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Evidence of Intraspecific Adaptive Variation in the American Pika (Ochotona princeps) on a Continental Scale Using a Target Enrichment and Mitochondrial Genome Skimming Approach. 利用目标富集和线粒体基因组撇取方法研究美洲鼠兔(Ochotona princeps)在大陆范围内的种内适应性变异证据。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-19 DOI: 10.1111/mec.17557
Zachery M Farrand, Kurt E Galbreath, Katherine C Teeter

Montane landscapes present an array of abiotic challenges that drive adaptive evolution amongst organisms. These adaptations can promote habitat specialisation, which may heighten the risk of extirpation from environmental change. For example, higher metabolic rates in an endothermic species may contribute to heightened cold tolerance, whilst simultaneously limiting heat tolerance. Here, using the climate-sensitive American pika (Ochotona princeps), we test for evidence of intraspecific adaptive variation amongst environmental gradients across the Intermountain West of North America. We leveraged results from previous studies on pika adaptation to generate a custom nuclear target enrichment design to sequence several hundred candidate genes related to cold, hypoxia and dietary detoxification. We also applied a 'genome skimming' approach to sequence mitochondrial DNA. Using genotype-environment association tests, we identified rare genomic variants associated with elevation and temperature variation amongst populations. Amongst mitochondrial genes, we identified intraspecific variation in selective signals and significant changes to the amino acid property equilibrium constant, which may relate to electron transport chain efficiency. These results illustrate a complex dynamic of adaptive variation amongst O. princeps where lineages and populations have adapted to unique regional conditions. Some of the clearest signals of selection were in a genetic lineage that includes pikas of the Great Basin region, which is also where recent localised extirpations have taken place and highlights the risk of losing adaptive alleles during environmental change.

山地景观带来了一系列非生物挑战,推动了生物的适应性进化。这些适应性会促进栖息地的特化,从而增加因环境变化而灭绝的风险。例如,内热物种较高的新陈代谢率可能有助于提高耐寒性,同时限制耐热性。在这里,我们利用对气候敏感的美洲鼠兔(Ochotona princeps),测试了北美西部中山区环境梯度中种内适应性变异的证据。我们利用之前关于鼠兔适应性的研究成果,生成了一个定制的核靶标富集设计,对数百个与寒冷、缺氧和饮食解毒相关的候选基因进行测序。我们还采用了 "基因组撇脂 "方法对线粒体DNA进行测序。通过基因型-环境关联测试,我们发现了与不同人群的海拔和温度变化相关的罕见基因组变异。在线粒体基因中,我们发现了选择信号的种内变异和氨基酸属性平衡常数的显著变化,这可能与电子传递链的效率有关。这些结果表明,王子鸥之间存在着复杂的适应性变异动态,其品系和种群已经适应了独特的区域条件。一些最明显的选择信号出现在包括大盆地地区鼠兔在内的一个遗传系中,这也是最近发生局部灭绝的地方,并凸显了在环境变化过程中丧失适应性等位基因的风险。
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引用次数: 0
Admixture With Cultivated Sunflower Likely Facilitated Establishment and Spread of Wild Sunflower (Helianthus annuus) in Argentina 与栽培向日葵的混合可能促进了野生向日葵(Helianthus annuus)在阿根廷的建立和传播。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-18 DOI: 10.1111/mec.17560
Fernando Hernández, Román B. Vercellino, Marco Todesco, Natalia Bercovich, Daniel Alvarez, Johanne Brunet, Alejandro Presotto, Loren H. Rieseberg

