Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids)

Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids) | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (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];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids) View ORCID Profile Yannick Woudstra , Paul Rees , View ORCID Profile Solofo E. Rakotoarisoa , View ORCID Profile Ronell R. Klopper , View ORCID Profile Gideon F. Smith , View ORCID Profile Nina Rønsted , View ORCID Profile Olwen M. Grace doi: https://doi.org/10.1101/2025.02.28.640761 Yannick Woudstra 1 Department for Ecology, Environment and Plant Sciences, Stockholm University , 106 91 Stockholm, Sweden 2 Royal Botanic Gardens , Kew, TW9 3AE Richmond, Surrey, United Kingdom 3 Natural History Museum of Denmark, University of Copenhagen , 1350 Copenhagen K, Denmark Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yannick Woudstra For correspondence: yannick.woudstra{at}su.se ograce{at}rbge.org.uk Paul Rees 2 Royal Botanic Gardens , Kew, TW9 3AE Richmond, Surrey, United Kingdom Find this author on Google Scholar Find this author on PubMed Search for this author on this site Solofo E. Rakotoarisoa 4 Conservation Allies , VO 12 Bis A, Manakambahiny, Antananarivo 101, Madagascar Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Solofo E. Rakotoarisoa Ronell R. Klopper 5 South Africa National Biodiversity Institute , 2 Cussonia Ave, Brummeria, 0184 Pretoria, Republic of South Africa 6 HGWJ Schweickerdt Herbarium, Department of Plant and Soil Sciences, University of Pretoria , Lynnwood Rd, Hatfield, 0002 Pretoria, Republic of South Africa Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Ronell R. Klopper Gideon F. Smith 7 Ria Oliver Herbarium, Department of Botany, Nelson Mandela University, University Way , Summerstrand, 6019 Gqeberha, South Africa Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Gideon F. Smith Nina Rønsted 3 Natural History Museum of Denmark, University of Copenhagen , 1350 Copenhagen K, Denmark Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Nina Rønsted Olwen M. Grace 2 Royal Botanic Gardens , Kew, TW9 3AE Richmond, Surrey, United Kingdom 8 Royal Botanic Garden Edinburgh , 20a Inverleith Row, EH3 5LR Edinburgh, United Kingdom Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Olwen M. Grace For correspondence: yannick.woudstra{at}su.se ograce{at}rbge.org.uk Abstract Full Text Info/History Metrics Supplementary material Data/Code Preview PDF Abstract Background and Aims With >700 species, Aloe and its generic kin (alooids) are a morphologically diverse group of succulent plants with a wide range across Africa, Madagascar and the Arabian Peninsula. Species such as Aloe vera and A. ferox are cultivated at scale for natural products, whole foods, and cosmetics. Despite substantial α-taxonomy contributions, infrageneric classification of Aloe has remained unresolved. Molecular systematics has been compromised by the lack of informative characters in standard markers and high costs of obtaining informative nuclear loci from large genomes (e.g. >15 Gbp); and the difficulty of obtaining quality DNA extractions from material of known provenance. Here these constraints are overcome with target capture sequencing that allows cost-effective sequencing of informative low-copy nuclear loci and unlocks genetic resources from preserved specimens in herbaria as well as silica-dried tissues. Methods Using a custom kit for alooids, 189 nuclear loci were sequenced in 294 species, including 50 herbarium specimens, to build a new phylogenomic framework for the big genus Aloe and 11 closely related genera in the alooid clade. Available taxonomic classifications for Aloe sensu stricto were contrasted against the obtained topology in an effort to stabilise taxonomy. Genus-level representations of the family Asphodelaceae were sequenced with the same tool. Key results The new phylogenomic framework demonstrates the monophyly of the alooids and confirms recent classifications in which smaller genera ( Aloidendron , Aloiampelos , Aristaloe , Gonialoe , Kumara ) are separated. Strong geographic patterns in the Aloe phylogeny are contrasted by less obvious phylogenetic structure in habit (growth form), and vegetative or reproductive morphology that are mainstays of α-taxonomy. Conclusion Repeated incidents of adaptive radiation and niche specialisation appear to underlie species diversity in Aloe . This study illustrates the power of combined (nuclear) phylogenomic and α-taxonomic inference, including the utility of herbarium genomics, in resolving the systematics of big genera. Lay summary The alooids are a group of >700 succulent plants, such as Aloe vera . Testing their taxonomy with genetics is difficult as Aloe genomes are large and very similar between species. A targeted approach was used to classify alooids with highly variable nuclear genes in ±300 species. The evolutionary relationships of alooids are determined principally by geographic distribution patterns, rather than plant morphology or flower shape. INTRODUCTION Molecular phylogenetics has become the framework for integrated systematics ( Grace et al ., 2021 ). Reconstructed evolutionary history can be contrasted with available taxonomic hypotheses to provide additional evidence for revised classifications. This has led to the presentation of revised systematics for morphologically diverse and taxonomically complex plant families [e.g. Fabaceae ( Legume Phylogeny Working Group, 2017 ), Asteraceae ( Mandel et al ., 2019 ), Poaceae ( Grass Phylogeny Working Group III, 2024 ), and, at a higher taxonomic rank, flowering plants in general ( The Angiosperm Phylogeny Group, 2016 )]. In addition, a phylogenetic tree provides meaningful insights about the evolutionary history that gave rise to observed morphological variation (e.g. Zuntini et al ., 2024 ). In many plant groups, however, the implementation of molecular systematics has unfortunately been hindered by: (i) a lack of variation in conventional DNA markers, leading to high levels of uncertainty in phylogenetic tree inference ( Hollingsworth et al ., 2011 ); and (ii) difficulties in obtaining high-quality DNA samples from taxonomically verified reference material. This is particularly the case for highly diverse, “big” genera, i.e. genera containing >500 species ( Frodin 2004 ), which are often characterised by high levels of rapid diversification and comprise many “difficult-to-collect” species, which may require considerable resource and skill to be collected for study. The emergence of nuclear phylogenomics, particularly with the use of target capture sequencing, has assisted with overcoming these limitations for many plant lineages ( Dodsworth et al ., 2019 ). With these modern techniques, hundreds of phylogenetically-informative nuclear loci can be sequenced with high coverage at a relatively low cost ( Woudstra et al ., 2022 ). Target capture sequencing also works well on degraded DNA from historical specimens ( Hart et al ., 2016 ; Quatela et al ., 2023 ), unlocking a “treasure vault” of genetic resources represented by centuries of botanical collecting with global coverage. The inclusion of herbarium specimens, particularly type specimens, is considered the gold standard in molecular systematics ( Renner et al ., 2024 ) because the application of taxonomic names is based on these specimens, thereby providing the best material with which to test taxonomic hypotheses using molecular data. Target capture sequencing tools are available as universal kits [e.g. Angiosperms353 ( Johnson et al ., 2019 )] or clade-specific ranging from family-[e.g. Asteraceae1061 ( Mandel et al ., 2014 )] to genus-level [e.g. Inga ( Nicholls et al ., 2015 )]. Although they are available at a lower cost, universal kits target more conserved loci and may therefore be less suitable for molecular systematics in big genera. In fact, most big-genus phylogenomic studies use a customised approach to target more variable loci [e.g. Dioscorea with >600 species (Soto Gomez et al ., 2019), Silene with >1000 species ( Quatela et al ., 2023 ) and Begonia with >2000 species ( Michel et al ., 2022 )]. In terms of morphology and ecology, Aloe sensu stricto is highly diverse and, in terms of species numbers, qualifies as a “big” genus comprising 591 species ( Newton, 2020 ) with a relatively recent evolutionary history (±15 million years) ( Grace et al ., 2015 ). Aloe and its generic kin (alooids) are a predominantly African group of succulent plants, with a natural geographical distribution range covering much of the continent, as well as Madagascar, the Mascarene Islands, Socotra, and the Arabian Peninsula. Several Aloe species are economically important, for example for the medicinal value derived from various fractions of their leaf extracts, supporting a global health products industry, most notably by Aloe vera and A. ferox . The inner leaf mesophyll tissue (clear gel) of these species is used in cosmetic products, while the leaf exudate of several species, rich in secondary metabolites with antioxidative properties, has been used in traditional medicine to treat, amongst others, indigestion, malaria, and cancer ( Grace, 2011 ; Amir et al ., 2019 ). Despite its relatively recent diversification, the genus presents a remarkable level of morphological and ecological variation ( Fig. 1 ), reflected by the publication of names for at least 56 infrageneric groups, some recognised at the ranks of section and series and others