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Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini) 螺旋角羚羊(Tragelaphini)进化史中基因流动和趋同的复杂模式。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-22 DOI: 10.1016/j.ympev.2024.108131
Andrinajoro R. Rakotoarivelo , Thabelo Rambuda , Ulrike H. Taron , Gabrielle Stalder , Paul O’Donoghue , Jan Robovský , Stefanie Hartmann , Michael Hofreiter , Yoshan Moodley

The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists and molecular geneticists for decades because its diversity is characterised by conflicts between morphological and molecular data as well as between mitochondrial, nuclear and chromosomal DNA. These inconsistencies point to a complex history of ecological diversification, coupled by either phenotypic convergence or introgression. Therefore, to unravel the phylogenetic relationships among spiral-horned antelopes, and to further investigate the role of divergence and gene flow in trait evolution, we sequenced genomes for all nine accepted species of the genus Tragelaphus, including a genome each for the highly divergent bushbuck lineages (T. s. scriptus and T. s. sylvaticus). We successfully reconstructed the Tragelaphus species tree, providing genome-level support for the early Pliocene divergence and monophyly of the nyala (T. angasii) and lesser kudu (T. imberbis), the monophyly of the two eland species (T. oryx and T. derbianus) and, importantly, the monophyly of kéwel (T. s. scriptus) and imbabala (T. s. sylvaticus) bushbuck. We found strong evidence for gene flow in at least four of eight nodes on the species tree. Among the six phenotypic traits assessed here, only habitat type mapped onto the species tree without homoplasy, showing that trait evolution was the result of complex patterns of divergence, introgression and convergent evolution.

羚羊科(Tragelaphini),又称螺旋角羚羊,是一个表型多样的哺乳动物部落,由一个属--羚羊属(Tragelaphus)组成。几十年来,该科的进化史一直吸引着分类学家和分子遗传学家的关注,因为其多样性的特点是形态学数据和分子数据之间以及线粒体、核DNA和染色体DNA之间的冲突。这些不一致性表明,该物种的生态多样化历史十分复杂,同时还存在表型趋同或外来引入的情况。因此,为了揭示旋角羚之间的系统发育关系,并进一步研究分化和基因流在性状进化中的作用,我们对旋角羚属所有九个公认物种的基因组进行了测序,包括高度分化的丛林羚系(T. s. scriptus和T. s. sylvaticus)的基因组。我们成功地重建了 Tragelaphus 的物种树,为尼亚拉(T. angasii)和小库杜(T. imberbis)在上新世早期的分化和单系化、两个伊兰种(T. oryx 和 T. derbianus)的单系化以及重要的凯威(T. s. scriptus)和伊姆巴拉(T. s. sylvaticus)丛林巴克的单系化提供了基因组水平的支持。在物种树的八个节点中,我们至少在四个节点上发现了基因流动的有力证据。在本文评估的六个表型特征中,只有栖息地类型映射到物种树上时没有同源现象,这表明特征的进化是复杂的分化、引入和趋同进化模式的结果。
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引用次数: 0
Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae) 矮牵牛及相关属(矮牵牛科,茄科)树种不一致的原因是不完全的世系分类和杂交。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-22 DOI: 10.1016/j.ympev.2024.108136
Pedro H. Pezzi , Lucas C. Wheeler , Loreta B. Freitas , Stacey D. Smith

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.

