Molecular Phylogenetics and Evolution最新文献

{"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}

{"title":"Phylogenetic relationships and species composition of host community influence the transmission of coronaviruses in sympatric bats","authors":"Chen Zhang ,&nbsp;Hao Gu ,&nbsp;Jie Peng ,&nbsp;Biao He ,&nbsp;Yuhang Liu ,&nbsp;Xiaomin Yan ,&nbsp;Jiang Feng ,&nbsp;Ying Liu","doi":"10.1016/j.ympev.2025.108343","DOIUrl":"10.1016/j.ympev.2025.108343","url":null,"abstract":"<div><div>Since the emergence of Severe Acute Respiratory Syndrome (SARS) in 2002, bats have been recognized as important reservoirs of diverse coronaviruses (CoVs). Despite extensive research on the broad geographic transmission of bat CoVs, there is a notable gap in understanding the transmission dynamics within sympatric bat communities. Using a phylogeographic Bayesian statistical framework, we examined CoV transmission patterns and their determinants in a region where four bat roosting caves coexist and CoVs circulate persistently. Our findings reveal that two subgenera of CoVs, α-CoVs and β-CoVs dominate different bat caves at varying times. Notably, β-CoVs show more frequent cross-species transmission events among the dominant reservoir hosts, bats of Rhinolophidae. Phylogenetic distance between host species emerges as the key influence factor of viral cross-species transmission, whereas cohabitation duration and the number of hosts sharing caves do not significantly influence viral transmission. In addition, we emphasize that the compositional similarity of species in the roosting caves is critical for the inter-cave transmission of bat-CoVs, rather than the distance between cave. These results provide novel insights into the complex transmission dynamics of bat CoVs within sympatric bat communities.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108343"},"PeriodicalIF":3.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726296","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":"Explosion of goby fish diversity at the Eocene-Oligocene transition","authors":"W. Tyler McCraney ,&nbsp;Christine E. Thacker ,&nbsp;Brant C. Faircloth ,&nbsp;Richard C. Harrington ,&nbsp;Thomas J. Near ,&nbsp;Michael E. Alfaro","doi":"10.1016/j.ympev.2025.108342","DOIUrl":"10.1016/j.ympev.2025.108342","url":null,"abstract":"<div><div>A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34–33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes (<em>Acanthomorpha</em>: <em>Percomorpha</em>: <em>Gobiiformes</em>) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hypothesis reconciles molecular clock- and fossil-based estimates for gobiiform diversification, dating the origin of <em>Apogonidae</em> and <em>Gobioidei</em> to the uppermost Late Cretaceous, with lower to middle Paleogene divergence of the gobioid backbone and an explosion of goby lineages at the EOT. Our results support a remarkably recent evolutionary origin of goby families and stimulate new questions on the seemingly exceptional diversity of the group.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108342"},"PeriodicalIF":3.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726295","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":"Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid speciation","authors":"Daniel Dols-Serrate ,&nbsp;Longhua Guo ,&nbsp;Leonid Kruglyak ,&nbsp;Marta Riutort","doi":"10.1016/j.ympev.2025.108339","DOIUrl":"10.1016/j.ympev.2025.108339","url":null,"abstract":"<div><div>Speciation is a complex process where many evolutionary forces interplay. The Mediterranean is acknowledged as one of the most relevant biodiverse areas in the Palearctic region and researchers have long studied the species inhabiting it to pursue the goals of evolutionary biology. Here, we study a complex of freshwater flatworm species of the genus <em>Dugesia</em> from Corsica and Sardinia using restriction site-associated DNA sequencing (specifically, 3RAD) data to unravel their evolutionary history and tackle the processes driving it. We assess the phylogenetic relationships and population structure within the group and evaluate new species boundaries using multispecies coalescent approaches. Furthermore, we offer insights into the environmental niche model of the group and use said model to guide our sampling efforts and collect and present molecular evidence for the first time of <em>Dugesia leporii</em> specimens, endemic from Sardinia last spotted in 1999. Our results indicate that paleoclimatic conditions rather than microplate tectonic dynamics were likely an important driver of diversification for the Corso-Sardinian group. Furthermore, our results warrant the taxonomic re-evaluation of the group as eight primary species candidates are established based on molecular data. Our study also reveals the first case of interspecific natural hybridization reported in Dugesiidae and, to our knowledge, in Tricladida. Finally, we discuss how this hybridization might constitute a new form of hybrid speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108339"},"PeriodicalIF":3.6,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712283","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":"Whole genome sequencing and phylogenetic analyses of the Sillaginidae family fish","authors":"Qi Liu ,&nbsp;Weihua Mao ,&nbsp;Yiting Wang ,&nbsp;Jiaguang Xiao ,&nbsp;Shilpi Saha ,&nbsp;Tianxiang Gao ,&nbsp;Fei Liu","doi":"10.1016/j.ympev.2025.108340","DOIUrl":"10.1016/j.ympev.2025.108340","url":null,"abstract":"<div><div>For a long time, the taxonomic study of the Sillaginidae family of fish has been relatively slow, leaving the evolutionary relationships among species unclear. Previous research has mainly relied on morphological characteristics, with molecular studies limited primarily to mitochondrial genomics, including analyses of gene fragments and whole mitochondrial genomic sequence. This approach resulted in less precise and comprehensive species identification. In this study, we employed high-depth whole-genome sequencing (WGS) and genome surveys on 13 specimens representing 9 species of Sillaginidae fish collected from the wild. Our analysis included a thorough genomic survey and the assembly of draft genomes for each specimen. The genome sizes of Sillaginidae species are highly similar, ranging from 511.71 Mb to 578.27 Mb, with most individuals exhibiting repeat sequences content below 34.69 %. After the genome draft assembly of each sample, we identified conserved genes and shared consistent sequences among individuals and constructed a species phylogenetic tree based on these data. The results revealed that <em>Sillago ingenua</em> occupies the basal branch, followed by <em>S. maculata</em> and <em>S. aeolus</em>, then <em>Sillaginopsis panijus</em>, <em>S. japonica</em> and <em>S. asiatica</em>, and finally <em>S. nigrofasciata</em> and <em>S.</em> cf. <em>sihama</em>. Subsequently, we validated the phylogenetic tree using genome-wide single nucleotide variations, and the results were highly consistent. This research provides, for the first time, a whole-genome perspective on the evolutionary relationships among Sillaginidae species, offering valuable insights into their taxonomy and historical evolution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108340"},"PeriodicalIF":3.6,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702272","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}