Molecular Phylogenetics and Evolution最新文献

{"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 ,&nbsp;Ragib Ahsan ,&nbsp;Marie Leleu ,&nbsp;George B. McManus ,&nbsp;Laura A. Katz ,&nbsp;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}

{"title":"A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity from the Indo-Pacific","authors":"Tullia I. Terraneo ,&nbsp;Francesca Benzoni ,&nbsp;Roberto Arrigoni ,&nbsp;Michael L. Berumen ,&nbsp;Kiruthiga G. Mariappan ,&nbsp;Chakkiath P. Antony ,&nbsp;Hugo B. Harrison ,&nbsp;Claude Payri ,&nbsp;Danwei Huang ,&nbsp;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}

{"title":"Evolution, range formation and a revised taxonomy of the disjunctly distributed European members of Astragalus sect. Caprini, an intricate group including highly endangered species of dry grasslands","authors":"Clemens Maylandt ,&nbsp;Philipp Kirschner ,&nbsp;Daniela Pirkebner ,&nbsp;Božo Frajman ,&nbsp;Julio Peñas de Giles ,&nbsp;Peter Schönswetter ,&nbsp;Pau Carnicero","doi":"10.1016/j.ympev.2024.108242","DOIUrl":"10.1016/j.ympev.2024.108242","url":null,"abstract":"<div><div>The Eurasian steppes are among the largest and most threatened biomes on Earth. During cold periods of the Pleistocene, the zonal Eurasian steppes had a much larger extent as compared to interglacial periods, and repeatedly expanded into large areas of present-day forested temperate Europe. Conversely, during warm periods, forest expansion recurrently forced Eurasian steppe biota into disjunct and small warm-stage refugia, i.e. today’s extrazonal steppes. The rare, threatened and disjunctly distributed northwestern African and European members of <em>Astragalus</em> sect. <em>Caprini</em> constitute an ideal model for gaining insights into the evolutionary dynamics of typical steppe biota. Here, we reconstructed the spatiotemporal diversification of northwestern African and European members of <em>Astragalus</em> sect. <em>Caprini</em> based on a combination of RADseq data, single gene markers (internal transcribed spacer, plastid <em>ycf1</em>), genome size measurements and multivariate morphometrics. We outline an evolutionary scenario in which the group originated in the Irano-Turanian region and started to diversify shortly after the Mid-Pleistocene-Transition (ca. 0.5 to 0.7 Ma). While lineages occurring in (sub-)mediterranean mountain ranges diverged early, lineages occurring in northern lowland steppes are much younger (ca. 0.2 to 0.3 Ma), emphasizing the importance of southern European mountain ranges as long-term refugia. Recurrent colonization of the western Mediterranean region by eastern Mediterranean lineages and secondary contacts of currently spatially isolated lineages have significantly (co-)shaped the genetic structure within the group; we assume that these events may be a consequence of cold-stage range expansions<em>.</em> Based on combined genetic and morphometric data, we suggest treating the ten lineages introduced in this study as independent species, contrasting previous taxonomic treatments.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108242"},"PeriodicalIF":3.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649563","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":"Nuclear phylogenomics of Eperua (Leguminosae) highlights the role of habitat and morphological lability in dispersal and diversification across Amazonia and in the Caatinga-Cerrado ecotone","authors":"Elenice A. Fortes ,&nbsp;Jacob B. Landis ,&nbsp;Hans ter Steege ,&nbsp;Chelsea D. Specht ,&nbsp;Jeff J. Doyle ,&nbsp;Vidal de F. Mansano","doi":"10.1016/j.ympev.2024.108236","DOIUrl":"10.1016/j.ympev.2024.108236","url":null,"abstract":"<div><div><em>Eperua</em> is a genus of Neotropical trees that forms a major component of tropical lowland forests in Amazonia, especially in the Guiana Shield and on white-sand forests. One species occurs in the Cerrado-Caatinga ecotone, and the genus also inhabits riverine and terra firme forests. Species in <em>Eperua</em> exhibit one of two drastically different floral architectures and inflorescence types, each associated with distinct pollinators. Prior phylogenetic studies of <em>Eperua</em> have revealed an unstructured topology concerning floral architectures and inflorescence types. In addition, no investigation has been conducted on how the evolution of these traits and habitat preferences influenced the dispersal and diversification of <em>Eperua</em>. Using target capture sequencing, we inferred the most comprehensive phylogeny for <em>Eperua</em> to date, sampling all 19 known species, five for the first time. We used coalescence, concatenation, and network methods to infer the <em>Eperua</em> phylogeny and investigate sources of incongruence impacting resolution and support. We reconstructed the biogeographic history and ancestral states for the flower architecture, inflorescence type, and habitat preference. Our phylogenomic analyses successfully resolved relationships within <em>Eperua</em>, attributing conflicts between the species tree and concatenated tree to gene tree discordance linked to reticulation events. Biogeographical analyses indicate that <em>Eperua</em> originated and initially diversified in the white-sand forests of the Guiana Shield. A subsequent adaptation to riverine and terra firme forests enabled <em>Eperua</em> to expand into new habitats and regions. Still, its historical preference for white-sand forests probably accounts for its absence in the southern and western parts of Amazonia. Ancestral geographic areas and corolla morphotype reconstructions suggest that speciation in <em>Eperua</em> has occurred in sympatry, likely driven by pollinator shifts mediated by drastic changes in floral architecture.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108236"},"PeriodicalIF":3.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644947","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 analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests","authors":"Xiu-Fei Qiu ,&nbsp;Yan-Yan Liu ,&nbsp;Ge Wu ,&nbsp;Cong-Hui Xu ,&nbsp;Xin-Quan Liu ,&nbsp;Xiao-Yan Xiang ,&nbsp;Xiao-Xin Wei ,&nbsp;Xiao-Quan Wang","doi":"10.1016/j.ympev.2024.108240","DOIUrl":"10.1016/j.ympev.2024.108240","url":null,"abstract":"<div><div>As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today’s forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time. We first reconstructed a highly resolved and robust phylogeny of <em>Larix</em> covering all widely recognized species, using both transcriptome-based 1,301 orthologous genes (OGs) and plastid genomes. In sharp contrast to previous studies, an unexpected deep split between the circumboreal and Qinghai-Tibetan Plateau (QTP) larches was revealed in our study. Within each lineage, two geographically distinct clades were further resolved. Biogeographical analyses suggest that <em>Larix</em> might have an origin of Eocene in high-latitude uplands, and during the Miocene, all extant species have appeared. Cenozoic climate- and orogeny-triggered vicariance likely played a major role in the divergence of global larches. Our results also demonstrate that the proto-boreal forest biome may have a relatively old origin back to the early Miocene, and significant winnowing and species alteration would have occurred as the climate shifted to much colder and drier conditions during the Neogene. Ecological niche analyses show various responses of the circumboreal and QTP larches under different climate scenarios, but both lineages are negatively impacted by warming climates. These findings have important conservation implications given the sensitivity of boreal forests in the face of global warming. Our work further emphasizes the importance of a solid phylogenetic framework for evolutionary and biogeographical inferences.