Molecular Phylogenetics and Evolution最新文献

{"title":"Molecular phylogeny of Hesperiidae (Lepidoptera) with an emphasis on Asian and African genera","authors":"Zhenfu Huang ,&nbsp;Hideyuki Chiba ,&nbsp;Yanqing Hu ,&nbsp;Xiaohua Deng ,&nbsp;Wen Fei ,&nbsp;Szabolcs Sáfián ,&nbsp;Liwei Wu ,&nbsp;Min Wang ,&nbsp;Xiaoling Fan","doi":"10.1016/j.ympev.2024.108119","DOIUrl":"10.1016/j.ympev.2024.108119","url":null,"abstract":"<div><p>Despite considerable research efforts in recent years, the deeper phylogenetic relationships among skipper butterflies (Hesperiidae) remain unresolved. This is primarily because of limited sampling, especially within Asian and African lineages. In this study, we consolidated previous data and extensively sampled Asian and African taxa to elucidate the phylogenetic relationships within Hesperiidae. The molecular dataset comprised sequences from two mitochondrial and two nuclear gene regions from 563 species that represented 353 genera. Our analyses revealed seven subfamilies within Hesperiidae: Coeliadinae, Euschemoninae, Eudaminae, Pyrginae, Heteropterinae, Trapezitinae, and Hesperiinae. The systematics of most tribes and genera aligned with those of prior studies. However, notable differences were observed in several tribes and genera. Overall, the position of taxa assigned to <em>incertae sedis</em> in Hesperiinae is largely clarified in this study. Our results strongly support the monophyly of the tribe Tagiadini (Pyrginae), and the systematics of some genera are clarified with comprehensive discussion. We recognize 15 tribes within the subfamily Hesperiinae. Of these, nine tribes are discussed in detail: Aeromachini, Astictopterini, Erionotini, Unkanini (new status), Ancistroidini, Ismini (confirmed status), Plastingini (new status), Gretnini (confirmed status), and Eetionini (confirmed status). We propose four subtribes within Astictopterini: Hypoleucina <strong>subtrib.n.</strong>, Aclerosina, Cupithina, and Astictopterina. Furthermore, we describe a new genus (<em>Hyarotoides</em> <strong>gen.n.</strong>) and reinstate two genera (<em>Zea</em> <strong>reinst.stat.</strong> and <em>Sepa</em> <strong>reinst.stat.</strong>) as valid. Additionally, we propose several new combinations: <em>Zea mytheca</em> <strong>comb.n.,</strong> <em>Sepa bononia</em> <strong>comb.n. &amp; reinst.stat.,</strong> and <em>Sepa umbrosa</em> <strong>comb.n.</strong> This study, with extensive sampling of Asian and African taxa, greatly enhances the understanding of the knowledge of the skipper tree of life.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"198 ","pages":"Article 108119"},"PeriodicalIF":4.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001118/pdfft?md5=219d4a76e376759b942ad88d260c7bd4&pid=1-s2.0-S1055790324001118-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288933","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}

{"title":"Sea anemone (Anthozoa, Actiniaria) diversity in Mo’orea (French Polynesia)","authors":"Charlotte Benedict ,&nbsp;Alonso Delgado ,&nbsp;Isabel Pen ,&nbsp;Claudia Vaga ,&nbsp;Marymegan Daly ,&nbsp;Andrea M. Quattrini","doi":"10.1016/j.ympev.2024.108118","DOIUrl":"10.1016/j.ympev.2024.108118","url":null,"abstract":"<div><p>Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo’orea (French Polynesia) with the use of a dataset from the Mo’orea Biocode’s “BioBlitz” initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo’orea’s diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera <em>Andvakia</em> and <em>Aiptasiomorpha</em>. This research unveils the diverse sea anemone ecosystem in Mo’orea, spotlighting the area’s ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"198 ","pages":"Article 108118"},"PeriodicalIF":4.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001106/pdfft?md5=fa0aef636cb361dc529c36a2e23263da&pid=1-s2.0-S1055790324001106-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141288959","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}

