Molecular Phylogenetics and Evolution最新文献_第7页

Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae) 杂交和不完全谱系分选是两个东亚茶属分支的进化历史特征。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-09-17 DOI: 10.1016/j.ympev.2025.108472

Han-Yang Lin , Miao Sun , Jian-Jun Jin , Cheng-Xin Fu , Douglas E. Soltis , Pamela S. Soltis , Yun-Peng Zhao

Reticulate evolution and recalcitrant phylogenetic relationships are common in the East Asian evergreen broad-leaved forests (EA-EBLFs),. Hybridization and incomplete lineage sorting (ILS) can both occur during diversification of these forests, yet the extent of ILS has often been overlooked. Among floristic elements in the EA-EBLFs, plant genera that are disjunctly distributed between eastern Asia and eastern North America (EA-ENA disjuncts) provide an excellent system to explore the magnitude of hybridization and ILS after vicariance and long-distance dispersal. Here, we investigated the evolutionary history of Stewartia L. (Theaceae), one of the EA-ENA disjuncts whose major members inhabit the EA-EBLFs (ca. 20 spp. in EA vs. two spp. in ENA) using target enrichment sequence data obtained from Angiosperms353. Based on nearly complete taxon sampling, we recovered two Stewartia clades (the EA deciduous and evergreen clades) in the EA-EBLFs. Our estimates indicate that these two clades started to diversify in the late Miocene, and the evergreen clade showed a higher diversification rate than the deciduous clade. The SNaQ and NANUQ analyses detected hybridization signals within both clades, primarily involving S. serrata and S. tonkinensis, respectively. In addition, the QuIBL analysis revealed co-occurring introgression and ILS in 98/105 and 318/360 tested triplets (Δ BIC < − 10) in the deciduous and evergreen clades, respectively. The Phytop analysis further supported ILS as the primary source of gene-tree discordance. Our study reveals complex phylogenetic and evolutionary patterns in EA-EBLF endemics and highlights the importance of hybridization and ILS in this region.

在东亚常绿阔叶林（EA-EBLFs）中，网状进化和顽固性系统发育关系是常见的。在这些森林中，杂交和不完全谱系分选（ILS）都可能在多样化过程中发生，但不完全谱系分选的程度往往被忽视。东亚-北美东部地区的植物属（EA-ENA disjuncts）是研究东亚-北美东部地区植物杂交和ILS程度的一个很好的系统。本文利用从被子植物（Angiosperms353）中获得的靶富集序列数据，研究了茶属植物（Stewartia L., Theaceae）的进化历史。茶属植物是EA-ENA分离科植物之一，其主要成员位于EA- eblfs中（EA约20种，ENA约2种）。通过几乎完整的分类群取样，我们在EA- eblf中恢复了两个Stewartia分支（EA落叶分支和常绿分支）。结果表明，这两个进化支在中新世晚期开始多样化，常绿进化支的多样化率高于落叶进化支。SNaQ和NANUQ分析在两个分支中检测到杂交信号，主要涉及S. serrata和S. tonkinensis。此外，QuIBL分析显示，在98/105和318/360测试的三胞胎中，基因渗入和ILS共同发生(Δ BIC

{"title":"Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae)","authors":"Han-Yang Lin , Miao Sun , Jian-Jun Jin , Cheng-Xin Fu , Douglas E. Soltis , Pamela S. Soltis , Yun-Peng Zhao","doi":"10.1016/j.ympev.2025.108472","DOIUrl":"10.1016/j.ympev.2025.108472","url":null,"abstract":"<div><div>Reticulate evolution and recalcitrant phylogenetic relationships are common in the East Asian evergreen broad-leaved forests (EA-EBLFs),. Hybridization and incomplete lineage sorting (ILS) can both occur during diversification of these forests, yet the extent of ILS has often been overlooked. Among floristic elements in the EA-EBLFs, plant genera that are disjunctly distributed between eastern Asia and eastern North America (EA-ENA disjuncts) provide an excellent system to explore the magnitude of hybridization and ILS after vicariance and long-distance dispersal. Here, we investigated the evolutionary history of <em>Stewartia</em> L. (Theaceae), one of the EA-ENA disjuncts whose major members inhabit the EA-EBLFs (ca. 20 spp. in EA vs. two spp. in ENA) using target enrichment sequence data obtained from Angiosperms353. Based on nearly complete taxon sampling, we recovered two <em>Stewartia</em> clades (the EA deciduous and evergreen clades) in the EA-EBLFs. Our estimates indicate that these two clades started to diversify in the late Miocene, and the evergreen clade showed a higher diversification rate than the deciduous clade. The SNaQ and NANUQ analyses detected hybridization signals within both clades, primarily involving <em>S. serrata</em> and <em>S. tonkinensis</em>, respectively. In addition, the QuIBL analysis revealed co-occurring introgression and ILS in 98/105 and 318/360 tested triplets (Δ BIC < − 10) in the deciduous and evergreen clades, respectively. The Phytop analysis further supported ILS as the primary source of gene-tree discordance. Our study reveals complex phylogenetic and evolutionary patterns in EA-EBLF endemics and highlights the importance of hybridization and ILS in this region.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108472"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093139","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

An integrated framework for evolution of ciliated protists (Protista, Ciliophora) from the perspective of comparative genomics 比较基因组学视角下纤毛原生生物（Protista, Ciliophora）进化的综合框架。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-09-05 DOI: 10.1016/j.ympev.2025.108468

Yuexin Wang , Didi Jin , Xiaopeng Hou , Khaled A.S. Al-Rasheid , Chen Shao , Tengteng Zhang

