Pub Date : 2024-11-26DOI: 10.1016/j.ympev.2024.108248
Alejandro Londoño-Burbano, Marcelo R. Britto
In the present study, we used DNA sequences from three mitochondrial (COI, Cytb, and nd2) and one nuclear (RAG2) marker, to perform species delimitation analyses (ABGD, GMYC, BPP, and bPTP) within Sturisoma to test the validity of currently recognized and potential new species for the genus. Additionally, a historical biogeographic analysis was carried out to test the age and centers of origin for species of the genus. Results found here indicate a high degree of genetic divergence with overlapping morphological characteristics suggesting a greater diversity than previously proposed for the genus. All valid species currently included in Sturisoma were confirmed here, and one potentially undescribed species was recovered. Based on genetic distances, geographical patterns and historical biogeography, the diversification of the group could be related to dispersal events from Western to Eastern Amazonia resulting in sympatric species that are highly divergent genetically but conservative morphologically. The lower (eastern) Amazonas and the Orinoco River basins were identified as the main centers of origin for the genus, with an approximate age of origin of 13 Mya, during the Miocene. The diversity of the genus is likely to be even higher because the Amazon River is a hotspot of hidden biodiversity.
{"title":"Species delimitation and historical biogeography of Sturisoma Swainson, 1838 (Loricariidae: Loricariinae): Hidden diversity along the Amazon River","authors":"Alejandro Londoño-Burbano, Marcelo R. Britto","doi":"10.1016/j.ympev.2024.108248","DOIUrl":"10.1016/j.ympev.2024.108248","url":null,"abstract":"<div><div>In the present study, we used DNA sequences from three mitochondrial (COI, Cytb, and nd2) and one nuclear (RAG2) marker, to perform species delimitation analyses (ABGD, GMYC, BPP, and bPTP) within <em>Sturisoma</em> to test the validity of currently recognized and potential new species for the genus. Additionally, a historical biogeographic analysis was carried out to test the age and centers of origin for species of the genus. Results found here indicate a high degree of genetic divergence with overlapping morphological characteristics suggesting a greater diversity than previously proposed for the genus. All valid species currently included in <em>Sturisoma</em> were confirmed here, and one potentially undescribed species was recovered. Based on genetic distances, geographical patterns and historical biogeography, the diversification of the group could be related to dispersal events from Western to Eastern Amazonia resulting in sympatric species that are highly divergent genetically but conservative morphologically. The lower (eastern) Amazonas and the Orinoco River basins were identified as the main centers of origin for the genus, with an approximate age of origin of 13 Mya, during the Miocene. The diversity of the genus is likely to be even higher because the Amazon River is a hotspot of hidden biodiversity.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108248"},"PeriodicalIF":3.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-26DOI: 10.1016/j.ympev.2024.108246
Ethan J. Briggs , Saoirse Foley , Lyn G. Cook
The composition of Australia’s fauna and flora has been largely assembled by two biogeographic processes, vicariance and long-distance dispersal and establishment. These patterns can be observed today through the survival of Gondwanan lineages contrasted with relatively recent colonization from south-east Asia, respectively. In general, the post-Gondwanan immigrant lineages from south-east Asia are taxa with traits that facilitate dispersal. Consequently, taxa like tarantulas (Araneae, Theraphosidae) that are largely pan-tropical but also have a low propensity for dispersal, are thought to be Gondwanan in origin. However, the Australian tarantulas are unsampled for phylogenomic studies and, as such, their classification and biogeographic origins have been long debated and are unresolved. Here we test if their current, morphology-based classification in Selenocosmiinae is accurate and assess whether the Australian tarantulas were present in Australia while it was part of Gondwana. We sample 369 tarantula specimens from across Australia, greatly expanding the geographic sampling of previous studies, to develop the first continent-wide phylogeny of the Australian tarantulas. To resolve the ‘back bone’ of the Australian tarantula phylogeny we generate 20 new transcriptomes for species of Australian tarantulas representing distinct lineages uncovered using mitochondrial sequence data and combine these new transcriptomes with published transcriptomic data. Through the recovery of ultra-conserved element (UCE) loci from transcriptomes and testing multiple data occupancy matrices, we find that the Australian clade is monophyletic and nested inside the largely Asian Selenocosmiinae. We find the Australian fauna are a relatively young radiation with a crown age of 18.8–8.3 Ma and we therefore reject the hypothesis of a Gondwanan origin for these animals and, instead, infer a recent dispersal from south-east Asia. Our findings indicate that they underwent a rapid radiation, possibly coinciding with their arrival into Australia. Our findings refute the monophyly of Selenocosmia and Coremiocnemis as currently recognised, and we remove Selenocosmia stalkeri from synonymy with Selenocosmia stirlingi.
