Molecular Phylogenetics and Evolution最新文献

{"title":"Plastid-nuclear coevolution of ribosomal protein genes in papilionoid legumes","authors":"Lydia G. Tressel ,&nbsp;Bikash Shrestha ,&nbsp;Chaehee Lee ,&nbsp;In-Su Choi ,&nbsp;Tracey A. Ruhlman ,&nbsp;Domingos Cardoso ,&nbsp;Martin F. Wojciechowski ,&nbsp;Robert K. Jansen","doi":"10.1016/j.ympev.2024.108281","DOIUrl":"10.1016/j.ympev.2024.108281","url":null,"abstract":"<div><div>In plants, cellular function is orchestrated by three distinct genomes located within the nucleus, mitochondrion, and plastid. These genomes are interdependent, requiring tightly coordinated maintenance and expression. Plastids host several multisubunit protein complexes encoded by both the plastid and nuclear genomes. To investigate plastid-nuclear coevolution, this study focused on plastid ribosomal protein genes that are encoded by both plastid and nuclear genomes from 50 taxa across 15 of the 22 early branching major clades of the legume subfamily Papilionoideae. Comparative analysis of substitution rates was conducted across five gene sets: nuclear-encoded plastid-targeted ribosomal protein genes (NuCpRP), nuclear-encoded cytosol-targeted ribosomal genes (NuCyRP), other nuclear-encoded plastid-targeted genes that are not involved in ribosomes (NuCpOT), plastid-encoded ribosomal protein genes (CpRP) and plastid-encoded photosynthesis genes (CpPS).<span><span>¹</span></span> Elevated nonsynonymous substitution rates (<em>d_N</em>) and ratios of nonsynonymous to synonymous substitution rates (<em>d_N</em>/<em>d_S</em>_; ω) were observed in both CpRP and NuCpRP compared to the other gene sets. Significant differences in <em>d_N</em> for CpRP and NuCpRP were found between the papilionoid 50-kb inversion clade and other legumes. Using coevolution statistics and evolutionary rate covariation, strong signals of cytonuclear coevolution were identified, where nonsynonymous substitutions in CpRP and NuCpRP genes co-occur along the same branches of the Papilionoideae phylogeny. Increased ω in a few CpRP genes was due to intensified positive selection whereas most of the CpRP and NuCpRP increased ω was caused by relaxed purifying selection. This pattern not only underscores the role of cytonuclear incompatibility in driving speciation but also highlights its constraints on the genetic enhancement of papilionoid crop species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108281"},"PeriodicalIF":3.6,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904175","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":"Genomic data support reticulate evolution in whiptail lizards from the Brazilian Caatinga","authors":"Felipe de M. Magalhães ,&nbsp;Eliana F. Oliveira ,&nbsp;Adrian A. Garda ,&nbsp;Frank T. Burbrink ,&nbsp;Marcelo Gehara","doi":"10.1016/j.ympev.2024.108280","DOIUrl":"10.1016/j.ympev.2024.108280","url":null,"abstract":"<div><div>Species relationships have traditionally been represented by phylogenetic trees, but not all evolutionary histories fit into bifurcating divergence models. Introgressive hybridization challenges this assumption by sometimes [or maybe often] leading to mitochondrial introgression, wherein one species’ mitochondrial genome is entirely replaced by another’s (mitochondrial capture). Such processes result in mitonuclear discrepancies, complicating species delimitation and phylogenetic inference. In our study, we used ultraconserved elements (UCE) and mitogenomic data to investigate the evolutionary history of the <em>Ameivula ocellifera</em> complex, a group of South American whiptail lizards widely distributed in semiarid environments of the Caatinga Domain in Brazil. We examine mitonuclear discordances, assessing reticulate evolution, evaluating species limits, and testing for adaptive mitochondrial capture that could explain higher introgression in the mitochondrial genome compared to nuclear DNA. Our findings support the occurrence of an ancient reticulation event during the diversification of these lizards, driven by introgressive hybridization, leading to mitochondrial capture, and explaining mitonuclear discrepancies. Overall, we did not find clear evidence of positive selection across mitochondrial protein-coding genes suggesting adaptive mitochondrial capture of individuals with introgressed mtDNA. Thus, the genetic diversification and mitogenome evolution could be neutral, with selection against hybridization in the autosomal loci only, or even mediated by mitonuclear incompatibilities. Analyses of mtDNA genomes alongside network and species delimitation methods were crucial for identifying and validating individuals with introgressed mtDNA as a distinct species, demonstrating the potential of genome sampling, and using innovative analytical techniques for elucidating speciation processes in the presence of introgressive hybridization.