Early-branching eukaryotes are associated with the early branching events during eukaryogenesis. Understanding their genomic diversity and evolution can provide insights into the origin and speciation of eukaryotes. Ciliated protists (ciliates) are a group of early-branching unicellular eukaryotes with a high biodiversity, making them excellent models for evolutionary studies. However, their genomic diversity and evolution remain insufficiently understood. In this study, the comparative genomic and phylogenomic analyses were conducted using well-annotated macronuclear genomes from 16 bulk-cultured ciliates across four major classes. Our results indicate that: a) ciliates exhibit significant genomic diversity, with genome sizes ranging from 18.4 Mb to 117.1 Mb, extensive stop codon rearrangements, and tens of thousands of nanochromosomes in Spirotrichea and Litostomatea, reflecting dynamic genome architecture and adaptive evolution; b) gene family expansions highlight divergent evolutionary trajectories among ciliate classes, with Heterotrichea enhancing cell division capacity and Spirotrichea focusing on signal transduction; c) phylogenetic and structural analyses of meiosis related zinc finger protein and calcium channel related calmodulin gene families indicate that they predate the divergence of ciliates with functional diversification; d) anaerobic Entodinium caudatum retains abundant ubiquitin-related genes, while halotolerant Fabrea salina enriches anaphase-promoting complex cofactors (a crucial E3 ubiquitin ligase), suggesting that the encystment might be enhanced for both species. In summary, we systematically investigated the genomic landscape of ciliates to broaden our understanding of the genomic diversity and evolutionary patterns of ciliates.

早期分支真核生物与真核发生过程中的早期分支事件有关。了解它们的基因组多样性和进化可以为真核生物的起源和物种形成提供见解。纤毛虫原生生物（Ciliated protists，简称纤毛虫）是一类具有高度生物多样性的早期分支单细胞真核生物，是进化研究的优秀模型。然而，它们的基因组多样性和进化仍然没有得到充分的了解。在这项研究中，使用来自4个主要分类的16只批量培养的纤毛虫的大核基因组进行了比较基因组学和系统基因组学分析。结果表明：a)纤毛虫具有显著的基因组多样性，其基因组大小在18.4 Mb至117.1 Mb之间，具有广泛的停止密码子重排和数万条纳米染色体，反映了动态的基因组结构和适应性进化；b)基因家族扩展突出了不同纤毛虫类的进化轨迹，异毛虫增强细胞分裂能力，螺毛虫专注于信号转导；C)与减数分裂相关的锌指蛋白和钙通道相关的钙调蛋白基因家族的系统发育和结构分析表明，它们早于具有功能多样化的纤毛虫的分化；d)厌氧尾状内胆保留了丰富的泛素相关基因，而耐盐Fabrea salina则丰富了促进后期的复杂辅助因子（一种至关重要的E3泛素连接酶），这表明两种物种的包囊可能都得到了增强。综上所述，我们系统地研究了纤毛虫的基因组景观，以扩大我们对纤毛虫基因组多样性和进化模式的理解。

{"title":"An integrated framework for evolution of ciliated protists (Protista, Ciliophora) from the perspective of comparative genomics","authors":"Yuexin Wang , Didi Jin , Xiaopeng Hou , Khaled A.S. Al-Rasheid , Chen Shao , Tengteng Zhang","doi":"10.1016/j.ympev.2025.108468","DOIUrl":"10.1016/j.ympev.2025.108468","url":null,"abstract":"<div><div>Early-branching eukaryotes are associated with the early branching events during eukaryogenesis. Understanding their genomic diversity and evolution can provide insights into the origin and speciation of eukaryotes. Ciliated protists (ciliates) are a group of early-branching unicellular eukaryotes with a high biodiversity, making them excellent models for evolutionary studies. However, their genomic diversity and evolution remain insufficiently understood. In this study, the comparative genomic and phylogenomic analyses were conducted using well-annotated macronuclear genomes from 16 bulk-cultured ciliates across four major classes. Our results indicate that: a) ciliates exhibit significant genomic diversity, with genome sizes ranging from 18.4 Mb to 117.1 Mb, extensive stop codon rearrangements, and tens of thousands of nanochromosomes in Spirotrichea and Litostomatea, reflecting dynamic genome architecture and adaptive evolution; b) gene family expansions highlight divergent evolutionary trajectories among ciliate classes, with Heterotrichea enhancing cell division capacity and Spirotrichea focusing on signal transduction; c) phylogenetic and structural analyses of meiosis related zinc finger protein and calcium channel related calmodulin gene families indicate that they predate the divergence of ciliates with functional diversification; d) anaerobic <em>Entodinium caudatum</em> retains abundant ubiquitin-related genes, while halotolerant <em>Fabrea salina</em> enriches anaphase-promoting complex cofactors (a crucial E3 ubiquitin ligase), suggesting that the encystment might be enhanced for both species. In summary, we systematically investigated the genomic landscape of ciliates to broaden our understanding of the genomic diversity and evolutionary patterns of ciliates.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108468"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145014485","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

Isolation and divergence of Greater Earless Lizards (Phrynosomatidae: Cophosaurus) in western North America support multiple diversification processes and a complex demographic history 北美西部大无耳蜥蜴的分离和分化支持多重多样化过程和复杂的人口历史。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-08-15 DOI: 10.1016/j.ympev.2025.108442

Christopher Blair , Carlos J. Pavón-Vázquez , Qaantah Rana , Keaka Farleigh , Erika Crispo , Thomas Panzera , Felipe de Medeiros Magalhães , Britt White , Uri Omar Garcia-Vazquez

The Southwestern US and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (Cophosaurus texanus) to examine diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population genomic and phylogenomic analyses support the existence of multiple lineages of C. texanus, with divergence following a southeast to northwest pattern. The geographic distribution of lineages, coupled with estimated divergence times, suggest a complex evolutionary history shaped by a combination of geomorphological shifts and ecological divergence in the Neogene. Our results also support the existence of a biogeographic barrier at the Continental Divide dating to the Pleistocene and the importance of isolation by distance. Migration rates between lineages are low, and multiple species delimitation analyses further support the distinctiveness of lineages. Species tree analyses show that C. texanus texanus is nested within lineages of C. texanus scitulus, supporting the hypothesis that this system may constitute a species complex in need of revision. In sum, we find evidence for multiple processes influencing lineage divergence, indicating that additional multipronged phylogeographic studies using genomic data are needed on diverse, widespread taxa throughout arid western North America.