informally named morphogroups. Download figure Open in new tab Fig. 1. Morphological and ecological diversity of alooid species. Growth form ranges from tall trees (A; Aloidendron barberae ) to clump-forming shrubs (B; Aloe framesii ) to small stemless plants (C; Aloe vera ). Alooids occupy a wide range of habitats (Supplementary Figure S2) ranging from hyper-arid cliff-faces (D; Aloe meyeri ) to forest understories (E; Aloe namorokoenesis ). Leaf shape is extremely variable with many species displaying spotted (maculate) patterns (F; Aloe davyana ), where sometimes the ends of the leaves dry up but stay on. More than 60 species form grass tuft-like leaves (G; Aloe chortolirioides ) acting as camouflage, whereas others display conspicuous black spines all over the leaves (H; Aloe melanacantha ). The arrangement of the leaves is usually in a rosette, the most striking example of which is found in the spiral arrangement of Aloe polyphylla (I), although distichous (plicate) arrangements are also found (J; Kumara plicatilis ). Finally, strikingly different inflorescence types are found among the alooids with ball-shaped terminal (capitate) arrangements (K; Aloe maculata ) and cylindrical racemose panicles (L; Aloe ferox ) the most common types. Nearly horizontal (oblique) arrangements of inflorescences are also found (M; Aloe marlothii ). Photo credits: A, I, L – N.R. Crouch; B – A.W. Klopper; C, F, G, J, K, M – G.F. Smith; D – E.J. van Jaarsveld; E – L. Nusbaumer, © Conservatoire & Jardin Botaniques Genève; H – H.M. Steyn. Although the formal nomenclatural and taxonomic history of Aloe dates back to 1753 ( Linnaeus, 1753 ), the first ‘modern’ monograph of the genus was only published more than 150 years later ( Berger, 1908 ). Berger (1908) recognised 181 species that he arranged in more than 30 infrageneric groups; many of these are still upheld today. Berger (1908) based his work on herbarium collections as well as living material cultivated in the Hanbury Garden at La Mortola, Italy. As far as is known, Berger never studied aloes in their natural habitats. Within 20 years following the publication of Berger’s (1908) classification, locally active botanists such as HB Christian (South-tropical Africa), H Perrier de la Bâthie (Madagascar), and GW Reynolds (southern Africa), together described more than 140 species that are still accepted today ( Klopper and Smith, 2013 ). Reynolds produced the most extensive monographs on Aloe to date, focusing on southern Africa first ( Reynolds, 1950 ) and later complementing this work with treatments of the Aloe taxa of Madagascar and tropical Africa ( Reynolds, 1966 ). In the South African monograph, Reynolds (1950) followed Berger’s classification (1908) but refined and expanded other formally published infrageneric groups. Many of the new species described from tropical Africa and Madagascar, however, did not comfortably fit within the framework of Berger (1908) , leading Reynolds (1966) to group them into newly circumscribed morphogroups. In subsequent decades the number of new species discovered and described increased steadily ( Klopper and Smith, 2013 ), with the novel material mainly originating from tropical Africa and Madagascar. By the early 21 st century, molecular phylogenetic studies started influencing the classification of the alooids, especially at the rank of genus. Historically, many genera were segregated from Aloe , but these were often eventually reincorporated. Notable alooid segregates reunited with Aloe are Leptaloe (grass aloes) and Lomatophyllum (berried aloes), with Leptaloe at present regarded as fitting in A . sect. Leptoaloe , along with the robust grass aloes, also referred to as slender aloes in the vernacular. The berried aloes are at present treated at the rank of section in the genus Aloe ( Glen and Hardy, 2000 ; Grace et al ., 2013 ; Newton, 2020 ). Representatives of Chortolirion (bulbous, grass-like aloes), which have a decidedly haworthioid appearance, are now similarly included in an expanded concept of Aloe ( Manning et al ., 2014 ). In contrast, several genera have been reinstated or newly published based on molecular evidence ( Grace et al ., 2013 ; Manning et al ., 2014 ; Grace et al ., 2015 ): Aloestrela [ancient aloe] ( Smith and Molteno, 2019 ) and Aristaloe [awn-leaf aloe] (both monotypic); Kumara ([fan aloes] two species); Aloiampelos ([rambling aloes] seven species); Aloidendron ([tree aloes] six species); and Gonialoe ([kanniedood aloes] four species). In addition, the genera Astroloba (11 species), Haworthia (57 species), Haworthiopsis (18 species), Gasteria (28 species), and Tulista (4 species) are all treated as accepted and distinct from Aloe sensu stricto ( Newton, 2020 ). As a result, Aloe sensu stricto now includes 591 species (excluding natural and artificial hybrids; CITES Secretariat, in press), many of which have never been placed in any of the infrageneric groups available for the genus. The taxonomy of Aloe and some of its generic kin is therefore in a state of flux. A lack of character variation (and thus resolution) in current molecular phylogenetics ( Manning et al ., 2014 ; Grace et al ., 2015 ; Dee et al ., 2018 ), however, resulted in authors of recent taxonomic treatments ( Carter et al ., 2011 ; Newton, 2020 ) being reluctant to incorporate at least some of the proposed changes at various generic and infrageneric ranks. Expanding the molecular dataset with plastid phylogenomics (e.g. using whole chloroplast genomes from genome skimming data) can improve this situation, particularly when herbarium material, including type specimens, is incorporated, as evidenced by Malakasi et al . (2019) in a study of the tree aloes ( Aloidendron ). For the big genus Aloe , however, more variable data from the nuclear genome is needed to track species boundaries ( Woudstra et al ., 2021 ). This study aimed to test a highly reduced representation approach to resolve long-standing phylogenetic uncertainties in Aloe with new nuclear phylogenomic data from an expanded sampling of species in the genus. A customised target capture sequencing tool ( Woudstra et al ., 2021 ) was applied to generate an adequate nuclear genomic reference database ( Woudstra et al ., 2024 ) from which a phylogenomic framework for the alooids (Asphodelaceae subf. Asphodeloideae) was built. The resulting phylogeny was then interpreted taxonomically to inform the stability, and remaining uncertainties, of the classification of Aloe and related genera. MATERIALS AND METHODS Sampling The basis of this study was formed by sampling preserved (herbarium and living) botanical collections at the Royal Botanic Gardens, Kew (K); Natural History Museum of Denmark, Copenhagen (C); East African Herbarium (EA), the Muséum National d’Histoire Naturelle, Paris (P); and the botanic gardens of the Universities of Potsdam, Uppsala, Göteborg, and Cambridge. The sampling was designed to build (i) a genus-level backbone phylogeny for the family Asphodelaceae and (ii) a comprehensive phylogeny for Aloe sensu stricto and related genera (the alooids). Here we apply the term “alooid” to all currently and formerly accepted species and infraspecific taxa of the genus Aloe and related genera. These comprise Aloe sensu stricto (591 species and 71 additional infraspecific taxa), the smaller genera Aloiampelos (seven species and three additional varieties), Aloidendron (six species), Gonialoe (four species), and Kumara (two species), the monotypic genera Aloestrela and Aristaloe , and the related genera Astroloba , Gasteria , Haworthia , Haworthiopsis and Tulista . All taxon names referred to in this study follow the checklist provided by World Flora Online (WFO, 2025), unless stated otherwise. For the Asphodelaceae backbone phylogeny, DNA extracts and ready-to-sequence DNA libraries for one member of each genus in the Asphodelaceae were obtained, except Kniphofia and Haworthia . These genera were sampled as part of the ongoing Plant and Fungal Tree of Life (PAFTOL) project at the Royal Botanic Gardens, Kew ( Baker et al ., 2022 ). This included samples from the related alooid genera Astroloba , Gasteria , Haworthia , Haworthiopsis and Tulista . For Haworthia , H. coarctata was sampled, which was since placed in Haworthiopsis ( Rowley 2013 ) and therefore samples representing Haworthia sensu stricto are lacking from this study. For the other alooids, we used samples from two previous studies ( Woudstra et al ., 2021 ; 2024 ) covering Aloe (401 samples, 378 species, four additional subspecies and eight additional varieties), Aloestrela (one species), Aloiampelos (three species), Aloidendron (four species), Aristaloe (one species), Gonialoe (one species), and Kumara (one species). The sampling for Aloe covered the main taxonomic groups ( Berger, 1908 ; Reynolds, 1950 , 1966 ; Glen and Hardy, 2000 ), phylogenetic clades ( Manning et al ., 2014 ; Grace et al ., 2015 ; Dee et al ., 2018 ), and geographic centres of diversity ( Carter et al ., 2011 ; Grace et al 2015 ). Detailed information on sample origins can be found in the Accession Information file (online supporting material). The procedure for sampling followed the methods outlined by Woudstra et al . (2024) . DNA isolation and sequencing DNA was isolated using either a Qiagen DNEasy kit (for high molecular weight DNA from silica-dried leaf material) using silica columns for purification (Qiagen, Holden, Germany) or using a CTAB protocol ( Doyle and Doyle, 1987 ) combined with a purification protocol optimised