Molecular Phylogenetics and Evolution最新文献_第8页

Little treasures hidden in the darkness: diversity and phylogeny of stygobiotic hydrobiidae (Mollusca: Gastropoda) of the Caucasus 隐藏在黑暗中的小宝藏：高加索地区茎生水螅科（软体动物：腹足类）的多样性和系统发育。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-14 DOI: 10.1016/j.ympev.2025.108439

Elizaveta Chertoprud , Irina Ekimova , Dmitry Palatov , Jozef Grego , Levan Mumladze , Maxim Vinarski

Hydrobiidae is the most diverse and species-rich freshwater gastropod family in the Palearctic. Their diversity in the Caucasus region remains largely unexplored and the phylogenetic relationships with European taxa have not been clarified yet. The primary objective of this study is to perform a molecular phylogenetic analysis of the stygobiotic Hydrobiidae of the Caucasus with an increased taxon sampling and incorporation of multiple molecular markers. We show that the Caucasian hydrobiids are represented by three distinct lineages of a subfamily rank: (1) Caucasopsiinae subfam.nov., comprises most of the stygobiotic hydrobiid genera endemic to Caucasus; (2) Belgrandiellinae includes a single stygobiotic genus Sitnikovia and a complex of crenobiotic genera; (3) Islamiinae is represented by a single monotypic genus. The Caucasian stygobiotic hydrobiids are represented by 13 genera, five of which were identified as new for science, and at least 37 species, including a significant number (20 species) of putative new taxa. Analysis of the soft-body anatomy revealed that the female reproductive system showed the best congruence with the phylogenetic relationships. Shell morphology showed high variability at both inter- and intrageneric level, questioning the generic assignment of species based on empty shells. The Caucasian stygobiotic Hydrobiidae show high endemism at all taxonomical levels from species to subfamilies, which probably reflects their long evolution in relative isolation from the hydrobiid clades inhabiting other regions.

水螅科是古北洋淡水腹足类动物中种类最丰富的一类。它们在高加索地区的多样性仍未得到充分研究，与欧洲分类群的系统发育关系也尚未明确。本研究的主要目的是通过增加分类单元采样和结合多种分子标记，对高加索地区的茎生水生生物进行分子系统发育分析。结果表明，高加索水合生物可分为三个不同的亚科谱系：1)高加索水合生物亚科（Caucasopsiinae）。它包括高加索特有的大部分茎生水生生物属；2) bel桔梗科包括一个单一的茎生属Sitnikovia和一个复合的茎生属；3) Islamiinae为单一的单型属。高加索地区有13个属，其中5个属为科学新发现，至少有37种，其中包括大量（20种）推定的新分类群。软体解剖分析表明，雌性生殖系统与系统发育关系最吻合。壳形态在种间和种内水平上都表现出高度的变异，这对基于空壳的种属分配提出了质疑。从种到亚科的所有分类水平上，高加索的水生生物都表现出高度的地方性，这可能反映了它们与其他地区的水生生物分支相对隔离的长期进化。

{"title":"Little treasures hidden in the darkness: diversity and phylogeny of stygobiotic hydrobiidae (Mollusca: Gastropoda) of the Caucasus","authors":"Elizaveta Chertoprud , Irina Ekimova , Dmitry Palatov , Jozef Grego , Levan Mumladze , Maxim Vinarski","doi":"10.1016/j.ympev.2025.108439","DOIUrl":"10.1016/j.ympev.2025.108439","url":null,"abstract":"<div><div>Hydrobiidae is the most diverse and species-rich freshwater gastropod family in the Palearctic. Their diversity in the Caucasus region remains largely unexplored and the phylogenetic relationships with European taxa have not been clarified yet. The primary objective of this study is to perform a molecular phylogenetic analysis of the stygobiotic Hydrobiidae of the Caucasus with an increased taxon sampling and incorporation of multiple molecular markers. We show that the Caucasian hydrobiids are represented by three distinct lineages of a subfamily rank: (1) Caucasopsiinae <strong>subfam.nov.</strong>, comprises most of the stygobiotic hydrobiid genera endemic to Caucasus; (2) Belgrandiellinae includes a single stygobiotic genus <em>Sitnikovia</em> and a complex of crenobiotic genera; (3) Islamiinae is represented by a single monotypic genus. The Caucasian stygobiotic hydrobiids are represented by 13 genera, five of which were identified as new for science, and at least 37 species, including a significant number (20 species) of putative new taxa. Analysis of the soft-body anatomy revealed that the female reproductive system showed the best congruence with the phylogenetic relationships. Shell morphology showed high variability at both inter- and intrageneric level, questioning the generic assignment of species based on empty shells. The Caucasian stygobiotic Hydrobiidae show high endemism at all taxonomical levels from species to subfamilies, which probably reflects their long evolution in relative isolation from the hydrobiid clades inhabiting other regions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108439"},"PeriodicalIF":3.6,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144862739","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

Population dynamics and evolutionary history of the genus Sakesphorus (Aves: Thamnophilidae) in the Amazonian floodplains 亚马逊河漫滩沙蝇属的种群动态与进化历史

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-14 DOI: 10.1016/j.ympev.2025.108435

Waleska Barbosa , Romina Batista , Eduardo D. Schultz , Camila C. Ribas

The genus Sakesphorus (Aves: Thamnophilidae) includes two species that are floodplain specialists within Amazonia. While S. luctuosus occupies floodplains of southeastern Amazonia and extends south along riparian habitats in central Brazil, S. canadensis occupies northern Amazonian floodplains and extends to other habitat types in northern South America, including mangroves, deciduous forests, and savannas. We reconstruct the historical diversification of the genus to investigate the landscape history of the Amazonian floodplains and their relationships with adjacent environments. We used reduced representation genomic data obtained with Ultra conserved Elements (UCE) probes and mtDNA from 26 S. canadensis and 30 S. luctuosus individuals. The phylogenetic analyses recovered each species as a well-supported clade. The split between the two species dates to 2.67 Ma (CI: 1.66–3.91), with a crown age of 620 Kya (CI: 0.37–0.91) for S. canadensis and 330 (CI: 0.2–0.49) Kya for S. luctuosus. Sakesphorus canadensis comprises three populations with low migration rates between them. Demographic expansion was unequivocal only for the Branco River population (S. c. fumosus), suggesting an association with the evolution of the Branco River drainage. Pleistocene diversification of the genus corroborates the dynamism of the Amazonian fluvial system during this period, affecting connectivity along Amazonian floodplains and driving population differentiation. Connectivity with adjacent biomes through riparian corridors was important for the evolution of Amazonian floodplain biodiversity and should be protected.

