Molecular Phylogenetics and Evolution最新文献

{"title":"Ecological divergence of marine bacteria Alteromonas mediterranea","authors":"Shuangfei Zhang,&nbsp;Chongran Sun","doi":"10.1016/j.ympev.2025.108359","DOIUrl":"10.1016/j.ympev.2025.108359","url":null,"abstract":"<div><div><em>Alteromonas mediterranea</em>, originally designated as <em>A. macleodii</em>, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that <em>A. mediterranea</em> members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of <em>A. mediterranea</em> members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of <em>A. mediterranea</em> strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome <em>o</em> ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of <em>A. mediterranea</em> relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of <em>A. mediterranea</em> members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of <em>A. mediterranea</em> in marine habitats. Given these data, these results are useful for information supplementation of <em>A. mediterranea</em> strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108359"},"PeriodicalIF":3.6,"publicationDate":"2025-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143864076","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 and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure","authors":"Veronika Bartáková ,&nbsp;Anna Bryjová ,&nbsp;Matej Polačik ,&nbsp;David O. Alila ,&nbsp;Béla Nagy ,&nbsp;Brian Watters ,&nbsp;Dirk Bellstedt ,&nbsp;Radim Blažek ,&nbsp;Jakub Žák ,&nbsp;Martin Reichard","doi":"10.1016/j.ympev.2025.108357","DOIUrl":"10.1016/j.ympev.2025.108357","url":null,"abstract":"<div><div>Annual killifishes of the genus <em>Nothobranchius</em> are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to <em>Nothobranchius</em> dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in <em>Nothobranchius</em> species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the <em>N. melanospilus</em> and <em>N. guentheri</em> species groups and placed <em>N. flammicomantis</em> outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among <em>N. eggersi</em>, <em>N. janpapi</em>, <em>N. melanospilus</em> and <em>N. ocellatus</em>. Populations of <em>Nothobranchius</em> species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins – in contrast to <em>Nothobranchius</em> species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108357"},"PeriodicalIF":3.6,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868471","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 the superfamily Lygaeoidea with proposals on taxonomic system (Hemiptera: Heteroptera)","authors":"Ying Lu ,&nbsp;Fei Ye ,&nbsp;Junlan Li ,&nbsp;Cuiqing Gao ,&nbsp;Yanhui Wang ,&nbsp;Xueqin Shi ,&nbsp;Yiqin Su ,&nbsp;Huaijun Xue ,&nbsp;Wenjun Bu ,&nbsp;Leyi Zheng ,&nbsp;Qiang Xie","doi":"10.1016/j.ympev.2025.108356","DOIUrl":"10.1016/j.ympev.2025.108356","url":null,"abstract":"<div><div>Lygaeoidea, one of the largest superfamilies of the true bugs (Hemiptera: Heteroptera), currently comprises 16 families and exhibits abundant diversification in habitats, body plans, and feeding habits. The relationships within this superfamily are complex, and comprehensive molecular phylogenetic studies, particularly those focusing on subfamilies and tribes within Rhyparochromidae, have been lacking. In the present study, we sampled 125 lygaeoid species representing all 16 families of Lygaeoidea, with a focus on two subfamilies and 12 tribes within Rhyparochromidae. A phylogenetic dataset with 102 genes was assembled, including two nuclear rRNA genes (18S rDNA, 28S rDNA), two mitochondrial rRNA genes (12S rDNA, 16S rDNA), 13 mitochondrial protein-coding genes (PCGs) and 85 nuclear PCGs generated from the low-coverage genomes. Our inferences indicate that Rhyparochromidae is not monophyletic, with one subfamily, one tribe, and one genus deserving elevation to the rank of family. Additionally, this phylogenetic result is also supported by corresponding morphological evidence. Besides, the transfer of the <em>Heissothignus</em> from Heterogastridae to Meschiidae is supported by molecular evidence in this study.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"209 ","pages":"Article 108356"},"PeriodicalIF":3.6,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947081","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":"Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata","authors":"Oscar Wallnoefer ,&nbsp;Alessandro Formaggioni ,&nbsp;Federico Plazzi,&nbsp;Marco Passamonti","doi":"10.1016/j.ympev.2025.108358","DOIUrl":"10.1016/j.ympev.2025.108358","url":null,"abstract":"<div><div>The order Squamata is a good candidate for detecting unusual patterns of mitochondrial evolution. The lineages leading to the snake and agamid clades likely experienced convergent evolution in mitochondrial OXidative PHOSphorylation (OXPHOS) genes, which provides strong support for the sister relationship of these two groups.