Molecular Phylogenetics and Evolution最新文献

{"title":"Generic delimitation in the Cyphotheca-Plagiopetalum-Sporoxeia clade","authors":"Qi-Yuan Zhuang ,&nbsp;Jin-Hong Dai ,&nbsp;Chun-Yu Zou ,&nbsp;Yan Liu ,&nbsp;Zhi-Yong Yu ,&nbsp;Xin Jiang ,&nbsp;Qiu-Jie Zhou ,&nbsp;Zheng-Ming Zhu ,&nbsp;Wen-Xiang Zhang ,&nbsp;Xi-Bin Guo ,&nbsp;Ren-Chao Zhou ,&nbsp;Ying Liu","doi":"10.1016/j.ympev.2025.108290","DOIUrl":"10.1016/j.ympev.2025.108290","url":null,"abstract":"<div><div>The <em>Cyphotheca</em>-<em>Plagiopetalum</em>-<em>Sporoxeia</em> clade (Sonerileae, Melastomataceae) comprises <em>Cyphotheca</em> Diels, <em>Plagiopetalum</em> Rehder, <em>Sporoxeia</em> W.W.Sm., and some species of the highly polyphyletic <em>Phyllagathis</em> Blume, as well as some undescribed species, which requires taxonomic revision at the generic level. In this study, we expanded taxon sampling of the CPS clade and reconstructed phylogenetic relationships using genomic SNPs and whole plastomes assembled from genome resequencing data. We recognized six subclades in the CPS clade and observed strong cytonuclear incongruences within and among subclades. Gene tree simulation and Patterson’s <em>D</em>-statistic indicated that the conflicting phylogenetic signals were mainly caused by incomplete lineage sorting and hybridization/introgression. Molecular and morphological divergence among species of the CPS clade were evaluated using principal component analysis. Genomic SNP data clearly separated the six subclades, whereas the boundaries of some subclades were obscure in the plots of morphological data. Through reconstruction of morphological characteristics, we found a high level of homoplasy for some characters but also identified potential synapomorphies for the lineages. Based on the results, a revised generic classification is proposed for the CPS clade. Specifically, we expand <em>Cyphotheca</em>, <em>Plagiopetalum</em>, and <em>Sporoxeia</em> to include additional species, and establish three new genera, namely <em>Chiehchenii</em>, <em>Neophyllagathis</em>, and <em>Sporocyphoxeia</em>. A description and a list of species are provided for each of the six genera. Four new species are described.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108290"},"PeriodicalIF":3.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973459","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 thorny tale: The origin and diversification of Cirsium (Compositae)","authors":"Lucía D. Moreyra ,&nbsp;Alfonso Susanna ,&nbsp;Juan Antonio Calleja ,&nbsp;Jennifer R. Ackerfield ,&nbsp;Turan Arabacı ,&nbsp;Carme Blanco-Gavaldà ,&nbsp;Christian Brochmann ,&nbsp;Tuncay Dirmenci ,&nbsp;Kazumi Fujikawa ,&nbsp;Mercè Galbany-Casals ,&nbsp;Tiangang Gao ,&nbsp;Abel Gizaw ,&nbsp;Iraj Mehregan ,&nbsp;Roser Vilatersana ,&nbsp;Juan Viruel ,&nbsp;Bayram Yıldız ,&nbsp;Frederik Leliaert ,&nbsp;Alexey P. Seregin ,&nbsp;Cristina Roquet","doi":"10.1016/j.ympev.2025.108285","DOIUrl":"10.1016/j.ympev.2025.108285","url":null,"abstract":"<div><div>Widely distributed plant genera offer insights into biogeographic processes and biodiversity. The Carduus-Cirsium group, with over 600 species in eight genera, is diverse across the Holarctic regions, especially in the Mediterranean Basin, Southwest Asia, Japan, and North America. Despite this diversity, evolutionary and biogeographic processes within the group, particularly for the genus <em>Cirsium</em>, remain underexplored. This study examines the biogeographic history and diversification of the group, focusing on <em>Cirsium</em>, using the largest molecular dataset for the group (299 plants from 251 taxa). Phylogenomic analyses based on 350 nuclear loci, derived from target capture sequencing, revealed highly resolved and consistent phylogenetic trees, with some incongruences likely due to hybridization and incomplete lineage sorting. Ancestral range estimations suggest that the Carduus-Cirsium group originated during the Late Miocene in the Western Palearctic, particularly in the Mediterranean, Eastern Europe, or Southwest Asia. A key dispersal event to tropical eastern Africa around 10.7 million years ago led to the genera Afrocarduus and Afrocirsium, which later diversified in the Afromontane region. The two subgenera of <em>Cirsium</em>—<em>Lophiolepis</em> and <em>Cirsium</em>—began diversifying around 7.2–7.3 million years ago in the Western Palearctic. During the Early Pliocene, diversification rates increased, with both subgenera dispersing to Southwest Asia, where extensive <em>in situ</em> diversification occurred. Rapid radiations in North America and Japan during the Pleistocene were triggered by jump-dispersals events from Asia, likely driven by geographic isolation and ecological specialization. This added further layers of complexity to the already challenging taxonomic classification of <em>Cirsium</em>.Keywords: Biogeography; Carduinae; <em>Cirsium</em>; Diversification; North Hemisphere; Target-enrichment; Taxonomy.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108285"},"PeriodicalIF":3.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)","authors":"Alden C. Dirks ,&nbsp;Andrew S. Methven ,&nbsp;Andrew N. Miller ,&nbsp;Michelle Orozco-Quime ,&nbsp;Sundy Maurice ,&nbsp;Gregory Bonito ,&nbsp;Judson Van Wyk ,&nbsp;Steven Ahrendt ,&nbsp;Alan Kuo ,&nbsp;William Andreopoulos ,&nbsp;Robert Riley ,&nbsp;Anna Lipzen ,&nbsp;Mansi Chovatia ,&nbsp;Emily Savage ,&nbsp;Kerrie Barry ,&nbsp;Igor V. Grigoriev ,&nbsp;Alexander J. Bradshaw ,&nbsp;Francis M. Martin ,&nbsp;A. Elizabeth Arnold ,&nbsp;Timothy Y. James","doi":"10.1016/j.ympev.2025.108286","DOIUrl":"10.1016/j.ympev.2025.108286","url":null,"abstract":"<div><div>Lorchels, also known as false morels (<em>Gyromitra sensu lato</em>), 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, <em>Discinaceae</em>, 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 <em>Discinaceae</em>. We recognized 10 genera across two tribes: tribe <em>Discineae</em> (<em>Discina</em>, <em>Maublancomyces</em>, <em>Neogyromitra</em>, <em>Piscidiscina</em>, and <em>Pseudodiscina</em>) and tribe <em>Gyromitreae</em> (<em>Gyromitra</em>, <em>Hydnotrya</em>, <em>Paragyromitra</em>, <em>Pseudorhizina</em>, and <em>Pseudoverpa</em>); <em>Piscidiscina</em> was newly erected and 26 new combinations were formalized. <em>Paradiscina melaleuca</em> and <em>Marcelleina donadinii</em> formed their own family-level clade sister to <em>Morchellaceae,</em> which merits further taxonomic study<em>.</em> Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (<em>Hydnotrya</em> spp.), whereas the other <em>Discinaceae</em> 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 <em>Gyromitra esculenta</em> 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 (<em>Gyromitra</em> and <em>Piscidiscina</em>) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of <em>Geomoriaceae</em> and <em>Helvellaceae</em>—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.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 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 ,&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}