Molecular Phylogenetics and Evolution最新文献

{"title":"Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis","authors":"Ricardo A.R. Machado ,&nbsp;Arthur Muller ,&nbsp;Alexandre Hiltmann ,&nbsp;Aashaq Hussain Bhat ,&nbsp;Vladimír Půža ,&nbsp;Antoinette P. Malan ,&nbsp;Carlos Castaneda-Alvarez ,&nbsp;Ernesto San-Blas ,&nbsp;Larry W. Duncan ,&nbsp;David Shapiro-Ilan ,&nbsp;Javad Karimi ,&nbsp;Lalramliana ,&nbsp;Hrang C. Lalramnghaki ,&nbsp;Hugues Baimey","doi":"10.1016/j.ympev.2025.108284","DOIUrl":"10.1016/j.ympev.2025.108284","url":null,"abstract":"<div><div>Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus <em>Heterorhabditis</em>. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus <em>Heterorhabditis</em>. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Using the inferred phylogenies, we then investigated co-phylogenetic relationships between <em>Heterorhabditis</em> and their <em>Photorhabdus</em> bacterial symbionts and biogeographical patterns. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species. In addition, two mitochondrial genes, the cytochrome <em>c</em> oxidase subunit I (<em>cox-1</em>) and the NADH dehydrogenase subunit 4 (<em>nad-4</em>), and two housekeeping genes, the fanconi-associated nuclease 1 (<em>fan-1</em>) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (<em>ppfr-1</em>), provided the most robust phylogenetic reconstructions compared to other individual genes. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus <em>Heterorhabditis</em>. If whole nuclear and/or mitochondrial genomes are unavailable, a combination of nuclear and mitochondrial genes can be used as an alternative. Under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analyzed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergence of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergence of some nuclear genes. On the other hand, we observed that the genera <em>Heterorhabditis</em> and <em>Photorhabdus</em> exhibit diverse biogeographic patterns, ranging from cosmopolitan species to potentially endemic species, and show high phylogenetic congruence, although host switches have also occurred. Our study contributes to a better understanding of the biodiversity and phylo- and co-phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108284"},"PeriodicalIF":3.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959251","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":"Biome conservatism prevailed in repeated long-distance colonization of Madagascar’s mountains by Helichrysum (Compositae, Gnaphalieae)","authors":"Carme Blanco-Gavaldà ,&nbsp;Cristina Roquet ,&nbsp;Genís Puig-Surroca ,&nbsp;Santiago Andrés-Sánchez ,&nbsp;Sylvain G. Razafimandimbison ,&nbsp;Rokiman Letsara ,&nbsp;Nicola Bergh ,&nbsp;Glynis V. Cron ,&nbsp;Lucía D. Moreyra ,&nbsp;Juan Antonio Calleja ,&nbsp;Òscar Castillo ,&nbsp;Randall J. Bayer ,&nbsp;Frederik Leliaert ,&nbsp;Alfonso Susanna ,&nbsp;Mercè Galbany-Casals","doi":"10.1016/j.ympev.2024.108283","DOIUrl":"10.1016/j.ympev.2024.108283","url":null,"abstract":"<div><div>Colonization and diversification processes are responsible for the distinctiveness of island biotas, with Madagascar standing out as a<!--> <!-->biodiversity hotspot exceptionally rich in species and endemism. Regardless of its significance, the evolutionary history and diversification drivers of Madagascar’s flora remain understudied. Here we focus on <em>Helichrysum</em> (Compositae, Gnaphalieae) to investigate the evolutionary and biogeographic origins of the Malagasy flora. We inferred a highly resolved phylogeny based on target-enrichment data from 327 species (including 51 % of Malagasy endemics) and conducted ancestral range estimation analyses. Our results revealed at least six <em>trans</em>-oceanic dispersal events from different African regions to Madagascar during the Pliocene. In this process, biome conservatism prevailed, as evidenced by similarities between Malagasy lineages and their African relatives. The southern African grasslands, known to be the center of diversification and the main source of African <em>Helichrysum</em> lineages, played a key role in the colonization of Madagascar as the ancestral source area of at least three clades. The Tropical Afromontane region was revealed as the source of at least two montane Malagasy lineages that substantially radiated <em>in-situ</em>. Finally, a dispersal event from southwestern Africa led to a lineage represented by a single species adapted to the island’s southwestern arid conditions. The main radiations of <em>Helichrysum</em> in Madagascar’s mountains occurred within the last 2 My, coinciding with a transition towards cooler and drier conditions and the expansion of open habitats, likely driven by a combination of geographic and ecological speciation. Overall, our findings highlight the affinities between the montane floras of continental Africa and Madagascar.