{"title":"Gondwanan relic or recent arrival? The biogeographic origins and systematics of Australian tarantulas","authors":"Ethan J. Briggs , Saoirse Foley , Lyn G. Cook","doi":"10.1016/j.ympev.2024.108246","DOIUrl":"10.1016/j.ympev.2024.108246","url":null,"abstract":"<div><div>The composition of Australia’s fauna and flora has been largely assembled by two biogeographic processes, vicariance and long-distance dispersal and establishment. These patterns can be observed today through the survival of Gondwanan lineages contrasted with relatively recent colonization from south-east Asia, respectively. In general, the post-Gondwanan immigrant lineages from south-east Asia are taxa with traits that facilitate dispersal. Consequently, taxa like tarantulas (Araneae, Theraphosidae) that are largely pan-tropical but also have a low propensity for dispersal, are thought to be Gondwanan in origin. However, the Australian tarantulas are unsampled for phylogenomic studies and, as such, their classification and biogeographic origins have been long debated and are unresolved. Here we test if their current, morphology-based classification in Selenocosmiinae is accurate and assess whether the Australian tarantulas were present in Australia while it was part of Gondwana. We sample 369 tarantula specimens from across Australia, greatly expanding the geographic sampling of previous studies, to develop the first continent-wide phylogeny of the Australian tarantulas. To resolve the ‘back bone’ of the Australian tarantula phylogeny we generate 20 new transcriptomes for species of Australian tarantulas representing distinct lineages uncovered using mitochondrial sequence data and combine these new transcriptomes with published transcriptomic data. Through the recovery of ultra-conserved element (UCE) loci from transcriptomes and testing multiple data occupancy matrices, we find that the Australian clade is monophyletic and nested inside the largely Asian Selenocosmiinae. We find the Australian fauna are a relatively young radiation with a crown age of 18.8–8.3 Ma and we therefore reject the hypothesis of a Gondwanan origin for these animals and, instead, infer a recent dispersal from south-east Asia. Our findings indicate that they underwent a rapid radiation, possibly coinciding with their arrival into Australia. Our findings refute the monophyly of <em>Selenocosmia</em> and <em>Coremiocnemis</em> as currently recognised, and we remove <em>Selenocosmia stalkeri</em> from synonymy with <em>Selenocosmia stirlingi</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108246"},"PeriodicalIF":3.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite Cuscuta campestris and other parasitic plant species, we identified a unique evolutionary history of rpl32 genes coding for an essential plastid ribosomal subunit in Cuscuta. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the Cuscuta subgenus Grammica. Oxalidales had suffered an ancestral EGT of rpl32 predating the evolution of the genus Cuscuta. The HGT subsequently relieved the plastid rpl32 from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in Cuscuta is supported by a high sequence similarity of the mature L32 protein between species of the subgenus Grammica and representatives of the Oxalidales, and by a surprisingly conserved transit peptide, whose functionality in Cuscuta was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.
