Molecular Phylogenetics and Evolution最新文献_第4页

Phylogenomics disentangles the evolutionary and biogeographic uncertainty in Apocissus (Vitaceae) 系统基因组学揭示了天麻属植物在进化和生物地理上的不确定性。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-21 DOI: 10.1016/j.ympev.2025.108525

Alberto J. Coello , Gabriel Johnson , Betsy R. Jackes , Jun Wen

Apocissus is an intriguing small genus in the grape family. It displays a tropical intercontinental disjunction with most species occurring in Australasia, and one in the Americas. Traditionally, its species were part of Cissus, but recent phylogenies have suggested that the Apocissus lineage diverged early from Cissus. Hence, Apocissus was formally described as a new genus, but its evolutionary history remains poorly understood. We herein conduct the first phylogenomic study on Apocissus using target-enriched genomic sequencing. We performed concatenated and coalescent-based analyses using 1,013 targeted nuclear loci of Vitaceae and 245 plastid loci. We assessed the hybridization using SNaQ and obtained a nuclear time-calibrated phylogeny with treePL. The biogeographic reconstructions were then performed with BioGeoBEARS. Nuclear reconstruction recovered the monophyly of Apocissus, and supported it as sister to Cissus, while the hybridization test did not support the hybrid origin of Apocissus. Our time-calibration and biogeographic reconstructions suggest a divergence from Cissus in the late Cretaceous and a later diversification in Australasia during the Oligocene, including a dispersal event from the Australasia to the Americas. Furthermore, our plastome reconstruction shows a close relationship between Cissus penninervis and Apocisssus, supporting the transfer of C. penninervis into Apocissus to ensure the monophyly of both genera. We herein made the taxonomic transfer, Apocissus penninervis (F.Muell.) J.Wen, Jackes & A.J.Coello, comb. nov.

罗经属是葡萄科中一个有趣的小属。它显示出一个热带洲际分离，大多数物种发生在澳大拉西亚，一个在美洲。传统上，它的物种是Cissus的一部分，但最近的系统发育表明，apoissus谱系从Cissus早期分化。因此，罗布森被正式描述为一个新的属，但它的进化历史仍然知之甚少。在此，我们使用目标富集的基因组测序对罗布施进行了首次系统基因组学研究。我们对1013个目标性核位点和245个质体位点进行了串联和聚结分析。我们使用SNaQ评估杂交，并使用treePL获得核时间校准的系统发育。利用biogeobars进行生物地理重建。核重建恢复了天麻的单系性，并支持它是天麻的姐妹株，而杂交试验不支持天麻的杂交起源。我们的时间校准和生物地理重建表明，在晚白垩世从Cissus开始分化，在渐新世在澳大拉西亚开始多样化，包括从澳大拉西亚到美洲的扩散事件。此外，我们的质体重建显示了Cissus penninervis和Apocisssus之间的密切关系，支持Cissus penninervis向Apocissus的转移，以确保两个属的单一性。我们在此进行了分类转移，Apocissus penninervis （F.Muell.）j·文，杰克和a·j·科罗，梳子。11月。

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引用次数: 0

Phylogeny, population structure, and conservation genomics of Galapagos vermilion flycatchers (genus Pyrocephalus) 加拉帕戈斯朱蝇属的系统发育、种群结构和保护基因组学。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-16 DOI: 10.1016/j.ympev.2025.108524

David J. Anchundia , Athena W. Lam , James B. Henderson , Matthew H. Van Dam , Courtney L. Pike , Sabine Tebbich , Birgit Fessl , Heinz Richner , John P. Dumbacher

