Comparative genomics of recent rapid adaptation in invasive spiders

Comparative genomics of recent rapid adaptation in invasive spiders | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Comparative genomics of recent rapid adaptation in invasive spiders Chao Tong, Kunyuan Wanghe, Miao Li This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7860671/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Understanding the genetic consequence of invasive success is crucial for biodiversity conservation under global change. Although various ecological traits common to invasive species have been identified, the genomic basis of invasive success and degree to which invasive species from different lineages have utilized common genes remain largely unknown. Here, we investigate 15 genomes of spider species, representing five instances of independent recent invasive success globally. By phylogenetically comparing the relative evolutionary rates between invasive and their non-invasive relatives, we reveal genome contents that associated with neurogenesis, brain development, mitochondria were under rapid molecular evolution in invasive spiders. We further identify genes involved in reproduction, larval development, immune response and nervous system developments that experienced convergent intensification of selection, while multiple metabolic processes associated genes underwent relaxed selection during the transition to invasive success. Our results also indicate that catabolic and metabolic gene repertoire under convergent positive selection may be associated with rapid adaptation to new environments in invasive spiders. Altogether, these findings pave the way towards a deeper understanding of recent rapid adaptation in invasive species. Biological sciences/Ecology/Biodiversity Biological sciences/Evolution/Molecular evolution comparative genomics invasive success spider rapid adaptation molecular evolution Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Introduction Biological invasions pose a significant threat to global biodiversity, invasive species have demonstrated remarkable success in colonizing new environments 1 . That is, invasive species have been introduced, either accidentally or intentionally, into regions outside their native range. Thus, invasive species often outcompete native species and disrupt local ecosystems 2 , which caused considerable ecological and economic damage 3 . Past studies suggest that rapid adaptation in novel and changing environments can rescue populations from extinction 4 and facilitate the spread of invasive species 3 , 5 , 6 . Species distributions and management strategies under current and future global change could benefit from a better understanding of the mechanism underlying rapid adaptation to novel niches. Decades of ecological studies have identified a set of ecological traits common to invasive species, such as rapid growth, high reproductive rate, wide environmental tolerance, strong competitive ability 7 . However, little is known about the genetic changes that may contribute to the invasive success. Recent advances in genomic technologies facilitate the increase in availability of invasive species genomic data 8 , 9 . Building on past studies focused on assessing the ecological impact of invasive species, increasing studies have begun to elucidate the genetic basis of rapid adaptation in invasive species, including invasive Argentine ant ( Linepithema humile ) 10 , cotton bollworm ( Helicoverpa armigera ) 11 , Asian longhorned beetle ( Anoplophora glabripennis ) 12 , and fall webworm ( Hyphantria cunea ) 3 . Despite research involving invasive arthropods (i.e. ants, beetles, and worms) having uncovered important insights into genomic changes associated with their rapid adaptations, the genomic underpinnings of invasive spiders have largely lagged behind. Specifically, among more than 40,000 known species of spiders, a number of invasive spider species have recently been identified, such as Australian redback spider ( Latrodectus hasseltii ) 13 , Mediterranean recluse spider ( Loxosceles rufescens ) 14 , huntsman spider ( Heteropoda venatoria ) 15 , jorō spider ( Trichonephila clavata ) 16 , brown widow spider ( Latrodectus geometricus ) 17 . Nevertheless, the genomic basis of rapid adaptation and degree to which invasive success has utilized common genes remain largely unknown. Here, we compiled a genomic dataset of invasive spiders and their non-invasive species focusing on genus level, which has been sequenced and made publicly available very recently 18 – 20 . By leveraging this high-quality omics dataset, we aimed to investigate the genomic convergence that may underlie rapid adaptation of invasive spiders across different lineages. Specifically, we identified genome-wide signature of molecular evolution that differ between invasive and non-invasive spiders, including rapid evolution, intensified or relaxed selection and positive selection. Collectively, our study provides insights into the genomic basis of rapid adaptation and molecular mechanism that contribute to the success of invasive spiders thriving in diverse environments. Results Invasive and non-invasive spiders exhibit distinct geographic distributions We performed cross search across multiple databases for spider species integrating both biogeographic / ecological and omics data and finalized a list of five invasive and ten closely related non-invasive spider species (Fig. 1 a, Table S1 ). Specifically, we found invasive spider species are: Australian redback spider ( Latrodectus hasseltii ) is originated in Australia, but now is listed as occurring in Southeast Asia and New Zealand 13 ; brown widow spider ( Latrodectus geometricus ) is suggested to originate in south Africa, while now it has been found in North America, Australia and many parts in Asia, especially in urban and suburban areas where it can displace native black widows 17 ; Mediterranean recluse spider ( Loxosceles rufescens ) is a species that originated in the Mediterranean region, now this species has been found in many parts of the world and listed as one of the most invasive spiders worldwide 14 ; a huntsman spider species Heteropoda venatoria is originated from Southeast Asia, but now it has been found in tropical and subtropical regions worldwide 15 , jorō spider ( Trichonephila clavata ) is native to East Asia, and has been spreading across North America since the 2010s 16 . Beside these five invasive spiders, 10 of their non-invasive relatives are narrowly distributed as shown in Fig. 1 a. Collectively, by comparing the updated biogeographic data, invasive and non-invasive spiders exhibit distinct geographic distributions. Instances of independent recent invasive success We retained the genomes or reference transcriptomes that included more than 90% completed BUSCO genes, and further identified 936 strict single-copy BUSCO genes aross all 15 spider species and an outgroup scorpion species (Table S2). Based on the concatenated single-copy BUSCO gene dataset, we inferred a genomic scale of phylogeny which was strongly supported (bootstrap value = 100) for all nodes, and estimated divergence time for each phylogenetic node (Fig. 1 b). Five invasive spiders species were confirmed at the genus level, including Trichonephila (family: Nephilidae), Latrodectus (family: Theridiidae), Heteropoda (family: Sparassidae), Loxosceles (family: Sicariidae), which also represented five instances of independent invasive success. Convergent rapid evolution is based on a shared neural and mitochondrial genome contents in invasive spiders We calculated the relative evolutionary rates (RER) for nodes on the phylogenetic tree by genes, and compared the RER representing invasive spiders (RER invasive ) and RER representing non-invasive spiders (RER non−invasive ), respectively. Out of 8095 orthologs that shared by 15 spiders, 153 genes showed convergent signature of rapid evolution in invasive spiders compared with their non-invasive relatives with significance (RER invasive >RER non−invasive , rho > 0, P < 0.05 Wilcoxon rank sum test), including NADH dehydrogenase 1 beta subcomplex subunit 7 (NDUFB7) (Fig. 2 a), Cyclin-C (CCNC), Cyclin-L1 (CCNL1), homeobox protein engrailed (EN1), serine proteinase stubble (Sb), 2-oxoglutarate dehydrogenase (OGDC), mitochondrial import receptor subunit TOM20 homolog (TOM20), E3 ubiquitin-protein ligase HUWE1 (Huwe1), Protein nervous wreck (Nwk) (Fig. 2 b, Table S3). However, 70 genes exhibited signature of convergent deceleration in invasive spiders with significance (RER invasive < RER non−invasive , rho < 0, P < 0.05 Wilcoxon rank sum test) (Table S4). Since we were interested in the genes under convergent rapid evolution in invasive spiders, we further did gene ontology enrichment to better understand which functional categories associated with the evolution of invasive spiders. Intriguingly, ontologies in neural and mitochondrial functions stood out of various significantly enriched GO terms, including mitochondrial electron transport, NADH to ubiquinone (GO:0006120), mitochondrion organization (GO:0007005), aerobic electron transport chain (GO:0019646), neuron projection development (GO:0031175), neuron development (GO:0048666), neurogenesis (GO:0022008) (Fig. 2 c, Table S5). Convergent shift in selective pressures associated with the evolution of invasive spiders Rapid evolution can be caused by intensified positive selection, relaxed purifying selection, or a combination of both 21 . RELAX, the model that we applied in this study, quantifies the degree which shifts in the distribution of Non-synonymous/Synonymous rate (dN/dS) across individual genes. Out of 6978 genes (codon alignments, minimum length > 50 codons), we identified 443 genes under convergent intensification of selection (K < 1) in invasive spider branches across the phylogeny, including glutamate receptor (GRIA) (K = 3.24, adjusted P →0, Fig. 3 a), putative inorganic phosphate cotransporter (Picot), alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT1), 2-oxoglutarate dehydrogenase (OGDC), serine proteinase stubble (Sb), innexin inx2 (inx) (Fig. 3 b, Table S6). In addition, we found 257 genes that experienced convergent relaxation in invasive spider branches relative to non-invasive spider branches, including ATPase family AAA domaincontaining protein 3A (K = 0.45, adjusted P→0, Fig. 4 a) (Fig. 3 b, Table S6). Moreover, GO enrichment analysis indicated that distinct functional terms were enriched for genes under convergent intensification or relaxation. Specifically, we found ontologies for genes under convergent intensification of selection in invasive spiders were mainly clustered in: (1) reproduction related terms, such as germ cell development (GO:0007281), spermatogenesis (GO:0007283), and oogenesis (GO:0048477); (2) larval development associated terms, such as instar larval or pupal development (GO:0002165), larval development (GO:0002164); (3) neural terms, such as central nervous system development (GO:0007417), neuron fate commitment (GO:0048663), neurotransmitter transport (GO:0006836) (Fig. 3 c, Table S7). For genes under convergent relaxation of selection in invasive spiders, we found enriched GO terms are mainly related to metabolic processes, such as amide metabolic process (GO:0043603), small molecule metabolic process (GO:0044281), cellular metabolic process (GO:0044237) (Fig. 3 c, Table S8). Convergent positive selection of catabolic and metabolic gene repertoire Positve selection can promote gene fast evolving 22 . BUSTED-PH, a newly developed model to detect the signature of positive selection repeatedly occurred in species across different lineages 23 , 24 . Out of 6978 genes that was the same dataset for RELAX, we identified 137 genes with the evidence of convergent positive selection in 5 invasive spider species, including innexin inx2 (inx2), serine proteinase stubble (Sb), mitochondrial import receptor subunit TOM20 homolog (TOM20) alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT1), putative inorganic phosphate cotransporter (Picot), glutamate receptor (GRIA) (Fig. 4 a, Table S9). Moreover, GO enrichment indicated that these positively selected genes in invasive spiders were mainly concentrated in catabolic and metabolic terms, such as primary metabolic process (GO:0044238), monocarboxylic acid metabolic process (GO:0032787), oxoacid metabolic process (GO:0043436), cellular lipid catabolic process (GO:0016042), fatty acid catabolic process (GO:0009062) (Fig. 4 b, Table S10). Genes with evidence from intersection of multiple selections By overlapping the sets of genes with evidence of convergent selections, we found various shared gene sets (Fig. 5 a, Table