{"title":"Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement","authors":"Karsten Fischer , Sondre Valentin Jordbræk , Stian Olsen , Mathias Bockwoldt , Rainer Schwacke , Björn Usadel , Kirsten Krause","doi":"10.1016/j.ympev.2024.108243","DOIUrl":"10.1016/j.ympev.2024.108243","url":null,"abstract":"<div><div>The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite <em>Cuscuta campestris</em> and other parasitic plant species, we identified a unique evolutionary history of <em>rpl32</em> genes coding for an essential plastid ribosomal subunit in <em>Cuscuta</em>. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the <em>Cuscuta</em> subgenus <em>Grammica</em>. Oxalidales had suffered an ancestral EGT of <em>rpl32</em> predating the evolution of the genus <em>Cuscuta</em>. The HGT subsequently relieved the plastid <em>rpl32</em> from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in <em>Cuscuta</em> is supported by a high sequence similarity of the mature L32 protein between species of the subgenus <em>Grammica</em> and representatives of the <em>Oxalidales</em>, and by a surprisingly conserved transit peptide, whose functionality in <em>Cuscuta</em> was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108243"},"PeriodicalIF":3.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-22DOI: 10.1016/j.ympev.2024.108250
Heidi M. Meudt , Sofie M. Pearson , Weixuan Ning , Jessica M. Prebble , Jennifer A. Tate
Island and mountain systems represent natural laboratories for studies of species radiations, but they often present several challenges for phylogenetic inference and species delimitation. The southern hemisphere forget-me-nots (Myosotis, Boraginaceae) comprise a geologically recent radiation centred in Aotearoa New Zealand, a mountainous archipelago, with about 50 species that are morphologically and ecologically divergent but lack genetic variation sufficient to resolve phylogenetic relationships and species boundaries using standard DNA Sanger sequencing markers, AFLPs, or microsatellites. Many of these Myosotis species are geographically restricted in alpine areas, uncommon or threatened, have polyploid and dysploid genomes, and are of high taxonomic and conservation priority. Here we present phylogenomic analyses using target-capture of Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to improve resolution of the radiation, explore biogeographic and morphological patterns within it, and address specific taxonomic questions for each species. Our comprehensive sampling includes over 300 individuals representing nearly all species from New Zealand and Australia, which is ∼ 2–3 × more taxon sampling and ∼ 80–120 × more molecular data than previously published for Myosotis. Exploration of different data filtering, curation and analyses (coalescent vs. concatenation) improved the resolution of the Angiosperms353 tree, which despite short backbone branches with low support values, showed taxonomic and geographic patterns, including multiple switches between ebracteate and bracteate inflorescences and multiple expansions within New Zealand from Te Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart Island, subantarctic islands, and Australia. Some of these patterns were also seen in the genome skimming datasets, and comparison of the three datasets was useful for improving our understanding of the taxonomy and resolution of this radiation. Although this phylogenomic study does not fully overcome all of the challenges regarding species delimitation of this rapid island and mountain species radiation, it nevertheless makes an important contribution to an integrative taxonomic revision of the southern hemisphere species of Myosotis.
岛屿和山地系统是研究物种辐射的天然实验室，但它们往往给系统发育推断和物种划分带来一些挑战。南半球的勿忘我（Myosotis，博拉金科）是以新西兰为中心的新近地质辐射，该群岛多山，约有 50 个物种，它们在形态和生态上存在差异，但缺乏足够的遗传变异，无法使用标准的 DNA 桑格测序标记、AFLPs 或微卫星来确定系统发育关系和物种界限。其中许多妙蛙属物种在地理上局限于高山地区，不常见或濒临灭绝，具有多倍体和二倍体基因组，在分类学和保护方面具有很高的优先性。在此，我们利用目标捕获的 Angiosperms353 诱饵以及全质粒和 nrDNA 的基因组撇取技术进行了系统发生组分析，以提高辐射的分辨率，探索其中的生物地理学和形态学模式，并解决每个物种的具体分类问题。我们的综合取样包括 300 多个个体，几乎代表了新西兰奥特亚罗瓦和澳大利亚的所有物种，这比以前发表的妙蛙花分类群取样多 2-3 倍，分子数据多 80-120 倍。对不同数据过滤、整理和分析（聚合与合并）的探索提高了 Angiosperms353 树的分辨率，尽管该树的主干分支较短且支持值较低，但仍显示出分类学和地理学模式，包括无苞片和有苞片花序之间的多次切换，以及新西兰境内从 Te Waipounamu 南岛到 Te Ika-a-Māui 北岛、Rakiura Stewart 岛、亚南极岛屿和澳大利亚的多次扩展。其中一些模式也出现在基因组取样数据集中，对这三个数据集进行比较有助于提高我们对这一辐射的分类和分辨率的理解。尽管这项系统发生组学研究并没有完全克服这一快速的岛屿和山地物种辐射所带来的物种划分方面的所有挑战，但它对南半球妙蛙属物种的综合分类学修订做出了重要贡献。