美国西南部和墨西哥北部仍然是研究影响谱系多样化的一系列生态和进化过程的理想地区。北美干旱地区复杂的地质历史，加上更新世时期的古气候变化和不同的生态区域，使得多管齐下的假设检验方法成为必要。我们将来自大无耳蜥蜴（Cophosaurus texanus）基因分型测序（GBS）方法的数千个位点与线粒体DNA （mtDNA）序列相结合，以检查多样性并测试隐种群结构。我们还在贝叶斯框架中应用最近开发的聚结方法来估计迁移率。种群基因组学和系统基因组学分析表明，该植物存在多支系，分化方向由东南向西北。谱系的地理分布，加上估计的分化时间，表明在新近纪，地貌变化和生态分化共同塑造了一个复杂的进化史。我们的研究结果还支持了更新世大陆分水岭生物地理屏障的存在，以及距离隔离的重要性。谱系之间的迁移率很低，多物种划分分析进一步支持了谱系的独特性。物种树分析表明，texanus texanus是在texanus scitulus的谱系中嵌套的，这支持了该系统可能构成一个需要修正的物种复合体的假设。总之，我们发现了影响谱系分化的多种过程的证据，表明需要对北美西部干旱地区广泛分布的多样化分类群进行更多的多管齐下的系统地理学研究。

{"title":"Isolation and divergence of Greater Earless Lizards (Phrynosomatidae: Cophosaurus) in western North America support multiple diversification processes and a complex demographic history","authors":"Christopher Blair , Carlos J. Pavón-Vázquez , Qaantah Rana , Keaka Farleigh , Erika Crispo , Thomas Panzera , Felipe de Medeiros Magalhães , Britt White , Uri Omar Garcia-Vazquez","doi":"10.1016/j.ympev.2025.108442","DOIUrl":"10.1016/j.ympev.2025.108442","url":null,"abstract":"<div><div>The Southwestern US and northern Mexico continue to serve as ideal regions to elucidate the suite of ecological and evolutionary processes influencing lineage diversification. The complex geological history of arid North America, coupled with paleoclimate change during the Pleistocene and diverse ecoregions makes a multipronged approach to hypothesis testing necessary. We combine thousands of loci from a genotyping-by-sequencing (GBS) approach along with mitochondrial DNA (mtDNA) sequences from the Greater Earless Lizard (<em>Cophosaurus texanus</em>) to examine diversity and test for cryptic population structure. We also apply recently developed coalescent approaches in a Bayesian framework to estimate migration rates. Population genomic and phylogenomic analyses support the existence of multiple lineages of <em>C. texanus</em>, with divergence following a southeast to northwest pattern. The geographic distribution of lineages, coupled with estimated divergence times, suggest a complex evolutionary history shaped by a combination of geomorphological shifts and ecological divergence in the Neogene. Our results also support the existence of a biogeographic barrier at the Continental Divide dating to the Pleistocene and the importance of isolation by distance. Migration rates between lineages are low, and multiple species delimitation analyses further support the distinctiveness of lineages. Species tree analyses show that <em>C. texanus texanus</em> is nested within lineages of <em>C. texanus scitulus</em>, supporting the hypothesis that this system may constitute a species complex in need of revision. In sum, we find evidence for multiple processes influencing lineage divergence, indicating that additional multipronged phylogeographic studies using genomic data are needed on diverse, widespread taxa throughout arid western North America.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108442"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876971","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

Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes 北美泥蛇和彩虹蛇的更新世物种形成和距离隔离。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-10-16 DOI: 10.1016/j.ympev.2025.108482

Edward A. Myers , Alexander D. McKelvy , Dirk J. Stevenson , Frank T. Burbrink

Understanding phylogeographic structure is a key step in examining the processes related to lineage divergence and speciation. It is often expected that wide-ranging taxa will be composed of deeply divergent lineages and that codistributed species will have similar population genetic structure. Within the southeastern coastal plain of North America, a biodiversity hotspot, the evolutionary processes that have led to the accumulation of diversity are underexplored. Several process within this region could be responsible for species diversification, including past changes in climate, fluctuating sea levels, and the formation of river systems. However, it is also possible that a pattern of isolation-by-distance can explain population genetic structure found in widely distributed species, which can serve as a null hypothesis for observed genetic structure. We generate a reduced representation genomic dataset with population level sampling for two sister species of snakes endemic to the southeastern coastal plain, the mudsnakes and rainbow snakes (Farancia abacura and F. erytrogramma, respectively). With these data we find a strong signal of population divergence in F. abacura, while isolation-by-distance alone explains genetic divergence in F. erytrogramma. We also identify several genomic regions associated with environmental variation that may be key to local adaptation. Lastly, we find that the best fit demographic model includes gene flow during the initial divergence of these two species. This model also suggests that there is current unidirectional gene flow from the eastern F. abacura lineage into F. erytrogramma. However, the two F. abacura lineages appear to be reproductively isolated. We suggest further comparative phylogeographic work to understand the full suite of evolutionary processes driving diversification and endemism in the southeastern coastal plain.

了解系统地理结构是研究谱系分化和物种形成过程的关键步骤。人们通常认为，广泛分布的分类群将由深度分化的谱系组成，而共分布的物种将具有相似的种群遗传结构。在生物多样性热点地区北美东南沿海平原，导致生物多样性积累的进化过程尚未得到充分探索。该地区的几个过程可能导致物种多样化，包括过去的气候变化、海平面波动和河流系统的形成。然而，距离隔离模式也有可能解释分布广泛的物种中发现的群体遗传结构，这可以作为观察到的遗传结构的零假设。我们对东南沿海平原特有的两种姐妹蛇——泥蛇和彩虹蛇（分别为Farancia abacura和F. erytrogramma）——进行种群水平采样，生成了一个简化的代表性基因组数据集。通过这些数据，我们发现了abacura种群分化的强烈信号，而单靠距离隔离解释了F. erytrogramma的遗传分化。我们还确定了与环境变化相关的几个基因组区域，这些区域可能是局部适应的关键。最后，我们发现最适合的人口统计学模型包含了这两个物种在初始分化过程中的基因流动。该模型还表明，目前存在从东部abacura谱系到F. erytrogramma的单向基因流动。然而，这两个abacura谱系似乎是生殖隔离的。我们建议进一步开展比较系统地理学工作，以了解东南沿海平原驱动多样性和地方性的整套进化过程。