S11). Specifically, we found 86 genes under both positive selection and intensification, namely intensified positive selection ( P = 0.0108, super exact test), including inx2, MGAT1, Picot, GRIA, TOM20. In addition, we identified five genes that underwent intensified positive selection and rapid evolution ( P = 0.0042, super exact test), including Sb. Moreover, we found 14 genes under both relaxation and rapid evolution, putatively under relaxed purifying selection ( P = 0.0046, super exact test), such as mitochondrial inner membrane protein OXA1L (OXA1L) (Fig. 5 b, Table S12). Discussion Invasive spiders shared the common ecological traits including fast growth rate, high reproductive rate, strong competitive ability, that had been identified by past studies. What is not known, however, is how convergences in genetic changes contribute to similarity in rapid adaptation in invasive species. Here we integrated biogeographic data mining, comparative genomics, and molecular evolution approaches to determine the degree to which invasive spiders have utilized common genes in their adaptations to new environment under global change. Maintenance of high reproductive rate is essential for expansion of population size for invasive species 4 , 7 . It is hypothesized that high fecundity would benefit from the intensified reproductive function in an organism. By comparing the selective pressure in invasive species with their non-invasive relatives, we observed reproductive genome contents were under significant intensification of selection, that may provide putative evidence to support this hypothesis. Besides, several candidate genes stand out. For instance, the gene innexin inx2 , which experienced both intensification and positive selection, regulates stretched cell morphogenesis in ovary of fly 25 and egg chamber formation in fly 26 . The gene relaxin receptor 2 , which experienced intensification of selection, involved in the regulation of male reproductive tract in rat 27 . In addition, the gene Cyclin-C , has been identified to be under rapid evolution in invasive spiders, is essential in cell cycle progression and is particularly active in spermatogenesis in mice 28 . Another gene Cyclin-L1 , also was detected under convergent rapid evolution, plays a role in spermatogenesis and oocyte maturation in C. elegans 29 . Here we provided preliminary evidence of convergent shift in selection putatively associated with the evolution of invasive spiders, further studies will be necessary to validate the function and mechanism of these candidates intensifying spider reproductive systems. Another feature common to invasive species, that is rapid growth rate, which facilitate the spread of invasive species 5 , 6 . Besides the enhanced function of multiple developmental processes, rapid growth also creates a high demand for energy and nutrients, which needs to be met. As a whole, this featured trait needs multiple biological processes to be involved, and the rapid adaptation of invasive spiders may be associated with the evolution of various genes involved these processes. Remarkably, we identified a set of genes under rapid evolution associated with pupal development or animal organ morphogenesis. One of Homeobox gene, homeobox protein engrailed , which exhibited rapid evolution in multiple invasive spider branches, involved in the wing development of fly 30 . The gene, nuclear hormone receptor E75 which involved in juvenile hormone signaling pathway that plays significant roles in insect development 31 , which was under intensification of selection in invasive spiders. Another gene, serine proteinase stubble , that was under intensification, positive selection and rapid evolution in invasive spiders, is required for required for hormone-dependent epithelial morphogenesis of imaginal discs, including the formation of bristles, legs, and wings of fly 32 . In addition, we identified abundant genes involved in metabolic or catabolic processes under convergent selection, which may supply the high demand of energy and nutrition uptake of invasive species, such as the genes, NADH dehydrogenase 1 beta subcomplex subunit 7 , ATPase family AAA domain containing protein 3A , 2-oxoglutarate dehydrogenase , mitochondrial import receptor subunit TOM20 homolog , alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase , putative inorganic phosphate cotransporter . Collectively, we suggested that the convergent evolution of developmental, catabolic and metabolic gene repertoires may be associated with the rapid adaptation of invasive spiders. Recent evidence shows enhanced cognitive ability in conjunction with behavioral flexibility are likely to be adaptive in invasive species 33 . Indeed, we identified numbers of genes under convergent shift in selections in invasive spiders, which supported this hypothesis. The gene, glutamate receptor , which experienced both positive evolution and intensification of selection in invasive spiders, contributed to synaptic transmission functions in learning and memory 34 . E3 ubiquitin-protein ligase HUWE1 involves in nervous system development and control neural differentiation 35 , was identified as a rapidly evolving gene specific to invasive spiders. Protein nervous wreck , an adaptor protein that regulates synaptic growth in fly 36 , was also one of the rapidly evolving genes in invasive spiders. Thus, these evidence may indicate that the repeated rapid evolution of neural genes in invasive spiders may facilitate the success of their invasive behaviors. Conclusions Our study presents three important findings. First, this present work suggests an evolutionary mechanism by which convergences in genomic changes at genome-wide level underlie the evolution of invasive spiders under current or future global change. Second, this study provides evidences for the genomic evolution of common ecological traits in invasive species. Third, our results support the hypothesis that adaptive evolution of cognitive ability can facilitate invasive success. Methods Invasive spiders and geographic distribution We assembled a curated list comprising spider species with records of description “invasive spider” as the search terms. In October 2024, we conducted thorough searches for each term in World Spider Catalog v25.5 ( https://wsc.nmbe.ch/ ) , Global Biodiversity Information Facility (GBIF, https://www.gbif.org/ ) and iNaturalist ( https://www.inaturalist.org/ ). We documented the taxonomy, environment, geographic distribution and accompanying images that corresponded to each search term (Table S1 ). Omics data collection We explored the genomic data of spiders species from online databases, NCBI Genome ( https://www.ncbi.nlm.nih.gov/genome ) and GigaDB ( http://gigadb.org/ ) , as of October 2024. Specifically, we downloaded the whole genome data of Latrodectus geometricus (GCA_026290005.1), Latrodectus hesperus (GCA_037975125.2) 19 , Trichonephila clavata (GCA_019973975.1), Trichonephila antipodiana 18 , Trichonephila clavipes (GCA_019973935.1) and Trichonephila inaurata (GCA_019973955.1). Finally, we employed the BUSCO pipeline 37 to assess the completeness of genome contents of these spider species based on the arachnida_odb10 single-copy orthologous gene set from OrthoDB v12 ( https://www.orthodb.org ) , which comprised 2,934 conserved genes. Reference transcriptome assembly and gene prediction In addition to the above five spider genomes, we sought to extend the omics dataset by including transcriptomes of closely related species from the same genus of species with genomic data. Specifically, we downloaded the raw RNA sequencing reads of Loxosceles rufescens , Loxosceles reclusa , Loxosceles deserta , Latrodectus hasselti , Trichonephila plumipes , Heteropoda venatoria , Heteropoda davidbowie , Heteropoda simplex , Heteropoda tetrica from NCBI SRA ( https://www.ncbi.nlm.nih.gov/sra ) (Table S2). Next, we performed de novo transcriptome assembly using rnaSPAdes 38 . Moreover, we used TransDecoder ( https://github.com/TransDecoder/TransDecoder ) to predict gene models in each assembled transcriptome. Similarly, we also used BUSCO pipeline to assess the quality of reference transcriptome assemblies. Phylogenetic tree construction and divergence time estimation We downloaded the genome of striped bark scorpion, Centruroides vittatus (GCF_030686945.1) for phylogeny construction as the requirement of an outgroup species. Building on the identified BUSCO gene repertoire within two categories “Complete and single-copy BUSCO” and “Complete and duplicated BUSCO” of six spider genomes, nine reference transcriptomes and a scorpion genome, we identified one-to-one single copy genes across all 16 species using OrthoFinder 39 . Next, we used a phylogenomic approach to reconstruct the phylogeny of 15 spider species, along with an outgroup species, based on a dataset of amino acid (AA) sequences corresponding to a pooled set of 1:1 single-copy orthologs. Further, we performed AA sequence alignment using MAFFT 40 , removed gaps using trimAL 41 , and assembled a concatenated dataset that included all 1:1 single-copy orthologs with a minimum length of 200 AA. Finally, we used ModelFinder 42 to determine best-fit model of sequence evolution and constructed the maximum likelihood (ML) phylogenetic tree using IQ-TREE2 43 with 1000 bootstrap replicates. We retrieved the documented divergence time between spiders on TimeTree database ( https://timetree.org/ ). Specifically, we included Trichonephila antipodiana - Trichonephila_clavata (min = 7.04 Million Years Ago, MYA , max = 11 MYA, median = 9.2 MYA), Trichonephila plumipes - Trichonephila clavata (median = 14.2 MYA); Trichonephila inaurata - Trichonephila clavipes (median = 15.1 MYA); Heteropoda davidbowie - Heteropoda venatoria (median = 22.9 MYA); Loxosceles deserta - Loxosceles reclusa (median = 10.8 MYA); Loxosceles rufescens - Loxosceles reclusa (min = 22.1 MYA, max = 43.4 MYA, median = 33 MYA); Loxosceles rufescens - Centruroides vittatus (min = 375.2 MYA, max = 442.3 MYA, median = 397). We estimated the divergence time for all nodes on the phylogeny using MCMCtree in PAML 44 with these calibration time. Finally, we used iTOL v6 ( https://itol.embl.de/ ) to visualize the phylogenetic tree and divergence time. Ortholog identification Beside BUSCO gene repertoire which only included curated single-copy orthologs from OrthoDB database, we employed OMA pipeline 45 to extend and further explore orthologous relationship of protein-coding genes across 15 spider species. Specifically, we compiled protein-coding gene dataset for each spider species and amalgamated them into a local pooled protein database. We performed parallel all-to-all BLAST using DIAMOND ( https://github.com/bbuchfink/diamond ) and identified putative orthologous groups (OGs). For each 1:1 ortholog pair, we selected the longest gene associated with curated OG as putative ortholog for each species. Relative evolutionary rate calculation To test whether signature of molecular evolution differ between invasive and their non-invasive spiders, we computed the relative evolutionary rate for each species at gene-wide scale. Specifically, we aligned the AA sequences of shared orthologs for the 15 spider species using MAFFT 40 . Next, we inferred gene tree and estimate branch length for each ortholog by pruning the reconstructed genome-wide phylogeny using R package, Phangorn 46 with the AA alignments. Finally, we calculated the relative evolutionary rate (RER) for each node on gene tree using R package, RERconverge 47 , and compared the RERs between invasive and non-invasive spiders with the Wilcoxon rank sum test. We defined the genes with RERs for invasive spiders significantly higher than RERs representing non-invasive spiders as rapid evolving genes or invasive-accelerated genes ( P < 0.05). Relaxed selection test To quantify the degree to which convergent shifts in the selection during transition to invasive success in spiders, we sought to detect the changes in nucleotide substitution rate (ω) and the selective strength (relaxation or intensification) acting on invasive transition. Specifically, we prepared the codon alignments of shared orthologs by 15 spider species, which derived from amino acid alignments and corresponding DNA sequences using PAL2NAL v.14 (-no gap) 48 . We retained the codon alignments with a minimum length of 50 codons, and prepared the corresponding tree for each ortholog by pruning the genome-scale phylogeny using R package, phytools 49 . Finally, we used RELAX 50 to test for a relaxation or intensification of selective pressure along invasive spider branches across the phylogeny. Rapid evolution (RER invasive >RER non−invasive ) can result from