Molecular Phylogenetics and Evolution最新文献_第7页

Genome-based phylogenetics and species delimitation for the narrowly distributed Pachyhynobius salamander (Caudata: Hynobiidae) reveal cryptic biodiversity 基于基因组的系统发育和物种划分揭示了分布狭窄的厚腹蝾螈（尾纲：厚腹蝾螈科）的隐伏生物多样性

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-30 DOI: 10.1016/j.ympev.2025.108458

Yongxuan Xiao , Tingli Hu , Suxin Shi , Hui Wang , Caiwen Zhang , Dapeng Pang , Yinfan Cai , Tao Pan , Pablo Orozco-terWengel , Baowei Zhang

Species delimitation is a challenging issue in taxonomy, especially in the absence of clear diagnostic morphological characters, a particular problem for cryptic species. In recent years, the rapid development of high-throughput sequencing technologies, when combined with genomic species delimitation methods such as the multispecies coalescent, has significantly improved the ability to resolve cryptic species. However, traditional methods like Bayesian phylogenetics and phylogeography often result in over-splitting due to their failure to fully consider factors such as gene flow. This study focuses on the genus Pachyhynobius, endemic to China, utilizing specific-locus amplified fragment sequencing technology to construct a high-quality nuclear genome SNP dataset. Systematic genomics combined with various species delimitation methods that incorporate the genealogical differentiation index and the isolation by distance model for geographic information was used to systematically evaluate the species boundaries of this genus. The results show that Pachyhynobius consists of four genetically independent, geographically disjunct lineages with deep genetic differentiation occurring over millions of years. Although these lineages have relatively close geographic distributions, long-term ecological niche conservatism and the sky island effect may be key driving forces responsible for their continued isolation and independent evolutionary paths. Multi-method species delimitation analysis further provides a comprehensive evaluation of the potentially distinct genetic lineages within the group, identifying them as potential cryptic species. Although new species have not yet been formally named, the evidence provided offers a new example for understanding the identification and evolutionary mechanisms of cryptic species in geographically restricted habitats.

物种划分是分类学中一个具有挑战性的问题，特别是在没有明确的诊断形态特征的情况下，这是一个特殊的问题。近年来，高通量测序技术的快速发展，与多物种聚结等基因组物种划分方法相结合，显著提高了对隐种的解析能力。然而，传统的贝叶斯系统遗传学和系统地理学等方法由于没有充分考虑基因流动等因素，往往导致过度分裂。本研究以中国特有的Pachyhynobius属植物为研究对象，利用特异位点扩增片段测序技术构建高质量的核基因组SNP数据集。采用系统基因组学结合多种物种划分方法，结合家谱分异指数和地理信息距离隔离模型对该属的种界进行了系统评价。结果表明，肿鼻虫由四个遗传上独立的、地理上不相交的谱系组成，这些谱系在数百万年的时间里发生了深刻的遗传分化。尽管这些世系的地理分布相对接近，但长期的生态位保守性和天空岛效应可能是它们持续隔离和独立进化路径的关键驱动力。多方法物种划分分析进一步提供了群体内潜在的不同遗传谱系的综合评估，确定它们为潜在的隐种。虽然新物种尚未正式命名，但提供的证据为理解地理受限生境中隐种的识别和进化机制提供了新的范例。

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引用次数: 0

Disjunct distributions and evolutionary diversification of Australasian geometrid moths: subfamilies Epidesmiinae, Desmobathrinae and Oenochrominae (Lepidopera) 澳洲几何蛾的不相交分布与进化多样性：鳞蛾亚科、鳞蛾亚科和鳞蛾亚科。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-29 DOI: 10.1016/j.ympev.2025.108450

Leidys Murillo-Ramos , Hamid Reza Ghanavi , Kyung Min Lee , Elina Laiho , Axel Hausmann , Hermann Staude , Egbert Friedrich , Gunnar Brehm , Pasi Sihvonen

