Molecular Phylogenetics and Evolution最新文献

筛选
英文 中文
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.
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-12-16 DOI: 10.1016/j.ympev.2024.108276
Daniel E Botello, Donald H Mansfield, Sven Buerki, Mary Ann E Feist, Mark Darrach, James F Smith
{"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, Donald H Mansfield, Sven Buerki, Mary Ann E Feist, Mark Darrach, James F Smith","doi":"10.1016/j.ympev.2024.108276","DOIUrl":"10.1016/j.ympev.2024.108276","url":null,"abstract":"<p><p>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 Lomatium foeniculaceum (Nutt.) Coult & 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: L. foeniculaceum var. foeniculaceum, L. foeniculaceum var. daucifolium (Torr. & A. Gray) Cronquist, L. foeniculaceum var. macdougalii (J.M. Coult. & Rose) Cronquist, L. foeniculaceum var. fimbriatum (W.L. Theob.) B. Boivin, and L. foeniculaceum var. inyoense (Mathias & 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 L. foeniculaceum var. macdougalii are in two clades with one sister to L. foeniculaceum var. foeniculaceum/L. foeniculaceum var. daucifolium the other sister to L. foeniculaceum var. fimbriatum. Most samples of L. foeniculaceum var. foeniculaceum are in the same clade; others are in the clade with L. foeniculaceum var. daucifolium 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: L. inyoense Mathias & Constance, L. macdougalii J. M. Coult. & Rose, L. fimbriatum (W.L. Theob.) Botello & J.F. Sm., L. semivaginatum Botello & J.F. Sm., and L. foeniculaceum with two varieties retained, L. foeniculaceum var. foeniculaceum and L. foeniculaceum var. daucifolium. The data suggest that the Continental Divide has been influential in the evolution of these species, acting as an effective barrier facilitating speciation.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
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.
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-12-16 DOI: 10.1016/j.ympev.2024.108274
Juan Vrdoljak, Kevin Imanol Sánchez, Andrea González-Marín, Mariana Morando, Luciano Javier Avila
{"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, Kevin Imanol Sánchez, Andrea González-Marín, Mariana Morando, Luciano Javier Avila","doi":"10.1016/j.ympev.2024.108274","DOIUrl":"10.1016/j.ympev.2024.108274","url":null,"abstract":"<p><p>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 Diplolaemus 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 post-hoc 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 Diplolaemus 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. In summary, our hierarchical workflow not only facilitated comprehensive comparisons but also enabled us to draw robust conclusions.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
A time-calibrated salamander phylogeny including 765 species and 503 genes.
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-12-15 DOI: 10.1016/j.ympev.2024.108272
Alexander A Stewart, John J Wiens
{"title":"A time-calibrated salamander phylogeny including 765 species and 503 genes.","authors":"Alexander A Stewart, John J Wiens","doi":"10.1016/j.ympev.2024.108272","DOIUrl":"10.1016/j.ympev.2024.108272","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae. 非洲热带特有的 Nomiinae 属 Trinomia(膜翅目:Halictidae)的系统发育、古老性和生态位占有。
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-12-13 DOI: 10.1016/j.ympev.2024.108273
Silas Bossert, Felipe V Freitas, Alain Pauly, Gengping Zhu, David W Crowder, Michael C Orr, James B Dorey, Elizabeth A Murray
{"title":"Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae.","authors":"Silas Bossert, Felipe V Freitas, Alain Pauly, Gengping Zhu, David W Crowder, Michael C Orr, James B Dorey, Elizabeth A Murray","doi":"10.1016/j.ympev.2024.108273","DOIUrl":"10.1016/j.ympev.2024.108273","url":null,"abstract":"<p><p>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 Trinomia. We analyzed a matrix of 59 species of Nomiinae using ultraconserved element (UCE) and whole genome data, including all six species of Trinomia, and estimated divergence times for the subfamily. We then generated distribution models for all six species of Trinomia using Maximum Entropy models (MaxEnt) and 671 spatial data points. From these methods, we discovered a monophyletic Trinomia with an unexpected sister group relationship to the Asian-endemic genus Gnathonomia, as well as a recent origin of Trinomia in the late Miocene (∼5.8 million years ago). From our results, we found hints of phylogenetic conservatism in distribution among sister-groups of Trinomia, 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Mystery on the Bounty: The family-level status of Pacificana cockayni Hogg, 1904 (Araneae).
