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A phylogenomic and morphometric reassessment of Ovulidae highlights host-related shell shape evolution 一项系统基因组学和形态计量学的重新评估突出了与寄主相关的外壳形状进化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-08 DOI: 10.1016/j.ympev.2026.108545
E. Nocella , G. Fassio , T. Lemarcis , P. Zaharias , D. Tamagnini , N. de Leo , N. Puillandre , M.V. Modica , M. Oliverio
The egg-cowries comprise a family of specialised carnivorous caenogastropods (Ovulidae Fleming, 1828) that feed by browsing on octocorals, hexacorals and stylasterid hydrozoans. A recent phylogenetic study, employing a Sanger-based multilocus nucleotide dataset, revealed numerous instances of morphological-molecular incongruence and raised the need for a revision of the current classification. To test alternative hypotheses of ovulid classifications, we applied a phylogenomic approach relying on an Exon-capture methodology to 41 samples from 26 genera and 41 species, representative of the subfamily- and genus-level diversity. Tree reconstructions were performed using both Maximum Likelihood and Bayesian inference methods, resulting in a total of five well-supported subfamily-level clades. The genera Jenneria and Pseudocypraea formed a monophyletic clade, sister to Pedicularia, altogether here considered as forming the subfamily Pediculariinae. The monophyly of Ovulinae was upheld, incorporating Quasisimnia. Prionovolvinae as traditionally recognised proved to be a melting pot of diverse genera and species, including Ovula isibasii, challenging conventional morphology-based classifications. To further investigate morphological variation within Ovulidae, we conducted 2D geometric morphometric analyses to assess shape differences. Groups emerging from Principal Component Analysis (PCA) aligned with the traditional, morphology-based classification. The weak phylogenetic signal associated with the morphometric patterns suggested that phylogeny had only a marginal influence on the morphological evolution of this clade, in contrast to the much stronger role played by host adaptation. This phylogenetic reassessment based on robust genomic data, not only helped to refine our taxonomic framework but also underscores the power of molecular insights in investigating complex evolutionary relationships within families such as the Ovulidae. Furthermore, the morphometric multivariate analysis proved efficient in revealing patterns and addressing eco-evolutionary links.
卵螺是一种专门的肉食性肠胃足类动物(ovuldae Fleming, 1828),它们以八爪珊瑚、六爪珊瑚和花柱类水生动物为食。最近的一项系统发育研究,采用基于sanger的多位点核苷酸数据集,揭示了许多形态-分子不一致的实例,并提出了对当前分类进行修订的必要性。为了验证卵泡分类的其他假设,我们采用基于外显子捕获方法的系统基因组学方法对来自26属和41种的41个样本进行了分析,这些样本代表了亚科和属水平的多样性。使用最大似然和贝叶斯推理方法进行树重建,共得到5个支持良好的亚科级进化枝。Jenneria属和pseudoypraia属形成了一个单系分支,是马先蒿属的姐妹,在这里被认为形成了马先蒿亚科。胚芽科的单一性得到了维持,并合并了准胚芽科。传统上认为的卵黄科是多种属和种的大熔炉,包括卵黄,挑战了传统的基于形态的分类。为了进一步研究紫堇科的形态差异,我们进行了二维几何形态分析来评估形状差异。从主成分分析(PCA)中出现的组与传统的基于形态的分类一致。与形态测量模式相关的微弱系统发育信号表明,系统发育对该支系的形态进化只有微弱的影响,而宿主适应则发挥了更大的作用。这种基于强大的基因组数据的系统发育重新评估,不仅有助于完善我们的分类框架,而且强调了分子洞察力在研究复杂进化关系中的力量,如卵科。此外,形态计量学多变量分析在揭示模式和解决生态进化联系方面被证明是有效的。
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引用次数: 0
Diversity, phylogeny, and biogeography of the subgenus Japonigekko (Gekkonidae: Gekko) 壁虎亚属(壁虎科:壁虎)的多样性、系统发育和生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-07 DOI: 10.1016/j.ympev.2025.108530
Jing Cao , Nikolay A. Poyarkov , Pingfan Wei , Minhua Tie , Tomoya Matsukoji , Chatmongkon Suwannapoom , Renda Ai , Wenzhu Lu , Phuping Sucharitakul , Haotian Wang , Siriwadee Chomdej , Zhiyong Yuan , Fang Yan
The subgenus Japonigekko, a monophyletic lineage, represents the most ecologically and morphologically diverse group within the genus Gekko, with a wide distribution across East Asia. Given the ecological significance and high diversity of Japonigekko, understanding its true species diversity and biogeographic history is crucial for biodiversity conservation in East Asia. However, research on this subgenus remains limited compared to other well-studied vertebrate groups such as mammals and amphibians. In this study, we conducted extensive sampling and integrated molecular data from 34 of the 38 known Japonigekko species using barcoding techniques for 331 samples from 129 sites, systematically elucidating their phylogenetic relationships. Further genomic analysis addressed longstanding taxonomic controversies, revealed previously underestimated species diversity, and clarified the historical biogeography of this group. Ultimately, we identified nine candidate new species. Phylogenetic analyses and ancestral area reconstructions suggest that Japonigekko originated in the Indochina Peninsula and southern China, subsequently dispersing northward and eastward during the Miocene in response to geological events and climatic fluctuations. The recurrent formation and disappearance of land bridges between the mainland and East Asian islands provided critical opportunities for both dispersal and isolation, revealing a unidirectional mainland-to-island dispersal pattern. These findings support to the “Ancient Species Divergence Hypothesis” in East Asia.
