Molecular Phylogenetics and Evolution最新文献_第4页

Integrative species delimitation methods infer species boundaries in the Lomatium foeniculaceum complex and indicate an evolutionary history from the Southwest towards the Northeast in western North America 综合物种划分方法推断了北美西部Lomatium foeniculaceum复合体的物种边界，并指出了其从西南向东北的进化史。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-12-16 DOI: 10.1016/j.ympev.2024.108276

Daniel E. Botello , Donald H. Mansfield , Sven Buerki , Mary Ann E. Feist , Mark Darrach , James F. Smith

Delimiting species boundaries is a perennial challenge in the field of systematics. Resolving whether morphological variation is the result of environmental parameters, incipient speciation, or complete speciation is especially challenging when the variation is subtle. Within the perennial endemic North American clade of Apiaceae (PENA) there are numerous examples in which widespread species have subtle geographically defined morphological variants that have typically been recognized at the subspecific rank. The Lomatium foeniculaceum (Nutt.) Coult & Rose species complex is a salient case that has long been treated as a single species with five infrataxa, spanning much of the western United States and western Canada in a morphological continuum: L. foeniculaceum var. foeniculaceum, L. foeniculaceum var. daucifolium (Torr. & A. Gray) Cronquist, L. foeniculaceum var. macdougalii (J.M. Coult. & Rose) Cronquist, L. foeniculaceum var. fimbriatum (W.L. Theob.) B. Boivin, and L. foeniculaceum var. inyoense (Mathias & Constance) B. Boivin. We utilized the Angiosperm353 baits kit to sample nuclear loci from these five taxa to determine if the subspecific taxa formed discrete genetic groups with the molecular data. Groups that were identified were then examined for a combination of morphological and ecological traits that corresponded to these groups and could be used to determine the most appropriate taxonomic ranks of recovered groups. Molecular data recovers six well-supported monophyletic clades and a seventh clade of a single individual. Samples initially identified as L. foeniculaceum var. macdougalii are in two clades with one sister to L. foeniculaceum var. foeniculaceum/L. foeniculaceum var. daucifolium the other sister to L. foeniculaceum var. fimbriatum. Most samples of L. foeniculaceum var. foeniculaceum are in the same clade; others are in the clade with L. foeniculaceum var. daucifolium depending on the analysis. Each clade can be defined with a distinct morphological diagnostic character state. We conclude that molecular data and morphology support the recognition of five distinct species within the complex: L. inyoense Mathias & Constance, L. macdougalii J. M. Coult. & Rose, L. fimbriatum (W.L. Theob.) Botello & J.F. Sm., L. semivaginatum Botello & J.F. Sm., and L. foeniculaceum with two varieties retained, L. foeniculaceum var. foeniculaceum and L. foeniculaceum var. daucifolium. The data suggest that the Continental Divide has been influential in the evolution of these species, acting as an effective barrier facilitating speciation.

物种边界的划定一直是系统学领域的难题。当变异很微妙时，要确定形态变异是环境参数、早期物种形成还是完全物种形成的结果尤其具有挑战性。在Apiaceae （PENA）的北美多年生特有种分支中，有许多例子表明，广泛分布的物种具有微妙的地理上定义的形态变异，这些变异通常被认为是亚种级。小茴香（坚果）库尔特和玫瑰物种复合体是一个突出的例子，长期以来一直被视为具有五个下丛的单一物种，在形态连续体中跨越了美国西部和加拿大西部的大部分地区：L. foeniculaceum var. foeniculaceum， L. foeniculacum var. dauciolium (Torr。克朗奎斯特，l.f eniculacum varmacdougalii （J.M. Coult）。克朗奎斯特，l.f eniculacum变种毡状体（W.L. Theob）B. Boivin，和L. foeniculacum var. inyoense （Mathias & Constance）利用Angiosperm353 baits试剂盒对这5个亚特异类群的核位点进行分析，以确定这些亚特异类群是否形成了离散的遗传群。然后，对鉴定出的类群进行形态学和生态学特征的综合检查，以确定恢复类群的最合适的分类等级。分子数据恢复了六个支持良好的单系进化枝和一个单一个体的第七枝。最初鉴定为L. foeniculacum var. macdougalii的样品分为两个分支，与L. foeniculacum var. foeniculacum /L有一个姊妹。鸢尾花是鸢尾花的另一个姐妹花。大部分样本在同一枝上；另一些则根据分析结果与L. foeniculacum var. daucifolium同属分支。每个分支都具有不同的形态诊断特征状态。我们的结论是，分子数据和形态学支持在复合体中识别五个不同的物种：L. inyoense Mathias & Constance， L. macdougalii J. M. Coult。&罗丝，l.f imbriatum （W.L. Theob）博特罗& J.F. Sm。， J.F. m.；和小叶乳香，保留了小叶乳香和小叶乳香两个品种。这些数据表明，大陆分水岭对这些物种的进化产生了影响，作为促进物种形成的有效屏障。