A better understanding of the genetic and ecological factors underlying successful invasions is critical to mitigate the negative impacts of invasive species. Here, we study the invasion history of Helianthus annuus populations from Argentina, with particular emphasis on the role of post-introduction admixture with cultivated sunflower (also H. annuus) and climate adaptation driven by large haploblocks. We conducted genotyping-by-sequencing of samples of wild populations as well as Argentinian cultivars and compared them with wild (including related annual Helianthus species) and cultivated samples from the native range. We also characterised samples for 11 known haploblocks associated with environmental variation in native populations to test whether haploblocks contributed to invasion success. Population genomics analyses supported two independent geographic sources for Argentinian populations, the central United States and Texas, but no significant contribution of related annual Helianthus species. We found pervasive admixture with cultivated sunflower, likely as result of post-introduction hybridization. Genomic scans between invasive populations and their native sources identified multiple genomic regions of divergence, possibly indicative of selection, in the invaded range. These regions significantly overlapped between the two native-invasive comparisons and showed disproportionally high crop ancestry, suggesting that crop alleles contributed to invasion success. We did not find evidence of climate adaptation mediated by haploblocks, yet outliers of genome scans were enriched in haploblock regions and, for at least two haploblocks, the cultivar haplotype was favoured in Argentina. Our results show that admixture with cultivated sunflower played a major role in the establishment and spread of H. annuus populations in Argentina.

更好地了解成功入侵的遗传和生态因素对于减轻入侵物种的负面影响至关重要。在这里,我们研究了阿根廷向日葵种群的入侵历史,特别强调了入侵后与栽培向日葵(也是向日葵)的混交以及大单倍群驱动的气候适应的作用。我们对野生种群和阿根廷栽培品种的样本进行了基因分型测序,并与原产地的野生(包括相关的一年生向日葵品种)和栽培样本进行了比较。我们还对与原生种群环境变异相关的 11 个已知单倍群样本进行了表征,以检验单倍群是否有助于入侵的成功。种群基因组学分析表明,阿根廷种群有两个独立的地理来源,即美国中部和德克萨斯州,但相关的一年生Helianthus物种并没有显著的贡献。我们发现向日葵普遍与栽培向日葵混交,这可能是入侵后杂交的结果。入侵种群与其本地种群之间的基因组扫描发现了多个基因组分异区域,这可能表明在入侵范围内进行了选择。这些区域在两个原生-入侵比较中明显重叠,并显示出不成比例的高作物祖先性,表明作物等位基因是入侵成功的原因之一。我们没有发现单倍群介导的气候适应证据,但基因组扫描的异常值却在单倍群区域中富集,而且至少有两个单倍群的栽培品种单倍型在阿根廷更受青睐。我们的研究结果表明,与栽培向日葵的混合在向日葵种群在阿根廷的建立和传播过程中发挥了重要作用。
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引用次数: 0
Gene Expression Shifts in Emperor Penguin Adaptation to the Extreme Antarctic Environment. 帝企鹅适应南极极端环境的基因表达变化。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-17 DOI: 10.1111/mec.17552
Josephine R Paris, Flávia A Nitta Fernandes, Federica Pirri, Samuele Greco, Marco Gerdol, Alberto Pallavicini, Marine Benoiste, Clément Cornec, Lorenzo Zane, Brian Haas, Céline Le Bohec, Emiliano Trucchi

Gene expression can accelerate ecological divergence by rapidly tweaking the response of an organism to novel environments, with more divergent environments exerting stronger selection and supposedly, requiring faster adaptive responses. Organisms adapted to extreme environments provide ideal systems to test this hypothesis, particularly when compared to related species with milder ecological niches. The Emperor penguin (Aptenodytes forsteri) is the only endothermic vertebrate breeding in the harsh Antarctic winter, in stark contrast with the less cold-adapted sister species, the King penguin (A. patagonicus). Assembling the first de novo transcriptomes and analysing multi-tissue (brain, kidney, liver, muscle, skin) RNA-Seq data from natural populations of both species, we quantified the shifts in tissue-enhanced genes, co-expression gene networks, and differentially expressed genes characterising Emperor penguin adaptation to the extreme Antarctic. Our analyses revealed the crucial role played by muscle and liver in temperature homeostasis, fasting, and whole-body energy metabolism (glucose/insulin regulation, lipid metabolism, fatty acid beta-oxidation, and blood coagulation). Repatterning at the regulatory level appears as more important in the brain of the Emperor penguin, showing the lowest signature of differential gene expression, but the largest co-expression gene network shift. Nevertheless, over-expressed genes related to mTOR signalling in the brain and the liver support their central role in cold and fasting responses. Besides contributing to understanding the genetics underlying complex traits, like body energy reservoir management, our results provide a first insight into the role of gene expression in adaptation to one of the most extreme environmental conditions endured by an endotherm.