尽管存在物种分化的总体历史,但系统发育研究经常揭示出基因组不同区域的不同拓扑结构。这些基因树不一致的原因多种多样,但不完全系谱分选(ILS)和杂交是其中最具生物学意义的原因。矮牵牛是研究野生杂交的经典系统。虽然野外研究表明杂交很频繁,但牵牛花及其近缘属内部的网状结构程度却从未从系统发育的角度进行过研究。在这项研究中,我们使用了来自 11 个矮牵牛属、16 个萼叶草属和 10 个法比亚娜属的转录组数据来阐明这些物种之间的关系,并研究杂交是否在该支系的多样化过程中发挥了重要作用。我们推断,属内基因树的不一致性与杂交事件有关,同时由于其快速多样化,ILS水平较高。此外,网络分析还估计了矮牵牛属和萼片草属之间更深层次的杂交事件,这两个属的染色体数目不同。虽然这两个属目前还不能杂交,但祖先的杂交可能在它们的平行辐射中起到了一定的作用,因为它们有着相同的栖息地和生活史。
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引用次数: 0
Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki) 利用 RADseq 和 Sanger 测序揭示天鹅绒蠕虫物种复合体(Onychophora: Peripatopsidae: Peripatopsis sedgwicki)中隐性宗族发生的一致模式。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-22 DOI: 10.1016/j.ympev.2024.108132
Angus Macgregor Myburgh , Aaron Barnes , Romina Henriques , Savel R. Daniels

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259–11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

本研究利用第一代 DNA 测序(线粒体细胞色素 c 氧化酶亚单位一,COI)和还原代表性基因组 RADseq 数据来了解绒毛虫 Peripatopsis sedgwicki 物种群在南非分布范围内的多样化模式和过程。为了评估该物种群的多样性和系统地理学,我们为 RADseq 数据生成了三个数据集(两个主要数据集和一个补充数据集),对应 1,259-11,468 个 SNPs。利用最大似然法和贝叶斯推断法推断了两个主要数据集的树拓扑结构。利用 COI 数据集进行的系统发育分析在该物种群中检索到四个不同的、支持良好的支系。应用于 COI 数据的五种物种划分方法(ASAP、bPTP、bGMYC、STACEY 和 iBPP)均支持福特斯堡自然保护区标本的区分。在主要的 P. sedgwicki 种群中,物种划分方法揭示了不同数量的可操作分类单元,并高估了推定类群的数量。分化时间估计值、物种的地理排他性和系统地理学结果表明,Plio/Pleistocene时期的宗族发生是最近发生的。在最大似然法框架下,对 RADseq 数据进行了主成分分析和主成分判别分析。后者的结果证实了利用 COI 数据观察到的四个主要支系,然而,应用额外的筛选方法发现了更多的多样性。RADseq 数据与 COI 数据之间的总体一致性很高,这表明第一代序列数据仍然是进化研究的一种廉价而有效的方法,尽管 RADseq 确实能提供更高的当代时空模式分辨率。
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引用次数: 0
Horizontally transferred glycoside hydrolase 26 may aid hemipteran insects in plant tissue digestion 水平转移的苷水解酶 26 可能有助于半翅目昆虫消化植物组织。
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-18 DOI: 10.1016/j.ympev.2024.108134
Hunter K. Walt , Seung-Joon Ahn , Federico G. Hoffmann

Glycoside hydrolases are enzymes that break down complex carbohydrates into simple sugars by catalyzing the hydrolysis of glycosidic bonds. There have been multiple instances of adaptive horizontal gene transfer of genes belonging to various glycoside hydrolase families from microbes to insects, as glycoside hydrolases can metabolize constituents of the carbohydrate-rich plant cell wall. In this study, we characterize the horizontal transfer of a gene from the glycoside hydrolase family 26 (GH26) from bacteria to insects of the order Hemiptera. Our phylogenies trace the horizontal gene transfer to the common ancestor of the superfamilies Pentatomoidea and Lygaeoidea, which include stink bugs and seed bugs. After horizontal transfer, the gene was assimilated into the insect genome as indicated by the gain of an intron, and a eukaryotic signal peptide. Subsequently, the gene has undergone independent losses and expansions in copy number in multiple lineages, suggesting an adaptive role of GH26s in some insects. Finally, we measured tissue-level gene expression of multiple stink bugs and the large milkweed bug using publicly available RNA-seq datasets. We found that the GH26 genes are highly expressed in tissues associated with plant digestion, especially in the principal salivary glands of the stink bugs. Our results are consistent with the hypothesis that this horizontally transferred GH26 was co-opted by the insect to aid in plant tissue digestion and that this HGT event was likely adaptive.