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引用次数: 0

A straightforward workflow to explore species diversity using the Patagonian lizards of the Diplolaemus genus (Iguania: Leiosauridae) as a study case, with the description of a new species 一个简单的工作流程来探索物种多样性，以巴塔哥尼亚蜥蜴属（鬣蜥属：Leiosauridae）为研究案例，描述一个新物种。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-12-16 DOI: 10.1016/j.ympev.2024.108274

Juan Vrdoljak , Kevin Imanol Sánchez , Andrea González-Marín , Mariana Morando , Luciano Javier Avila

Disputes over species descriptions, stemming from conceptual disparities and arbitrary species boundaries, are among the primary challenges of modern taxonomy. In this study, we introduce a straightforward workflow, grounded in evolutionary theory, designed to tackle these challenges. We exemplified this approach using Patagonian lizards from the Diplolaemus clade. This workflow involves assigning specimens to putative evolutionary lineages, conducting primary species delimitations, constructing a species tree, comparing lineages for evolutionary independence, and using post-hoc analyses to separate well-supported from ambiguous lineages. This approach aims to establish a reliable foundation for exploring the taxonomic and evolutionary diversity of challenging groups. Applying this workflow to the Diplolaemus clade, we used various analytical methods on genetic (mitochondrial and nuclear markers) and phenotypic data (meristic, linear, and geometric morphometrics). We identified ten lineages with varying degrees of evolutionary independence in a clade where only four species had been described. Among the newly identified lineages, two exhibited low support for evolutionary independence, three showed strong support but had non-conclusive information, and one was recognized and described as a new species. In summary, our hierarchical workflow not only facilitated comprehensive comparisons but also enabled us to draw robust conclusions.

关于物种描述的争论，源于概念上的差异和武断的物种边界，是现代分类学的主要挑战之一。在这项研究中，我们介绍了一个简单的工作流程，以进化理论为基础，旨在解决这些挑战。我们用巴塔哥尼亚蜥蜴为例说明了这种方法。该工作流程包括将标本分配给假定的进化谱系，进行主要物种划分，构建物种树，比较进化独立性的谱系，以及使用事后分析将有充分支持的谱系与不明确的谱系分开。该方法旨在为探索具有挑战性的类群的分类和进化多样性建立可靠的基础。将此工作流程应用于双扇门分支，我们对遗传（线粒体和核标记）和表型数据（分生、线性和几何形态计量学）使用了各种分析方法。我们在一个只被描述过4个物种的进化枝中鉴定出了10个具有不同程度的进化独立性的谱系。在新发现的谱系中，2个谱系对进化独立性的支持度较低，3个谱系对进化独立性的支持度较强，但信息不确定，1个谱系被认定为新种。总之，我们的分层工作流程不仅促进了全面的比较，而且使我们能够得出有力的结论。

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引用次数: 0

A time-calibrated salamander phylogeny including 765 species and 503 genes 包括765种和503个基因的时间校准蝾螈系统发育。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-12-15 DOI: 10.1016/j.ympev.2024.108272

Alexander A. Stewart, John J. Wiens

Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22–45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses.