{"title":"The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally","authors":"Yibo Ding ,&nbsp;Hongbo Guo ,&nbsp;Xinfang Hong ,&nbsp;Qiudi Li ,&nbsp;Zhijiang Miao ,&nbsp;Qiuwei Pan ,&nbsp;Kuiyang Zheng ,&nbsp;Wenshi Wang","doi":"10.1016/j.ympev.2024.108114","DOIUrl":"10.1016/j.ympev.2024.108114","url":null,"abstract":"<div><p>Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108114"},"PeriodicalIF":4.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201286","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}

{"title":"An ultraconserved element probe set for velvet worms (Onychophora)","authors":"Shoyo Sato ,&nbsp;Shahan Derkarabetian ,&nbsp;Arianna Lord ,&nbsp;Gonzalo Giribet","doi":"10.1016/j.ympev.2024.108115","DOIUrl":"10.1016/j.ympev.2024.108115","url":null,"abstract":"<div><p>Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families – Peripatopsidae and Peripatidae – and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics. Neopatida, the Neotropical clade of peripatids, has proved particularly difficult, with recalcitrant nodes and low resolution, potentially due to rapid radiation of the group during the Cretaceous. Previous studies have had to compromise between number of loci and number of taxa due to limitations of Sanger sequencing and phylotranscriptomics, respectively. Additionally, aspects of their genome size and structure have made molecular phylogenetics difficult and data matrices have been affected by missing data. To address these issues, we leveraged recent, published transcriptomes and the first high quality genome for the phylum and designed a high affinity ultraconserved element (UCE) probe set for Onychophora. This new probe set, consisting of ∼ 20,000 probes that target 1,465 loci across both families, has high locus recovery and phylogenetic utility. Phylogenetic analyses recovered the monophyly of major clades of Onychophora and revealed a novel lineage from the Neotropics that challenges our current understanding of onychophoran biogeographic endemicity. This new resource could drastically increase the power of molecular datasets and potentially allow access to genomic scale data from archival museum specimens to further tackle the issues exasperating onychophoran systematics.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108115"},"PeriodicalIF":4.1,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001076/pdfft?md5=b8befd6bdb00cdebaacbfc975838dd5d&pid=1-s2.0-S1055790324001076-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176883","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}

{"title":"Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae)","authors":"Yan Wang ,&nbsp;Xuexue Wu ,&nbsp;Yanyi Chen ,&nbsp;Chao Xu ,&nbsp;Yinghui Wang ,&nbsp;Qiang Wang","doi":"10.1016/j.ympev.2024.108112","DOIUrl":"10.1016/j.ympev.2024.108112","url":null,"abstract":"<div><p>Obtaining a robust phylogeny proves challenging due to the intricate evolutionary history of species, where processes such as hybridization and incomplete lineage sorting can introduce conflicting signals, thereby complicating phylogenetic inference. In this study, we conducted comprehensive sampling of Elsholtzieae, with a particular focus on its largest genus, <em>Elsholtzia</em>. We utilized 503 nuclear loci and complete plastome sequences obtained from 99 whole-genome sequencing datasets to elucidate the interspecific relationships within the Elsholtzieae. Additionally, we explored various sources of conflicts between gene trees and species trees. Fully supported backbone phylogenies were recovered, and the monophyly of <em>Elsholtzia</em> and <em>Keiskea</em> was not supported. Significant gene tree heterogeneity was observed at numerous nodes, particularly regarding the placement of <em>Vuhuangia</em> and the <em>E. densa</em> clade. Further investigations into potential causes of this discordance revealed that incomplete lineage sorting (ILS), coupled with hybridization events, has given rise to substantial gene tree discordance. Several species, represented by multiple samples, exhibited a closer association with geographical distribution rather than following a strictly monophyletic pattern in plastid trees, suggesting chloroplast capture within Elsholtzieae and providing evidence of hybridization. In conclusion, this study provides phylogenomic insights to untangle taxonomic problems in the tribe Elsholtzieae, especially the genus <em>Elsholtzia</em>.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"198 ","pages":"Article 108112"},"PeriodicalIF":4.1,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162559","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}