{"title":"Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)","authors":"Heidi M. Meudt , Sofie M. Pearson , Weixuan Ning , Jessica M. Prebble , Jennifer A. Tate","doi":"10.1016/j.ympev.2024.108250","DOIUrl":"10.1016/j.ympev.2024.108250","url":null,"abstract":"<div><div>Island and mountain systems represent natural laboratories for studies of species radiations, but they often present several challenges for phylogenetic inference and species delimitation. The southern hemisphere forget-me-nots (<em>Myosotis</em>, Boraginaceae) comprise a geologically recent radiation centred in Aotearoa New Zealand, a mountainous archipelago, with about 50 species that are morphologically and ecologically divergent but lack genetic variation sufficient to resolve phylogenetic relationships and species boundaries using standard DNA Sanger sequencing markers, AFLPs, or microsatellites. Many of these <em>Myosotis</em> species are geographically restricted in alpine areas, uncommon or threatened, have polyploid and dysploid genomes, and are of high taxonomic and conservation priority. Here we present phylogenomic analyses using target-capture of Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to improve resolution of the radiation, explore biogeographic and morphological patterns within it, and address specific taxonomic questions for each species. Our comprehensive sampling includes over 300 individuals representing nearly all species from New Zealand and Australia, which is ∼ 2–3 × more taxon sampling and ∼ 80–120 × more molecular data than previously published for <em>Myosotis.</em> Exploration of different data filtering, curation and analyses (coalescent vs. concatenation) improved the resolution of the Angiosperms353 tree, which despite short backbone branches with low support values, showed taxonomic and geographic patterns, including multiple switches between ebracteate and bracteate inflorescences and multiple expansions within New Zealand from Te Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart Island, subantarctic islands, and Australia. Some of these patterns were also seen in the genome skimming datasets, and comparison of the three datasets was useful for improving our understanding of the taxonomy and resolution of this radiation. Although this phylogenomic study does not fully overcome all of the challenges regarding species delimitation of this rapid island and mountain species radiation, it nevertheless makes an important contribution to an integrative taxonomic revision of the southern hemisphere species of <em>Myosotis</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108250"},"PeriodicalIF":3.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oceanic islands offer excellent opportunities to study the ecology, evolutionary biology, and biogeography of plants. To uncover the genetic basis of various evolutionary trends commonly observed on these islands, the origins and phylogenetic relationships of the species being studied should be understood. Callicarpa glabra, Callicarpa parvifolia, and Callicarpa subpubescens are evergreen woody plants endemic to the Ogasawara Islands, which are remote oceanic islands located off of the Japanese Archipelago. These species are ideal for studying evolutionary changes on oceanic islands because of their adaptive radiation and shift toward dioecious sex expression. We used a phylogenomic perspective to determine the evolutionary relationship of the three species within the genus and infer their colonization time. Based on the analysis of both chloroplast genomes and 86 nuclear single-copy genes, we found that these three species were monophyletic and embedded in a backbone clade that included multiple East Asian species. The phylogenetic tree based on over 10,000 nuclear genes placed the insular species in the East Asian clade, although the topology did not entirely correspond to the chloroplast tree, probably because of incomplete lineage sorting and interspecific hybridization. The three endemic species were estimated to have diverged from continental species approximately three million years ago (Mya). The results of this study suggested that the ancestor of the Ogasawara endemic species originated from long-distance dispersal from East Asia mainland in the late Pliocene, and then progressively speciated within the islands.
