Molecular Phylogenetics and Evolution最新文献

{"title":"Extensive cytonuclear discordance revealed by phylogenomic analyses suggests complex evolutionary history in the holly genus Ilex (Aquifoliaceae)","authors":"Ke-Wang Xu ,&nbsp;Yi Yang ,&nbsp;Hong Chen ,&nbsp;Chen-Xue Lin ,&nbsp;Lei Jiang ,&nbsp;Zhong-Long Guo ,&nbsp;Meng Li ,&nbsp;Ming-Zhuo Hao ,&nbsp;Kai-Kai Meng","doi":"10.1016/j.ympev.2024.108255","DOIUrl":"10.1016/j.ympev.2024.108255","url":null,"abstract":"<div><div><em>Ilex</em> L., the exclusive genus of Aquifoliaceae, encompasses over 600 dioecious wood species with a highly irregular distribution, predominantly found in South America and Asia. The phylogeny and classification of this genus remain enigmatic due to significant early extinctions, constrained morphological diversity, recent hybridization/introgression, and conflicting signals from previously utilized markers. This study presents phylogenetic reconstructions based on complete chloroplast genome sequences and single nucleotide polymorphisms (SNPs) derived from genome resequencing data. A total of 116 accessions of <em>Ilex</em>, representing approximately 108 taxa, were included as the ingroup, with five accessions of two species serving as outgroups. Analysis of the chloroplast genome and nuclear SNP data individually resulted in two robust phylogenetic trees, revealing substantial discrepancies between the chloroplast genome and nuclear SNP phylogenies at both the species and clade levels. The chloroplast genome sequences successfully resolved relationships within this genus into eight strongly supported major clades, while the nuclear SNPs resolved relationships into seven highly supported major clades. Our nuclear SNP phylogenetic tree, in comparison to the chloroplast genome tree, aligns more closely with the recently updated classification of <em>Ilex</em> in multiple instances. The extensive cytonuclear discordance identified may be attributed to recent hybridization events and incomplete lineage sorting (ILS).</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108255"},"PeriodicalIF":3.6,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774811","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 analyses unravel the tangled evolutionary history of Genisteae (Fabaceae)","authors":"Sarah Hunter ,&nbsp;Domingos Cardoso ,&nbsp;Tracey A. Ruhlman ,&nbsp;Robert K. Jansen","doi":"10.1016/j.ympev.2024.108249","DOIUrl":"10.1016/j.ympev.2024.108249","url":null,"abstract":"<div><div>Genisteae, a tribe in the subfamily Papilionoideae (Fabaceae), is characterized by the production of quinolizidine alkaloids that confer pest resistance in most of its members. Many relationships at the generic level remain unresolved due largely to a lack of modern attempts to reconstruct the phylogeny. Previous studies with limited taxon sampling and only a few molecular loci indicated the presence of three clades within the tribe: the <em>Lupinus</em> clade, the <em>Cytisus-Genista</em> complex and the <em>Argyrolobium</em> group. There are also two historical genera, <em>Teline</em> and <em>Chamaecytisus,</em> that have been reclassified over the years with some controversy. Species from <em>Teline</em> are currently classified in <em>Genista</em>, and <em>Chamaecytisus</em> species are placed inside of <em>Cytisus. Sellocharis</em> is another genus with vague placement inside of Genisteae near <em>Anarthrophyllum</em>, based mostly on morphology and cytology. Representative taxa from 24 of the 25 genera of Genisteae, along with species of historical genera <em>Teline</em> and <em>Chamaecytisus,</em> were sampled and utilized in a phylogenomic investigation using both plastid and nuclear data to resolve relationships at the generic level. Whole genomic DNA was sequenced and complete plastomes were assembled and annotated. Low-copy nuclear genes were retrieved from the genomic DNA sequences using a mapping-assembly-scaffold approach. Phylogenetic analyses using maximum likelihood, Bayesian and coalescence methods resulted in fully resolved and strongly supported trees for both nuclear and plastid data that show four major clades inside of Genisteae: <em>Cytisus-Genista</em> complex, <em>Lupinus</em> clade, <em>Argyrolobium</em> group and the novel <em>Anarthrophyllum</em> group. The resulting phylogenetic trees also supported the transfer of the <em>Argyrolobium</em> group from Crotalarieae to Genisteae, and the reclassification of <em>Teline</em> inside of <em>Genista,</em> both of which were previously suggested in literature<em>.