Molecular Phylogenetics and Evolution最新文献

{"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}

{"title":"Integrative species delimitation methods infer species boundaries in the Lomatium foeniculaceum complex and indicate an evolutionary history from the Southwest towards the Northeast in western North America","authors":"Daniel E. Botello ,&nbsp;Donald H. Mansfield ,&nbsp;Sven Buerki ,&nbsp;Mary Ann E. Feist ,&nbsp;Mark Darrach ,&nbsp;James F. Smith","doi":"10.1016/j.ympev.2024.108276","DOIUrl":"10.1016/j.ympev.2024.108276","url":null,"abstract":"<div><div>Delimiting species boundaries is a perennial challenge in the field of systematics. Resolving whether morphological variation is the result of environmental parameters, incipient speciation, or complete speciation is especially challenging when the variation is subtle. Within the perennial endemic North American clade of Apiaceae (PENA) there are numerous examples in which widespread species have subtle geographically defined morphological variants that have typically been recognized at the subspecific rank. The <em>Lomatium foeniculaceum</em> (Nutt.) Coult &amp; Rose species complex is a salient case that has long been treated as a single species with five infrataxa, spanning much of the western United States and western Canada in a morphological continuum: <em>L</em>. <em>foeniculaceum</em> var. <em>foeniculaceum</em>, <em>L</em>. <em>foeniculaceum</em> var. <em>daucifolium</em> (Torr. &amp; A. Gray) Cronquist, <em>L</em>. <em>foeniculaceum</em> var. <em>macdougalii</em> (J.M. Coult. &amp; Rose) Cronquist, <em>L</em>. <em>foeniculaceum</em> var. <em>fimbriatum</em> (W.L. Theob.) B. Boivin, and <em>L</em>. <em>foeniculaceum</em> var. <em>inyoense</em> (Mathias &amp; Constance) B. Boivin. We utilized the Angiosperm353 baits kit to sample nuclear loci from these five taxa to determine if the subspecific taxa formed discrete genetic groups with the molecular data. Groups that were identified were then examined for a combination of morphological and ecological traits that corresponded to these groups and could be used to determine the most appropriate taxonomic ranks of recovered groups. Molecular data recovers six well-supported monophyletic clades and a seventh clade of a single individual. Samples initially identified as <em>L. foeniculaceum</em> var. <em>macdougalii</em> are in two clades with one sister to <em>L. foeniculaceum</em> var. <em>foeniculaceum/L. foeniculaceum</em> var. <em>daucifolium</em> the other sister to <em>L. foeniculaceum</em> var. <em>fimbriatum.</em> Most samples of <em>L. foeniculaceum</em> var. <em>foeniculaceum</em> are in the same clade; others are in the clade with <em>L. foeniculaceum</em> var. <em>daucifolium</em> depending on the analysis. Each clade can be defined with a distinct morphological diagnostic character state. We conclude that molecular data and morphology support the recognition of five distinct species within the complex: <em>L</em>. <em>inyoense</em> Mathias &amp; Constance, <em>L</em>. <em>macdougalii</em> J. M. Coult. &amp; Rose, <em>L. fimbriatum</em> (W.L. Theob.) Botello &amp; J.F. Sm., <em>L. semivaginatum</em> Botello &amp; J.F. Sm., and <em>L. foeniculaceum</em> with two varieties retained, <em>L. foeniculaceum</em> var. <em>foeniculaceum</em> and <em>L. foeniculaceum</em> var. <em>daucifolium</em>. The data suggest that the Continental Divide has been influential in the evolution of these species, acting as an effective barrier facilitating speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108276"},"PeriodicalIF":3.6,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856988","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 straightforward workflow to explore species diversity using the Patagonian lizards of the Diplolaemus genus (Iguania: Leiosauridae) as a study case, with the description of a new species","authors":"Juan Vrdoljak ,&nbsp;Kevin Imanol Sánchez ,&nbsp;Andrea González-Marín ,&nbsp;Mariana Morando ,&nbsp;Luciano Javier Avila","doi":"10.1016/j.ympev.2024.108274","DOIUrl":"10.1016/j.ympev.2024.108274","url":null,"abstract":"<div><div>Disputes over species descriptions, stemming from conceptual disparities and arbitrary species boundaries, are among the primary challenges of modern taxonomy. In this study, we introduce a straightforward workflow, grounded in evolutionary theory, designed to tackle these challenges. We exemplified this approach using Patagonian lizards from the <em>Diplolaemus</em> clade. This workflow involves assigning specimens to putative evolutionary lineages, conducting primary species delimitations, constructing a species tree, comparing lineages for evolutionary independence, and using <em>post-hoc</em> analyses to separate well-supported from ambiguous lineages. This approach aims to establish a reliable foundation for exploring the taxonomic and evolutionary diversity of challenging groups. Applying this workflow to the <em>Diplolaemus</em> clade, we used various analytical methods on genetic (mitochondrial and nuclear markers) and phenotypic data (meristic, linear, and geometric morphometrics). We identified ten lineages with varying degrees of evolutionary independence in a clade where only four species had been described. Among the newly identified lineages, two exhibited low support for evolutionary independence, three showed strong support but had non-conclusive information, and one was recognized and described as a new species<em>.