{"title":"Phylogenetic origin of dioecious Callicarpa (Lamiaceae) species endemic to the Ogasawara Islands revealed by chloroplast and nuclear whole genome analyses","authors":"Kazutoshi Masuda , Hiroaki Setoguchi , Koki Nagasawa , Suzuki Setsuko , Shosei Kubota , Shin S. Satoh , Shota Sakaguchi","doi":"10.1016/j.ympev.2024.108234","DOIUrl":"10.1016/j.ympev.2024.108234","url":null,"abstract":"<div><div>Oceanic islands offer excellent opportunities to study the ecology, evolutionary biology, and biogeography of plants. To uncover the genetic basis of various evolutionary trends commonly observed on these islands, the origins and phylogenetic relationships of the species being studied should be understood. <em>Callicarpa glabra</em>, <em>Callicarpa parvifolia</em>, and <em>Callicarpa subpubescens</em> are evergreen woody plants endemic to the Ogasawara Islands, which are remote oceanic islands located off of the Japanese Archipelago. These species are ideal for studying evolutionary changes on oceanic islands because of their adaptive radiation and shift toward dioecious sex expression. We used a phylogenomic perspective to determine the evolutionary relationship of the three species within the genus and infer their colonization time. Based on the analysis of both chloroplast genomes and 86 nuclear single-copy genes, we found that these three species were monophyletic and embedded in a backbone clade that included multiple East Asian species. The phylogenetic tree based on over 10,000 nuclear genes placed the insular species in the East Asian clade, although the topology did not entirely correspond to the chloroplast tree, probably because of incomplete lineage sorting and interspecific hybridization. The three endemic species were estimated to have diverged from continental species approximately three million years ago (Mya). The results of this study suggested that the ancestor of the Ogasawara endemic species originated from long-distance dispersal from East Asia mainland in the late Pliocene, and then progressively speciated within the islands.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108234"},"PeriodicalIF":3.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1016/j.ympev.2024.108247
Sarah A. Morris , Nicolas A. Hazzi , Gustavo Hormiga
Pisauridae Simon, 1890, or nursery web spiders, are a large family with a worldwide distribution and very diverse life history strategies. Despite being named for their nursery webs, similar structures are built by some members of Ctenidae, Trechaleidae, and Oxyopidae. Pisauridae has no known morphological synapomorphies that circumscribe all members of the family, and delineation of subfamilies has been a longstanding issue. In addition, several recent molecular phylogenetic studies have called into question the monophyly of Pisauridae. Here, we infer a phylogeny of Pisauridae with nine genetic markers (12S, 16S, 18S, 28S, actin, COI, histone H3, ITS2, and NADH) combined with ultraconserved elements (UCEs) to test the monophyly of the group and determine intrafamilial relationships. Our study includes a total of 81 terminals (59 of them pisaurids). Our maximum likelihood and gene coalescence analyses strongly suggest that as currently circumscribed, the family Pisauridae is not monophyletic. To circumscribe Pisauridae as a monophyletic group, based on our molecular results, we propose the restoration of the family Dolomedidae Simon, 1876 (rank resurrected) to include the genera DolomedesLatreille, 1804 and BradystichusSimon, 1884. In addition, based on morphological evidence, we also place in Dolomedidae the genera MegadolomedesDavies & Raven, 1980; Tasmomedes Raven, 2018; Mangromedes Raven, 2018; OrnodolomedesRaven & Hebron, 2018; and CaledomedesRaven & Hebron, 2018. We provide a phylogenetic delimitation of the three subfamilies of Pisauridae: Halinae, Thaumasiinae, and Pisaurinae. Ten pisaurid genera are deemed incertae sedis in terms of their placement. In light of our hypothesized molecular phylogeny, we discuss the morphological characters and putative synapomorphies of Pisauridae and propose diagnostic characters for its subfamilies and for the family Dolomedidae, along with taxonomic notes about genera not included in our study.
{"title":"Molecular phylogenetics of nursery web spiders (Araneae: Pisauridae)","authors":"Sarah A. Morris , Nicolas A. Hazzi , Gustavo Hormiga","doi":"10.1016/j.ympev.2024.108247","DOIUrl":"10.1016/j.ympev.2024.108247","url":null,"abstract":"<div><div>Pisauridae Simon, 1890, or nursery web spiders, are a large family with a worldwide distribution and very diverse life history strategies. Despite being named for their nursery webs, similar structures are built by some members of Ctenidae, Trechaleidae, and Oxyopidae. Pisauridae has no known morphological synapomorphies that circumscribe all members of the family, and delineation of subfamilies has been a longstanding issue. In addition, several recent molecular phylogenetic studies have called into question the monophyly of Pisauridae. Here, we infer a phylogeny of Pisauridae with nine genetic markers (12S, 16S, 18S, 28S, actin, COI, histone H3, ITS2, and NADH) combined with ultraconserved elements (UCEs) to test the monophyly of the group and determine intrafamilial relationships. Our study includes a total of 81 terminals (59 of them pisaurids). Our maximum likelihood and gene coalescence analyses strongly suggest that as currently circumscribed, the family