基因表达可以通过快速调整生物体对新环境的反应来加速生态分化,分化程度越高的环境会产生越强的选择,因此需要更快的适应性反应。适应极端环境的生物为检验这一假说提供了理想的系统,尤其是与生态位较温和的相关物种相比。帝企鹅(Aptenodytes forsteri)是唯一一种在严酷的南极冬季繁殖的内温脊椎动物,这与不太适应寒冷环境的姊妹物种帝企鹅(A. patagonicus)形成了鲜明对比。我们组装了第一个全新的转录组,并分析了来自这两个物种自然种群的多组织(脑、肾、肝、肌肉、皮肤)RNA-Seq数据,量化了组织增强基因、共表达基因网络和差异表达基因的变化,这些都是帝企鹅适应极端南极环境的特征。我们的分析揭示了肌肉和肝脏在温度平衡、禁食和全身能量代谢(葡萄糖/胰岛素调节、脂质代谢、脂肪酸β-氧化和血液凝固)中的关键作用。在帝企鹅的大脑中,调控水平上的重组显得更为重要,显示出最低的差异基因表达特征,但共表达基因网络的变化却最大。尽管如此,大脑和肝脏中与mTOR信号有关的基因过度表达,支持了它们在寒冷和禁食反应中的核心作用。除了有助于理解复杂性状(如体内能量储备管理)的遗传学基础外,我们的研究结果还首次揭示了基因表达在适应内温动物所经受的最极端环境条件中的作用。
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引用次数: 0
Contrasting Genomic Diversity and Inbreeding Levels Among Two Closely Related Falcon Species With Overlapping Geographic Distributions. 地理分布重叠的两种近缘猎鹰物种基因组多样性和近交水平的对比。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-14 DOI: 10.1111/mec.17549
Audrey M Martin, Jeff A Johnson, Robert B Berry, Matthew Carling, Carlos Martínez Del Rio

Genomic resources are valuable to examine historical demographic patterns and their effects to better inform management and conservation of threatened species. We evaluated population trends and genome-wide variation in the near-threatened Orange-breasted Falcon (Falco deiroleucus) and its more common sister species, the Bat Falcon (F. rufigularis), to explore how the two species differ in genomic diversity as influenced by their contrasting long-term demographic histories. We generated and aligned whole genome resequencing data for 12 Orange-breasted Falcons and 9 Bat Falcons to an annotated Gyrfalcon (F. rusticolus) reference genome that retained approximately 22.4 million biallelic autosomal SNPs (chromosomes 1-22). Our analyses indicated much lower genomic diversity in Orange-breasted Falcons compared to Bat Falcons. All sampled Orange-breasted Falcons were significantly more inbred than the sampled Bat Falcons, with values similar to those observed in island-mainland species comparisons. The distribution of runs of homozygosity showed variation suggesting long-term low population size and the possibility of bottlenecks in Orange-breasted Falcons contrasting with consistently larger populations in Bat Falcons. Analysis of genetic load suggests that Orange-breasted Falcons are less likely to experience inbreeding depression than Bat Falcons due to reduced inbreeding load but are at elevated risk from fixation of deleterious gene variants and perhaps a reduced adaptive potential. These genomic analyses highlight differences in the historical demography of two closely related species that have influenced their current genomic diversity and should result in differing strategies for their continued conservation.

