Molecular Phylogenetics and Evolution最新文献

Corrigendum to "Harmony in diversity: Reorganizing the families within the order Pseudomonadales" [Mol. Phylogenet. Evol. 206 (2025) 108321]. 《多样性中的和谐：重组假单胞目的科》的勘误[摩尔。系统发育学]。进化。206 (2025)108321 [j]。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-07-18 DOI: 10.1016/j.ympev.2025.108409

José David Flores-Félix, Paula García-Fraile, Zaki Saati-Santamaría

引用次数: 0

Population-level phylogenomic analysis yields insights into species cohesion and population substructure of Lobelia section Lobelia (Campanulaceae) 种群水平的系统基因组分析揭示了半边莲属植物的种内聚性和种群亚结构。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-07-14 DOI: 10.1016/j.ympev.2025.108410

Grant T. Godden , Andrew A. Crowl , Stephen R. Patten , Princess Abu , Svea Hall , Mark O. Johnston , Douglas W. Schemske , T. Wayne Barger , Miguel A. Pérez-Pérez , Christopher R. Herlihy , Lynda F. Delph , Christopher B. Blackwood , Andrea L. Case , Nico Cellinese

{"title":"Population-level phylogenomic analysis yields insights into species cohesion and population substructure of Lobelia section Lobelia (Campanulaceae)","authors":"Grant T. Godden , Andrew A. Crowl , Stephen R. Patten , Princess Abu , Svea Hall , Mark O. Johnston , Douglas W. Schemske , T. Wayne Barger , Miguel A. Pérez-Pérez , Christopher R. Herlihy , Lynda F. Delph , Christopher B. Blackwood , Andrea L. Case , Nico Cellinese","doi":"10.1016/j.ympev.2025.108410","DOIUrl":"10.1016/j.ympev.2025.108410","url":null,"abstract":"<div><div>How close relatives maintain species boundaries in sympatry remains a critical question in biodiversity research. Here we introduce <em>Lobelia</em> sect. <em>Lobelia</em> (Campanulaceae) as a useful clade for investigating such questions. Polyphyly within this clade was strongly suspected because many of the 26 species are cross-compatible and show remarkable overlap in distribution, morphology, ecology, and life history. Indeed, the species <em>Lobelia</em> × <em>rogersii</em> has a purported hybrid origin from <em>Lobelia puberula</em> and <em>Lobelia brevifolia</em>, and the well-known cultivar <em>Lobelia</em> × <em>speciosa</em> results from mating between <em>Lobelia siphilitica</em> and <em>Lobelia cardinalis</em>. We carried out a comprehensive evolutionary investigation of <em>Lobelia</em> sect. <em>Lobelia</em>, including phylogenetic inference, divergence time estimates, and population structure analyses using 729 accessions from 193 natural population sites representing 1–13 individuals per population per species. In contrast to expectations, nearly all species were recovered as reciprocally monophyletic with strong topological support and low levels of interspecific gene flow. An exception to this general pattern is observed in the Florida panhandle, where <em>Lobelia glandulosa</em> and <em>Lobelia apalachicolensis</em> co-occur and appear to be actively hybridizing. We conclude that North American <em>Lobelia</em> species are genetically cohesive, despite significant geographic overlap, frequent co-occurrence, morphological similarity, and broad interfertility in artificial crosses.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"212 ","pages":"Article 108410"},"PeriodicalIF":3.6,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651279","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

Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus 从副葡萄球菌泛基因组和色素谱的进化见解。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-07-10 DOI: 10.1016/j.ympev.2025.108408

