Molecular Phylogenetics and Evolution最新文献

{"title":"Limits of exon capture efficiency for phylogenomics using nudibranch gastropods (Mollusca: Heterobranchia) as a case study.","authors":"Sofía Paz-Sedano, Ángel Valdés, Carla C Stout, Kendall Feliciano, Sandra Muro, Nerida G Wilson, Kara K S Layton, Jessica A Goodheart","doi":"10.1016/j.ympev.2026.108630","DOIUrl":"https://doi.org/10.1016/j.ympev.2026.108630","url":null,"abstract":"<p><p>Target capture is an effective tool for phylogenomic reconstruction of evolutionary histories. This sequencing methodology is cost-effective and allows the use of older or poorly preserved specimens. One important consideration while applying target capture is the rate of divergence of the group under study. The success of this approach depends on the distance of the bait set with the target taxon, affecting the sequencing efficiency and the ability to extract the target loci. However, the threshold distance at which the efficiency decreases is still unclear, varying between studies and taxonomic groups. In nudibranch mollusks, an exon capture bait set was designed for the suborder Doridina. However, the usefulness of this bait set in other clades has not been explored. We investigate the efficiency and taxonomic limits of target capture sequencing in evolutionarily distant taxa, testing the capacity of inferring the evolutionary relationships throughout the order Nudibranchia. Seventy-nine species across two diverse suborders and 12 superfamilies were sequenced using an exon capture bait set designed for Doridina. Although species of the suborder Cladobranchia were successfully sequenced, a decrease in the number of captured genes is observed, showing that the capture efficiency significantly decreases after a threshold bait-to-target DNA distance of 18%. Even so, the results obtained from phylogenetic analyses shed light on relationships among nudibranch taxa, addressing questions that have remained controversial due to the lack of support in previous analyses, such as the position of the genus Doridoxa within Doridina, supporting Phyllidioidea as monophyletic or the paraphyletic nature of Chromodoridoidea.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108630"},"PeriodicalIF":3.6,"publicationDate":"2026-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790289","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, biogeography, and description of a new subfamily and genus of African characiform fishes (Teleostei: Alestidae)","authors":"Alice Wang ,&nbsp;Melanie L.J. Stiassny ,&nbsp;Bruno F. Melo","doi":"10.1016/j.ympev.2026.108546","DOIUrl":"10.1016/j.ympev.2026.108546","url":null,"abstract":"<div><div>The Congo River, with the highest diversity of riverine fishes in Africa, only recently established its contemporary outlet into the Atlantic around the Miocene-Pliocene transition (∼5 millions of years ago; Ma). Yet, its role in shaping ichthyofaunal diversification across central Africa through interactions with adjacent Atlantic coastal rivers remains unexplored at both regional and local scales. The African characiform family Alestidae, with lineages distributed across the entire region, offers an ideal system to investigate inland-coastal biogeographic connections. However, phylogenetic relationships within Alestidae remain unresolved, particularly with respect to two key genera, <em>Brachypetersius</em> and <em>Nannopetersius</em>, which inhabit both regions of interest. Applying likelihood and species-tree inferences using 1,759 nuclear ultraconserved elements (UCEs) and 13 protein-coding genes of mitochondrial genomes from 42 alestid taxa, we resolve both <em>Brachypetersius</em> and <em>Nannopetersius</em> as polyphyletic and identify a distinct clade warranting recognition as a new genus: <em>Clavocharax</em>. External morphological and osteological data from museum specimens corroborate this finding by providing diagnostic characters for the new genus. Our molecular and morphological data also support the revalidation of Clupeocharacinae as an inclusive subfamily, encompassing the new genus and seven other West and Central African genera, marking the first phylogenetically supported subfamily within Alestidae. Divergence time estimates suggest that <em>Clavocharax</em> originated in the early Miocene (23.2–15.0 Ma), coinciding with climatic shifts and potential river capture events across the region of the Congo River outflow and lower Guinean coastal systems. Ancestral range estimation implicates Miocene climatic and geological events, including the formation of Congo’s current Atlantic outlet, in driving repeated geodispersal and diversification across inland and coastal drainages. This study highlights the influence of historical hydrological connectivity on African freshwater fish diversity and resolves previous gaps in our understanding of regional ichthyofaunal evolution and biogeography.