Sakesphorus属（鸟类：Thamnophilidae）包括两个物种，它们是亚马逊河流域洪泛区的专家。虽然S. luctuosus占据了亚马逊东南部的洪泛平原，并沿着巴西中部的河岸栖息地向南延伸，但S. canadensis占据了亚马逊北部的洪泛平原，并扩展到南美洲北部的其他栖息地类型，包括红树林、落叶林和稀树草原。我们重建了该属的历史多样性，以研究亚马逊洪泛区的景观历史及其与邻近环境的关系。我们使用超保守元件（Ultra conservative Elements， UCE）探针和mtDNA从26个加拿大S. canadensis和30个S. luctuosus个体中获得的简化代表性基因组数据。系统发育分析恢复了每个物种作为一个良好支持的分支。两种间的分裂时间为2.67 Ma (CI: 1.66 ~ 3.91)，其中加拿大杉的树冠年龄为620 Kya (CI: 0.37 ~ 0.91)， luctuosus的树冠年龄为330 Kya （CI: 0.2 ~ 0.49）。加拿大Sakesphorus包括三个种群，它们之间的迁移率很低。只有布兰科河种群（S. c. fumosus）的人口扩张是明确的，这表明与布兰科河流域的演变有关。该属的更新世多样化证实了这一时期亚马逊河流系统的活力，影响了亚马逊漫滩沿线的连通性，并推动了种群分化。通过河岸走廊与邻近生物群落的连通性对亚马逊洪泛区生物多样性的演变至关重要，应予以保护。

{"title":"Population dynamics and evolutionary history of the genus Sakesphorus (Aves: Thamnophilidae) in the Amazonian floodplains","authors":"Waleska Barbosa , Romina Batista , Eduardo D. Schultz , Camila C. Ribas","doi":"10.1016/j.ympev.2025.108435","DOIUrl":"10.1016/j.ympev.2025.108435","url":null,"abstract":"<div><div>The genus <em>Sakesphorus</em> (Aves: Thamnophilidae) includes two species that are floodplain specialists within Amazonia. While <em>S. luctuosus</em> occupies floodplains of southeastern Amazonia and extends south along riparian habitats in central Brazil, <em>S. canadensis</em> occupies northern Amazonian floodplains and extends to other habitat types in northern South America, including mangroves, deciduous forests, and savannas. We reconstruct the historical diversification of the genus to investigate the landscape history of the Amazonian floodplains and their relationships with adjacent environments. We used reduced representation genomic data obtained with Ultra conserved Elements (UCE) probes and mtDNA from 26 <em>S. canadensis</em> and 30 <em>S. luctuosus</em> individuals. The phylogenetic analyses recovered each species as a well-supported clade. The split between the two species dates to 2.67 Ma (CI: 1.66–3.91), with a crown age of 620 Kya (CI: 0.37–0.91) for <em>S. canadensis</em> and 330 (CI: 0.2–0.49) Kya for <em>S. luctuosus</em>. <em>Sakesphorus canadensis</em> comprises three populations with low migration rates between them. Demographic expansion was unequivocal only for the Branco River population (<em>S. c. fumosus)</em>, suggesting an association with the evolution of the Branco River drainage. Pleistocene diversification of the genus corroborates the dynamism of the Amazonian fluvial system during this period, affecting connectivity along Amazonian floodplains and driving population differentiation. Connectivity with adjacent biomes through riparian corridors was important for the evolution of Amazonian floodplain biodiversity and should be protected.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108435"},"PeriodicalIF":3.6,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852538","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

Reticulate evolution in terrestrial snails of Euhadra peliomphala species complex 陆生蜗牛种群的网状进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-13 DOI: 10.1016/j.ympev.2025.108437

Yasuto Ishii , Shun Ito , Yuichi Kameda , Tsuyoshi Takano , Tsukasa Waki , Satoshi Chiba , Takahiro Hirano

Recent studies have shown the significant role of introgression in evolution, yet the confident evidence of introgression has come from biased taxa. Although the Mollusca were representative taxa to show introgression-driven evolution, conclusive examination has been rare. Here, we investigated the genetic structure and evolutionary history of terrestrial snails in the Euhadra peliomphala species complex (Heterobranchia: Camaenidae). We collected 197 individuals from 196 sites in Japan, covering the entire distribution, and obtained genome-wide single nucleotide polymorphisms (SNPs) using double digest restriction site-associated DNA sequencing. The population genetic analysis showed that the study individuals are clustered into 12 lineages, which are distributed parapatrically. Our hybrid test detected hybrid zones between several pairs of the lineages. Additionally, we reconstructed a phylogenetic network of these lineages and detected three reticulate events, including introgression from an extinct lineage. The ages of the introgression events suggests that geological activity and climate change were involved. We also found human-induced introgression. Overall, the present research showed a highly reticulated evolutionary history of the E. peliomphala species complex, and provided confident evidence of introgression in terrestrial snails. This study should play a major role as a basis for further research on introgression-driven evolution within the E. peliomphala species complex.

近年来的研究表明，基因渗入在进化过程中起着重要的作用，但基因渗入的可靠证据来自有偏见的分类群。虽然软体动物是表现渐渗驱动进化的代表性类群，但结论性的研究很少。本文研究了陆生钉螺的遗传结构和进化历史。我们从日本196个位点收集了197个个体，覆盖了整个分布，并使用双消化限制性内切位点相关DNA测序获得了全基因组单核苷酸多态性（snp）。群体遗传分析表明，研究个体可聚为12个类群，类群分布近似于类群。我们的杂交试验在几对世系之间发现了杂交带。此外，我们重建了这些谱系的系统发育网络，并检测到三个网状事件，包括来自已灭绝谱系的渗入。侵润事件的年龄表明，地质活动和气候变化参与了侵润事件。我们还发现了人类引起的基因渗入。总的来说，本研究显示了一个高度网状的peliomphala物种复合体的进化史，并为陆地蜗牛的渐渗提供了可靠的证据。该研究可为进一步研究褐包黄种群的基因渗入驱动进化奠定基础。