Jie Tang , Zhe Hu , Xinping Zhang , Qiaohui Mou , Lianming Du , Maurycy Daroch

{"title":"Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus","authors":"Jie Tang , Zhe Hu , Xinping Zhang , Qiaohui Mou , Lianming Du , Maurycy Daroch","doi":"10.1016/j.ympev.2025.108408","DOIUrl":"10.1016/j.ympev.2025.108408","url":null,"abstract":"<div><div><em>Parasynechococcus</em> is one of the two essential alongside <em>Prochlorococcus</em> photosynthetic cyanobacteria that contribute primary productivity in the ocean. Despite its global importance its specie delimitation remains controversial. Herein, a pangenome analysis of 39 high-quality genomes was conducted to delineate <em>Parasynechococcus</em> species. Core-gene phylogram revealed the classification of these genomes into 18 well-defined putative genospecies, which was corroborated by ANI index and GTDB classification. Moreover, numerous interspecies and intraspecies HGT events were detected, some of which may be responsible for the inconsistencies between core-gene and pan-gene phylograms. Besides, the profiling of phycobilisome rod region in <em>Parasynechococcus</em> genomes unraveled intriguing diversity of their genomic organization, pigment type and genomic cluster variants. The diversification process was hypothesized to be mediated by the putative mobile elements located in these regions. Moreover, phylogeny incongruence between the genes within phycobilisome rod region and the core genome indicate distinct evolutionary history, which could be ascribed to lateral gene transfer. Conclusively, the results provide insights into the diversity and evolution of <em>Parasynechococcus</em> from the perspective of pangenome and pigment type, facilitating the evolutionary research and exploration of this important taxon.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"212 ","pages":"Article 108408"},"PeriodicalIF":3.6,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621273","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

Speciation continuum in non-model organisms: Revisiting the species-pair concept in lichens 非模式生物的物种形成连续体：重新审视地衣的物种对概念。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-07-10 DOI: 10.1016/j.ympev.2025.108407

Ana Otero , H. Thorsten Lumbsch , Polina Degtjarenko , Felix Grewe

{"title":"Speciation continuum in non-model organisms: Revisiting the species-pair concept in lichens","authors":"Ana Otero , H. Thorsten Lumbsch , Polina Degtjarenko , Felix Grewe","doi":"10.1016/j.ympev.2025.108407","DOIUrl":"10.1016/j.ympev.2025.108407","url":null,"abstract":"<div><div>Evolutionary biologists have long pursued understanding the continuum in which populations flow, interact, and evolve, which can ultimately lead to divergence into distinct species. Lichens, which are often defined as intricate ecosystems, exhibit remarkable evolutionary mechanisms that challenge conventional definitions of speciation. A particularly notable phenomenon in lichens is the species-pair concept, in which closely related taxa only differ in their reproductive strategies − one reproducing sexually, the other asexually. We investigated this concept in the iconic beard-like lichen <em>Usnea</em> by comparing three species pairs: <em>U. aurantiacoatra/U. antarctica</em>, <em>U. florida/U. subfloridana</em> and <em>U. intermedia/U. perplexans.</em> Using reference-based RADseq data and applying multivariate and model-based genomic population methods, we evaluated genomic differentiation across each pair. Our results revealed a gradient of divergence: <em>U. aurantiacoatra</em>/<em>U. antarctica</em> showed strong lineage separation with no genomic admixture, <em>U. intermedia</em>/<em>U. perplexans</em> exhibited moderate differentiation with signs of gene flow, and <em>U. florida</em>/<em>U. subfloridana</em> formed a largely unstructured clade with substantial genomic overlap. These findings place the three species pairs at different positions along the speciation continuum and highlight reproductive mode as a key factor influencing lineage divergence. Our study reframes the species-pair concept within a continuum framework and provides new genomic insights from a non-model system, enhancing our understanding of speciation in lichen-forming fungi.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"212 ","pages":"Article 108407"},"PeriodicalIF":3.6,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621274","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

Museomics reveals the phylogenetic position of an enigmatic vertebrate family (Lophiiformes: Lophichthyidae) 博物馆组学揭示了一个神秘的脊椎动物家族的系统发育位置（水母目：水母科）。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-07-01 DOI: 10.1016/j.ympev.2025.108406

