Molecular Phylogenetics and Evolution最新文献

{"title":"Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota).","authors":"Alden C Dirks, Andrew S Methven, Andrew N Miller, Michelle Orozco-Quime, Sundy Maurice, Gregory Bonito, Judson Van Wyk, Steven Ahrendt, Alan Kuo, William Andreopoulos, Robert Riley, Anna Lipzen, Mansi Chovatia, Emily Savage, Kerrie Barry, Igor V Grigoriev, Alexander J Bradshaw, Francis M Martin, A Elizabeth Arnold, Timothy Y James","doi":"10.1016/j.ympev.2025.108286","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108286","url":null,"abstract":"<p><p>Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108286"},"PeriodicalIF":3.6,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959254","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 analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis.","authors":"Ricardo A R Machado, Arthur Muller, Alexandre Hiltmann, Aashaq Hussain Bhat, Vladimír Půža, Antoinette P Malan, Carlos Castaneda-Alvarez, Ernesto San-Blas, Larry W Duncan, David Shapiro-Ilan, Javad Karimi, Lalramliana, Hrang C Lalramnghaki, Hugues Baimey","doi":"10.1016/j.ympev.2025.108284","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108284","url":null,"abstract":"<p><p>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 Heterorhabditis. 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 Heterorhabditis. 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 Heterorhabditis and their Photorhabdus 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 c oxidase subunit I (cox-1) and the NADH dehydrogenase subunit 4 (nad-4), and two housekeeping genes, the fanconi-associated nuclease 1 (fan-1) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (ppfr-1), 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 Heterorhabditis. 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 Heterorhabditis and Photorhabdus 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"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":"","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, Min Deng, Xuan Dai, Wei Wang, Xing Wang, Liu-Sheng Chen, 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":" ","pages":"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, Stephanie Koster, W Babik, J France, K Kalaentzis, C Kazilas, I Martínez-Solano, M C de Visser, B Wielstra","doi":"10.1016/j.ympev.2024.108282","DOIUrl":"10.1016/j.ympev.2024.108282","url":null,"abstract":"<p><p>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 Lissotriton, 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 L. italicus and the L. vulgaris species complex. Yet, we also observe deviations between the phylogenetic hypotheses resulting from the different analyses. We interpret the placement of L. montandoni deep within the L. vulgaris species complex by SNAPPER, rather than as the sister taxon to the remainder of the L. vulgaris 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 L. kosswigi and L. graecus and propose that L. v. lantzi and L. v. schmidtleri had better be treated as subspecies. Our work also highlights areas for further taxonomic research: range-wide phylogenomic data are required to disentangle the L. boscai - L. maltzani species complex and the northern and southern lineages of L. v. vulgaris. 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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":"","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, Bikash Shrestha, Chaehee Lee, In-Su Choi, Tracey A Ruhlman, Domingos Cardoso, Martin F Wojciechowski, Robert K Jansen","doi":"10.1016/j.ympev.2024.108281","DOIUrl":"10.1016/j.ympev.2024.108281","url":null,"abstract":"<p><p>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).¹ Elevated nonsynonymous substitution rates (d_N) and ratios of nonsynonymous to synonymous substitution rates (d_N/d_S_; ω) were observed in both CpRP and NuCpRP compared to the other gene sets. Significant differences in d_N 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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, Eliana F Oliveira, Adrian A Garda, Frank T Burbrink, Marcelo Gehara","doi":"10.1016/j.ympev.2024.108280","DOIUrl":"https://doi.org/10.1016/j.ympev.2024.108280","url":null,"abstract":"<p><p>Species relationships and speciation 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 Ameivula ocellifera complex, a group of South American whiptail lizards widely distributed in arid environments, such as the Caatinga Domain in Brazil. Our focus was on understanding mitonuclear discordances, assessing reticulate evolution, evaluating species limits, and testing for adaptive mitochondrial capture that could explain a 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 wide genome sampling and innovative analytical techniques for elucidating speciation processes in the presence of introgressive hybridization.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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":"","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.","authors":"Courtney Whitcher, Victor Goyannes Dill Orrico, Santiago Ron, Mariana L Lyra, Carla Santana Cassini, Rodrigo B Ferreira, Daniel Y M Nakamura, Pedro Peloso, Marco Rada, Mauricio Rivera-Correa, Marcelo José Sturaro, Paula H Valdujo, Célio F B Haddad, Taran Grant, Julian Faivovich, Alan Lemmon, Emily Moriarty Lemmon","doi":"10.1016/j.ympev.2024.108275","DOIUrl":"https://doi.org/10.1016/j.ympev.2024.108275","url":null,"abstract":"<p><p>Dendropsophusis one of the most species-rich genera of 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 formerD. ruschiigroup to theD. decipiensgroup and redefined theD. leucophyllatusgroup 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. Dendropsophuslikely originated ∼ 57 mya, predating the Andean uplift, with some taxa showing dispersal patterns less constrained by ecological changes than previously thought.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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, Athena Lam, Matthew H Van Dam, Agnes Scheunert, Jiří Hájek, Lars Hendrich, Mariano C Michat, Yoandri Megna, Luis Figueroa, Nilver Zenteno, Julieta Ledezma, Fernando Guerra-Serrudo, Michael Balke","doi":"10.1016/j.ympev.2024.108279","DOIUrl":"10.1016/j.ympev.2024.108279","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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, Tomoaki Noda, Mikiko Hayashi, Yuko Fujii, Noriko Iwata, Yuko Yokota, Masanori Murata, Chisato Tatematsu, Hideshi Naka, Akio Tera, Katsumi Ono, Kakeru Yokoi, Takanori Kato, Tomoko Okamoto, Koji Tsuchida","doi":"10.1016/j.ympev.2024.108278","DOIUrl":"10.1016/j.ympev.2024.108278","url":null,"abstract":"<p><p>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 (Parnassius glacialis) 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 P. glacialis 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. P. glacialis 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 P. glacialis diverged from the continental P. glacialis and expanded its range across the Japanese Archipelago via western routes, leading to its current distribution.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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":"","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, Nils Bourland, Bente Klitgård, Rowan Schley, Steven B Janssens, Olivier J Hardy","doi":"10.1016/j.ympev.2024.108277","DOIUrl":"10.1016/j.ympev.2024.108277","url":null,"abstract":"<p><p>Reliable species delimitation is fundamental for establishing clear and equitable guidelines on the sustainable harvest of economically important organisms. Pterocarpus (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 Pterocarpus populations under CITES regulations (CoP19). In our study, we addressed this issue by reassessing species delimitation of all twelve accepted African Pterocarpus 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 Pterocarpus species. This involved reconstructing chloroplast and ribosomal DNA phylogenies, using genome skimming and maximum likelihood approaches. Our results confirmed the monophyly of eleven Pterocarpus species and a paraphyletic P. rotundifolius, which presented geographically coherent subclades, suggesting the possibility of cryptic diversity within the complex. A similar situation arose in P. lucens, 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 Pterocarpus species identification. Our findings give valuable insights into African Pterocarpus species delimitation, highlighting the need for further investigation of potential cryptic diversity within a clade including P. rotundifolius, P. brenanii and P. lucens. Finally, our study lays the groundwork for developing DNA-based tools aimed at improving logging regulations for African Pterocarpus species.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}