{"title":"Reticulate evolution in terrestrial snails of Euhadra peliomphala species complex","authors":"Yasuto Ishii , Shun Ito , Yuichi Kameda , Tsuyoshi Takano , Tsukasa Waki , Satoshi Chiba , Takahiro Hirano","doi":"10.1016/j.ympev.2025.108437","DOIUrl":"10.1016/j.ympev.2025.108437","url":null,"abstract":"<div><div>Recent studies have shown the significant role of introgression in evolution, yet the confident evidence of introgression has come from biased taxa. Although the Mollusca were representative taxa to show introgression-driven evolution, conclusive examination has been rare. Here, we investigated the genetic structure and evolutionary history of terrestrial snails in the <em>Euhadra peliomphala</em> species complex (Heterobranchia: Camaenidae). We collected 197 individuals from 196 sites in Japan, covering the entire distribution, and obtained genome-wide single nucleotide polymorphisms (SNPs) using double digest restriction site-associated DNA sequencing. The population genetic analysis showed that the study individuals are clustered into 12 lineages, which are distributed parapatrically. Our hybrid test detected hybrid zones between several pairs of the lineages. Additionally, we reconstructed a phylogenetic network of these lineages and detected three reticulate events, including introgression from an extinct lineage. The ages of the introgression events suggests that geological activity and climate change were involved. We also found human-induced introgression. Overall, the present research showed a highly reticulated evolutionary history of the <em>E. peliomphala</em> species complex, and provided confident evidence of introgression in terrestrial snails. This study should play a major role as a basis for further research on introgression-driven evolution within the <em>E. peliomphala</em> species complex.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108437"},"PeriodicalIF":3.6,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859934","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

Phylogenomic incongruence in Castanopsis (Fagaceae) is primarily caused by gene flow rather than incomplete lineage sorting 蓖麻（壳斗科）的系统发育不一致主要是由基因流动而不是不完整的谱系分类引起的

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-13 DOI: 10.1016/j.ympev.2025.108444

Shimei Tang , Si Yin , Yang Wu , Ye Sun

Reticulate evolution complicates phylogenetic reconstruction and obscures species delimitation. Investigating gene flow and its evolutionary consequences across the phylogenetic breadth of the genus provides critical insights into the mechanisms causing diversification within this lineage. By utilizing RAD-seq data from 39 Castanopsis species, we reconstructed phylogenetic relationships through both concatenation- and coalescent-based methods. To disentangle the contributions of gene flow and incomplete lineage sorting (ILS) to phylogenetic discordance, we employed an integrative approach combining topological analyses, polytomy tests, coalescent simulations, and phylogenetic network inference. Furthermore, we tracked the evolutionary trajectory of a key morphological trait across the genus. Despite pervasive gene tree incongruence, we recovered a well-supported species tree. Our analyses identified gene flow as the primary cause of phylogenomic discordance in Castanopsis, though the role of ILS could not be entirely ruled out. Ancient hybridization events along the phylogenetic backbone played a pivotal role in shaping the major clades of Castanopsis. The genus underwent an early rapid diversification during the Eocene, with speciation rates gradually declining thereafter. This study establishes a reliable phylogenetic framework for the examined Castanopsis species and demonstrates the utility of RAD-seq data in resolving complex evolutionary relationships. Our results provide novel insights into the diversification mechanisms of Castanopsis in China, emphasizing the profound impact of reticulate evolution on its evolutionary trajectory.

网状进化使系统发育重建变得复杂，并模糊了物种界限。研究基因流动及其在整个属的系统发育广度上的进化后果，为这一谱系内引起多样化的机制提供了关键的见解。利用39种栲属植物的RAD-seq数据，通过串联和聚结两种方法重建了系统发育关系。为了解开基因流和不完全谱系分类（ILS）对系统发育不一致的贡献，我们采用了一种综合方法，结合拓扑分析、多切分测试、聚结模拟和系统发育网络推断。此外，我们还追踪了整个属中一个关键形态特征的进化轨迹。尽管普遍存在基因树不一致，但我们恢复了一个良好支持的物种树。虽然不能完全排除ILS的作用，但我们的分析发现基因流动是导致Castanopsis系统发育不一致的主要原因。沿着系统发育主干的古代杂交事件在形成Castanopsis主要分支中发挥了关键作用。该属在始新世经历了早期的快速多样化，此后物种形成率逐渐下降。本研究为研究的Castanopsis物种建立了一个可靠的系统发育框架，并证明了RAD-seq数据在解决复杂进化关系中的实用性。我们的研究结果为中国栲的多样化机制提供了新的见解，强调了网状进化对其进化轨迹的深刻影响。

{"title":"Phylogenomic incongruence in Castanopsis (Fagaceae) is primarily caused by gene flow rather than incomplete lineage sorting","authors":"Shimei Tang , Si Yin , Yang Wu , Ye Sun","doi":"10.1016/j.ympev.2025.108444","DOIUrl":"10.1016/j.ympev.2025.108444","url":null,"abstract":"<div><div>Reticulate evolution complicates phylogenetic reconstruction and obscures species delimitation. Investigating gene flow and its evolutionary consequences across the phylogenetic breadth of the genus provides critical insights into the mechanisms causing diversification within this lineage. By utilizing RAD-seq data from 39 <em>Castanopsis</em> species, we reconstructed phylogenetic relationships through both concatenation- and coalescent-based methods. To disentangle the contributions of gene flow and incomplete lineage sorting (ILS) to phylogenetic discordance, we employed an integrative approach combining topological analyses, polytomy tests, coalescent simulations, and phylogenetic network inference. Furthermore, we tracked the evolutionary trajectory of a key morphological trait across the genus. Despite pervasive gene tree incongruence, we recovered a well-supported species tree. Our analyses identified gene flow as the primary cause of phylogenomic discordance in <em>Castanopsis</em>, though the role of ILS could not be entirely ruled out. Ancient hybridization events along the phylogenetic backbone played a pivotal role in shaping the major clades of <em>Castanopsis</em>. The genus underwent an early rapid diversification during the Eocene, with speciation rates gradually declining thereafter. This study establishes a reliable phylogenetic framework for the examined <em>Castanopsis</em> species and demonstrates the utility of RAD-seq data in resolving complex evolutionary relationships. Our results provide novel insights into the diversification mechanisms of <em>Castanopsis</em> in China, emphasizing the profound impact of reticulate evolution on its evolutionary trajectory.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108444"},"PeriodicalIF":3.6,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852569","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