最近的时间校准两栖动物系统进化论在现存蝾螈的科级关系上达成了一致，但采样机制不同，推断的分化时间也大相径庭。例如，最近一项基于 220 个核基因位点的系统发生组研究对分类群取样有限（41 个物种），估计的分化时间相对较短，而一项基于 15 个基因和 481 个物种的更广泛的超矩阵研究估计的主要支系的分化时间要早 2200-4500 万年。在这里，我们结合了系统发生组和超级矩阵方法，根据分子标记估计了迄今为止最大的蝾螈系统发生。我们的矩阵包含 765 个蝾螈物种和 503 个基因（总体数据缺失率为 92.3%）。与之前最大的蝾螈系统发育相比，我们多包含了 284 个物种（增加了 59%），并对目前描述的所有蝾螈物种中的约 93% 进行了采样。我们的年代分析纳入的蝾螈化石校准点是之前研究的两倍多。对树状拓扑结构的最大似然估计得出的科级关系与之前的研究一致。尽管许多物种的数据缺失严重，但几乎所有物种都被归入了预期的属。整个树的 Bootstrap 支持率普遍较高，但在一些基因取样有限的支系中支持率较低（如一些蝾螈属）。年代分析得出的主要支系的年龄估计值一般介于之前的系统发生学分析和超矩阵分析得出的年龄估计值之间。我们还提供了一组 200 个时间校准树，用于比较分析。

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引用次数: 0

Phylogeny, antiquity, and niche occupancy of Trinomia (Hymenoptera: Halictidae), an Afrotropical endemic genus of Nomiinae 非洲热带特有的 Nomiinae 属 Trinomia（膜翅目：Halictidae）的系统发育、古老性和生态位占有。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-12-13 DOI: 10.1016/j.ympev.2024.108273

Silas Bossert , Felipe V. Freitas , Alain Pauly , Gengping Zhu , David W. Crowder , Michael C. Orr , James B. Dorey , Elizabeth A. Murray

The Afrotropical region is home to many endemic bee groups, yet almost none have been studied from an integrated, holistic perspective. Among them, the halictid subfamily Nomiinae contains exceptional African diversity with variable distributions and life histories. Here, we combine phylogenomics, molecular dating, and distributional modelling to explore the evolutionary ecology of the genus Trinomia. We analyzed a matrix of 59 species of Nomiinae using ultraconserved element (UCE) and whole genome data, including all six species of Trinomia, and estimated divergence times for the subfamily. We then generated distribution models for all six species of Trinomia using Maximum Entropy models (MaxEnt) and 671 spatial data points. From these methods, we discovered a monophyletic Trinomia with an unexpected sister group relationship to the Asian-endemic genus Gnathonomia, as well as a recent origin of Trinomia in the late Miocene (∼5.8 million years ago). From our results, we found hints of phylogenetic conservatism in distribution among sister-groups of Trinomia, however, our results also highlight the need for additional efforts inventorying, identifying, and sharing data on African bees. This study represents an exemplary first step into studying bee spatial phylogenomics of African endemic bees.

非洲热带地区是许多地方性蜂群的家园，但几乎没有一个从综合、整体的角度进行过研究。其中，halictid Nomiinae亚科具有独特的非洲多样性，其分布和生活史各异。在这里，我们结合系统基因组学、分子测年和分布模型来探索Trinomia属的进化生态学。利用超保守元件（UCE）和全基因组数据分析了59种triniinae属（包括所有6种Trinomia）的矩阵，并估计了该亚科的分化时间。利用最大熵模型（MaxEnt）和671个空间数据点建立了6种三棱藓属植物的分布模型。从这些方法中，我们发现了一种单系的Trinomia，它与亚洲特有的Gnathonomia属有着意想不到的姐妹群关系，并且在中新世晚期（~ 580万年前）发现了Trinomia的起源。从我们的研究结果中，我们发现了Trinomia姐妹群体分布的系统发育保守性，然而，我们的研究结果也强调了对非洲蜜蜂进行额外的调查、鉴定和共享数据的必要性。本研究代表了非洲特有蜜蜂空间系统基因组学研究的典范性第一步。