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-12-02 DOI: 10.1016/j.ympev.2024.108256
Jacob A Gorneau, Franklyn Cala-Riquelme, Sarah C Crews, Katherine O Montana, Joseph C Spagna, Cor J Vink, Lauren A Esposito
{"title":"Mystery on the Bounty: The family-level status of Pacificana cockayni Hogg, 1904 (Araneae).","authors":"Jacob A Gorneau, Franklyn Cala-Riquelme, Sarah C Crews, Katherine O Montana, Joseph C Spagna, Cor J Vink, Lauren A Esposito","doi":"10.1016/j.ympev.2024.108256","DOIUrl":"10.1016/j.ympev.2024.108256","url":null,"abstract":"<p><p>The family-level placement of the species Pacificana cockayniHogg, 1904 (Araneae, Miturgidae) has been ambiguous for over a century, with the monotypic genus Pacificana 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 c 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 Pacificana Hogg, 1904 to Cycloctenidae Simon, 1898 (new family placement).</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Extensive cytonuclear discordance revealed by phylogenomic analyses suggests complex evolutionary history in the holly genus Ilex (Aquifoliaceae).
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-11-30 DOI: 10.1016/j.ympev.2024.108255
Ke-Wang Xu, Yi Yang, Hong Chen, Chen-Xue Lin, Lei Jiang, Zhong-Long Guo, Meng Li, Ming-Zhuo Hao, Kai-Kai Meng
{"title":"Extensive cytonuclear discordance revealed by phylogenomic analyses suggests complex evolutionary history in the holly genus Ilex (Aquifoliaceae).","authors":"Ke-Wang Xu, Yi Yang, Hong Chen, Chen-Xue Lin, Lei Jiang, Zhong-Long Guo, Meng Li, Ming-Zhuo Hao, Kai-Kai Meng","doi":"10.1016/j.ympev.2024.108255","DOIUrl":"10.1016/j.ympev.2024.108255","url":null,"abstract":"<p><p>Ilex 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 Ilex, 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 Ilex in multiple instances. The extensive cytonuclear discordance identified may be attributed to recent hybridization events and incomplete lineage sorting (ILS).</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Phylogenomic analyses unravel the tangled evolutionary history of Genisteae (Fabaceae).
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-11-30 DOI: 10.1016/j.ympev.2024.108249
Sarah Hunter, Domingos Cardoso, Tracey A Ruhlman, Robert K Jansen
{"title":"Phylogenomic analyses unravel the tangled evolutionary history of Genisteae (Fabaceae).","authors":"Sarah Hunter, Domingos Cardoso, Tracey A Ruhlman, Robert K Jansen","doi":"10.1016/j.ympev.2024.108249","DOIUrl":"10.1016/j.ympev.2024.108249","url":null,"abstract":"<p><p>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 Lupinus clade, the Cytisus-Genista complex and the Argyrolobium group. There are also two historical genera, Teline and Chamaecytisus, that have been reclassified over the years with some controversy. Species from Teline are currently classified in Genista, and Chamaecytisus species are placed inside of Cytisus. Sellocharis is another genus with vague placement inside of Genisteae near Anarthrophyllum, based mostly on morphology and cytology. Representative taxa from 24 of the 25 genera of Genisteae, along with species of historical genera Teline and Chamaecytisus, 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: Cytisus-Genista complex, Lupinus clade, Argyrolobium group and the novel Anarthrophyllum group. The resulting phylogenetic trees also supported the transfer of the Argyrolobium group from Crotalarieae to Genisteae, and the reclassification of Teline inside of Genista, both of which were previously suggested in literature. The phylogenetic trees also determined a placement for Sellocharis in the new Anarthrophyllum 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets.