糖苷水解酶是一种通过催化水解糖苷键将复杂碳水化合物分解为单糖的酶。由于糖苷水解酶可以代谢富含碳水化合物的植物细胞壁成分,属于各种糖苷水解酶家族的基因从微生物向昆虫进行了多次适应性水平基因转移。在这项研究中,我们描述了糖苷水解酶家族 26(GH26)的一个基因从细菌向半翅目昆虫水平转移的特征。我们的系统发生学将该基因水平转移追溯到了包括蝽和种子蝽在内的五蠹目和姬蛙目超家族的共同祖先。水平转移后,该基因被同化到昆虫基因组中,表现为获得了一个内含子和一个真核信号肽。随后,该基因在多个品系中经历了独立的拷贝数丢失和扩增,这表明 GH26s 在某些昆虫中具有适应性作用。最后,我们利用公开的 RNA-seq 数据集测量了多种蝽类和大型乳草蝽的组织级基因表达。我们发现,GH26 基因在与植物消化相关的组织中高度表达,尤其是在蝽的主要唾液腺中。我们的研究结果符合这样的假设,即这种横向转移的 GH26 被昆虫共同利用来帮助植物组织消化,而且这种 HGT 事件很可能是适应性的。
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引用次数: 0
Phylogenomics and biogeography of the small carpenter bees (Apidae: Xylocopinae: Ceratina) 小木匠蜂(Apidae: Xylocopinae: Ceratina)的系统发生组学和生物地理学。
IF 4.1 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-17 DOI: 10.1016/j.ympev.2024.108133
Trevor J.L. Sless , Michael G. Branstetter , Michael Mikát , Katherine A. Odanaka , Kerrigan B. Tobin , Sandra M. Rehan

Small carpenter bees in the genus Ceratina are behaviourally diverse, species-rich, and cosmopolitan, with over 370 species and a range including all continents except Antarctica. Here, we present the first comprehensive phylogeny of the genus based on ultraconserved element (UCE) phylogenomic data, covering a total of 185 ingroup specimens representing 22 of the 25 current subgenera. Our results support most recognized subgenera as natural groups, but we also highlight several groups in need of taxonomic revision – particularly the nominate subgenus Ceratina sensu stricto – and several clades that likely need to be described as new subgenera. In addition to phylogeny, we explore the evolutionary history of Ceratina through divergence time estimation and biogeographic reconstruction. Our findings suggest that Ceratinini split from its sister tribe Allodapini about 72 million years ago. The common ancestor of Ceratina emerged in the Afrotropical realm approximately 42 million years ago, near the Middle Eocene Climatic Optimum. Multiple subsequent dispersal events led to the present cosmopolitan distribution of Ceratina, with the majority of transitions occurring between the Afrotropics, Indomalaya, and the Palearctic. Additional movements also led to the arrival of Ceratina in Madagascar, Australasia, and a single colonization of the Americas. Dispersal events were asymmetrical overall, with temperate regions primarily acting as destinations for migrations from tropical source regions.

小木匠蜂属(Ceratina)行为多样、物种丰富且具有世界性,有 370 多个物种,分布范围包括除南极洲以外的所有大陆。在此,我们基于超保守元素(UCE)系统发生组数据首次提出了该属的全面系统发生,涵盖了代表目前 25 个亚属中 22 个亚属的总共 185 个内群标本。我们的研究结果支持大多数公认的亚属为自然类群,但我们也强调了几个需要进行分类学修订的类群--特别是严格意义上的提名亚属 Ceratina,以及几个可能需要描述为新亚属的支系。除了系统发育外,我们还通过分歧时间估计和生物地理重建来探索 Ceratina 的进化史。我们的研究结果表明,Ceratinini大约在7200万年前从其姊妹族Allodapini中分离出来。Ceratina 的共同祖先出现在大约 4200 万年前的非洲热带地区,接近中始新世气候最适宜期。随后的多次扩散事件导致了 Ceratina 目前的世界性分布,其中大部分过渡发生在非洲热带地区、印度河流域和古北区之间。其他的迁移还导致 Ceratina 来到马达加斯加、大洋洲和美洲的一次殖民。传播事件总体上是不对称的,温带地区主要是热带来源地区迁徙的目的地。
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引用次数: 0
Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles 基因组 SNP 解决了塞舌尔群岛古老两栖动物岛屿辐射的系统发育问题
IF 3.6 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-16 DOI: 10.1016/j.ympev.2024.108130
Miranda B. Sherlock , Jeffrey W. Streicher , David J. Gower , Simon T. Maddock , Ronald A. Nussbaum , Oommen V. Oommen , Ana Serra Silva , Julia J. Day , Mark Wilkinson