The Galapagos archipelago in the Eastern Tropical Pacific is known for its isolation, island endemism, and rapid diversification. Despite considerable scientific research many groups remain poorly studied. One of these groups is the genus Pyrocephalus, a group of brightly-colored and charismatic flycatchers whose populations have declined significantly in recent decades. To study the evolution and diversification of Pyrocephalus, we used samples from 53 individuals across 11 Galapagos Islands (Pyrocephalus dubius and P. nanus) and a continental outgroup (P. obscurus) and reconstructed a phylogeny using 233,916 genome-wide SNPs. The data revealed that Pyrocephalus colonized Galapagos earlier than previously estimated, approximately 1.3 million years ago (MYA), and diversified into at least eight genetically distinct clades. These include P. dubius, a species endemic to San Cristobal Island, now extinct, and P. nanus across the remaining islands. The P. nanus population on Floreana Island has been isolated for at least 1.2 MYA, along with additional divergent groups from Santa Cruz, Pinzon + Rabida, Isabela + Fernandina, Santiago, Marchena and Pinta, which have each been isolated for 0.89–0.15 million years. Morphometric, plumage and acoustic comparisons corroborate many of these genetic clades. Specifically for Santa Cruz Island, population genetic analyses indicate a significant reduction in nucleotide diversity, but no evidence of inbreeding, suggesting a minimal recent migration and rapid population decline. Our data on genetic diversification are critical for identifying evolutionary distinct populations and guiding translocations to restore extirpated or diminished island populations.

加拉帕戈斯群岛位于东热带太平洋，以其孤立、岛屿特有和快速多样化而闻名。尽管有大量的科学研究，但对许多群体的研究仍然很少。其中一种是Pyrocephalus属，这是一种色彩鲜艳、魅力十足的捕蝇鸟，其种群数量在最近几十年里显著下降。为了研究Pyrocephalus的进化和多样化，我们使用了来自加拉帕戈斯群岛11个岛屿（Pyrocephalus dubius和P. nanus）和大陆外群（P. obscurus）的53个个体的样本，并使用233,916个全基因组snp重建了系统发育。数据显示，Pyrocephalus在加拉帕戈斯群岛定居的时间比之前估计的要早，大约在130万年前（MYA），并分化成至少8个遗传上不同的分支。其中包括P. dubius，一种圣克里斯托瓦尔岛特有的物种，现在已经灭绝，以及P. nanus遍布其余岛屿。弗洛里亚纳岛上的南猿种群已经分离了至少1.2万年，另外还有来自圣克鲁斯、Pinzon + Rabida、伊莎贝拉 + 费尔南迪纳、圣地亚哥、马尔切纳和平塔的不同种群，它们分别分离了89至15万年。形态计量学、羽毛学和声学比较证实了许多这些遗传分支。特别是在圣克鲁斯岛，种群遗传分析表明核苷酸多样性显著减少，但没有近亲繁殖的证据，这表明最近的迁移很少，种群数量迅速下降。我们关于遗传多样化的数据对于识别进化上不同的种群和指导易位以恢复灭绝或减少的岛屿种群至关重要。

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引用次数: 0

Unpouching Peracarida relationships with ultraconserved elements 揭示超保守元素的超囊胞关系。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-16 DOI: 10.1016/j.ympev.2025.108523

Tammy Iwasa-Arai , Katrin Linse , Sónia C.S. Andrade , Gonzalo Giribet

Peracarida is a large group containing twelve orders of brooding crustaceans, including the large orders Amphipoda, Isopoda, Tanaidacea and Cumacea, and a series of smaller orders, some restricted to isolated habitats. The relationships of Peracarida have been disputed and little effo has been made to use extensive taxon sampling with a modern genetic approach. Here we present a novel probe set of ultraconserved elements (UCEs) developed for peracarids to investigate higher-level relationships using newly collected Antarctic material and collection-based specimens. Concatenated and coalescent-based analyses across different levels of occupancy matrices recovered strong support for the monophyly of Peracarida and for the clade Mancoida (Isopoda + Tanaidacea + Cumacea). Thermosbaenacea was consistently resolved as the sister group to all remaining peracarids. Within Amphipoda, our results contrast with previous phylogenies by placing Corophiida and Hyperiidea as early-branching lineages. In Isopoda, Oniscidea was recovered as monophyletic and concordant with morphological hypotheses. These findings provide one of the first phylogenomic frameworks for Peracarida and demonstrate the promise of UCEs for resolving long-standing questions in malacostracan evolution.