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108546"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145949480","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":"Single-cell phylogenomics identifies major groups of marine eugregarine endosymbionts (Apicomplexa)","authors":"Eunji Park ,&nbsp;Ina Na ,&nbsp;Alana Closs ,&nbsp;Kyle Hall ,&nbsp;Tyrel Froese ,&nbsp;Danja Currie-Olsen ,&nbsp;Ondine Pontier ,&nbsp;Niels Van Steenkiste ,&nbsp;Patrick J. Keeling ,&nbsp;Brian S. Leander","doi":"10.1016/j.ympev.2026.108548","DOIUrl":"10.1016/j.ympev.2026.108548","url":null,"abstract":"<div><div>Gregarines are a large group of apicomplexan parasites that infect a wide range of invertebrate hosts, including diverse and speciose groups, such as annelids and arthropods. Marine eugregarines represent the majority of gregarine diversity, but remain poorly understood, especially their deepest phylogenetic relationships. To expand knowledge of marine eugregarine diversity and their evolutionary history, we surveyed marine invertebrates, with a particular focus on annelids, across multiple locations in British Columbia, Canada. From this effort, we obtained high-quality, single-cell transcriptomes from 20 different species of marine eugregarines, including nine previously described species and 11 novel ones, which more than doubles the amount of phylogenomic data for the group. These data, which comprehensively represent the known diversity of marine gregarines in annelid hosts, allowed us to construct an expanded phylogenetic tree based on small subunit ribosomal DNA sequences and a phylogenomic tree inferred from 142 proteins and 44,802 amino acid sequences. Our analyses show that marine eugregarines form six major lineages, five of which include species infecting annelid hosts: The Ancoroidea, Lecudinoidea, Loxomorphoidea n. superfam., Paralecudinoidea n. superfam., and a distinct lineage represented by <em>Belladina schistomeringa</em> n. gen. et sp. These findings contribute to ongoing efforts to build a robust molecular phylogenetic framework for gregarine diversity and refine gregarine classification. However, some of the deepest evolutionary relationships among these superfamilies remain unresolved, highlighting the need for expanded taxon sampling to better capture the true diversity of eugregarine parasites.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108548"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145999364","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":"Diversity, phylogeny, and biogeography of the subgenus Japonigekko (Gekkonidae: Gekko)","authors":"Jing Cao ,&nbsp;Nikolay A. Poyarkov ,&nbsp;Pingfan Wei ,&nbsp;Minhua Tie ,&nbsp;Tomoya Matsukoji ,&nbsp;Chatmongkon Suwannapoom ,&nbsp;Renda Ai ,&nbsp;Wenzhu Lu ,&nbsp;Phuping Sucharitakul ,&nbsp;Haotian Wang ,&nbsp;Siriwadee Chomdej ,&nbsp;Zhiyong Yuan ,&nbsp;Fang Yan","doi":"10.1016/j.ympev.2025.108530","DOIUrl":"10.1016/j.ympev.2025.108530","url":null,"abstract":"<div><div>The subgenus <em>Japonigekko</em>, a monophyletic lineage, represents the most ecologically and morphologically diverse group within the genus <em>Gekko</em>, with a wide distribution across East Asia. Given the ecological significance and high diversity of <em>Japonigekko</em>, understanding its true species diversity and biogeographic history is crucial for biodiversity conservation in East Asia. However, research on this subgenus remains limited compared to other well-studied vertebrate groups such as mammals and amphibians. In this study, we conducted extensive sampling and integrated molecular data from 34 of the 38 known <em>Japonigekko</em> species using barcoding techniques for 331 samples from 129 sites, systematically elucidating their phylogenetic relationships. Further genomic analysis addressed longstanding taxonomic controversies, revealed previously underestimated species diversity, and clarified the historical biogeography of this group. Ultimately, we identified nine candidate new species. Phylogenetic analyses and ancestral area reconstructions suggest that <em>Japonigekko</em> originated in the Indochina Peninsula and southern China, subsequently dispersing northward and eastward during the Miocene in response to geological events and climatic fluctuations. The recurrent formation and disappearance of land bridges between the mainland and East Asian islands provided critical opportunities for both dispersal and isolation, revealing a unidirectional mainland-to-island dispersal pattern. These findings support to the “Ancient Species Divergence Hypothesis” in East Asia.