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands. These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

对于海洋岛屿来说,塞舌尔群岛的花岗岩质地非常罕见,这里有多个特有的两栖动物品系。其中包括一个古老的(可能约 6000 万年前)八种凯西拉类,它们中的大多数出现在多个岛屿上。这些无尾类有着复杂的分类历史,其物种间的系统发育关系一直难以解决。双位 RAD 测序(ddRADseq)已被广泛应用于系统地理学,并越来越多地应用于系统发育学,但其在解决远古分化方面的实用性还不太成熟。为了解决这个问题,我们应用 ddRADseq 生成了一个全基因组 SNP 面板,用于塞舌尔群岛无尾类的系统发生学分析。基于 129,154 个 SNPs,我们解决了深层和浅层分裂问题,并获得了强有力的支持。我们的研究结果证明了全基因组 SNP 在多个分类水平上的进化推断能力,并支持最近提出的 Grandisonia Taylor, 1968 与 Hypogeophis Peters, 1879 的同义。我们揭示了 Hypogeophis 的三个支系(大体型、中体型和短体型),并确定了体型矮小、体格粗壮和尖嘴表型的单一起源。
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引用次数: 0
Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia) 测试双壳类动物(软体动物门:双壳类)中用于系统发育推断的超保守元素(UCE)。
IF 4.1 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-13 DOI: 10.1016/j.ympev.2024.108129
Sara González-Delgado , Paula C. Rodríguez-Flores , Gonzalo Giribet

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

双壳类动物是重要的渔业资源和文物。利用形态学和分子特征进行双壳类动物系统发育的传统由来已久,许多具有重要商业价值的物种都有基因组资源。然而,双壳类家族之间的关系一直不稳定,有丝分裂基因组学与基于桑格扩增子测序或系统转录组学的结果之间存在重大冲突。在这里,我们设计并测试了双壳纲的超保守元素探针集,目的是使用数百个位点,而无需对昂贵且复杂的全基因组或转录组进行测序分析,并将双壳纲系统发生学应用于博物馆标本。我们的探针集成功捕获了 1,513 个 UCE,总长度为 263,800 bp,每个 UCE 的平均长度为 174.59 ± 3.44(从 28 到 842 bp 不等)。利用不同的数据矩阵和系统发育推断方法,在双壳纲和多纳科内对该 UCE 探针集进行了系统发育测试,结果表明在多个分类水平上都取得了良好的效果。此外,我们的探针集还能捕捉到 1900 年前采集的博物馆标本中的大量 UCE。总之,这是双壳类系统发生学的一个新颖而有用的资源。
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引用次数: 0
Artificial intelligence enables unified analysis of historical and landscape influences on genetic diversity 人工智能可对遗传多样性的历史和景观影响进行统一分析。
IF 4.1 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-12 DOI: 10.1016/j.ympev.2024.108116
Emanuel M. Fonseca , Bryan C. Carstens

While genetic variation in any species is potentially shaped by a range of processes, phylogeography and landscape genetics are largely concerned with inferring how environmental conditions and landscape features impact neutral intraspecific diversity. However, even as both disciplines have come to utilize SNP data over the last decades, analytical approaches have remained for the most part focused on either broad-scale inferences of historical processes (phylogeography) or on more localized inferences about environmental and/or landscape features (landscape genetics). Here we demonstrate that an artificial intelligence model-based analytical framework can consider both deeper historical factors and landscape-level processes in an integrated analysis. We implement this framework using data collected from two Brazilian anurans, the Brazilian sibilator frog (Leptodactylus troglodytes) and granular toad (Rhinella granulosa). Our results indicate that historical demographic processes shape most the genetic variation in the sibulator frog, while landscape processes primarily influence variation in the granular toad. The machine learning framework used here allows both historical and landscape processes to be considered equally, rather than requiring researchers to make an a priori decision about which factors are important.