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引用次数: 0

Mystery on the Bounty: The family-level status of Pacificana cockayni Hogg, 1904 (Araneae) 赏金之谜：1904年（Araneae） Pacificana cockayni Hogg的家庭地位。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-12-02 DOI: 10.1016/j.ympev.2024.108256

Jacob A. Gorneau , Franklyn Cala-Riquelme , Sarah C. Crews , Katherine O. Montana , Joseph C. Spagna , Cor J. Vink , Lauren A. Esposito

The family-level placement of the species Pacificana cockayni Hogg, 1904 (Araneae, Miturgidae) has been ambiguous for over a century, with the monotypic genus Pacificana initially placed in Agelenidae, later transferred to Amaurobioidinae (Anyphaenidae), and presently in Miturgidae. A recent work describing the male and molecular data consisting of a single mitochondrial gene, cytochrome c oxidase subunit I, confirmed that the species is part of the marronoid clade; however, these data did not result in a conclusive family-level placement. Here, we use low-coverage whole genome sequencing (lcWGS) combined with data from the Sequence Read Archive to infer a phylogeny from ultraconserved elements (UCEs) and six legacy Sanger loci. Indications of potential family placements from prior work and the topologies from this study support a transfer of Pacificana Hogg, 1904 to Cycloctenidae Simon, 1898 (new family placement).

Pacificana cockayni Hogg, 1904（蜘蛛目，Miturgidae）的科级归属在一个多世纪以来一直很模糊，单型属最初被置于Agelenidae，后来被转移到Amaurobioidinae (amyphaenidae)，目前在Miturgidae。最近的一项工作描述了由单个线粒体基因（细胞色素c氧化酶亚基I）组成的雄性和分子数据，证实了该物种是马龙鱼枝的一部分；然而，这些数据并没有得出决定性的家庭安置结果。在这里，我们使用低覆盖全基因组测序（lcWGS）结合Sequence Read Archive的数据，从超保守元件（UCEs）和六个遗留Sanger位点推断出系统发育。从先前的工作和本研究的拓扑结构中得出的潜在家族定位的迹象支持将Pacificana Hogg， 1904年转移到Cycloctenidae Simon， 1898年（新的家族定位）。

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引用次数: 0

Extensive cytonuclear discordance revealed by phylogenomic analyses suggests complex evolutionary history in the holly genus Ilex (Aquifoliaceae) 系统基因组学分析揭示了冬青属植物广泛的细胞核不一致，表明冬青属植物具有复杂的进化历史。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-30 DOI: 10.1016/j.ympev.2024.108255

Ke-Wang Xu , Yi Yang , Hong Chen , Chen-Xue Lin , Lei Jiang , Zhong-Long Guo , Meng Li , Ming-Zhuo Hao , Kai-Kai Meng

Ilex L., the exclusive genus of Aquifoliaceae, encompasses over 600 dioecious wood species with a highly irregular distribution, predominantly found in South America and Asia. The phylogeny and classification of this genus remain enigmatic due to significant early extinctions, constrained morphological diversity, recent hybridization/introgression, and conflicting signals from previously utilized markers. This study presents phylogenetic reconstructions based on complete chloroplast genome sequences and single nucleotide polymorphisms (SNPs) derived from genome resequencing data. A total of 116 accessions of Ilex, representing approximately 108 taxa, were included as the ingroup, with five accessions of two species serving as outgroups. Analysis of the chloroplast genome and nuclear SNP data individually resulted in two robust phylogenetic trees, revealing substantial discrepancies between the chloroplast genome and nuclear SNP phylogenies at both the species and clade levels. The chloroplast genome sequences successfully resolved relationships within this genus into eight strongly supported major clades, while the nuclear SNPs resolved relationships into seven highly supported major clades. Our nuclear SNP phylogenetic tree, in comparison to the chloroplast genome tree, aligns more closely with the recently updated classification of Ilex in multiple instances. The extensive cytonuclear discordance identified may be attributed to recent hybridization events and incomplete lineage sorting (ILS).