壁虎亚属是壁虎属中生态和形态最多样化的类群,在东亚地区分布广泛。鉴于日本虎的生态意义和高度多样性,了解其真实的物种多样性和生物地理历史对东亚生物多样性保护至关重要。然而,与哺乳动物和两栖动物等其他研究充分的脊椎动物群体相比,对这一亚属的研究仍然有限。在本研究中,我们利用条形码技术对已知的38种日本虎中的34种进行了广泛的采样和分子数据整合,系统地阐明了它们的系统发育关系。进一步的基因组分析解决了长期存在的分类学争议,揭示了以前被低估的物种多样性,并澄清了该类群的历史生物地理学。最终,我们确定了9个候选的新物种。系统发育分析和祖先区域重建表明,日本虎起源于印度支那半岛和中国南部,随后在中新世期间因地质事件和气候波动而向北和向东分散。大陆和东亚岛屿之间陆桥的反复形成和消失为扩散和隔离提供了重要机会,揭示了大陆到岛屿的单向扩散模式。这些发现支持了东亚“古物种分化假说”。
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引用次数: 0
UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard genus Barisia (Squamata: Anguidae) UCE系统基因组学揭示了山地墨西哥壁虎属Barisia的造山带变异和渐入形成多样化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-05 DOI: 10.1016/j.ympev.2026.108531
E. Karen López-Estrada , Alejandro Zaldívar-Riverón , Jovana M. Jasso-Martínez , Ernesto Samacá-Sáenz , Jorge Gutiérrez-Rodríguez , Pilar Benites , Valeria B. Salinas-Ramos , John E. McCormack , Robert W. Bryson Jr.
The Mexican Transition Zone is a biogeographic area where the Nearctic and Neotropical regions overlap, encompassing mountain ranges formed during different geological periods. Its complex geological and paleoclimatic history has promoted evolutionary processes such as introgression through hybridization, which can bias phylogenetic inferences and species delimitation. Here, we investigated evolutionary relationships among species of the endemic Mexican lizard genus Barisia using nuclear ultraconserved elements (UCEs). We analyzed samples largely overlapping with a previous study based on mitochondrial DNA (mtDNA) and compared topologies to evaluate mito-nuclear discordance. We also examined population structure, introgression, species boundaries, and biogeographic history of Barisia using molecular dating and ancestral area reconstruction. The strongly supported UCE phylogeny challenges the current species classification of the genus, revealing lineages structured by mountain ranges. Both UCE and previous mtDNA datasets revealed introgression between populations of B. imbricata and B. ciliaris in the southern Central Mexican Plateau and between B. imbricata and B. jonesi in the western Trans-Mexican Volcanic Belt (TMVB), which was further supported by structure and introgression analyses. Our results support the recognition of seven species within Barisia, with the reassignment of populations of B. imbricata, B. ciliaris, and B. jonesi. Overall, diversification within the genus was primarily driven by orogenic vicariance. This study highlights the utility of UCEs for reconstructing robust phylogenies, assessing species limits and genetic structure, as well as to inferring biogeographic patterns.
墨西哥过渡带是一个生物地理区域,新北极和新热带地区重叠,包括不同地质时期形成的山脉。其复杂的地质和古气候历史促进了杂交渗入等进化过程,这可能会影响系统发育推断和物种划分。本文利用核超保守元素(UCEs)研究了墨西哥特有的Barisia蜥蜴属物种间的进化关系。我们分析了与先前基于线粒体DNA (mtDNA)的研究大部分重叠的样本,并比较了拓扑结构以评估mito-nuclear不一致性。利用分子定年和祖先区重建等方法,研究了巴利沙蚤的种群结构、入侵、物种边界和生物地理历史。强有力的支持UCE系统发育挑战了目前属的物种分类,揭示了由山脉结构的谱系。UCE和mtDNA数据均显示,中墨西哥高原南部地区的brbricata和B. ciliaris种群之间以及西部跨墨西哥火山带(TMVB)地区的brbricata和B. jonesi种群之间存在渐近现象,结构和渐近分析进一步支持了这一结论。我们的研究结果支持在Barisia中对7个物种的识别,并重新分配了B. brbricata、B. ciliaris和B. jonesi的种群。总体而言,属内的多样化主要是由造山带变异驱动的。本研究强调了UCEs在重建强健的系统发育、评估物种限制和遗传结构以及推断生物地理模式方面的效用。
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引用次数: 0
Large-scale phylogenomics reveals convergent genome evolution across repeated transitions to endosymbiosis in Enterobacterales 大规模系统基因组学揭示了肠杆菌在重复过渡到内共生过程中的趋同基因组进化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-05 DOI: 10.1016/j.ympev.2026.108532
Giobbe Forni , Jacopo Martelossi , Benoit Morel , Dario Pistone , Claudio Bandi , Matteo Montagna
Symbiogenesis stands among the major transitions in the history of life on Earth. Over the past three decades, extensive research has focused on specific host-symbiont associations to investigate their genome evolution. However, the idiosyncratic sequence evolution of endosymbionts has made it challenging to establish a robust phylogenetic framework for identifying broad-scale evolutionary patterns. Here, we establish the first genome-scale phylogenomic resolution for the Enterobacterales order, encompassing both free-living and endosymbiont species, and provide an analysis of gene loss and acquisition dynamics at scale. By examining over 200 genomes, we show remarkable consistency in phenomena previously known from scattered observations: a spike in gene loss invariably accompanies the shift to endosymbiosis, followed by a slower but continuous rate of gene erosion; gene acquisition processes are reduced after the lifestyle shift. Furthermore, convergence in gene family loss across independent and distantly related symbiotic lineages is observed, with genes having conserved functions and evolving under strong constraints lost at lower rates. Our results unify scattered observations into a broad-scale view of the consequences of endosymbiont genome evolution and highlight the roles of gene essentiality and dispensability in shaping convergent evolutionary trajectories.