</div><div>The OXPHOS subunits are encoded by both the nuclear and mitochondrial genomes, which are subject to distinct evolutionary pressures. Nevertheless, the cooperation between OXPHOS subunits is essential for proper OXPHOS function, as incompatibilities between subunits can be highly deleterious.</div><div>In the present study, we annotated OXPHOS genes of 56 Squamata species. The nuclear OXPHOS subunits that physically interact with mitochondrial proteins also support the clade sister relationship between snakes and agamids. Additionally, we found a significant number of convergent amino acid changes between agamids and snakes, not only in mitochondrial OXPHOS genes, but also in nuclear ones, with a higher rate of convergence in the nuclear OXPHOS subunits that play central roles in the OXPHOS complexes, like COX4 and NDUFA4.</div><div>Overall, the common selective pressures in two distinct lineages can lead two sets of genes, encoded by two different genomes, to exhibit similar patterns of convergent evolution, as well as similar evolutionary rates. As a consequence, the coevolution of interdependent subunits and their adaptation to specific evolutionary pressures can heavily influence the molecular structure of cytonuclear enzyme complexes and blur phylogenetic signals.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108358"},"PeriodicalIF":3.6,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835287","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":"Deciphering the patterns and timing of diversification of the genus Melanastera (Hemiptera: Psylloidea: Liviidae) in the Neotropics","authors":"Liliya Štarhová Serbina ,&nbsp;Daniel Burckhardt ,&nbsp;Lenka Petráková Dušátková ,&nbsp;Dalva L. Queiroz ,&nbsp;Renato Goldenberg ,&nbsp;Hannes Schuler ,&nbsp;Diana M. Percy ,&nbsp;Igor Malenovský","doi":"10.1016/j.ympev.2025.108347","DOIUrl":"10.1016/j.ympev.2025.108347","url":null,"abstract":"<div><div>Even after decades of research on diversification in the Neotropics, our understanding of the evolutionary processes that shaped Neotropical clades is still incomplete. In the present study, we used different divergence times and likelihood-based methods to investigate the influence of biogeography and host plant associations on the diversification of the most species-rich psyllid genus <em>Melanastera</em> (Liviidae) from the Neotropics as a model group of herbivorous insects. We used molecular phylogenetic data from seven gene fragments (four mitochondrial and three nuclear). The putatively monophyletic group of Neotropical <em>Melanastera</em> species has an estimated crown node age of 20.2 Ma (ML, CI 20.2–30.6) or 23.2 Ma (BI, 95 % HPD 16.6–32.6), with diversification occurring mainly in the Upper Miocene, although some species groups diversified in the Pliocene or Pleistocene. Biogeographic analysis suggests that the Neotropical <em>Melanastera</em> originated from the Pacific region of South and Central America. We detected a shift in diversification rates that likely occurred either at the time of origin of <em>Melanastera</em> or during the main colonisation of the Atlantic and Amazon Forests, followed by a subsequent slowdown in speciation rates. State-dependent speciation and extinction models revealed a significant relationship between this diversification shift and the shift of <em>Melanastera</em> to the plant families Melastomataceae and Annonaceae, reflecting the impact of host switching on speciation rates in this group. This period also coincides with several independent dispersal events from the Atlantic and Amazon Forests to other parts of the Neotropics. Taken together, the results of the current study suggest that diversification of <em>Melanastera</em> was facilitated by shifts to new host families, which may have promoted the dispersal of <em>Melanastera</em> into new adaptive zones with subsequent processes of local speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108347"},"PeriodicalIF":3.6,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813016","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":"Total-evidence phylogenetic analysis resolves the evolutionary timescale of mantis shrimps (Stomatopoda) and provides insights into their molecular and morphological evolutionary rates","authors":"Cara Van Der Wal ,&nbsp;Shane T. Ahyong ,&nbsp;Maxim W.D. Adams ,&nbsp;Nathan Lo ,&nbsp;Simon Y.W. Ho","doi":"10.1016/j.ympev.2025.108346","DOIUrl":"10.1016/j.ympev.2025.108346","url":null,"abstract":"<div><div>The