Desert ecosystems shape diversification in glossy snakes (genus Arizona) requiring a re-alignment of evolutionary and conservation units 沙漠生态系统塑造了光泽蛇（亚利桑那属）的多样化，需要重新调整进化和保护单位。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-13 DOI: 10.1016/j.ympev.2025.108441

Dustin A. Wood , Jonathan Q. Richmond , Michael F. Westphal , Bradford D. Hollingsworth , Robert N. Fisher , Amy G. Vandergast

Subspecies are often targets for conservation, yet many lack the genetic data necessary to validate their status as distinctive evolutionary lineages. In 2016, conservationists faced this issue when designating the California glossy snake, Arizona elegans occidentalis, as a Species of Special Concern in California, a decision prompted by population declines and habitat loss but absent of genetic information about its evolutionary integrity. To address this knowledge gap, we collected genomic and mitochondrial data from a rangewide sample of the Arizona elegans complex (n = 257) and characterized genetic structure at varying spatial scales. We confirmed an east–west phyletic division within the A. elegans complex that correlates with an ecotone between the Sonoran and Chihuahuan Deserts and pinpoint the separation to a ∼20 km area in southeastern Arizona, USA. Individuals recognized as A. e. occidentalis do not form a genetically cohesive unit within a more inclusive western clade that is sister to the endemic Arizona pacata in Baja California, México. We synonymize four subspecies circumscribed by the western clade and recognize a new species Arizona occidentalis to re-align the taxonomy with the phylogeographic structure. Most of the diversity within A. occidentalis occurs in California, with three major lineages corresponding separate desert biomes. We revise the conservation units within A. occidentalis to mirror these lineages and address concerns regarding habitat loss in transitional environments along the western edge of its range. This work underscores the importance of aligning taxonomy, evolutionary identity, and management units to design the most effective conservation strategies.

亚种通常是保护的目标，但许多亚种缺乏必要的遗传数据来验证它们作为独特进化谱系的地位。2016年，自然资源保护主义者在将加利福尼亚的光泽蛇亚利桑那elegans occidentalis指定为加利福尼亚州特别关注的物种时面临着这个问题，这一决定是由人口下降和栖息地丧失引起的，但缺乏有关其进化完整性的遗传信息。为了解决这一知识差距，我们从亚利桑那秀丽隐杆线虫复群（n = 257）的广泛样本中收集了基因组和线粒体数据，并在不同的空间尺度上表征了遗传结构。我们确认了秀丽隐杆线虫复合体的东西向种系分裂，该分裂与索诺兰沙漠和奇瓦瓦沙漠之间的过渡带有关，并将其分离定位在美国亚利桑那州东南部约20 km的区域。在一个更具包容性的西部进化支中，被认为是西方猿猴的个体并没有形成一个遗传上有凝聚力的单位，而西部进化支是下加利福尼亚的亚利桑那州特有的帕卡塔的姐妹。我们将以西部支系为界的4个亚种同义化，并确认了一个新种，以重新调整分类与系统地理结构。美国西部野刺的多样性主要集中在加利福尼亚，有三个主要的谱系对应着不同的沙漠生物群系。我们修改了西方桤木的保护单元，以反映这些谱系，并解决了其分布范围西部边缘过渡环境中栖息地丧失的问题。这项工作强调了协调分类、进化认同和管理单位以设计最有效的保护策略的重要性。

{"title":"Desert ecosystems shape diversification in glossy snakes (genus Arizona) requiring a re-alignment of evolutionary and conservation units","authors":"Dustin A. Wood , Jonathan Q. Richmond , Michael F. Westphal , Bradford D. Hollingsworth , Robert N. Fisher , Amy G. Vandergast","doi":"10.1016/j.ympev.2025.108441","DOIUrl":"10.1016/j.ympev.2025.108441","url":null,"abstract":"<div><div>Subspecies are often targets for conservation, yet many lack the genetic data necessary to validate their status as distinctive evolutionary lineages. In 2016, conservationists faced this issue when designating the California glossy snake, <em>Arizona elegans occidentalis</em>, as a Species of Special Concern in California, a decision prompted by population declines and habitat loss but absent of genetic information about its evolutionary integrity. To address this knowledge gap, we collected genomic and mitochondrial data from a rangewide sample of the <em>Arizona elegans</em> complex (<em>n</em> = 257) and characterized genetic structure at varying spatial scales. We confirmed an east–west phyletic division within the <em>A. elegans</em> complex that correlates with an ecotone between the Sonoran and Chihuahuan Deserts and pinpoint the separation to a ∼20 km area in southeastern Arizona, USA. Individuals recognized as <em>A. e. occidentalis</em> do not form a genetically cohesive unit within a more inclusive western clade that is sister to the endemic <em>Arizona pacata</em> in Baja California, México. We synonymize four subspecies circumscribed by the western clade and recognize a new species <em>Arizona occidentalis</em> to re-align the taxonomy with the phylogeographic structure. Most of the diversity within <em>A. occidentalis</em> occurs in California, with three major lineages corresponding separate desert biomes. We revise the conservation units within <em>A. occidentalis</em> to mirror these lineages and address concerns regarding habitat loss in transitional environments along the western edge of its range. This work underscores the importance of aligning taxonomy, evolutionary identity, and management units to design the most effective conservation strategies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108441"},"PeriodicalIF":3.6,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859933","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

Target-enriched multilocus assay on poriferan museum collections unsettles tethyid classification 博物馆收藏的多孔蛋白靶富集多位点测定扰乱了甲状腺分类。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-13 DOI: 10.1016/j.ympev.2025.108436

Dirk Erpenbeck , Fabian Deister , Merrick Ekins , Nora Dotzler , John N.A. Hooper , Toufiek Samaai , Simone Schätzle , Joëlle van der Sprong , Sergio Vargas , Gert Wörheide

