Molecular Phylogenetics and Evolution最新文献

{"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}

{"title":"Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies","authors":"Matthew P. Greenwood ,&nbsp;Thibaut Capblancq ,&nbsp;Niklas Wahlberg ,&nbsp;Laurence Després","doi":"10.1016/j.ympev.2024.108222","DOIUrl":"10.1016/j.ympev.2024.108222","url":null,"abstract":"<div><div>Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of <em>Coenonympha</em> (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of <em>Coenonympha</em> and within a rapidly diversifying subclade (the <em>hero</em> group) remain difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108222"},"PeriodicalIF":3.6,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549190","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":"Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera","authors":"Xuanzeng Liu ,&nbsp;Nian Liu ,&nbsp;Xuan Jing ,&nbsp;Hashim Khan ,&nbsp;Kaiyan Yang ,&nbsp;Yanna Zheng ,&nbsp;Yimeng Nie ,&nbsp;Hojun Song ,&nbsp;Yuan Huang","doi":"10.1016/j.ympev.2024.108221","DOIUrl":"10.1016/j.ympev.2024.108221","url":null,"abstract":"<div><div>Nuclear mitochondrial pseudogenes (NUMTs) result from the transfer of mitochondrial DNA (mtDNA) to the nuclear genome. NUMTs, as “frozen” snapshots of mitochondria, can provide insights into diversification patterns. In this study, we analyzed the origins and insertion frequency of NUMTs using genome assembly data from ten species in Orthoptera. We found divergences between NUMTs and contemporary mtDNA in Orthoptera ranging from 0 % to 23.78 %. The results showed that the number of NUMT insertions was significantly positively correlated with the content of transposable elements in the genome. We found that 39.09 %-68.65 % of the NUMTs flanking regions (2,000 bp) contained retrotransposons, and more NUMTs originated from mitochondrial rDNA regions. Based on the analysis of the mitochondrial transcriptome, we found a potential mechanism of NUMT integration: mitochondrial transcripts are reverse transcribed into double-stranded DNA and then integrated into the genome. The probability of this mechanism occurring accounts for 0.30 %-1.02 % of total mitochondrial nuclear transfer events. Finally, based on the phylogenetic tree constructed using NUMTs and contemporary mtDNA, we provide insights into ancient evolutionary events such as species-specific “autaponumts” and “synaponumts” shared among different species, as well as post-integration duplication events.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108221"},"PeriodicalIF":3.6,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513600","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":"Jumping through hoops: Structural rearrangements and accelerated mutation rates on Dendrodorididae (Mollusca: Nudibranchia) mitogenomes rumble their evolution","authors":"Carles Galià-Camps ,&nbsp;Tilman Schell ,&nbsp;Alba Enguídanos ,&nbsp;Cinta Pegueroles ,&nbsp;Miquel A. Arnedo ,&nbsp;Manuel Ballesteros ,&nbsp;Ángel Valdés ,&nbsp;Carola Greve","doi":"10.1016/j.ympev.2024.108218","DOIUrl":"10.1016/j.ympev.2024.108218","url":null,"abstract":"<div><div>The systematics of the family Dendrodorididae, with only three valid genera, is a challenge for integrative taxonomists. Its members lack hard structures for morphological comparisons and their mitochondrial and nuclear markers provide contradictory phylogenetic signals, making phylogenetic reconstructions difficult. This molecular discordance has been hypothesized to be the result of nuclear pseudogenes or exogenous contamination. However, these hypotheses have not been tested. Here, we assembled the first genome drafts of seven Dendrodorididae species to investigate the evolutionary processes of this family. Two of the mitogenomes displayed an identical structural rearrangement involving the translocation of three coding genes and five tRNAs, described for the first time in nudibranchs. In addition, we found particularly high d<em>N</em> and d<em>N</em>/d<em>S</em> values and multiple insertions and deletions on the mitochondrial genes of smooth <em>Dendrodoris</em>. In contrast, nuclear single-copy ortholog genes showed no such mutational differences. Models of protein structures from mitochondrial genes are conserved, suggesting conserved functionality. Phylogenies using mitogenomic and nuclear data showed that species with rearranged mitogenomes form a clade, although Dendrodorididae relationships remained unresolved<em>.