Disjunct distribution patterns have long intrigued biogeographers, sparking ongoing debates about the mechanisms driving the current distribution of biodiversity. Among the most discussed patterns are long-distance dispersal and vicariance. While these patterns have been extensively studied in plants, marine taxa, mammals, and some invertebrates, they remain less explored in groups like moths. In this study, we use the Epidesmiinae + Oenochrominae + Desmobathrinae complex—three closely related subfamilies within the Geometridae family—as a model to examine disjunct distribution patterns in Australasian moths. Epidesmiinae + Oenochrominae moths are primarily distributed within the Australasian region, with some taxa being endemic to New Zealand. In contrast, their sister group, Desmobathrinae, exhibits a trans-continental and mainly pantropical distribution. The biogeography and evolution of these subfamilies, which currently have different distribution areas, have not been analysed in an evolutionary context before. To investigate this, we inferred phylogenetic trees using a Maximum-Likelihood approach and used the topology to estimate time-calibrated trees and reconstruct ancestral biogeographical areas using a Bayesian method. Additionally, we explored the diversification rates of these lineages. Our results suggest that the ancestor of the three subfamilies most likely originated in Australasia during the Eocene (∼58 Ma). Bayesian biogeographical analyses suggested dispersal events of the Desmobathrinae into the Indo-Malayan region and other areas, with an important jump to the Neotropics, while Epidesmiinae and Oenochrominae dispersed mainly within Australasia. Diversification analysis revealed no significant shifts in diversification rates, with the phylogeny showing a pattern of declining speciation rates over time. Our study exemplifies how phylogenetics in combination with biogeographical reconstruction uncovers macroevolutionary patterns in moths.

分离的分布模式长期以来一直引起生物地理学家的兴趣，引发了关于驱动当前生物多样性分布机制的持续争论。其中讨论最多的模式是长距离扩散和迁移。虽然这些模式已经在植物、海洋分类群、哺乳动物和一些无脊椎动物中得到了广泛的研究，但在飞蛾等群体中却很少被探索。在这项研究中，我们使用尺蠖科中三个密切相关的亚科Epidesmiinae + Oenochrominae + Desmobathrinae复合物作为模型来研究澳大利亚飞蛾的不间断分布模式。Epidesmiinae + Oenochrominae蛾主要分布在澳大利亚地区，部分类群为新西兰特有。相比之下，它们的姐妹类群，假蝇科，表现出跨大陆和主要的泛热带分布。这些亚科的生物地理学和进化，目前有不同的分布区域，以前没有在进化背景下分析过。为了研究这一点，我们使用最大似然方法推断系统发育树，并使用拓扑来估计时间校准树，并使用贝叶斯方法重建祖先生物地理区域。此外，我们探索了这些谱系的多样化率。我们的研究结果表明，这三个亚科的祖先最有可能起源于始新世（~ 58 Ma）的澳大利亚。贝叶斯生物地理分析表明，Desmobathrinae扩散到印度-马来亚地区和其他地区，并有一个重要的跳跃到新热带地区，而epidesminae和Oenochrominae主要分布在澳大拉西亚。多样化分析显示多样化率没有显著变化，系统发育表现出物种形成率随时间下降的模式。我们的研究举例说明了系统发育与生物地理重建相结合如何揭示飞蛾的宏观进化模式。

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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 : 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。

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引用次数: 0

Estimated timeline for the evolution of symbiotic nitrogen fixing Paraburkholderia 共生固氮Paraburkholderia进化的估计时间

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-25 DOI: 10.1016/j.ympev.2025.108447

Lazarus Mavima , Emma T. Steenkamp , Chrizelle W. Beukes , Marike Palmer , Sofie E. De Meyer , Euan K. James , Stephanus N. Venter , Martin P.A. Coetzee

The nitrogen-fixing and nodule-forming symbionts of legumes, which belong to the class Betaproteobacteria, are informally known as beta-rhizobia. Thus far, members of this group have only been found in the genera Paraburkholderia, Trinickia and Cupriavidus. In this study, we investigate the poorly characterized evolutionary history of this trait in the predominant beta-rhizobial genus, Paraburkholderia. This was determined in the context of the current evolutionary theories and date estimates of rhizobia, the genus Paraburkholderia and the earth. Evolutionary divergence dates of rhizobial Paraburkholderia as well as their ancestral nodulation states were estimated using over 800 diverse proteobacterial genomes. Molecular dating was carried out using the software BEAST (Bayesian Evolutionary Analysis Sampling Trees) and APE (using the ‘chronopl’ function). Our results showed that the most recent common ancestor (MRCA) of the extant beta-rhizobial species emerged between 2744 and 1752 million years ago (Ma) and later (2135–514 Ma) diverged into the lineages Cupriavidus, Trinickia and Paraburkholderia. However, major diversifications of rhizobial Paraburkholderia occurred in three phases: (i) during the Permian and Triassic periods (400–200 Ma) when Pangaea was fully assembled and its landmass filling up with flora and fauna, (ii) during the Jurassic period (200–150 Ma) when fauna and flora were flourishing in Pangaea, and (iii) during the Cretaceous and Paleogene periods (150–23 Ma) when Gondwana was breaking up. Furthermore, Paraburkholderia were estimated to have acquired their precursor nodulation loci that evolved into their current nodulation loci from different sources between 103 and 48 Ma. Accordingly, our study describes the evolutionary history of rhizobial Paraburkholderia, thus enabling us to understand the past environmental factors that shaped the current geographical distribution of these agriculturally important bacteria, and to identify locations potentially rich in beta-rhizobia.