共生现象是地球生命史上的重大转变之一。在过去的三十年里,广泛的研究集中在特定的宿主-共生体关联上,以研究它们的基因组进化。然而,内共生体的特殊序列进化使得建立一个强大的系统发育框架来识别大范围的进化模式具有挑战性。在这里,我们建立了肠杆菌目的第一个基因组尺度的系统基因组分辨率,包括自由生活和内共生物种,并提供了大规模的基因丢失和获得动力学分析。通过对200多个基因组的研究,我们发现了先前从分散观察中所知道的现象的显著一致性:基因丢失的峰值总是伴随着向内共生的转变,随后是一个缓慢但持续的基因侵蚀速率;改变生活方式后,基因获取过程减少。此外,在独立的和远亲的共生谱系中观察到基因家族丢失的趋同,具有保守功能和在强约束下进化的基因以较低的速率丢失。我们的研究结果将分散的观察结果统一为内共生体基因组进化后果的广泛观点,并强调了基因的必要性和可有可无在形成趋同进化轨迹中的作用。
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引用次数: 0
Lizards on a sky archipelago: Genomic approaches to the evolution of the mountain genus Iberolacerta 天空群岛上的蜥蜴:山地Iberolacerta属进化的基因组方法
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-04 DOI: 10.1016/j.ympev.2025.108527
Adrián Talavera , Bernat Burriel-Carranza , Gabriel Mochales-Riaño , Maria Estarellas , Oscar Arribas , Héctor Tejero-Cicuéndez , Judit Salces-Ortiz , Daniel Fernández- Guiberteau , Fèlix Amat , Manel Niell , Rosa Fernández , Alexander S. Mikheyev , Salvador Carranza
The mountain-dwelling lizards of the genus Iberolacerta inhabit several isolated massifs across central and southwestern Europe. Their restricted and fragmented ranges, coupled with high altitude specialization in most species, entail a significant threat in the context of climate change for this group of lizards that has attracted interest from different fields. On the one hand, the alpine confinement of these relict species precedes the Pleistocene glacial cycles, and a few hypotheses have been proposed to explain it: from competitive exclusion by the wall lizards of the genus Podarcis, to adaptations to either cold or hypoxia, that would prevent them from expanding into lowlands. On the other hand, extensive research on chromosome evolution has shown Iberolacerta karyotypes to fairly differ from other lacertid lizards, exhibiting reductions in chromosome numbers and multiple sex chromosome determination systems. Here, we present a chromosome-level genome assembly for Iberolacerta aurelioi, an endangered rock lizard endemic to the Pyrenees. This genome has shed light on a genome architecture shaped by chromosome fusions, whose adaptive potential we discuss, as well as on expression shifts towards a hemoglobin isoform of enhanced oxygen affinity, as an adaptation to altitudinal hypoxia. In addition, medium coverage whole-genome sequencing (WGS) data from 12 representatives encompassing all species and subspecies within the genus allowed us to address phylogenomic relationships, unveiling introgression events, gathering evidence in support of the competitive exclusion hypothesis through past demographic inference, and providing insights into homozygosity burdens, which offer valuable information for conservation efforts.
伊比利亚蜥蜴属的山地蜥蜴栖息在欧洲中部和西南部的几个孤立的山体上。它们有限而分散的活动范围,加上大多数物种的高海拔特化,在气候变化的背景下,对这类蜥蜴构成了重大威胁,引起了不同领域的兴趣。一方面,这些遗存物种在更新世冰川循环之前就被限制在高山,有人提出了一些假说来解释这一点:从足蜥属壁蜥的竞争排斥,到适应寒冷或缺氧,这将阻止它们向低地扩张。另一方面,对染色体进化的广泛研究表明,Iberolacerta的核型与其他蜥类相当不同,表现出染色体数量减少和多重性染色体决定系统。在这里,我们提出了一个染色体水平的基因组组装的伊比利牛斯岛特有的濒危岩蜥蜴。该基因组揭示了由染色体融合形成的基因组结构,我们讨论了其适应潜力,以及向增强氧亲和力的血红蛋白同型的表达转变,作为对海拔缺氧的适应。此外,来自该属内所有物种和亚种的12个代表的中等覆盖全基因组测序(WGS)数据使我们能够解决系统基因组关系,揭示渗透事件,通过过去的人口统计学推断收集支持竞争排斥假说的证据,并提供对纯合性负担的见解,为保护工作提供有价值的信息。
{"title":"Lizards on a sky archipelago: Genomic approaches to the evolution of the mountain genus Iberolacerta","authors":"Adrián Talavera ,&nbsp;Bernat Burriel-Carranza ,&nbsp;Gabriel Mochales-Riaño ,&nbsp;Maria Estarellas ,&nbsp;Oscar Arribas ,&nbsp;Héctor Tejero-Cicuéndez ,&nbsp;Judit Salces-Ortiz ,&nbsp;Daniel Fernández- Guiberteau ,&nbsp;Fèlix Amat ,&nbsp;Manel Niell ,&nbsp;Rosa Fernández ,&nbsp;Alexander S. Mikheyev ,&nbsp;Salvador Carranza","doi":"10.1016/j.ympev.2025.108527","DOIUrl":"10.1016/j.ympev.2025.108527","url":null,"abstract":"<div><div>The mountain-dwelling lizards of the genus <em>Iberolacerta</em> inhabit several isolated massifs across central and southwestern Europe. Their restricted and fragmented ranges, coupled with high altitude specialization in most species, entail a significant threat in the context of climate change for this group of lizards that has attracted interest from different fields. On the one hand, the alpine confinement of these relict species precedes the Pleistocene glacial cycles, and a few hypotheses have been proposed to explain it: from competitive exclusion by the wall lizards of the genus <em>Podarcis</em>, to adaptations to either cold or hypoxia, that would prevent them from expanding into lowlands. On the other hand, extensive research on chromosome evolution has shown <em>Iberolacerta</em> karyotypes to fairly differ from other lacertid lizards, exhibiting reductions in chromosome numbers and multiple sex chromosome determination systems. Here, we present a chromosome-level genome assembly for <em>Iberolacerta aurelioi</em>, an endangered rock lizard endemic to the Pyrenees. This genome has shed light on a genome architecture shaped by chromosome fusions, whose adaptive potential we discuss, as well as on expression shifts towards a hemoglobin isoform of enhanced oxygen affinity, as an adaptation to altitudinal hypoxia. In addition, medium coverage whole-genome sequencing (WGS) data from 12 representatives encompassing all species and subspecies within the genus allowed us to address phylogenomic relationships, unveiling introgression events, gathering evidence in support of the competitive exclusion hypothesis through past demographic inference, and providing insights into homozygosity burdens, which offer valuable information for conservation efforts.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108527"},"PeriodicalIF":3.6,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145904201","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