crustacean order Stomatopoda comprises approximately 500 species of mantis shrimps. These marine predators, common in tropical and subtropical waters, possess sophisticated visual systems and specialized hunting appendages. In this study, we infer the evolutionary relationships within Stomatopoda using a combined data set of 77 morphological characters, whole mitochondrial genomes, and three nuclear markers. Our data set includes representatives from all seven stomatopod superfamilies, including the first sequence data from Erythrosquilloidea. Using a Bayesian relaxed molecular clock with fossil-based calibration priors, we estimate that crown-group unipeltatan stomatopods appeared ∼ 143 (95 % credible interval 199–98) million years ago in the Mesozoic. Additionally, our results support the hypothesis that specialized smashing and spearing appendages appeared early in the evolutionary history of Unipeltata. We found no evidence of a correlation between rates of morphological and molecular evolution across the phylogeny, but identified very high levels of among-lineage rate variation in the morphological characters. Our total-evidence analysis recovered evolutionary signals from both molecular and morphological data sets, demonstrating the merit in combining these sources of information for phylogenetic inference and evolutionary analysis.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108346"},"PeriodicalIF":3.6,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143799323","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":"Cryptic species, biogeography, and patterns of introgression in the fish genus Mogurnda (Eleotridae) from the Australian wet tropics: A purple patch for purple-spots","authors":"Samuel R. Amini ,&nbsp;Mark Adams ,&nbsp;Michael P. Hammer ,&nbsp;Glenn Briggs ,&nbsp;James A. Donaldson ,&nbsp;Brendan C. Ebner ,&nbsp;Peter J. Unmack","doi":"10.1016/j.ympev.2025.108344","DOIUrl":"10.1016/j.ympev.2025.108344","url":null,"abstract":"<div><div>Accurately delimiting species is an essential first step towards understanding the true biodiversity of an ecosystem and any subsequent efforts to identify and protect taxa at risk of extinction. Current molecular evidence suggests that purple-spotted gudgeons (genus <em>Mogurnda</em>) harbour high levels of cryptic biodiversity across their broad distributional range. The present study uses a large single nucleotide polymorphism (SNP) dataset plus a companion allozyme dataset to clarify taxonomic uncertainty, patterns of introgression, and biogeographic relationships among <em>Mogurnda</em> populations within the Queensland Wet Tropics (QWT), a known biodiversity hotspot. Both datasets were strongly concordant in identifying a total of seven taxa split among distinct southern, northern, and lowlands groups. No two taxa were found in strict sympatry, but many appear to be parapatric and occur within the same drainage basin. Although clear evidence of introgression was only evident at six sites (∼4%), the genomic signature of modest historic admixture between proximally-distributed taxa was detected at multiple other sites. Nevertheless, all primary genetic and phylogenetic analyses strongly supported the integrity and diagnosability of these seven taxa. We therefore nominate these as novel candidate species for what appears to be yet another hyper-cryptic complex within the Australian freshwater ichthyological fauna. These results offer up intriguing ecological scenarios and conservation implications for multiple candidate species with narrow ranges in specialised habitat. We conclude by exploring the major biogeographic patterns displayed by QWT <em>Mogurnda</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108344"},"PeriodicalIF":3.6,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797154","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":"Exploring the evolution of anaerobes within ciliate class Prostomatea by transcriptomics","authors":"Jiahui Xu ,&nbsp;Zhuo Shen ,&nbsp;Tingting Hao ,&nbsp;Hua Su ,&nbsp;Miaoying Chen ,&nbsp;Xuming Pan ,&nbsp;Zhenzhen Yi","doi":"10.1016/j.ympev.2025.108345","DOIUrl":"10.1016/j.ympev.2025.108345","url":null,"abstract":"<div><div>Mitochondrion-related organelles (MROs) enable anaerobic eukaryotes to thrive in anoxic environments, and the independent ciliate lineages of anaerobes serve as excellent candidates for investigating the convergent evolutionary transition from mitochondria to MROs. Previous studies have demonstrated that the adaptations of ciliates to anaerobic conditions may be lineage-specific. However, our understanding of the diverse metabolic peculiarities of MROs is limited to a few ciliate lineages. In