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108283"},"PeriodicalIF":3.6,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962600","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":"Retraction notice to “Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)” [Mol. Phylogenet. Evol. 197 (2024) 108113]","authors":"Qi Chen ,&nbsp;Min Deng ,&nbsp;Xuan Dai ,&nbsp;Wei Wang ,&nbsp;Xing Wang ,&nbsp;Liu-Sheng Chen ,&nbsp;Guo-Hua Huang","doi":"10.1016/j.ympev.2024.108251","DOIUrl":"10.1016/j.ympev.2024.108251","url":null,"abstract":"","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"202 ","pages":"Article 108251"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756025","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 yields new systematic and taxonomical insights for Lissotriton newts, a genus with a strong legacy of introgressive hybridization","authors":"J. Mars ,&nbsp;Stephanie Koster ,&nbsp;W. Babik ,&nbsp;J. France ,&nbsp;K. Kalaentzis ,&nbsp;C. Kazilas ,&nbsp;I. Martínez-Solano ,&nbsp;M.C. de Visser ,&nbsp;B. Wielstra","doi":"10.1016/j.ympev.2024.108282","DOIUrl":"10.1016/j.ympev.2024.108282","url":null,"abstract":"<div><div>The ease with which genome-wide data can nowadays be collected allows complicated phylogenetic questions to be re-evaluated. Phylogenetic relationships among newts have often proven difficult to resolve due to the prevalence of incomplete lineage sorting and introgressive hybridization. For the newt genus <em>Lissotriton</em>, phylogenetic relationships are not settled and there is controversy surrounding the species status of several taxa. We obtain c. 7 k nuclear DNA markers with target enrichment by sequence capture and conduct a concatenated analysis with RAxML, gene-tree summarization with ASTRAL, and species tree estimation with SNAPPER. We explore introgression between evolutionary lineages with TreeMix and Dsuite and compare how introgression events influence the different phylogenetic tools employed. We retrieve tree topologies that are discordant with previous mtDNA-based attempts, particularly concerning the phylogenetic placement of <em>L. italicus</em> and the <em>L. vulgaris</em> species complex. Yet, we also observe deviations between the phylogenetic hypotheses resulting from the different analyses. We interpret the placement of <em>L. montandoni</em> deep within the <em>L. vulgaris</em> species complex by SNAPPER, rather than as the sister taxon to the remainder of the <em>L. vulgaris</em> species complex according to RAxML and ASTRAL, as an artifact of introgression – well-documented in previous work and backed up by TreeMix and Dsuite analyses. Our analyses allow us to make some taxonomical recommendations: we confirm the recently proposed species status of <em>L. kosswigi</em> and <em>L. graecus</em> and propose that <em>L. v. lantzi</em> and <em>L. v. schmidtleri</em> had better be treated as subspecies. Our work also highlights areas for further taxonomic research: range-wide phylogenomic data are required to disentangle the <em>L. boscai</em> – <em>L. maltzani</em> species complex and the northern and southern lineages of <em>L. v. vulgaris</em>. Our study illustrates the power of target enrichment by sequence capture in tackling longstanding questions in taxa with an extensive history of hybridization and introgression.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108282"},"PeriodicalIF":3.6,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923287","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":"Plastid-nuclear coevolution of ribosomal protein genes in papilionoid legumes","authors":"Lydia G. Tressel ,&nbsp;Bikash Shrestha ,&nbsp;Chaehee Lee ,&nbsp;In-Su Choi ,&nbsp;Tracey A. Ruhlman ,&nbsp;Domingos Cardoso ,&nbsp;Martin F. Wojciechowski ,&nbsp;Robert K. Jansen","doi":"10.1016/j.ympev.2024.108281","DOIUrl":"10.1016/j.ympev.2024.108281","url":null,"abstract":"<div><div>In plants, cellular function is orchestrated by three distinct genomes located within the nucleus, mitochondrion, and plastid. These genomes are interdependent, requiring