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108280"},"PeriodicalIF":3.6,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900733","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":"Phylogenetics, biogeography, and life history evolution in the broadly distributed treefrog genus Dendropsophus (Anura: Hylidae: Hylinae)","authors":"Courtney Whitcher ,&nbsp;Victor G.D. Orrico ,&nbsp;Santiago Ron ,&nbsp;Mariana L. Lyra ,&nbsp;Carla S. Cassini ,&nbsp;Rodrigo B. Ferreira ,&nbsp;Daniel Y.M. Nakamura ,&nbsp;Pedro L.V. Peloso ,&nbsp;Marco A. Rada ,&nbsp;Mauricio Rivera-Correa ,&nbsp;Marcelo J. Sturaro ,&nbsp;Paula H. Valdujo ,&nbsp;Célio F.B. Haddad ,&nbsp;Taran Grant ,&nbsp;Julian Faivovich ,&nbsp;Alan Lemmon ,&nbsp;Emily Moriarty Lemmon","doi":"10.1016/j.ympev.2024.108275","DOIUrl":"10.1016/j.ympev.2024.108275","url":null,"abstract":"<div><div><em>Dendropsophus<!--> </em>is one of the most species-rich genera of hylid treefrogs. Recent studies integrating Sanger-generated mitochondrial and nuclear loci with phenomic characters (SP) have advanced understanding of this clade, but questions about its internal relationships and biogeographic history persist. To address these questions, we used anchored hybrid enrichment (AHE) to combine 432 nuclear loci for 78 taxa (72 % of species) with published data. Quantitatively, the impact of the AHE data was modest, with compositional differences in only three recognized clades and more than 80 % of the clades in the AHE + SP analyses also supported in the SP-only analyses. Nevertheless, the impact of AHE was crucial for resolving and increasing support for multiple nodes. We transferred one species of the former<!--> <em>D. ruschii<!--> </em>group to the<!--> <em>D. decipiens</em> <!-->group and redefined the<!--> <em>D. leucophyllatus<!--> </em>group to avoid paraphyly. We estimated divergence times to reconstruct the clade’s biogeographic history. We also examined evolution of oviposition sites and assessed its effect on lineage accumulation. <em>Dendropsophus<!--> </em>likely originated ∼ 57 mya, predating the Andean uplift, with some taxa showing dispersal patterns less constrained by ecological changes than previously thought.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108275"},"PeriodicalIF":3.6,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900736","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":"Plate tectonics, cold adaptation and long-distance range expansion to remote archipelagos and the high Andes as drivers of a circumantarctic freshwater arthropod radiation","authors":"Adrián Villastrigo ,&nbsp;Athena Lam ,&nbsp;Matthew H. Van Dam ,&nbsp;Agnes Scheunert ,&nbsp;Jiří Hájek ,&nbsp;Lars Hendrich ,&nbsp;Mariano C. Michat ,&nbsp;Yoandri Megna ,&nbsp;Luis Figueroa ,&nbsp;Nilver Zenteno ,&nbsp;Julieta Ledezma ,&nbsp;Fernando Guerra-Serrudo ,&nbsp;Michael Balke","doi":"10.1016/j.ympev.2024.108279","DOIUrl":"10.1016/j.ympev.2024.108279","url":null,"abstract":"<div><div>Disjunct distributions, characterised by spatially separated populations of related species, offer insights into historical biogeographic patterns and evolutionary processes. This study investigates the evolutionary history of the diving beetle subfamily Lancetinae through a phylogenomic approach incorporating ultraconserved elements (UCEs) and heritage genetic markers. Our findings support an early Miocene origin for Lancetinae, with subsequent diversification influenced by historical vicariance events and long-distance dispersal. The divergence from the closely related subfamily Coptotominae in the late Cretaceous is not consistent with a Gondwanan origin, although highlights a likely Pangean origin for these taxa. This research underscores the significant impact of Gondwanan fragmentation on biogeographic patterns and highlights the remarkable dispersal capabilities of Lancetinae beetles.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108279"},"PeriodicalIF":3.