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108240"},"PeriodicalIF":3.6,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644949","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 analyses of hamsters (Cricetinae) inferred from GBS data and mitochondrial genomes","authors":"Xuan Pan ,&nbsp;Xuming Wang ,&nbsp;Yingxun Liu ,&nbsp;Yuchun Li ,&nbsp;Rui Liao ,&nbsp;Zhongzheng Chen ,&nbsp;Buqing Peng ,&nbsp;Xichao Zhu ,&nbsp;Jiatang Li ,&nbsp;Shaoying Liu","doi":"10.1016/j.ympev.2024.108241","DOIUrl":"10.1016/j.ympev.2024.108241","url":null,"abstract":"<div><div>Accurate species delimitation and identification is crucial for species conservation, providing a foundation for studies on evolutionary biology, ecology, and essentially all biological disciplines. The subfamily Cricetinae (Cricetidae, Rodentia), known as hamsters, is widely distributed in the Palearctic region. At present, there are nine genera and 18 species of hamsters are recognized worldwide, although the taxonomic status of certain taxa remains unclear. In this study, we collected 146 hamster specimens representing 14 species and generated new mitochondrial genomes and nuclear genome-wide single nucleotide polymorphisms (SNPs) to explore their relationships among these hamsters using multiple species delimitation approaches. Results showed: (1) strong phylogenetic support for the classification of <em>Urocricetus, Nothocricetulus</em>, and <em>Cansumys</em> as separate genera; (2) <em>Urocricetus</em> contained two separate species, <em>U. kamensis</em> and <em>U. lama</em>, with <em>U. alticola</em> and <em>U. tibetanus</em> considered synonyms of <em>U. lama</em>; (3) <em>U. kamensis</em> and <em>U. lama</em> are separated by the Nujiang River, with the matching divergence time suggesting that the formation of the river was the primary evolutionary factor driving the species differentiation, and (4) genetic differentiation occurred within the <em>Tscherskia</em> genus, which included two cryptic species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108241"},"PeriodicalIF":3.6,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640352","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":"Reticulate Evolution in Japanese Sceptridium (Ophioglossaceae), including diploid, tetraploid, and hexaploid species","authors":"Sousuke Ishii ,&nbsp;Norio Sahashi ,&nbsp;Atushi Ebihara ,&nbsp;Shun K. Hirota ,&nbsp;Yoshihisa Suyama ,&nbsp;Yasuyuki Watano","doi":"10.1016/j.ympev.2024.108244","DOIUrl":"10.1016/j.ympev.2024.108244","url":null,"abstract":"<div><div>Homospory represents an intriguing reproductive strategy, including the potential for gametophytic selfing, considered the ultimate form of selfing. The plants of the fern genus <em>Sceptridium</em> (Ophioglossaceae) are generally considered to be predominantly selfing, making them suitable for analyzing speciation patterns and intraspecific variation characteristic of homosporous plants. The <em>Sceptridium</em> species in Japan not only exhibit variations in ploidy, including diploids, tetraploids, and hexaploids, but also pose taxonomic challenges due to morphologically distinctive forms that are difficult to be assigned to previously described species. We developed multiple single-copy nuclear markers and aimed to identify ancestral species of the polyploids and to elucidate the evolutionary entity of an undescribed species. Chromosome counts and analyses of individual gene trees confirmed that <em>S. japonicum, S. atrovirens,</em> and the undescribed species are allohexaploids originating through hybridization between a maternal tetraploid ancestor closely related to <em>S. formosanum</em> and a paternal diploid ancestor closely related to extant diploid species. By identifying homoeologs derived from the diploid ancestor, we successfully analyzed the phylogenetic relationship between the diploid ancestor of the hexaploid species and extant diploid species using the multispecies coalescent model. The examined undescribed species could not be distinguished from <em>S. atrovirens</em> by multiple nuclear markers or by SNP data obtained from multiplexed ISSR genotyping by sequencing. This species appears to represent one of the polymorphisms of <em>S. atrovirens</em>, which was fixed through gametophytic selfing.