豆科植物的固氮和结瘤共生体，属于β变形菌纲，被非正式地称为β根瘤菌。到目前为止，只在Paraburkholderia、Trinickia和Cupriavidus属中发现了这一类群的成员。在这项研究中，我们研究了该性状在主要的β -根瘤菌属Paraburkholderia中的进化历史。这是在当前的进化理论和根瘤菌，Paraburkholderia属和地球的日期估计的背景下确定的。利用800多个不同的蛋白质细菌基因组估计了根瘤菌副芽孢杆菌的进化分化日期及其祖先结瘤状态。使用软件BEAST（贝叶斯进化分析采样树）和APE（使用‘ chronopl ’函数）进行分子定年。结果表明，现存β -根瘤菌物种的最近共同祖先（MRCA）出现在2744 ~ 1752亿年前（Ma），之后（2135 ~ 514 Ma）分化为Cupriavidus、Trinickia和Paraburkholderia谱系。然而，根瘤菌Paraburkholderia的主要多样化发生在三个阶段：(i)在二叠纪和三叠纪时期（400-200 Ma），当时泛大陆完全组装，其陆地上充满了动植物；（ii）在侏罗纪时期（200-150 Ma），当时泛大陆动植物繁盛；（iii）在白垩纪和古近纪时期（150-23 Ma），当时冈瓦纳大陆正在分裂。此外，据估计，Paraburkholderia在103至48 Ma之间从不同的来源获得了它们的前体细胞结瘤位点，并进化成它们现在的结瘤位点。因此，我们的研究描述了根瘤菌副根瘤菌的进化历史，从而使我们能够了解过去的环境因素，这些环境因素塑造了这些农业上重要的细菌的当前地理分布，并确定了潜在丰富的-根瘤菌的位置。

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引用次数: 0

Diversification and differentiation of Stipa species shed light on the regional evolutionary history of the eastern Eurasian steppe 针虫种类的多样化和分化对欧亚东部草原的区域进化史具有重要意义

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-25 DOI: 10.1016/j.ympev.2025.108449

Dongqing Yan , Yanyan Fan , Xiaoru Jiang , Yang Ma , Kejian Lin , Zhenhua Dang , Jianming Niu

Understanding the evolutionary history of the Eurasian steppe is crucial for restoring severely degraded ecosystems and mitigating the impact of future climate change. Stipa species, which demonstrate zonal and extrazonal distribution patterns across the eastern Eurasian steppe, serve as a noteworthy example for elucidating the evolution of this biome. In this paper, we explored the phylogeny of the genus Stipa using transcriptome data, while examined the genetic differentiation, demographic history, and adaptive evolution of S. baicalensis, S. grandis, and S. krylovii using RAD-seq data. We found that from mid-Miocene to early-Pliocene, the Qinghai-Tibet Plateau (QTP) uplift triggered the formation of the Asian monsoon and progressive aridification of Asian interior, fostering Stipa species emergence and out-of-QTP. During the Pleistocene, glacial-interglacial cycles and East Asian monsoon fluctuations led to alternations of cold-dry and warm-wet climate, facilitating the differentiation and migration of these three species across Mongolian Plateau, Loess Plateau, and Central Asia. These climatic oscillations shaped distinct genetic variations among these species in different geographical regions. Furthermore, annual precipitation and total soil nitrogen content were the primary drivers of their adaptive evolution. Noticeably, the evolution of Stipa species exhibits prominent spatio-temporal integration characteristics. Conclusively, we proposed a comprehensive regional evolution framework for plants in the eastern Eurasian steppe. Our research fills gaps in understanding the evolutionary history of the entire Eurasian steppe and the impact of evolutionary processes on contemporary plant distributions, which is vital for assessing steppe vegetation shifts and plant genomic vulnerability under climate change scenarios.