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873590","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":"Unraveling the potential structure of a Parnassius butterfly in Japan: Insights into the expansion history","authors":"Hideyuki Tamura,&nbsp;Tomoaki Noda,&nbsp;Mikiko Hayashi,&nbsp;Yuko Fujii,&nbsp;Noriko Iwata,&nbsp;Yuko Yokota,&nbsp;Masanori Murata,&nbsp;Chisato Tatematsu,&nbsp;Hideshi Naka ,&nbsp;Akio Tera,&nbsp;Katsumi Ono,&nbsp;Kakeru Yokoi ,&nbsp;Takanori Kato,&nbsp;Tomoko Okamoto,&nbsp;Koji Tsuchida","doi":"10.1016/j.ympev.2024.108278","DOIUrl":"10.1016/j.ympev.2024.108278","url":null,"abstract":"<div><div>The Japanese Archipelago consists of a series of isolated yet interconnected islands off the Eurasian continent. The linear topography of the archipelago presents a unique biogeographic context for the dispersal of organisms from the continent. In this study, mitochondrial DNA (mtDNA) and single-nucleotide polymorphism (SNP) variation were employed to elucidate the dispersal history of the Japanese clouded butterfly (<em>Parnassius glacialis</em>) across the Japanese Archipelago, including the northern island (Hokkaido), the main island (Honshu), and Shikoku Island. Network analysis of 1192 bp of mtDNA (cytochrome oxidase I and II) regions revealed 49 haplotypes and three distinct haplotype groups, which correspond geographically to Eastern Japan, Western Japan, and Chugoku–Shikoku. The Chugoku–Shikoku group is the most ancient lineage. Divergence time estimates using whole-genome sequencing of mtDNA suggest that the Japanese lineage diverged from the continental <em>P. glacialis</em> approximately 3.08 million years ago (Ma). Subsequently, the Eastern Japan and Western Japan lineages diverged from the Chugoku–Shikoku lineage around 1.06 Ma, with subsequent divergence of the Eastern and Western Japan lineages at approximately 0.62 Ma. <em>P. glacialis</em> is estimated to have expanded its distribution via a land bridge that once connected China and the Japanese Archipelago. Population structure analysis based on 3067 SNP genotypes revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. Through mtDNA and SNP variation analyses, four primary genetic barriers were identified: between Hokkaido and Honshu, between Eastern and Central Japan, within the Kansai region, and in the Chugoku region. The first three barriers correspond to notable geographical features, the Blakiston Line, a line parallel to the Itoigawa–Shizuoka Tectonic Line, and a boundary crossing Lake Biwa. These findings suggest that Japanese <em>P. glacialis</em> diverged from the continental <em>P. glacialis</em> and expanded its range across the Japanese Archipelago via western routes, leading to its current distribution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108278"},"PeriodicalIF":3.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873593","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":"Species delimitation and phylogenomics of economically important African Pterocarpus trees, with an implication for the development of DNA-based species identification tools","authors":"Laura Albreht ,&nbsp;Nils Bourland ,&nbsp;Bente Klitgård ,&nbsp;Rowan Schley ,&nbsp;Steven B. Janssens ,&nbsp;Olivier J. Hardy","doi":"10.1016/j.ympev.2024.108277","DOIUrl":"10.1016/j.ympev.2024.108277","url":null,"abstract":"<div><div>Reliable species delimitation is fundamental for establishing clear and equitable guidelines on the sustainable harvest of economically important organisms. <em>Pterocarpus</em> (Fabaceae) is a pantropical tree genus including several highly valuable timber-producing species, that face significant threats from intensive logging. However, a lack of taxonomic clarity has hindered the advance of logging regulations and has led to the inclusion of all African <em>Pterocarpus</em> populations under CITES regulations (CoP19). In our study, we addressed this issue by reassessing species delimitation of all twelve accepted African <em>Pterocarpus</em> species, including neotropical samples of the two trans-Atlantic species. Based on DNA sequences obtained by the Angiosperms353 probe set, we reconstructed a comprehensive phylogeny applying maximum likelihood and multispecies coalescent approaches. Additionally, we explored the potential of high-copy DNA for identifying African <em>Pterocarpus</em> species. This involved reconstructing chloroplast and ribosomal DNA phylogenies, using genome skimming and maximum likelihood approaches. Our results confirmed the monophyly of eleven <em>Pterocarpus</em> species and a paraphyletic <em>P. rotundifolius</em>, which presented geographically coherent subclades, suggesting the possibility of cryptic diversity within the complex. A