Moritz Muschick , Lukas Rüber , Michael Matschiner

{"title":"Museomics reveals the phylogenetic position of an enigmatic vertebrate family (Lophiiformes: Lophichthyidae)","authors":"Moritz Muschick , Lukas Rüber , Michael Matschiner","doi":"10.1016/j.ympev.2025.108406","DOIUrl":"10.1016/j.ympev.2025.108406","url":null,"abstract":"<div><div><em>Lophichthys boschmai</em>, the only member of the family Lophichthyidae, is an elusive lophiiform fish whose phylogenetic associations are debated. This family is among the last two vertebrate families lacking DNA sequence data, primarily due to the species’ rarity, lack of fresh material and challenges associated with sequencing formalin-treated museum specimens. In this study, we provide mitochondrial and nuclear DNA sequences obtained from two museum specimens of <em>Lophichthys boschmai</em>. Employing ancient DNA techniques, we successfully extracted and analyzed the degraded and fragmented DNA. Our findings, derived from both mitochondrial genomes and nuclear ultra-conserved elements (UCE), reveal the Lophichthyidae as sister lineage to Tathicarpidae within the Antennarioidei. This study showcases the use of whole-genome “shotgun” sequencing data from formalin-fixed museum specimens in the context of an available UCE dataset. Given the enhanced versatility in data reusability this approach offers, we suggest it should be a favored approach when studying rare specimens.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108406"},"PeriodicalIF":3.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562102","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 taxonomic challenges in Calibrachoa (Solanaceae) and sheds light on the origins of cultivated million bells 系统基因组学揭示了calbrachoa（茄科）的分类挑战，并揭示了栽培百万个铃铛的起源。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-06-30 DOI: 10.1016/j.ympev.2025.108405

Alice Backes , Leonardo T. Gonçalves , Pedro H. Pezzi, Loreta B. Freitas

{"title":"Phylogenomics reveals taxonomic challenges in Calibrachoa (Solanaceae) and sheds light on the origins of cultivated million bells","authors":"Alice Backes , Leonardo T. Gonçalves , Pedro H. Pezzi, Loreta B. Freitas","doi":"10.1016/j.ympev.2025.108405","DOIUrl":"10.1016/j.ympev.2025.108405","url":null,"abstract":"<div><div>Phylogenies are essential for understanding evolutionary relationships, testing species boundaries, and defining species status. However, hybridization and incomplete lineage sorting (ILS) can obscure these relationships in recently diversified plant lineages by creating conflicting signals across the genome and reducing phylogenetic resolution. <em>Calibrachoa</em> (million bells), a Neotropical genus of ornamental plants with high ecological diversity, underwent rapid diversification during the Pleistocene, leading to extensive ILS and interspecific hybridization. In this study, we sampled multiple individuals from all recognized species, a potential new species, and a commercial cultivar of <em>Calibrachoa</em>. We used genome-wide genotyping to investigate phylogenetic relationships, species cohesion, hybridization, and the origin of one commercial cultivar. Our results confirm the division of the genus into two subgenera: <em>Calibrachoa</em> sensu stricto and <em>Stimomphis</em>. Within <em>Stimomphis</em>, we observed paraphyly and polyphyly, with low support for several phylogenetic nodes. This uncertainty likely reflects challenges in species delimitation, high ILS due to recent diversification, and ongoing hybridization. We also confirm the hybrid origin of the commercial cultivar. Our findings provide new insights into the evolutionary history of <em>Calibrachoa</em>, improving our understanding of its taxonomy and hybridization dynamics. These results illustrate the need to account for reticulate evolution and ILS when resolving phylogenies in rapidly diversifying plant groups.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108405"},"PeriodicalIF":3.6,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144555943","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 climate-driven range expansion of the antlion tribe Megistopini (Neuroptera: Myrmeleontidae: Nemoleontinae) during the Oligocene-Miocene transition 系统基因组学揭示了渐新世-中新世过渡时期，气候驱动的蚁族Megistopini（神经翅目：Myrmeleontidae: Nemoleontinae）的范围扩张。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-06-29 DOI: 10.1016/j.ympev.2025.108401

Yuchen Zheng , Yuezheng Tu , Xuankun Li , André Nel , Davide Badano , Xingyue Liu