基因组资源非常宝贵,可用于研究历史人口模式及其影响,从而为濒危物种的管理和保护提供更好的信息。我们评估了濒临灭绝的橙胸隼(Falco deiroleucus)及其更常见的姊妹物种蝙蝠隼(F. rufigularis)的种群趋势和全基因组变异,以探索这两个物种在基因组多样性方面的差异是如何受其截然不同的长期人口历史影响的。我们生成了12只橙胸隼和9只蝙蝠隼的全基因组重测序数据,并将其与注释过的石隼(F. rusticolus)参考基因组进行了比对,该参考基因组保留了约2240万个双偶联常染色体SNP(1-22号染色体)。我们的分析表明,与蝙蝠隼相比,橙胸隼的基因组多样性要低得多。所有取样的橙胸隼都明显比取样的蝙蝠隼近亲繁殖,其数值与岛屿-大陆物种比较中观察到的数值相似。同源性分布的变化表明,橙胸隼的种群数量长期偏低,有可能出现瓶颈,而蝙蝠隼的种群数量则一直较大。遗传负荷分析表明,由于近亲繁殖负荷降低,橙胸隼比蝙蝠隼更不可能出现近亲繁殖抑制,但有害基因变异固定的风险却很高,适应潜力也可能降低。这些基因组分析凸显了这两个密切相关物种在历史人口统计方面的差异,这种差异影响了它们目前的基因组多样性,并应导致它们采取不同的持续保护策略。
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引用次数: 0
A Latitudinal Gradient of Reference Genomes. 参考基因组的纬度梯度。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-14 DOI: 10.1111/mec.17551
Ethan B Linck, Carlos Daniel Cadena

Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes, while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state-of-the-art methods. Here, we ask whether a fundamental biogeographic pattern-the latitudinal gradient of species richness in tetrapods-is reflected in the available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last 5 years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes and that reduced representation and whole-genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics.

殖民主义和不平衡发展遗留下来的全球不平等会导致科学知识的系统性偏差。在生态学和进化生物学领域,研究成果、资金和研究力量不成比例地集中在高纬度地区,而生物多样性则集中在低纬度地区。这种差异可能对系统地理学、分子生态学和保护遗传学等领域产生特殊影响,因为基因组学的兴起增加了应用最先进方法所需的成本和专业技术。在这里,我们要问的是,一个基本的生物地理格局--四足动物物种丰富度的纬度梯度--是否反映在现有的参考基因组中,而参考基因组是将分子工具应用于生物多样性研究和保护的重要数据资源。我们还询问了全球南方和全球北方在测序方法上是否存在差异,并回顾了过去 5 年中四种主要期刊上的保护遗传学研究。我们发现,相对于低纬度地区的物种丰富度而言,现存的参考基因组非常稀少,而降低代表性和全基因组测序则不成比例地应用于全球北方的类群。最后,我们提出了缩小这一差距和加强生物多样性基因组学国际合作的建议。
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引用次数: 0
Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands 适应性辐射的种群基因组学:加那利群岛特有蜘蛛的超高遗传多样性和重组水平。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-14 DOI: 10.1111/mec.17547
Paula Escuer, Sara Guirao-Rico, Miquel A. Arnedo, Alejandro Sánchez-Gracia, Julio Rozas

The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage-based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterised genome-wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems.

在加那利群岛的海洋群岛中,蜘蛛属(Dysdera)经历了显著的多样化,自群岛起源以来的 2,000 万年中,共出现了约 60 种特有物种。这种进化辐射伴随着饮食结构的巨大变化,通常表现为包括形态、新陈代谢和行为变化在内的表型改变。因此,这些特有的蜘蛛是了解进化驱动因素和确定适应性辐射基因组决定因素的绝佳模型。最近,我们首次完成了地方性物种之一 D. silvatica 的染色体组水平的基因组组装,为进化基因组学研究提供了高质量的参考序列。在这里,我们对拉戈梅拉岛的一个 D. silvatica 自然种群进行了基于低覆盖率的重测序研究。利用新的高质量基因组,我们描述了全基因组核苷酸多态性、分化和连锁不平衡水平,并推断了该种群的人口历史。我们还对最近的正选择进行了全面的全基因组扫描。我们的研究结果表明,在这一受地理限制的地方性物种中,核苷酸多样性和重组水平极高,表明历史上的有效种群规模很大。我们还发现了几个可能受到正选择的候选基因组区域,突出了相关的生物过程,如视觉和氮提取等潜在的适应目标。这些过程可能最终推动该属的物种多样化。这项对海洋群岛特有蜘蛛的开创性研究为更广泛的种群基因组学分析奠定了基础,旨在了解驱动岛屿生态系统适应性辐射的遗传机制。
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引用次数: 0
Decrypting Corals: Does Regulatory Evolution Underlie Environmental Specialisation of Coral Cryptic Lineages? 解密珊瑚:调控进化是珊瑚隐生系环境特化的基础吗?
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-14 DOI: 10.1111/mec.17546
Dominique N Gallery, John P Rippe, Mikhail V Matz