</em> The phylogenetic trees also determined a placement for <em>Sellocharis</em> in the new <em>Anarthrophyllum</em> group. Although both nuclear and plastid trees were congruent with respect to the monophyly and relationships among the four major clades, incongruence was detected within some of the major clades and the potential causes are discussed.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108249"},"PeriodicalIF":3.6,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774812","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":"Endogean habits drove cryptic diversification in Appalachian Lathrobium Gravenhorst (Coleoptera, Staphylinidae)","authors":"Adam Haberski ,&nbsp;Michael S. Caterino","doi":"10.1016/j.ympev.2024.108252","DOIUrl":"10.1016/j.ympev.2024.108252","url":null,"abstract":"<div><div>The southern Appalachian Mountains are a biodiverse region with high levels of endemism. Shared biogeographic patterns among co-distributed, but independent taxa might illuminate common drivers of Appalachian endemism. <em>Lathrobium</em> is a Holarctic genus with 38 species described form North America, six of which are flightless and endemic to the high Appalachians. We use an integrative morphological and multi-locus molecular dataset to study phylogenetic and biogeographical relationships of Appalachian <em>Lathrobium</em> and test subgeneric hypotheses. A phylogeny based on 176 samples from 67 taxa supported three independent arrivals in the Appalachian Mountains. Divergence times estimated in BEAST2 were concurrent for all three lineages and fell between the Miocene or early Pliocene (16.4 – 4.6 Ma). Speciation within Appalachians occurred during the Pleistocene (2.3 – 0.1 Ma). Monophyly of existing subgenera was supported except for <em>Abletobium</em> Casey. <em>Abletobium</em> is <strong>placed in synonymy</strong> with <em>Glyptomerus</em> Müller. Our results reveal the importance of cold-climate refugia within the Appalachian Mountains for the persistence and in-situ diversification of endemic endogean taxa. We hypothesize that the xeric climate of the Miocene drove <em>Lathrobium</em> lineages into the mountains and subsequent isolation in mountaintop refugia during warm Pleistocene interglacials led to speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108252"},"PeriodicalIF":3.6,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774810","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 Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets","authors":"Jing Zhao ,&nbsp;Zhen-Long Liang ,&nbsp;Shao-Li Fang ,&nbsp;Rong-Juan Li ,&nbsp;Chuan-Jie Huang ,&nbsp;Li-Bing Zhang ,&nbsp;Tanner Robison ,&nbsp;Zhang-Ming Zhu ,&nbsp;Wen-Jing Cai ,&nbsp;Hong Yu ,&nbsp;Zhao-Rong He ,&nbsp;Xin-Mao Zhou","doi":"10.1016/j.ympev.2024.108253","DOIUrl":"10.1016/j.ympev.2024.108253","url":null,"abstract":"<div><div>Previous studies have shown that at least six genera of the Cheilanthoideae, a subfamily of the fern family Pteridaceae, may not be monophyletic. In these non-monophyletic genera, the Old-World genus <em>Paragymnopteris</em> including approximately five species have long been controversial. In this study, with an extensive taxon sampling of <em>Paragymnopteris</em>, we assembled 19 complete plastomes of all recognized <em>Paragymnopteris</em> species, plastomes of <em>Pellaea</em> (3 species) and <em>Argyrochosma</em> (1 species), as well as transcriptomes from <em>Paragymnopteris</em> (6 species) and <em>Argyrochosma</em> (1 species). We conducted a comprehensive and systematic phylogenomic analysis focusing on the contentious relationships among the genus of <em>Paragymnopteris</em> through 9 plastid makers, the plastomes, mitochondria, nuclear ribosomal cistron genomes, and single-copy nuclear genes. Moreover, we further combined distribution, ploidy, and morphological features to investigate the evolution of <em>Paragymnopteris</em>. The backbone of <em>Paragymnopteris</em> was resolved consistently in the nuclear and plastid phylogenies. Our major results include: (1) <em>Paragymnopteris</em> is not monophyletic including two fully supported clades; (2) confirming that <em>Paragymnopteris delavayi</em> var. <em>intermedia</em> is a close relative of <em>P. delavayi</em> instead of <em>P. marantae</em> var. <em>marantae</em>; (3) the chromosome base number may not be a stable trait which has previously been used as an important character to divide <em>Paragymnopteris</em> into two groups; and (4) gene flow or introgression might be the main reason for the gene trees conflict of <em>Paragymnopteris</em>, but both gene flow and ILS might simultaneously and/or cumulatively act on the conflict of core pellaeids. The robust phylogeny of <em>Paragymnopteris</em> presented here will help us for the future studies of the arid to semi-arid ferns of Cheilanthoideae at the evolutionary, physiological, developmental, and omics-based levels.