{"title":"Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci","authors":"Drew R. Schield ,&nbsp;Clare E. Brown ,&nbsp;Subir B. Shakya ,&nbsp;Gina M. Calabrese ,&nbsp;Rebecca J. Safran ,&nbsp;Frederick H. Sheldon","doi":"10.1016/j.ympev.2024.108111","DOIUrl":"10.1016/j.ympev.2024.108111","url":null,"abstract":"<div><p>Swallows (Hirundinidae) are a globally distributed family of passerine birds that exhibit remarkable similarity in body shape but tremendous variation in plumage, sociality, nesting behavior, and migratory strategies. As a result, swallow species have become models for empirical behavioral ecology and evolutionary studies, and variation across the Hirundinidae presents an excellent opportunity for comparative analyses of trait evolution. Exploiting this potential requires a comprehensive and well-resolved phylogenetic tree of the family. To address this need, we estimated swallow phylogeny using genetic data from thousands of ultraconserved element (UCE) loci sampled from nearly all recognized swallow species. Maximum likelihood, coalescent-based, and Bayesian approaches yielded a well-resolved phylogenetic tree to the generic level, with minor disagreement among inferences at the species level, which likely reflect ongoing population genetic processes. The UCE data were particularly useful in helping to resolve deep nodes, which previously confounded phylogenetic reconstruction efforts. Divergence time estimates from the improved swallow tree support a Miocene origin of the family, roughly 13 million years ago, with subsequent diversification of major groups in the late Miocene and Pliocene. Our estimates of historical biogeography support the hypothesis that swallows originated in the Afrotropics and have subsequently expanded across the globe, with major <em>in situ</em> diversification in Africa and a secondary major radiation following colonization of the Neotropics. Initial examination of nesting and sociality indicates that the origin of mud nesting – a relatively rare nest construction phenotype in birds – was a major innovation coincident with the origin of a clade giving rise to over 40% of extant swallow diversity. In contrast, transitions between social and solitary nesting appear less important for explaining patterns of diversification among swallows.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108111"},"PeriodicalIF":4.1,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158965","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}

{"title":"Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)","authors":"Qi Chen ,&nbsp;Min Deng ,&nbsp;Xuan Dai ,&nbsp;Wei Wang ,&nbsp;Xing Wang ,&nbsp;Liu-Sheng Chen ,&nbsp;Guo-Hua Huang","doi":"10.1016/j.ympev.2024.108113","DOIUrl":"10.1016/j.ympev.2024.108113","url":null,"abstract":"<div><p>A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order in the world following Coleoptera and Diptera, Lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such a charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly resolved. Compared to earlier phylogenomic studies, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa) and acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling with significant increases in the number of included genes on tree topology by considering a series of systematic errors using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias giving rise to unstable positions of ditrysian groups in phylogenomic reconstruction. Phylogenetic inference showed the most comprehensive framework to reveal the relationships among lepidopteran superfamilies, and presented some newly relationships with strong supports (Papilionoidea was sister to Gelechioidea and Immoidea was sister to Galacticoidea, respectively), but limited by taxon sampling, the relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly resolved, which need to increase taxon sampling for further phylogenomic reconstruction. The present study demonstrates that taxon sampling is an important determinant for an accurate lepidopteran tree of life and provides some essential insights for future lepidopteran phylogenomic studies.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108113"},"PeriodicalIF":4.1,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141139977","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}

{"title":"Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective","authors":"Chuanqi Jiang ,&nbsp;Siyu Gu ,&nbsp;Tingting Pan ,&nbsp;Xueyan Wang ,&nbsp;Weiwei Qin ,&nbsp;Guangying Wang ,&nbsp;Xinxin Gao ,&nbsp;Jing Zhang ,&nbsp;Kai Chen ,&nbsp;Alan Warren ,&nbsp;Jie Xiong ,&nbsp;Wei Miao","doi":"10.1016/j.ympev.2024.108110","DOIUrl":"10.1016/j.ympev.2024.108110","url":null,"abstract":"<div><p>Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108110"},"PeriodicalIF":4.1,"publicationDate":"2024-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072365","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}