Orogeny and climate change jointly shaped elevational speciation and introgression within Pachygrontha antennata and closely related species (Heteroptera: Pachygronthidae) 造山运动和气候变化共同影响了肿腹蛛及其近缘种(异翅目:肿腹蛛科)在海拔高度的物种形成和进化。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-03 DOI: 10.1016/j.ympev.2025.108529
Kaibin Wang , Ying Wang , Zechen Tang , Xiuxiu Zhu , Cuiqing Gao , Jiayue Zhou , Siying Fu , Wenjun Bu
The formation and evolution of biogeographic processes are shaped by the long-term interplay of multiple biotic and abiotic factors. Compared with the Qinghai–Tibetan Plateau and Himalayas, the Hengduan Mountains region experienced rapid and relatively recent orogenic activity, primarily between the late Miocene to late Pliocene, a period marked by significant climatic change. This makes the Hengduan Mountains an ideal system for investigating how orogeny, climate change, and biological processes collectively influence species divergence and distribution patterns. Using ddRAD-seq data, we reconstructed the divergence history of Pachygrontha antennata and its closely related species. Our results indicate that the speciation of four clearly delineated lineages occurred near the Miocene-Pliocene boundary along the eastern margin of the Qinghai-Tibet Plateau, coinciding with major tectonic events and paleoclimatic oscillations. Orogeny generated diverse ecological niches along elevational gradients, while pronounced climatic shifts facilitated their expansion and colonization. Notably, during interglacial dispersal, populations at the leading edge of the low-elevation species P. antennata came into secondary contact with high-elevation P. sp. along the western margin of the Sichuan Basin. This interaction resulted in bidirectional but asymmetric gene flow, allowing P. antennata to retain ancestral genetic components shared with P. sp. and develop analogous genetic characteristics, which may have enhanced the high-elevation adaptability of the P. antennata population. Overall, our research reveals how abiotic factors—including orogeny and climate change—interact with biotic processes such as adaptive evolution and genetic introgression to shape species divergence and distribution dynamics.
生物地理过程的形成和演化是多种生物和非生物因素长期相互作用的结果。与青藏高原和喜马拉雅地区相比,横断山区的造山活动相对较晚,主要发生在晚中新世至晚上新世,这是一个气候变化显著的时期。这使得横断山脉成为研究造山运动、气候变化和生物过程如何共同影响物种分化和分布格局的理想系统。利用ddRAD-seq数据,重建了触角肿龙(Pachygrontha antennata)及其近缘种的分化历史。结果表明,青藏高原东缘中新世-上新世界线附近出现了四个清晰的物种谱系,与主要的构造事件和古气候振荡相吻合。造山运动沿海拔梯度产生了多种生态位,而明显的气候变化促进了生态位的扩张和定植。值得注意的是,在间冰期的扩散过程中,低海拔物种的前缘种群。天线开始与高海拔地区发生二次接触。沿四川盆地西部边缘生长。这种相互作用导致了双向但不对称的基因流动,使得触角楠保留了与触角楠共享的祖先遗传成分,并发展出类似的遗传特征,这可能增强了触角楠种群的高海拔适应性。总体而言,我们的研究揭示了非生物因素(包括造山运动和气候变化)如何与生物过程(如适应性进化和遗传渗入)相互作用,以塑造物种分化和分布动态。
{"title":"Orogeny and climate change jointly shaped elevational speciation and introgression within Pachygrontha antennata and closely related species (Heteroptera: Pachygronthidae)","authors":"Kaibin Wang ,&nbsp;Ying Wang ,&nbsp;Zechen Tang ,&nbsp;Xiuxiu Zhu ,&nbsp;Cuiqing Gao ,&nbsp;Jiayue Zhou ,&nbsp;Siying Fu ,&nbsp;Wenjun Bu","doi":"10.1016/j.ympev.2025.108529","DOIUrl":"10.1016/j.ympev.2025.108529","url":null,"abstract":"<div><div>The formation and evolution of biogeographic processes are shaped by the long-term interplay of multiple biotic and abiotic factors. Compared with the Qinghai–Tibetan Plateau<!--> <!-->and Himalayas, the Hengduan Mountains region experienced rapid and relatively recent orogenic activity, primarily between the late Miocene to late Pliocene, a period marked by significant climatic change. This makes the Hengduan Mountains an ideal system for investigating how orogeny, climate change, and biological processes collectively influence species divergence and distribution patterns. Using ddRAD-seq data, we reconstructed the divergence history of <em>Pachygrontha antennata</em> and its closely related species. Our results indicate that the speciation of four clearly delineated lineages occurred near the Miocene-Pliocene boundary along the eastern margin of the Qinghai-Tibet Plateau, coinciding with major tectonic events and paleoclimatic oscillations. Orogeny generated diverse ecological niches along elevational gradients, while pronounced climatic shifts facilitated their expansion and colonization. Notably, during interglacial dispersal, populations at the leading edge of<!--> <!-->the low-elevation species<!--> <em>P. antennata</em> <!-->came into secondary contact with high-elevation<!--> <em>P.</em> sp.<!--> <!-->along the western margin of the Sichuan Basin. This<!--> <!-->interaction resulted in bidirectional but asymmetric gene flow, allowing <em>P. antennata</em> to retain ancestral genetic components shared with <em>P.</em> sp.<!--> <!-->and develop analogous genetic characteristics, which may have enhanced the high-elevation adaptability of the <em>P. antennata</em> population. Overall, our research reveals how abiotic factors—including orogeny and climate change—interact with biotic processes such as adaptive evolution and genetic introgression to shape species divergence and distribution dynamics.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"217 ","pages":"Article 108529"},"PeriodicalIF":3.6,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145906752","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