A recent sequencing study has shown that two common Caribbean corals, Montastraea cavernosa and Siderastrea siderea, each consist of four genetically distinct lineages in the Florida Keys. These lineages are specialised to a certain depth and, to a lesser extent, to nearshore or offshore habitats. We hypothesised that the lineages' environmental specialisation is at least in part due to regulatory evolution, which would manifest as the emergence of groups of coregulated genes ('modules') demonstrating lineage-specific responses to different reef environments. Our hypothesis also predicted that genes belonging to such modules would show greater genetic divergence between lineages than other genes. Contrary to these expectations, responses of cryptic lineages to natural environmental variation were essentially the same at the genome-wide gene coexpression network level, with much fewer differences in gene expression between lineages compared to between habitats. Moreover, none of the identified coregulated gene expression modules exhibit elevated genetic divergence between lineages. Possible explanations of these unexpected results range from the leading role of algal symbionts and/or microbiome in adaptation to strong action of spatially varying selection equalising gene expression patterns despite different genetic background. We discuss how future studies could assist in discriminating between these possibilities.

最近的一项测序研究表明,在佛罗里达礁岛群,两种常见的加勒比珊瑚(Montastraea cavernosa 和 Siderastrea siderea)分别由四个基因不同的品系组成。这些品系专精于一定的深度,其次是近岸或离岸栖息地。我们假设,这些品系的环境特化至少有一部分是由于调控进化造成的,这种进化将表现为核心基因组("模块")的出现,显示出品系对不同珊瑚礁环境的特异性反应。我们的假设还预测,与其他基因相比,属于这类模块的基因在不同种系之间会表现出更大的遗传差异。与预期相反的是,在全基因组基因共表达网络水平上,隐性种系对自然环境变化的反应基本相同,种系间基因表达的差异远远小于栖息地间的差异。此外,在已确定的核心基因表达模块中,没有一个表现出系间遗传差异的增加。这些意外结果的可能解释包括:藻类共生体和/或微生物群在适应过程中发挥了主导作用,以及尽管遗传背景不同,但不同空间选择的强大作用使基因表达模式趋于一致。我们将讨论未来的研究如何帮助区分这些可能性。
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引用次数: 0
Sexual Selection on Non-Ornamental Traits Is Underpinned by Evidence of Genetic Constraints on Sex-Biased Expression in Dusky Pipefish. 在暗色琵琶鱼中,非基本性状的性选择受到性别表达遗传限制的证据的支持。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-14 DOI: 10.1111/mec.17550
Nicole M Tosto, Emily Rose, Heather D Mason, Judith E Mank, Sarah P Flanagan

Species lacking distinct secondary sex characteristics, such as differences in size or morphology, are often thought to experience lower levels of sex-specific selection in comparison to highly sexually dimorphic organisms. However, monomorphism in classic visible traits could be a result of genetic or physiological constraints that prevent the sexes from reaching divergent fitness optima. Additionally, biochemical and molecular work have revealed a variety of less easily observed phenotypes that nonetheless exhibit profound dimorphism. Sex-specific selection could act on these more subtle, less visible, traits. We investigate sex-specific selection in the polygynandrous dusky pipefish (Syngnathus floridae), which lacks distinct secondary sexual characteristics such as size, colour and morphological dimorphism. Using experimental breeding populations, we revealed that although males and females have similar opportunities for sexual selection, only males experience significant sexual selection pressures on body size. We also investigated patterns of sex-biased and sex-specific gene expression in gonads, livers and gills, and tested whether genes with highly divergent expression patterns between the sexes are more likely to be tissue-specific, and therefore relieved of genetic constraints. Sex bias in gene expression was widespread, although the reproductive organs had the most sex-biased and sex-specific genes. Sex-specific selection on gene expression in gills was primarily related to immune response, whereas the liver and gonads had a wide variety of cellular processes, as well as reproductive proteins, showing sex-biased expression. These sex-biased genes showed higher organ-specificity in their expression patterns, suggesting that pleiotropic constraints might have historically impacted the evolution of sex-specific expression patterns. Altogether, we find evidence for ongoing and historical sex-specific selection in the dusky pipefish.