</em> The present study provides novel evidence for accelerated mutation rates in the mitogenomes of Dendrodorididae, which presumably have implications on respiratory adaptation, and highlights the importance of using genomic data to unveil rare evolutionary processes, crucial for correctly inferring phylogenies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108218"},"PeriodicalIF":3.6,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481851","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 insights into the worldwide evolutionary relationships of the stingless bees (Apidae, Meliponini)","authors":"Anderson Lepeco ,&nbsp;Michael G. Branstetter ,&nbsp;Gabriel A.R. Melo ,&nbsp;Felipe V. Freitas ,&nbsp;Kerrigan B. Tobin ,&nbsp;Jenny Gan ,&nbsp;Jeremy Jensen ,&nbsp;Eduardo A.B. Almeida","doi":"10.1016/j.ympev.2024.108219","DOIUrl":"10.1016/j.ympev.2024.108219","url":null,"abstract":"<div><div>Stingless bees (tribe Meliponini) are remarkable for their characteristically large social colonies, their capacity to produce honey and other useful products, and their morphological and behavioral diversity. They have a disjunct pan-tropical distribution, primarily occurring in warm and humid environments in the Neotropical, Afrotropical, and Indo-Australasian regions. Even though phylogenetic hypotheses have been proposed for Meliponini based on morphology and molecular data, many questions are still unsolved regarding the evolutionary relationships and systematics of the tribe. In this contribution, we present a large phylogenomic dataset comprising over 2500 ultra-conserved element (UCE) loci sequenced for 153 species of Meliponini, representing all known genera of stingless bees. The genera <em>Camargoia</em>, <em>Paratrigonoides</em>, <em>Plectoplebeia, Cleptotrigona</em>, <em>Ebaiotrigona</em>, <em>Papuatrigona</em>, <em>Pariotrigona</em>, <em>Platytrigona</em>, and <em>Sahulotrigona</em> were included in molecular phylogenetic analyses for the first time. Concatenated and species-tree analyses were performed using different partitioning strategies and summary methods. We performed gene-genealogy interrogation (GGI) on several recalcitrant nodes to resolve discordances among recovered tree topologies. Results were mostly consistent among analyses, recovering three main lineages of Meliponini congruent with the biogeographic domains to which they are associated. Within major clades, discordances were found in relation to previous works. The genus <em>Frieseomelitta</em> was recovered as paraphyletic in relation to <em>Trichotrigona</em>, and the genus <em>Lepidotrigona</em> was revealed to be composed of two independent lineages. Even though concatenated and weighted ASTRAL analyses were mostly effective in recovering the relationships favored by GGI, they retrieved different results in relation to the phylogenetic placements of <em>Oxytrigona</em> and <em>Cephalotrigona</em>. The most favored hypothesis in GGI analyses was not found in any other analyses, being more congruent with morphological evidence and highlighting the relevance of exploring the support given to alternative hypotheses through topological tests. Recent advances in our capacity to generate molecular sequences from old specimens using modern sequencing methods allowed for unparalleled sampling across genera, yielding a backbone for the phylogenetic relationships of stingless bees, which will further investigations into their systematics and evolution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108219"},"PeriodicalIF":3.6,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481852","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":"Genome-wide species delimitation and quantification of the extent of introgression in eriophyoid mite Epitrimerus sabinae complex (Acariformes: Eriophyoidea)","authors":"Liang-Fei Yao,&nbsp;Zi-Kai Shao,&nbsp;Ni Li,&nbsp;Yue Hu,&nbsp;Xiao-Feng Xue","doi":"10.1016/j.ympev.2024.108220","DOIUrl":"10.1016/j.ympev.2024.108220","url":null,"abstract":"<div><div>Species complex hinders the exploration of terrestrial species diversity, particularly in small arthropod lineages that are morphologically indistinguishable from each other. The <em>Epitrimerus sabinae</em> complex in the Eriophyoidea provides a valuable case study in species complex delimitation, as they exhibit limited morphological variations. In this study, we obtained thousands of nuclear genomic single-nucleotide polymorphisms via whole-genome sequencing from 55 <em>E. sabinae</em> complex specimens, covering their potential all known distribution ranges. We implemented a framework to infer cryptic speciation, which involved phylogenetic and genetic clustering to identify potential species, followed by population demographic assessment to confirm lineage independence (and thus species status). Our results demonstrate that the <em>E. sabinae</em> complex comprises ten distinct species. These species range from highly divergent, genetically isolated lineages, to differentiated populations involving gene flow. This gene flow is widespread across species boundaries, indicating potential genetic introgression among them. Additionally, demographic analyses revealed that the ten species have followed unique trajectories in size change during the Quaternary period. Time-calibrated phylogenies further showed that speciation in the <em>E. sabinae</em> complex occurred rapidly, resulting in