</em> In summary, our hierarchical workflow not only facilitated comprehensive comparisons but also enabled us to draw robust conclusions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108274"},"PeriodicalIF":3.6,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856968","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 time-calibrated salamander phylogeny including 765 species and 503 genes","authors":"Alexander A. Stewart,&nbsp;John J. Wiens","doi":"10.1016/j.ympev.2024.108272","DOIUrl":"10.1016/j.ympev.2024.108272","url":null,"abstract":"<div><div>Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22–45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108272"},"PeriodicalIF":3.6,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840342","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":"Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae","authors":"Silas Bossert ,&nbsp;Felipe V. Freitas ,&nbsp;Alain Pauly ,&nbsp;Gengping Zhu ,&nbsp;David W. Crowder ,&nbsp;Michael C. Orr ,&nbsp;James B. Dorey ,&nbsp;Elizabeth A. Murray","doi":"10.1016/j.ympev.2024.108273","DOIUrl":"10.1016/j.ympev.2024.108273","url":null,"abstract":"<div><div>The Afrotropical region is home to many endemic bee groups, yet almost none have been studied from an integrated, holistic perspective. Among them, the halictid subfamily Nomiinae contains exceptional African diversity with variable distributions and life histories. Here, we combine phylogenomics, molecular dating, and distributional modelling to explore the evolutionary ecology of the genus <em>Trinomia</em>. We analyzed a matrix of 59 species of Nomiinae using ultraconserved element (UCE) and whole genome data, including all six species of <em>Trinomia</em>, and estimated divergence times for the subfamily. We then generated distribution models for all six species of <em>Trinomia</em> using Maximum Entropy models (MaxEnt) and 671 spatial data points. From these methods, we discovered a monophyletic <em>Trinomia</em> with an unexpected sister group relationship to the Asian-endemic genus <em>Gnathonomia</em>, as well as a recent origin of <em>Trinomia</em> in the late Miocene (∼5.8 million years ago). From our results, we found hints of phylogenetic conservatism in distribution among sister-groups of <em>Trinomia</em>, however, our results also highlight the need for additional efforts inventorying, identifying, and sharing data on African bees. This study represents an exemplary first step into studying bee spatial phylogenomics of African endemic bees.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108273"},"PeriodicalIF":3.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830472","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":"Mystery on the Bounty: The family-level status of Pacificana cockayni Hogg, 1904 (Araneae)","authors":"Jacob A. Gorneau ,&nbsp;Franklyn Cala-Riquelme ,&nbsp;Sarah C. Crews ,&nbsp;Katherine O. Montana ,&nbsp;Joseph C. Spagna ,&nbsp;Cor J. Vink ,&nbsp;Lauren A. Esposito","doi":"10.1016/j.ympev.2024.108256","DOIUrl":"10.1016/j.ympev.2024.108256","url":null,"abstract":"<div><div>The family-level placement of the species <em>Pacificana cockayni</em> <span><span>Hogg, 1904</span></span> (Araneae, Miturgidae) has been ambiguous for over a century, with the monotypic genus <em>Pacificana</em> initially placed in Agelenidae, later transferred to Amaurobioidinae (Anyphaenidae), and presently in Miturgidae. A recent work describing the male and molecular data consisting of a single mitochondrial gene, cytochrome <em>c</em> oxidase subunit I, confirmed that the species is part of the marronoid clade; however, these data did not result in a conclusive family-level placement. Here, we use low-coverage whole genome sequencing (lcWGS) combined with data from the Sequence Read Archive to infer a phylogeny from ultraconserved elements (UCEs) and six legacy Sanger loci. Indications of potential family placements from prior work and the topologies from this study support a transfer of <em>Pacificana</em> Hogg, 1904 to Cycloctenidae Simon, 1898 (<strong>new family placement</strong>).</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108256"},"PeriodicalIF":3.6,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781937","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":"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}