Marine biodiversity collections are critical resources for understanding biodiversity and evolutionary patterns. However, their taxonomic utility is limited due to challenges in morphological identification and cryptic speciation, particularly in sponges (Porifera). This study applied a novel target-enriched multilocus assay to a decades-old unidentified collection of Tethyidae from the Queensland Museum. Target-specific baits were designed based on Tethya genome data, enabling the sequencing of nuclear ultraconserved elements (UCEs) and mitochondrial genomes, even from degraded samples. In the study, 40 specimens were sequenced, and we found up to 4,440 UCEs per sample. The phylogenies were based on up to 2,788 loci and demonstrated overall high bootstrap support. Results include robust support for earlier findings on the non-monophyly of Tethya, with lineages linking to other genera (e.g., Stellitethya, Tethycometes), suggesting that Tethya is a paraphyletic group foundational to Tethyidae. Morphological subgroupings, previously hypothesized, were validated genetically, though several novel relationships emerged. This approach highlights the suitability of target-enriched multilocus assays for archival collections, enabling detailed biodiversity assessments using collection material initially not sampled for molecular work. Our Tethya case study underlines that this methodology provides a framework for broader applications in marine biodiversity conservation, facilitating the understanding and preservation of past and present biodiversity to guide future efforts.

海洋生物多样性收集是了解生物多样性和进化模式的重要资源。然而，由于形态学鉴定和隐物种形成方面的挑战，特别是在海绵（Porifera）中，它们的分类学应用受到限制。这项研究应用了一种新的富含靶标的多位点测定方法，对昆士兰博物馆几十年前的一组未确定的Tethyidae藏品进行了分析。基于Tethya基因组数据设计了目标特异性诱饵，使核超保守元件（UCEs）和线粒体基因组测序成为可能，甚至来自降解样品。在这项研究中，我们对40个样本进行了测序，每个样本中发现了4440个UCEs。系统发育基于2788个位点，总体上具有较高的自举支持度。结果有力地支持了早期关于Tethya非单系的发现，与其他属（例如，Stellitethya, Tethycometes）有联系的谱系，表明Tethya是Tethyidae的一个副类群。形态亚群，先前的假设，被证实遗传，虽然一些新的关系出现。这种方法强调了目标丰富的多位点分析对档案馆藏的适用性，使详细的生物多样性评估能够使用最初未为分子工作采样的馆藏材料。我们的Tethya案例研究强调，该方法为海洋生物多样性保护提供了一个更广泛应用的框架，促进了对过去和现在生物多样性的理解和保护，以指导未来的工作。

{"title":"Target-enriched multilocus assay on poriferan museum collections unsettles tethyid classification","authors":"Dirk Erpenbeck , Fabian Deister , Merrick Ekins , Nora Dotzler , John N.A. Hooper , Toufiek Samaai , Simone Schätzle , Joëlle van der Sprong , Sergio Vargas , Gert Wörheide","doi":"10.1016/j.ympev.2025.108436","DOIUrl":"10.1016/j.ympev.2025.108436","url":null,"abstract":"<div><div>Marine biodiversity collections are critical resources for understanding biodiversity and evolutionary patterns. However, their taxonomic utility is limited due to challenges in morphological identification and cryptic speciation, particularly in sponges (Porifera). This study applied a novel target-enriched multilocus assay to a decades-old unidentified collection of Tethyidae from the Queensland Museum. Target-specific baits were designed based on <em>Tethya</em> genome data, enabling the sequencing of nuclear ultraconserved elements (UCEs) and mitochondrial genomes, even from degraded samples. In the study, 40 specimens were sequenced, and we found up to 4,440 UCEs per sample. The phylogenies were based on up to 2,788 loci and demonstrated overall high bootstrap support. Results include robust support for earlier findings on the non-monophyly of <em>Tethya</em>, with lineages linking to other genera (e.g., <em>Stellitethya</em>, <em>Tethycometes</em>), suggesting that <em>Tethya</em> is a paraphyletic group foundational to Tethyidae. Morphological subgroupings, previously hypothesized, were validated genetically, though several novel relationships emerged. This approach highlights the suitability of target-enriched multilocus assays for archival collections, enabling detailed biodiversity assessments using collection material initially not sampled for molecular work. Our <em>Tethya</em> case study underlines that this methodology provides a framework for broader applications in marine biodiversity conservation, facilitating the understanding and preservation of past and present biodiversity to guide future efforts.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108436"},"PeriodicalIF":3.6,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859935","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

From marine sand to land and rivers: A combined phylogenomic strategy unveils the evolution of minute Acochlidimorpha slugs (Gastropoda: Heterobranchia) 从海洋沙子到陆地和河流：一个综合的系统基因组策略揭示了微小的Acochlidimorpha蛞蝓（腹足目：异鳃目）的进化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-12 DOI: 10.1016/j.ympev.2025.108443

Jose Fernández-Simón , Katharina M. Jörger , Bastian Brenzinger , Michael Schrödl , Nerida G. Wilson , Timea P. Neusser , Juan Moles

The repeated colonisation of non-marine environments in panpulmonate molluscs represents a major evolutionary transition, yet many lineages remain poorly understood. Among gastropods, Acochlidimorpha stands out for its ecological and morphological diversity, originating in marine interstitial habitats before independently invading freshwater and terrestrial ecosystems. Here, we present the most complete phylogeny of Acochlidimorpha to date based on a global taxon sampling collected over several decades. We integrate ultra-conserved element (UCE) data from 58 museum-preserved specimens—comprising over 1,700 nuclear loci—with all publicly available Sanger-sequencing markers, totalling more than 150 specimens. This pioneering approach sets a new benchmark for phylogenomic studies in minute molluscan lineages. Our results resolve long-standing systematic ambiguities, reinstating Pontohedylidae stat. rest. and Strubelliidae stat. rest. and establishing Helicohedylidae fam. nov. Within Acochlidioidea, Strubelliidae is recovered as the sister to Pseudunelidae + (Tantulidae + Acochlidiidae). At the species level, we clarify the position of key taxa, including Asperspina loricata and two unidentified species of Hedylopsis. Ancestral habitat reconstruction analyses reveal at least four independent transitions to freshwater and terrestrial environments, highlighting the anatomical innovations facilitating these shifts, and further reinforcing the Indo-West Pacific as the centre of origin and diversification of most extant acochlids. Altogether, our study provides a robust evolutionary framework for Acochlidimorpha, offering new insights into the processes underlying terrestrialisation, morphological evolution, and ecological diversification in a lineage characterised by both extreme miniaturisation and evolutionary dynamism.