{"title":"Pleistocene speciation and isolation-by-distance within North American mud and rainbow snakes","authors":"Edward A. Myers , Alexander D. McKelvy , Dirk J. Stevenson , Frank T. Burbrink","doi":"10.1016/j.ympev.2025.108482","DOIUrl":"10.1016/j.ympev.2025.108482","url":null,"abstract":"<div><div>Understanding phylogeographic structure is a key step in examining the processes related to lineage divergence and speciation. It is often expected that wide-ranging taxa will be composed of deeply divergent lineages and that codistributed species will have similar population genetic structure. Within the southeastern coastal plain of North America, a biodiversity hotspot, the evolutionary processes that have led to the accumulation of diversity are underexplored. Several process within this region could be responsible for species diversification, including past changes in climate, fluctuating sea levels, and the formation of river systems. However, it is also possible that a pattern of isolation-by-distance can explain population genetic structure found in widely distributed species, which can serve as a null hypothesis for observed genetic structure. We generate a reduced representation genomic dataset with population level sampling for two sister species of snakes endemic to the southeastern coastal plain, the mudsnakes and rainbow snakes (<em>Farancia abacura</em> and <em>F. erytrogramma</em>, respectively). With these data we find a strong signal of population divergence in <em>F. abacura</em>, while isolation-by-distance alone explains genetic divergence in <em>F. erytrogramma</em>. We also identify several genomic regions associated with environmental variation that may be key to local adaptation. Lastly, we find that the best fit demographic model includes gene flow during the initial divergence of these two species. This model also suggests that there is current unidirectional gene flow from the eastern <em>F. abacura</em> lineage into <em>F. erytrogramma</em>. However, the two <em>F. abacura</em> lineages appear to be reproductively isolated. We suggest further comparative phylogeographic work to understand the full suite of evolutionary processes driving diversification and endemism in the southeastern coastal plain.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108482"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318985","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

Incomplete lineage sorting, hybridization and polyploidization blurred phylogenetic relationships of gentians from the Qinghai-Tibetan Plateau

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-10-05 DOI: 10.1016/j.ympev.2025.108476

Shan-Shan Sun , Shu-Han Xu , Wen-Jie Yi , Shi-Long Chen , Pan Li , Daiki Takahashi , Harue Abe , Xiao-Lei Ma , Peng-Cheng Fu

Resolving evolutionary relationships among species undergoing radiation is challenging. Gentiana is a species-rich genus with a sub-cosmopolitan distribution, in which several sections have undergone recent radiation. In this study, we reassessed the phylogeny of Gentiana with particular focus on the controversial section Kudoa, and elucidated the complex phylogenetic relationship as well as their underlying causes in this section. Combining with a large number of single-copy orthologous genes and complete chloroplast genome sequences, we revised the delimitation of sections Kudoa and Isomeria, and proposed a new section Uniflorae. Our results suggested that G. yakushimensis, one of the most controversial species in Gentiana, should be transferred from section Kudoa to Pneumonanthe. The revised section Kudoa comprised two morphologically distinct series, and was composed of five genetic clades, with one clade corresponding to series Verticilatae. Although the backbone of Kudoa phylogeny was clear, current genetic data were insufficient to clarify species boundaries for several species. Evidence from single-copy orthologous genes and genome-wide SNPs revealed widespread hybridization against a background of extensive incomplete lineage sorting (ILS) in section Kudoa, accounting for the gene tree discordance. Genome size data indicated that tetraploids occurred in three out of the five clades, demonstrating that polyploidization further complicated the phylogeny of section Kudoa. In summary, Gentiana comprises 14 sections under our revised classification, and ILS, hybridization and polyploidization collectively contributed to the phylogenetic ambiguity of section Kudoa.

解决受辐射的物种之间的进化关系是具有挑战性的。龙胆属是一个种类丰富的属，具有亚世界性分布，其中几个部分经历了最近的辐射。在本研究中，我们重新评估了龙胆属的系统发育，特别是对有争议的Kudoa区段进行了重点研究，并阐明了该区段复杂的系统发育关系及其潜在原因。结合大量的单拷贝同源基因和完整的叶绿体基因组序列，我们修改了Kudoa和Isomeria的划分，并提出了一个新的Uniflorae分类。结果表明，龙胆属最具争议种之一的yakushimensis应该从Kudoa区转移到Pneumonanthe区。修订后的Kudoa由两个形态上不同的系列组成，由5个遗传支系组成，其中一个支系对应于Verticilatae系列。虽然Kudoa系统发育的主干是明确的，但目前的遗传数据不足以明确一些物种的物种边界。来自单拷贝同源基因和全基因组snp的证据显示，Kudoa区段广泛存在不完全谱系分类（ILS）背景下的广泛杂交，这是基因树不一致的原因。基因组大小数据显示，5个分支中有3个发生了四倍体，表明多倍体化进一步使Kudoa分支的系统发育复杂化。综上所述，龙胆属在修订后的分类中包括14个区段，而ILS、杂交和多倍体化共同导致了Kudoa区段的系统发育不明确。

{"title":"Incomplete lineage sorting, hybridization and polyploidization blurred phylogenetic relationships of gentians from the Qinghai-Tibetan Plateau","authors":"Shan-Shan Sun , Shu-Han Xu , Wen-Jie Yi , Shi-Long Chen , Pan Li , Daiki Takahashi , Harue Abe , Xiao-Lei Ma , Peng-Cheng Fu","doi":"10.1016/j.ympev.2025.108476","DOIUrl":"10.1016/j.ympev.2025.108476","url":null,"abstract":"<div><div>Resolving evolutionary relationships among species undergoing radiation is challenging. <em>Gentiana</em> is a species-rich genus with a sub-cosmopolitan distribution, in which several sections have undergone recent radiation. In this study, we reassessed the phylogeny of <em>Gentiana</em> with particular focus on the controversial section <em>Kudoa</em>, and elucidated the complex phylogenetic relationship as well as their underlying causes in this section. Combining with a large number of single-copy orthologous genes and complete chloroplast genome sequences, we revised the delimitation of sections <em>Kudoa</em> and <em>Isomeria</em>, and proposed a new section <em>Uniflorae</em>. Our results suggested that <em>G. yakushimensis</em>, one of the most controversial species in <em>Gentiana</em>, should be transferred from section <em>Kudoa</em> to <em>Pneumonanthe</em>. The revised section <em>Kudoa</em> comprised two morphologically distinct series, and was composed of five genetic clades, with one clade corresponding to series <em>Verticilatae</em>. Although the backbone of <em>Kudoa</em> phylogeny was clear, current genetic data were insufficient to clarify species boundaries for several species. Evidence from single-copy orthologous genes and genome-wide SNPs revealed widespread hybridization against a background of extensive incomplete lineage sorting (ILS) in section <em>Kudoa</em>, accounting for the gene tree discordance. Genome size data indicated that tetraploids occurred in three out of the five clades, demonstrating that polyploidization further complicated the phylogeny of section <em>Kudoa</em>. In summary, <em>Gentiana</em> comprises 14 sections under our revised classification, and ILS, hybridization and polyploidization collectively contributed to the phylogenetic ambiguity of section <em>Kudoa</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108476"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145246028","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