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108530"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145946852","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":"Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus) in southern South America","authors":"Maria Recuerda ,&nbsp;Cecilia Kopuchian ,&nbsp;Pablo Andrés Fracas ,&nbsp;Pablo Luis Tubaro ,&nbsp;Leonardo Campagana ,&nbsp;Darío Alejandro Lijtmaer","doi":"10.1016/j.ympev.2026.108544","DOIUrl":"10.1016/j.ympev.2026.108544","url":null,"abstract":"<div><div>Understanding how the evolutionary dynamics of widespread species unfold in space and time is critical for uncovering the processes shaping biodiversity. We integrated mitochondrial DNA and genome-wide SNPs to investigate the diversification of the widespread Southern House Wren (<em>Troglodytes musculus</em>) in southern South America and its insular relative, Cobb’s Wren (<em>T. cobbi</em>) from the Malvinas/Falkland Islands (MFI). We aim to reveal processes shaping their evolutionary history and potentially that of other co-distributed taxa. Our analyses indicate a pattern of latitudinal divergence, with an initial split between northern populations (Bolivia, Northern and Central Argentina, Uruguay) and southern populations from Patagonia and the MFI. Shortly after, further diversification occurred, including the colonization of the MFI from Patagonia, where the insular population became isolated, and a split between an Andean lineage and a widespread lowland lineage. Both the timing of these splits and the mitochondrial and genomic patterns suggest a major role of glaciations, particularly the Great Patagonian Glaciation, in the diversification of these species in the southern Neotropics. The colonization of the MFI and negligible gene flow with the continent led to the formation of<!--> <em>T. cobbi</em>, contrasting with the notable post-glacial gene flow between the continental northern and southern lineages, although with reduced gene flow between Andean and lowland populations. These results underscore how historical divergence, ecological barriers, and secondary contact jointly shape population structure and genetic diversity, with implications for understanding diversification in widespread species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108544"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145949491","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 of poachers (Agonidae) and the evolution of armor in cottoid fishes (Perciformes: Cottoidei)","authors":"Megan L. Vandenberg ,&nbsp;Zach Heiple ,&nbsp;Matthew A. Kolmann ,&nbsp;Thaddaeus Buser ,&nbsp;Adam P. Summers ,&nbsp;Fernando Meléndez-Vazquez ,&nbsp;Dahiana Arcila ,&nbsp;Katherine P. Maslenikov ,&nbsp;Luke Tornabene","doi":"10.1016/j.ympev.2026.108552","DOIUrl":"10.1016/j.ympev.2026.108552","url":null,"abstract":"<div><div>Cottoid fishes represent a morphologically diverse radiation of perciforms, yet their phylogenetic relationships and higher-level taxonomy remain unstable. In particular, the limits of the family Agonidae (poachers) and the placement of closely related lineages have remained uncertain. Here, we used genomic and morphological data to reconstruct relationships across major cottoid clades, and to assess the evolution of dermal armor across this group. Our analyses support a monophyletic Agonidae only when restricted to fully armored poachers and resolve seven well-supported subfamilies. Ancestral-state reconstructions reveal multiple gains of armor plates following a transition from scales to minute dermal spines. These gains coincide with ecological transitions onto continental shelf habitats, where armor likely provided protection from predators and the environment. Given the high diversity of armor morphology in Agonidae, this study enables fine-scalemapping of armor traits and provides a basis for testing the selective pressure shaping performance.