虽然任何物种的遗传变异都可能受到一系列过程的影响,但系统地理学和景观遗传学主要关注的是推断环境条件和景观特征如何影响中性的种内多样性。然而,即使这两个学科在过去几十年中都开始利用 SNP 数据,分析方法在很大程度上仍然集中在对历史进程的大范围推断(系统地理学)或对环境和/或景观特征的局部推断(景观遗传学)上。在这里,我们证明了基于人工智能模型的分析框架可以在综合分析中同时考虑更深层次的历史因素和景观层面的过程。我们利用从两种巴西无尾类动物--巴西咝蛙(Leptodactylus troglodytes)和颗粒蟾蜍(Rhinella granulosa)--收集到的数据实施了这一框架。我们的研究结果表明,历史人口统计过程决定了箭蛙的大部分遗传变异,而景观过程则主要影响颗粒蟾蜍的变异。这里使用的机器学习框架允许同时考虑历史和景观过程,而不是要求研究人员先验地决定哪些因素是重要的。
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引用次数: 0
Phylogenomic analyses of ochrophytes (stramenopiles) with an emphasis on neglected lineages 以被忽视的品系为重点的赭藻(葡萄孢藻)系统发生组分析
IF 4.1 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-07 DOI: 10.1016/j.ympev.2024.108120
Anna Cho, Gordon Lax, Patrick J. Keeling

Ochrophyta is a photosynthetic lineage that crowns the phylogenetic tree of stramenopiles, one of the major eukaryotic supergroups. Due to their ecological impact as a major primary producer, ochrophytes are relatively well-studied compared to the rest of the stramenopiles, yet their evolutionary relationships remain poorly understood. This is in part due to a number of missing lineages in large-scale multigene analyses, and an apparently rapid radiation leading to many short internodes between ochrophyte subgroups in the tree. These short internodes are also found across deep-branching lineages of stramenopiles with limited phylogenetic signal, leaving many relationships controversial overall. We have addressed this issue with other deep-branching stramenopiles recently, and now examine whether contentious relationships within the ochrophytes may be resolved with the help of filling in missing lineages in an updated phylogenomic dataset of ochrophytes, along with exploring various gene filtering criteria to identify the most phylogenetically informative genes. We generated ten new transcriptomes from various culture collections and a single-cell isolation from an environmental sample, added these to an existing phylogenomic dataset, and examined the effects of selecting genes with high phylogenetic signal or low phylogenetic noise. For some previously contentious relationships, we find a variety of analyses and gene filtering criteria consistently unite previously unstable groupings with strong statistical support. For example, we recovered a robust grouping of Eustigmatophyceae with Raphidophyceae-Phaeophyceae-Xanthophyceae while Olisthodiscophyceae formed a sister-lineage to Pinguiophyceae. Selecting genes with high phylogenetic signal or data quality recovered more stable topologies. Overall, we find that adding under-represented groups across different lineages is still crucial in resolving phylogenetic relationships, and discrete gene properties affect lineages of stramenopiles differently. This is something which may be explored to further our understanding of the molecular evolution of stramenopiles.