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108244"},"PeriodicalIF":3.6,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640415","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":"A phylogenomic tree of wood-warblers (Aves: Parulidae): Dealing with good, bad, and ugly samples","authors":"Min Zhao ,&nbsp;Jessica A. Oswald ,&nbsp;Julie M. Allen ,&nbsp;Hannah L. Owens ,&nbsp;Peter A. Hosner ,&nbsp;Robert P. Guralnick ,&nbsp;Edward L. Braun ,&nbsp;Rebecca T. Kimball","doi":"10.1016/j.ympev.2024.108235","DOIUrl":"10.1016/j.ympev.2024.108235","url":null,"abstract":"<div><div>The New World warblers (Parulidae) are a model group for ecological and evolutionary analyses. However, current phylogenetic relationships across this family are based upon few loci. Here we use ultraconserved elements (UCEs) to estimate a rigorous species-level phylogeny for the family. As is true for many groups, high-quality tissues were unavailable for some taxa. Thus, we explored methods for incorporating sequences derived from historical (toe pad) samples to expand the phylogenetic datasets. We recovered an average of 4,186 UCE loci and mitochondrial bycatch data (supplemented with published mitochondrial data) from 96% of all currently recognized species. We found that the UCE phylogeny built with alignments with less than 70% of gaps and ambiguities recovered the most robust phylogenetic relationships for this family, representing 101 species. Using this phylogeny as a topological backbone and adding ten fair quality “bad” samples effectively generated an overall well supported phylogeny, representing 108 species (∼90% of all species). Based on this tree, we then added in seven poor quality “ugly” samples and six of those were placed within their expected genera. We also explored the phylogenetic positions of the likely extinct <em>Leucopeza semperi</em> and the endangered <em>Catharopeza bishopi</em> where limited data was obtained. Overall, taxonomic placements in our UCE trees largely correspond to previously published studies with the recovery of all currently recognized genera as monophyletic except for <em>Basileuterus</em> which was rendered paraphyletic by <em>B. lachrymosus</em>. Our study provides insights in understanding the phylogenetic relationships of a model Passeriformes family and outlines effective practices for managing sparse genomic data sourced from historical museum specimens. Variable topological arrangements across datasets and analyses reflect the evolutionary complexity of this group and provide future topics for in-depth studies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108235"},"PeriodicalIF":3.6,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633476","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":"Unveiling hidden diversity: Phylogenomics of neotomine rodents and taxonomic implications for the genus Peromyscus","authors":"Susette Castañeda-Rico ,&nbsp;Jesús E. Maldonado ,&nbsp;Melissa T.R. Hawkins ,&nbsp;Cody W. Edwards","doi":"10.1016/j.ympev.2024.108233","DOIUrl":"10.1016/j.ympev.2024.108233","url":null,"abstract":"<div><div>Neotomine rodents (Cricetidae, Neotominae) represent one of the most commonly encountered and diverse group of rodents in North America, yet phylogenetic relationships within this group remain uncertain. This subfamily is known for its rapid evolution, adding more complexity to our efforts to unravel their evolutionary history. The main debate revolves around the recognition of the genus <em>Peromyscus</em> as monophyletic or paraphyletic due to its relationship with other genera such as <em>Habromys</em>, <em>Megadontomys</em>, <em>Podomys</em>, <em>Neotomodon</em>, and <em>Osgoodomys</em>. Here, we aim to resolve phylogenetic relationships within Neotominae, to further explore their evolutionary history and taxonomic boundaries. We used target capture and high-throughput sequencing of complete mitogenomes and thousands of genome-wide ultraconserved elements loci (UCEs). Our comprehensive analyses encompassed 53 species of Neotominae spanning 12 previously described genera, along with one yet-undescribed genus. We also investigated 12 out of the 13 species groups within <em>Peromyscus</em>. Our analyses, including Maximum Likelihood and Bayesian Inference with both mitogemomes and UCEs, as well as the coalescent species-tree-based approach with UCEs, consistently recovered concordant and well-resolved phylogenies with high levels of nodal support. We identified seven main clades within Neotominae that could potentially be recognized