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108552"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047550","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":"Phylogenetic analysis of the New Guinean forest wallabies, Dorcopsis and Dorcopsulus reveals cryptic divergent lineages impacted by highland and lowland barriers","authors":"Mark D.B. Eldridge ,&nbsp;Matthew J. Phillips ,&nbsp;Renae C. Pratt ,&nbsp;Linda E. Neaves ,&nbsp;Kristofer M. Helgen ,&nbsp;Sally Potter","doi":"10.1016/j.ympev.2026.108542","DOIUrl":"10.1016/j.ympev.2026.108542","url":null,"abstract":"<div><div>Amongst the Macropodidae (kangaroos and wallabies) the morphologically distinct forest wallabies are the most poorly studied. Modern forest wallabies are confined to the rainforests of New Guinea, with three species inhabiting the lowlands (<em>Dorcopsis</em>), two species in the highlands (<em>Dorcopsulus</em>)<em>,</em> and one satellite island endemic (<em>Dorcopsis atrata</em>). Due to limited sampling in previous studies, our understanding of the evolutionary history and systematics of these genera is unresolved. We obtained tissue samples from 17 individual <em>Dorcopsis</em> and 26 <em>Dorcopsulus</em> including representatives from five of the six currently recognised species. DNA sequence data was generated from up to three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis resolved six major lineages and showed that <em>Dorcopsulus</em> was embedded within <em>Dorcopsis</em>, making the latter paraphyletic. Within <em>Dorcopsis</em>, two lineages corresponded to <em>D. hageni</em> and <em>D. muelleri</em>, which were sister taxa. Another two divergent lineages were identified within sampled <em>D. luctuosa</em>, both of which appear to represent distinct species. Within <em>Dorcopsulus</em>, two major lineages were present, distributed north and south of the Central Ranges, at odds with current taxonomy. Major diversification within <em>Dorcopsis/Dorcopsulus</em> occurred during the late Miocene and the mid-Pliocene, the latter likely associated in New Guinea with lowland barriers and orogenic processes including the uplift of the Central Ranges. The paraphyly of <em>Dorcopsis</em> and detection of divergent lineages within some sampled species indicate that some adjustments to current taxonomy are warranted. We recommend the recognition of a single genus of forest wallabies (<em>Dorcopsis</em>) and provisionally recognise seven species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108542"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013482","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 reveals the backbone phylogeny of Systellognatha (Insecta: Plecoptera)","authors":"Xiao Yang ,&nbsp;Yehao Wang ,&nbsp;Qing-Bo Huo ,&nbsp;Abdur Rehman ,&nbsp;Scott A. Grubbs ,&nbsp;Chenyang Cai ,&nbsp;Yu-Zhou Du","doi":"10.1016/j.ympev.2026.108547","DOIUrl":"10.1016/j.ympev.2026.108547","url":null,"abstract":"<div><div>Phylogenomics has greatly deepened our understanding of insect evolution, yet significant gaps remain in certain ancient and fast-evolving lineages. Plecoptera (stoneflies), one of the earliest-diverging groups of winged insects with fossil records dating back to the Carboniferous, remain underrepresented in nuclear genomic studies. Within Plecoptera, the suborder Systellognatha, which accounts for nearly half of extant stonefly diversity, has long presented challenges for phylogenetic resolution due to limited taxon sampling and conflicting signals from different molecular datasets. In this study, we performed low-coverage whole-genome sequencing on 16 Systellognatha specimens from China representing nine genera across five families, including the first-ever nuclear genomic data for the understudied family Styloperlidae. Combined with public transcriptomic datasets, our analysis comprises 68 species and covers all seven families of Systellognatha. Phylogenomic analyses using both site-homogeneous and site-heterogeneous models consistently reject the monophyly of Pteronarcyoidea and identify Styloperlidae as the earliest-diverging lineage within the suborder. Meanwhile, comparative analysis based on molecular systematics and morphology indicates that the number of common derived features during the differentiation process of Pteronarcyidae and Perloidea has decreased sharply. However, Pteronarcyidae exhibits ancestral characteristics. This study not only clarifies key evolutionary relationships within Systellognatha with exceptional certainty but also develops a comprehensive phylogenomic framework that will serve as a resource for future global studies on Plecoptera systematics, biogeography, and early insect evolution in general.