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-11-29 DOI: 10.1016/j.ympev.2024.108253
Jing Zhao, Zhen-Long Liang, Shao-Li Fang, Rong-Juan Li, Chuan-Jie Huang, Li-Bing Zhang, Tanner Robison, Zhang-Ming Zhu, Wen-Jing Cai, Hong Yu, Zhao-Rong He, Xin-Mao Zhou
{"title":"Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets.","authors":"Jing Zhao, Zhen-Long Liang, Shao-Li Fang, Rong-Juan Li, Chuan-Jie Huang, Li-Bing Zhang, Tanner Robison, Zhang-Ming Zhu, Wen-Jing Cai, Hong Yu, Zhao-Rong He, Xin-Mao Zhou","doi":"10.1016/j.ympev.2024.108253","DOIUrl":"10.1016/j.ympev.2024.108253","url":null,"abstract":"<p><p>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 Paragymnopteris including approximately five species have long been controversial. In this study, with an extensive taxon sampling of Paragymnopteris, we assembled 19 complete plastomes of all recognized Paragymnopteris species, plastomes of Pellaea (3 species) and Argyrochosma (1 species), as well as transcriptomes from Paragymnopteris (6 species) and Argyrochosma (1 species). We conducted a comprehensive and systematic phylogenomic analysis focusing on the contentious relationships among the genus of Paragymnopteris 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 Paragymnopteris. The backbone of Paragymnopteris was resolved consistently in the nuclear and plastid phylogenies. Our major results include: (1) Paragymnopteris is not monophyletic including two fully supported clades; (2) confirming that Paragymnopteris delavayi var. intermedia is a close relative of P. delavayi instead of P. marantae var. marantae; (3) the chromosome base number may not be a stable trait which has previously been used as an important character to divide Paragymnopteris into two groups; and (4) gene flow or introgression might be the main reason for the gene trees conflict of Paragymnopteris, but both gene flow and ILS might simultaneously and/or cumulatively act on the conflict of core pellaeids. The robust phylogeny of Paragymnopteris 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Endogean habits drove cryptic diversification in Appalachian Lathrobium Gravenhorst (Coleoptera, Staphylinidae).
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-11-29 DOI: 10.1016/j.ympev.2024.108252
Adam Haberski, Michael S Caterino
{"title":"Endogean habits drove cryptic diversification in Appalachian Lathrobium Gravenhorst (Coleoptera, Staphylinidae).","authors":"Adam Haberski, Michael S Caterino","doi":"10.1016/j.ympev.2024.108252","DOIUrl":"10.1016/j.ympev.2024.108252","url":null,"abstract":"<p><p>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. Lathrobium 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 Lathrobium 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 Abletobium Casey. Abletobium is placed in synonymy with Glyptomerus 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 Lathrobium lineages into the mountains and subsequent isolation in mountaintop refugia during warm Pleistocene interglacials led to speciation.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
Phylogenomics reveals a new generic delimitation of Asian Millettia, with reinstatements of Pongamia and Otosema (Fabaceae: Millettieae).
IF 3.6 1区 生物学
Molecular Phylogenetics and Evolution Pub Date : 2024-11-28 DOI: 10.1016/j.ympev.2024.108254
Zhuqiu Song, Liansheng Xu, Anoop Puthuparampil Balan, Myriam Gaudeul, Yiyong Zhao, Kaiwen Jiang, Tian Li, Shijin Li
{"title":"Phylogenomics reveals a new generic delimitation of Asian Millettia, with reinstatements of Pongamia and Otosema (Fabaceae: Millettieae).","authors":"Zhuqiu Song, Liansheng Xu, Anoop Puthuparampil Balan, Myriam Gaudeul, Yiyong Zhao, Kaiwen Jiang, Tian Li, Shijin Li","doi":"10.1016/j.ympev.2024.108254","DOIUrl":"10.1016/j.ympev.2024.108254","url":null,"abstract":"<p><p>The generic relationships within the core Millettieae have not been well resolved to date. Millettia 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 Millettia 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 Millettia. 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 Millettia were grouped into three distinct, well-supported subclades, leading us to propose a much narrower generic concept of Millettia, along with the reinstatements of the genera Pongamia and Otosema. Millettia s.str. was restricted to include only seven species. Pongamia was recognized as a medium-sized genus that includes Fordia and Ibatiria, with approximately 56 species. Otosema, usually treated as a subgenus or section of Millettia, was resurrected as a distinct genus with three species. Our findings also indicated that the sampled African Millettia species belong to three subclades distinct from the Asian Millettia 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 Derris s.lato, Lonchocarpus s.lato, and Millettia 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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信