冬青（Ilex L.）是水合木科的唯一属，包括600多种雌雄异株木材，分布极不均匀，主要分布在南美洲和亚洲。由于显著的早期灭绝、有限的形态多样性、最近的杂交/渗入以及先前利用的标记的相互矛盾的信号，该属的系统发育和分类仍然是一个谜。本研究基于完整的叶绿体基因组序列和来自基因组重测序数据的单核苷酸多态性（SNPs）进行系统发育重建。其中，116个冬青属属（约108个分类群）为内群，2个属（共5个）为外群。对叶绿体基因组和核SNP数据的分析分别产生了两个强大的系统发生树，揭示了叶绿体基因组和核SNP系统发生在物种和进化支水平上的巨大差异。叶绿体基因组序列成功地将该属内的关系划分为8个强烈支持的主要分支，而核snp则将关系划分为7个高度支持的主要分支。与叶绿体基因组树相比，我们的核SNP系统发育树在多个实例中与最近更新的冬青分类更接近。所发现的广泛的细胞核不一致可能归因于最近的杂交事件和不完整的谱系分类（ILS）。

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引用次数: 0

Phylogenomic analyses unravel the tangled evolutionary history of Genisteae (Fabaceae) 系统基因组学分析揭示了金Genisteae （Fabaceae）错综复杂的进化史。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-30 DOI: 10.1016/j.ympev.2024.108249

Sarah Hunter , Domingos Cardoso , Tracey A. Ruhlman , Robert K. Jansen

Genisteae, a tribe in the subfamily Papilionoideae (Fabaceae), is characterized by the production of quinolizidine alkaloids that confer pest resistance in most of its members. Many relationships at the generic level remain unresolved due largely to a lack of modern attempts to reconstruct the phylogeny. Previous studies with limited taxon sampling and only a few molecular loci indicated the presence of three clades within the tribe: the Lupinus clade, the Cytisus-Genista complex and the Argyrolobium group. There are also two historical genera, Teline and Chamaecytisus, that have been reclassified over the years with some controversy. Species from Teline are currently classified in Genista, and Chamaecytisus species are placed inside of Cytisus. Sellocharis is another genus with vague placement inside of Genisteae near Anarthrophyllum, based mostly on morphology and cytology. Representative taxa from 24 of the 25 genera of Genisteae, along with species of historical genera Teline and Chamaecytisus, were sampled and utilized in a phylogenomic investigation using both plastid and nuclear data to resolve relationships at the generic level. Whole genomic DNA was sequenced and complete plastomes were assembled and annotated. Low-copy nuclear genes were retrieved from the genomic DNA sequences using a mapping-assembly-scaffold approach. Phylogenetic analyses using maximum likelihood, Bayesian and coalescence methods resulted in fully resolved and strongly supported trees for both nuclear and plastid data that show four major clades inside of Genisteae: Cytisus-Genista complex, Lupinus clade, Argyrolobium group and the novel Anarthrophyllum group. The resulting phylogenetic trees also supported the transfer of the Argyrolobium group from Crotalarieae to Genisteae, and the reclassification of Teline inside of Genista, both of which were previously suggested in literature. The phylogenetic trees also determined a placement for Sellocharis in the new Anarthrophyllum group. Although both nuclear and plastid trees were congruent with respect to the monophyly and relationships among the four major clades, incongruence was detected within some of the major clades and the potential causes are discussed.