甲壳纲是一个包含12目孵化甲壳类动物的大群，包括大目片足目、等足目、鱼足目和Cumacea，以及一系列较小的目，其中一些仅限于孤立的栖息地。Peracarida的关系一直存在争议，并且没有尝试使用现代遗传方法进行广泛的分类群抽样。在这里，我们提出了一种新的超保守元素（UCEs）探针集，用于研究使用新收集的南极材料和基于采集的标本的高水平关系。在不同层次的占用矩阵中，基于串联和聚结的分析恢复了对Peracarida和Mancoida分支（等足目 + Tanaidacea + Cumacea）的单系性的有力支持。Thermosbaenacea一直被认为是所有剩余的peracarids的姐妹群。在Amphipoda中，我们的结果与之前的系统发育形成对比，将corophhiida和hyperidea作为早期分支谱系。在等足目中，蛇尾纲被恢复为单系，与形态学假设一致。这些发现提供了第一个系统基因组框架，并展示了UCEs在解决malacostracan进化中长期存在的问题方面的前景。

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引用次数: 0

Disentangling subspecies delimitation in Heldreichia bupleurifolia Boiss. (Brassicaceae) through genomic and quantitative morphological approaches 柴胡属植物亚种划分的分离。（芸苔科）通过基因组学和定量形态学方法。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-13 DOI: 10.1016/j.ympev.2025.108518

Ilgın Deniz Can , Emrullah Yılmaz , Kurtuluş Özgişi , Hakan Gür , İsmail Kudret Sağlam , Barış Özüdoğru

Heldreichia bupleurifolia Boiss., the only species in its genus, is distributed across the Taurus and Anatolian Diagonal Mountains in Türkiye and presents considerable taxonomic challenges. The species is currently divided into five subspecies and one variety and has long posed challenges for infraspecific classification due to overlapping morphological traits and unresolved phylogenetic relationships. To address these issues and clarify the boundaries of the described subspecies and their evolutionary history, this study integrates comprehensive morphometric analyses of 502 individuals from 36 populations, as well as SNP- and locus-based genomic analyses from RAD-seq data of 136 individuals from 20 populations. While morphometric assessments showed significant differentiation in foliar and fruit traits, especially between western and eastern populations, genomic analyses identified distinct genetic clusters corresponding to geographic regions. High levels of genetic admixture and morphological plasticity were seen in the Central Taurus populations, indicating either historical hybridization or the preservation of ancestral polymorphisms. In accordance with morphological and admixture analyses, coalescent-based subspecies delimitation supported a three-subspecies model, resulting in revised taxonomic classifications that included new combinations. To further contextualize these results within an evolutionary perspective, we adopted the speciation continuum framework, interpreting morphological, genetic, and reproductive differentiation as components of a continuous process of divergence. These results emphasize the drawbacks of using morphology alone for taxonomy and the value of integrative methods for determining subspecies boundaries in areas with complex topography.

柴胡属植物。是其属中唯一的一种，分布在 rkiye的金牛座和安纳托利亚对角山脉，并提出了相当大的分类挑战。该物种目前分为5个亚种和1个变种，由于重叠的形态特征和未解决的系统发育关系，长期以来对种下分类提出了挑战。为了解决这些问题并澄清所描述亚种的界限及其进化史，本研究整合了来自36个种群的502个个体的综合形态计量学分析，以及来自20个种群的136个个体的RAD-seq数据的SNP和基于位点的基因组分析。虽然形态计量学评估显示叶片和果实性状存在显著差异，特别是在西部和东部种群之间，但基因组分析发现了与地理区域相对应的不同遗传簇。在中部金牛座群体中发现了高度的遗传混合和形态可塑性，表明要么是历史杂交，要么是祖先多态性的保存。根据形态学和混合分析，基于聚结的亚种划分支持三亚种模型，导致修订的分类分类包括新的组合。为了从进化的角度进一步解释这些结果，我们采用了物种形成连续体框架，将形态、遗传和生殖分化解释为连续分化过程的组成部分。这些结果强调了单独使用形态学进行分类的缺点和综合方法在复杂地形地区确定亚种边界的价值。

