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Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae). 勿忘我系统发生组学:提高新西兰奥特亚罗瓦岛和山区快速辐射的分辨率和分类学(Myosotis;Boraginaceae)。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-22 DOI: 10.1016/j.ympev.2024.108250
Heidi M Meudt, Sofie Pearson, Weixuan Ning, Jessica M Prebble, Jennifer A Tate

Island and mountain systems represent natural laboratories for studies of species radiations, but they often present several challenges for phylogenetic inference and species delimitation. The southern hemisphere forget-me-nots (Myosotis, Boraginaceae) comprise a geologically recent radiation centred in New Zealand, a mountainous archipelago, with about 50 species that are morphologically and ecologically divergent but lack genetic variation sufficient to resolve phylogenetic relationships and species boundaries using standard DNA Sanger sequencing markers, AFLPs, or microsatellites. Many of these Myosotis species are geographically restricted in alpine areas, uncommon or threatened, have polyploid and dysploid genomes, and are of high taxonomic and conservation priority. Here we present phylogenomic analyses using target-capture of Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to improve resolution of the radiation, explore biogeographic and morphological patterns within it, and address specific taxonomic questions for each species. Our comprehensive sampling includes over 300 individuals representing nearly all species from Aotearoa New Zealand and Australia, which is ∼ 2-3 × more taxon sampling and ∼ 80-120 × more molecular data than previously published for Myosotis. Exploration of different data filtering, curation and analyses (coalescent vs. concatenation) improved the resolution of the Angiosperms353 tree, which despite short backbone branches with low support values, showed taxonomic and geographic patterns, including multiple switches between ebracteate and bracteate inflorescences and multiple expansions within New Zealand from Te Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart Island, subantarctic islands, and Australia. Some of these patterns were also seen in the genome skimming datasets, and comparison of the three datasets was useful for improving our understanding of the taxonomy and resolution of this radiation. Although this phylogenomic study does not fully overcome all of the challenges regarding species delimitation of this rapid island and mountain species radiation, it nevertheless makes an important contribution to an integrative taxonomic revision of the southern hemisphere species of Myosotis.

岛屿和山地系统是研究物种辐射的天然实验室,但它们往往给系统发育推断和物种划分带来一些挑战。南半球的勿忘我(Myosotis,博拉金科)是以新西兰为中心的新近地质辐射,该群岛多山,约有 50 个物种,它们在形态和生态上存在差异,但缺乏足够的遗传变异,无法使用标准的 DNA 桑格测序标记、AFLPs 或微卫星来确定系统发育关系和物种界限。其中许多妙蛙属物种在地理上局限于高山地区,不常见或濒临灭绝,具有多倍体和二倍体基因组,在分类学和保护方面具有很高的优先性。在此,我们利用目标捕获的 Angiosperms353 诱饵以及全质粒和 nrDNA 的基因组撇取技术进行了系统发生组分析,以提高辐射的分辨率,探索其中的生物地理学和形态学模式,并解决每个物种的具体分类问题。我们的综合取样包括 300 多个个体,几乎代表了新西兰奥特亚罗瓦和澳大利亚的所有物种,这比以前发表的妙蛙花分类群取样多 2-3 倍,分子数据多 80-120 倍。对不同数据过滤、整理和分析(聚合与合并)的探索提高了 Angiosperms353 树的分辨率,尽管该树的主干分支较短且支持值较低,但仍显示出分类学和地理学模式,包括无苞片和有苞片花序之间的多次切换,以及新西兰境内从 Te Waipounamu 南岛到 Te Ika-a-Māui 北岛、Rakiura Stewart 岛、亚南极岛屿和澳大利亚的多次扩展。其中一些模式也出现在基因组取样数据集中,对这三个数据集进行比较有助于提高我们对这一辐射的分类和分辨率的理解。尽管这项系统发生组学研究并没有完全克服这一快速的岛屿和山地物种辐射所带来的物种划分方面的所有挑战,但它对南半球妙蛙属物种的综合分类学修订做出了重要贡献。
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引用次数: 0
Taken to extremes: Loss of plastid rpl32 in Streptophyta and Cuscuta's unconventional solution for its replacement. 走向极端:裸子植物质体 rpl32 的丧失和菟丝子对其替代的非传统解决方案。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-22 DOI: 10.1016/j.ympev.2024.108243
Karsten Fischer, Sondre Valentin Jordbræk, Stian Olsen, Mathias Bockwoldt, Rainer Schwacke, Björn Usadel, Kirsten Krause