金凤花科是凤蝶亚科（豆科）中的一个分支，其特点是产生喹啉类生物碱，使其大多数成员具有抗虫性。由于缺乏重建系统发育的现代尝试，许多在一般水平上的关系仍未得到解决。以往的研究通过有限的分类单元采样和少量的分子位点表明，该部落中存在三个分支：Lupinus分支，Cytisus-Genista复合体和Argyrolobium组。历史上还有两个属，Teline和Chamaecytisus，多年来一直被重新分类，但存在一些争议。来自Teline的物种目前被分类在Genista中，Chamaecytisus物种被放在Cytisus中。Sellocharis是另一个定位模糊的属，主要基于形态学和细胞学。本文选取了金雀花科25属中24属的代表性分类群，以及历史上的Teline属和Chamaecytisus属的种，利用质体和核数据进行了系统基因组学研究，以解决属水平上的关系。测序全基因组DNA，组装完整质体并进行注释。利用定位-组装-支架方法从基因组DNA序列中检索低拷贝核基因。利用最大似然、贝叶斯和聚结方法进行系统发育分析，得到了核和质体数据的完全解析和强有力支持的树，显示了金雀亚科内部的四个主要分支：Cytisus-Genista复合体、Lupinus分支、Argyrolobium类群和新的Anarthrophyllum类群。所得到的系统发育树也支持了Argyrolobium类群从crotalariae向gensteae的转移，以及Genista内部的Teline的重新分类，这两个都是之前文献中提出的。系统发育树还确定了Sellocharis在新的节肢动物组中的位置。尽管核树和质体树在四个主要分支的单系和关系方面是一致的，但在一些主要分支中发现了不一致，并讨论了可能的原因。

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引用次数: 0

Endogean habits drove cryptic diversification in Appalachian Lathrobium Gravenhorst (Coleoptera, Staphylinidae) 内源习性驱动了Appalachian Lathrobium Gravenhorst（鞘翅目，葡萄球菌科）的隐多样性。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-29 DOI: 10.1016/j.ympev.2024.108252

Adam Haberski , Michael S. Caterino

The southern Appalachian Mountains are a biodiverse region with high levels of endemism. Shared biogeographic patterns among co-distributed, but independent taxa might illuminate common drivers of Appalachian endemism. Lathrobium is a Holarctic genus with 38 species described form North America, six of which are flightless and endemic to the high Appalachians. We use an integrative morphological and multi-locus molecular dataset to study phylogenetic and biogeographical relationships of Appalachian Lathrobium and test subgeneric hypotheses. A phylogeny based on 176 samples from 67 taxa supported three independent arrivals in the Appalachian Mountains. Divergence times estimated in BEAST2 were concurrent for all three lineages and fell between the Miocene or early Pliocene (16.4 – 4.6 Ma). Speciation within Appalachians occurred during the Pleistocene (2.3 – 0.1 Ma). Monophyly of existing subgenera was supported except for Abletobium Casey. Abletobium is placed in synonymy with Glyptomerus Müller. Our results reveal the importance of cold-climate refugia within the Appalachian Mountains for the persistence and in-situ diversification of endemic endogean taxa. We hypothesize that the xeric climate of the Miocene drove Lathrobium lineages into the mountains and subsequent isolation in mountaintop refugia during warm Pleistocene interglacials led to speciation.

南部阿巴拉契亚山脉是一个生物多样性的地区，具有高度的地方性。在共同分布但独立的分类群之间共享的生物地理模式可能阐明阿巴拉契亚地区特有的共同驱动因素。Lathrobium是一个全北极属，在北美有38种，其中6种是不会飞的，是阿巴拉契亚山脉特有的。我们使用一个完整的形态学和多位点分子数据集来研究Appalachian Lathrobium的系统发育和生物地理关系，并测试亚属假设。基于来自67个分类群的176个样本的系统发育支持了三次在阿巴拉契亚山脉的独立到达。在BEAST2中估计的三个谱系的分化时间是同步的，并且在中新世和上新世早期之间（16.4 - 4.6 Ma）。阿巴拉契亚山脉的物种形成发生在更新世（2.3 - 0.1 Ma）。除Abletobium Casey外，现有亚属均支持单系性。Abletobium与glytomerus myller同义。我们的研究结果揭示了阿巴拉契亚山脉寒冷气候避难所对地方性内源分类群的持久性和原位多样性的重要性。我们假设中新世的干旱气候驱使Lathrobium谱系进入山区，随后在温暖的更新世间冰期在山顶避难的隔离导致了物种形成。