Integrative phylogenetics and geography unveil Quaternary diversification and mitochondrial-nuclear discordance in Odorrana schmackeri sensu lato (Anura, Ranidae): Roles of Qinghai-Tibetan uplift, climate oscillations, and asymmetric gene flow 青藏隆升、气候振荡和不对称基因流的作用:第四纪多样性和线粒体核不一致性的综合系统发育和地理揭示
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2026-01-01 DOI: 10.1016/j.ympev.2025.108528
Yanjun Zhu , Zhuo Chen , Yuxiao He , Xinyue Yang , Xiaofei Zhai , Qiuya Wang , Xiaohong Chen , Xiang Ji
Odorrana schmackeri sensu lato, a group of montane stream-dwelling amphibians in southern China, provides an ideal model for deciphering how Cenozoic geological and climatic dynamics drive cryptic diversification. By integrating mitochondrial 12S/16S rRNA sequences from 1,398 samples spanning 107 populations and genome-wide SNP data from 193 individuals across 18 populations, we reconstruct the geographic structure and speciation history of O. schmackeri sensu lato. Our analyses resolved six evolutionarily distinct lineages in O. schmackeri sensu lato, i.e., Odorrana hejiangensis, Odorrana ichangensis, Odorrana kweichouensis, Odorrana schmackeri, Odorrana tianmuii, and Odorrana huanggangensis. A pronounced east–west geographic break aligned with the stepped topography shaped by Qinghai-Tibetan Plateau uplift, while Late Miocene-Pleistocene climatic oscillations and drainage reorganizations drove lineage diversification through cyclical habitat fragmentation and secondary contact. We observed topological incongruence between mitochondrial and SNP-based phylogenies. Multiple lines of evidence provided strong support for historical gene flow and hybridization events, primarily between O. huanggangensis, O. schmackeri, O. tianmuii, and O. kweichowensis. The initial divergence within O. schmackeri sensu lato dates to the late Miocene, with subsequent speciation events occurring throughout the Pliocene and early Pleistocene. Demographic expansions during the Early Pleistocene facilitated niche differentiation and Ecological Niche Modeling indicated that each species has maintained distinct geographical distributions across different climatic periods (LIG, LGM, Current), with suitable habitats responding differently to Pleistocene climatic fluctuations. This study resolved the taxonomic complexity of O. schmackeri sensu lato and contributed to biogeographic theory by demonstrating how heterogeneous landscapes drive speciation through cyclical isolation, secondary contact, and adaptive radiation.
中国南方山区溪流两栖动物的一群,为解释新生代地质和气候动力学如何驱动隐生多样性提供了一个理想的模型。通过整合107个种群1398个样本的线粒体12S/16S rRNA序列和18个种群193个个体的全基因组SNP数据,重建了沙马基猴(O. schmackeri sensu lato)的地理结构和物种形成历史。通过分析,我们确定了猕猴桃的6个进化谱系,即合江气味、昌味气味、贵州气味、猕猴桃气味、天籁气味和黄冈气味。明显的东西断裂与青藏高原隆起形成的阶梯地形一致,而晚中新世-更新世气候振荡和排水重组通过周期性栖息地破碎化和二次接触推动了谱系多样化。我们观察到线粒体和基于snp的系统发育之间的拓扑不一致。多种证据有力地支持了黄岗O.、schmackeri O.、tianmuii O.和贵州O.之间的历史基因流动和杂交事件。O. schmackeri sensu lato的最初分化可以追溯到中新世晚期,随后的物种形成事件发生在上新世和更新世早期。早更新世的种群扩展促进了生态位的分化,生态位模型表明,各物种在不同气候时期(LIG、LGM、Current)保持了不同的地理分布,适合的栖息地对更新世气候波动的响应不同。本研究通过揭示异质景观如何通过周期性隔离、二次接触和适应性辐射驱动物种形成,解决了沙马基利植物分类的复杂性,并为生物地理学理论做出了贡献。
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引用次数: 0
Polyploid evolution, phylogenetic relationships, and biogeography of sub-Saharan Africa’s only tetraploid fish group – Pseudobarbus and allies (Teleostei: Cyprinidae) 撒哈拉以南非洲唯一的四倍体鱼类群——拟barbus及其同族(拟barbus:鲤科)的多倍体进化、系统发育关系和生物地理学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-21 DOI: 10.1016/j.ympev.2025.108526
Lei Yang , Paul H. Skelton , Gavin J.P. Naylor
The tetraploid smiliogastrines (Pseudobarbus & allies) constitute a small group of cyprinids that are endemic to freshwaters of southern Africa. How and when these polyploids originated has remained a mystery to researchers for years. Their phylogenetic relationships and biogeographical history also need further investigation. In this study, we reconstructed the phylogenetic relationships of this group using DNA sequences from both mitochondrial and nuclear genes. The initial split occurred between Namaquacypris hospes and all other tetraploid smiliogastrines. Amatolacypris is sister to the clade formed by Sedercypris and Cheilobarbus, which are reciprocally monophyletic. The clade formed by these three genera is sister to the monophyletic Pseudobarbus. For the three nuclear genes (i.e., RAG1, IRBP2, and EGR2B) used, we attempted to separate the two gene copies for each gene and each polyploid species. On the phylogenetic trees inferred from individual nuclear genes, one gene copy of Pseudobarbus & allies was clustered with African Enteromius & allies, whereas the other gene copy seen to be more closely related to Asian Puntius & allies. These results suggest that this tetraploid group likely originated through hybridization, although additional nuclear genomic data will be needed to rigorously test this hypothesis. The maternal progenitor of this group is likely a lineage from African Enteromius & allies, while the paternal progenitor likely came from an extinct Asian lineage (“Lineage P”) closely related to Puntius & allies. Our results suggest that the Lineage P might have originated earlier than the common ancestor of all African smiliogastrines. The tetraploid smiliogastrines may have originated at late Paleogene to Eocene (58.9–36.5 Ma). They established themselves in the Orange River and later colonized all major rivers and lakes to the south. During this process, the tetraploid ancestor diverged into the current generic and specific diversity.