了解欧亚草原的进化史对于恢复严重退化的生态系统和减轻未来气候变化的影响至关重要。在欧亚东部大草原上，针虫物种表现出地带性和非地带性分布模式，为阐明该生物群系的演变提供了一个值得注意的例子。本研究利用转录组数据对针蚜属植物的系统发育进行了研究，并利用RAD-seq数据对黄芩、大针蚜和克氏针蚜的遗传分化、种群历史和适应进化进行了研究。更新世期间，冰期-间冰期旋回和东亚季风波动导致了干冷和暖湿气候的交替，促进了这三种植物在蒙古高原、黄土高原和中亚地区的分化和迁移。这些气候波动在不同地理区域的这些物种之间形成了不同的遗传变异。年降水量和土壤全氮含量是其适应进化的主要驱动力。值得注意的是，针茅种的进化具有明显的时空整合特征。最后，我们提出了欧亚东部草原植物区域进化的综合框架。我们的研究填补了了解整个欧亚草原的进化史和进化过程对当代植物分布的影响的空白，这对于评估气候变化情景下草原植被转移和植物基因组脆弱性至关重要。

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引用次数: 0

Sink or swim: Phylogenomic analysis of Baikal sculpins reveals multiple transformations to pelagic, bathybenthic, and lotic ecomorphologies 下沉或游泳：贝加尔湖雕塑的系统基因组分析揭示了向远洋、深海和海洋生态形态的多重转变

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-25 DOI: 10.1016/j.ympev.2025.108451

Michael W. Sandel , Andres Aguilar , Sergei Kirilchik , David A. Neely , Bakhtiar E. Bogdanov , Kayla M. Fast , Joshua D. Millwood

Lake Baikal ranks among the world’s most species-rich freshwater ecosystems; however, the evolutionary histories of endemic taxa remain poorly understood. The unique abiotic environments of Lake Baikal include the only bathybenthic, bathypelagic, and deep hydrothermal vent communities in freshwater, each of which supports species with derived morphological and physiological traits. As the only known vertebrate radiation endemic to a non-tropical ancient lake, Baikal sculpins represent an underappreciated resource for investigating evolutionary processes that underlie adaptive radiation. We examined morphological and ecological diversity among Baikal sculpins and present the first interspecific phylogeny inferred from dense nuclear genomic sampling (ddRADseq). The new phylogeny supports a holarctic lotic ancestor to a limnetic radiation and reveals reticulate adaptations to lotic, bathyal, and pelagic habitats.

We apply the new phylogeny to revise Baikal sculpin taxonomy, and we resurrect Uranidea as a monotypic sister-group to the Baikal sculpin radiation. Our data support independent evolution of pelagic and bathypelagic ecomorphs and multiple invasions of aphotic habitats. Concordant ecomorphological shifts involved dramatic modification of skeletal elements, sensory systems, and reproductive mode. Habitat depth is highlighted as an important abiotic factor associated with adaptive radiation, but more research is needed to address potentially confounding effects of thermal and photic zonation. We discuss the geoclimatic processes that may explain this rapid radiation, and conclude by highlighting the anthropogenic changes that threaten this irreplaceable natural resource.

贝加尔湖是世界上物种最丰富的淡水生态系统之一；然而，地方性分类群的进化历史仍然知之甚少。贝加尔湖独特的非生物环境包括淡水中唯一的深海底栖、深海底栖和深海热液喷口群落，每一种都支持具有衍生形态和生理特征的物种。作为唯一已知的非热带古湖泊特有的脊椎动物辐射，贝加尔湖雕塑代表了一种未被充分重视的资源，用于研究适应性辐射的进化过程。我们研究了贝加尔湖雕塑的形态和生态多样性，并提出了第一个通过密集核基因组抽样（ddRADseq）推断的种间系统发育。新的系统发育支持一个全北极的深海祖先到一个海洋辐射，并揭示了对深海、深海和远洋栖息地的网状适应。我们应用新的系统发育来修正贝加尔湖雕塑分类，并将天王星作为贝加尔湖雕塑辐射的单型姐妹群复活。我们的数据支持远洋和深海生态形态的独立进化和多栖栖息地的入侵。和谐的生态形态变化包括骨骼元素、感觉系统和生殖模式的显著改变。生境深度是与适应性辐射相关的重要非生物因子，但需要更多的研究来解决热和光带的潜在混淆效应。我们讨论了可能解释这种快速辐射的地理气候过程，并通过强调威胁这种不可替代的自然资源的人为变化来结束。

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引用次数: 0

Hidden diversity in the driest desert on Earth: genomics unveils cryptic diversity in an ancient South American gecko lineage (Phyllodactylidae, Garthia) 地球上最干燥沙漠中隐藏的多样性：基因组学揭示了古代南美壁虎谱系的神秘多样性（Phyllodactylidae, Garthia）