Phylogenetic reconstruction of African weakly electric fish (Campylomormyrus spp.) is suggestive of ancient introgression events 非洲弱电鱼（Campylomormyrus spp.）的系统发育重建提示了古代的遗传渗入事件。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-08-25 DOI: 10.1016/j.ympev.2025.108452

Julia Canitz , Frank Kirschbaum , David L.J. Vendrami , Victor Mamonekene , Ralph Tiedemann

The African weakly electric fish genus Campylomormyrus belongs to the species-rich family Mormyridae and comprises 15 described species. Previous species trees that focus on the genus, have included at most ten species. The resulting phylogenies have been used to explain the evolution of the species-specific electrical organ discharge (EOD) and interpreted in the context of sympatric speciation caused by disruptive selection. However, available molecular phylogenies that are focused on the Campylomormyrus genus rely only on a limited number of genetic markers. Here, we used ddRAD sequencing to genotype 65 individuals from twelve Campylomormyrus species and Gnathonemus petersii at more than 8,000 SNPs. We reconstruct a robust species tree that is suggestive of ancient introgression events between different species, which might affect both genetic and trait variability in the genus. Different levels of genetic and EOD diversity in two significant Campylomormyrus clades reveals that i) certain species might be in early stages of their speciation process, ii) that hybridization/introgression occurs in mormyrids and iii) that EOD-related genes could be potential speciation genes. Our genomic approach demonstrates the significance of these findings in understanding the evolution of Campylomormyrus.

非洲弱电鱼属Campylomormyrus属于种类丰富的Mormyridae家族，包括15个已描述的物种。以前着重于属的种树，最多包括10个物种。由此产生的系统发生被用来解释物种特异性电器官放电（EOD）的进化，并在由破坏性选择引起的同域物种形成的背景下进行解释。然而，现有的弯曲菌属分子系统发育只依赖于有限数量的遗传标记。在这里，我们使用ddRAD测序对来自12种弯曲菌和petergnathonemus的65个个体进行了超过8000个snp的基因型分析。我们重建了一个健壮的物种树，这暗示了不同物种之间的古老渗入事件，这可能会影响属的遗传和性状变异。在两个重要的弯曲菌分支中，不同水平的遗传和EOD多样性表明，i)某些物种可能处于物种形成过程的早期阶段，ii)杂交/渐渗发生在形态中，iii) EOD相关基因可能是潜在的物种形成基因。我们的基因组方法证明了这些发现对理解弯曲菌进化的重要性。

{"title":"Phylogenetic reconstruction of African weakly electric fish (Campylomormyrus spp.) is suggestive of ancient introgression events","authors":"Julia Canitz , Frank Kirschbaum , David L.J. Vendrami , Victor Mamonekene , Ralph Tiedemann","doi":"10.1016/j.ympev.2025.108452","DOIUrl":"10.1016/j.ympev.2025.108452","url":null,"abstract":"<div><div>The African weakly electric fish genus <em>Campylomormyrus</em> belongs to the species-rich family Mormyridae and comprises 15 described species. Previous species trees that focus on the genus, have included at most ten species. The resulting phylogenies have been used to explain the evolution of the species-specific electrical organ discharge (EOD) and interpreted in the context of sympatric speciation caused by disruptive selection. However, available molecular phylogenies that are focused on the <em>Campylomormyrus</em> genus rely only on a limited number of genetic markers. Here, we used ddRAD sequencing to genotype 65 individuals from twelve <em>Campylomormyrus</em> species and <em>Gnathonemus petersii</em> at more than 8,000 SNPs. We reconstruct a robust species tree that is suggestive of ancient introgression events between different species, which might affect both genetic and trait variability in the genus. Different levels of genetic and EOD diversity in two significant <em>Campylomormyrus</em> clades reveals that i) certain species might be in early stages of their speciation process, ii) that hybridization/introgression occurs in mormyrids and iii) that EOD-related genes could be potential speciation genes. Our genomic approach demonstrates the significance of these findings in understanding the evolution of <em>Campylomormyrus</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108452"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phylogenomics of an early-branching clade of Orthocladiinae (Diptera: Chironomidae) 正枝蝇科早期分支分支的系统基因组学研究（双翅目：手蛾科）。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-09-30 DOI: 10.1016/j.ympev.2025.108477

Hai-Feng Xu , Zhi-Chao Zhang , Dan Zhang , Viktor Baranov , Chen-Hong Li , Xiao-Long Lin

The early-branching clade of Orthocladiinae and Prodiamesinae represent ancient, highly diverse, and ecologically adaptable key groups within Chironomidae (Diptera). Their larvae are widely distributed in freshwater ecosystems and serve as core bioindicators for water quality monitoring. However, due to historically incomplete geographical sampling and insufficient resolution of molecular markers, the taxonomic status of Prodiamesinae and the phylogenetic relationships among several problematic genera within the early-branching clade of Orthocladiinae have remained unresolved. This study systematically selected representative species from Prodiamesinae and the early-branching clade of Orthocladiinae to construct a highly confident molecular phylogenetic framework using universal single-copy orthologous nuclear genomic data. Key findings include: Prodiamesinae should be subsumed within Orthocladiinae, forming a sister group with Propsilocerus and treated as a synonym of Orthocladiinae (= Prodiamesinae syn. n.); the phylogenetic relationships among the early-branching clade of Orthocladiinae have been conclusively resolved; the origin of Orthocladiinae sensu lato (including Prodiamesinae and the early-branching clade of Orthocladiinae) dates back to the Early-Middle Jurassic (ca. 199–165 million years ago). These results reshape the higher-level classification system of Chironomidae, providing a reliable taxonomic foundation and evolutionary framework for future studies.