{"title":"Phylogenomics reveals climate-driven range expansion of the antlion tribe Megistopini (Neuroptera: Myrmeleontidae: Nemoleontinae) during the Oligocene-Miocene transition","authors":"Yuchen Zheng , Yuezheng Tu , Xuankun Li , André Nel , Davide Badano , Xingyue Liu","doi":"10.1016/j.ympev.2025.108401","DOIUrl":"10.1016/j.ympev.2025.108401","url":null,"abstract":"<div><div>Myrmeleontidae (antlions and owlflies) represents the most diverse family of Neuroptera (lacewings), while the higher-level classification and evolutionary history has yet been investigated comprehensively. Here we present a comprehensive molecular phylogenetic and biogeographic analysis of the antlion tribe Megistopini, a poorly known group without the well-known pitfall-building larval behavior but primarily inhabiting sand or rock debris, based on Ultraconserved Elements (UCE) data. The monophyly of Megistopini was strongly supported, comprising some genera previously considered as members of Nemoleontini, i.e., Indoleon Banks, 1913, Negrokus Navás, 1930, Paraglenurus van der Weele, 1909, Thaumatoleon <span><span>Esben-Petersen, 1921</span></span>, and Yunleon Yang, 1986. The attribution of Gymnocnemia Schneider, 1845, Nedroledon Navás, 1914 to Megistopini was also confirmed by the molecular analysis. We establish a new genus Himaleon gen. n. to accommodate some species that are classified as incertae sedis within Nemoleontinae, i.e., H. binatus (<span><span>Yang, 1987</span></span>) comb. n., H. cancellosus (<span><span>Yang, 1987</span></span>) comb. n., and H. vartianorum (<span><span>Hölzel, 1972</span></span>) comb. n. Our biogeographic study suggests that Megistopini likely originated in the Zagros-Iranian Plateau-Himalayas-Hengduan Mountains during the mid-Oligocene. Later, the uplift of the Qinghai-Xizang Plateau, along with the surrounding orogenic movements and climatic changes, led to a radiation of Megistopini during the Miocene, which spread in Eurasia. Moreover, our results suggest that the presence of opposable pretarsal claw, a common character in slender-legged antlions, is the ancestral state of Megistopini and was secondarily lost in some genera, also not appearing correlated to habitat choice.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108401"},"PeriodicalIF":3.6,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546313","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

Novel phylogenomic and biogeographic insights into Palaquium and tribe Isonandreae (Sapotaceae) 枇杷科枇杷属和枇杷族的系统发育学和生物地理学新见解。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-06-29 DOI: 10.1016/j.ympev.2025.108403

A. Phang , M.A. Niissalo , L. Herrera-Alsina , F.F. Pezzini , R. Hollands , D.F.R.P. Burslem , M. Ruhsam , D.J. Middleton , P. Wilkie , G.S. Khew

{"title":"Novel phylogenomic and biogeographic insights into Palaquium and tribe Isonandreae (Sapotaceae)","authors":"A. Phang , M.A. Niissalo , L. Herrera-Alsina , F.F. Pezzini , R. Hollands , D.F.R.P. Burslem , M. Ruhsam , D.J. Middleton , P. Wilkie , G.S. Khew","doi":"10.1016/j.ympev.2025.108403","DOIUrl":"10.1016/j.ympev.2025.108403","url":null,"abstract":"<div><div><em>Palaquium</em> is currently the largest genus in the sapodilla family Sapotaceae. Previous studies of relationships within <em>Palaquium</em> and its tribe Isonandreae have been based on limited sampling and loci, which have failed to resolve taxonomic boundaries and hindered the understanding of evolution in this Malesian-centric genus. This study uses high-throughput, target capture DNA sequence data to recover phylogenetic relationships in the most comprehensive near species-level sampling to date (∼80 % of 120 recognised <em>Palaquium</em> species as well as representatives of all seven genera in tribe Isonandreae). The analyses confirm that <em>Palaquium</em> is not monophyletic as currently circumscribed. There is a divergent Asian clade more closely related to the genus <em>Isonandra</em>, and the genus <em>Aulandra</em> is nested within <em>Palaquium</em>. The enhanced phylogenetic dataset provided the opportunity to reconstruct biogeographic history, applying both traditional dispersal-extinction-cladogenesis models and a newer modelling framework that accounts for unrecorded extinctions. The results support previous findings of west to east colonisation in the Malesian archipelago, similar to several other plant groups. Recovered diversification timings of <em>Palaquium</em> and tribe Isonandreae are however older than in previous studies, pointing to a boreotropical vicariant signature and ancestral range possibilities within Sundaland that reconcile more closely to Eocene fossil records. These findings enhance our understanding of biogeographic patterns in the biodiversity-rich and geologically dynamic region of Southeast Asia.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"212 ","pages":"Article 108403"},"PeriodicalIF":3.6,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546312","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

Genomic insights into the reticulate evolution of viviparous Phrynocephalus lizards on the Qinghai-Tibetan Plateau 青藏高原胎生龙头蜥网状进化的基因组研究。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-06-29 DOI: 10.1016/j.ympev.2025.108404

Xianguang Guo , Zhongyi Yao , Bo Cai , Xiao Xiao , Qiwei Xu , Ying Chen , Lin Cui , Xia Qiu , Jinzhong Fu , Yin Qi , Weizhao Yang