缺乏明显第二性征的物种,如体型或形态上的差异,通常被认为与高度性别二形的生物相比,会经历较低水平的性别特异性选择。然而,典型可见性状的单态性可能是遗传或生理限制的结果,这些限制阻止了两性达到不同的最佳适应度。此外,生化和分子研究还揭示了各种不易观察到的表型,但这些表型却表现出深刻的二态性。性别特异性选择可能会作用于这些更微妙、更不明显的特征。我们研究了雌雄同体的暗色琵琶鱼(Syngnathus floridae)的性别选择,这种鱼缺乏明显的第二性特征,如体型、颜色和形态二态性。通过实验繁殖种群,我们发现虽然雄性和雌性有相似的性选择机会,但只有雄性在体型上经历了显著的性选择压力。我们还研究了性腺、肝脏和鳃中有性别偏向和性别特异性的基因表达模式,并检验了性别间表达模式高度不同的基因是否更有可能具有组织特异性,从而摆脱遗传限制。基因表达的性别偏向非常普遍,但生殖器官的性别偏向和性别特异性基因最多。鳃中基因表达的性别特异性选择主要与免疫反应有关,而肝脏和性腺中的各种细胞过程以及生殖蛋白则表现出性别偏向表达。这些具有性别偏向的基因在其表达模式中表现出更高的器官特异性,这表明多效制约因素可能在历史上影响了性别特异性表达模式的进化。总之,我们发现了暗色琵琶鱼性别特异性选择的持续性和历史性证据。
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引用次数: 0
Evolution and Plasticity of Gene Expression Under Progressive Warming in Drosophila subobscura 亚马逊果蝇在逐渐变暖条件下基因表达的进化与可塑性
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-08 DOI: 10.1111/mec.17548
Marta A. Antunes, Marta A. Santos, Ana S. Quina, Mauro Santos, Margarida Matos, Pedro Simões

Understanding the molecular mechanisms of thermal adaptation is crucial to predict the impacts of global warming. However, there is still a lack of research on the effects of rising temperatures over time and of studies involving different populations from the same species. The present study focuses on these two aspects, which are of great importance in understanding how organisms cope and adapt to ongoing changes in their environment. This study investigates the impact of global warming on the gene expression patterns of Drosophila subobscura populations from two different latitudinal locations after 23 generations of evolution. Our results indicate that evolutionary changes depend on the genetic background of the populations, with different starting points for thermal evolution, and that high-latitude populations show more pronounced evolutionary changes, with some evidence of convergence towards low-latitude populations. We found an interplay between plasticity and selection, with the high-latitude population showing fewer initial plastic genes and lower levels of adaptive plasticity, but a greater magnitude of change in both plastic and selective responses during evolution under warming conditions compared with its low-latitude counterpart. A substantial proportion of the transcriptome was observed to be evolving, despite the lack of observable response at higher-order phenotypic traits. The interplay between plasticity and selection may prove to be an essential component in shaping species’ evolutionary responses to climate change. Furthermore, the value of conducting studies on multiple populations of the same species is emphasised, given the identification of differences between populations with different backgrounds in several contexts.