The evolution of plant genomes is riddled with exchanges of genetic material within one plant (endosymbiotic gene transfer/EGT) and between unrelated plants (horizontal gene transfer/HGT). These exchanges have left their marks on plant genomes. Parasitic plants with their special evolutionary niche provide ample examples for these processes because they are under a reduced evolutionary pressure to maintain autotrophy and thus to conserve their plastid genomes. On the other hand, the close physical connections with different hosts enabled them to acquire genetic material from other plants. Based on an analysis of an extensive dataset including the parasite Cuscuta campestris and other parasitic plant species, we identified a unique evolutionary history of rpl32 genes coding for an essential plastid ribosomal subunit in Cuscuta. Our analysis suggests that the gene was most likely sequestered by HGT from a member of the Oxalidales order serving as host to an ancestor of the Cuscuta subgenus Grammica. Oxalidales had suffered an ancestral EGT of rpl32 predating the evolution of the genus Cuscuta. The HGT subsequently relieved the plastid rpl32 from its evolutionary constraint and led to its loss from the plastid genome. The HGT-based acquisition in Cuscuta is supported by a high sequence similarity of the mature L32 protein between species of the subgenus Grammica and representatives of the Oxalidales, and by a surprisingly conserved transit peptide, whose functionality in Cuscuta was experimentally verified. The findings are discussed in view of an overall pattern of EGT events for plastid ribosomal subunits in Streptophyta.

植物基因组的进化过程充满了植物内部(内共生基因转移/EGT)和非亲缘植物之间(水平基因转移/HGT)的遗传物质交换。这些交换在植物基因组上留下了痕迹。寄生植物以其特殊的进化生态位为这些过程提供了大量实例,因为寄生植物在进化过程中承受着较小的压力,需要保持自养,从而保护其质体基因组。另一方面,寄生植物与不同宿主的密切物理联系使它们能够从其他植物获取遗传物质。基于对包括菟丝子寄生虫和其他寄生植物物种在内的大量数据集的分析,我们发现了菟丝子中编码重要质体核糖体亚基的 rpl32 基因的独特进化史。我们的分析表明,该基因很可能是通过 HGT 从作为菟丝子亚属 Grammica 祖先宿主的 Oxalidales 目成员中分离出来的。在菟丝子属进化之前,Oxalidales 曾遭受过 rpl32 的祖先 EGT。随后的 HGT 解除了质体 rpl32 的进化限制,导致其从质体基因组中消失。菟丝子亚属物种与 Oxalidales 代表物种之间成熟 L32 蛋白的序列高度相似,以及一个令人惊讶的保守转运肽(其在菟丝子中的功能已得到实验验证),都支持了菟丝子中基于 HGT 的获取。本文从链格植物界质体核糖体亚基 EGT 事件的总体模式角度讨论了这些发现。
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引用次数: 0
Phylogenetic origin of dioecious Callicarpa (Lamiaceae) species endemic to the Ogasawara Islands revealed by chloroplast and nuclear whole genome analyses 通过叶绿体和核全基因组分析揭示小笠原群岛特有的雌雄异株Callicarpa(Lamiaceae)物种的系统发育起源。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-20 DOI: 10.1016/j.ympev.2024.108234
Kazutoshi Masuda , Hiroaki Setoguchi , Koki Nagasawa , Suzuki Setsuko , Shosei Kubota , Shin S. Satoh , Shota Sakaguchi
Oceanic islands offer excellent opportunities to study the ecology, evolutionary biology, and biogeography of plants. To uncover the genetic basis of various evolutionary trends commonly observed on these islands, the origins and phylogenetic relationships of the species being studied should be understood. Callicarpa glabra, Callicarpa parvifolia, and Callicarpa subpubescens are evergreen woody plants endemic to the Ogasawara Islands, which are remote oceanic islands located off of the Japanese Archipelago. These species are ideal for studying evolutionary changes on oceanic islands because of their adaptive radiation and shift toward dioecious sex expression. We used a phylogenomic perspective to determine the evolutionary relationship of the three species within the genus and infer their colonization time. Based on the analysis of both chloroplast genomes and 86 nuclear single-copy genes, we found that these three species were monophyletic and embedded in a backbone clade that included multiple East Asian species. The phylogenetic tree based on over 10,000 nuclear genes placed the insular species in the East Asian clade, although the topology did not entirely correspond to the chloroplast tree, probably because of incomplete lineage sorting and interspecific hybridization. The three endemic species were estimated to have diverged from continental species approximately three million years ago (Mya). The results of this study suggested that the ancestor of the Ogasawara endemic species originated from long-distance dispersal from East Asia mainland in the late Pliocene, and then progressively speciated within the islands.
