Molecular Phylogenetics and Evolution最新文献

{"title":"Molecular phylogenetics of nursery web spiders (Araneae: Pisauridae)","authors":"Sarah A. Morris ,&nbsp;Nicolas A. Hazzi ,&nbsp;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 &amp; Raven, 1980</span></span>; <em>Tasmomedes</em> Raven, 2018; <em>Mangromedes</em> Raven, 2018; <em>Ornodolomedes</em> <span><span>Raven &amp; Hebron, 2018</span></span>; and <em>Caledomedes</em> <span><span>Raven &amp; 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}

{"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 ,&nbsp;Hannah M. Wood ,&nbsp;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}

{"title":"Phylogenomics resolves the puzzling phylogeny of banded newts (genus Ommatotriton)","authors":"Konstantinos Kalaentzis ,&nbsp;Stephanie Koster ,&nbsp;Jan W. Arntzen ,&nbsp;Sergé Bogaerts ,&nbsp;James France ,&nbsp;Michael Franzen ,&nbsp;Christos Kazilas ,&nbsp;Spartak N. Litvinchuk ,&nbsp;Kurtuluş Olgun ,&nbsp;Manon de Visser ,&nbsp;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}

{"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}