Pisauridae is not monophyletic. To circumscribe Pisauridae as a monophyletic group, based on our molecular results, we propose the restoration of the family Dolomedidae <span><span>Simon, 1876</span></span> (rank resurrected) to include the genera <em>Dolomedes</em> <span><span>Latreille, 1804</span></span> and <em>Bradystichus</em> <span><span>Simon, 1884</span></span>. In addition, based on morphological evidence, we also place in Dolomedidae the genera <em>Megadolomedes</em> <span><span>Davies & Raven, 1980</span></span>; <em>Tasmomedes</em> Raven, 2018; <em>Mangromedes</em> Raven, 2018; <em>Ornodolomedes</em> <span><span>Raven & Hebron, 2018</span></span>; and <em>Caledomedes</em> <span><span>Raven & Hebron, 2018</span></span>. We provide a phylogenetic delimitation of the three subfamilies of Pisauridae: Halinae, Thaumasiinae, and Pisaurinae. Ten pisaurid genera are deemed <em>incertae sedis</em> in terms of their placement. In light of our hypothesized molecular phylogeny, we discuss the morphological characters and putative synapomorphies of Pisauridae and propose diagnostic characters for its subfamilies and for the family Dolomedidae, along with taxonomic notes about genera not included in our study.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108247"},"PeriodicalIF":3.6,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1016/j.ympev.2024.108245
Nicolas A. Hazzi , Hannah M. Wood , Gustavo Hormiga
Tropical wandering spiders (Ctenidae) are a diverse family of cursorial predators whose species richness peaks in the tropics. The phylogeny of Ctenidae has been examined using morphology and Sanger-based sequencing data, but these studies have been limited by taxon sampling and have often recovered low branch support for many intrafamilial phylogenetic relationships. Herein, we present the most extensive phylogenetic sampling of this family using genome-scale data, leveraging museum collections of all ctenid subfamilies from across the world. We obtained a well-resolved phylogeny of Ctenidae, with the majority of nodes showing maximal nodal support and topological congruence across different phylogenetic analyses. For the first time, we show with high support that Ancylometes is not within Ctenidae but is the sister lineage to all the remaining lycosoid families. Therefore, we propose Ancylometidae as a new family. We assess the phylogenetic position of Ctenidae within Lycosoidea using a variety of phylogenetic methods and tests, demonstrating that the previously proposed position of Ctenidae as the sister clade of Psechridae, based on phylotranscriptomic analyses, lacks phylogenetic support. As a new finding, this study shows that the subfamily Acantheinae, as currently delimited, is polyphyletic. Therefore, we erect the new ctenid subfamily Enoplocteninae to accommodate the Neotropical genera Enoploctenus, Chococtenus, and Phymatoctenus. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Califorctenus and Acantheis) and add support to other parts of the tree that received low support in the most recent Sanger-based phylogeny. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework provided by the molecular phylogenetic results of this study.
{"title":"Reassessing the evolutionary relationships of tropical wandering spiders using phylogenomics: A UCE-based phylogeny of Ctenidae (Araneae) with the discovery of a new lycosoid family","authors":"Nicolas A. Hazzi , Hannah M. Wood , Gustavo Hormiga","doi":"10.1016/j.ympev.2024.108245","DOIUrl":"10.1016/j.ympev.2024.108245","url":null,"abstract":"<div><div>Tropical wandering spiders (Ctenidae) are a diverse family of cursorial predators whose species richness peaks in the tropics. The phylogeny of Ctenidae has been examined using morphology and Sanger-based sequencing data, but these studies have been limited by taxon sampling and have often recovered low branch support for many intrafamilial phylogenetic relationships. Herein, we present the most extensive phylogenetic sampling of this family using genome-scale data, leveraging museum collections of all ctenid subfamilies from across the world. We obtained a well-resolved phylogeny of Ctenidae, with the majority of nodes showing maximal nodal support and topological congruence across different phylogenetic analyses. For the first time, we show with high support that <em>Ancylometes</em> is not within Ctenidae but is the sister lineage to all the remaining lycosoid families. Therefore, we propose Ancylometidae as a new family. We assess the phylogenetic position of Ctenidae within Lycosoidea using a variety of phylogenetic methods and tests, demonstrating that the previously proposed position of Ctenidae as the sister clade of Psechridae, based on phylotranscriptomic analyses, lacks phylogenetic support. As a new finding, this study shows that the subfamily Acantheinae, as currently delimited, is polyphyletic. Therefore, we erect the new ctenid subfamily Enoplocteninae to accommodate the Neotropical genera <em>Enoploctenus</em>, <em>Chococtenus</em>, and <em>Phymatoctenus</em>. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., <em>Califorctenus</em> and <em>Acantheis</em>) and add support to other parts of the tree that received low support in the most recent Sanger-based phylogeny. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework provided by the molecular phylogenetic results of this study.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108245"},"PeriodicalIF":3.6,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-17DOI: 10.1016/j.ympev.2024.108237