{"title":"Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)","authors":"Guilherme H.F. Azevedo ,&nbsp;Marshal Hedin ,&nbsp;Wayne P. Maddison","doi":"10.1016/j.ympev.2024.108109","DOIUrl":"10.1016/j.ympev.2024.108109","url":null,"abstract":"<div><p>We use ultraconserved elements (UCE) and Sanger data to study the phylogeny, age, and biogeographical history of harmochirine jumping spiders, a group that includes the species-rich genus <em>Habronattus</em>, whose remarkable courtship has made it the focus of studies of behaviour, sexual selection, and diversification. We recovered 1947 UCE loci from 43 harmochirine taxa and 4 outgroups, yielding a core dataset of 193 UCEs with at least 50 % occupancy. Concatenated likelihood and ASTRAL analyses confirmed the separation of harmochirines into two major clades, here designated the infratribes Harmochirita and Pellenita. Most are African or Eurasian with the notable exception of a clade of pellenites containing <em>Habronattus</em> and <em>Pellenattus</em> of the Americas and <em>Havaika</em> and <em>Hivanua</em> of the Pacific Islands. Biogeographical analysis using the DEC model favours a dispersal of the clade’s ancestor from Eurasia to the Americas, from which <em>Havaika</em>’s ancestor dispersed to Hawaii and <em>Hivanua</em>’s ancestor to the Marquesas Islands. Divergence time analysis on 32 loci with 85 % occupancy, calibrated by fossils and island age, dates the dispersal to the Americas at approximately 4 to 6 million years ago. The explosive radiation of <em>Habronattus</em> perhaps began only about 4 mya. The phylogeny clarifies both the evolution of sexual traits (e.g., the terminal apophyses was enlarged in <em>Pellenes</em> and not subsequently lost) and the taxonomy. <em>Habronattus</em> is confirmed as monophyletic. <em>Pellenattus</em> is raised to the status of genus, and 13 species moved into it as new combinations. <em>Bianor stepposus</em> Logunov, 1991 is transferred to <em>Sibianor</em>, and <em>Pellenes bulawayoensis</em> Wesołowska, 1999 is transferred to <em>Neaetha</em>. A molecular clock rate estimate for spider UCEs is presented and its utility to inform prior distributions is discussed.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108109"},"PeriodicalIF":4.1,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1055790324001015/pdfft?md5=986ae4a61e4be84a6ea946819fcd187c&pid=1-s2.0-S1055790324001015-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141072321","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}

{"title":"Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae)","authors":"Francois S. Becker ,&nbsp;Graham J. Alexander ,&nbsp;Krystal A. Tolley","doi":"10.1016/j.ympev.2024.108104","DOIUrl":"10.1016/j.ympev.2024.108104","url":null,"abstract":"<div><p>Barking geckos (genus <em>Ptenopus</em>) are terrestrial, burrowing lizards endemic to southern Africa, currently with three recognised species. Two species are range-restricted (<em>P. kochi</em> and <em>P. carpi</em>) and display clear differences in substrate preference (soft sand vs. hard gravel). The third and most widespread species, <em>P. garrulus,</em> occurs on a variety of substrates of differing hardness, across potential geographic barriers, and over a steep climatic gradient. Variations in morphology and advertisement calls indicates that <em>P. garrulus</em> may be a species complex. Two subspecies of <em>P. garrulus</em> are currently recognised: <em>P. g. maculatus</em> and <em>P. g. garrulus</em>. To investigate species boundaries, we produced the first comprehensive phylogeny for the genus. We used a novel application of multiple regression on matrices models to assess multiple environmental drivers of diversification, as contrasted to isolation by distance. We show that <em>P. kochi, P. carpi,</em> and <em>P. g. garrulus</em> are valid species, but that <em>P. g. maculatus</em> is a paraphyletic complex of five previously unrecognised taxa. Specialisation onto different substrates was likely the main driver of divergence, with parapatric occurrence of two to four clades occurring at each of the three substrate transition zones identified <em>a priori</em>. The region encompasses diverse bioclimatic regions and potential geographic barriers, and these likely played a role in some divergence events.</p></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"197 ","pages":"Article 108104"},"PeriodicalIF":4.1,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140944282","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}