海洋岛屿为研究植物的生态学、进化生物学和生物地理学提供了绝佳的机会。要揭示这些岛屿上常见的各种进化趋势的遗传基础,就必须了解所研究物种的起源和系统发育关系。Callicarpa glabra、Callicarpa parvifolia 和 Callicarpa subpubescens 是小笠原群岛特有的常绿木本植物。这些物种是研究海洋岛屿进化变化的理想对象,因为它们具有适应性辐射和向雌雄异体性别表达的转变。我们从系统发生学的角度确定了该属三个物种的进化关系,并推断了它们的殖民时间。基于对叶绿体基因组和 86 个核单拷贝基因的分析,我们发现这三个物种是单系的,并嵌入到一个包括多个东亚物种的主干支系中。基于 10,000 多个核基因的系统发生树将海岛物种置于东亚支系中,尽管拓扑结构与叶绿体树并不完全一致,这可能是由于不完全的世系分类和种间杂交造成的。据估计,这三个地方物种是在大约三百万年前(Mya)从大陆物种分化而来的。该研究结果表明,小笠原特有种的祖先起源于上新世晚期从东亚大陆的远距离扩散,然后在群岛内逐步分化。
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引用次数: 0
Molecular phylogenetics of nursery web spiders (Araneae: Pisauridae) 育儿网蜘蛛(Araneae: Pisauridae)的分子系统学。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-19 DOI: 10.1016/j.ympev.2024.108247
Sarah A. Morris , Nicolas A. Hazzi , Gustavo Hormiga
Pisauridae Simon, 1890, or nursery web spiders, are a large family with a worldwide distribution and very diverse life history strategies. Despite being named for their nursery webs, similar structures are built by some members of Ctenidae, Trechaleidae, and Oxyopidae. Pisauridae has no known morphological synapomorphies that circumscribe all members of the family, and delineation of subfamilies has been a longstanding issue. In addition, several recent molecular phylogenetic studies have called into question the monophyly of Pisauridae. Here, we infer a phylogeny of Pisauridae with nine genetic markers (12S, 16S, 18S, 28S, actin, COI, histone H3, ITS2, and NADH) combined with ultraconserved elements (UCEs) to test the monophyly of the group and determine intrafamilial relationships. Our study includes a total of 81 terminals (59 of them pisaurids). Our maximum likelihood and gene coalescence analyses strongly suggest that as currently circumscribed, the family Pisauridae is not monophyletic. To circumscribe Pisauridae as a monophyletic group, based on our molecular results, we propose the restoration of the family Dolomedidae Simon, 1876 (rank resurrected) to include the genera Dolomedes Latreille, 1804 and Bradystichus Simon, 1884. In addition, based on morphological evidence, we also place in Dolomedidae the genera Megadolomedes Davies & Raven, 1980; Tasmomedes Raven, 2018; Mangromedes Raven, 2018; Ornodolomedes Raven & Hebron, 2018; and Caledomedes Raven & Hebron, 2018. We provide a phylogenetic delimitation of the three subfamilies of Pisauridae: Halinae, Thaumasiinae, and Pisaurinae. Ten pisaurid genera are deemed incertae sedis in terms of their placement. In light of our hypothesized molecular phylogeny, we discuss the morphological characters and putative synapomorphies of Pisauridae and propose diagnostic characters for its subfamilies and for the family Dolomedidae, along with taxonomic notes about genera not included in our study.