for herbarium material ( Quatela et al ., 2023 ) using AMPure XP beads (Beckman Coulter, Brea, California, USA). For some herbarium samples, a cleaning step was performed before CTAB extraction in an effort to remove high amounts of polysaccharides and polyphenol ( Shepherd and McLay, 2011 ). High-molecular weight DNA samples were fragmented by ultrasonication (Covaris M220, Covaris, Woburn, Massachusetts, USA). Libraries were prepared using NEBNext Ultra II library preparation kits for Illumina sequencing using Multiplex Dual Index sets 1&2 (New England Biolabs, Ipswich, Massachusetts, USA). Pools of 8–27 equimolar indexed library samples were then enriched with the alooid target capture bait panel ( Woudstra et al ., 2021 ), which uses myBaits ® v3 chemistry (Daicel Arbor, Ann Arbor, Michigan, USA). High-throughput Illumina ® paired end sequence data was obtained for the samples described above. As datasets from different studies were combined ( Woudstra et al 2021 ; Woudstra et al 2024 , the sequence platform and read length varied from 350 bp PE on Illumina MiSeq to 150 bp PE on Illumina HiSeq. Four samples were generated from Illumina RNAseq data assembled into transcripts ( Woudstra et al ., 2021 ). Details for each included sample can be found in the sequencing information file (online supporting material). Phylogenomics Sequence data were analysed to produce an updated phylogenomic framework for (i) genus-level infrafamilial relationships for genera in Asphodelaceae and (ii) species-level inter- and infrageneric relationships among species in the alooid clade in the subfamily Asphodeloideae ( Fig. 2 ). For the Asphodelaceae backbone phylogeny, a subsampling with one representative of each genus were used, together with four representatives for the big genus Aloe : the southern African Aloe polyphylla , the eastern African A. secundiflora , the Mascarene A. tormentorii , and the iconic A. vera that has a strong affinity with Arabian aloes. For the alooid species tree, all suitable samples were used, together with Bulbine frutescens as outgroup. Download figure Open in new tab Fig. 2. Coalescent summary tree (generated with ASTRAL-III) of the genus-level backbone phylogeny for Asphodelaceae. The tree was manually rooted at the branch for Xanthorrhoea preissii , causing the absence of a node support for nodes between subfamilies. Nodes that are fully supported (LPP=1) are indicated with a light green circle and are specified in full if lower (<1). All three defined subfamilies are monophyletic, with the alooid clade being part of the Asphodelaceae subf. Asphodeloideae. The tree can be explored using the following link: https://itol.embl.de/shared/YWoudstra . A conservative and curated approach was taken to the phylogenomic analysis to minimise issues with sequence alignment and paralogy affecting the inference of phylogenetic relationships. Firstly, information from (overhanging) off-target reads, which can sometimes be assembled in intronic and intergenic regions, were not used as the recovery and coverage of these regions would be relatively random due to the baits being designed to capture exons ( Woudstra et al ., 2021 ). Secondly, all loci with high rates of paralogy were removed, as identified by the HybPiper paralogy warning script ( Johnson et al ., 2016 ) and visual inspection of alignments ( Woudstra et al ., 2021 ). Thirdly, poorly recovered loci (<200 samples) and samples with <50% total recovered target length (≤175 kbp) were excluded. Finally, the resulting phylogeny was curated by removing all samples with questionable phylogenomic placement due to human error in mislabelling of original DNA isolates or in DNA library preparation (Sequencing Information file, online supporting material). Sequence reads were assembled into contigs and processed into clean, multiple-sequence alignments (MSAs) using the following pipeline: (1) Raw reads were trimmed using Trimmomatic v0.39 ( Bolger et al ., 2014 ) to remove low-quality (terminal parts of) reads (phred-33 score below 30 - <99.9% accuracy); (2) Trimmed reads were assembled into 189 low-copy nuclear target loci using HybPiper v1.3.1 ( Johnson et al ., 2016 ) against reference sequences from the original transcriptomes used for the aloe TCS design ( Woudstra et al ., 2021 ); (3) Assembled target exon sequences were assembled into MSAs using MAFFT v7.429 ( Katoh and Standley, 2013 ); which were subsequently trimmed to remove (4a) insertions (<650 bp) and deletions that are present in less than half of all samples using CIAlign v1.0.14 ( Tumescheit et al ., 2022 ); (4b) nucleotide sites covered by less than a fifth of all samples using Phyutility v2.2 ( Smith and Dunn, 2008 ); and (4c) previously undiscovered putative paralogous regions by visualisation and manual cleaning in Geneious 9.1 Pro. Sequences <100 bp were removed from the multiple sequence alignments. Woudstra et al . (2024) provide more information. To estimate phylogenetic relationships, maximum likelihood gene trees were generated using IQ-Tree v1.6.12 ( Nguyen et al ., 2015 ) for each of the loci remaining after the filtering, trimming, and manual cleaning steps. A general time reversible model (GTR) for substitution rates combined with a gamma-distribution for rate heterogeneity (option +G) and a correction for invariable sites (option +I) were deployed. Node support was calculated using 1000 ultra-fast bootstrap replications (option -bb). The 173 resulting gene trees were summarised into a species tree using the coalescent-based model implemented in ASTRAL-III ( Zhang et al ., 2018 ). This model accounts for incomplete lineage sorting, which is estimated through gene tree discordance, and defined as the ratio of quartets shared between all gene trees and the species tree. The resulting summary trees were visualised and annotated in the interactive Tree of Life programme ( Letunic and Bork, 2021 ). The Asphodelaceae tree was rooted on the branch containing the Xanthorrhoea preissii sample, following the Kew Tree of Life ( Baker et al ., 2022 ) for Asphodelaceae. The alooid species tree was rooted on the branch containing the outgroup sample for Bulbine frutescens (subf. Asphodeloideae). Taxonomic hypothesis testing The most comprehensive treatments for Aloe were used as taxonomic hypotheses for phylogenetic testing: the monograph of Aloe by Berger (1908) ; the expanded treatments of Reynolds for southern Africa ( Reynolds, 1950 ), tropical Africa ( Reynolds, 1966 ), and Madagascar ( Reynolds, 1966 ); and the floristic treatment of Aloe by Glen and Hardy (2000) as part of the Flora of Southern Africa series. The groups of Malagasy aloes recognised by Castillon and Castillon (2010) were not tested as the sampling in the present study did not have sufficient coverage of all the groups recognised. Using the taxonomic concepts for sections and series described in these publications, validly published species names were allocated to taxonomic groups (online supporting material). Using the interactive Tree of Life annotation software ( Letunic and Bork, 2021 ) the alooid phylogeny was then annotated with the main infrageneric groups (sections and series) in Aloe according to Berger (1908) before adding additional detail from other treatments by Reynolds (1950 ; 1966 ) and Glen & Hardy (2000) . Finally, phylogenetic patterns for geographic distribution were tested with eight different areas of diversity distinguished, based on Carter et al . (2011) and Grace et al . (2015): Southern Africa, including all of South Africa, Lesotho, and Eswatini; Southwestern Africa, including all of Namibia and the dry, southwestern parts of Angola; South Tropical Africa, corresponding roughly to Zambezia including Botswana, Mozambique, Zambia, Zimbabwe, and the eastern parts of Angola; Tropical East Africa, including all of Kenya, Uganda, Tanzania, Rwanda, and Burundi; Tropical West Africa, including the tropical wetter parts of the Congo and the Gold Coast; the Horn of Africa, including all of Ethiopia, Somalia, Eritrea, Djibouti, Sudan, and South Sudan; the Arabian Peninsula, including all of Saudi Arabia, Oman, and Yemen, including Socotra; Madagascar and the Mascarene islands, including La Réunion, Mauritius, Mayotte, the Comoros, and the southern Seychelles. RESULTS This study presents a considerable increase in sequence information for the alooids (Asphodelaceae subf. Asphodeloideae; Aloe and related genera) covering all 12 genera (with the exception of Haworthia sensu stricto) and 303 taxa (294 species, of which 278 belong to Aloe ) in total. 