正枝蝇科和原枝蝇科的早期分支分支是手蛾科（双翅目）中古老、多样性高、生态适应性强的关键类群。其幼虫广泛分布于淡水生态系统中，是水质监测的核心生物指标。然而，由于历史上地理采样的不完整和分子标记的解析不足，原枝科的分类地位以及在正枝科早期分支分支中几个问题属之间的系统发育关系仍未得到解决。本研究系统地选择了原齿亚科和正齿亚科早期分支分支的代表性物种，利用通用的单拷贝同源核基因组数据构建了一个高度可信的分子系统发育框架。主要发现包括：Prodiamesinae应归入正枝亚科，与prosilocerus形成姊妹类群，并被视为正枝亚科的同义词（= Prodiamesinae synn .）；正枝目早期分支分支之间的系统发育关系得到了最终的解决；正枝虫科（包括原枝虫科和正枝虫科的早期分支分支）的起源可以追溯到早中侏罗世（约1.99 - 1.65亿年前）。这些结果重塑了手蛾科的高级分类体系，为今后的研究提供了可靠的分类学基础和进化框架。

{"title":"Phylogenomics of an early-branching clade of Orthocladiinae (Diptera: Chironomidae)","authors":"Hai-Feng Xu , Zhi-Chao Zhang , Dan Zhang , Viktor Baranov , Chen-Hong Li , Xiao-Long Lin","doi":"10.1016/j.ympev.2025.108477","DOIUrl":"10.1016/j.ympev.2025.108477","url":null,"abstract":"<div><div>The early-branching clade of Orthocladiinae and Prodiamesinae represent ancient, highly diverse, and ecologically adaptable key groups within Chironomidae (Diptera). Their larvae are widely distributed in freshwater ecosystems and serve as core bioindicators for water quality monitoring. However, due to historically incomplete geographical sampling and insufficient resolution of molecular markers, the taxonomic status of Prodiamesinae and the phylogenetic relationships among several problematic genera within the early-branching clade of Orthocladiinae have remained unresolved. This study systematically selected representative species from Prodiamesinae and the early-branching clade of Orthocladiinae to construct a highly confident molecular phylogenetic framework using universal single-copy orthologous nuclear genomic data. Key findings include: Prodiamesinae should be subsumed within Orthocladiinae, forming a sister group with <em>Propsilocerus</em> and treated as a synonym of Orthocladiinae (= Prodiamesinae <strong>syn. n.</strong>); the phylogenetic relationships among the early-branching clade of Orthocladiinae have been conclusively resolved; the origin of Orthocladiinae <em>sensu lato</em> (including Prodiamesinae and the early-branching clade of Orthocladiinae) dates back to the Early-Middle Jurassic (<em>ca.</em> 199–165 million years ago). These results reshape the higher-level classification system of Chironomidae, providing a reliable taxonomic foundation and evolutionary framework for future studies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108477"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214482","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

Widespread incongruence in the phylogenomics of the ancient land plant lineage, Selaginellaceae (lycophytes) 古代陆地植物谱系卷柏科（石松类）系统基因组学的广泛不一致。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-09-04 DOI: 10.1016/j.ympev.2025.108454

Jing Zhao , Hong Yu , Carl J. Rothfels , Jian-Jun Yang , Shao-Li Fang , Zhao-Rong He , Li-Bing Zhang , Xin-Mao Zhou

The advent of high-throughput genomic sequencing has provided unprecedented access to genome-scale data. This deluge of data has yielded new insights into phylogenetic relationships across the tree of life. However, incongruent results arising from different data partitions or from the use of different analyses have often been overlooked or insufficiently explored. In this study, we analyze the transcriptomes and plastomes of Selaginellaceae, an important land plant lineage and an ideal system to thoroughly explore phylogenomic incongruence. We aimed to reconstruct the most likely phylogenetic relationships in Selaginaceae and to examine the underlying causes of incongruence using various tests. Our major findings include: (1) phylogenomic incongruence in Selaginellaceae is quite common; (2) some plastid genes did not evolve as a linked unit, different from what is generally thought in vascular plants; (3) quantifying phylogenetic signal across different sites and genes that cause significant incongruence is necessary in phylogenomic analysis; (4) cytonuclear discordance and gene-tree conflict can be explained by incomplete lineage sorting, hybridization, and unique plastome traits; and (5) the most likely relationships “true tree” based on different datasets and phylogenetic analyses within Selaginellaceae are (Selaginoidoideae, (Boreoselaginelloideae, (Gymnogynoideae, (Sinoselaginelloideae, (Pulvinielloideae, (Lycopodioidoideae + Selaginelloideae))))). The data-analysis workflows established here might offer a framework for future phylogenomic studies for other complicated lineages.

高通量基因组测序的出现为获取基因组规模数据提供了前所未有的途径。海量的数据让我们对整个生命之树的系统发育关系有了新的认识。然而，由于不同的数据分区或使用不同的分析而产生的不一致的结果往往被忽视或没有得到充分的探讨。在这项研究中，我们分析了卷柏科的转录组和质体组，这是一个重要的陆地植物谱系，也是一个彻底探索系统基因组不一致的理想系统。我们的目的是重建最可能的系统发育关系在柏树科和检查不一致的潜在原因使用各种测试。主要发现有：(1)卷柏科植物系统发育不一致现象较为普遍；(2)一些质体基因没有作为一个连接的单位进化，这与维管植物中普遍认为的不同；(3)在系统基因组分析中，对不同位点和基因间的系统发育信号进行量化是必要的；(4)细胞核不一致和基因树冲突可以通过不完整的谱系分类、杂交和独特的质体性状来解释；（5)基于不同的数据集和系统发育分析，卷柏科内最可能的亲缘关系“真树”是（Selaginoidoideae）、（boreoselagineloideae、（Gymnogynoideae）、（sinoselagineloideae、（pulvinieloideae、（Lycopodioidoideae + ）））））)。这里建立的数据分析工作流程可能为未来其他复杂谱系的系统基因组研究提供一个框架。