Konstantinos Kalaentzis , Stephanie Koster , Jan W. Arntzen , Sergé Bogaerts , James France , Michael Franzen , Christos Kazilas , Spartak N. Litvinchuk , Kurtuluş Olgun , Manon de Visser , Ben Wielstra
Resolving the order of speciation events that occurred in rapid succession is inherently hard and typically requires a phylogenomic approach. A case in point concerns the previously unresolved phylogeny of the three species of banded newt (genus Ommatotriton). We obtain c. 7k nuclear DNA markers using target enrichment by sequence capture and analyze the dataset using maximum likelihood inference of concatenated data with RAxML, summary multi-species coalescent analysis with ASTRAL and Bayesian species tree inference using a diffusion model with SNAPPER, and use TreeMix and PhyloNet to test for interspecific gene flow. All analyses recover three distinct species with no evidence of interspecific gene flow. All analyses retrieved the topology (O. nesterovi, (O. ophryticus, O. vittatus)), with high support. SNAPPER did show the tendency to get stuck in a local optimum, resulting in a different but still highly supported topology. Furthermore, we notice that fewer SNAPPER runs get stuck in a local optimum when we include an outgroup. Therefore, we recommend the exploration of multiple independent runs and the use of an outgroup with this approach. The banded newt radiation illustrates the use of genome-wide data to tackle formerly unresolved phylogenies.
{"title":"Phylogenomics resolves the puzzling phylogeny of banded newts (genus Ommatotriton)","authors":"Konstantinos Kalaentzis , Stephanie Koster , Jan W. Arntzen , Sergé Bogaerts , James France , Michael Franzen , Christos Kazilas , Spartak N. Litvinchuk , Kurtuluş Olgun , Manon de Visser , Ben Wielstra","doi":"10.1016/j.ympev.2024.108237","DOIUrl":"10.1016/j.ympev.2024.108237","url":null,"abstract":"<div><div>Resolving the order of speciation events that occurred in rapid succession is inherently hard and typically requires a phylogenomic approach. A case in point concerns the previously unresolved phylogeny of the three species of banded newt (genus <em>Ommatotriton</em>). We obtain c. 7k nuclear DNA markers using target enrichment by sequence capture and analyze the dataset using maximum likelihood inference of concatenated data with RAxML, summary multi-species coalescent analysis with ASTRAL and Bayesian species tree inference using a diffusion model with SNAPPER, and use TreeMix and PhyloNet to test for interspecific gene flow. All analyses recover three distinct species with no evidence of interspecific gene flow. All analyses retrieved the topology (<em>O. nesterovi</em>, (<em>O. ophryticus</em>, <em>O. vittatus</em>)), with high support. SNAPPER did show the tendency to get stuck in a local optimum, resulting in a different but still highly supported topology. Furthermore, we notice that fewer SNAPPER runs get stuck in a local optimum when we include an outgroup. Therefore, we recommend the exploration of multiple independent runs and the use of an outgroup with this approach. The banded newt radiation illustrates the use of genome-wide data to tackle formerly unresolved phylogenies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108237"},"PeriodicalIF":3.6,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-17DOI: 10.1016/j.ympev.2024.108239
Shahed U.A. Shazib , Ragib Ahsan , Marie Leleu , George B. McManus , Laura A. Katz , Luciana F. Santoferrara
Phylogenetic analyses increasingly rely on genomic and transcriptomic data to produce better supported inferences on the evolutionary relationships among microbial eukaryotes. Such phylogenomic analyses, however, require robust workflows, bioinformatic expertise and computational power. Microbial eukaryotes pose additional challenges given the complexity of their genomes and the presence of non-target sequences (e.g., symbionts, prey) in data obtained from single cells of uncultivable lineages. To address these challenges, we developed a phylogenomic workflow based on single-cell RNA sequencing, integrating all essential steps from cell isolation to data curation and species tree inference. We assessed our workflow by using publicly available and newly generated transcriptomes (11 and 28, respectively) from the Oligotrichea, a diverse group of marine planktonic ciliates. This group’s phylogenetic relationships have been relatively well-studied based on ribosomal RNA gene markers, which we reconstructed by read mapping of transcriptome sequences and compared to our phylogenomic inferences. We also compared phylogenomic analyses based on single-copy protein-coding genes (well-curated orthologs) and multi-copy genes (including paralogs) by sequence concatenation and a coalescence approach (Asteroid), respectively. Finally, using subsets of up to 1,014 gene families (GFs), we assessed the influence of missing data in our phylogenomic inferences. All our analyses yielded similar results, and most inferred relationships were consistent and well-supported. Overall, we found that Asteroid provides robust support for species tree inferences, while simplifying curation steps, minimizing the effects of missing data and maximizing the number of GFs represented in the analyses. Our workflow can be adapted for phylogenomic analyses based on single-cell RNA sequencing of other uncultivable microbial eukaryotes.