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引用次数: 0

Evolutionary history of Ridge-nosed Rattlesnakes (Crotalus willardi): A specialized and diverse montane species 脊鼻响尾蛇（Crotalus willardi）的进化史：一种特殊的、多样化的山地物种。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-13 DOI: 10.1016/j.ympev.2025.108522

Michael J. Buontempo , Philip Lavretsky , Rhett M. Rautsaw , Lauren M. McFarland , Ramses Alejandro Rosales-García , Jason L. Strickland , Miguel Borja , Jason Jones , Ricardo Ramírez Chaparro , Robert W. Bryson Jr. , Christopher L. Parkinson , Michael G. Harvey

Mountain organisms often exhibit complex distributions, patterns of variation, and evolutionary histories due to the topographical, climatic, and orogenic complexity of the areas in which they occur. Many montane taxa, however, lack the detailed sampling across space and the genome required to characterize diversity or estimate key evolutionary parameters. Here, we leverage comprehensive sampling, genome-wide data, and a draft genome assembly to investigate patterns of diversity and evolutionary history within a widespread but poorly studied snake, the Ridge-nosed Rattlesnake (Crotalus willardi), that inhabits the montane pine-oak woodlands in the Sierra Madre Occidental and Madrean Archipelago. We test for population genetic structure, measure gene flow and admixture between populations, and estimate phylogenetic history and divergence times among groups. We find substantial genetic structure, with up to seven differentiated populations, only three of which correspond with existing subspecific taxonomy. We identify one putative recent admixture event as well as evidence of historical gene flow among populations. We find that southern populations are generally older than those currently occurring in the Madrean Archipelago, which diverged within the last 0.6 million years. Together, our results reveal that current taxonomy fails to capture the substantial diversity and complex evolutionary processes at work in this species of montane snake and suggest that high-resolution sampling is crucial to understanding the biotic history of complex montane regions.

山地生物由于其所在地区的地形、气候和造山带的复杂性，往往表现出复杂的分布、变异模式和进化历史。然而，许多山地分类群缺乏详细的跨空间采样和基因组，以表征多样性或估计关键的进化参数。在这里，我们利用全面的采样、全基因组数据和基因组组装草图来研究一种分布广泛但研究较少的蛇的多样性模式和进化史，脊鼻响尾蛇（Crotalus willardi），它生活在西马德雷山脉和马德雷群岛的山地松橡树林地。我们测试群体遗传结构，测量群体之间的基因流动和混合，并估计群体之间的系统发育历史和分化时间。我们发现了大量的遗传结构，有多达7个不同的群体，其中只有3个与现有的亚特异性分类相对应。我们确定了一个假定的近期混合事件以及种群间历史基因流动的证据。我们发现，南方的种群通常比目前在马德兰群岛出现的种群更古老，马德兰群岛在过去的60万年里出现了分化。总之，我们的研究结果表明，目前的分类方法未能捕捉到这种山地蛇的大量多样性和复杂的进化过程，并表明高分辨率采样对了解复杂山地地区的生物历史至关重要。

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引用次数: 0

Structural dynamics of chloroplast genome in Paphiopedilum (Orchidaceae): in response to natural hybridization 兰属植物叶绿体基因组的结构动态：对自然杂交的响应。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-10 DOI: 10.1016/j.ympev.2025.108521

Xue-Ying Wei , Ai-Qun Hu , Jin Zhou , Jiang-Ping Shu , Wei-Yue Sun , Li-Qiang Li , Jian-Wen Shao , Hui Wang , Yue-Hong Yan