142 of these taxa (133 species) have never been sequenced before (Species Information file, online supporting material). The amount of sequence data underlying the phylogeny was considerably increased for all species, from up to seven plastid and nuclear ribosomal markers (previous studies) to 173 low-copy nuclear genes (this study), discounting 16 genes removed due to paralogy or low recovery. The total target dataset (all 189 genes) comprised 350,347 bp compared to 4,693 bp using traditional markers ( Woudstra et al ., 2021 ). A fully resolved backbone phylogeny for Asphodelaceae The final backbone phylogeny of Asphodelaceae ( Fig. 2 ) comprises all but two (Kniphofia and Haworthia) of the currently accepted genera. Both Hemerocallidoideae (20 genera) and Asphodeloideae (19 genera) are monophyletic, with the monogeneric Xanthorrhoeoideae sister to Asphodeloideae. The alooids (12 genera) comprise a monophyletic clade embedded within subfamily Asphodeloideae. All except five nodes were fully supported (Local Posterior Probability (LPP) >1), with relationships between Gonialoe , Aristaloe , and Gasteria receiving the lowest support. In Asphodeloideae, Asphodelus is monophyletic with Asphodeline in a clade that is sister to the rest of the genera. Trachyandra and Eremurus are also monophyletic, while Bulbinella is recovered on a separate branch. Bulbine and Jodrellia are sister to the monophyletic alooid clade. Within this, Aloidendron and Aloestrela form a monophyletic clade that, together with Aloiampelos , are sister to the rest of the alooid genera. Kumara is recovered on a distinct branch, sister to the “core” alooids. Aloe sensu stricto is monophyletic and distinct from a clade comprising Gonialoe and Aristaloe which were previously included in Aloe (clade C, Fig. 2 ). In clade C, Astroloba is sister genus to the rest, but the nodes separating Gonialoe and Aristaloe are poorly supported (LPP=0.56 and 0.44, respectively). Haworthiopsis tessellata is separate from Haworthia coarctata (i.e. Haworthiopsis coarctata ), which is monophyletic together with Tulista . Haworthiopsis is therefore paraphyletic in this topology. Two monophyletic clades are recovered in Asphodelaceae subf. Hemerocallidoideae. In the smaller clade, the genus Pasithea is sister to eight other genera and Phormium is sister to the remaining seven. Geitonoplesium and Agrostocrinum are monophyletic, as are Herpolirion and Thelionema . The monophyly of Stypandra with Dianella and Excremis is poorly supported (LPP=0.64), while there is full support for monophyly between the latter two. The larger clade involves Hemerocallis , which is monophyletic together with Simethis and Chamaescilla . This group is sister to the former Johnsoniaceae (clade B, Fig. 2 ), comprising Tricoryne , Corynotheca , Caesia , Arnocrinum , Stawellia , Hodgsoniola , Johnsonia , and Hensmania . Hodgsoniola is monophyletic with Stawellia with moderate support (LPP=0.75), while the monophyly of Johnsonia and Hensmania is fully supported. The genera of the alooid clade The species-level topology for alooids confirms the separation of Aloestrela , Aloidendron , Aristaloe , Gonialoe , and Kumara from Aloe sensu stricto with full support ( Fig. 3A ). Aloestrela is nested within Aloidendron and together they form a fully supported monophyletic clade of five species in this topology. Aloiampelos ciliaris and A. striatula are monophyletic and form a larger monophyletic clade together with Aloidendron . Kumara is sister to the remaining members of the alooid clade, with the 279 species of Aloe sensu stricto forming a large, fully supported monophyletic clade. Although two out of the three sequenced species of Aloiampelos are phylogenetically distinct from Aloe sensu stricto, Aloiampelos is not resolved as a monophyletic clade because Aloiampelos commixta is sister to Aloe sensu stricto ( Fig. 3A ). Download figure Open in new tab Fig. 3. Phylogenetic relationships within the alooids as determined with a coalescent-based summary tree from 173 low-copy nuclear gene trees. (A) Cladogram displaying intergeneric relationships in the alooid clade. (B) Detailed infrageneric cladogram for Aloe sensu stricto with labels coloured according to fully supported taxonomic sections ( Fig. 4 ) or geographic distribution ( Fig. 5 ). The tree can be explored using the following link: https://itol.embl.de/shared/YWoudstra . Gonialoe and Aristaloe form a fully supported clade with the larger genera Haworthiopsis and Gasteria , as well as Astroloba , and Tulista . The genus-level phylogeny of Asphodelaceae (clade C, Fig. 2 ) and the species-level phylogeny of the alooids ( Fig. 3A ) disagree about the relationship between Gonialoe , Astroloba , and the other genera: in the former, Astroloba is sister to the rest, while in the latter Gonialoe is in this position. In both cases these nodes are not supported (LPP=0.56 and 0.36, respectively) and the sister genus placement therefore remains ambiguous. Both topologies do, however, agree on the placement of Aristaloe as sister to Gasteria , Haworthiopsis , and Tulista , with the latter three forming a monophyletic clade. Infrageneric relationships in Aloe sensu stricto The final phylogeny of Aloe sensu stricto presented here comprises 279 species with five additional subspecies and three additional varieties ( Fig. 3B ). Support was generally high (LPP ≥0.80), particularly for the deeper nodes. Gene tree discordance was detected with a normalised quartet score of 0.625, causing low support in some of the shallower nodes of diverse clades (e.g. Maculate aloes). The new topology generally favours the classification of Berger (1908) for the southern African clades ( Fig. 4A ), whereas the tropical African clades, which are younger, are better characterised by geographic distribution patterns ( Fig. 5 ) than by morphology ( Fig. 4B ). Download figure Open in new tab Fig. 4. Phylogenetic testing of standing taxonomic hypotheses for the genus Aloe sensu stricto. (A) Main sections, following the classification by Berger (1908) with amendments by Reynolds (1950) and Glen and Hardy (2000) . (B) Morphogroups for the aloes of tropical Africa and the Arabian Peninsula following the classification by Reynolds (1966) . (C) Morphogroups for the aloes of Madagascar and the Mascarene islands, including Aloe sect. Lomatophyllum as circumscribed by Rowley (1996) , and following the classification by Reynolds (1966) . Topologies correspond to the coalescent-based summary tree for the alooids ( Fig. 3 ) and can be explored using the following link: https://itol.embl.de/shared/YWoudstra . Download figure Open in new tab Fig. 5. Phylogenomic patterns of geographic distribution in the alooids. Geographic regions are based on the classifications by Carter et al . (2011) and Grace et al . (2015). Topology corresponds to the coalescent-based summary tree for alooids ( Fig. 3 ) and can be explored using the following link: https://itol.embl.de/shared/YWoudstra . The older clades are predominantly formed by southern African taxa ( Fig. 5 ). Among these, many of the sections, especially those first included in the monograph of Berger (1908) , form clear phylogenetic patterns ( Fig. 4A ). Aloe sect. Aloe is sister to the rest of the genus with two species from A . sect. Echinatae (i.e. A. erinacea and A. melanacantha ) embedded within it. Aloe sect. Leptoaloe is a monophyletic clade (LPP = 0.73) with the only exception being the bulb-forming A. buettneri , which is sister to A . sect. Pictae . In A . sect. Pictae , A . ser. Paniculatae is embedded as a paraphyletic clade. Aloe sect. Latebracteatae is monophyletic and forms a clade with two paraphyletic members of A . sect. Anguialoe (i.e. A. alooides and A. vryheidensis ) and A. globuligemma ( A . sect. Ortholophae ). With the exception of one species ( A. rupicola ), A . sect. Pachydendron (single-stemmed, tree-like aloes) is monophyletic and comprised only of southern African species with A . sect. Pachythamnos embedded within it, along with A. marlothii (placed by Berger (1908) in A . sect. Ortholophae ). Aloe rupicola ( A . sect. Pachydendron ) is instead embedded within the monophyletic A . sect. Asperifoliae , which comprises species predominantly from Southwestern Africa. Although paraphyletic, the three members of A . sect. Longistylae (i.e. A. broomii , A. chlorantha , and A. longistyla ) are all in the same clade together with three of the five members of A . sect. Purpurascentes (i.e. A. framesii , A. khamiesensis , and A. microstigma ) and two monophyletic members of A . sect. Rhodocanthae (i.e. A. glauca and A. lineata ). Also included in this clade are A. humilis and A. pictifolia (from A. sect. Echinatae ), but A. humilis resolves as sister to the clade containing the two species of A . sect. Rhodocanthae , while A. pictifolia is sister to A. microstigma . Aloe arborescens and A. mutabilis from A . sect. Arborescentes are monophyletic, while A. pluridens is sister to A. succotrina (from A . sect. Purpurascentes ). Another Southern African clade comprises A. comosa (from A. sect. Rhodacanthae ), A. gariepensis (from A. sect. Purpurascentes ), and A. krapohliana (from A. sect. Echinatae ). While southern African taxa of A. sect. Aloe , A . sect. Latebracteatae , A . sect. Leptoaloe , A . sect. Pachydendron , and A . sect. Pictae form strongly supported coherent clades, several sections are polyphyletic: A. sect. Arborescentes , A. sect. Echinatae , A. sect. Purpurascentes , and A. sect. Rhodacanthae . The taxonomic sections hitherto recognised in Aloe are not recovered intact in the phylogenetic clades of tropical Africa ( Fig. 4A ). Aloe sect. Chabaudia (seven species), A . sect. Ortholophae (10 species), and A . sect. Pachydendron (six species) are all represented by species spread across three clades covering substantial phylogenetic distances. A similar pattern is found for the three Tropical African members of A . sect. Pictae , which are spread across two clades. Aloe sect. Latebracteatae is the only monophyletic section among the tropical African aloes, though separated from the southern African taxa. All of the tropical African morphogroups recognised by Reynolds (1966) are polyphyletic ( Fig. 4B ) with only a few groups forming monophyletic clades, but never with all members sampled. Of these, the strongest coherence is found in Group 9 of Reynolds (1966) , which is an expanded version of A . sect. Verae , where only two members are