a rapid radiation during the Neogene period. Collectively, parallelism/convergence and recent divergence involving multiple gene flows may explain the homoplasy of <em>E. sabinae</em> complex. Our results highlight the integrated approach in species complex delimitation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108220"},"PeriodicalIF":3.6,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481853","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":"Revisiting evolutionary relationships of Antrodiaetus (Araneae, Mygalomorphae, Antrodiaetidae) using phylogenomics; implications for species diversity and biogeography of a persistent Holarctic lineage","authors":"Erik Ciaccio ,&nbsp;Jason E. Bond ,&nbsp;Marshal Hedin ,&nbsp;Chris A. Hamilton","doi":"10.1016/j.ympev.2024.108206","DOIUrl":"10.1016/j.ympev.2024.108206","url":null,"abstract":"<div><div><em>Antrodiaetus</em> is a lineage of mygalomorph spider (Mygalomorphae: Antrodiaetidae) that has persisted since the late Cretaceous and has a disjunct Holarctic distribution and strong morphological conservatism. These folding-door spiders possess a life history (i.e., limited dispersal, conserved environmental niche) that closely ties their evolution to geology. This study produces a robust, well-supported phylogenomic inference of all currently recognized <em>Antrodiaetus</em> species using UCEs (Ultraconserved Elements), corroborates previous biogeographical hypotheses, and proposes new hypotheses about diversification patterns. We also confirm that previously suspected cryptic diversity within <em>A. pacificus</em> is underestimated, as this nominal species comprises multiple divergent and cryptic lineages. Our phylogeny now serves as a foundation for understanding <em>Antrodiaetus</em> species relationships, biogeography, and speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108206"},"PeriodicalIF":3.6,"publicationDate":"2024-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481854","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 multi-gene phylogeny of the Asian kukri snakes (Oligodon Fitzinger, 1826): Sharpening the blade of the second largest serpent radiation (Reptilia: Squamata: Colubridae)","authors":"Justin L. Lee ,&nbsp;Platon V. Yushchenko ,&nbsp;Chatmongkon Suwannapoom ,&nbsp;Parinya Pawangkhanant ,&nbsp;L. Lee Grismer ,&nbsp;Tan Van Nguyen ,&nbsp;V. Deepak ,&nbsp;Surya Narayanan ,&nbsp;Sandeep Das ,&nbsp;Thy Neang ,&nbsp;H.T. Lalremsanga ,&nbsp;Jian-Huan Yang ,&nbsp;Daniel Jablonski ,&nbsp;Mustafa Erkaya ,&nbsp;Gernot Vogel ,&nbsp;Aaron M. Bauer ,&nbsp;Nikolay A. Poyarkov","doi":"10.1016/j.ympev.2024.108215","DOIUrl":"10.1016/j.ympev.2024.108215","url":null,"abstract":"<div><div>With 90 recognized species, kukri snakes in the genus <em>Oligodon</em> Fitzinger constitute the second largest snake radiation in the world. <em>Oligodon</em> species are collectively distributed across the Asian continent and possess several ecological and morphological attributes that are unique amongst other snakes. Despite their high levels of species richness, evolutionary relationships within <em>Oligodon</em> are poorly understood due to a limited number of samples and genetic markers available in earlier phylogenies. In this study, we assembled the largest molecular dataset of <em>Oligodon</em> to date, which we use to assess the systematics and biogeography of the entire genus. Based on a combination of maximum likelihood and Bayesian phylogenies using fragments of three mitochondrial genes (12 s, 16 s, CytB) and three nuclear genes (Rag1, C-mos, BDNF), we identify eight deeply divergent clades within <em>Oligodon</em>, of which only two correspond with species groupings that were recognized by previous morphological classifications. Four species delimitation methods employed on the mitochondrial portion of the dataset resulted in dramatically divergent estimations of molecular operational taxonomic units (mOTUs). When combined, all four methods support the existence of unrecognized species-level lineages, but also indicate that several other <em>Oligodon</em> species are poorly differentiated genetically and require additional integrative taxonomic research to properly resolve. Based on divergence dating, we demonstrate that <em>Oligodon</em> began to diversify during the early Neogene and hypothesize that the most recent common ancestor of the genus originated in mainland Southeast Asia. We conclude by recognizing eight phylogenetically defined species groups and identify sampling gaps that require further investigation once new data becomes available. This study contributes to a greater understanding of snake evolution on the Asian continent and acts as a baseline for future studies of this speciose genus.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"201 ","pages":"Article 108215"},"PeriodicalIF":3.6,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481850","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}