Chloroplast genomes, once considered highly conserved, have been shown to exhibit significant structural variations, though the underlying mechanisms remain unclear. In this study, we investigated the chloroplast genome structure of eight populations comprising 76 individuals of Paphiopedilum barbigerum, P. helenae, and P. vejvarutianum. By using chloroplast genome sequences and 15,924 nuclear SNP loci, we conducted analyses and validations of chloroplast genome structural recombination and natural hybridization. Our key findings include the following: (1) Structural variations in the chloroplast genomes were found to be stable and heritable across populations. (2) In P. barbigerum, populations exhibiting structural variation contained an unidentified insertion sequence in the SSC region, which was associated with a significant reduction in GC content within this region. (3) The presence of non-LTR retrotransposons suggests their potential role in the expansion and contraction of the IR region in Paphiopedilum, with this chloroplast variation potentially linked to natural hybridization events. (4) The incongruent phylogenetic relationships, gene flow and gene introgression among P. barbigerum, P. helenae, and P. vejvarutianum point to a history of hybridization within these species. Our study proposes that both transposon activity and hybridization play crucial roles in driving chloroplast structural variations. For the first time, the structural variations of chloroplasts have been linked to transposons and natural hybridization, breaking the traditional stereotype of chloroplasts being highly conserved. This discovery enhances our understanding of how natural hybridization contributes to species formation and provides a basis for exploring the evolutionary mechanisms of chloroplast genomes.

叶绿体基因组，一度被认为是高度保守的，已经显示出显著的结构变异，尽管潜在的机制尚不清楚。本研究对8个居群（76个个体）的barbigerum、P. helenae和P. vejvarutianum进行了叶绿体基因组结构分析。利用叶绿体基因组序列和15924个核SNP位点，对叶绿体基因组结构重组和自然杂交进行了分析和验证。我们的主要发现包括：(1)叶绿体基因组的结构变异在种群中是稳定的和可遗传的。(2) barbigerum的结构变异种群在SSC区含有一个未知的插入序列，这与该区域GC含量的显著降低有关。(3)非ltr逆转录转座子的存在表明，它们可能在Paphiopedilum IR区的扩张和收缩中发挥作用，这种叶绿体变异可能与自然杂交事件有关。(4) barbigerum、P. helenae和P. vejvarutianum之间不一致的系统发育关系、基因流动和基因渗入表明这些物种之间存在杂交史。我们的研究表明转座子活性和杂交在驱动叶绿体结构变化中起着至关重要的作用。首次将叶绿体的结构变异与转座子和自然杂交联系起来，打破了叶绿体高度保守的传统刻板印象。这一发现增强了我们对自然杂交如何促进物种形成的理解，并为探索叶绿体基因组的进化机制提供了基础。

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引用次数: 0

Erratum to “Target sequence capture informs generic delimitation and hybridization in the tribe Lasiopetaleae (Malvaceae)”. [Mol. Phylogenetics Evol. 213 (2025) 108445] “靶序列捕获为部落Lasiopetaleae （Malvaceae）的属界划分和杂交提供了信息”的勘误。[j].中国生物医学工程学报，2013(5):444 - 444。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-05 DOI: 10.1016/j.ympev.2025.108501

Benjamin M. Anderson , Todd G.B. McLay , Carolyn F. Wilkins , Kelly A. Shepherd

引用次数: 0

Diversification and hybridization in Andinocleome (Cleomaceae) 山铁锤科山铁锤属植物的多样化与杂交。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-05 DOI: 10.1016/j.ympev.2025.108517