relaxed purifying selection or intensified positive selection 21 . Briefly, RELAX distinguishes between the signals by modeling how codons with different ω categories (ω > 1 and ω 1 indicates the signature of intensified selection, whereas K < 1 indicates a relaxed selection strength at invasive spider branches 21 , 51 . We employed a log-likelihood ratio test (LRT) to compare the supports for the null model (K = 1) and the alternative model (K > 1 or K < 1), which further corrected P values using the Benjamini-Hochberg method to control for multiple comparisons. We defined the genes under convergent relaxation which showed K < and adjusted P 1 and adjusted P < 0.05 are considered to be under convergent intensification in invasive spider branches. Positive selection test To determine whether convergent positive selection associated with the evolution of invasive species, we sought to detect the signal of positive selection in invasive spider branches across the phylogeny using BUSTED-PH ( https://github.com/veg/hyphy-analyses/tree/master/BUSTED-PH ) with the codon alignments and gene trees for each shared ortholog as described above. We used LRT to calculate adjusted P values for focal foreground branches (adjusted P value-foreground), background branches (adjusted P value-background), and difference between focal foreground and background (adjusted P value-diff) following Benjamini–Hochberg adjustment. We defined genes with significant signals of convergent positive selection in invasive branches (adjusted P invasive < 0.05) and difference between invasive and non-invasive branches (adjusted P diff < 0.05), while no significant signals in non-invasive branches (adjusted P non−invasive < 0.05) as positively selected genes in invasive spiders. Gene ontology enrichment analysis We performed Gene Ontology (GO) enrichment analysis for genes under rapid evolution, intensification or relaxation, and positive selection in invasive spiders using GOTermFinder 52 . In addition, we corrected P value for each enriched GO term following Benjamini–Hochberg adjustment. We considered the GO terms (Biological Processes) with adjusted P < 0.05 to be significant. Authors’ contributions C.T.: conceptualization, data curation, formal analysis, investigation, supervision, visualization, writing—original draft; W.K. and M.L.: data curation, formal analysis, writing—review and editing. All authors gave final approval for publication and agreed to be held accountable for the work performed therein. Declarations Data accessibility All data and scripts required to generate figures, tables, and perform statistical analyses are available on GitHub ( https://github.com/jiyideanjiao/invasive_genomics ). All other data needed are provided in either the main text or in the Supplementary material. Acknowledgements We are grateful for computational support from Biomix HPC Cluster at the University of Delaware. References Early, R., et al.: Global threats from invasive alien species in the twenty-first century and national response capacities. Nat. Commun. 7 , 12485 (2016) Charles, H., Dukes, J.S.: Impacts of invasive species on ecosystem services. Biol. Invasions. (2007). 10.1007/978-3-540-36920-2.pdf Wu, N., et al.: Fall webworm genomes yield insights into rapid adaptation of invasive species. Nat. Ecol. Evol. 3 , 105–115 (2019) Bell, G., Gonzalez, A.: Evolutionary rescue can prevent extinction following environmental change. Ecol. Lett. 12 , 942–948 (2009) Perkins, T.A., Phillips, B.L., Baskett, M.L., Hastings, A.: Evolution of dispersal and life history interact to drive accelerating spread of an invasive species. Ecol. Lett. 16 , 1079–1087 (2013) Wu, Y., Colautti, R.I.: Evidence for continent-wide convergent evolution and stasis throughout 150 y of a biological invasion. Proc. Natl. Acad. Sci. U. S. A. 119, e2107584119 (2022) Stapley, J., Santure, A.W., Dennis, S.R.: Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol. Ecol. 24 , 2241–2252 (2015) North, H.L., McGaughran, A., Jiggins, C.D.: Insights into invasive species from whole-genome resequencing. Mol. Ecol. 30 , 6289–6308 (2021) Matheson, P., McGaughran, A.: Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates. Sci. Rep. 12 , 13987 (2022) Smith, C.D., et al.: Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc. Natl. Acad. Sci. U. S. A. 108, 5673–5678 (2011) Jones, C.M., et al.: Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest. Mol. Ecol. 24 , 4901–4911 (2015) McKenna, D.D., et al.: Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biol. 17 , 227 (2016) Vink, C.J., Derraik, J.G.B., Phillips, C.B., Sirvid, P.J.: The invasive Australian redback spider, Latrodectus hasseltii Thorell 1870 (Araneae: Theridiidae): current and potential distributions, and likely impacts. Biol. Invasions. 13 , 1003–1019 (2011) Nentwig, W., Pantini, P., Vetter, R.S.: Distribution and medical aspects of Loxosceles rufescens, one of the most invasive spiders of the world (Araneae: Sicariidae). Toxicon. 132 , 19–28 (2017) Ratão, S.S., Adrião, A., Silva, H., Cardoso, I.: Presence of an invasive huntsman spider species Heteropoda venatoria in Porto Inglês, Maio Island, Cabo Verde Archipelago. Zoologia Caboverdiana (2021) Davis, A.K., Frick, B.L.: Physiological evaluation of newly invasive jorō spiders (Trichonephila clavata) in the southeastern USA compared to their naturalized cousin, Trichonephila clavipes. Physiol. Entomol. 47 , 170–175 (2022) Chapman, C.S.: Measuring the Success of the Invasive Brown Widow Spider (Latrodectus Geometricus) and Its Impact on the Native Western Black Widow Spider (Latrodectus Hesperus). California State University, Fresno (2022) Fan, Z., et al.: A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. Gigascience 10 , (2021) Miles, L.S., et al.: Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. J. Hered. 115 , 241–252 (2024) Arakawa, K., et al.: 1000 spider silkomes: Linking sequences to silk physical properties. Sci. Adv. 8 , eabo6043 (2022) Tong, C., Avilés, L., Rayor, L.S., Mikheyev, A.S., Linksvayer, T.A.: Genomic signatures of recent convergent transitions to social life in spiders. Nat. Commun. 13 , 6967 (2022) Torgerson, D.G., Kulathinal, R.J., Singh, R.S.: Mammalian sperm proteins are rapidly evolving: evidence of positive selection in functionally diverse genes. Mol. Biol. Evol. 19 , 1973–1980 (2002) Ludington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L.: New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol. 21 , 284 (2023) Barkdull, M., Moreau, C.: Worker reproduction and caste polymorphism impact genome evolution and social genes across the ants. Genome Biol. Evol. 15 , (2023) Huang, Y.-C., et al.: βPS-Integrin acts downstream of Innexin 2 in modulating stretched cell morphogenesis in the Drosophila ovary, vol. G3. Genes|Genomes|Genetics 11 (2021) Mukai, M., et al.: Innexin2 gap junctions in somatic support cells are required for cyst formation and for egg chamber formation in Drosophila. Mech. Dev. 128 , 510–523 (2011) Filonzi, M., et al.: Relaxin family peptide receptors Rxfp1 and Rxfp2: mapping of the mRNA and protein distribution in the reproductive tract of the male rat. Reprod. Biol. Endocrinol. 5 , 29 (2007) Bruter, A.V., et al.: Knockout of cyclin dependent kinases 8 and 19 leads to depletion of cyclin C and suppresses spermatogenesis and male fertility in mice. eLife (2024). 10.7554/elife.96465 Williams, C.W., Iyer, J., Liu, Y., O’Connell, K.F.: CDK-11-Cyclin L is required for gametogenesis and fertility in C. elegans. Dev. Biol. 441 , 52–66 (2018) Layalle, S., et al.: Engrailed homeoprotein acts as a signaling molecule in the developing fly. Development. 138 , 2315–2323 (2011) Jindra, M., Palli, S.R., Riddiford, L.M.: The juvenile hormone signaling pathway in insect development. Annu. Rev. Entomol. 58 , 181–204 (2013) Appel, L.F., et al.: The Drosophila Stubble-stubbloid gene encodes an apparent transmembrane serine protease required for epithelial morphogenesis. Proc. Natl. Acad. Sci. U. S. A. 90, 4937–4941 (1993) Szabo, B., Damas-Moreira, I., Whiting, M.J.: Can cognitive ability give invasive species the means to succeed? A review of the evidence. Front. Ecol. Evol. 8 , (2020) Riedel, G., Platt, B., Micheau, J.: Glutamate receptor function in learning and memory. Behav. Brain Res. (2003) Zhao, X., et al.: The HECT-domain ubiquitin ligase Huwe1 controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein. Nat. Cell. Biol. 10 , 643–653 (2008) Coyle, I.P., et al.: Nervous wreck, an SH3 adaptor protein that interacts with Wsp, regulates synaptic growth in Drosophila. Neuron. 41 , 521–534 (2004) Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., Zdobnov, E.M.: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 31 , 3210–3212 (2015) Nurk, S., et al.: Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comput. Biol. 20 , 714–737 (2013) Emms, D.M., Kelly, S.: OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20 , 238 (2019) Katoh, K., Standley, D.M.: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30 , 772–780 (2013) Capella-Gutiérrez, S., Silla-Martínez, J.M., Gabaldón, T.: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25 , 1972–1973 (2009) Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., Jermiin, L.S.: ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. 14 , 587–589 (2017) Minh, B.Q., et al.: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 37 , 1530–1534 (2020) Yang, Z.: PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24 , 1586–1591 (2007) Altenhoff, A.M., et al.: OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Res. 49 , D373–D379 (2021) Schliep, K.P.: phangorn: phylogenetic analysis in R. Bioinformatics 27, 592–593 (2011) Kowalczyk, A., et al.: RERconverge: an R package for associating evolutionary rates with convergent traits. Bioinformatics. 35 , 4815–4817 (2019) Suyama, M., Torrents, D., Bork, P.: PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34 , W609–W612 (2006) Revell, L.J.: phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ. 12 , e16505 (2024) Wertheim, J.O., Murrell, B., Smith, M.D., Pond, K., S. L., Scheffler, K.: RELAX: detecting relaxed selection in a phylogenetic framework. Mol. Biol. Evol. 32 , 820–832 (2015) Chak, S.T.C., Baeza, J.A., Barden, P.: Eusociality shapes convergent patterns of molecular evolution across mitochondrial genomes of snapping shrimps. Mol. Biol. Evol. 38 , 1372–1383 (2021) Boyle, E.I., et al.: GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 20 , 3710–3715 (2004) Additional Declarations There is NO Competing Interest. Supplementary Files Supplementarytables.xlsx Supplementary tables Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7860671","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":531185597,"identity":"f96f2557-4694-4a5b-9f0a-e80b3dc6484f","order_by":0,"name":"Chao Tong","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA80lEQVRIiWNgGAWjYLACxgYGBjb25gMHPjCAGARU88C08PEcS3w4A6SFmVgtchI5xsZgHiEt9uy9h1/83GEnxyaRYyZt82ubPB8zA+OHjzl4bOE5l2bZeybZmI3nWZl0bt9twzZmBmbJmdvwaAEabszYxpzYxp68TTq35zaQDfQOL2Et9YltDAlm0pY9t+2J0WL8mLHtcGIbR4qxMcOP24mEtZw5Y8bY23Yc6BdgIPc23E5uY2ZsxusX9vYe4w8/26rl5NuBUfnjz23b+e3NBz98xKMFCNgk4EzGNjDZgFc9EDB/QLD/EFI8CkbBKBgFIxEAAEMYTfmIJfdEAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0001-5202-5507","institution":"Arizona State University","correspondingAuthor":true,"prefix":"","firstName":"Chao","middleName":"","lastName":"Tong","suffix":""},{"id":531185598,"identity":"14dea1d7-f735-4d11-97d4-d576e7bae533","order_by":1,"name":"Kunyuan 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13:42:05","extension":"html","order_by":12,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":121183,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/3518320d786188452916bca1.html"},{"id":93941965,"identity":"d5d787da-e62c-4c91-81ba-77709e607b43","added_by":"auto","created_at":"2025-10-20 13:42:04","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":541828,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGeographic distribution of invasive/non-invasive spiders and genome-scale phylogeny of spiders.\u003c/strong\u003e (\u003cstrong\u003ea\u003c/strong\u003e) Blue dots represent the recorded geographic distributions of invasive spiders, and orange dots represent the recorded geographic distributions of non-invasive spiders. The world map is generated using packages, ggplots, sf, rnaturalearth, rnaturalearthdata and ggspatial in R software. (\u003cstrong\u003eb\u003c/strong\u003e) The maximum likelihood phylogenetic tree with estimated divergence time of 15 spider species and an outgroup scorpion included in the study. The genome-scale phylogeny was inferred from 936 strict single-copy completed BUSCO genes. Blue dots represent five invasive spiders, orange dots represent ten non-invasive spiders, and dark dots represent six calibration time points from Timetree database version 5 (\u003ca href=\"https://timetree.org/\"\u003ehttps://timetree.org/\u003c/a\u003e). Pictures of invasive spiders: \u003cem\u003eTrichonephila clavata\u003c/em\u003e(credit: Trey Wardlaw), \u003cem\u003eLatrodectus geometricus\u003c/em\u003e (credit: Eduardo Ingani), \u003cem\u003eLatrodectus hasselti\u003c/em\u003e (credit: Zyoute And Djigr), \u003cem\u003eHeteropoda venatoria\u003c/em\u003e (credit: Chengtao Lin), and \u003cem\u003eLoxosceles rufescens\u003c/em\u003e (credit: Steven Wang).