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108253"},"PeriodicalIF":3.6,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774994","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 a new generic delimitation of Asian Millettia, with reinstatements of Pongamia and Otosema (Fabaceae: Millettieae)","authors":"Zhuqiu Song ,&nbsp;Liansheng Xu ,&nbsp;Anoop Puthuparampil Balan ,&nbsp;Myriam Gaudeul ,&nbsp;Yiyong Zhao ,&nbsp;Kaiwen Jiang ,&nbsp;Tian Li ,&nbsp;Shijin Li","doi":"10.1016/j.ympev.2024.108254","DOIUrl":"10.1016/j.ympev.2024.108254","url":null,"abstract":"<div><div>The generic relationships within the core Millettieae have not been well resolved to date. <em>Millettia</em> is considered one of the most problematic genera to classify within the core Millettieae, with approximately 150 species found in Asia and Africa. Recent molecular evidence has indicated that <em>Millettia</em> is highly polyphyletic. In this study, we utilized plastomes and single-copy nuclear genes from genome skimming sequencing to reconstruct the generic relationships and estimate the divergence time for the core Millettieae, focusing on the Asian species of <em>Millettia</em>. Our results revealed a broader circumscription of the core Millettieae with the inclusion of the Phaseoleae subtribe Ophrestiinae, consisting of 7 clades and 14 subclades within two main groups (canavanine and non-canavanine). The Asian species of <em>Millettia</em> were grouped into three distinct, well-supported subclades, leading us to propose a much narrower generic concept of <em>Millettia</em>, along with the reinstatements of the genera <em>Pongamia</em> and <em>Otosema</em>. <em>Millettia</em> s.str. was restricted to include only seven species. <em>Pongamia</em> was recognized as a medium-sized genus that includes <em>Fordia</em> and <em>Ibatiria</em>, with approximately 56 species. <em>Otosema</em>, usually treated as a subgenus or section of <em>Millettia</em>, was resurrected as a distinct genus with three species. Our findings also indicated that the sampled African <em>Millettia</em> species belong to three subclades distinct from the Asian <em>Millettia</em> subclades, warranting further investigation in future studies. The dating result showed that the early rapid diversification of the core Millettieae during the Mid-Miocene Climatic Optimum involved several major problematic genera, including <em>Derris</em> s.lato, <em>Lonchocarpus</em> s.lato, and <em>Millettia</em> s.lato, which may explain why these plant groups are difficult to classify. These results offer new insights into the phylogeny and taxonomy of the core Millettieae.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108254"},"PeriodicalIF":3.6,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774998","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 historical biogeography of Sturisoma Swainson, 1838 (Loricariidae: Loricariinae): Hidden diversity along the Amazon River","authors":"Alejandro Londoño-Burbano,&nbsp;Marcelo R. Britto","doi":"10.1016/j.ympev.2024.108248","DOIUrl":"10.1016/j.ympev.2024.108248","url":null,"abstract":"<div><div>In the present study, we used DNA sequences from three mitochondrial (COI, Cytb, and nd2) and one nuclear (RAG2) marker, to perform species delimitation analyses (ABGD, GMYC, BPP, and bPTP) within <em>Sturisoma</em> to test the validity of currently recognized and potential new species for the genus. Additionally, a historical biogeographic analysis was carried out to test the age and centers of origin for species of the genus. Results found here indicate a high degree of genetic divergence with overlapping morphological characteristics suggesting a greater diversity than previously proposed for the genus. All valid species currently included in <em>Sturisoma</em> were confirmed here, and one potentially undescribed species was recovered. Based on genetic distances, geographical patterns and historical biogeography, the diversification of the group could be related to dispersal events from Western to Eastern Amazonia resulting in sympatric species that are highly divergent genetically but conservative morphologically. The lower (eastern) Amazonas and the Orinoco River basins were identified as the main centers of origin for the genus, with an approximate age of origin of 13 Mya, during the Miocene. The diversity of the genus is likely to be even higher because the Amazon River is a hotspot of hidden biodiversity.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108248"},"PeriodicalIF":3.