四倍体smiliogastrines (Pseudobarbus & allies)是非洲南部淡水特有的一小群鲤科动物。这些多倍体是如何以及何时起源的,多年来一直是研究人员的一个谜。它们的系统发育关系和生物地理历史也有待进一步研究。在这项研究中,我们利用线粒体和核基因的DNA序列重建了这一群体的系统发育关系。最初的分裂发生在Namaquacypris hospes和所有其他四倍体smiliogastres之间。Amatolacypris是由sedercyis和Cheilobarbus组成的分支的姐妹,它们是相互单系的。由这三个属组成的分支是单系假刺属的姐妹。对于使用的三个核基因(RAG1, IRBP2和EGR2B),我们试图对每个基因和每个多倍体物种分离两个基因拷贝。在由单个核基因推断的系统发育树中,Pseudobarbus & allies的一个基因拷贝与非洲Enteromius & allies聚集在一起,而另一个基因拷贝与亚洲puntus & allies的关系更为密切。这些结果表明,这个四倍体群体可能起源于杂交,尽管需要额外的核基因组数据来严格验证这一假设。这个群体的母系祖先可能来自非洲的Enteromius及其盟友,而父系祖先可能来自与Puntius及其盟友密切相关的已灭绝的亚洲谱系(“谱系P”)。我们的研究结果表明,谱系P的起源可能早于所有非洲smiliogastra的共同祖先。四倍体smiliogastres可能起源于晚古近纪至始新世(58.9-36.5 Ma)。他们在奥兰治河建立了自己的殖民地,后来在南部的所有主要河流和湖泊都建立了殖民地。在这一过程中,四倍体祖先分化为现在的属和特异多样性。
{"title":"Polyploid evolution, phylogenetic relationships, and biogeography of sub-Saharan Africa’s only tetraploid fish group – Pseudobarbus and allies (Teleostei: Cyprinidae)","authors":"Lei Yang ,&nbsp;Paul H. Skelton ,&nbsp;Gavin J.P. Naylor","doi":"10.1016/j.ympev.2025.108526","DOIUrl":"10.1016/j.ympev.2025.108526","url":null,"abstract":"<div><div>The tetraploid smiliogastrines (<em>Pseudobarbus</em> &amp; allies) constitute a small group of cyprinids that are endemic to freshwaters of southern Africa. How and when these polyploids originated has remained a mystery to researchers for years. Their phylogenetic relationships and biogeographical history also need further investigation. In this study, we reconstructed the phylogenetic relationships of this group using DNA sequences from both mitochondrial and nuclear genes. The initial split occurred between <em>Namaquacypris hospes</em> and all other tetraploid smiliogastrines. <em>Amatolacypris</em> is sister to the clade formed by <em>Sedercypris</em> and <em>Cheilobarbus</em>, which are reciprocally monophyletic. The clade formed by these three genera is sister to the monophyletic <em>Pseudobarbus</em>. For the three nuclear genes (i.e., RAG1, IRBP2, and EGR2B) used, we attempted to separate the two gene copies for each gene and each polyploid species. On the phylogenetic trees inferred from individual nuclear genes, one gene copy of <em>Pseudobarbus</em> &amp; allies was clustered with African <em>Enteromius</em> &amp; allies, whereas the other gene copy seen to be more closely related to Asian <em>Puntius</em> &amp; allies. These results suggest that this tetraploid group likely originated through hybridization, although additional nuclear genomic data will be needed to rigorously test this hypothesis. The maternal progenitor of this group is likely a lineage from African <em>Enteromius</em> &amp; allies, while the paternal progenitor likely came from an extinct Asian lineage (“Lineage P”) closely related to <em>Puntius</em> &amp; allies. Our results suggest that the Lineage P might have originated earlier than the common ancestor of all African smiliogastrines. The tetraploid smiliogastrines may have originated at late Paleogene to Eocene (58.9–36.5 Ma). They established themselves in the Orange River and later colonized all major rivers and lakes to the south. During this process, the tetraploid ancestor diverged into the current generic and specific diversity.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"216 ","pages":"Article 108526"},"PeriodicalIF":3.6,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822188","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 disentangles the evolutionary and biogeographic uncertainty in Apocissus (Vitaceae) 系统基因组学揭示了天麻属植物在进化和生物地理上的不确定性。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-21 DOI: 10.1016/j.ympev.2025.108525
Alberto J. Coello , Gabriel Johnson , Betsy R. Jackes , Jun Wen
Apocissus is an intriguing small genus in the grape family. It displays a tropical intercontinental disjunction with most species occurring in Australasia, and one in the Americas. Traditionally, its species were part of Cissus, but recent phylogenies have suggested that the Apocissus lineage diverged early from Cissus. Hence, Apocissus was formally described as a new genus, but its evolutionary history remains poorly understood. We herein conduct the first phylogenomic study on Apocissus using target-enriched genomic sequencing. We performed concatenated and coalescent-based analyses using 1,013 targeted nuclear loci of Vitaceae and 245 plastid loci. We assessed the hybridization using SNaQ and obtained a nuclear time-calibrated phylogeny with treePL. The biogeographic reconstructions were then performed with BioGeoBEARS. Nuclear reconstruction recovered the monophyly of Apocissus, and supported it as sister to Cissus, while the hybridization test did not support the hybrid origin of Apocissus. Our time-calibration and biogeographic reconstructions suggest a divergence from Cissus in the late Cretaceous and a later diversification in Australasia during the Oligocene, including a dispersal event from the Australasia to the Americas. Furthermore, our plastome reconstruction shows a close relationship between Cissus penninervis and Apocisssus, supporting the transfer of C. penninervis into Apocissus to ensure the monophyly of both genera. We herein made the taxonomic transfer, Apocissus penninervis (F.Muell.) J.Wen, Jackes & A.J.Coello, comb. nov.