Theresa Saunders, Henry Landis, Eric H. Roalson

Andinocleome sensu lato of the Andean clade of Cleomaceae contains eight species and presents an important study group for research in population dynamics, species boundaries, and hybridization as there are morphological variations within species (particularly A. anomala), questionable species boundaries, and hypothesized hybridization in the genus. In this research, we used target sequence capture and the Angiosperms353 probe set to generate data from 65 herbarium vouchers. These data were combined with previously published sequence data from an additional 112 specimens in the genus to resolve species boundaries and identify genetic diversity within species. The Hyb-Seq nuclear phylogenetic tree resolved species boundaries and provides an important framework for future studies in Andinocleome. Few studies in plants have applied the Angiosperms353 probe set to address population level dynamics using herbarium specimens, and our study expands on this research. We identified genetic variation between intraspecific populations by sampling from two “mass collections” representing morphological variation in the species A. anomala, in addition to sampling across the genus. We also used off-target chloroplast regions to construct a chloroplast phylogenetic tree; discordance between the nuclear and chloroplast trees indicated introgressive hybridization within Andinocleome. STRUCTURE, principal component analyses, SNaQ, and HyDe analyses further supported hybridization between multiple species within the clade. Our study resolves species boundaries despite significant hybridization and represents the most comprehensive genetic study to date in Andinocleome. We demonstrate that the Angiosperms353 probe set can be appropriate for identifying population structuring within species, even when utilizing herbarium specimens.

山蕨科安第斯支系的长尾蕨（Andinocleome sensu lato）包含8个种，是种群动态、种界和杂交研究的重要研究群体，因为种内存在形态变异（特别是A. anomala），种界存在问题，属内存在假设杂交。在这项研究中，我们使用靶序列捕获和Angiosperms353探针集从65份植物标本室凭证中生成数据。这些数据与先前发表的来自该属另外112个标本的序列数据相结合，以确定物种边界并确定物种内的遗传多样性。Hyb-Seq核系统发育树解决了物种边界问题，为今后的研究提供了重要框架。很少有研究利用植物标本室标本来研究被子植物的种群水平动态，本研究在此基础上进行了扩展。除了跨属取样外，我们还从代表A. anomala物种形态变异的两个“大规模收集”中取样，确定了种内种群之间的遗传变异。我们还利用非靶叶绿体区域构建了叶绿体系统发育树；核树和叶绿体树之间的不一致表明了颖花体内的渐渗杂交。结构分析、主成分分析、SNaQ和HyDe分析进一步支持了分支内多个物种之间的杂交。我们的研究解决了物种边界，尽管有显著的杂交，代表了迄今为止最全面的遗传研究。我们证明，即使在利用植物标本室标本时，Angiosperms353探针集也可以用于识别物种内的种群结构。

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引用次数: 0

Toward a new phylogeny-based classification of Flatidae (Hemiptera: Fulgoromorpha): a diversification shaped by angiosperm expansion 基于系统发育的新Flatidae分类（半翅目：Fulgoromorpha）：由被子植物扩张形成的多样化。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-04 DOI: 10.1016/j.ympev.2025.108508

Deqiang Ai , Bourgoin Thierry , Wenjun Bu , Yalin Zhang

Despite being one of the most diverse planthopper families with broad distribution and ecological significance, the internal classification of Flatidae has remained largely phenetic and of limited phylogenetic relevance. Here, we present the first comprehensive phylogenetic analysis of Flatidae, based on a multilocus dataset and broad, though still incomplete, genus-level sampling. Our results challenge the monophyly of most traditional subfamilies, tribes, and subtribes, and reveal three previously unrecognized major lineages with strong biogeographic structure: the siphantinian, flatinian, and selizinian lineages. The latter two comprise, respectively, three and five well-supported sublineages: phromniinan, phyllyphantinan, and flatinan for the former; and sisciinan, phantinan, selizinan, cryptoflatinan, and the Makaya⁺ sublineage for the latter. The origin of Flatidae is estimated to date back to the Late Jurassic, with diversification in their ancestral area, likely the Oriental region or the Old World, occurring during the Early Cretaceous. The geographic distributions of the newly emerged lineages show strong coherence with their phylogenetic structure. We interpret the early diversification of Flatidae as closely tied to the rise of angiosperms during the Cretaceous, which provided novel ecological opportunities and facilitated both radiation and long-term persistence across continents. Herein, we provide a new evolutionary framework for future morphological, ecological, and taxonomic research on Flatidae, and we contribute to a deeper understanding of diversification patterns among higher Fulgoroidea.