Zoobank: urn:lsid:zoobank.org:pub:264EB1DD-A0B1-4D30-94B3-8AEA2D41C34B.

在泛肺软体动物中，非海洋环境的反复殖民化代表了一个主要的进化转变，但许多谱系仍然知之甚少。在腹足类动物中，Acochlidimorpha因其生态和形态的多样性而引人注目，它们起源于海洋间质栖息地，然后独立入侵淡水和陆地生态系统。在这里，我们基于几十年来收集的全球分类群样本，提出了迄今为止最完整的Acochlidimorpha系统发育。我们将来自58个博物馆保存的标本（包括1700多个核位点）的超保守元素（UCE）数据与所有公开可用的桑格测序标记整合在一起，总共超过150个标本。这种开创性的方法为微小软体动物谱系的系统基因组研究设定了新的基准。我们的结果解决了长期存在的系统歧义，恢复了Pontohedylidae stat. rest。和蛋卷菌科。建立Helicohedylidae家族。11 .在松毛虫总科中，松毛虫科被恢复为拟松毛虫科+（松毛虫科 + 松毛虫科）的姐妹。在种水平上，我们明确了关键分类群的位置，包括loricata Asperspina和两个未确定的Hedylopsis种。祖先栖息地重建分析揭示了至少四次向淡水和陆地环境的独立转变，强调了促进这些转变的解剖学创新，并进一步加强了印度-西太平洋作为大多数现存水螅类起源和多样化中心的地位。总之，我们的研究为Acochlidimorpha提供了一个强大的进化框架，为一个以极端小型化和进化动力为特征的谱系的陆地化、形态进化和生态多样化过程提供了新的见解。Zoobank: urn: lsid zoobank.org:酒吧:264 eb1dd a0b1 - 4 d30 - 94 - b3 - 8 aea2d41c34b。

{"title":"From marine sand to land and rivers: A combined phylogenomic strategy unveils the evolution of minute Acochlidimorpha slugs (Gastropoda: Heterobranchia)","authors":"Jose Fernández-Simón , Katharina M. Jörger , Bastian Brenzinger , Michael Schrödl , Nerida G. Wilson , Timea P. Neusser , Juan Moles","doi":"10.1016/j.ympev.2025.108443","DOIUrl":"10.1016/j.ympev.2025.108443","url":null,"abstract":"<div><div>The repeated colonisation of non-marine environments in panpulmonate molluscs represents a major evolutionary transition, yet many lineages remain poorly understood. Among gastropods, Acochlidimorpha stands out for its ecological and morphological diversity, originating in marine interstitial habitats before independently invading freshwater and terrestrial ecosystems. Here, we present the most complete phylogeny of Acochlidimorpha to date based on a global taxon sampling collected over several decades. We integrate ultra-conserved element (UCE) data from 58 museum-preserved specimens—comprising over 1,700 nuclear loci—with all publicly available Sanger-sequencing markers, totalling more than 150 specimens. This pioneering approach sets a new benchmark for phylogenomic studies in minute molluscan lineages. Our results resolve long-standing systematic ambiguities, reinstating <strong>Pontohedylidae stat. rest.</strong> and <strong>Strubelliidae stat. rest.</strong> and establishing <strong>Helicohedylidae fam. nov.</strong> Within Acochlidioidea, Strubelliidae is recovered as the sister to Pseudunelidae + (Tantulidae + Acochlidiidae). At the species level, we clarify the position of key taxa, including <em>Asperspina loricata</em> and two unidentified species of <em>Hedylopsis</em>. Ancestral habitat reconstruction analyses reveal at least four independent transitions to freshwater and terrestrial environments, highlighting the anatomical innovations facilitating these shifts, and further reinforcing the Indo-West Pacific as the centre of origin and diversification of most extant acochlids. Altogether, our study provides a robust evolutionary framework for Acochlidimorpha, offering new insights into the processes underlying terrestrialisation, morphological evolution, and ecological diversification in a lineage characterised by both extreme miniaturisation and evolutionary dynamism.</div><div>Zoobank: urn:lsid:zoobank.org:pub:264EB1DD-A0B1-4D30-94B3-8AEA2D41C34B.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108443"},"PeriodicalIF":3.6,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144857130","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

Whole-genome resequencing unveils the phylogeographic coevolution of Oncomelania hupensis with Yangtze River dynamics in China 全基因组重测序揭示了中国湖北钉螺与长江动态的系统地理共同进化

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-11 DOI: 10.1016/j.ympev.2025.108440

Lei Duan , Fang Luo , Qin Liu , Shen Chen , Xia Tian , Wen-Wen Lv , Lu He , Zi-Rui Ren , Jing Xu , Xiao-Nong Zhou , Shi-Zhu Li , Shan Lv , Wei Hu

The freshwater snail Oncomelania hupensis is the only intermediate host of Schistosoma japonicum and is currently mainly distributed in the middle and lower reaches of the Yangtze River in China. To explore the evolutionary history and adaptations of O. hupensis, we re-sequenced 283O. hupensis accessions from 30 geographic locations across the middle and lower Yangtze River. Our study raises and proves an intriguing hypothesis: O. hupensis has its distribution and adaptation closely tied to the geological evolution of the Yangtze River. Despite varying degrees of isolation and differentiation, lake-type snail populations in the middle and lower reaches may migrate westward to eastward (from middle to lower reaches) via water flow, while hill ecotype snails in the middle reaches potentially disperse from hilly region to lake areas. Population genetics and evolutionary analyses revealed that O. hupensis exhibits a gradual dispersal history from hilly region to downstream areas, closely mirroring the Yangtze River’s flow and geological evolution. Compared to hill ecotype populations, lake populations displayed higher genetic diversity, consistent with dynamic habitats and increased gene flow. This west-to-east migration pattern may be driven by the Yangtze River’s geological dynamics and associated climatic-ecological shifts. Notably, we found genes under strong positive selection differed between lake and hill ecotype populations. Our study provides comprehensive insights into the population dynamics and genetic architecture of O. hupensis, underscoring its coevolution with the Yangtze River’s geological history. These findings advance the genetic understanding of O. hupensis adaptation to different ecological environments and inform schistosomiasis control strategies.