\u003c/p\u003e","description":"","filename":"11.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/28be8da6529788b614c00e55.jpg"},{"id":93942771,"identity":"824a2849-dac5-4b3c-8594-2feea195d8b8","added_by":"auto","created_at":"2025-10-20 13:50:04","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":436861,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenes and ontologies under convergent rapid evolution in invasive spider branches.\u003c/strong\u003e (\u003cstrong\u003ea\u003c/strong\u003e) Scatter plot depicting the relative evolutionary rate (RER) for each nodes on the phylogeny of gene, NADH dehydrogenase 1 beta subcomplex subunit 7. Orange dots represent the RERs of non-invasive spider branches, blue dots represent the RERs of invasive spider branches. Rho and \u003cem\u003eP\u003c/em\u003e value are shown, which p value is calculated by a Wilcoxon rank sum test. (\u003cstrong\u003eb\u003c/strong\u003e) Scatter plot depicting the rho values of rapidly evolving genes in invasive spider branches with significance (\u003cem\u003eP\u003c/em\u003e value \u0026lt; 0.05). A number of candidata genes are labeled in blue, including NADH dehydrogenase 1 beta subcomplex subunit 7 (NDUFB7), Cyclin-C (CCNC), Cyclin-L1 (CCNL1), homeobox protein engrailed (EN1), serine proteinase stubble (Sb), 2-oxoglutarate dehydrogenase (OGDC), mitochondrial import receptor subunit TOM20 homolog (TOMM20), E3 ubiquitin-protein ligase HUWE1 (Huwe1), Protein nervous wreck (Nwk). (\u003cstrong\u003ec\u003c/strong\u003e) REVIEGO plot depicting the significantly enriched gene ontology terms for genes under convergent rapid evolution in invasive spiders. The bubble size represents the log size, which is the log-transformed \u003cem\u003eP\u003c/em\u003e-value or the frequency of GO terms in the dataset. The color scale represents the -LOG10(\u003cem\u003eP\u003c/em\u003e-value) of enriched GO terms.\u003c/p\u003e","description":"","filename":"12.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/0342c31afa080c7dc8fa7a5e.jpg"},{"id":93942772,"identity":"53ddbaee-e85c-4a86-8e22-edbc698004df","added_by":"auto","created_at":"2025-10-20 13:50:04","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":559121,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenes and ontologies under convergent relaxation or intensification of selection in invasive spiders.\u003c/strong\u003e (\u003cstrong\u003ea\u003c/strong\u003e) Multi-bar plots depicting the example of gene under convergent intensification of selection (glutamate receptor, K \u0026gt; 1, \u003cem\u003eP\u003c/em\u003e \u0026lt; 0.05) and convergent relaxation of selection (ATPase family AAA domaincontaining protein 3A, K \u0026lt; 1, \u003cem\u003eP\u003c/em\u003e\u0026lt; 0.05). \u003cem\u003eP\u003c/em\u003e value as calculated by using Likelihood-ratio test (LRT). The distribution of dN/dS across sites in a gene, are illustrated by three categories of dN/dS for non-invasive (orange) and invasive (blue) branches. The vertical dashed line at dN/dS = 1 represents neutral evolution, bars at dN/dS \u0026gt; 1 represent sites experiencing positive selection, and bars at dN/dS \u0026lt;1 represent sites experiencing purifying selection. The arrows show the direction of change in dN/dS between non-invasive and invasive branches. Relaxation of selection (K \u0026lt; 1) would push all ω categories toward 1, while intensification of selection (K \u0026gt; 1) would pull all ω categories away from 1. (\u003cstrong\u003eb\u003c/strong\u003e) Scatter plots depicting the genes under convergent relaxation of selection (0 \u0026lt; K \u0026lt; 1), and intensification of selection (1 \u0026lt; K \u0026lt; 50). The color scale of dots are ranged from navy to red, representing the adjusted \u003cem\u003eP\u003c/em\u003e-value of each gene. A number of candidate genes are labeled and annotated, including ATPase family AAA domain containing protein 3A (ATAD3A), innexin inx2 (inx2), serine proteinase stubble (Sb), 2-oxoglutarate dehydrogenase (OGDC), alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT1), putative inorganic phosphate cotransporter (Picot), glutamate receptor (GRIA). (\u003cstrong\u003ec\u003c/strong\u003e) REVIEGO plot depicting the significantly enriched gene ontology terms for genes under convergent intensification or relaxation of selections in invasive spiders. The bubble size represents the log size, which is the log-transformed \u003cem\u003eP\u003c/em\u003e-value or the frequency of GO terms in the dataset. The color scale represents the -LOG10(\u003cem\u003eP\u003c/em\u003e-value) of enriched GO terms.\u003c/p\u003e","description":"","filename":"13.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/3c1ce083e7c342775cb3fb38.jpg"},{"id":93941968,"identity":"786bb374-6160-43ef-8fc2-68ed75306553","added_by":"auto","created_at":"2025-10-20 13:42:04","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":305760,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenes and ontologies under convergent positive selection in invasive spiders.\u003c/strong\u003e (\u003cstrong\u003ea\u003c/strong\u003e) 3D scatter plot depicting the genes under positive selection with significance, adjusted-\u003cem\u003eP\u003c/em\u003e-value-invasive spider \u0026lt; 0.05, adjusted-P-value between invasive spider and non-invasive spiders \u0026lt; 0.05, adjusted-\u003cem\u003eP\u003c/em\u003e-value-non-invasive spider \u0026gt; 0.05. The log-transformed adjusted-P-values are shown on X-axis (invasive spiders), Y-axis (non-invasive spiders), and Z-axis (between invasive and non-invasive spiders). A number of candidate genes are annotated and labeled in dark, including innexin inx2 (inx2), serine proteinase stubble (Sb), mitochondrial import receptor subunit TOM20 homolog (TOM20), alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase, (MGAT1), putative inorganic phosphate cotransporter (Picot), glutamate receptor (GRIA). (\u003cstrong\u003eb\u003c/strong\u003e) REVIEGO plot depicting the significantly enriched gene ontology terms for genes under convergent positive selection in invasive spiders.\u003c/p\u003e","description":"","filename":"14.jpg","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/2d2ac3aef55e46edd1920164.jpg"},{"id":93943815,"identity":"3d1ed728-0d8e-42d5-8f03-1105f8a3e4e3","added_by":"auto","created_at":"2025-10-20 13:58:04","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":5713,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenes and ontologies under convergent positive selection in invasive spiders.\u003c/strong\u003e (\u003cstrong\u003ea\u003c/strong\u003e) 3D scatter plot depicting the genes under positive selection with significance, adjusted-\u003cem\u003eP\u003c/em\u003e-value-invasive spider \u0026lt; 0.05, adjusted-P-value between invasive spider and non-invasive spiders \u0026lt; 0.05, adjusted-\u003cem\u003eP\u003c/em\u003e-value-non-invasive spider \u0026gt; 0.05. The log-transformed adjusted-P-values are shown on X-axis (invasive spiders), Y-axis (non-invasive spiders), and Z-axis (between invasive and non-invasive spiders). A number of candidate genes are annotated and labeled in dark, including innexin inx2 (inx2), serine proteinase stubble (Sb), mitochondrial import receptor subunit TOM20 homolog (TOM20), alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase, (MGAT1), putative inorganic phosphate cotransporter (Picot), glutamate receptor (GRIA). (\u003cstrong\u003eb\u003c/strong\u003e) REVIEGO plot depicting the significantly enriched gene ontology terms for genes under convergent positive selection in invasive spiders.\u003c/p\u003e","description":"","filename":"placeholderimage.png","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/1a962335d589b36c9b2a327a.png"},{"id":94985890,"identity":"54e94af5-48ff-428c-add0-9e416cf33cc6","added_by":"auto","created_at":"2025-11-03 06:59:12","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2912976,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/f19883d1-f441-4c4b-9ba8-eb027a75ff7b.pdf"},{"id":93941971,"identity":"84a39753-1b42-42d1-82d7-ae41a4933ae2","added_by":"auto","created_at":"2025-10-20 13:42:04","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":145339,"visible":true,"origin":"","legend":"Supplementary tables","description":"","filename":"Supplementarytables.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7860671/v1/43c30a2ccf4ac3c152b72363.xlsx"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Comparative genomics of recent rapid adaptation in invasive spiders","fulltext":[{"header":"Introduction","content":"\u003cp\u003eBiological invasions pose a significant threat to global biodiversity, invasive species have demonstrated remarkable success in colonizing new environments \u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e. That is, invasive species have been introduced, either accidentally or intentionally, into regions outside their native range. Thus, invasive species often outcompete native species and disrupt local ecosystems \u003csup\u003e\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e, which caused considerable ecological and economic damage \u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u003c/sup\u003e. Past studies suggest that rapid adaptation in novel and changing environments can rescue populations from extinction \u003csup\u003e\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u003c/sup\u003e and facilitate the spread of invasive species \u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e,\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e,\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e. Species distributions and management strategies under current and future global change could benefit from a better understanding of the mechanism underlying rapid adaptation to novel niches.\u003c/p\u003e\u003cp\u003eDecades of ecological studies have identified a set of ecological traits common to invasive species, such as rapid growth, high reproductive rate, wide environmental tolerance, strong competitive ability \u003csup\u003e\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. However, little is known about the genetic changes that may contribute to the invasive success. Recent advances in genomic technologies facilitate the increase in availability of invasive species genomic data \u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e,\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u003c/sup\u003e. Building on past studies focused on assessing the ecological impact of invasive species, increasing studies have begun to elucidate the genetic basis of rapid adaptation in invasive species, including invasive Argentine ant (\u003cem\u003eLinepithema humile\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u003c/sup\u003e, cotton bollworm (\u003cem\u003eHelicoverpa armigera\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e, Asian longhorned beetle (\u003cem\u003eAnoplophora glabripennis\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e, and fall webworm (\u003cem\u003eHyphantria cunea\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u003c/sup\u003e. Despite research involving invasive arthropods (i.e. ants, beetles, and worms) having uncovered important insights into genomic changes associated with their rapid adaptations, the genomic underpinnings of invasive spiders have largely lagged behind. Specifically, among more than 40,000 known species of spiders, a number of invasive spider species have recently been identified, such as Australian redback spider (\u003cem\u003eLatrodectus hasseltii\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e, Mediterranean recluse spider (\u003cem\u003eLoxosceles rufescens\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e, huntsman spider (\u003cem\u003eHeteropoda venatoria\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e, jorō spider (\u003cem\u003eTrichonephila clavata\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e, brown widow spider (\u003cem\u003eLatrodectus geometricus\u003c/em\u003e) \u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e. Nevertheless, the genomic basis of rapid adaptation and degree to which invasive success has utilized common genes remain largely unknown.