裸子植物是一种光合作用植物,在真核生物超群之一--石蒜科植物的系统发育树中居于首位。由于其作为主要初级生产者对生态环境的影响,与其他石龙子类相比,对水华藻的研究相对较多,但对其进化关系的了解仍然很少。这部分是由于在大规模多基因分析中缺失了一些世系,以及明显的快速辐射导致树上的赭藻亚群之间出现了许多短节间。这些短节间也出现在系统发育信号有限的石莲花类深枝系中,使得许多关系在整体上存在争议。最近,我们通过其他深枝葡萄科植物解决了这一问题,现在我们要研究的是,是否可以通过在最新的赭藻系统发生组数据集中填补缺失的世系,同时探索各种基因筛选标准来确定最具系统发生信息的基因,从而解决赭藻内部有争议的关系问题。我们从各种培养物和环境样本的单细胞分离中生成了十个新的转录组,将这些转录组添加到现有的系统发生组数据集中,并研究了选择具有高系统发生信号或低系统发生噪声的基因的效果。对于一些以前有争议的关系,我们发现各种分析和基因筛选标准都能以强有力的统计支持将以前不稳定的分组统一起来。例如,我们恢复了红叶石龙子科(Eustigmatophyceae)与石龙子科(Raphidophyceae)-白叶石龙子科(Phaeophyceae)-黄叶石龙子科(Xanthophyceae)的稳健分组关系,而橄榄叶石龙子科(Olisthodiscophyceae)则与红叶石龙子科(Pinguiophyceae)形成姊妹系。选择具有高系统发育信号或数据质量的基因可以恢复更稳定的拓扑结构。总之,我们发现,在不同种系中增加代表性不足的类群对于解决系统发生关系仍然至关重要,而且离散基因的特性对葡萄孢植物的种系有着不同的影响。为了进一步了解石龙子的分子进化,我们可以对这一点进行探索。
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引用次数: 0
Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon 南美洲热带草原鸟类的物种变异:亚马逊河内外的最小夜鹰 Chordeiles pusillus(鸟类:Caprimulgidae)的案例。
IF 4.1 1区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-07 DOI: 10.1016/j.ympev.2024.108117
Alexandre M. Fernandes , Mario Cohn-Haft , Luís Fábio Silveira , Alexandre Aleixo , Nathália Nascimento , Urban Olsson

The Least Nighthawk Chordeiles pusillus is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of C. pusillus to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050–2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Marajó island during favourable climatic conditions in the Pleistocene.

在南美洲热带地区,只要有热带稀树草原的地方,就有夜鹰(Least Nighthawk Chordeiles pusillus)的踪迹,它们通常分布在亚马逊热带雨林地区的白沙稀树草原等孤立区域。在这里,我们通过比较来自白沙稀树草原的样本和来自亚马逊热带雨林地区以外的其他稀树草原的样本,研究最矮夜鹰种群之间的遗传关系,以了解导致其多样化的历史进程,并通过三条假定的扩散走廊来确定南北稀树草原之间的扩散路线。我们利用来自 C. pusillus 分布区的 32 个 mtDNA 样本推断出了一个有年代的系统发育。在 17 个样本的子集中,我们使用猎枪序列来推断基于距离的系统发育,并估计个体的混杂比例。我们使用 ABBA-BABA 检验(D 统计量)和主成分分析(PCA)计算白沙种群和非亚马逊种群之间的基因流和共享等位基因,以考察种系内部和种系之间的遗传结构。最后,我们利用物种分布模型(SDM)对末次冰川极盛时期(LGM)、当前和未来(2050-2080 年)的条件进行模拟,以预测气候变化情景下可能出现的物种。利用 mtDNA 序列和单核苷酸多态性(SNPs)发现了两个主要支系(估计在距今约 107 万年前分化),并得到了 NGSadmix 和 PCA 的支持:一个支系位于亚马逊盆地的白沙稀树草原,另一个支系位于非亚马逊稀树草原。北部非亚马孙种群与白沙稀树草原种群之间的 D 统计表明,这些支系之间可能存在等位基因共享,但掺杂分析并未证实这一点。北部非亚马孙种群之间的扩散可能发生在圭亚那和巴西地盾之间的干旱走廊,该走廊后来向东移动。我们的数据表明,这些种群早在末次冰川极盛期之前就已分离,因此扩散可能发生在气候条件相似的任何更早的时期。随后,非亚马孙河流域的世系之间变得更加分化,可能在更新世有利的气候条件下连接并扩散到马拉霍岛对面的亚马孙河口。
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Molecular Phylogenetics and Evolution
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