育儿网蜘蛛(Pisauridae Simon,1890 年)是一个庞大的家族,分布于世界各地,生活史策略多种多样。尽管因其育儿网而得名,但栉蛛科(Ctenidae)、蛛蛛科(Trechaleidae)和蛛蛛科(Oxyopidae)的成员也有类似的结构。栉水母科(Pisauridae)没有已知的形态同形异构体来限定该科的所有成员,因此亚科的划分一直是一个长期的问题。此外,最近的几项分子系统发育研究也对鱼龙科的单系性提出了质疑。在此,我们利用 9 个遗传标记(12S、16S、18S、28S、肌动蛋白、COI、组蛋白 H3、ITS2 和 NADH)结合超保守元素(UCE)推断了鱼龙科的系统发育,以检验鱼龙科的单系性并确定科内关系。我们的研究共包括 81 个终端(其中 59 个是比索类)。我们的最大似然法和基因凝聚分析强烈表明,按照目前的划分,雉科并非单系。基于我们的分子研究结果,我们建议恢复 Dolomedidae Simon, 1876 科(等级复活),以包括 Dolomedes Latreille, 1804 属和 Bradystichus Simon, 1884 属,从而将 Pisauridae 定义为单系群。此外,根据形态学证据,我们还将 Megadolomedes 属 Davies & Raven, 1980 年;Tasmomedes 属 Raven, 2018 年;Mangromedes 属 Raven, 2018 年;Ornodolomedes 属 Raven & Hebron, 2018 年;以及 Caledomedes 属 Raven & Hebron, 2018 年归入 Dolomedidae。我们提供了雉龙科三个亚科的系统发育划分:Halinae、Thaumasiinae 和 Pisaurinae。有 10 个鱼龙亚科属的位置被认为是不确定的。根据我们假定的分子系统发育,我们讨论了鱼龙亚科的形态特征和假定的同形异构体,并提出了鱼龙亚科和鱼龙科的诊断特征,以及未包括在我们研究中的属的分类说明。
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引用次数: 0
Reassessing the evolutionary relationships of tropical wandering spiders using phylogenomics: A UCE-based phylogeny of Ctenidae (Araneae) with the discovery of a new lycosoid family 利用系统发生组学重新评估热带游走蜘蛛的进化关系:基于 UCE 的栉水母科(Araneae)系统发育,发现一个新的茄科。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-19 DOI: 10.1016/j.ympev.2024.108245
Nicolas A. Hazzi , Hannah M. Wood , Gustavo Hormiga
Tropical wandering spiders (Ctenidae) are a diverse family of cursorial predators whose species richness peaks in the tropics. The phylogeny of Ctenidae has been examined using morphology and Sanger-based sequencing data, but these studies have been limited by taxon sampling and have often recovered low branch support for many intrafamilial phylogenetic relationships. Herein, we present the most extensive phylogenetic sampling of this family using genome-scale data, leveraging museum collections of all ctenid subfamilies from across the world. We obtained a well-resolved phylogeny of Ctenidae, with the majority of nodes showing maximal nodal support and topological congruence across different phylogenetic analyses. For the first time, we show with high support that Ancylometes is not within Ctenidae but is the sister lineage to all the remaining lycosoid families. Therefore, we propose Ancylometidae as a new family. We assess the phylogenetic position of Ctenidae within Lycosoidea using a variety of phylogenetic methods and tests, demonstrating that the previously proposed position of Ctenidae as the sister clade of Psechridae, based on phylotranscriptomic analyses, lacks phylogenetic support. As a new finding, this study shows that the subfamily Acantheinae, as currently delimited, is polyphyletic. Therefore, we erect the new ctenid subfamily Enoplocteninae to accommodate the Neotropical genera Enoploctenus, Chococtenus, and Phymatoctenus. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Califorctenus and Acantheis) and add support to other parts of the tree that received low support in the most recent Sanger-based phylogeny. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework provided by the molecular phylogenetic results of this study.