{"title":"Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing − A case study with planktonic ciliates (Ciliophora, Oligotrichea)","authors":"Shahed U.A. Shazib , Ragib Ahsan , Marie Leleu , George B. McManus , Laura A. Katz , Luciana F. Santoferrara","doi":"10.1016/j.ympev.2024.108239","DOIUrl":"10.1016/j.ympev.2024.108239","url":null,"abstract":"<div><div>Phylogenetic analyses increasingly rely on genomic and transcriptomic data to produce better supported inferences on the evolutionary relationships among microbial eukaryotes. Such phylogenomic analyses, however, require robust workflows, bioinformatic expertise and computational power. Microbial eukaryotes pose additional challenges given the complexity of their genomes and the presence of non-target sequences (e.g., symbionts, prey) in data obtained from single cells of uncultivable lineages. To address these challenges, we developed a phylogenomic workflow based on single-cell RNA sequencing, integrating all essential steps from cell isolation to data curation and species tree inference. We assessed our workflow by using publicly available and newly generated transcriptomes (11 and 28, respectively) from the Oligotrichea, a diverse group of marine planktonic ciliates. This group’s phylogenetic relationships have been relatively well-studied based on ribosomal RNA gene markers, which we reconstructed by read mapping of transcriptome sequences and compared to our phylogenomic inferences. We also compared phylogenomic analyses based on single-copy protein-coding genes (well-curated orthologs) and multi-copy genes (including paralogs) by sequence concatenation and a coalescence approach (Asteroid), respectively. Finally, using subsets of up to 1,014 gene families (GFs), we assessed the influence of missing data in our phylogenomic inferences. All our analyses yielded similar results, and most inferred relationships were consistent and well-supported. Overall, we found that Asteroid provides robust support for species tree inferences, while simplifying curation steps, minimizing the effects of missing data and maximizing the number of GFs represented in the analyses. Our workflow can be adapted for phylogenomic analyses based on single-cell RNA sequencing of other uncultivable microbial eukaryotes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108239"},"PeriodicalIF":3.6,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-16DOI: 10.1016/j.ympev.2024.108238
Tullia I. Terraneo , Francesca Benzoni , Roberto Arrigoni , Michael L. Berumen , Kiruthiga G. Mariappan , Chakkiath P. Antony , Hugo B. Harrison , Claude Payri , Danwei Huang , Andrew H. Baird
Porites corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of Porites spp. as models for research, the richness and evolutionary relationships of species within the genus remain elusive. In this study, we analyzed genomic data from 330 colonies of Porites from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 25,163 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any nominal species. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, a series of divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about Porites species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. A precise understanding of Porites species and their diversity and distributions is necessary for effective reef conservation and management.
{"title":"A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity from the Indo-Pacific","authors":"Tullia I. Terraneo , Francesca Benzoni , Roberto Arrigoni , Michael L. Berumen , Kiruthiga G. Mariappan , Chakkiath P. Antony , Hugo B. Harrison , Claude Payri , Danwei Huang , Andrew H. Baird","doi":"10.1016/j.ympev.2024.108238","DOIUrl":"10.1016/j.ympev.2024.108238","url":null,"abstract":"<div><div><em>Porites</em> corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of <em>Porites</em> spp. as models for research, the richness and evolutionary relationships of species within the genus remain elusive. In this study, we analyzed genomic data from 330 colonies of <em>Porites</em> from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 25,163 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any nominal species. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, a series of divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about <em>Porites</em> species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. A precise understanding of <em>Porites</em> species and their diversity and distributions is necessary for effective reef conservation and management.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108238"},"PeriodicalIF":3.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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