淡水蜗牛钉螺是日本血吸虫唯一的中间宿主，目前主要分布在中国长江中下游地区。为了探索湖北钉螺的进化历史和适应性，我们对2830o进行了重新测序。来自长江中下游30个地理位置的甲型h1n1流感病例。我们的研究提出并证明了一个有趣的假设：湖北钉螺的分布和适应与长江的地质演化密切相关。中下游湖泊生态型钉螺种群虽有不同程度的隔离和分化，但可通过水流向西向东迁移（由中下游迁移），中游丘陵生态型钉螺有从丘陵向湖泊分散的潜力。种群遗传学和进化分析表明，湖北钉螺呈现出从丘陵地区向下游地区逐渐扩散的历史，与长江的流向和地质演化密切相关。与山地生态型种群相比，湖泊种群表现出更高的遗传多样性，与动态生境一致，基因流量增加。这种西向东迁移模式可能是由长江的地质动力和相关的气候生态变化驱动的。值得注意的是，我们发现湖泊生态型和丘陵生态型群体之间存在强正向选择的基因差异。我们的研究为湖北钉螺的种群动态和遗传结构提供了全面的见解，强调了其与长江地质历史的共同进化。这些发现促进了对湖北血吸虫适应不同生态环境的遗传学认识，并为血吸虫病控制策略提供了信息。

{"title":"Whole-genome resequencing unveils the phylogeographic coevolution of Oncomelania hupensis with Yangtze River dynamics in China","authors":"Lei Duan , Fang Luo , Qin Liu , Shen Chen , Xia Tian , Wen-Wen Lv , Lu He , Zi-Rui Ren , Jing Xu , Xiao-Nong Zhou , Shi-Zhu Li , Shan Lv , Wei Hu","doi":"10.1016/j.ympev.2025.108440","DOIUrl":"10.1016/j.ympev.2025.108440","url":null,"abstract":"<div><div>The freshwater snail <em>Oncomelania hupensis</em> is the only intermediate host of <em>Schistosoma japonicum</em> and is currently mainly distributed in the middle and lower reaches of the Yangtze River in China. To explore the evolutionary history and adaptations of <em>O. hupensis</em>, we re-sequenced 283<em>O. hupensis</em> accessions from 30 geographic locations across the middle and lower Yangtze River. Our study raises and proves an intriguing hypothesis: <em>O. hupensis</em> has its distribution and adaptation closely tied to the geological evolution of the Yangtze River. Despite varying degrees of isolation and differentiation, lake-type snail populations in the middle and lower reaches may migrate westward to eastward (from middle to lower reaches) via water flow, while hill ecotype snails in the middle reaches potentially disperse from hilly region to lake areas. Population genetics and evolutionary analyses revealed that <em>O. hupensis</em> exhibits a gradual dispersal history from hilly region to downstream areas, closely mirroring the Yangtze River’s flow and geological evolution. Compared to hill ecotype populations, lake populations displayed higher genetic diversity, consistent with dynamic habitats and increased gene flow. This west-to-east migration pattern may be driven by the Yangtze River’s geological dynamics and associated climatic-ecological shifts. Notably, we found genes under strong positive selection differed between lake and hill ecotype populations. Our study provides comprehensive insights into the population dynamics and genetic architecture of <em>O. hupensis</em>, underscoring its coevolution with the Yangtze River’s geological history. These findings advance the genetic understanding of <em>O. hupensis</em> adaptation to different ecological environments and inform schistosomiasis control strategies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108440"},"PeriodicalIF":3.6,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144828299","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 African Labeo (Cypriniformes: Cyprinidae) emphasizing central African species 非洲鳗鲡的系统基因组学研究（鲤形目：鲤科），重点研究中非物种。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-05 DOI: 10.1016/j.ympev.2025.108427

Tobit L.D. Liyandja , Brian T. Smith , S. Elizabeth Alter , Brian L. Sidlauskas , Melanie L.J. Stiassny

Labeo constitutes the largest genus within the cyprinid tribe Labeonini with over 110 recognized species in Africa and Asia. The clade comprises a major component of the herbivore/detritivore guild with considerable socio-economic importance to artisanal and commercial fisheries. A pan-African distribution and wide variety of habitat occupancy make the group a model to investigate diversification patterns, eco-phenotypic variation, and biogeographical events underpinning their radiation at a continental scale. However, previous attempts to elucidate Labeo systematics using either molecular or morphological data have failed to produce congruent and robust results, and much taxonomic and nomenclatural confusion remains. Here we present the first phylogenomic analysis of the genus using 2,187 ultraconserved elements from 85 taxa, including 56 recognized species, 27 cryptic (candidate) species, and outgroups from the Asian Labeonini. Both concatenated and coalescence-based phylogenetic analyses strongly support monophyly of African Labeo and recover three major clades comprising at least nine species groups. Two main clades are pan-African, while the third is restricted to four ichthyofaunal provinces. With the single exception of the L. umbratus group, none of the previously proposed morphological groupings are resolved as monophyletic, suggesting rampant morphological convergence across the radiation. In this study, interspecific relationships are well resolved and time calibration results corroborate the key role of the Miocene in the radiation of African freshwater fishes. We identify numerous previously unrecognized taxa, and our study provides a much-needed framework for the taxonomic revision of Labeo, a task critical for the development of sound management of these important food fishes.

在非洲和亚洲有超过110个已知的物种，Labeo是塞普里德部落Labeonini中最大的属。该支系是草食/食腐动物支系的主要组成部分，对手工和商业渔业具有相当大的社会经济重要性。泛非分布和广泛的栖息地占用使该群体成为研究多样性模式、生态表型变异和支撑其在大陆范围内辐射的生物地理事件的模型。然而，以前的尝试阐明Labeo系统使用无论是分子或形态数据都未能产生一致和有力的结果，和许多分类和命名混淆仍然存在。本文首次利用来自85个分类群的2187个超保守元件对该属进行系统基因组分析，其中包括56个已知种、27个隐种（候选）种和亚洲Labeonini的外群。基于串联和聚结的系统发育分析都有力地支持非洲拉贝的单系性，并恢复了包括至少9个物种群的三个主要分支。两个主要分支是泛非分支，而第三个分支则局限于四个鱼类学省份。除了L. umbratus类群外，所有先前提出的形态类群都不能确定为单系的，这表明在整个辐射中形态趋同非常猖獗。在本研究中，种间关系得到了很好的解决，时间校准结果证实了中新世在非洲淡水鱼辐射中的关键作用。我们确定了许多以前未被认识的分类群，我们的研究为Labeo的分类修订提供了一个急需的框架，这是对这些重要食用鱼类进行健全管理的关键任务。