了解热适应的分子机制对于预测全球变暖的影响至关重要。然而,目前仍然缺乏对气温升高随时间推移产生的影响的研究,也缺乏涉及同一物种不同种群的研究。本研究主要关注这两个方面,这对于了解生物如何应对和适应环境的持续变化非常重要。本研究调查了全球变暖对来自两个不同纬度地区的亚种果蝇种群经过 23 代进化后的基因表达模式的影响。我们的结果表明,进化变化取决于种群的遗传背景,热进化的起点不同,高纬度种群表现出更明显的进化变化,并有一些向低纬度种群趋同的证据。我们发现可塑性和选择之间存在相互作用,高纬度种群显示出较少的初始可塑性基因和较低的适应可塑性水平,但与低纬度种群相比,在变暖条件下的进化过程中,可塑性和选择性反应的变化幅度更大。尽管在高阶表型特征上缺乏可观察到的反应,但仍观察到很大一部分转录组在进化。可塑性和选择之间的相互作用可能会成为物种进化过程中对气候变化做出反应的重要组成部分。此外,对同一物种的多个种群进行研究的价值也得到了强调,因为不同背景的种群之间在多种情况下存在差异。
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引用次数: 0
Comparative Population Genomic Diversity and Differentiation in Trapdoor Spiders and Relatives (Araneae, Mygalomorphae) Trapdoor Spiders and Relatives (Araneae, Mygalomorphae) 的种群基因组多样性和分化比较。
IF 4.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-08 DOI: 10.1111/mec.17540
Rodrigo Monjaraz-Ruedas, James Starrett, Lacie Newton, Jason E. Bond, Marshal Hedin

Although patterns of population genomic variation are well-studied in animals, there remains room for studies that focus on non-model taxa with unique biologies. Here we characterise and attempt to explain such patterns in mygalomorph spiders, which are generally sedentary, often occur as spatially clustered demes and show remarkable longevity. Genome-wide single nucleotide polymorphism (SNP) data were collected for 500 individuals across a phylogenetically representative sample of taxa. We inferred genetic populations within focal taxa using a phylogenetically informed clustering approach, and characterised patterns of diversity and differentiation within- and among these genetic populations, respectively. Using phylogenetic comparative methods we asked whether geographical range sizes and ecomorphological variables (behavioural niche and body size) significantly explain patterns of diversity and differentiation. Specifically, we predicted higher genetic diversity in genetic populations with larger geographical ranges, and in small-bodied taxa. We also predicted greater genetic differentiation in small-bodied taxa, and in burrowing taxa. We recovered several significant predictors of genetic diversity, but not genetic differentiation. However, we found generally high differentiation across genetic populations for all focal taxa, and a consistent signal for isolation-by-distance irrespective of behavioural niche or body size. We hypothesise that high population genetic structuring, likely reflecting combined dispersal limitation and microhabitat specificity, is a shared trait for all mygalomorphs. Few studies have found ubiquitous genetic structuring for an entire ancient and species-rich animal clade.

虽然对动物种群基因组变异模式的研究很深入,但对具有独特生物学特性的非模式类群的研究仍有很大的空间。在这里,我们描述并试图解释巨型蜘蛛的这种模式,这种蜘蛛通常是定居性的,经常以空间集群的形式出现,而且寿命极长。我们收集了具有系统发育代表性的分类群样本中 500 个个体的全基因组单核苷酸多态性(SNP)数据。我们利用系统发育信息聚类方法推断了重点类群内部的遗传种群,并分别描述了这些遗传种群内部和之间的多样性和分化模式。利用系统发育比较方法,我们提出了地理范围大小和生态形态变量(行为生态位和体型)是否能显著解释多样性和分化模式的问题。具体来说,我们预测地理范围较大的遗传种群和小体型类群的遗传多样性较高。我们还预测小体型类群和穴居类群的遗传分化程度更高。我们发现了几个重要的遗传多样性预测因子,但没有发现遗传分化。不过,我们发现所有重点类群的遗传种群之间的分化程度普遍较高,而且无论行为生态位或体型大小如何,距离隔离的信号都是一致的。我们假设,高种群遗传结构可能反映了扩散限制和微生境特异性,是所有巨蜥的共同特征。很少有研究发现整个古老而物种丰富的动物支系具有普遍的遗传结构。
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Molecular Ecology
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