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-25 DOI: 10.1016/j.ympev.2025.108448

Kamryn Carter , Claudio Reyes-Olivares , Jonathan Eubanks , Hayden Hanna , Stuart V. Nielsen , Damien Esquerré

Quantifying and delimiting biodiversity is a critical challenge in modern biology, particularly in taxa where species boundaries are unclear or poorly defined. In many cases, traditional morphological approaches are insufficient or even misleading when delimiting taxonomic units. Modern genomic methods offer a powerful tool to gain an in-depth perspective of evolutionary history and genetic variation across populations. The Chilean Marked Geckos (genus Garthia) currently comprise two species, G. gaudichaudii and G. penai, endemic to the semi-arid coastal regions of North-Central Chile. Although additional species/subspecies have been proposed, a recent study went so far as to suggest that just one species should be recognized. However, no study to date has evaluated their diversity using genetic tools. For the first time, we used phylogenomic and population genetic methods to better understand diversity across the entire distribution of Garthia. Using both mtDNA and nDNA data, we reconstruct the phylogeny, assess population structure, and delimit species. Our phylogenetic analyses reveal deep evolutionary divergence strongly supporting the existence of at least the two nominate species. However, our species delimitation and population structure analyses suggest alpha-level diversity could be even higher, with evidence supporting a cryptic species complex of between three and eleven species, including deep divergences between geographically proximate populations. We discuss the impact these findings have on our understanding of Chilean gecko diversity and biogeographic patterns in the world’s driest desert.

定量和划分生物多样性是现代生物学的一个关键挑战，特别是在物种边界不清楚或定义不清的分类群中。在许多情况下，传统的形态学方法在划分分类单位时是不充分的，甚至是误导性的。现代基因组方法提供了一个强大的工具，以获得一个深入的视角的进化史和遗传变异的人群。智利标记壁虎（Garthia属）目前包括两个物种，G. gaudichadii和G. penai，特有于智利中北部半干旱的沿海地区。虽然已经提出了更多的物种/亚种，但最近的一项研究甚至认为应该只承认一个物种。然而，迄今为止还没有研究使用遗传工具评估它们的多样性。我们首次使用系统基因组学和群体遗传学方法来更好地了解加西亚整个分布的多样性。利用mtDNA和nDNA数据，我们重建了系统发育，评估了种群结构，并划分了物种。我们的系统发育分析揭示了深层的进化分歧，有力地支持了至少两个指定物种的存在。然而，我们的物种划分和种群结构分析表明，α水平的多样性可能更高，有证据支持3到11种之间的隐种复合物，包括地理上接近的种群之间的深度分歧。我们讨论了这些发现对我们理解智利壁虎多样性和世界上最干旱沙漠的生物地理格局的影响。

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引用次数: 0

Target sequence capture informs generic delimitation and hybridization in the tribe Lasiopetaleae (Malvaceae) 靶序列捕获为部落Lasiopetaleae （Malvaceae）的属界划分和杂交提供了信息。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-22 DOI: 10.1016/j.ympev.2025.108445

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

The tribe Lasiopetaleae (Malvaceae subfamily Byttnerioideae) consists of nine genera largely distributed in Australia. Boundaries between genera have historically been contentious, with many species being described in one genus and variously transferred to others. Previous phylogenetic studies using morphology and plastid DNA have mostly resolved relationships within the tribe except for a group of genera allied to Lasiopetalum. To clarify generic boundaries and the phylogeny of this group, we generated and analyzed target sequence capture data for 144 samples across 8 genera, focusing on denser sampling within Guichenotia, Lasiopetalum, Lysiosepalum and Thomasia, using two bait sets: Angiosperms353 and OzBaits. Sequences for 388 nuclear loci were assembled using two approaches: HybPiper and SECAPR (with some modifications), and results were compared. We used concatenation and coalescent analyses, with and without putative hybrids, to generate new phylogenetic hypotheses for the group. Potential hybrids were investigated using HybPhaser and by assembling phased high-copy portions of the genome, as well as by quantifying potential parentage from heterozygous sites in alignments. Our results indicate that current genera in the group are paraphyletic, and there are examples of hybridization within and between them. Gene concordance for backbone relationships in the group was low, likely caused by gene tree estimation error and taxon instability among closely-related species as well as incomplete lineage sorting during rapid diversification. Despite discordance and hybridization, morphologically diagnosable genomic clades could be recognized. Paraphyly might be resolved by expanding one or two existing genera substantially (subsuming c. 108 taxa) or, for less taxonomic disruption, reinstating two former genera and recognizing two new genera.