recovered in a separate clade. Aloe dorotheae (Reynolds Group 5) forms a monophyletic clade with two of its close relatives but with a third species separate ( A. canarina ). Based on perianth structure, two groups can be formed: those with striped perianths (Reynolds Group 4; clade I, Fig. 4B ; five species) that comprise the A. somaliensis species complex ( Fig. 3B ); and those with clavate perianths (Reynolds Group 13; clade II, Fig. 4B ; four species). Geography ( Fig. 5 ) is a better classifier than morphology in Aloe sensu stricto, with the Tropical African aloes roughly falling into three geographic clades: Southwestern Africa, Tropical East Africa, and aloes from the Horn of African and Arabian Peninsula. A shrubby growth form is the predominant type of habit among tropical East African species of Aloe (24 species, Reynolds Group 19, Fig. 4B ; Supplementary Figure S1). The A. somaliensis cluster of species mentioned above is nested within the Tropical East African clade and A . sect. Verae comprises predominantly Arabian aloes. Within A . sect. Pictae , a monophyletic group is formed by aloes from tropical East Africa and the Horn of Africa. The Malagasy taxa in Aloe sensu stricto form a fully supported monophyletic clade with the monophyletic clade with A . sect. Lomatophyllum embedded in it ( Fig. 4C ). As is the case for the tropical African aloes, the Malagasy morphogroups recognised by Reynolds (1966) are not recovered as phylogenetic units. The only coherent group of species from Madagascar comprises three paraphyletic species with capitate inflorescences. DISCUSSION AND CONCLUSIONS The alooid clade The findings of this study bring hitherto-elusive phylogenomic evidence to stabilise the current classification of the alooids. The taxonomy of the alooids has been revised significantly in the last three decades, with several genera being split from the core Aloe genus ( Grace et al ., 2013 ; Manning et al ., 2014 ; Smith and Molteno, 2019 ), and older genera being reincorporated ( Rowley, 1996 ; Glen and Hardy, 2000 ; Grace et al ., 2013 ). With a few minor changes, which are detailed below, an intergeneric classification of eleven alooid genera (comprising 730 species) can be stabilised. The present study furthermore provides a framework and genomic tool with which to add previously-uninvestigated species as sequences become available to complete the Aloe tree of life. One of the more easily distinguishable groups of alooids is the tree aloes, i.e. the genus Aloidendron , based on their distinctive arborescent, often multi-branched growth form ( Malakasi et al ., 2019 ). Nevertheless, the systematics surrounding this group has become rather complicated in recent years. Although the arborescent growth form has likely evolved multiple times in the alooids (Supplementary Figure S1), species included in Aloidendron are distinct from often single-stemmed trees included in Aloe sensu stricto by their height (>3 m), dichotomous branching and non-retention of dead leaves on the stem and branches ( Grace et al ., 2013 ). For these reasons, the (usually) unbranched Malagasy tree aloe Aloe suzannae , which showed phylogenetic affinity with Aloidendron , was raised to its own monotypic genus Aloestrela ( Smith and Molteno, 2019 ). Aloe sabaea , on the other hand, was placed in Aloidendron ( Manning et al ., 2014 ) based on an erroneous record of a 9 m-tall specimen by Reynolds (1966) ( Malakasi et al ., 2019 ). Kumara , the other genus of which one representative attains tree-like dimensions, has distinctly distichous (plicate) leaves. Following the results by Malakasi et al . (2019) , the present detailed nuclear phylogenomic study of the alooids now reinforces the acceptance of Aloidendron and Kumara at the rank of genus. Aloestrela suzannae is nested well within Aloidendron sensu stricto and could be transferred to Aloidendron . Aloe sabaea is clearly distinct from Aloidendron and is related to tropical African tree-like species, such as Aloe ballyi , included in Aloe sensu stricto, and has already been returned to the genus Aloe ( Smith et al ., 2019 ). Kumara plicatilis is also clearly distinct, occurring on a separate branch as sister to the remaining genera in the alooid clade, and the reinstatement of this genus is therefore warranted. Although Aloidendron pillansii was not sequenced in this study, its placement in Aloidendron was confirmed by Malakasi et al . (2019) . This species was, however, paraphyletic in that study and thus requires further investigation for its taxonomic status. Aloidendron tongaense has yet to be sequenced and investigated phylogenetically and therefore requires further attention to complete systematic studies on Aloidendron. At present, the genus Aloidendron should therefore comprise seven species, with the inclusion of Aloestrela suzannae . The genus Aloiampelos also comprises seven species and is distinguishable by its variously rambling, leaning, or creeping habit, characteristic leaf sheaths and comparatively long internodes ( Grace et al ., 2013 ). Contrary to Aloidendron , this genus is polyphyletic in the present topology ( Fig. 3A ) with two species showing strong affinity with Aloidendron and one, i.e. Aloiampelos commixta , being sister to Aloe sensu stricto. The placement of this Aloiampelos commixta sample was also recovered using the Angiosperms-353 universal target capture kit ( Baker et al . 2022 ). In a taxonomic study of Aloiampelos by Ellis (2013) , A. commixta consistently resolved within Aloiampelos , often sister to A. juddii . However, the various gene trees (based on ITS sequences) presented in that study generally did not show good node support ( Ellis, 2013 ). Further phylogenomic investigation using other accessions, preferably including the type specimen of A. commixta and material from A. juddii , should confirm whether this taxon does indeed not belong to Aloiampelos. Returning this taxon to Aloe sensu stricto would be one possible solution, but further investigation is required before any changes to the circumscription of the genus Aloiampelos is made. The kanniedood aloes (genus Gonialoe ) and the awn-leaf aloe (monotypic genus Aristaloe ) were separated from Aloe based on their phylogenetic affinity with Haworthia and Gasteria ( Manning et al ., 2014 ). The results presented here support this separation showing Gonialoe variegata and Aristaloe aristata as phylogenetically distinct from Aloe sensu stricto. Gonialoe is based on A . sect. Serrulatae and now includes four species. To test the monophyly of this small genus of alooids, phylogenomic analysis of the remaining members should be prioritised. In summary, our data currently support an alooid classification of 11 genera, recognising Aloe sensu stricto, Aloiampelos , Aloidendron , Aristaloe , Astroloba , Gasteria , Gonialoe , Haworthia , Haworthiopsis , Kumara and Tulista at this rank; with Aloestrela incorporated into Aloidendron . Aloe sensu stricto The 278 species of Aloe sensu stricto included in the present study are monophyletic. The use of nuclear phylogenomics through target capture sequencing has afforded a significant improvement in the molecular systematics of this big genus. Herbarium genomics furthermore allowed the inclusion of many difficult-to-collect and difficult-to-cultivate (e.g. grass aloes) species in the present study, expanding the phylogenetic framework from 197 species of Aloe ( Grace et al ., 2015 ) to 279 out of the 591 currently accepted species. With this expanded phylogenomic framework, it was possible to test existing taxonomic hypotheses based mostly based on vegetative and reproductive morphology using molecular data. The results confirm strong geographic patterns in the evolutionary history of Aloe , and the monophyly of five large sections for predominantly southern African taxa and one section for Arabian taxa. Historically, southern African alooid genera have received more taxonomic attention because of a considerable number of botanists working on the group in the region. Dedicated collecting trips by botanists working with institutes such as the Royal Botanic Gardens, Kew, the South African National Biodiversity Institute, and some South African universities have expanded the available living and preserved collections. As this present study was, for the main part, based on the collections at Kew, good coverage is available for this region. The general emerging pattern is that the infrageneric groupings recognised by Berger (1908) , often as they were expanded by Reynolds (1950) , are coherent, whereas the groupings published later, e.g. by Reynolds (1966) and Glen and Hardy (2000) are often polyphyletic. Several well-defined groups can be distinguished with, necessarily, their circumscription refined as new taxa are described. Aptly, the clade that is sister to all other groups recognised in Aloe sensu stricto is A . sect. Aloe , currently comprising the mitre-forming aloes (following the concept of Glen and Hardy, 2000 ), e.g. A. arenicola , A. mitriformis , and A. pearsonii . These species with their capitate inflorescences are predominantly distributed along the west coast of the Western and Northern Cape provinces of South Africa, as well as in southern Namibia. In the phylogenomic inference presented here, this clade also includes two species, i.e. A. erinacea and A. melanacantha , both in A . sect. Echinatae , with sharper, more pronounced teeth on the leaf margins and scattered on one or both leaf surfaces. Like representatives