similar situation arose in <em>P. lucens</em>, exhibiting two sister clades with disjunct distributions. Species delimitation based on high-copy DNA was congruent with the Angiosperms353 data for most species, indicating the reliability of chloroplast and ribosomal DNA markers for <em>Pterocarpus</em> species identification. Our findings give valuable insights into African <em>Pterocarpus</em> species delimitation, highlighting the need for further investigation of potential cryptic diversity within a clade including <em>P. rotundifolius</em>, <em>P. brenanii</em> and <em>P. lucens</em>. Finally, our study lays the groundwork for developing DNA-based tools aimed at improving logging regulations for African <em>Pterocarpus</em> species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108277"},"PeriodicalIF":3.6,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866533","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":"Integrative species delimitation methods infer species boundaries in the Lomatium foeniculaceum complex and indicate an evolutionary history from the Southwest towards the Northeast in western North America","authors":"Daniel E. Botello ,&nbsp;Donald H. Mansfield ,&nbsp;Sven Buerki ,&nbsp;Mary Ann E. Feist ,&nbsp;Mark Darrach ,&nbsp;James F. Smith","doi":"10.1016/j.ympev.2024.108276","DOIUrl":"10.1016/j.ympev.2024.108276","url":null,"abstract":"<div><div>Delimiting species boundaries is a perennial challenge in the field of systematics. Resolving whether morphological variation is the result of environmental parameters, incipient speciation, or complete speciation is especially challenging when the variation is subtle. Within the perennial endemic North American clade of Apiaceae (PENA) there are numerous examples in which widespread species have subtle geographically defined morphological variants that have typically been recognized at the subspecific rank. The <em>Lomatium foeniculaceum</em> (Nutt.) Coult &amp; Rose species complex is a salient case that has long been treated as a single species with five infrataxa, spanning much of the western United States and western Canada in a morphological continuum: <em>L</em>. <em>foeniculaceum</em> var. <em>foeniculaceum</em>, <em>L</em>. <em>foeniculaceum</em> var. <em>daucifolium</em> (Torr. &amp; A. Gray) Cronquist, <em>L</em>. <em>foeniculaceum</em> var. <em>macdougalii</em> (J.M. Coult. &amp; Rose) Cronquist, <em>L</em>. <em>foeniculaceum</em> var. <em>fimbriatum</em> (W.L. Theob.) B. Boivin, and <em>L</em>. <em>foeniculaceum</em> var. <em>inyoense</em> (Mathias &amp; Constance) B. Boivin. We utilized the Angiosperm353 baits kit to sample nuclear loci from these five taxa to determine if the subspecific taxa formed discrete genetic groups with the molecular data. Groups that were identified were then examined for a combination of morphological and ecological traits that corresponded to these groups and could be used to determine the most appropriate taxonomic ranks of recovered groups. Molecular data recovers six well-supported monophyletic clades and a seventh clade of a single individual. Samples initially identified as <em>L. foeniculaceum</em> var. <em>macdougalii</em> are in two clades with one sister to <em>L. foeniculaceum</em> var. <em>foeniculaceum/L. foeniculaceum</em> var. <em>daucifolium</em> the other sister to <em>L. foeniculaceum</em> var. <em>fimbriatum.</em> Most samples of <em>L. foeniculaceum</em> var. <em>foeniculaceum</em> are in the same clade; others are in the clade with <em>L. foeniculaceum</em> var. <em>daucifolium</em> depending on the analysis. Each clade can be defined with a distinct morphological diagnostic character state. We conclude that molecular data and morphology support the recognition of five distinct species within the complex: <em>L</em>. <em>inyoense</em> Mathias &amp; Constance, <em>L</em>. <em>macdougalii</em> J. M. Coult. &amp; Rose, <em>L. fimbriatum</em> (W.L. Theob.) Botello &amp; J.F. Sm., <em>L. semivaginatum</em> Botello &amp; J.F. Sm., and <em>L. foeniculaceum</em> with two varieties retained, <em>L. foeniculaceum</em> var. <em>foeniculaceum</em> and <em>L. foeniculaceum</em> var. <em>daucifolium</em>. The data suggest that the Continental Divide has been influential in the evolution of these species, acting as an effective barrier facilitating speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108276"},"PeriodicalIF":3.6,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856988","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":"A