热带游走蜘蛛(栉水母科)是一个种类繁多的游走性食肉动物家族,其物种丰富度在热带地区达到顶峰。栉水母科的系统发育已利用形态学和基于 Sanger 的测序数据进行了研究,但这些研究受到类群取样的限制,许多科内系统发育关系的分支支持率往往很低。在本文中,我们利用世界各地博物馆收藏的所有栉水母亚科的基因组规模数据,对该科进行了最广泛的系统发育取样。我们获得了栉水母科的系统发育,大多数节点在不同的系统发育分析中显示出最大的节点支持和拓扑一致性。我们首次以高支持度表明,Ancylometes 并不属于栉水母科,而是所有其余类狼尾草科的姊妹系。因此,我们提议将 Ancylometidae 作为一个新的科。我们使用多种系统发生学方法和检验方法评估了栉水母科在茄形目中的系统发生学位置,证明之前基于系统转录组学分析提出的栉水母科作为栉水母科姊妹支系的位置缺乏系统发生学支持。作为一项新发现,本研究表明,目前划分的 Acantheinae 亚科具有多系性。因此,我们建立了新的 Enoplocteninae 亚科,以容纳新热带属 Enoploctenus、Chococtenus 和 Phymatoctenus。我们使用 UCE 数据的系统发生结果解决了几个有问题的属(如 Califorctenus 和 Acantheis)的位置问题,并为该树的其他部分提供了支持,这些部分在基于 Sanger 的最新系统发生中支持率较低。我们将在本研究的分子系统发育结果所提供的系统发育框架内讨论主要栉水母系的一些假定形态同形异构体。
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引用次数: 0
Phylogenomics resolves the puzzling phylogeny of banded newts (genus Ommatotriton) 系统发生组学解析了带状蝾螈(Ommatotriton 属)令人费解的系统发生。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-17 DOI: 10.1016/j.ympev.2024.108237
Konstantinos Kalaentzis , Stephanie Koster , Jan W. Arntzen , Sergé Bogaerts , James France , Michael Franzen , Christos Kazilas , Spartak N. Litvinchuk , Kurtuluş Olgun , Manon de Visser , Ben Wielstra
Resolving the order of speciation events that occurred in rapid succession is inherently hard and typically requires a phylogenomic approach. A case in point concerns the previously unresolved phylogeny of the three species of banded newt (genus Ommatotriton). We obtain c. 7k nuclear DNA markers using target enrichment by sequence capture and analyze the dataset using maximum likelihood inference of concatenated data with RAxML, summary multi-species coalescent analysis with ASTRAL and Bayesian species tree inference using a diffusion model with SNAPPER, and use TreeMix and PhyloNet to test for interspecific gene flow. All analyses recover three distinct species with no evidence of interspecific gene flow. All analyses retrieved the topology (O. nesterovi, (O. ophryticus, O. vittatus)), with high support. SNAPPER did show the tendency to get stuck in a local optimum, resulting in a different but still highly supported topology. Furthermore, we notice that fewer SNAPPER runs get stuck in a local optimum when we include an outgroup. Therefore, we recommend the exploration of multiple independent runs and the use of an outgroup with this approach. The banded newt radiation illustrates the use of genome-wide data to tackle formerly unresolved phylogenies.
解决快速连续发生的物种变异事件的顺序问题本身就很困难,通常需要采用系统发生学方法。带状蝾螈(Ommatotriton 属)三个物种的系统发育之前尚未解决,这就是一个很好的例子。我们通过序列捕获目标富集法获得了约 7k 个核 DNA 标记,并使用 RAxML 对连接数据进行最大似然推断,使用 ASTRAL 进行多物种聚合分析,使用 SNAPPER 的扩散模型进行贝叶斯物种树推断,并使用 TreeMix 和 PhyloNet 测试种间基因流。所有分析都恢复了三个不同的物种,没有证据表明存在种间基因流。所有分析都检索到了拓扑结构(O. nesterovi、(O. ophryticus、O. vittatus)),支持率很高。SNAPPER 确实显示出陷入局部最优的趋势,从而产生了不同的拓扑结构,但支持率仍然很高。此外,我们注意到,当我们包含一个外群时,陷入局部最优的 SNAPPER 运行次数较少。因此,我们建议使用这种方法探索多个独立运行并使用外群。带状蝾螈辐射说明了如何利用全基因组数据来解决以前悬而未决的系统发育问题。
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引用次数: 0
A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity from the Indo-Pacific 用基因组学方法研究印度洋-太平洋海鹦(Anthozoa: Scleractinia)的巨型多样性。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-16 DOI: 10.1016/j.ympev.2024.108238
Tullia I. Terraneo , Francesca Benzoni , Roberto Arrigoni , Michael L. Berumen , Kiruthiga G. Mariappan , Chakkiath P. Antony , Hugo B. Harrison , Claude Payri , Danwei Huang , Andrew H. Baird
Porites corals are vital components of tropical reef ecosystems worldwide, serving as ecosystem engineers and hubs of biodiversity in shallow water coral reefs. Despite their ecological significance and the widespread use of Porites spp. as models for research, the richness and evolutionary relationships of species within the genus remain elusive. In this study, we analyzed genomic data from 330 colonies of Porites from 17 localities across the Indo-Pacific region based on the reduced representation genomic approach ezRAD. We retrieved 25,163 SNPs and provided a phylogenomic hypothesis for 29 nominal species and 10 unknown morphologies, recovering 15 deeply rooted molecular clades. Among these, 12 clades included samples corresponding to single distinct morphospecies. One did not match any nominal species. The remaining two clades comprised species complexes, which included various massive and encrusting morphologies commonly used in experimental biology. Within these complexes, we observed additional geographic or morphological structure, indicating complex evolutionary dynamics, possibly reflecting distinct species, isolated populations or hybridization. Additionally, a series of divergent samples underscored the importance of more sampling to define species boundaries and refine phylogenomic relationships. We also integrated our findings with previous phylogenetic datasets and their respective sampling localities, challenging traditional notions about Porites species geographic distributions. Overall, our findings indicate a need to revise past synonymies and to formally establish new species. A precise understanding of Porites species and their diversity and distributions is necessary for effective reef conservation and management.