罗经属是葡萄科中一个有趣的小属。它显示出一个热带洲际分离,大多数物种发生在澳大拉西亚,一个在美洲。传统上,它的物种是Cissus的一部分,但最近的系统发育表明,apoissus谱系从Cissus早期分化。因此,罗布森被正式描述为一个新的属,但它的进化历史仍然知之甚少。在此,我们使用目标富集的基因组测序对罗布施进行了首次系统基因组学研究。我们对1013个目标性核位点和245个质体位点进行了串联和聚结分析。我们使用SNaQ评估杂交,并使用treePL获得核时间校准的系统发育。利用biogeobars进行生物地理重建。核重建恢复了天麻的单系性,并支持它是天麻的姐妹株,而杂交试验不支持天麻的杂交起源。我们的时间校准和生物地理重建表明,在晚白垩世从Cissus开始分化,在渐新世在澳大拉西亚开始多样化,包括从澳大拉西亚到美洲的扩散事件。此外,我们的质体重建显示了Cissus penninervis和Apocisssus之间的密切关系,支持Cissus penninervis向Apocissus的转移,以确保两个属的单一性。我们在此进行了分类转移,Apocissus penninervis (F.Muell.)j·文,杰克和a·j·科罗,梳子。11月。
{"title":"Phylogenomics disentangles the evolutionary and biogeographic uncertainty in Apocissus (Vitaceae)","authors":"Alberto J. Coello ,&nbsp;Gabriel Johnson ,&nbsp;Betsy R. Jackes ,&nbsp;Jun Wen","doi":"10.1016/j.ympev.2025.108525","DOIUrl":"10.1016/j.ympev.2025.108525","url":null,"abstract":"<div><div><em>Apocissus</em> is an intriguing small genus in the grape family. It displays a tropical intercontinental disjunction with most species occurring in Australasia, and one in the Americas. Traditionally, its species were part of <em>Cissus</em>, but recent phylogenies have suggested that the <em>Apocissus</em> lineage diverged early from <em>Cissus</em>. Hence, <em>Apocissus</em> was formally described as a new genus, but its evolutionary history remains poorly understood. We herein conduct the first phylogenomic study on <em>Apocissus</em> using target-enriched genomic sequencing. We performed concatenated and coalescent-based analyses using 1,013 targeted nuclear loci of Vitaceae and 245 plastid loci. We assessed the hybridization using SNaQ and obtained a nuclear time-calibrated phylogeny with treePL. The biogeographic reconstructions were then performed with BioGeoBEARS. Nuclear reconstruction recovered the monophyly of <em>Apocissus</em>, and supported it as sister to <em>Cissus</em>, while the hybridization test did not support the hybrid origin of <em>Apocissus</em>. Our time-calibration and biogeographic reconstructions suggest a divergence from <em>Cissus</em> in the late Cretaceous and a later diversification in Australasia during the Oligocene, including a dispersal event from the Australasia to the Americas. Furthermore, our plastome reconstruction shows a close relationship between <em>Cissus penninervis</em> and <em>Apocisssus</em>, supporting the transfer of <em>C. penninervis</em> into <em>Apocissus</em> to ensure the monophyly of both genera. We herein made the taxonomic transfer, <em>Apocissus penninervis</em> (F.Muell.) J.Wen, Jackes &amp; A.J.Coello, comb. nov.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"216 ","pages":"Article 108525"},"PeriodicalIF":3.6,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822102","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, population structure, and conservation genomics of Galapagos vermilion flycatchers (genus Pyrocephalus) 加拉帕戈斯朱蝇属的系统发育、种群结构和保护基因组学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-12-16 DOI: 10.1016/j.ympev.2025.108524
David J. Anchundia , Athena W. Lam , James B. Henderson , Matthew H. Van Dam , Courtney L. Pike , Sabine Tebbich , Birgit Fessl , Heinz Richner , John P. Dumbacher
The Galapagos archipelago in the Eastern Tropical Pacific is known for its isolation, island endemism, and rapid diversification. Despite considerable scientific research many groups remain poorly studied. One of these groups is the genus Pyrocephalus, a group of brightly-colored and charismatic flycatchers whose populations have declined significantly in recent decades. To study the evolution and diversification of Pyrocephalus, we used samples from 53 individuals across 11 Galapagos Islands (Pyrocephalus dubius and P. nanus) and a continental outgroup (P. obscurus) and reconstructed a phylogeny using 233,916 genome-wide SNPs. The data revealed that Pyrocephalus colonized Galapagos earlier than previously estimated, approximately 1.3 million years ago (MYA), and diversified into at least eight genetically distinct clades. These include P. dubius, a species endemic to San Cristobal Island, now extinct, and P. nanus across the remaining islands. The P. nanus population on Floreana Island has been isolated for at least 1.2 MYA, along with additional divergent groups from Santa Cruz, Pinzon + Rabida, Isabela + Fernandina, Santiago, Marchena and Pinta, which have each been isolated for 0.89–0.15 million years. Morphometric, plumage and acoustic comparisons corroborate many of these genetic clades. Specifically for Santa Cruz Island, population genetic analyses indicate a significant reduction in nucleotide diversity, but no evidence of inbreeding, suggesting a minimal recent migration and rapid population decline. Our data on genetic diversification are critical for identifying evolutionary distinct populations and guiding translocations to restore extirpated or diminished island populations.