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741474","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":"Gondwanan relic or recent arrival? The biogeographic origins and systematics of Australian tarantulas","authors":"Ethan J. Briggs ,&nbsp;Saoirse Foley ,&nbsp;Lyn G. Cook","doi":"10.1016/j.ympev.2024.108246","DOIUrl":"10.1016/j.ympev.2024.108246","url":null,"abstract":"<div><div>The composition of Australia’s fauna and flora has been largely assembled by two biogeographic processes, vicariance and long-distance dispersal and establishment. These patterns can be observed today through the survival of Gondwanan lineages contrasted with relatively recent colonization from south-east Asia, respectively. In general, the post-Gondwanan immigrant lineages from south-east Asia are taxa with traits that facilitate dispersal. Consequently, taxa like tarantulas (Araneae, Theraphosidae) that are largely pan-tropical but also have a low propensity for dispersal, are thought to be Gondwanan in origin. However, the Australian tarantulas are unsampled for phylogenomic studies and, as such, their classification and biogeographic origins have been long debated and are unresolved. Here we test if their current, morphology-based classification in Selenocosmiinae is accurate and assess whether the Australian tarantulas were present in Australia while it was part of Gondwana. We sample 369 tarantula specimens from across Australia, greatly expanding the geographic sampling of previous studies, to develop the first continent-wide phylogeny of the Australian tarantulas. To resolve the ‘back bone’ of the Australian tarantula phylogeny we generate 20 new transcriptomes for species of Australian tarantulas representing distinct lineages uncovered using mitochondrial sequence data and combine these new transcriptomes with published transcriptomic data. Through the recovery of ultra-conserved element (UCE) loci from transcriptomes and testing multiple data occupancy matrices, we find that the Australian clade is monophyletic and nested inside the largely Asian Selenocosmiinae. We find the Australian fauna are a relatively young radiation with a crown age of 18.8–8.3 Ma and we therefore reject the hypothesis of a Gondwanan origin for these animals and, instead, infer a recent dispersal from south-east Asia. Our findings indicate that they underwent a rapid radiation, possibly coinciding with their arrival into Australia. Our findings refute the monophyly of <em>Selenocosmia</em> and <em>Coremiocnemis</em> as currently recognised, and we remove <em>Selenocosmia stalkeri</em> from synonymy with <em>Selenocosmia stirlingi</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108246"},"PeriodicalIF":3.6,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741471","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":"Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta’s unconventional solution for its replacement","authors":"Karsten Fischer ,&nbsp;Sondre Valentin Jordbræk ,&nbsp;Stian Olsen ,&nbsp;Mathias Bockwoldt ,&nbsp;Rainer Schwacke ,&nbsp;Björn Usadel ,&nbsp;Kirsten Krause","doi":"10.1016/j.ympev.2024.108243","DOIUrl":"10.1016/j.ympev.2024.108243","url":null,"abstract":"<div><div>The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite <em>Cuscuta campestris</em> and other parasitic plant species, we identified a unique evolutionary history of <em>rpl32</em> genes coding for an essential plastid ribosomal subunit in <em>Cuscuta</em>. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the <em>Cuscuta</em> subgenus <em>Grammica</em>. Oxalidales had suffered an ancestral EGT of <em>rpl32</em> predating the evolution of the genus <em>Cuscuta</em>. The HGT subsequently relieved the plastid <em>rpl32</em> from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in <em>Cuscuta</em> is supported by a high sequence similarity of the mature L32 protein between species of the subgenus <em>Grammica</em> and representatives of the <em>Oxalidales</em>, and by a surprisingly conserved transit peptide, whose functionality in <em>Cuscuta</em> was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108243"},"PeriodicalIF":3.