茯苓珊瑚是全球热带珊瑚礁生态系统的重要组成部分,是浅水珊瑚礁生态系统的工程师和生物多样性的枢纽。尽管波罗的海珊瑚具有重要的生态意义,而且被广泛用作研究模型,但该属物种的丰富性和进化关系仍然难以捉摸。在本研究中,我们基于缩减代表基因组学方法 ezRAD,分析了印度洋-太平洋地区 17 个地方的 330 个茯苓群落的基因组数据。我们检索了 25,163 个 SNPs,并为 29 个标称物种和 10 个未知形态提供了系统发生学假设,恢复了 15 个根深蒂固的分子支系。其中,12 个支系包括与单一不同形态物种相对应的样本。一个支系与任何标称物种都不匹配。其余两个支系由物种复合体组成,其中包括实验生物学中常用的各种块状和包壳形态。在这些复合体中,我们观察到了更多的地理或形态结构,表明了复杂的进化动态,可能反映了不同的物种、孤立的种群或杂交。此外,一系列不同的样本凸显了进行更多取样以确定物种边界和完善系统进化关系的重要性。我们还将研究结果与之前的系统发育数据集及其各自的采样地点相结合,对传统的海鲈物种地理分布观念提出了挑战。总之,我们的研究结果表明有必要修订过去的异名并正式建立新物种。要想有效地保护和管理珊瑚礁,就必须准确了解海茯苓的种类及其多样性和分布情况。
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引用次数: 0
Nuclear phylogenomics of Eperua (Leguminosae) highlights the role of habitat and morphological lability in dispersal and diversification across Amazonia and in the Caatinga-Cerrado ecotone Eperua(豆科)的核系统发生组学突显了栖息地和形态易变性在整个亚马孙和卡廷加--塞拉多生态区域的扩散和多样化中的作用。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-15 DOI: 10.1016/j.ympev.2024.108236
Elenice A. Fortes , Jacob B. Landis , Hans ter Steege , Chelsea D. Specht , Jeff J. Doyle , Vidal de F. Mansano
Eperua is a genus of Neotropical trees that forms a major component of tropical lowland forests in Amazonia, especially in the Guiana Shield and on white-sand forests. One species occurs in the Cerrado-Caatinga ecotone, and the genus also inhabits riverine and terra firme forests. Species in Eperua exhibit one of two drastically different floral architectures and inflorescence types, each associated with distinct pollinators. Prior phylogenetic studies of Eperua have revealed an unstructured topology concerning floral architectures and inflorescence types. In addition, no investigation has been conducted on how the evolution of these traits and habitat preferences influenced the dispersal and diversification of Eperua. Using target capture sequencing, we inferred the most comprehensive phylogeny for Eperua to date, sampling all 19 known species, five for the first time. We used coalescence, concatenation, and network methods to infer the Eperua phylogeny and investigate sources of incongruence impacting resolution and support. We reconstructed the biogeographic history and ancestral states for the flower architecture, inflorescence type, and habitat preference. Our phylogenomic analyses successfully resolved relationships within Eperua, attributing conflicts between the species tree and concatenated tree to gene tree discordance linked to reticulation events. Biogeographical analyses indicate that Eperua originated and initially diversified in the white-sand forests of the Guiana Shield. A subsequent adaptation to riverine and terra firme forests enabled Eperua to expand into new habitats and regions. Still, its historical preference for white-sand forests probably accounts for its absence in the southern and western parts of Amazonia. Ancestral geographic areas and corolla morphotype reconstructions suggest that speciation in Eperua has occurred in sympatry, likely driven by pollinator shifts mediated by drastic changes in floral architecture.