\u003c/p\u003e\u003cp\u003eHere, we compiled a genomic dataset of invasive spiders and their non-invasive species focusing on genus level, which has been sequenced and made publicly available very recently \u003csup\u003e\u003cspan additionalcitationids=\"CR19\" citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e. By leveraging this high-quality omics dataset, we aimed to investigate the genomic convergence that may underlie rapid adaptation of invasive spiders across different lineages. Specifically, we identified genome-wide signature of molecular evolution that differ between invasive and non-invasive spiders, including rapid evolution, intensified or relaxed selection and positive selection. Collectively, our study provides insights into the genomic basis of rapid adaptation and molecular mechanism that contribute to the success of invasive spiders thriving in diverse environments.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003eInvasive and non-invasive spiders exhibit distinct geographic distributions\u003c/h2\u003e\u003cp\u003eWe performed cross search across multiple databases for spider species integrating both biogeographic / ecological and omics data and finalized a list of five invasive and ten closely related non-invasive spider species (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea, Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). Specifically, we found invasive spider species are: Australian redback spider (\u003cem\u003eLatrodectus hasseltii\u003c/em\u003e) is originated in Australia, but now is listed as occurring in Southeast Asia and New Zealand \u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e; brown widow spider (\u003cem\u003eLatrodectus geometricus\u003c/em\u003e) is suggested to originate in south Africa, while now it has been found in North America, Australia and many parts in Asia, especially in urban and suburban areas where it can displace native black widows \u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e; Mediterranean recluse spider (\u003cem\u003eLoxosceles rufescens\u003c/em\u003e) is a species that originated in the Mediterranean region, now this species has been found in many parts of the world and listed as one of the most invasive spiders worldwide \u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e; a huntsman spider species \u003cem\u003eHeteropoda venatoria\u003c/em\u003e is originated from Southeast Asia, but now it has been found in tropical and subtropical regions worldwide \u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e, jorō spider (\u003cem\u003eTrichonephila clavata\u003c/em\u003e) is native to East Asia, and has been spreading across North America since the 2010s \u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e. Beside these five invasive spiders, 10 of their non-invasive relatives are narrowly distributed as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea. Collectively, by comparing the updated biogeographic data, invasive and non-invasive spiders exhibit distinct geographic distributions.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eInstances of independent recent invasive success\u003c/h3\u003e\n\u003cp\u003eWe retained the genomes or reference transcriptomes that included more than 90% completed BUSCO genes, and further identified 936 strict single-copy BUSCO genes aross all 15 spider species and an outgroup scorpion species (Table S2). Based on the concatenated single-copy BUSCO gene dataset, we inferred a genomic scale of phylogeny which was strongly supported (bootstrap value\u0026thinsp;=\u0026thinsp;100) for all nodes, and estimated divergence time for each phylogenetic node (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eb). Five invasive spiders species were confirmed at the genus level, including \u003cem\u003eTrichonephila\u003c/em\u003e (family: Nephilidae), \u003cem\u003eLatrodectus\u003c/em\u003e (family: Theridiidae), \u003cem\u003eHeteropoda\u003c/em\u003e (family: Sparassidae), \u003cem\u003eLoxosceles\u003c/em\u003e (family: Sicariidae), which also represented five instances of independent invasive success.\u003c/p\u003e\u003cp\u003e\u003cb\u003eConvergent rapid evolution is based on a shared neural and mitochondrial genome contents in invasive spiders\u003c/b\u003e\u003c/p\u003e\u003cp\u003eWe calculated the relative evolutionary rates (RER) for nodes on the phylogenetic tree by genes, and compared the RER representing invasive spiders (RER\u003csub\u003einvasive\u003c/sub\u003e) and RER representing non-invasive spiders (RER\u003csub\u003enon\u0026minus;invasive\u003c/sub\u003e), respectively. Out of 8095 orthologs that shared by 15 spiders, 153 genes showed convergent signature of rapid evolution in invasive spiders compared with their non-invasive relatives with significance (RER\u003csub\u003einvasive\u003c/sub\u003e \u0026gt;RER\u003csub\u003enon\u0026minus;invasive\u003c/sub\u003e, rho\u0026thinsp;\u0026gt;\u0026thinsp;0, \u003cem\u003eP\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05 Wilcoxon rank sum test), including NADH dehydrogenase 1 beta subcomplex subunit 7 (NDUFB7) (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea), Cyclin-C (CCNC), Cyclin-L1 (CCNL1), homeobox protein engrailed (EN1), serine proteinase stubble (Sb), 2-oxoglutarate dehydrogenase (OGDC), mitochondrial import receptor subunit TOM20 homolog (TOM20), E3 ubiquitin-protein ligase HUWE1 (Huwe1), Protein nervous wreck (Nwk) (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eb, Table S3). However, 70 genes exhibited signature of convergent deceleration in invasive spiders with significance (RER\u003csub\u003einvasive\u003c/sub\u003e \u0026lt; RER\u003csub\u003enon\u0026minus;invasive\u003c/sub\u003e, rho\u0026thinsp;\u0026lt;\u0026thinsp;0, \u003cem\u003eP\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05 Wilcoxon rank sum test) (Table S4). Since we were interested in the genes under convergent rapid evolution in invasive spiders, we further did gene ontology enrichment to better understand which functional categories associated with the evolution of invasive spiders. Intriguingly, ontologies in neural and mitochondrial functions stood out of various significantly enriched GO terms, including mitochondrial electron transport, NADH to ubiquinone (GO:0006120), mitochondrion organization (GO:0007005), aerobic electron transport chain (GO:0019646), neuron projection development (GO:0031175), neuron development (GO:0048666), neurogenesis (GO:0022008) (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ec, Table S5).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\n\u003ch3\u003eConvergent shift in selective pressures associated with the evolution of invasive spiders\u003c/h3\u003e\n\u003cp\u003eRapid evolution can be caused by intensified positive selection, relaxed purifying selection, or a combination of both \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. RELAX, the model that we applied in this study, quantifies the degree which shifts in the distribution of Non-synonymous/Synonymous rate (dN/dS) across individual genes. Out of 6978 genes (codon alignments, minimum length\u0026thinsp;\u0026gt;\u0026thinsp;50 codons), we identified 443 genes under convergent intensification of selection (K\u0026thinsp;\u0026lt;\u0026thinsp;1) in invasive spider branches across the phylogeny, including glutamate receptor (GRIA) (K\u0026thinsp;=\u0026thinsp;3.24, adjusted \u003cem\u003eP\u003c/em\u003e\u0026rarr;0, Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ea), putative inorganic phosphate cotransporter (Picot), alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT1), 2-oxoglutarate dehydrogenase (OGDC), serine proteinase stubble (Sb), innexin inx2 (inx) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eb, Table S6). In addition, we found 257 genes that experienced convergent relaxation in invasive spider branches relative to non-invasive spider branches, including ATPase family AAA domaincontaining protein 3A (K\u0026thinsp;=\u0026thinsp;0.45, adjusted P\u0026rarr;0, Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ea) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eb, Table S6). Moreover, GO enrichment analysis indicated that distinct functional terms were enriched for genes under convergent intensification or relaxation. Specifically, we found ontologies for genes under convergent intensification of selection in invasive spiders were mainly clustered in: (1) reproduction related terms, such as germ cell development (GO:0007281), spermatogenesis (GO:0007283), and oogenesis (GO:0048477); (2) larval development associated terms, such as instar larval or pupal development (GO:0002165), larval development (GO:0002164); (3) neural terms, such as central nervous system development (GO:0007417), neuron fate commitment (GO:0048663), neurotransmitter transport (GO:0006836) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ec, Table S7). For genes under convergent relaxation of selection in invasive spiders, we found enriched GO terms are mainly related to metabolic processes, such as amide metabolic process (GO:0043603), small molecule metabolic process (GO:0044281), cellular metabolic process (GO:0044237) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ec, Table S8).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\n\u003ch3\u003eConvergent positive selection of catabolic and metabolic gene repertoire\u003c/h3\u003e\n\u003cp\u003ePositve selection can promote gene fast evolving \u003csup\u003e\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e. BUSTED-PH, a newly developed model to detect the signature of positive selection repeatedly occurred in species across different lineages \u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e,\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e\u003c/sup\u003e. Out of 6978 genes that was the same dataset for RELAX, we identified 137 genes with the evidence of convergent positive selection in 5 invasive spider species, including innexin inx2 (inx2), serine proteinase stubble (Sb), mitochondrial import receptor subunit TOM20 homolog (TOM20)\u003c/p\u003e\u003cp\u003ealpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (MGAT1), putative inorganic phosphate cotransporter (Picot), glutamate receptor (GRIA) (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ea, Table S9). Moreover, GO enrichment indicated that these positively selected genes in invasive spiders were mainly concentrated in catabolic and metabolic terms, such as primary metabolic process (GO:0044238), monocarboxylic acid metabolic process (GO:0032787), oxoacid metabolic process (GO:0043436), cellular lipid catabolic process (GO:0016042), fatty acid catabolic process (GO:0009062) (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eb, Table S10).\u003c/p\u003e\n\u003ch3\u003eGenes with evidence from intersection of multiple selections\u003c/h3\u003e\n\u003cp\u003eBy overlapping the sets of genes with evidence of convergent selections, we found various shared gene sets (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003ea, Table S11). Specifically, we found 86 genes under both positive selection and intensification, namely intensified positive selection (\u003cem\u003eP\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.0108, super exact test), including inx2, MGAT1, Picot, GRIA, TOM20. In addition, we identified five genes that underwent intensified positive selection and rapid evolution (\u003cem\u003eP\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.0042, super exact test), including Sb. Moreover, we found 14 genes under both relaxation and rapid evolution, putatively under relaxed purifying selection (\u003cem\u003eP\u003c/em\u003e\u0026thinsp;=\u0026thinsp;0.0046, super exact test), such as mitochondrial inner membrane protein OXA1L (OXA1L) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eb, Table S12).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eInvasive spiders shared the common ecological traits including fast growth rate, high reproductive rate, strong competitive ability, that had been identified by past studies. What is not known, however, is how convergences in genetic changes contribute to similarity in rapid adaptation in invasive species. Here we integrated biogeographic data mining, comparative genomics, and molecular evolution approaches to determine the degree to which invasive spiders have utilized common genes in their adaptations to new environment under global change.