straightforward workflow to explore species diversity using the Patagonian lizards of the Diplolaemus genus (Iguania: Leiosauridae) as a study case, with the description of a new species","authors":"Juan Vrdoljak ,&nbsp;Kevin Imanol Sánchez ,&nbsp;Andrea González-Marín ,&nbsp;Mariana Morando ,&nbsp;Luciano Javier Avila","doi":"10.1016/j.ympev.2024.108274","DOIUrl":"10.1016/j.ympev.2024.108274","url":null,"abstract":"<div><div>Disputes over species descriptions, stemming from conceptual disparities and arbitrary species boundaries, are among the primary challenges of modern taxonomy. In this study, we introduce a straightforward workflow, grounded in evolutionary theory, designed to tackle these challenges. We exemplified this approach using Patagonian lizards from the <em>Diplolaemus</em> clade. This workflow involves assigning specimens to putative evolutionary lineages, conducting primary species delimitations, constructing a species tree, comparing lineages for evolutionary independence, and using <em>post-hoc</em> analyses to separate well-supported from ambiguous lineages. This approach aims to establish a reliable foundation for exploring the taxonomic and evolutionary diversity of challenging groups. Applying this workflow to the <em>Diplolaemus</em> clade, we used various analytical methods on genetic (mitochondrial and nuclear markers) and phenotypic data (meristic, linear, and geometric morphometrics). We identified ten lineages with varying degrees of evolutionary independence in a clade where only four species had been described. Among the newly identified lineages, two exhibited low support for evolutionary independence, three showed strong support but had non-conclusive information, and one was recognized and described as a new species<em>.</em> In summary, our hierarchical workflow not only facilitated comprehensive comparisons but also enabled us to draw robust conclusions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108274"},"PeriodicalIF":3.6,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856968","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":"A time-calibrated salamander phylogeny including 765 species and 503 genes","authors":"Alexander A. Stewart,&nbsp;John J. Wiens","doi":"10.1016/j.ympev.2024.108272","DOIUrl":"10.1016/j.ympev.2024.108272","url":null,"abstract":"<div><div>Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22–45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108272"},"PeriodicalIF":3.6,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840342","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, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae","authors":"Silas Bossert ,&nbsp;Felipe V. Freitas ,&nbsp;Alain Pauly ,&nbsp;Gengping Zhu ,&nbsp;David W. Crowder ,&nbsp;Michael C. Orr ,&nbsp;James B. Dorey ,&nbsp;Elizabeth A. Murray","doi":"10.1016/j.ympev.2024.108273","DOIUrl":"10.1016/j.ympev.2024.108273","url":null,"abstract":"<div><div>The Afrotropical region is home to many endemic bee groups, yet almost none have been studied from an integrated, holistic perspective. Among them, the halictid subfamily Nomiinae contains exceptional African diversity with variable distributions and life histories. Here, we combine phylogenomics, molecular dating, and distributional modelling to explore the evolutionary ecology of the genus <em>Trinomia</em>. We analyzed a matrix of 59 species of Nomiinae using ultraconserved element (UCE) and whole genome data, including all six species of <em>Trinomia</em>, and estimated divergence times for the subfamily. We then generated distribution models for all six species of <em>Trinomia</em> using Maximum Entropy models (MaxEnt) and 671 spatial data points. From these methods, we discovered a monophyletic <em>Trinomia</em> with an unexpected sister group relationship to the Asian-endemic genus <em>Gnathonomia</em>, as well as a recent origin of <em>Trinomia</em> in the late Miocene (∼5.8 million years ago). From our results, we found hints of phylogenetic conservatism in distribution among sister-groups of <em>Trinomia</em>, however, our results also highlight the need for additional efforts inventorying, identifying, and sharing data on African bees. This study represents an exemplary first step into studying bee spatial phylogenomics of African endemic bees.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108273"},"PeriodicalIF":3.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830472","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}