tightly coordinated maintenance and expression. Plastids host several multisubunit protein complexes encoded by both the plastid and nuclear genomes. To investigate plastid-nuclear coevolution, this study focused on plastid ribosomal protein genes that are encoded by both plastid and nuclear genomes from 50 taxa across 15 of the 22 early branching major clades of the legume subfamily Papilionoideae. Comparative analysis of substitution rates was conducted across five gene sets: nuclear-encoded plastid-targeted ribosomal protein genes (NuCpRP), nuclear-encoded cytosol-targeted ribosomal genes (NuCyRP), other nuclear-encoded plastid-targeted genes that are not involved in ribosomes (NuCpOT), plastid-encoded ribosomal protein genes (CpRP) and plastid-encoded photosynthesis genes (CpPS).<span><span>¹</span></span> Elevated nonsynonymous substitution rates (<em>d_N</em>) and ratios of nonsynonymous to synonymous substitution rates (<em>d_N</em>/<em>d_S</em>_; ω) were observed in both CpRP and NuCpRP compared to the other gene sets. Significant differences in <em>d_N</em> for CpRP and NuCpRP were found between the papilionoid 50-kb inversion clade and other legumes. Using coevolution statistics and evolutionary rate covariation, strong signals of cytonuclear coevolution were identified, where nonsynonymous substitutions in CpRP and NuCpRP genes co-occur along the same branches of the Papilionoideae phylogeny. Increased ω in a few CpRP genes was due to intensified positive selection whereas most of the CpRP and NuCpRP increased ω was caused by relaxed purifying selection. This pattern not only underscores the role of cytonuclear incompatibility in driving speciation but also highlights its constraints on the genetic enhancement of papilionoid crop species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108281"},"PeriodicalIF":3.6,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic data support reticulate evolution in whiptail lizards from the Brazilian Caatinga","authors":"Felipe de M. Magalhães ,&nbsp;Eliana F. Oliveira ,&nbsp;Adrian A. Garda ,&nbsp;Frank T. Burbrink ,&nbsp;Marcelo Gehara","doi":"10.1016/j.ympev.2024.108280","DOIUrl":"10.1016/j.ympev.2024.108280","url":null,"abstract":"<div><div>Species relationships have traditionally been represented by phylogenetic trees, but not all evolutionary histories fit into bifurcating divergence models. Introgressive hybridization challenges this assumption by sometimes [or maybe often] leading to mitochondrial introgression, wherein one species’ mitochondrial genome is entirely replaced by another’s (mitochondrial capture). Such processes result in mitonuclear discrepancies, complicating species delimitation and phylogenetic inference. In our study, we used ultraconserved elements (UCE) and mitogenomic data to investigate the evolutionary history of the <em>Ameivula ocellifera</em> complex, a group of South American whiptail lizards widely distributed in semiarid environments of the Caatinga Domain in Brazil. We examine mitonuclear discordances, assessing reticulate evolution, evaluating species limits, and testing for adaptive mitochondrial capture that could explain higher introgression in the mitochondrial genome compared to nuclear DNA. Our findings support the occurrence of an ancient reticulation event during the diversification of these lizards, driven by introgressive hybridization, leading to mitochondrial capture, and explaining mitonuclear discrepancies. Overall, we did not find clear evidence of positive selection across mitochondrial protein-coding genes suggesting adaptive mitochondrial capture of individuals with introgressed mtDNA. Thus, the genetic diversification and mitogenome evolution could be neutral, with selection against hybridization in the autosomal loci only, or even mediated by mitonuclear incompatibilities. Analyses of mtDNA genomes alongside network and species delimitation methods were crucial for identifying and validating individuals with introgressed mtDNA as a distinct species, demonstrating the potential of genome sampling, and using innovative analytical techniques for elucidating speciation processes in the presence of introgressive hybridization.