{"title":"Genomic insights into the reticulate evolution of viviparous Phrynocephalus lizards on the Qinghai-Tibetan Plateau","authors":"Xianguang Guo , Zhongyi Yao , Bo Cai , Xiao Xiao , Qiwei Xu , Ying Chen , Lin Cui , Xia Qiu , Jinzhong Fu , Yin Qi , Weizhao Yang","doi":"10.1016/j.ympev.2025.108404","DOIUrl":"10.1016/j.ympev.2025.108404","url":null,"abstract":"<div><div>The contribution of hybridization to the speciation and diversification of organisms remains a topic of ongoing debate. While ancient reticulate events have been increasingly recognized as a common feature in evolutionary history of many species, the role of hybridization in driving adaptation, especially in extreme environments, is still unclear. The viviparouslizards present an excellent system to investigate this question, which are distributed across the Qinghai-Tibetan Plateau (QTP) with most species occurring above 2,300 m above sea level. In this study, we employed an integrative approach combining population genetics, phylogenomics and gene flow assessment to unravel the evolutionary history of this clade using genome-wide dataset. Our results revealed a robust phylogenetic relationship between these species with evidence of multiple reticulate events throughout their colonization to the challenging QTP environments. Notably, we found the two highest-altitude species, <em>P. erythrurus</em> and <em>P. theobaldi</em>, received approximately 41% and 14% of their alleles via interspecific gene flow, respectively. Coding genes in these introgressed regions exhibited significantly accelerated evolution, and were over-represented in functions such as “response to temperature stimulus” and “circulatory system process”, including key genes such as <em>ACE</em> and <em>VEGFC</em>, potentially facilitating their adaptation to high-altitude environments. This study suggests the broader relevance of gene flow in shaping evolutionary trajectories of species in extreme environments, and provides novel insights into the understanding of natural hybridization.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108404"},"PeriodicalIF":3.6,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546311","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 of Orthoptera (Insecta) using targeted ultraconserved element data 利用定向超保守元件数据研究直翅目昆虫的系统发育。

IF 3.6 1区生物学

Molecular Phylogenetics and Evolution Pub Date : 2025-06-29 DOI: 10.1016/j.ympev.2025.108402

Jovana M. Jasso-Martínez, Rubén Castañeda-Osorio, Diana A. Mil-Salazar, Karla F. Pintos-Garduño

{"title":"Phylogeny of Orthoptera (Insecta) using targeted ultraconserved element data","authors":"Jovana M. Jasso-Martínez, Rubén Castañeda-Osorio, Diana A. Mil-Salazar, Karla F. Pintos-Garduño","doi":"10.1016/j.ympev.2025.108402","DOIUrl":"10.1016/j.ympev.2025.108402","url":null,"abstract":"<div><div>Target capture of Ultraconserved Elements (UCEs) is a widely used technique in insect phylogenomic research, with various probe sets developed for different insect orders. However, the use of this approach in the order Orthoptera remains unexplored. In this study, we designed a novel probe set to capture UCE loci in Orthoptera by leveraging annotated Orthoptera genomes. Our designed bait set “Orthoptera-UCEbaitset-v1” contains 15,651 probes of 120 bp each, targeting 1,361 UCE loci. We tested our probe set <em>in-silico</em> by identifying and extracting UCE loci from publicly available genomic and transcriptomic datasets of Orthoptera and additionally, provide alternatives for applying the UCE approach to Orthoptera phylogenomics. The resulting phylogeny from the UCE <em>in-silico</em> test was well-supported and highly similar to the current classification for the group, which is supported by various studies employing diverse sources of evidence. In this study we show that the UCE-based approach provides a compelling alternative to exonic-only genomic targeting, as UCEs span exonic, intronic, and intergenic regions, offering a robust and adaptable solution for Orthoptera phylogenomics. Furthermore, the use of well-established methodologies for probe design and UCE loci capture makes this approach both efficient and scalable, which is particularly valuable for Orthoptera, a group known for its challenging genomic characteristics, including the large genome sizes of many species. Nevertheless, it is crucial to consider that a single strategy may not be universally optimal for phylogenomics of this insect group, and that further studies are needed to evaluate and integrate different approaches for advancing phylogenomic research in Orthoptera.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108402"},"PeriodicalIF":3.6,"publicationDate":"2025-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546324","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