尽管飞虱科是分布最广、生态意义最丰富的飞虱科之一，但飞虱科的内部分类在很大程度上仍然是表型的，系统发育相关性有限。在这里，我们提出了第一个全面的系统发育分析，基于多位点数据集和广泛的，尽管仍然不完整，属水平的抽样。我们的研究结果挑战了大多数传统亚科、部落和亚部落的单一性，并揭示了三个以前未被认识到的具有强大生物地理结构的主要谱系：西phantinian、flatinian和selizinian谱系。后两者分别包括三个和五个支持良好的亚系：phromniinan， phyllyphantinan和flatinan（前者）；还有七剑麻、幻地楠、七剑麻、隐扁豆，以及后者的Makaya+子系。据估计，Flatidae的起源可以追溯到晚侏罗世，它们的祖先地区（可能是东方地区或旧大陆）的多样化发生在早白垩纪。新出现的谱系的地理分布与其系统发育结构具有很强的一致性。我们认为，Flatidae的早期多样化与白垩纪被子植物的兴起密切相关，被子植物的兴起提供了新的生态机会，并促进了跨大陆的辐射和长期持久性。本研究为今后Flatidae的形态学、生态学和分类学研究提供了一个新的进化框架，并有助于更深入地了解高等富氏总科的多样化模式。

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引用次数: 0

Multilocus phylogeny of the land snail Helix differs substantially from the mitochondrial gene tree 地螺螺旋的多位点系统发育与线粒体基因树有很大的不同。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-12-04 DOI: 10.1016/j.ympev.2025.108516

Ondřej Korábek , Bernhard Hausdorf

The phylogeny of the western Palaearctic land snail genus Helix was previously studied using only a few partial mitochondrial genes. The mitochondrial phylogeny was not well resolved, and frequent mitochondrial introgressions indicated that the mitochondrial phylogeny may not correspond to the species tree. We analysed genome-wide ddRAD data to obtain a reliable species tree and re-analysed the mitochondrial phylogeny with mitogenome-scale data from selected species to investigate the extent and causes of mitonuclear discordance. The ddRAD phylogeny resolved the position of previously problematic species, elucidated the biogeographic history of the genus, and confirmed the monophyly of some species that was not unambiguously supported by the mitochondrial data. Helix arnautorum is shown here to be a distinct species, separate from Helix dormitoris. Mitochondrial introgressions indeed cause discordances between the mitochondrial and species trees. The most significant case, the nearly complete replacement of the original mitochondrion of Helix buchii, is associated with relaxed selection and accelerated substitution rate in the original mitochondrial lineage. However, robustly estimating the mitochondrial phylogeny turned out to be difficult even with complete mitochondrial genomes. This is probably due to a combination of short internal branches and variation in substitution rate and nucleotide composition. Alignment filtering and site-heterogeneous mixture models yielded estimates more concordant with the species tree than partitioned analysis of complete protein-coding sequences.

在此之前，人们仅利用少数部分线粒体基因研究了古北缘西部陆地蜗牛属Helix的系统发育。线粒体系统发育未得到很好的解决，频繁的线粒体渗入表明线粒体系统发育可能与物种树不对应。我们分析了全基因组的ddRAD数据，以获得可靠的物种树，并使用来自选定物种的有丝分裂基因组规模数据重新分析了线粒体系统发育，以研究有丝分裂核不一致的程度和原因。ddRAD系统发育解决了以前有问题的物种的位置，阐明了该属的生物地理历史，并证实了一些线粒体数据不明确支持的物种的单系性。此处显示的螺旋arnautorum是一个独特的物种，与螺旋宿舍分开。线粒体渗入确实导致线粒体树和物种树之间的不一致。最显著的例子是，Helix buchii的原始线粒体几乎完全被替换，这与原始线粒体谱系中的宽松选择和加速替换率有关。然而，即使有完整的线粒体基因组，也很难可靠地估计线粒体系统发育。这可能是由于短的内部分支和取代率和核苷酸组成的变化的结合。比对滤波和位点异质混合模型比完整蛋白质编码序列的分割分析更符合物种树的估计。

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