at the generic level, mostly to categorize the genus <em>Peromyscus</em> as a monophyletic group, including one species group within “<em>Peromyscus</em>”. Furthermore, our divergence dating estimates place the crown age of Neotominae to be around the late Miocene at ca. 7.9 – 10.7 mya. While generic level diversification continued through the Pliocene, species level diversification predominantly occurred during the late Pliocene, extending through the Pleistocene and Holocene. These epochs have been recognized as periods with significant changes in flora and fauna, driving ecological transformations on a global scale. We hypothesized that climatic and vegetation shifts during the Neogene and Quaternary, coupled with geological events, topographical features, and the presence of biogeographical corridors played a pivotal role in the speciation and diversification of Neotominae. Recognizing the importance of generating genomic-scale data coupled with a broad taxonomic sampling, our study, for the first time, offers resolution of the relationships among the main lineages of Neotominae. We expect that the phylogeny presented here will serve as a foundational resource for future systematic and evolutionary studies. This includes facilitating a proper comprehensive taxonomic revision of the group and the formal description and naming of new genera.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108233"},"PeriodicalIF":3.6,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633517","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 comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography","authors":"Yun-He Wu ,&nbsp;Man-Hao Xu ,&nbsp;Chatmongkon Suwannapoom ,&nbsp;Sang Ngoc Nguyen ,&nbsp;Robert W. Murphy ,&nbsp;Theodore J. Papenfuss ,&nbsp;Amy Lathrop ,&nbsp;Felista Kasyoka Kilunda ,&nbsp;Wei Gao ,&nbsp;Zhi-Yong Yuan ,&nbsp;Jin-Min Chen ,&nbsp;Liang Zhang ,&nbsp;Hai-Peng Zhao ,&nbsp;Li-Jun Wang ,&nbsp;Md Mizanur Rahman ,&nbsp;Lotanna Micah Nneji ,&nbsp;Gui-Gang Zhao ,&nbsp;Yun-Yu Wang ,&nbsp;Jie-Qiong Jin ,&nbsp;Peng Zhang ,&nbsp;Jing Che","doi":"10.1016/j.ympev.2024.108223","DOIUrl":"10.1016/j.ympev.2024.108223","url":null,"abstract":"<div><div>The genus <em>Sylvirana</em> includes 12 species widely distributed in South China and Southeast Asia. The phylogenetic relationships and species diversity for <em>Sylvirana</em> and allied genera remain unresolved and controversial due to insufficient data and incomplete taxon sampling. Using a combined dataset of mitochondrial genes (16S and <em>COI</em>) and 101 nuclear genes obtained through the amplicon sequence capture approach, we generated the most comprehensive phylogenetic analysis for the genus <em>Sylvirana</em> to date, inferring diversity, phylogenetic relationships, and historical biogeography with unprecedented levels of taxon and geographic sampling. Our results conservatively reveal six undescribed species, mostly distributed in peninsular Indochina. Phylogenetic analyses strongly support the non-monophyly of <em>Sylvirana</em> with respect to <em>Pterorana.</em> Additionally, phylogenetic results place <em>Sylvirana guentheri</em> and <em>Pelophylax lateralis</em> into genus <em>Humerana</em>, supporting the inclusion of <em>Hylarana latouchii</em>, <em>Papurana milleti</em>, and <em>Hylarana attigua</em> within <em>Pterorana + Sylvirana</em>. The long-disputed species of <em>Hylarana bannanica</em> (previously <em>Sylvirana</em>) cluster with genus <em>Papurana</em>. Because the results of multiple non-monophyletic genera create taxonomic confusion, we suggest relegating all genera to subgenus rank of <em>Hylarana. Sylvirana</em> is a junior synonym of the <em>Pterorana</em>. Biogeographically, we trace the origin of <em>Pterorana</em> to Southeast Asia during the early Miocene, with subsequent dispersal thereafter. Our study shows that climatic changes may have profoundly influenced the diversification of <em>Pterorana</em> during the Miocene.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108223"},"PeriodicalIF":3.6,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142559579","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}