Eperua 是新热带树木的一个属,是亚马逊热带低地森林的主要组成部分,尤其是在圭亚那盾和白沙森林中。其中一个物种出现在塞拉多-卡廷加生态区,该属还栖息在河流和陆地森林中。Eperua 的物种有两种截然不同的花结构和花序类型,每种都与不同的授粉者有关。之前的 Eperua 系统发育研究显示,花结构和花序类型的拓扑结构并不稳定。此外,关于这些特征和栖息地偏好的进化如何影响 Eperua 的扩散和多样化,还没有进行过研究。通过目标捕获测序,我们推断出了迄今为止最全面的Eperua系统发生,对所有19个已知物种进行了取样,其中5个物种是首次发现。我们使用聚合、连接和网络方法来推断 Eperua 系统发生,并研究影响分辨率和支持率的不一致性来源。我们重建了花的结构、花序类型和栖息地偏好的生物地理历史和祖先状态。我们的系统发生学分析成功地解析了Eperua内部的关系,将物种树与连接树之间的冲突归因于与网状结构事件相关的基因树不一致。生物地理学分析表明,Eperua起源于圭亚那地盾的白沙森林,并在那里进行了最初的多样化。随后对河流和陆地森林的适应使Eperua得以扩展到新的栖息地和地区。不过,Eperua历来偏爱白沙森林,这可能是其在亚马逊南部和西部缺失的原因。始祖地理区域和花冠形态类型的重建表明,Eperua的物种变异发生在同域中,很可能是由授粉者的转移和花卉结构的急剧变化所引起的。
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引用次数: 0
Phylogenomic analyses shed new light on the spatiotemporal evolution of global larches: Implications for the dynamics of boreal forests 系统发生组分析为全球落叶松的时空演变提供了新线索:对北方森林动态的影响。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-15 DOI: 10.1016/j.ympev.2024.108240
Xiu-Fei Qiu , Yan-Yan Liu , Ge Wu , Cong-Hui Xu , Xin-Quan Liu , Xiao-Yan Xiang , Xiao-Xin Wei , Xiao-Quan Wang
As the Earth warms, understanding the long-term dynamics of forest ecosystems is essential for guiding forest management and biodiversity conservation. Insights from past dynamics may provide valuable lessons for managing today’s forests. Here, we investigated the spatiotemporal evolution of global larches to gain further insights into how boreal forests change over time. We first reconstructed a highly resolved and robust phylogeny of Larix covering all widely recognized species, using both transcriptome-based 1,301 orthologous genes (OGs) and plastid genomes. In sharp contrast to previous studies, an unexpected deep split between the circumboreal and Qinghai-Tibetan Plateau (QTP) larches was revealed in our study. Within each lineage, two geographically distinct clades were further resolved. Biogeographical analyses suggest that Larix might have an origin of Eocene in high-latitude uplands, and during the Miocene, all extant species have appeared. Cenozoic climate- and orogeny-triggered vicariance likely played a major role in the divergence of global larches. Our results also demonstrate that the proto-boreal forest biome may have a relatively old origin back to the early Miocene, and significant winnowing and species alteration would have occurred as the climate shifted to much colder and drier conditions during the Neogene. Ecological niche analyses show various responses of the circumboreal and QTP larches under different climate scenarios, but both lineages are negatively impacted by warming climates. These findings have important conservation implications given the sensitivity of boreal forests in the face of global warming. Our work further emphasizes the importance of a solid phylogenetic framework for evolutionary and biogeographical inferences.