{"title":"Widespread incongruence in the phylogenomics of the ancient land plant lineage, Selaginellaceae (lycophytes)","authors":"Jing Zhao , Hong Yu , Carl J. Rothfels , Jian-Jun Yang , Shao-Li Fang , Zhao-Rong He , Li-Bing Zhang , Xin-Mao Zhou","doi":"10.1016/j.ympev.2025.108454","DOIUrl":"10.1016/j.ympev.2025.108454","url":null,"abstract":"<div><div>The advent of high-throughput genomic sequencing has provided unprecedented access to genome-scale data. This deluge of data has yielded new insights into phylogenetic relationships across the tree of life. However, incongruent results arising from different data partitions or from the use of different analyses have often been overlooked or insufficiently explored. In this study, we analyze the transcriptomes and plastomes of Selaginellaceae, an important land plant lineage and an ideal system to thoroughly explore phylogenomic incongruence. We aimed to reconstruct the most likely phylogenetic relationships in Selaginaceae and to examine the underlying causes of incongruence using various tests. Our major findings include: (1) phylogenomic incongruence in Selaginellaceae is quite common; (2) some plastid genes did not evolve as a linked unit, different from what is generally thought in vascular plants; (3) quantifying phylogenetic signal across different sites and genes that cause significant incongruence is necessary in phylogenomic analysis; (4) cytonuclear discordance and gene-tree conflict can be explained by incomplete lineage sorting, hybridization, and unique plastome traits; and (5) the most likely relationships “true tree” based on different datasets and phylogenetic analyses within Selaginellaceae are (Selaginoidoideae, (Boreoselaginelloideae, (Gymnogynoideae, (Sinoselaginelloideae, (Pulvinielloideae, (Lycopodioidoideae + Selaginelloideae))))). The data-analysis workflows established here might offer a framework for future phylogenomic studies for other complicated lineages.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108454"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008676","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

Diversification in Amazonian Hypocnemis antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs) 从超保守元件（UCEs）推断亚马孙地区矮蚁蚁的多样性（鸟类：蚁科）

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-08-31 DOI: 10.1016/j.ympev.2025.108456

Áurea Cronemberger , Camila C. Ribas , Alexandre Aleixo

Warbling antbirds consist of an avian genus (Hypocnemis) with a wide distribution, confined to the Amazon basin, and whose true diversity and evolutionary history remain poorly understood. Here, we used sequences of 2,222 Ultra-conserved Elements (UCEs) and 30 exons loci from 58 specimens belonging to all currently recognized Hypocnemis species and all but one subspecies to infer phylogenies, population structure, interspecific limits, and the genus’ biogeographic history. A consensus of phylogenies, networks, and phylogeographic structure analyses recovered up to thirteen independent evolutionary units within the genus, which currently has eight named species. Except for one case, these lineages corroborate currently recognized taxa; based on our analyses, we propose the recognition of two additional species in the genus: H. implicata and H. ochraceiventris. From a biogeographic perspective, our estimated scenarios indicate separation of the two main Hypocnemis lineages during the Miocene, subsequent concentration of Pliocene splits in western and northern Amazonia, and more recent Pleistocene diversification in the southeastern part of the basin. Lineage relationships in the southeastern group are complex, and support a pattern whereby lineages in close contact on the Brazilian shield are not each other’s closest relatives. This pattern challenges simplistic biogeographic interpretations and suggests that independent range-expansion and admixture events, local extinction, and even behavioral attributes under strong divergent selection, may be coupled with vicariant scenarios.

鸣唱蚁鸟是一种鸟类属，分布广泛，局限于亚马逊盆地，其真正的多样性和进化历史仍然知之甚少。在此，我们利用来自58个标本的2222个超保守元件（UCEs）和30个外显子位点的序列来推断该属的系统发育、种群结构、种间界限和生物地理历史。系统发育、网络和系统地理结构分析的共识在该属中恢复了多达13个独立的进化单位，目前有8个已命名的物种。除了一个例子外，这些谱系证实了目前公认的分类群；基于我们的分析，我们建议在该属中识别另外两个种：H. implicata和H. ochraceiventris。从生物地理学的角度来看，我们估计的情景表明，中新世两个主要的低洼洼谱系分离，随后在亚马逊河西部和北部集中了上新世的分裂，而在盆地东南部更近的更新世多样化。东南族群的血统关系是复杂的，并且支持一种模式，即在巴西盾上密切接触的血统不是彼此的近亲。这一模式挑战了简单的生物地理学解释，表明独立的范围扩张和混合事件、局部灭绝，甚至是强分化选择下的行为属性，都可能与替代情景相结合。

{"title":"Diversification in Amazonian Hypocnemis antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs)","authors":"Áurea Cronemberger , Camila C. Ribas , Alexandre Aleixo","doi":"10.1016/j.ympev.2025.108456","DOIUrl":"10.1016/j.ympev.2025.108456","url":null,"abstract":"<div><div>Warbling antbirds consist of an avian genus (<em>Hypocnemis</em>) with a wide distribution, confined to the Amazon basin, and whose true diversity and evolutionary history remain poorly understood. Here, we used sequences of 2,222 Ultra-conserved Elements (UCEs) and 30 exons loci from 58 specimens belonging to all currently recognized <em>Hypocnemis</em> species and all but one subspecies to infer phylogenies, population structure, interspecific limits, and the genus’ biogeographic history. A consensus of phylogenies, networks, and phylogeographic structure analyses recovered up to thirteen independent evolutionary units within the genus, which currently has eight named species. Except for one case, these lineages corroborate currently recognized taxa; based on our analyses, we propose the recognition of two additional species in the genus: <em>H. implicata</em> and <em>H. ochraceiventris</em>. From a biogeographic perspective, our estimated scenarios indicate separation of the two main <em>Hypocnemis</em> lineages during the Miocene, subsequent concentration of Pliocene splits in western and northern Amazonia, and more recent Pleistocene diversification in the southeastern part of the basin. Lineage relationships in the southeastern group are complex, and support a pattern whereby lineages in close contact on the Brazilian shield are not each other’s closest relatives. This pattern challenges simplistic biogeographic interpretations and suggests that independent range-expansion and admixture events, local extinction, and even behavioral attributes under strong divergent selection, may be coupled with vicariant scenarios.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108456"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933764","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