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引用次数: 0

Phylogenomics of Paragymnopteris (Cheilanthoideae, Pteridaceae): Insights from plastome, mitochondrial, and nuclear datasets 副翼蕨的系统基因组学：来自质体、线粒体和核数据集的见解。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-29 DOI: 10.1016/j.ympev.2024.108253

Jing Zhao , Zhen-Long Liang , Shao-Li Fang , Rong-Juan Li , Chuan-Jie Huang , Li-Bing Zhang , Tanner Robison , Zhang-Ming Zhu , Wen-Jing Cai , Hong Yu , Zhao-Rong He , Xin-Mao Zhou

Previous studies have shown that at least six genera of the Cheilanthoideae, a subfamily of the fern family Pteridaceae, may not be monophyletic. In these non-monophyletic genera, the Old-World genus Paragymnopteris including approximately five species have long been controversial. In this study, with an extensive taxon sampling of Paragymnopteris, we assembled 19 complete plastomes of all recognized Paragymnopteris species, plastomes of Pellaea (3 species) and Argyrochosma (1 species), as well as transcriptomes from Paragymnopteris (6 species) and Argyrochosma (1 species). We conducted a comprehensive and systematic phylogenomic analysis focusing on the contentious relationships among the genus of Paragymnopteris through 9 plastid makers, the plastomes, mitochondria, nuclear ribosomal cistron genomes, and single-copy nuclear genes. Moreover, we further combined distribution, ploidy, and morphological features to investigate the evolution of Paragymnopteris. The backbone of Paragymnopteris was resolved consistently in the nuclear and plastid phylogenies. Our major results include: (1) Paragymnopteris is not monophyletic including two fully supported clades; (2) confirming that Paragymnopteris delavayi var. intermedia is a close relative of P. delavayi instead of P. marantae var. marantae; (3) the chromosome base number may not be a stable trait which has previously been used as an important character to divide Paragymnopteris into two groups; and (4) gene flow or introgression might be the main reason for the gene trees conflict of Paragymnopteris, but both gene flow and ILS might simultaneously and/or cumulatively act on the conflict of core pellaeids. The robust phylogeny of Paragymnopteris presented here will help us for the future studies of the arid to semi-arid ferns of Cheilanthoideae at the evolutionary, physiological, developmental, and omics-based levels.

先前的研究表明，在蕨类植物翼蕨科的一个亚科中，至少有六个属可能不是单系的。在这些非单系属中，包括大约5种的旧大陆副羽翼属长期以来一直存在争议。本研究通过对Paragymnopteris的广泛分类取样，收集了所有已识别的Paragymnopteris种的19个完整质体组，以及Pellaea（3种）和Argyrochosma（1种）的质体组，以及Paragymnopteris（6种）和Argyrochosma（1种）的转录组。通过9个质体制造体、质体体、线粒体、核糖体反扰子基因组和单拷贝核基因，对副蹼翅虫属植物间存在争议的关系进行了全面系统的系统基因组分析。此外，我们进一步结合分布、倍性和形态特征来研究副羽翼虫的进化。副翅虫的骨干在核和质体系统发育中是一致的。我们的主要结果包括：(1)副羽翼不是单系的，包括两个完全支持的分支；(2)证实了中庸副阳翅虫不是黄翅虫的近亲，而是黄翅虫的近亲；(3)染色体碱基数可能不是一个稳定的性状，而染色体碱基数曾被认为是将副羽翼虫分为两类的重要特征；(4)基因流或基因渗入可能是副羽翼虫基因树冲突的主要原因，但基因流和基因流可能同时或累积作用于核心鳞片虫的冲突。本文所介绍的副蕨类植物强健的系统发育将有助于我们今后在进化、生理、发育和组学水平上对蕨类植物进行进一步的研究。