加拉帕戈斯群岛位于东热带太平洋,以其孤立、岛屿特有和快速多样化而闻名。尽管有大量的科学研究,但对许多群体的研究仍然很少。其中一种是Pyrocephalus属,这是一种色彩鲜艳、魅力十足的捕蝇鸟,其种群数量在最近几十年里显著下降。为了研究Pyrocephalus的进化和多样化,我们使用了来自加拉帕戈斯群岛11个岛屿(Pyrocephalus dubius和P. nanus)和大陆外群(P. obscurus)的53个个体的样本,并使用233,916个全基因组snp重建了系统发育。数据显示,Pyrocephalus在加拉帕戈斯群岛定居的时间比之前估计的要早,大约在130万年前(MYA),并分化成至少8个遗传上不同的分支。其中包括P. dubius,一种圣克里斯托瓦尔岛特有的物种,现在已经灭绝,以及P. nanus遍布其余岛屿。弗洛里亚纳岛上的南猿种群已经分离了至少1.2万年,另外还有来自圣克鲁斯、Pinzon + Rabida、伊莎贝拉 + 费尔南迪纳、圣地亚哥、马尔切纳和平塔的不同种群,它们分别分离了89至15万年。形态计量学、羽毛学和声学比较证实了许多这些遗传分支。特别是在圣克鲁斯岛,种群遗传分析表明核苷酸多样性显著减少,但没有近亲繁殖的证据,这表明最近的迁移很少,种群数量迅速下降。我们关于遗传多样化的数据对于识别进化上不同的种群和指导易位以恢复灭绝或减少的岛屿种群至关重要。
{"title":"Phylogeny, population structure, and conservation genomics of Galapagos vermilion flycatchers (genus Pyrocephalus)","authors":"David J. Anchundia ,&nbsp;Athena W. Lam ,&nbsp;James B. Henderson ,&nbsp;Matthew H. Van Dam ,&nbsp;Courtney L. Pike ,&nbsp;Sabine Tebbich ,&nbsp;Birgit Fessl ,&nbsp;Heinz Richner ,&nbsp;John P. Dumbacher","doi":"10.1016/j.ympev.2025.108524","DOIUrl":"10.1016/j.ympev.2025.108524","url":null,"abstract":"<div><div>The Galapagos archipelago in the Eastern Tropical Pacific is known for its isolation, island endemism, and rapid diversification. Despite considerable scientific research many groups remain poorly studied. One of these groups is the genus <em>Pyrocephalus</em>, a group of brightly-colored and charismatic flycatchers whose populations have declined significantly in recent decades. To study the evolution and diversification of <em>Pyrocephalus</em>, we used samples from 53 individuals across 11 Galapagos Islands (<em>Pyrocephalus dubius</em> and <em>P. nanus</em>) and a continental outgroup (<em>P. obscurus</em>) and reconstructed a phylogeny using 233,916 genome-wide SNPs. The data revealed that <em>Pyrocephalus</em> colonized Galapagos earlier than previously estimated, approximately 1.3 million years ago (MYA), and diversified into at least eight genetically distinct clades. These include <em>P. dubius</em>, a species endemic to San Cristobal Island, now extinct, and <em>P. nanus</em> across the remaining islands. The <em>P. nanus</em> population on Floreana Island has been isolated for at least 1.2 MYA, along with additional divergent groups from Santa Cruz, Pinzon + Rabida, Isabela + Fernandina, Santiago, Marchena and Pinta, which have each been isolated for 0.89–0.15 million years. Morphometric, plumage and acoustic comparisons corroborate many of these genetic clades. Specifically for Santa Cruz Island, population genetic analyses indicate a significant reduction in nucleotide diversity, but no evidence of inbreeding, suggesting a minimal recent migration and rapid population decline. Our data on genetic diversification are critical for identifying evolutionary distinct populations and guiding translocations to restore extirpated or diminished island populations.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"216 ","pages":"Article 108524"},"PeriodicalIF":3.6,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145783765","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
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Molecular Phylogenetics and Evolution
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