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712101","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":"Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)","authors":"Heidi M. Meudt ,&nbsp;Sofie M. Pearson ,&nbsp;Weixuan Ning ,&nbsp;Jessica M. Prebble ,&nbsp;Jennifer A. Tate","doi":"10.1016/j.ympev.2024.108250","DOIUrl":"10.1016/j.ympev.2024.108250","url":null,"abstract":"<div><div>Island and mountain systems represent natural laboratories for studies of species radiations, but they often present several challenges for phylogenetic inference and species delimitation. The southern hemisphere forget-me-nots (<em>Myosotis</em>, Boraginaceae) comprise a geologically recent radiation centred in Aotearoa New Zealand, a mountainous archipelago, with about 50 species that are morphologically and ecologically divergent but lack genetic variation sufficient to resolve phylogenetic relationships and species boundaries using standard DNA Sanger sequencing markers, AFLPs, or microsatellites. Many of these <em>Myosotis</em> species are geographically restricted in alpine areas, uncommon or threatened, have polyploid and dysploid genomes, and are of high taxonomic and conservation priority. Here we present phylogenomic analyses using target-capture of Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to improve resolution of the radiation, explore biogeographic and morphological patterns within it, and address specific taxonomic questions for each species. Our comprehensive sampling includes over 300 individuals representing nearly all species from New Zealand and Australia, which is ∼ 2–3 × more taxon sampling and ∼ 80–120 × more molecular data than previously published for <em>Myosotis.</em> Exploration of different data filtering, curation and analyses (coalescent vs. concatenation) improved the resolution of the Angiosperms353 tree, which despite short backbone branches with low support values, showed taxonomic and geographic patterns, including multiple switches between ebracteate and bracteate inflorescences and multiple expansions within New Zealand from Te Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart Island, subantarctic islands, and Australia. Some of these patterns were also seen in the genome skimming datasets, and comparison of the three datasets was useful for improving our understanding of the taxonomy and resolution of this radiation. Although this phylogenomic study does not fully overcome all of the challenges regarding species delimitation of this rapid island and mountain species radiation, it nevertheless makes an important contribution to an integrative taxonomic revision of the southern hemisphere species of <em>Myosotis</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108250"},"PeriodicalIF":3.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712058","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":"Phylogenetic origin of dioecious Callicarpa (Lamiaceae) species endemic to the Ogasawara Islands revealed by chloroplast and nuclear whole genome analyses","authors":"Kazutoshi Masuda ,&nbsp;Hiroaki Setoguchi ,&nbsp;Koki Nagasawa ,&nbsp;Suzuki Setsuko ,&nbsp;Shosei Kubota ,&nbsp;Shin S. Satoh ,&nbsp;Shota Sakaguchi","doi":"10.1016/j.ympev.2024.108234","DOIUrl":"10.1016/j.ympev.2024.108234","url":null,"abstract":"<div><div>Oceanic islands offer excellent opportunities to study the ecology, evolutionary biology, and biogeography of plants. To uncover the genetic basis of various evolutionary trends commonly observed on these islands, the origins and phylogenetic relationships of the species being studied should be understood. <em>Callicarpa glabra</em>, <em>Callicarpa parvifolia</em>, and <em>Callicarpa subpubescens</em> are evergreen woody plants endemic to the Ogasawara Islands, which are remote oceanic islands located off of the Japanese Archipelago. These species are ideal for studying evolutionary changes on oceanic islands because of their adaptive radiation and shift toward dioecious sex expression. We used a phylogenomic perspective to determine the evolutionary relationship of the three species within the genus and infer their colonization time. Based on the analysis of both chloroplast genomes and 86 nuclear single-copy genes, we found that these three species were monophyletic and embedded in a backbone clade that included multiple East Asian species. The phylogenetic tree based on over 10,000 nuclear genes placed the insular species in the East Asian clade, although the topology did not entirely correspond to the chloroplast tree, probably because of incomplete lineage sorting and interspecific hybridization. The three endemic species were estimated to have diverged from continental species approximately three million years ago (Mya). The results of this study suggested that the ancestor of the Ogasawara endemic species originated from long-distance dispersal from East Asia mainland in the late Pliocene, and then progressively speciated within the islands.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"203 ","pages":"Article 108234"},"PeriodicalIF":3.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689772","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}