随着地球变暖,了解森林生态系统的长期动态对于指导森林管理和生物多样性保护至关重要。从过去的动态中获得的启示可能会为今天的森林管理提供宝贵的经验。在这里,我们研究了全球落叶松的时空演化,以进一步了解北方森林是如何随时间变化的。我们首先利用基于转录组的 1,301 个直向同源基因(OGs)和质体基因组,重建了一个高度解析和稳健的拉里克系统发育,涵盖了所有公认的物种。与之前的研究形成鲜明对比的是,我们的研究发现,在环周和青藏高原(QTP)落叶松之间出现了意想不到的深度分裂。在每一系中,又进一步分出了两个地理上不同的支系。生物地理学分析表明,落叶松可能起源于始新世的高纬度高地,在中新世出现了所有现存物种。新生代气候和造山运动引发的沧海桑田可能在全球落叶松的分化中扮演了重要角色。我们的研究结果还表明,原生林生物群落的起源可能要追溯到中新世早期,随着新近纪气候变得更加寒冷和干旱,原生林生物群落会发生重大的筛选和物种改变。生态位分析表明,在不同的气候情景下,环坡落叶松和QTP落叶松会有不同的反应,但这两个品系都会受到气候变暖的负面影响。鉴于北方森林对全球变暖的敏感性,这些发现对保护具有重要意义。我们的工作进一步强调了坚实的系统发生学框架对于进化和生物地理推断的重要性。
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引用次数: 0
Evolution, range formation and a revised taxonomy of the disjunctly distributed European members of Astragalus sect. Caprini, an intricate group including highly endangered species of dry grasslands. 黄芪科(Astragalus sect.Caprini是一个复杂的群体,包括干旱草原上的高度濒危物种。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-11-15 DOI: 10.1016/j.ympev.2024.108242
Clemens Maylandt, Philipp Kirschner, Daniela Pirkebner, Božo Frajman, Julio Peñas, Peter Schönswetter, Pau Carnicero

The Eurasian steppes are among the largest and most threatened biomes on Earth. During cold periods of the Pleistocene, the zonal Eurasian steppes had a much larger extent as compared to interglacial periods, and repeatedly expanded into large areas of present-day forested temperate Europe. Conversely, during warm periods, forest expansion recurrently forced Eurasian steppe biota into disjunct and small warm-stage refugia, i.e. today's extrazonal steppes. The rare, threatened and disjunctly distributed northwestern African and European members of Astragalus sect. Caprini constitute an ideal model for gaining insights into the evolutionary dynamics of typical steppe biota. Here, we reconstructed the spatiotemporal diversification of northwestern African and European members of Astragalus sect. Caprini based on a combination of RADseq data, single gene markers (internal transcribed spacer, plastid ycf1), genome size measurements and multivariate morphometrics. We outline an evolutionary scenario in which the group originated in the Irano-Turanian region and started to diversify shortly after the Mid-Pleistocene-Transition (ca. 0.5 to 0.7 Ma). While lineages occurring in (sub-)mediterranean mountain ranges diverged early, lineages occurring in northern lowland steppes are much younger (ca. 0.2 to 0.3 Ma), emphasizing the importance of southern European mountain ranges as long-term refugia. Recurrent colonization of the western Mediterranean region by eastern Mediterranean lineages and secondary contacts of currently spatially isolated lineages have significantly (co-)shaped the genetic structure within the group; we assume that these events may be a consequence of cold-stage range expansions. Based on combined genetic and morphometric data, we suggest treating the ten lineages introduced in this study as independent species, contrasting previous taxonomic treatments.

欧亚大草原是地球上面积最大、受威胁最严重的生物群落之一。在更新世的寒冷时期,欧亚草原地带的范围比间冰期大得多,并一再扩展到今天温带欧洲森林覆盖的大片地区。相反,在温暖时期,森林的扩张经常迫使欧亚大草原生物群进入不连续性的小型温暖阶段避难所,即今天的地带外大草原。稀有、濒危和分布不均的西北非和欧洲黄芪科成员,构成了一个理想的黄芪研究模式。Caprini 是了解典型草原生物群进化动态的理想模型。在这里,我们根据黄芪科(Astragalus sect.这里,我们结合 RADseq 数据、单基因标记(内部转录间隔、质体 ycf1)、基因组大小测量和多元形态计量学,重建了非洲西北部和欧洲黄芪科成员的时空多样性。我们勾勒出这样一种进化情景:该类群起源于伊朗-都兰地区,在中更新世过渡(约 0.5 至 0.7 马年)后不久开始分化。发生在(亚)地中海山脉的世系分化较早,而发生在北部低地草原的世系分化则要年轻得多(约 0.2 至 0.3 Ma),这强调了南欧山脉作为长期避难所的重要性。地中海东部各系对地中海西部地区的反复殖民以及目前在空间上相互隔离的各系之间的二次接触极大地(共同)塑造了该类群的遗传结构;我们认为这些事件可能是寒冷阶段范围扩张的结果。根据遗传学和形态计量学的综合数据,我们建议将本研究中引入的 10 个品系视为独立的物种,与之前的分类学处理方法形成对比。
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引用次数: 0
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Molecular Phylogenetics and Evolution
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