Spatio-temporal evolution of shrub willows (Salix subgenus Vetrix clade) on a global scale 全球尺度下灌木柳树亚属的时空演化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2026-01-01 Epub Date: 2025-10-17 DOI: 10.1016/j.ympev.2025.108480

Pia Marinček , Jing Vir Leong , Loic Pittet , Ètienne Léveillé-Bourret , Tommi Nyman , Maria Tomoshevich , Evgeny Banaev , Li He , Elvira Hörandl , Martin Volf , Natascha D. Wagner

The spatio-temporal evolution of woody plant lineages in the Holarctic is still understudied, limiting our understanding of evolutionary processes that promote higher diversity at higher latitudes in some lineages, which contradicts the latitudinal gradient hypothesis which predicts higher species richness in the tropics. Shrub willows (Salix subgenus Vetrix) comprise about 350 species of which many are adapted to arctic-alpine ecosystems and thus form an important element across the Holarctic region. In this study, we utilized RAD sequencing to estimate the spatio-temporal evolution of the Vetrix clade based on about 140 species covering most of its morphological and geographical diversity. The resolved phylogeny revealed four lineages: the Pan-Himalayan clade, the North American clade and two clades containing species from Eurasia. Widespread circumpolar species form a hybridogenetic grade between the Eurasian and North American clades. Our results confirm that shrub willows originated in the Tertiary, probably in Asia, and that diversification coincided with the climatic cooling in the Pleistocene. At least two radiations were observed, in the Pan Himalayas and in North America. Speciation was further shaped by migration and dispersal in Eurasia, likely accelerated by the uplift of mountain chains, the closure of the Turgai Strait and expansion of suitable habitats. The dated phylogeny revealed that speciation of arctic lineages predates adaptation to high latitudes, as also evident from the fossil record. Small wind-dispersed seeds enabled shrub willows to colonize the expanding arctic tundra regions in the Miocene and their recolonization after the LGM. Given the high observed number of polyploid species equally distributed in all clades and indications of genetic admixture, we assume that species diversity in shrub willows was additionally increased by hybridization and polyploidization.

全北极地区木本植物谱系的时空演化研究尚不充分，这限制了我们对某些谱系在高纬度地区促进更高物种多样性的进化过程的理解，这与预测热带地区物种丰富度更高的纬度梯度假说相矛盾。灌木柳树（柳树亚属）包括约350种，其中许多适应北极-高山生态系统，因此形成整个全北极地区的重要组成部分。在本研究中，我们利用RAD测序方法对覆盖其大部分形态和地理多样性的约140种Vetrix支系进行了时空演化估算。解决的系统发育揭示了四个分支：泛喜马拉雅分支，北美分支和两个包含欧亚物种的分支。广泛分布的环极物种形成欧亚和北美分支之间的杂交进化等级。我们的研究结果证实，灌木柳树起源于第三纪，可能在亚洲，并且多样化与更新世气候变冷相吻合。在泛喜马拉雅和北美至少观测到两次辐射。欧亚大陆的迁徙和分散进一步塑造了物种形成，可能是由于山脉的隆起、图尔盖海峡的关闭和适宜栖息地的扩大而加速的。确定年代的系统发育表明，北极谱系的物种形成早于对高纬度地区的适应，这一点也从化石记录中得到了证明。风吹散的小种子使灌木柳树能够在中新世殖民不断扩大的北极苔原地区，并在LGM之后重新殖民。鉴于观察到的多倍体物种数量多，分布均匀，且存在遗传混杂现象，我们认为杂交和多倍体化增加了灌木柳树的物种多样性。

{"title":"Spatio-temporal evolution of shrub willows (Salix subgenus Vetrix clade) on a global scale","authors":"Pia Marinček , Jing Vir Leong , Loic Pittet , Ètienne Léveillé-Bourret , Tommi Nyman , Maria Tomoshevich , Evgeny Banaev , Li He , Elvira Hörandl , Martin Volf , Natascha D. Wagner","doi":"10.1016/j.ympev.2025.108480","DOIUrl":"10.1016/j.ympev.2025.108480","url":null,"abstract":"<div><div>The spatio-temporal evolution of woody plant lineages in the Holarctic is still understudied, limiting our understanding of evolutionary processes that promote higher diversity at higher latitudes in some lineages, which contradicts the latitudinal gradient hypothesis which predicts higher species richness in the tropics. Shrub willows (<em>Salix</em> subgenus <em>Vetrix</em>) comprise about 350 species of which many are adapted to arctic-alpine ecosystems and thus form an important element across the Holarctic region. In this study, we utilized RAD sequencing to estimate the spatio-temporal evolution of the <em>Vetrix</em> clade based on about 140 species covering most of its morphological and geographical diversity. The resolved phylogeny revealed four lineages: the Pan-Himalayan clade, the North American clade and two clades containing species from Eurasia. Widespread circumpolar species form a hybridogenetic grade between the Eurasian and North American clades. Our results confirm that shrub willows originated in the Tertiary, probably in Asia, and that diversification coincided with the climatic cooling in the Pleistocene. At least two radiations were observed, in the Pan Himalayas and in North America. Speciation was further shaped by migration and dispersal in Eurasia, likely accelerated by the uplift of mountain chains, the closure of the Turgai Strait and expansion of suitable habitats. The dated phylogeny revealed that speciation of arctic lineages predates adaptation to high latitudes, as also evident from the fossil record. Small wind-dispersed seeds enabled shrub willows to colonize the expanding arctic tundra regions in the Miocene and their recolonization after the LGM. Given the high observed number of polyploid species equally distributed in all clades and indications of genetic admixture, we assume that species diversity in shrub willows was additionally increased by hybridization and polyploidization.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108480"},"PeriodicalIF":3.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145330835","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