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108280"},"PeriodicalIF":3.6,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetics, biogeography, and life history evolution in the broadly distributed treefrog genus Dendropsophus (Anura: Hylidae: Hylinae)","authors":"Courtney Whitcher ,&nbsp;Victor G.D. Orrico ,&nbsp;Santiago Ron ,&nbsp;Mariana L. Lyra ,&nbsp;Carla S. Cassini ,&nbsp;Rodrigo B. Ferreira ,&nbsp;Daniel Y.M. Nakamura ,&nbsp;Pedro L.V. Peloso ,&nbsp;Marco A. Rada ,&nbsp;Mauricio Rivera-Correa ,&nbsp;Marcelo J. Sturaro ,&nbsp;Paula H. Valdujo ,&nbsp;Célio F.B. Haddad ,&nbsp;Taran Grant ,&nbsp;Julian Faivovich ,&nbsp;Alan Lemmon ,&nbsp;Emily Moriarty Lemmon","doi":"10.1016/j.ympev.2024.108275","DOIUrl":"10.1016/j.ympev.2024.108275","url":null,"abstract":"<div><div><em>Dendropsophus<!--> </em>is one of the most species-rich genera of hylid treefrogs. Recent studies integrating Sanger-generated mitochondrial and nuclear loci with phenomic characters (SP) have advanced understanding of this clade, but questions about its internal relationships and biogeographic history persist. To address these questions, we used anchored hybrid enrichment (AHE) to combine 432 nuclear loci for 78 taxa (72 % of species) with published data. Quantitatively, the impact of the AHE data was modest, with compositional differences in only three recognized clades and more than 80 % of the clades in the AHE + SP analyses also supported in the SP-only analyses. Nevertheless, the impact of AHE was crucial for resolving and increasing support for multiple nodes. We transferred one species of the former<!--> <em>D. ruschii<!--> </em>group to the<!--> <em>D. decipiens</em> <!-->group and redefined the<!--> <em>D. leucophyllatus<!--> </em>group to avoid paraphyly. We estimated divergence times to reconstruct the clade’s biogeographic history. We also examined evolution of oviposition sites and assessed its effect on lineage accumulation. <em>Dendropsophus<!--> </em>likely originated ∼ 57 mya, predating the Andean uplift, with some taxa showing dispersal patterns less constrained by ecological changes than previously thought.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108275"},"PeriodicalIF":3.6,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plate tectonics, cold adaptation and long-distance range expansion to remote archipelagos and the high Andes as drivers of a circumantarctic freshwater arthropod radiation","authors":"Adrián Villastrigo ,&nbsp;Athena Lam ,&nbsp;Matthew H. Van Dam ,&nbsp;Agnes Scheunert ,&nbsp;Jiří Hájek ,&nbsp;Lars Hendrich ,&nbsp;Mariano C. Michat ,&nbsp;Yoandri Megna ,&nbsp;Luis Figueroa ,&nbsp;Nilver Zenteno ,&nbsp;Julieta Ledezma ,&nbsp;Fernando Guerra-Serrudo ,&nbsp;Michael Balke","doi":"10.1016/j.ympev.2024.108279","DOIUrl":"10.1016/j.ympev.2024.108279","url":null,"abstract":"<div><div>Disjunct distributions, characterised by spatially separated populations of related species, offer insights into historical biogeographic patterns and evolutionary processes. This study investigates the evolutionary history of the diving beetle subfamily Lancetinae through a phylogenomic approach incorporating ultraconserved elements (UCEs) and heritage genetic markers. Our findings support an early Miocene origin for Lancetinae, with subsequent diversification influenced by historical vicariance events and long-distance dispersal. The divergence from the closely related subfamily Coptotominae in the late Cretaceous is not consistent with a Gondwanan origin, although highlights a likely Pangean origin for these taxa. This research underscores the significant impact of Gondwanan fragmentation on biogeographic patterns and highlights the remarkable dispersal capabilities of Lancetinae beetles.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108279"},"PeriodicalIF":3.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the potential structure of a Parnassius butterfly in Japan: Insights into the expansion history","authors":"Hideyuki Tamura,&nbsp;Tomoaki Noda,&nbsp;Mikiko Hayashi,&nbsp;Yuko Fujii,&nbsp;Noriko Iwata,&nbsp;Yuko Yokota,&nbsp;Masanori Murata,&nbsp;Chisato Tatematsu,&nbsp;Hideshi Naka ,&nbsp;Akio Tera,&nbsp;Katsumi Ono,&nbsp;Kakeru Yokoi ,&nbsp;Takanori Kato,&nbsp;Tomoko Okamoto,&nbsp;Koji Tsuchida","doi":"10.1016/j.ympev.2024.108278","DOIUrl":"10.1016/j.ympev.2024.108278","url":null,"abstract":"<div><div>The Japanese Archipelago consists of a series of isolated yet interconnected islands off the Eurasian continent. The linear topography of the archipelago presents a unique biogeographic context for the dispersal of organisms from the continent. In this study, mitochondrial DNA (mtDNA) and single-nucleotide polymorphism (SNP) variation were employed to elucidate the dispersal history of the Japanese clouded butterfly (<em>Parnassius glacialis</em>) across the Japanese Archipelago, including the northern island (Hokkaido), the main island (Honshu), and Shikoku Island. Network analysis of 1192 bp of mtDNA (cytochrome oxidase I and II) regions revealed 49 haplotypes and three distinct haplotype groups, which correspond geographically to Eastern Japan, Western Japan, and Chugoku–Shikoku. The Chugoku–Shikoku group is the most ancient lineage. Divergence time estimates using whole-genome sequencing of mtDNA suggest that the Japanese lineage diverged from the continental <em>P. glacialis</em> approximately 3.08 million years ago (Ma). Subsequently, the Eastern Japan and Western Japan lineages diverged from the Chugoku–Shikoku lineage around 1.06 Ma, with subsequent divergence of the Eastern and Western Japan lineages at approximately 0.62 Ma. <em>P. glacialis</em> is estimated to have expanded its distribution via a land bridge that once connected China and the Japanese Archipelago. Population structure analysis based on 3067 SNP genotypes revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. Through mtDNA and SNP variation analyses, four primary genetic barriers were identified: between Hokkaido and Honshu, between Eastern and Central Japan, within the Kansai region, and in the Chugoku region. The first three barriers correspond to notable geographical features, the Blakiston Line, a line parallel to the Itoigawa–Shizuoka Tectonic Line, and a boundary crossing Lake Biwa. These findings suggest that Japanese <em>P. glacialis</em> diverged from the continental <em>P. glacialis</em> and expanded its range across the Japanese Archipelago via western routes, leading to its current distribution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108278"},"PeriodicalIF":3.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Species delimitation and phylogenomics of economically important African Pterocarpus trees, with an implication for the development of DNA-based species identification tools","authors":"Laura Albreht ,&nbsp;Nils Bourland ,&nbsp;Bente Klitgård ,&nbsp;Rowan Schley ,&nbsp;Steven B. Janssens ,&nbsp;Olivier J. Hardy","doi":"10.1016/j.ympev.2024.108277","DOIUrl":"10.1016/j.ympev.2024.108277","url":null,"abstract":"<div><div>Reliable species delimitation is fundamental for establishing clear and equitable guidelines on the sustainable harvest of economically important organisms. <em>Pterocarpus</em> (Fabaceae) is a pantropical tree genus including several highly valuable timber-producing species, that face significant threats from intensive logging. However, a lack of taxonomic clarity has hindered the advance of logging regulations and has led to the inclusion of all African <em>Pterocarpus</em> populations under CITES regulations (CoP19). In our study, we addressed this issue by reassessing species delimitation of all twelve accepted African <em>Pterocarpus</em> species, including neotropical samples of the two trans-Atlantic species. Based on DNA sequences obtained by the Angiosperms353 probe set, we reconstructed a comprehensive phylogeny applying maximum likelihood and multispecies coalescent approaches. Additionally, we explored the potential of high-copy DNA for identifying African <em>Pterocarpus</em> species. This involved reconstructing chloroplast and ribosomal DNA phylogenies, using genome skimming and maximum likelihood approaches. Our results confirmed the monophyly of eleven <em>Pterocarpus</em> species and a paraphyletic <em>P. rotundifolius</em>, which presented geographically coherent subclades, suggesting the possibility of cryptic diversity within the complex. A similar situation arose in <em>P. lucens</em>, exhibiting two sister clades with disjunct distributions. Species delimitation based on high-copy DNA was congruent with the Angiosperms353 data for most species, indicating the reliability of chloroplast and ribosomal DNA markers for <em>Pterocarpus</em> species identification. Our findings give valuable insights into African <em>Pterocarpus</em> species delimitation, highlighting the need for further investigation of potential cryptic diversity within a clade including <em>P. rotundifolius</em>, <em>P. brenanii</em> and <em>P. lucens</em>. Finally, our study lays the groundwork for developing DNA-based tools aimed at improving logging regulations for African <em>Pterocarpus</em> species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108277"},"PeriodicalIF":3.6,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}