of A . sect. Aloe , these two species also sucker basally to form clumps of variable density, but their racemes are conical-cylindric and not capitate. With their grass tuft-like habit and capitate to near-capitate inflorescences, the grass aloes, i.e. A . sect. Leptoaloe , form one of the most distinctive and visually recognisable clades of aloes. Their association with grasslands and grassy patches on cliffs provides effective camouflage to limit herbivory. These species generally do not succumb to veld fires and are able to resprout from their basally thickened stems and often fusiform roots ( Cousins and Witkowski, 2012 ). These ecological innovations have allowed this group to diversify significantly and it currently includes 62 accepted species (Species and Sections file, online supporting material), >10% of the Aloe taxa recognised at present. One grass aloe, Aloe myriacantha , has the widest natural geographical distribution of all the aloes, ranging from southern South Africa in a northerly direction to well beyond the equator ( Newton, 2020 ). The grass aloes are clearly monophyletic in the present study with a fully supported node, the only exception being the bulb-forming A. buettneri , which resolves here as a member of the “maculate aloes” clade. The maculate aloes, i.e. A . sect. Pictae , are the most diverse section in Aloe , represented in the present study by 32 out of 90 currently accepted species ( Fig. 3B , 4A). Although typical characters of this group, such as (generally) transversely arranged leaf maculations (spots) and flower tubes that are constricted above the ovaries, are not unique to A . sect. Pictae , they are well defined on a combination of these characters and their leaf surface sculpturing ( Grace et al ., 2009 ). The nuclear phylogenomic results presented here confirm the monophyly of this group for all southern African species and most of the tropical African species. Aloe ser. Paniculatae , the coral aloes, is embedded within A . sect. Pictae . The floral morphology of A. buettneri and the coral aloes is similar to those of the maculate aloes, supporting their possible inclusion in A. sect. Pictae . Although Aloe swynnertonii appears on a separate branch in the final phylogeny, the node is not supported (LPP<0.60) and in many of the gene trees this species is part of A. sect. Pictae , being sister to the other members. The tropical aloes A. citrina , A. congdonii , and A. weloensis are clearly not part of A . sect. Pictae because they are placed at some distance to the rest of this section ( Fig. 4A ). Further investigation of the tropical members of A . sect. Pictae would therefore be warranted to determine their placement as part of the section. The only section that is monophyletic for both Southern African and tropical African aloes, albeit in two separate clades, respectively, is A . sect. Latebracteatae , indicating the likely loss and subsequent gain of shared features used to define the section (large floral bracts, flowers on long pedicels (>10 mm), anthers and styles not (or very shortly) exserted from the flower tube; Glen & Hardy 2000 ). This is a general pattern across the Aloe phylogeny, perhaps best exemplified by the multiple separate occurrences of the (generally single-stemmed) tree-habit (>3 m, Supplementary Figure S1). Unbranched trees occur in the Southern African (e.g. Aloe ferox ), Malagasy (e.g. A. helenae ), Tropical East African (e.g. A. volkensii ), and Horn of Africa (e.g. A. gracilicaulis ) clades. It is therefore not surprising that A . sect. Pachydendron is polyphyletic. Other monophyletic groups among the tropical African aloes are Aloe sect. Verae (Reynolds’ group 9), which includes the popular Aloe vera , and a group of small montane aloes from Somalia (Somaliensis group, Fig. 3B ). This last group has been treated previously by Carter et al . (1984) and includes several members of Reynolds’ group 4 (striped perianth): A. somaliensis , A. hemmingii (synonymised by Carter et al . under A. somaliensis ), A. jucunda and A. peckii ; with A. mcloughlinii and A. erensii considered to be close relatives. The nuclear phylogenomic topology in this study clarifies the monophyly of the four species in this group together with A. mcloughlinii and the Northern Ethiopian A. monticola . The Kenyan A. erensii , however, is more distantly related and is monophyletic with A. diolii from South Sudan. The monophyly of A. hemmingii with A. somaliensis would support its synonymy. The non-alooid members of Asphodelaceae subf. Asphodeloideae The arrangement of the other genera in the subfamily Asphodeloideae agrees with previous phylogenetic studies ( Seberg et al ., 2012 ; Grace et al ., 2015 ; McLay and Bayly, 2016 ) in the monophyly of Asphodeline-Asphodelus and the sister relationship of Bulbine to the alooid clade. Disagreement is, however, found in the relationships between Bulbinella , Eremurus , and Trachyandra . The present topology agrees with Seberg et al . (2012) in placing Eremurus and Trachyandra together and recovering Bulbinella on a separate branch. Kniphofia is expected to occupy a separate branch nested among the non-alooid members of the subfamily, according to nuclear data ( Baker et al . 2022 ). The monotypic Jodrellia is currently synonymised with Bulbine ( Boatwright and Manning, 2010 ), a decision that is supported by the data from the present study, although additional species of Bulbine need to be investigated to confirm the monophyly of this genus. Asphodelaceae subf. Hemerocallidoideae The present study presents a fully resolved and, with the exception of two nodes, fully supported phylogeny of the monophyletic subfamily Hemerocallidoideae. Several taxonomic and phylogenetic uncertainties are resolved. Geitonoplesium is confirmed as a member of this subfamily, sister to Agrostocrinum , and Chamaescilla is confirmed as sister to a monophyletic clade of Hemerocallis and Simethis ( McLay and Bayly, 2016 ). The historical polytomy at the base of the clade with Dianella , Excremis , Stypandra , Thelionema , and Herpolirion (core phormioids, clade A in Fig. 2 ) is resolved and broadly agrees with the topology presented by McLay and Bayly (2016) , with Thelionema recovered together with Herpolirion and Dianella with Excremis . The previously-recognised family Johnsoniaceae forms a monophyletic clade (clade B in Fig. 2 ). In line with previous phylogenetic efforts ( Wurdack and Dorr, 2009 ; Seberg et al ., 2012 ; McLay and Bayly, 2016 ), Tricoryne is sister to the rest of the group in the present phylogeny, followed by Corynotheca , Caesia , Arnocrinum , and the core group formed by Hodgsoniola , Hensmania , Johnsonia , and Stawellia . Only one of the aforementioned studies included Hodgsoniola ( McLay and Bayly, 2016 ) where it was placed with Hensmania . The phylogenomic inference presented here disagrees with this and recovers Hodgsoniola with Johnsonia instead. Hensmania is monophyletic with Stawellia with full support. The monotypic Hodgsoniola and Stawellia (five species) can be united on morphological basis as well, with both genera having basally united tepals ( Clifford and Conran, 1998 ). A possible synapomorphy between Johnsonia and Hensmania could be the presence of bracts around the flowers. Future work One of the most taxonomically problematic groups in Aloe , A . sect. Purpurascentes , remains polyphyletic in the present phylogenomic treatment. Despite recent work to stabilise the taxonomy of this group ( Klopper et al ., 2023 ), further adjustment may be necessary. Three of the five representatives of this section included in the present study form a coherent but paraphyletic group: Aloe framesii , A. khamiesensis , and A. microstigma . The phylogenetic distance between the three groupings of species from A . sect. Purpurascentes supports Klopper et al .’s (2023) findings that A. gariepensis and especially A. succotrina comprise monophyletic clades separate to the rest of the core-Purpurascentes group (i.e. Aloe framesii , A. khamiesensis , and A. microstigma ). Based on their morphological analyses, Klopper et al . (2023) concluded that A. pictifolia , a species regarded by some as a relative of A. microstigma , probably does not belong to the A . sect. Purpurascentes , despite some morphological similarities that might support such a relationship. However, A. pictifolia was not included in the molecular analysis of Klopper et al . (2023) and in results from the present study, it resolves as sister to A. microstigma . Its sectional placement could therefore be reconsidered. A detailed study of all ten species and infraspecific taxa currently included in this section, as well as A. pictifolia , using our target capture tool may suggest a refined classification for A . sect. Purpurascentes . Another predominantly Southern African section that requires further investigation is A. sect Echinatae , which clearly does not consist of a natural grouping of species based on molecular data. Members of this section resolve in four different phylogenetically distant clades in the phylogenomic results presented here. As mentioned above, the placement of A. erinacea and A. melanacantha within the clade comprising A . sect. Aloe , and the sister-relationship of A. pictifolia and A. microstigma (from A . sect. Purpurascentes ) could be morphologically justified. More difficult to explain from a morphological perspective is the placement of A. humilis as sister to A. glauca and A. lineata (from A. sect. Rhodacanthae ), as well as the placement of A. krapohliana in a clade with A. comosa (from A . sect. Rhodacanthae ) and A. gariepensis (from A . sect. Purpurascentes ). Beyond Southern Africa, there are three coherent monophyletic groups: A . sect. Asperifoliae , comprising arid-adapted aloes distributed in Southwestern Africa; the A. somaliensis species complex, comprising small aloes from the Horn of Africa; and A . sect. Verae comprising mainly Arabian aloes, including the iconic Aloe vera . The origins of A. vera have long been enigmatic ( Grace et al . 