本科由9个属组成，主要分布于澳大利亚。在历史上，属之间的界限一直是有争议的，许多物种被描述在一个属中，并以各种方式转移到其他属中。以前使用形态学和质体DNA的系统发育研究主要解决了部落内部的关系，除了与Lasiopetalum相关的一组属。为了明确该类群的属界和系统发育，我们生成并分析了8个属144个样本的目标序列捕获数据，重点对Guichenotia、Lasiopetalum、Lysiosepalum和Thomasia进行了密集采样，使用了两种诱饵：Angiosperms353和OzBaits。采用HybPiper和SECAPR两种方法（进行了一些修改）对388个核位点进行序列组装，并对结果进行比较。我们使用串联和聚结分析，有或没有假定的杂交，为该群体产生新的系统发育假设。利用HybPhaser，通过组装基因组的阶段性高拷贝部分，以及通过对杂种组合中杂合位点的潜在亲本进行量化，来研究潜在的杂种。我们的结果表明，目前属的群体是副葡萄，有杂交的例子和他们之间。基因一致性较低，可能是由于基因树估计错误、近缘物种间分类单元不稳定以及快速多样化过程中谱系分类不完整所致。尽管不一致和杂交，形态学上可诊断的基因组枝可以被识别。Paraphyly可以通过大量扩展一个或两个现有的属（包括约108个分类群）来解决，或者为了减少分类上的破坏，可以恢复两个以前的属并识别两个新属。

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引用次数: 0

Geographic isolation, ecological adaptation, and hybridization influenced fast divergence of a Solanaceae plant group from subtropical highland grasslands 地理隔离、生态适应和杂交影响了亚热带高原草原茄科植物类群的快速分化

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2025-08-17 DOI: 10.1016/j.ympev.2025.108446

Luana S. Soares , Aureliano Bombarely , Loreta B. Freitas

Several processes influence species establishment in nature, with evolutionary radiations playing a critical role in biodiversity evolution. Ecological adaptation, progenitor-derivative speciation, pollinator shifts, and geographic isolation followed by local adaptation can lead to plant radiations in montane systems. This study investigated the rapid divergence and migration of highland Petunia species. Employing reduced representation genome sequencing and a genomic population approach, we focused on detecting structuration, ecological inference, hybridization/introgression, and evolutionary patterns. Our findings revealed an intricate and complex array of factors, including ecological adaptation without marked genetic diversity, hybridization, and geographic isolation, which led to species divergence in a short period. Ancestral polymorphism sharing maintained genetic diversity could facilitate rapid divergence among the highland species by providing variation to natural selection. During the Pleistocene, Petunia species expanded and contracted their ranges in response to the alternance of climate cycles. This period of environmental changes was pivotal in promoting rapid speciation through geographic isolation. Here, we highlight the multifaceted nature of species diversification, influenced by a confluence of geographic distribution, demographic history, and hybridization. The interplay of these factors highlights the diverse and dynamic pathways to speciation in a model plant genus, thereby contributing to a deeper understanding of species diversification and the role of genetic and environmental factors in shaping biodiversity.

自然界中有几个过程影响物种的建立，其中进化辐射在生物多样性进化中起着关键作用。生态适应、祖-衍生物种形成、传粉媒介转移和地理隔离以及随后的局部适应都可能导致山地系统中的植物辐射。研究了高原矮牵牛的快速分化和迁移。采用减少代表性的基因组测序和基因组群体方法，我们专注于检测结构、生态推断、杂交/渐渗和进化模式。我们的研究结果揭示了一系列复杂而复杂的因素，包括没有明显遗传多样性的生态适应、杂交和地理隔离，导致物种在短时间内分化。祖先多态性共享维持了遗传多样性，为自然选择提供了变异，促进了高原物种间的快速分化。更新世期间，矮牵牛花的分布范围随着气候周期的变化而扩大和缩小。这一时期的环境变化是通过地理隔离促进物种快速形成的关键。在这里，我们强调了物种多样化的多面性，受地理分布、人口历史和杂交的影响。这些因素的相互作用突出了模式植物属物种形成的多样性和动态途径，从而有助于更深入地了解物种多样化以及遗传和环境因素在塑造生物多样性中的作用。

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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 : 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。

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引用次数: 0