this study, we sequenced the transcriptomes of four anaerobic species from two genera (<em>Apolagynus</em> and <em>Holophrya</em>), which are classified within the predominantly aerobic class Prostomatea, and predicted their mitochondrial metabolisms. The ecological niches of prostomatean anaerobes were mapped onto newly constructed phylogenomic trees and small subunit (SSU) rDNA trees. Results showed that paraphyletic class Prostomatea containing six clades (Clade Ⅰ–Ⅵ) has a close relationship with Oligohymenophorea and Plagiopylea. Notably, all prostomatean species within Clade Ⅱ are anaerobic, while anaerobes are only sporadically present in other clades. The MROs of anaerobic prostomatean species display at least two distinct phenotypes. <em>Holophrya ovum</em> in Clade Ⅰ produces ATP by oxidative phosphorylation under aerobic conditions and via substrate-level phosphorylation via acetate: succinate CoA transferase (ASCT) and succinyl CoA synthetase (SCS) as well as adenylate kinase (AK) under anaerobic conditions. In contrast, three species of <em>Apolagynus</em> in Clade Ⅱ possess reduced electron transport chain (ETC), and are capable of ATP generation via substrate-level phosphorylation mediated by ASCT/SCS and propionyl-CoA. Additionally, these three <em>Apolagynus</em> species possess [FeFe] hydrogenase probably producing H₂. A comparison of the ETC pathways among various anaerobic ciliates further showed that the MROs of these organisms have originated from repeated convergent evolution. Our findings shed lights on evolutionary history of anaerobes within the ciliate class Prostomatea.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108345"},"PeriodicalIF":3.6,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143774943","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":"Novel island species elucidate a species complex of Neotropical crocodiles","authors":"Jose Avila-Cervantes ,&nbsp;Pierre Charruau ,&nbsp;J. Rogelio Cedeño-Vázquez ,&nbsp;Hoai-Nam Bui ,&nbsp;Miryam Venegas-Anaya ,&nbsp;Marta Vargas ,&nbsp;Marco A. López-Luna ,&nbsp;Héctor González-Cortés ,&nbsp;David A. Macías-Díaz ,&nbsp;Jonathan S. Pérez-Flores ,&nbsp;Gabriel Barrios-Quiroz ,&nbsp;J. Miguel Salazar ,&nbsp;W. Owen McMillan ,&nbsp;Hans C.E. Larsson","doi":"10.1016/j.ympev.2025.108341","DOIUrl":"10.1016/j.ympev.2025.108341","url":null,"abstract":"<div><div>The evolutionary history of Neotropical crocodiles has remained elusive. They inhabit a broad geographic range with populations spanning from coastal, inland, and insular locations. Using a selection of natural insular, coastal, and one inland population of <em>C. acutus</em>, coastal <em>C. moreletii</em>, and the single surviving population of <em>C. rhombifer</em>, we discovered a remarkable genetic diversity for the group. Moreover, geometric morphometric results of skull shapes shows that these crocodylus species span a morphological cline. We recovered a high genetic differentiation between <em>C. moreletii</em>, <em>C. rhombifer</em>, and five clusters of <em>C. acutus</em>. The genetic and geographic differences among the <em>C. acutus</em> clusters were used to suggest these may be a species complex. Several ecological, morphological and genetics traits are identified in the well-studied populations from Banco Chinchorro and Cozumel islands off the Mexican Yucatan Peninsula to support discrete species designations for these populations. This work suggests the presence of rapid, recent evolution of several cryptic <em>Crocodylus</em> species throughout the Neotropics.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108341"},"PeriodicalIF":3.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143739269","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":"Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes – with particular focus on Hymenocoleus Robbr.","authors":"Lovisa Thilén ,&nbsp;Olivier Lachenaud ,&nbsp;Olle Thureborn ,&nbsp;Sylvain G. Razafimandimbison ,&nbsp;Catarina Rydin","doi":"10.1016/j.ympev.2025.108338","DOIUrl":"10.1016/j.ympev.2025.108338","url":null,"abstract":"<div><div>Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus <em>Hymenocoleus</em>. Using coalescent-based inference methods, we find that <em>Puffia gerrardii</em> (recently separated from <em>Geophila</em>) is sister to <em>Hymenocoleus</em>. The deepest split in <em>Hymenocoleus</em> is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in <em>Hymenocoleus</em> could be confidently resolved and while Robbrecht’s traditional infrageneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108338"},"PeriodicalIF":3.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756155","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}