\u003c/p\u003e\u003cp\u003eMaintenance of high reproductive rate is essential for expansion of population size for invasive species \u003csup\u003e\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e,\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. It is hypothesized that high fecundity would benefit from the intensified reproductive function in an organism. By comparing the selective pressure in invasive species with their non-invasive relatives, we observed reproductive genome contents were under significant intensification of selection, that may provide putative evidence to support this hypothesis. Besides, several candidate genes stand out. For instance, the gene \u003cem\u003einnexin inx2\u003c/em\u003e, which experienced both intensification and positive selection, regulates stretched cell morphogenesis in ovary of fly \u003csup\u003e\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e\u003c/sup\u003e and egg chamber formation in fly \u003csup\u003e\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e. The gene \u003cem\u003erelaxin receptor 2\u003c/em\u003e, which experienced intensification of selection, involved in the regulation of male reproductive tract in rat \u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e. In addition, the gene \u003cem\u003eCyclin-C\u003c/em\u003e, has been identified to be under rapid evolution in invasive spiders, is essential in cell cycle progression and is particularly active in spermatogenesis in mice \u003csup\u003e\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e. Another gene \u003cem\u003eCyclin-L1\u003c/em\u003e, also was detected under convergent rapid evolution, plays a role in spermatogenesis and oocyte maturation in \u003cem\u003eC. elegans\u003c/em\u003e \u003csup\u003e\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e\u003c/sup\u003e. Here we provided preliminary evidence of convergent shift in selection putatively associated with the evolution of invasive spiders, further studies will be necessary to validate the function and mechanism of these candidates intensifying spider reproductive systems.\u003c/p\u003e\u003cp\u003eAnother feature common to invasive species, that is rapid growth rate, which facilitate the spread of invasive species \u003csup\u003e\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e,\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e. Besides the enhanced function of multiple developmental processes, rapid growth also creates a high demand for energy and nutrients, which needs to be met. As a whole, this featured trait needs multiple biological processes to be involved, and the rapid adaptation of invasive spiders may be associated with the evolution of various genes involved these processes. Remarkably, we identified a set of genes under rapid evolution associated with pupal development or animal organ morphogenesis. One of \u003cem\u003eHomeobox\u003c/em\u003e gene, \u003cem\u003ehomeobox protein engrailed\u003c/em\u003e, which exhibited rapid evolution in multiple invasive spider branches, involved in the wing development of fly \u003csup\u003e\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e\u003c/sup\u003e. The gene, \u003cem\u003enuclear hormone receptor E75\u003c/em\u003e which involved in juvenile hormone signaling pathway that plays significant roles in insect development \u003csup\u003e\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u003c/sup\u003e, which was under intensification of selection in invasive spiders. Another gene, \u003cem\u003eserine proteinase stubble\u003c/em\u003e, that was under intensification, positive selection and rapid evolution in invasive spiders, is required for required for hormone-dependent epithelial morphogenesis of imaginal discs, including the formation of bristles, legs, and wings of fly \u003csup\u003e\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e\u003c/sup\u003e. In addition, we identified abundant genes involved in metabolic or catabolic processes under convergent selection, which may supply the high demand of energy and nutrition uptake of invasive species, such as the genes, \u003cem\u003eNADH dehydrogenase 1 beta subcomplex subunit 7\u003c/em\u003e, \u003cem\u003eATPase family AAA domain containing protein 3A\u003c/em\u003e, \u003cem\u003e2-oxoglutarate dehydrogenase\u003c/em\u003e, \u003cem\u003emitochondrial import receptor subunit TOM20 homolog\u003c/em\u003e, \u003cem\u003ealpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase\u003c/em\u003e, \u003cem\u003eputative inorganic phosphate cotransporter\u003c/em\u003e. Collectively, we suggested that the convergent evolution of developmental, catabolic and metabolic gene repertoires may be associated with the rapid adaptation of invasive spiders.\u003c/p\u003e\u003cp\u003eRecent evidence shows enhanced cognitive ability in conjunction with behavioral flexibility are likely to be adaptive in invasive species \u003csup\u003e\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. Indeed, we identified numbers of genes under convergent shift in selections in invasive spiders, which supported this hypothesis. The gene, \u003cem\u003eglutamate receptor\u003c/em\u003e, which experienced both positive evolution and intensification of selection in invasive spiders, contributed to synaptic transmission functions in learning and memory \u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. \u003cem\u003eE3 ubiquitin-protein ligase HUWE1\u003c/em\u003e involves in nervous system development and control neural differentiation \u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e, was identified as a rapidly evolving gene specific to invasive spiders. \u003cem\u003eProtein nervous wreck\u003c/em\u003e, an adaptor protein that regulates synaptic growth in fly \u003csup\u003e\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u003c/sup\u003e, was also one of the rapidly evolving genes in invasive spiders. Thus, these evidence may indicate that the repeated rapid evolution of neural genes in invasive spiders may facilitate the success of their invasive behaviors.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eOur study presents three important findings. First, this present work suggests an evolutionary mechanism by which convergences in genomic changes at genome-wide level underlie the evolution of invasive spiders under current or future global change. Second, this study provides evidences for the genomic evolution of common ecological traits in invasive species. Third, our results support the hypothesis that adaptive evolution of cognitive ability can facilitate invasive success.\u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\u003ch2\u003eInvasive spiders and geographic distribution\u003c/h2\u003e\u003cp\u003eWe assembled a curated list comprising spider species with records of description \u0026ldquo;invasive spider\u0026rdquo; as the search terms. In October 2024, we conducted thorough searches for each term in World Spider Catalog v25.5 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://wsc.nmbe.ch/\u003c/span\u003e\u003cspan address=\"https://wsc.nmbe.ch/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e, Global Biodiversity Information Facility (GBIF, \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.gbif.org/\u003c/span\u003e\u003cspan address=\"https://www.gbif.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e and iNaturalist (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.inaturalist.org/\u003c/span\u003e\u003cspan address=\"https://www.inaturalist.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e).\u003c/span\u003e We documented the taxonomy, environment, geographic distribution and accompanying images that corresponded to each search term (Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e).\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\u003ch2\u003eOmics data collection\u003c/h2\u003e\u003cp\u003eWe explored the genomic data of spiders species from online databases, NCBI Genome (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/genome\u003c/span\u003e\u003cspan address=\"https://www.ncbi.nlm.nih.gov/genome\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e and GigaDB (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://gigadb.org/\u003c/span\u003e\u003cspan address=\"http://gigadb.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e, as of October 2024. Specifically, we downloaded the whole genome data of \u003cem\u003eLatrodectus geometricus\u003c/em\u003e (GCA_026290005.1), \u003cem\u003eLatrodectus hesperus\u003c/em\u003e (GCA_037975125.2) \u003csup\u003e19\u003c/sup\u003e, \u003cem\u003eTrichonephila clavata\u003c/em\u003e (GCA_019973975.1), \u003cem\u003eTrichonephila antipodiana\u003c/em\u003e \u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e, \u003cem\u003eTrichonephila clavipes\u003c/em\u003e (GCA_019973935.1) and \u003cem\u003eTrichonephila inaurata\u003c/em\u003e (GCA_019973955.1). Finally, we employed the BUSCO pipeline \u003csup\u003e\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e to assess the completeness of genome contents of these spider species based on the arachnida_odb10 single-copy orthologous gene set from OrthoDB v12 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.orthodb.org\u003c/span\u003e\u003cspan address=\"https://www.orthodb.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e, which comprised 2,934 conserved genes.\u003c/p\u003e\u003cp\u003e\u003cb\u003eReference transcriptome assembly and gene prediction\u003c/b\u003e\u003c/p\u003e\u003cp\u003eIn addition to the above five spider genomes, we sought to extend the omics dataset by including transcriptomes of closely related species from the same genus of species with genomic data. Specifically, we downloaded the raw RNA sequencing reads of \u003cem\u003eLoxosceles rufescens\u003c/em\u003e, \u003cem\u003eLoxosceles reclusa\u003c/em\u003e, \u003cem\u003eLoxosceles deserta\u003c/em\u003e, \u003cem\u003eLatrodectus hasselti\u003c/em\u003e, \u003cem\u003eTrichonephila plumipes\u003c/em\u003e, \u003cem\u003eHeteropoda venatoria\u003c/em\u003e, \u003cem\u003eHeteropoda davidbowie\u003c/em\u003e, \u003cem\u003eHeteropoda simplex\u003c/em\u003e, \u003cem\u003eHeteropoda tetrica\u003c/em\u003e from NCBI SRA (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/sra\u003c/span\u003e\u003cspan address=\"https://www.ncbi.nlm.nih.gov/sra\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e (Table S2). Next, we performed \u003cem\u003ede novo\u003c/em\u003e transcriptome assembly using rnaSPAdes \u003csup\u003e\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e. Moreover, we used TransDecoder (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/TransDecoder/TransDecoder\u003c/span\u003e\u003cspan address=\"https://github.com/TransDecoder/TransDecoder\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e to predict gene models in each assembled transcriptome. Similarly, we also used BUSCO pipeline to assess the quality of reference transcriptome assemblies.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\u003ch2\u003ePhylogenetic tree construction and divergence time estimation\u003c/h2\u003e\u003cp\u003eWe downloaded the genome of striped bark scorpion, \u003cem\u003eCentruroides vittatus\u003c/em\u003e (GCF_030686945.1) for phylogeny construction as the requirement of an outgroup species. Building on the identified BUSCO gene repertoire within two categories \u0026ldquo;Complete and single-copy BUSCO\u0026rdquo; and \u0026ldquo;Complete and duplicated BUSCO\u0026rdquo; of six spider genomes, nine reference transcriptomes and a scorpion genome, we identified one-to-one single copy genes across all 16 species using OrthoFinder \u003csup\u003e\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e\u003c/sup\u003e. Next, we used a phylogenomic approach to reconstruct the phylogeny of 15 spider species, along with an outgroup species, based on a dataset of amino acid (AA) sequences corresponding to a pooled set of 1:1 single-copy orthologs. Further, we performed AA sequence alignment using MAFFT \u003csup\u003e\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u003c/sup\u003e, removed gaps using trimAL \u003csup\u003e\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e\u003c/sup\u003e, and assembled a concatenated dataset that included all 1:1 single-copy orthologs with a minimum length of 200 AA. Finally, we used ModelFinder \u003csup\u003e\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e\u003c/sup\u003e to determine best-fit model of sequence evolution and constructed the maximum likelihood (ML) phylogenetic tree using IQ-TREE2 \u003csup\u003e43\u003c/sup\u003e with 1000 bootstrap replicates.\u003c/p\u003e\u003cp\u003eWe retrieved the documented divergence time between spiders on TimeTree database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://timetree.org/\u003c/span\u003e\u003cspan address=\"https://timetree.