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引用次数: 0

Phylogenomics reveals a new generic delimitation of Asian Millettia, with reinstatements of Pongamia and Otosema (Fabaceae: Millettieae) 系统基因组学揭示了亚洲粟属植物的新属划分，恢复了粟科粟属植物Pongamia和Otosema。

IF 3.6 1区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Phylogenetics and Evolution

Pub Date : 2024-11-28 DOI: 10.1016/j.ympev.2024.108254

Zhuqiu Song , Liansheng Xu , Anoop Puthuparampil Balan , Myriam Gaudeul , Yiyong Zhao , Kaiwen Jiang , Tian Li , Shijin Li

The generic relationships within the core Millettieae have not been well resolved to date. Millettia is considered one of the most problematic genera to classify within the core Millettieae, with approximately 150 species found in Asia and Africa. Recent molecular evidence has indicated that Millettia is highly polyphyletic. In this study, we utilized plastomes and single-copy nuclear genes from genome skimming sequencing to reconstruct the generic relationships and estimate the divergence time for the core Millettieae, focusing on the Asian species of Millettia. Our results revealed a broader circumscription of the core Millettieae with the inclusion of the Phaseoleae subtribe Ophrestiinae, consisting of 7 clades and 14 subclades within two main groups (canavanine and non-canavanine). The Asian species of Millettia were grouped into three distinct, well-supported subclades, leading us to propose a much narrower generic concept of Millettia, along with the reinstatements of the genera Pongamia and Otosema. Millettia s.str. was restricted to include only seven species. Pongamia was recognized as a medium-sized genus that includes Fordia and Ibatiria, with approximately 56 species. Otosema, usually treated as a subgenus or section of Millettia, was resurrected as a distinct genus with three species. Our findings also indicated that the sampled African Millettia species belong to three subclades distinct from the Asian Millettia subclades, warranting further investigation in future studies. The dating result showed that the early rapid diversification of the core Millettieae during the Mid-Miocene Climatic Optimum involved several major problematic genera, including Derris s.lato, Lonchocarpus s.lato, and Millettia s.lato, which may explain why these plant groups are difficult to classify. These results offer new insights into the phylogeny and taxonomy of the core Millettieae.

到目前为止，核心小米内部的一般关系还没有得到很好的解决。Millettia被认为是在核心Millettieae中分类最困难的属之一，在亚洲和非洲发现了大约150种。最近的分子证据表明，粟粒粟粒具有高度的多系性。本研究以亚洲种为研究对象，利用基因组略读测序的质体和单拷贝核基因，重建了密菇科核心种的属类关系，并估计了其分化时间。我们的研究结果揭示了一个更广泛的核心milletiae的范围，包括Phaseoleae亚部落Ophrestiinae，由7个分支和14个亚分支组成，分为两个主要类群（canavine和non- canavine）。我们把粟属的亚洲种划分为三个不同的、有充分证据支持的亚支，使我们提出了一个更狭窄的粟属的一般概念，同时恢复了粟属和粟属。Millettia s.str。被限制只包括五种。Pongamia被认为是一个中等大小的属，包括Fordia和Ibatiria，大约有58种。Otosema，通常被认为是Millettia的一个亚属或部分，被复活为一个独特的属，有三个种。研究结果还表明，非洲粟子属属与亚洲粟子属属不同的3个亚支，值得进一步研究。结果表明，中新世中期气候最适期的早期快速多样化涉及了几个主要的问题属，包括Derris s.l、Lonchocarpus s.l和Millettia s.l，这可能解释了这些植物群难以分类的原因。这些结果为核心粟科的系统发育和分类提供了新的认识。

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引用次数: 0