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108547"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145967945","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":"UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard genus Barisia (Squamata: Anguidae)","authors":"E. Karen López-Estrada ,&nbsp;Alejandro Zaldívar-Riverón ,&nbsp;Jovana M. Jasso-Martínez ,&nbsp;Ernesto Samacá-Sáenz ,&nbsp;Jorge Gutiérrez-Rodríguez ,&nbsp;Pilar Benites ,&nbsp;Valeria B. Salinas-Ramos ,&nbsp;John E. McCormack ,&nbsp;Robert W. Bryson Jr.","doi":"10.1016/j.ympev.2026.108531","DOIUrl":"10.1016/j.ympev.2026.108531","url":null,"abstract":"<div><div>The Mexican Transition Zone is a biogeographic area where the Nearctic and Neotropical regions overlap, encompassing mountain ranges formed during different geological periods. Its complex geological and paleoclimatic history has promoted evolutionary processes such as introgression through hybridization, which can bias phylogenetic inferences and species delimitation. Here, we investigated evolutionary relationships among species of the endemic Mexican lizard genus <em>Barisia</em> using nuclear ultraconserved elements (UCEs). We analyzed samples largely overlapping with a previous study based on mitochondrial DNA (mtDNA) and compared topologies to evaluate mito-nuclear discordance. We also examined population structure, introgression, species boundaries, and biogeographic history of <em>Barisia</em> using molecular dating and ancestral area reconstruction. The strongly supported UCE phylogeny challenges the current species classification of the genus, revealing lineages structured by mountain ranges. Both UCE and previous mtDNA datasets revealed introgression between populations of <em>B. imbricata</em> and <em>B. ciliaris</em> in the southern Central Mexican Plateau and between <em>B. imbricata</em> and <em>B. jonesi</em> in the western Trans-Mexican Volcanic Belt (TMVB), which was further supported by structure and introgression analyses. Our results support the recognition of seven species within <em>Barisia</em>, with the reassignment of populations of <em>B. imbricata</em>, <em>B. ciliaris</em>, and <em>B. jonesi</em>. Overall, diversification within the genus was primarily driven by orogenic vicariance. This study highlights the utility of UCEs for reconstructing robust phylogenies, assessing species limits and genetic structure, as well as to inferring biogeographic patterns.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108531"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145918991","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":"Diversification and biogeographic history of African dormice (genus Graphiurus) revealed by ultraconserved elements and mitochondrial data","authors":"Kenneth Otieno Onditi ,&nbsp;Terrence C. Demos ,&nbsp;Julian C. Kerbis Peterhans ,&nbsp;Violaine Nicolas ,&nbsp;Ondřej Mikula ,&nbsp;Anna Bryjová ,&nbsp;Amétépé Hounmavo ,&nbsp;Ara Monadjem ,&nbsp;Josef Bryja","doi":"10.1016/j.ympev.2026.108549","DOIUrl":"10.1016/j.ympev.2026.108549","url":null,"abstract":"<div><div>The sub-Saharan Africa endemic dormouse genus <em>Graphiurus</em> is a morphologically diverse group of rodents that has lacked a genus-wide genetic framework, hindering inference of their evolution and biogeography. Here, we assembled the first comprehensive, range-wide genomic dataset for <em>Graphiurus</em>, including ultraconserved elements and the cytochrome <em>b</em> gene. We used phylogenetic reconstruction, divergence-time estimation, and ancestral area reconstruction to clarify biogeographic histories and evaluate how historical range dynamics may have influenced lineage diversification. <em>Graphiurus</em> is the earliest-diverging lineage within Gliridae sister to all other extant genera. Within <em>Graphiurus</em>, we recovered 24 molecular operational taxonomic units (MOTUs) forming two reciprocally monophyletic, deeply divergent clades: a West African lineage comprising three MOTUs and a pan-sub-Saharan Africa lineage comprising 21 MOTUs. Genetic distances between these clades are equal to or greater than those used to distinguish genera. Diversification within <em>Graphiurus</em> started in the middle Miocene, peaking in a rapid radiation during the Plio-Pleistocene. These diversification events coincided with increased climatic instability that fragmented forests into isolated refugia. Ancestral-area reconstructions suggest a <em>Graphiurus</em> origin in the Upper Guinean rainforest, followed by jump dispersal across the Afrotropics, with most subsequent divergences occurring in East Africa. As the first comprehensive phylogenetic analysis of <em>Graphiurus</em>, our study underscores the urgent need for an integrated taxonomic revision of the genus that couples genomic data with detailed morphology and critical re-examination of type material to resolve species limits and formally describe the recovered MOTUs. Many MOTUs appear range restricted, underscoring vulnerability to ongoing habitat loss within montane refugia.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108549"},"PeriodicalIF":3.6,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146020876","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}