2015 ) as it is only known from cultivation and individuals that have likely escaped from cultivation. The prolific plantations and wild growth of A. vera in the Caribbean have led to the popularisation of the now synonymous name A. barbadensis ( Grace 2011 ). Taxonomically, however, it has often been recognised as a close relative of extant wild species on the Arabian Peninsula and the placement of A. vera in A . sect. Verae along with other Arabian aloes in the present study supports this hypothesis. To further investigate the Dianella , Excremis , Stypandra , Thelionema , and Herpolirion clade in Asphodelaceae subf. Hemerocallidoideae, it would be useful to sequence the monotypic genus Rhuacophila , which is often synonymised with Dianella but shows strong affinity with Stypandra ( Wurdack and Dorr, 2009 ; McLay and Bayly, 2016 ). Conclusion The customised target capture sequencing method has proved highly suitable as a pragmatic solution to expand sequencing efforts in the alooids, despite the large numbers of species and large genome sizes. Strong geographic patterns in the present evidence provide a key to further resolve the infrageneric classification of Aloe . Reclassification of Aloe sensu stricto will therefore have to build on the approach of Reynolds (1950 , 1966 ): with separate treatments for Southern Africa, Madagascar, and tropical Africa. Much work is still needed for Madagascar and tropical Africa, where the existing morphogroup classifications cannot be upheld ( Fig. 4B & 4C) and where many recently described species have yet to be sampled and sequenced. A collaborative approach is therefore advocated, involving local botanists and large regional herbaria, such as those of the South African National Biodiversity Institute (SANBI) in Pretoria (PRE) and Cape Town (NBG) for southern Africa and Madagascar, the East African Herbarium (EA) for tropical East Africa and Tsimbazaza Herbarium (TAN) for Madagascar, to achieve a comprehensive revision to the infrageneric classification of Aloe . FUNDING This work was supported by funding from the European Union’s Horizon 2020 framework, as part of the MSCA-ITN-ETN PlantID [grant number 765000] and a personal stipend from the Sven & Lily Lawski fond för naturvetenskaplig forskning (Sweden) [N2023-0017] to Y.W. CONFLICT OF INTEREST The authors have declared that there is no conflict of interest applicable to this study. AUTHOR CONTRIBUTIONS Conceptualisation: O.M.G., Y.W., & N.R.; Specimen curation: P.R., O.M.G., R.R.K., G.F.S. & S.E.R.; Data generation (DNA sequences): Y.W.; Data curation (taxonomic): R.R.K., G.F.S.; Data curation (traits): Y.W.; Analysis (phylogenomic inference): Y.W.; Manuscript writing: Y.W. with help of all co-authors. SUPPLEMENTARY DATA Supplementary Data is available in the PDF file named “Supporting Information” and contains two graphs displaying alooid topologies annotated with habit (growth form) and habitat, respectively. DATA AVAILABILITY STATEMENT Raw sequencing data used in this study are deposited in the Sequence Read Archive (SRA) of the U.S. National Center for Biotechnology Information (NCBI) under Bioprojects PRJNA1120847 (for alooids), PRJNA1122593 (for other members of the Asphodelaceae), and PRJNA1120785 (for data from the alooid target capture tool design study ( Woudstra et al ., 2021 )). Other data related to this manuscript are available through online supporting material deposited in FigShare at DOI 10.6084/m9.figshare.28435394. These include (i) the reference sequences for the four species used in the design of the alooid target capture tool, (ii) Accession Information file, (iii) Sequence Information file, (iv) Species Information file containing info on the taxonomy, geographic distribution and growth form of species investigated in this study, (v) Species-and-Sections file containing taxonomic information on all Aloe names published to date, and (vi) a directory containing the assembled sequences, cleaned alignments, gene trees, species trees and the code to produce these. ACKNOWLEDGEMENTS The authors thank collectors, horticulturalists and herbarium curators at the different botanical institutes that provided provenanced reference material to the study: Royal Botanic Gardens, Kew, and Kew Herbarium (K); Royal Botanic Garden Edinburgh (E); East Africa Herbarium (EA); Herbarium of the Musée National d’Histoire Naturelle, Paris (P); University of Uppsala Herbarium (UPS) and Uppsala Botanic Garden, Gothenburg Botanic Garden; Potsdam Botanic Garden; and Cambridge University Botanic Garden. We thank Anne-Sophie Quatela for advice on DNA extractions from herbarium material; and Kennedy Matheka for providing material of Aloe ngutwaensis before the official publication of the species description. Computational resources were provided by UNINETT Sigma2 - the National Infrastructure for High Performance Computing and Data Storage in Norway. Footnotes https://doi.org/10.6084/m9.figshare.28435394 LITERATURE CITED ↵ Amir HM , Grace OM , Wabuyele E , Manoko MLK . 2019 . Ethnobotany of Aloe L. (Asphodelaceae) in Tanzania . South African Journal of Botany 122 : 330 – 335 . OpenUrl CrossRef ↵ Baker WJ , Bailey P , Barber V , et al. 2022 . A comprehensive phylogenomic platform for exploring the Angiosperm Tree of Life . Systematic Biology 71 : 301 – 319 . OpenUrl CrossRef PubMed ↵ Engler A Berger A . 1908 . Liliaceae-Asphodeloideae-Aloineae . In: Engler A , ed., Das Pflanzenreich: regni vegetablilis conspectus . Leipzig : W. Engelmann , 1 – 360 . ↵ Boatwright JS , Manning JC . 2010 . Asphodelaceae. Inclusion of the genus Jodrellia in Bulbine (Asphodelaceae) . Bothalia 40 : 59 . OpenUrl CrossRef ↵ Bolger AM , Lohse M , Usadel B . 2014 . Trimmomatic: a flexible trimmer for Illumina sequence data . Bioinformatics 30 : 2114 – 2120 . OpenUrl CrossRef PubMed Web of Science ↵ Carter S , Cutler DF , Reynolds T , Brandham PE . 1984 . A multidisciplinary approach to a revision of the aloe somaliensis complex (Liliaceae) . Kew Bulletin 39 : 611 – 633 . OpenUrl CrossRef ↵ Carter S , Lavranos JJ , Newton LE , Walker CC . 2011 . Aloes: the definitive guide . London : Royal Botanic Gardens , Kew & British Cactus and Succulent Society . ↵ Castillon JB , Castillon JP . 2010 . Les aloe de Madagascar / The aloes of Madagascar . Antananarivo : J.-P. Castillon . CITES Secretariat . In press. CITES Checklist for aloe species: an updated checklist to the aloes of the world . Compiled by: Klopper RR , Carter-Holmes S , Demissew S , Figueiredo E , Grace OM , Neale S , Newton LE , Rakotoarisoa SE , Smith GF , Walker CC , eds. Pretoria : South African National Biodiversity Institute . ↵ Kubitzki K Clifford HT , Conran JG . 1998 . Johnsoniaceae . In: Kubitzki K , ed., The families and genera of vascular plants, Vol. III: Flowering Plants. Monocotyledons: Lilianae (except Orchidaceae) . Berlin, Heidelberg : Springer , 336 – 340 . ↵ Cousins SR , Witkowski ETF . 2012 . African aloe ecology: a review . Journal of Arid Environments 85 : 1 – 17 . OpenUrl CrossRef ↵ Dee R , Malakasi P , Rakotoarisoa SE , Grace OM . 2018 . A phylogenetic analysis of the genus Aloe (Asphodelaceae) in Madagascar and the Mascarene Islands . Botanical Journal of the Linnean Society 187 : 428 – 440 . OpenUrl CrossRef ↵ Dodsworth S , Pokorny L , Johnson MG , et al. 2019 . Hyb-Seq for flowering plant systematics . Trends in Plant Science 24 : 887 – 891 . OpenUrl CrossRef PubMed ↵ Doyle JJ , Doyle JL . 1987 . A rapid DNA isolation procedure for small quantities of fresh leaf tissue . Phytochemical Bulletin 19 : 11 – 15 . OpenUrl ↵ Ellis K. 2013 . Revision of Aloiampelos Klopper & Gideon F. Sm.(Xanthorrhoeaceae subfam. Asphodeloideae) . MSc Thesis, Nelson Mandela Metropolitan University, Gqeberha, South Africa . http://hdl.handle.net/10948/d1020955 ↵ Frodin DG . 2004 . History and concepts of big plant genera . Taxon 53 : 753 – 776 . OpenUrl CrossRef Web of Science ↵ Germishuizen , G Glen HF , Hardy DS . 2000 . Aloaceae (First part): Aloe . In: Germishuizen , G . (ed.), Flora of Southern Africa 5 , Part 1, Fascicle 1. Pretoria : National Botanical Institute . Govaerts R , Nic Lughada E , Black N , Turner R , Paton A . 2021 . The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity . Scientific Data 8 : 215 . DOI: 10.1038/s41597-021-00997-6 OpenUrl CrossRef PubMed ↵ Grace OM , Buerki S , Symonds MR , et al. 2015 . Evolutionary history and leaf succulence as explanations for medicinal use in aloes and the global popularity of Aloe vera . BMC Evolutionary Biology 15 : e29 . DOI: 10.1186/s12862-015-0291-7 OpenUrl CrossRef ↵ Grace OM , Klopper RR , Smith GF , et al. 2013 . A revised generic classification for Aloe (Xanthorrhoeaceae subfam . Asphodeloideae). Phytotaxa 76 : 7 – 14 . OpenUrl CrossRef ↵ Grace OM , Pérez-Escobar OA , Lucas EJ , et al. 2021 . Botanical monography in the Anthropocene . Trends in Plant Science 26 : 433 – 441 . OpenUrl CrossRef PubMed ↵ Grace OM , Simmonds MSJ , Smith GF , Van Wyk AE . 