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e).\u003c/span\u003e Specifically, we included \u003cem\u003eTrichonephila antipodiana\u003c/em\u003e - \u003cem\u003eTrichonephila_clavata\u003c/em\u003e (min\u0026thinsp;=\u0026thinsp;7.04\u0026nbsp;Million Years Ago, \u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eMYA\u003c/span\u003e, max\u0026thinsp;=\u0026thinsp;11 MYA, median\u0026thinsp;=\u0026thinsp;9.2 MYA), \u003cem\u003eTrichonephila plumipes\u003c/em\u003e - \u003cem\u003eTrichonephila clavata\u003c/em\u003e (median\u0026thinsp;=\u0026thinsp;14.2 MYA); \u003cem\u003eTrichonephila inaurata\u003c/em\u003e - \u003cem\u003eTrichonephila clavipes\u003c/em\u003e (median\u0026thinsp;=\u0026thinsp;15.1 MYA); \u003cem\u003eHeteropoda davidbowie\u003c/em\u003e - \u003cem\u003eHeteropoda venatoria\u003c/em\u003e (median\u0026thinsp;=\u0026thinsp;22.9 MYA); \u003cem\u003eLoxosceles deserta\u003c/em\u003e - \u003cem\u003eLoxosceles reclusa\u003c/em\u003e (median\u0026thinsp;=\u0026thinsp;10.8 MYA); \u003cem\u003eLoxosceles rufescens\u003c/em\u003e - \u003cem\u003eLoxosceles reclusa\u003c/em\u003e (min\u0026thinsp;=\u0026thinsp;22.1 MYA, max\u0026thinsp;=\u0026thinsp;43.4 MYA, median\u0026thinsp;=\u0026thinsp;33 MYA); \u003cem\u003eLoxosceles rufescens\u003c/em\u003e - \u003cem\u003eCentruroides vittatus\u003c/em\u003e (min\u0026thinsp;=\u0026thinsp;375.2 MYA, max\u0026thinsp;=\u0026thinsp;442.3 MYA, median\u0026thinsp;=\u0026thinsp;397). We estimated the divergence time for all nodes on the phylogeny using MCMCtree in PAML \u003csup\u003e\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e\u003c/sup\u003e with these calibration time. Finally, we used iTOL v6 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://itol.embl.de/\u003c/span\u003e\u003cspan address=\"https://itol.embl.de/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e to visualize the phylogenetic tree and divergence time.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e\u003ch2\u003eOrtholog identification\u003c/h2\u003e\u003cp\u003eBeside BUSCO gene repertoire which only included curated single-copy orthologs from OrthoDB database, we employed OMA pipeline \u003csup\u003e\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e to extend and further explore orthologous relationship of protein-coding genes across 15 spider species. Specifically, we compiled protein-coding gene dataset for each spider species and amalgamated them into a local pooled protein database. We performed parallel all-to-all BLAST using DIAMOND (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/bbuchfink/diamond\u003c/span\u003e\u003cspan address=\"https://github.com/bbuchfink/diamond\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e and identified putative orthologous groups (OGs). For each 1:1 ortholog pair, we selected the longest gene associated with curated OG as putative ortholog for each species.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec15\" class=\"Section2\"\u003e\u003ch2\u003eRelative evolutionary rate calculation\u003c/h2\u003e\u003cp\u003eTo test whether signature of molecular evolution differ between invasive and their non-invasive spiders, we computed the relative evolutionary rate for each species at gene-wide scale. Specifically, we aligned the AA sequences of shared orthologs for the 15 spider species using MAFFT \u003csup\u003e\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u003c/sup\u003e. Next, we inferred gene tree and estimate branch length for each ortholog by pruning the reconstructed genome-wide phylogeny using R package, Phangorn \u003csup\u003e\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e\u003c/sup\u003e with the AA alignments. Finally, we calculated the relative evolutionary rate (RER) for each node on gene tree using R package, RERconverge \u003csup\u003e\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e\u003c/sup\u003e, and compared the RERs between invasive and non-invasive spiders with the Wilcoxon rank sum test. We defined the genes with RERs for invasive spiders significantly higher than RERs representing non-invasive spiders as rapid evolving genes or invasive-accelerated genes (\u003cem\u003eP\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05).\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec16\" class=\"Section2\"\u003e\u003ch2\u003eRelaxed selection test\u003c/h2\u003e\u003cp\u003eTo quantify the degree to which convergent shifts in the selection during transition to invasive success in spiders, we sought to detect the changes in nucleotide substitution rate (ω) and the selective strength (relaxation or intensification) acting on invasive transition. Specifically, we prepared the codon alignments of shared orthologs by 15 spider species, which derived from amino acid alignments and corresponding DNA sequences using PAL2NAL v.14 (-no gap) \u003csup\u003e\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e\u003c/sup\u003e. We retained the codon alignments with a minimum length of 50 codons, and prepared the corresponding tree for each ortholog by pruning the genome-scale phylogeny using R package, phytools \u003csup\u003e\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e\u003c/sup\u003e. Finally, we used RELAX \u003csup\u003e\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e\u003c/sup\u003e to test for a relaxation or intensification of selective pressure along invasive spider branches across the phylogeny. Rapid evolution (RER\u003csub\u003einvasive\u003c/sub\u003e \u0026gt;RER\u003csub\u003enon\u0026minus;invasive\u003c/sub\u003e) can result from relaxed purifying selection or intensified positive selection \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. Briefly, RELAX distinguishes between the signals by modeling how codons with different ω categories (ω\u0026thinsp;\u0026gt;\u0026thinsp;1 and ω\u0026thinsp;\u0026lt;\u0026thinsp;1) respond to a single selection intensity parameter K. Relaxation of selection would push all ω categories toward 1, while intensification of selection would pull all ω categories away from 1. K\u0026thinsp;\u0026gt;\u0026thinsp;1 indicates the signature of intensified selection, whereas K\u0026thinsp;\u0026lt;\u0026thinsp;1 indicates a relaxed selection strength at invasive spider branches \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e,\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e\u003c/sup\u003e. We employed a log-likelihood ratio test (LRT) to compare the supports for the null model (K\u0026thinsp;=\u0026thinsp;1) and the alternative model (K\u0026thinsp;\u0026gt;\u0026thinsp;1 or K\u0026thinsp;\u0026lt;\u0026thinsp;1), which further corrected \u003cem\u003eP\u003c/em\u003e values using the Benjamini-Hochberg method to control for multiple comparisons. We defined the genes under convergent relaxation which showed K\u0026thinsp;\u0026lt;\u0026thinsp;and adjusted \u003cem\u003eP\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05, while genes with K\u0026thinsp;\u0026gt;\u0026thinsp;1 and adjusted \u003cem\u003eP\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05 are considered to be under convergent intensification in invasive spider branches.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec17\" class=\"Section2\"\u003e\u003ch2\u003ePositive selection test\u003c/h2\u003e\u003cp\u003eTo determine whether convergent positive selection associated with the evolution of invasive species, we sought to detect the signal of positive selection in invasive spider branches across the phylogeny using BUSTED-PH (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/veg/hyphy-analyses/tree/master/BUSTED-PH\u003c/span\u003e\u003cspan address=\"https://github.com/veg/hyphy-analyses/tree/master/BUSTED-PH\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e with the codon alignments and gene trees for each shared ortholog as described above. We used LRT to calculate adjusted \u003cem\u003eP\u003c/em\u003e values for focal foreground branches (adjusted \u003cem\u003eP\u003c/em\u003e value-foreground), background branches (adjusted P value-background), and difference between focal foreground and background (adjusted \u003cem\u003eP\u003c/em\u003e value-diff) following Benjamini\u0026ndash;Hochberg adjustment. We defined genes with significant signals of convergent positive selection in invasive branches (adjusted \u003cem\u003eP\u003c/em\u003e\u003csub\u003einvasive\u003c/sub\u003e \u0026lt; 0.05) and difference between invasive and non-invasive branches (adjusted \u003cem\u003eP\u003c/em\u003e\u003csub\u003ediff\u003c/sub\u003e \u0026lt; 0.05), while no significant signals in non-invasive branches (adjusted \u003cem\u003eP\u003c/em\u003e\u003csub\u003enon\u0026minus;invasive\u003c/sub\u003e \u0026lt; 0.05) as positively selected genes in invasive spiders.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec18\" class=\"Section2\"\u003e\u003ch2\u003eGene ontology enrichment analysis\u003c/h2\u003e\u003cp\u003eWe performed Gene Ontology (GO) enrichment analysis for genes under rapid evolution, intensification or relaxation, and positive selection in invasive spiders using GOTermFinder \u003csup\u003e\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e\u003c/sup\u003e. In addition, we corrected \u003cem\u003eP\u003c/em\u003e value for each enriched GO term following Benjamini\u0026ndash;Hochberg adjustment. We considered the GO terms (Biological Processes) with adjusted \u003cem\u003eP\u003c/em\u003e\u0026thinsp;\u0026lt;\u0026thinsp;0.05 to be significant.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec19\" class=\"Section2\"\u003e\u003ch2\u003eAuthors\u0026rsquo; contributions\u003c/h2\u003e\u003cp\u003eC.T.: conceptualization, data curation, formal analysis, investigation, supervision, visualization, writing\u0026mdash;original draft; W.K. and M.L.: data curation, formal analysis, writing\u0026mdash;review and editing. All authors gave final approval for publication and agreed to be held accountable for the work performed therein.\u003c/p\u003e\u003c/div\u003e"},{"header":"Declarations","content":"\u003c/p\u003e\u003cp\u003e\u003ch2\u003eData accessibility\u003c/h2\u003e\u003cp\u003eAll data and scripts required to generate figures, tables, and perform statistical analyses are available on GitHub (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/jiyideanjiao/invasive_genomics\u003c/span\u003e\u003cspan address=\"https://github.com/jiyideanjiao/invasive_genomics\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e).\u003c/span\u003e All other data needed are provided in either the main text or in the Supplementary material.\u003c/p\u003e\u003c/p\u003e\u003ch2\u003eAcknowledgements\u003c/h2\u003e\u003cp\u003eWe are grateful for computational support from Biomix HPC Cluster at the University of Delaware.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eEarly, R., et al.: Global threats from invasive alien species in the twenty-first century and national response capacities. Nat. Commun. \u003cb\u003e7\u003c/b\u003e, 12485 (2016)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCharles, H., Dukes, J.S.: Impacts of invasive species on ecosystem services. Biol. Invasions. (2007). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1007/978-3-540-36920-2.pdf\u003c/span\u003e\u003cspan address=\"10.1007/978-3-540-36920-2.pdf\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWu, N., et al.: Fall webworm genomes yield insights into rapid adaptation of invasive species. Nat. Ecol. Evol. \u003cb\u003e3\u003c/b\u003e, 105\u0026ndash;115 (2019)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBell, G., Gonzalez, A.: Evolutionary rescue can prevent extinction following environmental change. Ecol. Lett. \u003cb\u003e12\u003c/b\u003e, 942\u0026ndash;948 (2009)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003ePerkins, T.A., Phillips, B.L., Baskett, M.L., Hastings, A.: Evolution of dispersal and life history interact to drive accelerating spread of an invasive species. Ecol. Lett. \u003cb\u003e16\u003c/b\u003e, 1079\u0026ndash;1087 (2013)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWu, Y., Colautti, R.I.: Evidence for continent-wide convergent evolution and stasis throughout 150 y of a biological invasion. Proc. Natl. Acad. Sci. U. S. A. 119, e2107584119 (2022)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eStapley, J., Santure, A.W., Dennis, S.R.: Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol. Ecol. \u003cb\u003e24\u003c/b\u003e, 2241\u0026ndash;2252 (2015)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNorth, H.L., McGaughran, A., Jiggins, C.D.: Insights into invasive species from whole-genome resequencing. Mol. Ecol. \u003cb\u003e30\u003c/b\u003e, 6289\u0026ndash;6308 (2021)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMatheson, P., McGaughran, A.: Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates. Sci. Rep. \u003cb\u003e12\u003c/b\u003e, 13987 (2022)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSmith, C.D., et al.: Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc. Natl. Acad. Sci. U. S. A. 108, 5673\u0026ndash;5678 (2011)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eJones, C.M., et al.: Genomewide transcriptional signatures of migratory flight activity in a globally invasive insect pest. Mol. Ecol. \u003cb\u003e24\u003c/b\u003e, 4901\u0026ndash;4911 (2015)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMcKenna, D.D., et al.: Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface. Genome Biol. \u003cb\u003e17\u003c/b\u003e, 227 (2016)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eVink, C.J., Derraik, J.G.B., Phillips, C.B., Sirvid, P.J.: The invasive Australian redback spider, Latrodectus hasseltii Thorell 1870 (Araneae: Theridiidae): current and potential distributions, and likely impacts. Biol. Invasions. \u003cb\u003e13\u003c/b\u003e, 1003\u0026ndash;1019 (2011)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNentwig, W., Pantini, P., Vetter, R.S.: Distribution and medical aspects of Loxosceles rufescens, one of the most invasive spiders of the world (Araneae: Sicariidae). Toxicon. \u003cb\u003e132\u003c/b\u003e, 19\u0026ndash;28 (2017)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eRat\u0026atilde;o, S.S., Adri\u0026atilde;o, A., Silva, H., Cardoso, I.: Presence of an invasive huntsman spider species Heteropoda venatoria in Porto Ingl\u0026ecirc;s, Maio Island, Cabo Verde Archipelago. Zoologia Caboverdiana (2021)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eDavis, A.K., Frick, B.L.: Physiological evaluation of newly invasive jorō spiders (Trichonephila clavata) in the southeastern USA compared to their naturalized cousin, Trichonephila clavipes. Physiol. Entomol. \u003cb\u003e47\u003c/b\u003e, 170\u0026ndash;175 (2022)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChapman, C.S.: Measuring the Success of the Invasive Brown Widow Spider (Latrodectus Geometricus) and Its Impact on the Native Western Black Widow Spider (Latrodectus Hesperus). California State University, Fresno (2022)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eFan, Z., et al.: A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event. Gigascience \u003cb\u003e10\u003c/b\u003e, (2021)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMiles, L.S., et al.: Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider. J. Hered. \u003cb\u003e115\u003c/b\u003e, 241\u0026ndash;252 (2024)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eArakawa, K., et al.: 1000 spider silkomes: Linking sequences to silk physical properties. Sci. Adv. \u003cb\u003e8\u003c/b\u003e, eabo6043 (2022)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eTong, C., Avil\u0026eacute;s, L., Rayor, L.S., Mikheyev, A.S., Linksvayer, T.A.: Genomic signatures of recent convergent transitions to social life in spiders. Nat. Commun. \u003cb\u003e13\u003c/b\u003e, 6967 (2022)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eTorgerson, D.G., Kulathinal, R.J., Singh, R.S.: Mammalian sperm proteins are rapidly evolving: evidence of positive selection in functionally diverse genes. Mol. Biol. Evol. \u003cb\u003e19\u003c/b\u003e, 1973\u0026ndash;1980 (2002)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLudington, A.J., Hammond, J.M., Breen, J., Deveson, I.W., Sanders, K.L.: New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol. \u003cb\u003e21\u003c/b\u003e, 284 (2023)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBarkdull, M., Moreau, C.: Worker reproduction and caste polymorphism impact genome evolution and social genes across the ants. Genome Biol. Evol. \u003cb\u003e15\u003c/b\u003e, (2023)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHuang, Y.-C., et al.: βPS-Integrin acts downstream of Innexin 2 in modulating stretched cell morphogenesis in the Drosophila ovary, vol. G3. Genes|Genomes|Genetics 11 (2021)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMukai, M., et al.: Innexin2 gap junctions in somatic support cells are required for cyst formation and for egg chamber formation in Drosophila. Mech. Dev. \u003cb\u003e128\u003c/b\u003e, 510\u0026ndash;523 (2011)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eFilonzi, M., et al.: Relaxin family peptide receptors Rxfp1 and Rxfp2: mapping of the mRNA and protein distribution in the reproductive tract of the male rat. Reprod. Biol. Endocrinol. \u003cb\u003e5\u003c/b\u003e, 29 (2007)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBruter, A.V., et al.: Knockout of cyclin dependent kinases 8 and 19 leads to depletion of cyclin C and suppresses spermatogenesis and male fertility in mice. eLife (2024). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.7554/elife.96465\u003c/span\u003e\u003cspan address=\"10.7554/elife.96465\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWilliams, C.W., Iyer, J., Liu, Y., O\u0026rsquo;Connell, K.F.: CDK-11-Cyclin L is required for gametogenesis and fertility in C. elegans. Dev. Biol. \u003cb\u003e441\u003c/b\u003e, 52\u0026ndash;66 (2018)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eLayalle, S., et al.: Engrailed homeoprotein acts as a signaling molecule in the developing fly. Development. \u003cb\u003e138\u003c/b\u003e, 2315\u0026ndash;2323 (2011)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eJindra, M., Palli, S.R., Riddiford, L.M.: The juvenile hormone signaling pathway in insect development. Annu. Rev. Entomol. \u003cb\u003e58\u003c/b\u003e, 181\u0026ndash;204 (2013)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eAppel, L.F., et al.: The Drosophila Stubble-stubbloid gene encodes an apparent transmembrane serine protease required for epithelial morphogenesis. Proc. Natl. Acad. Sci. U. S. A. 90, 4937\u0026ndash;4941 (1993)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSzabo, B., Damas-Moreira, I., Whiting, M.J.: Can cognitive ability give invasive species the means to succeed? A review of the evidence. Front. Ecol. Evol. \u003cb\u003e8\u003c/b\u003e, (2020)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eRiedel, G., Platt, B., Micheau, J.: Glutamate receptor function in learning and memory. Behav. Brain Res. (2003)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eZhao, X., et al.: The HECT-domain ubiquitin ligase Huwe1 controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein. Nat. Cell. Biol. \u003cb\u003e10\u003c/b\u003e, 643\u0026ndash;653 (2008)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCoyle, I.P., et al.: Nervous wreck, an SH3 adaptor protein that interacts with Wsp, regulates synaptic growth in Drosophila. Neuron. \u003cb\u003e41\u003c/b\u003e, 521\u0026ndash;534 (2004)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSim\u0026atilde;o, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., Zdobnov, E.M.: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. \u003cb\u003e31\u003c/b\u003e, 3210\u0026ndash;3212 (2015)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eNurk, S., et al.: Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comput. Biol. \u003cb\u003e20\u003c/b\u003e, 714\u0026ndash;737 (2013)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eEmms, D.M., Kelly, S.: OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. \u003cb\u003e20\u003c/b\u003e, 238 (2019)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eKatoh, K., Standley, D.M.: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. \u003cb\u003e30\u003c/b\u003e, 772\u0026ndash;780 (2013)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eCapella-Guti\u0026eacute;rrez, S., Silla-Mart\u0026iacute;nez, J.M., Gabald\u0026oacute;n, T.: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. \u003cb\u003e25\u003c/b\u003e, 1972\u0026ndash;1973 (2009)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eKalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., Jermiin, L.S.: ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. \u003cb\u003e14\u003c/b\u003e, 587\u0026ndash;589 (2017)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eMinh, B.Q., et al.: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. \u003cb\u003e37\u003c/b\u003e, 1530\u0026ndash;1534 (2020)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eYang, Z.: PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. \u003cb\u003e24\u003c/b\u003e, 1586\u0026ndash;1591 (2007)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eAltenhoff, A.M., et al.: OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Res. \u003cb\u003e49\u003c/b\u003e, D373\u0026ndash;D379 (2021)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSchliep, K.P.: phangorn: phylogenetic analysis in R. Bioinformatics 27, 592\u0026ndash;593 (2011)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eKowalczyk, A., et al.: RERconverge: an R package for associating evolutionary rates with convergent traits. Bioinformatics. \u003cb\u003e35\u003c/b\u003e, 4815\u0026ndash;4817 (2019)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eSuyama, M., Torrents, D., Bork, P.: PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. \u003cb\u003e34\u003c/b\u003e, W609\u0026ndash;W612 (2006)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eRevell, L.J.: phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ. \u003cb\u003e12\u003c/b\u003e, e16505 (2024)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eWertheim, J.O., Murrell, B., Smith, M.D., Pond, K., S. L., Scheffler, K.: RELAX: detecting relaxed selection in a phylogenetic framework. Mol. Biol. Evol. \u003cb\u003e32\u003c/b\u003e, 820\u0026ndash;832 (2015)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eChak, S.T.C., Baeza, J.A., Barden, P.: Eusociality shapes convergent patterns of molecular evolution across mitochondrial genomes of snapping shrimps. Mol. Biol. Evol. \u003cb\u003e38\u003c/b\u003e, 1372\u0026ndash;1383 (2021)\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eBoyle, E.I., et al.: GO::TermFinder\u0026mdash;open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. \u003cb\u003e20\u003c/b\u003e, 3710\u0026ndash;3715 (2004)\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"comparative genomics, invasive success, spider, rapid adaptation, molecular evolution ","lastPublishedDoi":"10.21203/rs.3.rs-7860671/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7860671/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eUnderstanding the genetic consequence of invasive success is crucial for biodiversity conservation under global change. Although various ecological traits common to invasive species have been identified, the genomic basis of invasive success and degree to which invasive species from different lineages have utilized common genes remain largely unknown. Here, we investigate 15 genomes of spider species, representing five instances of independent recent invasive success globally. By phylogenetically comparing the relative evolutionary rates between invasive and their non-invasive relatives, we reveal genome contents that associated with neurogenesis, brain development, mitochondria were under rapid molecular evolution in invasive spiders. We further identify genes involved in reproduction, larval development, immune response and nervous system developments that experienced convergent intensification of selection, while multiple metabolic processes associated genes underwent relaxed selection during the transition to invasive success. Our results also indicate that catabolic and metabolic gene repertoire under convergent positive selection may be associated with rapid adaptation to new environments in invasive spiders. Altogether, these findings pave the way towards a deeper understanding of recent rapid adaptation in invasive species.\u003c/p\u003e","manuscriptTitle":"Comparative genomics of recent rapid adaptation in invasive spiders","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-10-20 13:42:00","doi":"10.21203/rs.3.rs-7860671/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"f63403ea-af07-4706-b42f-22c0b50f10cc","owner":[],"postedDate":"October 20th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":56472372,"name":"Biological sciences/Ecology/Biodiversity"},{"id":56472373,"name":"Biological sciences/Evolution/Molecular evolution"}],"tags":[],"updatedAt":"2025-10-31T15:51:25+00:00","versionOfRecord":[],"versionCreatedAt":"2025-10-20 13:42:00","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7860671","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7860671","identity":"rs-7860671","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}