{"title":"Phylogenomics of African Labeo (Cypriniformes: Cyprinidae) emphasizing central African species","authors":"Tobit L.D. Liyandja , Brian T. Smith , S. Elizabeth Alter , Brian L. Sidlauskas , Melanie L.J. Stiassny","doi":"10.1016/j.ympev.2025.108427","DOIUrl":"10.1016/j.ympev.2025.108427","url":null,"abstract":"<div><div><em>Labeo</em> constitutes the largest genus within the cyprinid tribe Labeonini with over 110 recognized species in Africa and Asia. The clade comprises a major component of the herbivore/detritivore guild with considerable socio-economic importance to artisanal and commercial fisheries. A pan-African distribution and wide variety of habitat occupancy make the group a model to investigate diversification patterns, eco-phenotypic variation, and biogeographical events underpinning their radiation at a continental scale. However, previous attempts to elucidate <em>Labeo</em> systematics using either molecular or morphological data have failed to produce congruent and robust results, and much taxonomic and nomenclatural confusion remains. Here we present the first phylogenomic analysis of the genus using 2,187 ultraconserved elements from 85 taxa, including 56 recognized species, 27 cryptic (candidate) species, and outgroups from the Asian Labeonini. Both concatenated and coalescence-based phylogenetic analyses strongly support monophyly of African <em>Labeo</em> and recover three major clades comprising at least nine species groups. Two main clades are pan-African, while the third is restricted to four ichthyofaunal provinces. With the single exception of the <em>L. umbratus</em> group, none of the previously proposed morphological groupings are resolved as monophyletic, suggesting rampant morphological convergence across the radiation. In this study, interspecific relationships are well resolved and time calibration results corroborate the key role of the Miocene in the radiation of African freshwater fishes. We identify numerous previously unrecognized taxa, and our study provides a much-needed framework for the taxonomic revision of <em>Labeo</em>, a task critical for the development of sound management of these important food fishes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"213 ","pages":"Article 108427"},"PeriodicalIF":3.6,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144796254","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

Divergence time and biogeography of the fungal genus Porodaedalea (Basidiomycota, Hymenochaetales), obligate phytopathogens on coniferous trees 针叶树上专性植物病原体孢子菌属（担子菌科，膜膜菌科）的分化时间和生物地理

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-07-28 DOI: 10.1016/j.ympev.2025.108425

Heng Zhao , Fang Wu , Yu-Cheng Dai , Josef Vlasák , Masoomeh Ghobad-Nejhad , Hong-Gao Liu , Yuan Yuan

Porodaedalea is one of the core genera of Hymenochaetaceae, comprising 19 species widespread in the Northern Hemisphere. Its members grow on conifers and cause white pocket rot. Nevertheless, the origin, evolution and dispersal of Porodaedalea have remained unclear. In this study, a robust phylogeny of the genus is reconstructed using molecular sequences from four loci (ITS + LSU rDNA + rpb2 + tef1α). Molecular clock analyses suggest that the ancestor of Porodaedalea probably occurred at the Late Cretaceous (80 millions of years ago (Mya) with a 95 % highest posterior density (HPD) of 112–51 Mya), and diverse species mainly emerged between Pliocene and Miocene of Neogene (20–4 Mya of mean stem age). Biogeographic analyses propose that Porodaedalea originated in Asia and diversified in the Northern Hemisphere. After that, the genus evolved with ten global dispersal events and five global vicariance events. Finally, geographic separation and host tree preference provided niches for Porodaedalea species.

Porodaedalea是膜毛科（Hymenochaetaceae）的核心属之一，共有19种，分布在北半球。它的成员生长在针叶树上，引起白色袋腐病。尽管如此，Porodaedalea的起源、进化和传播仍然不清楚。在本研究中，利用ITS + LSU rDNA + rpb2 + tef1α四个位点的分子序列重建了该属的强健系统发育。分子钟分析表明，Porodaedalea的祖先可能出现在晚白垩世（8000万年前），95%的最高后密度（HPD）为112-51万年前)，多种物种主要出现在上新世-中新世（平均茎龄20-4万年前）之间。生物地理分析表明，Porodaedalea起源于亚洲，并在北半球多样化。此后，该属经历了10次全球扩散事件和5次全球变异事件。最后，地理分离和寄主树偏好为螺藻提供了生态位。

{"title":"Divergence time and biogeography of the fungal genus Porodaedalea (Basidiomycota, Hymenochaetales), obligate phytopathogens on coniferous trees","authors":"Heng Zhao , Fang Wu , Yu-Cheng Dai , Josef Vlasák , Masoomeh Ghobad-Nejhad , Hong-Gao Liu , Yuan Yuan","doi":"10.1016/j.ympev.2025.108425","DOIUrl":"10.1016/j.ympev.2025.108425","url":null,"abstract":"<div><div><em>Porodaedalea</em> is one of the core genera of Hymenochaetaceae, comprising 19 species widespread in the Northern Hemisphere. Its members grow on conifers and cause white pocket rot. Nevertheless, the origin, evolution and dispersal of <em>Porodaedalea</em> have remained unclear. In this study, a robust phylogeny of the genus is reconstructed using molecular sequences from four loci (ITS + LSU rDNA + <em>rpb2</em> + <em>tef1α</em>). Molecular clock analyses suggest that the ancestor of <em>Porodaedalea</em> probably occurred at the Late Cretaceous (80 millions of years ago (Mya) with a 95 % highest posterior density (HPD) of 112–51 Mya), and diverse species mainly emerged between Pliocene and Miocene of Neogene (20–4 Mya of mean stem age). Biogeographic analyses propose that <em>Porodaedalea</em> originated in Asia and diversified in the Northern Hemisphere. After that, the genus evolved with ten global dispersal events and five global vicariance events. Finally, geographic separation and host tree preference provided niches for <em>Porodaedalea</em> species.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"212 ","pages":"Article 108425"},"PeriodicalIF":3.6,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144739097","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