2009 . Taxonomic significance of leaf surface morphology in Aloe section Pictae (Xanthorrhoeaceae) . Botanical Journal of the Linnean Society 160 : 418 – 428 . OpenUrl CrossRef ↵ Grace OM . 2011 . Current perspectives on the economic botany of the genus Aloe L . ( Xanthorrhoeaceae). South African Journal of Botany 77 : 980 – 987 . OpenUrl CrossRef ↵ Grass Phylogeny Working Group III . 2024 . Nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence . New Phytologist 245 : 818 – 834 . OpenUrl PubMed ↵ Hart ML , Forrest LL , Nicholls JA , Kidner CA . 2016 . Retrieval of hundreds of nuclear loci from herbarium specimens . Taxon 65 : 1081 – 1092 . OpenUrl CrossRef ↵ Hollingsworth PM , Graham SW , Little DP . 2011 . Choosing and using a plant DNA barcode . PLoS ONE 6 : e19254 . DOI: 10.1371/journal.pone.0019254 OpenUrl CrossRef PubMed ↵ Johnson MG , Gardner EM , Liu Y , et al. 2016 . HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment . Applications in Plant Sciences 4 : e1600016 . DOI: doi.org/ 10.3732/apps.1600016 OpenUrl CrossRef ↵ Johnson MG , Pokorny L , Dodsworth S , et al. 2019 . A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering . Systematic Biology 68 : 594 – 606 . OpenUrl CrossRef PubMed ↵ Katoh K , Standley DM . 2013 . MAFFT multiple sequence alignment software version 7: improvements in performance and usability . Molecular Biology and Evolution 30 : 772 – 780 . OpenUrl CrossRef PubMed Web of Science ↵ Klopper RR , Grace OM , Klopper AW , Smith GF , Van Wyk AE . 2023 . A taxonomic revision of Aloe sect . Purpurascentes (Asphodelaceae subfam. Alooideae). Phytotaxa 628 : 1 – 64 . OpenUrl ↵ Klopper RR , Smith GF . 2013 . Aloes of the world: when, where and who? Aloe 50 : 44 – 52 . OpenUrl ↵ Legume Phylogeny Working Group . 2017 . A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny: The Legume Phylogeny Working Group (LPWG) . Taxon 66 : 44 – 77 . OpenUrl CrossRef ↵ Letunic I , Bork P . 2021 . Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation . Nucleic Acids Research 49 : W293 – W296 . OpenUrl CrossRef PubMed ↵ Linnaeus C . 1753 . Species Plantarum 1 . Stockholm : Impensis Laurentii Salvii . ↵ Malakasi P , Bellot S , Dee R , Grace OM . 2019 . Museomics clarifies the classification of Aloidendron (Asphodelaceae), the iconic african tree aloes . Frontiers in Plant Science 10 : e1227 . DOI: doi.org/ 10.3389/fpls.2019.01227 OpenUrl CrossRef ↵ Mandel JR , Dikow RB , Funk VA , et al. 2014 . A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae . Applications in Plant Sciences 2 : e1300085 . DOI: doi.org/ 10.3732/apps.1300085 OpenUrl CrossRef ↵ Mandel JR , Dikow RB , Siniscalchi CM , et al. 2019 . A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae . Proceedings of the National Academy of Sciences of the United States of America 116 : 14083 – 14088 OpenUrl Abstract / FREE Full Text ↵ Manning JC , Boatwright JS , Daru BH , Maurin O , Van der Bank M . 2014 . A molecular phylogeny and generic classification of Asphodelaceae subfamily Alooideae: a final resolution of the prickly issue of polyphyly in the alooids? Systematic Botany 39 : 55 – 74 . OpenUrl CrossRef ↵ McLay TGB , Bayly MJ . 2016 . A new family placement for Australian blue squill, Chamaescilla : Xanthorrhoeaceae (Hemerocallidoideae), not Asparagaceae . Phytotaxa 275 : 97 – 111 . OpenUrl CrossRef ↵ Michel T , Tseng Y-H , Wilson H , Chung K-F , Thomas DC , Kidner C . 2022 . A hybrid capture bait set for Begonia . Edinburgh Journal of Botany 79 : 1 – 33 . OpenUrl ↵ Eggli U , Nyffeler R Newton LE . 2020 . Aloe (Asphodelaceae) . In: Eggli U , Nyffeler R , eds., Illustrated handbook of succulent plants. Monocotyledons . Berlin, Heidelberg : Springer , 485 – 696 . ↵ Nguyen L-T , Schmidt HA , Von Haeseler A , Minh BQ. 2015 . IQ-TREE: a Ffst and effective stochastic algorithm for estimating maximum-likelihood phylogenies . Molecular Biology and Evolution 32 : 268 – 274 . OpenUrl CrossRef PubMed ↵ Nicholls JA , Pennington RT , Koenen EJ , et al. 2015 . Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae) . Frontiers in Plant Science 6 : e710 . DOI: 10.3389/fpls.2015.00710 OpenUrl CrossRef ↵ Quatela A-S , Cangren P , Jafari F , Michel T , De Boer HJ , Oxelman B . 2023 . Retrieval of long DNA reads from herbarium specimens . AoB PLANTS 15 : plad074. DOI: 10.1093/aobpla/plad074 OpenUrl CrossRef ↵ Renner SS , Scherz MD , Schoch CL , Gottschling M , Vences M . 2024 . Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains . Systematic Biology 73 : 486 – 494 . OpenUrl CrossRef PubMed ↵ Reynolds GW . 1950 . The aloes of South Africa . Johannesburg : The Trustees of the Aloes of South Africa Book Fund . ↵ Reynolds GW . 1966 . The aloes of Tropical Africa and Madagascar . Mbabane : The Trustees of the Aloes Book Fund . ↵ Rowley GD . 1996 . The berried aloes: Aloe section Lomatophyllum . Excelsa 17 : 59 – 62 . OpenUrl ↵ Rowley GD . 2013 . Generic concepts in the Alooideae — part 3. The phylogenetic story . Alsterworthia International Special Issue 10 : 3 – 6 . OpenUrl ↵ Seberg O , Petersen G , Davis JI , et al. 2012 . Phylogeny of the Asparagales based on three plastid and two mitochondrial genes . American Journal of Botany 99 : 875 – 889 . OpenUrl Abstract / FREE Full Text ↵ Shepherd LD , McLay TGB . 2011 . Two micro-scale protocols for the isolation of DNA from polysaccharide-rich plant tissue . Journal of Plant Research 124 : 311 – 314 . OpenUrl CrossRef PubMed Web of Science ↵ Smith GF , Klopper RR , Grace OM . 2019 . Aloidendron (Asphodelaceae subfam. Alooideae) consists of six species, not seven: Aloe sabaea is a true aloe . Phytotaxa 416 : 88 – 90 . OpenUrl CrossRef ↵ Smith GF , Molteno S . 2019 . Aloestrela Molteno & Gideon F.Sm. (Asphodelaceae: Alooideae), a new alooid genus with A. suzannae (Decary) Molteno & Gideon F.Sm. as the only species . Bradleya 2019 : 3 – 7 . OpenUrl CrossRef ↵ Smith SA , Dunn CW . 2008 . Phyutility: a phyloinformatics tool for trees, alignments and molecular data . Bioinformatics 24 : 715 – 716 . OpenUrl CrossRef PubMed Web of Science Soto Gomez M , Pokorny L , Kantar MB , et al. 2019 . A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae) . Applications in Plant Sciences 7 : e11254 . DOI: 10.1002/aps3.11254 OpenUrl CrossRef PubMed ↵ The Angiosperm Phylogeny Group . 2016 . An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV . Botanical Journal of the Linnean Society 181 : 1 – 20 . OpenUrl CrossRef ↵ Tumescheit C , Firth AE , Brown K . 2022 . CIAlign - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments . PeerJ 10 : e12983 . DOI: 10.7717/peerj.12983 OpenUrl CrossRef WFO: World Flora Online . 2025 . Published on the Internet; http://www.worldfloraonline.org . Accessed on: 27 Feb 2025 . ↵ De Boer H , Rydmark MO , Verstraete B , Gravendeel B Woudstra Y , Quatela A-S , Kidner C , et al. 2022 . Chapter 14: Target capture . In: De Boer H , Rydmark MO , Verstraete B , Gravendeel B , eds, Molecular identification of plants: from sequence to species . Sofia : Pensoft Publishers, Advanced Books , 190 – 212 . ↵ Woudstra Y , Rees P , Rakotoarisoa SE , Rønsted N , Howard C , Grace OM. 2024 . An updated DNA barcoding tool for Aloe vera and related CITES-regulated species . BioRxiv . DOI: 10.1101/2024.07.09.602761 OpenUrl Abstract / FREE Full Text ↵ Woudstra Y , Viruel J , Fritzsche M , et al. 2021 . A customised target capture sequencing tool for molecular identification of Aloe vera and relatives . Scientific Reports 11 : e24347 . DOI: 10.1038/s41598-021-03300-0 OpenUrl CrossRef ↵ Wurdack KJ , Dorr LJ . 2009 . The South American genera of Hemerocallidaceae ( Eccremis and Pasithea ): two introductions to the New World . Taxon 58 : 1122 – 1132 . OpenUrl CrossRef ↵ Zhang C , Rabiee M , Sayyari E , Mirarab S . 2018 . ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees . BMC Bioinformatics 19 : e153 . DOI: 10.1186/s12859-018-2129-y OpenUrl CrossRef ↵ Zuntini AR , Carruthers T , Maurin O , et al. 2024 . Phylogenomics and the rise of the angiosperms . Nature 629 : 843 – 850 . OpenUrl CrossRef PubMed View the discussion thread. Back to top Previous Next Posted March 05, 2025. Download PDF Supplementary Material Data/Code Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids) Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids) Yannick Woudstra , Paul Rees , Solofo E. Rakotoarisoa , Ronell R. Klopper , Gideon F. Smith , Nina Rønsted , Olwen M. Grace bioRxiv 2025.02.28.640761; doi: https://doi.org/10.1101/2025.02.28.640761 Share This Article: Copy Citation Tools Nuclear phylogenomics reveals strong geographic patterns in the evolutionary history of Aloe and related genera (alooids) Yannick Woudstra , Paul Rees , Solofo E. Rakotoarisoa , Ronell R. Klopper , Gideon F. Smith , Nina Rønsted , Olwen M. Grace bioRxiv 2025.02.28.640761; doi: https://doi.org/10.1101/2025.02.28.640761 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Evolutionary Biology Subject Areas All Articles Animal Behavior and Cognition (7642) Biochemistry (17715) Bioengineering (13907) Bioinformatics (42003) Biophysics (21470) Cancer Biology (18624) Cell Biology (25533) Clinical Trials (138) Developmental Biology (13390) Ecology (19935) Epidemiology (2067) Evolutionary Biology (24356) Genetics (15617) Genomics (22529) Immunology (17753) Microbiology (40432) Molecular Biology (17200) Neuroscience (88681) Paleontology (667) Pathology (2840) Pharmacology and Toxicology (4828) Physiology (7653) Plant Biology (15161) Scientific Communication and Education (2046) Synthetic Biology (4304) Systems Biology (9826) Zoology (2271)