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An enigmatic translocation of the vertebrate primordial eye field. 脊椎动物原始视野的神秘移位。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-10-02 DOI: 10.1186/s12862-020-01693-6
R G Loosemore, S D Matthaei, T C Stanger

The primordial eye field of the vertebrate embryo is a single entity of retinal progenitor cells spanning the anterior neural plate before bifurcating to form bilateral optic vesicles. Here we review fate mapping data from zebrafish suggesting that prior to evagination of the optic vesicles the eye field may undergo a Maypole-plait migration of progenitor cells through the midline influenced by the anteriorly subducting diencephalon. Such an enigmatic translocation of scaffolding progenitors could have evolutionary significance if pointing, by way of homology, to an ancient mechanism for transition of the single eye field in chordates to contralateral eye fields in vertebrates.

脊椎动物胚胎的原始视野是横跨前神经板的视网膜祖细胞的单一实体,然后分叉形成双侧视神经泡。在这里,我们回顾了斑马鱼的命运图谱数据,表明在视神经囊外翻之前,视野可能经历了受前隐伏间脑影响的祖细胞通过中线的梅pole-plait迁移。如果通过同源性的方式指出脊索动物的单眼视野向脊椎动物的对侧眼视野过渡的一种古老机制,那么这种支架祖细胞的神秘易位可能具有进化意义。
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引用次数: 0
Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae. 通过麦角酵母中的 mtDNA 置换揭示线粒体与核的共同适应。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-25 DOI: 10.1186/s12862-020-01685-6
Tuc H M Nguyen, Sargunvir Sondhi, Andrew Ziesel, Swati Paliwal, Heather L Fiumera

Background: Mitochondrial function requires numerous genetic interactions between mitochondrial- and nuclear- encoded genes. While selection for optimal mitonuclear interactions should result in coevolution between both genomes, evidence for mitonuclear coadaptation is challenging to document. Genetic models where mitonuclear interactions can be explored are needed.

Results: We systematically exchanged mtDNAs between 15 Saccharomyces cerevisiae isolates from a variety of ecological niches to create 225 unique mitochondrial-nuclear genotypes. Analysis of phenotypic profiles confirmed that environmentally-sensitive interactions between mitochondrial and nuclear genotype contributed to growth differences. Exchanges of mtDNAs between strains of the same or different clades were just as likely to demonstrate mitonuclear epistasis although epistatic effect sizes increased with genetic distances. Strains with their original mtDNAs were more fit than strains with synthetic mitonuclear combinations when grown in media that resembled isolation habitats.

Conclusions: This study shows that natural variation in mitonuclear interactions contributes to fitness landscapes. Multiple examples of coadapted mitochondrial-nuclear genotypes suggest that selection for mitonuclear interactions may play a role in helping yeasts adapt to novel environments and promote coevolution.

背景:线粒体功能需要线粒体编码基因与核编码基因之间的大量基因相互作用。虽然选择最佳的线粒体核相互作用应导致两个基因组的共同进化,但线粒体核共同适应的证据却难以记录。我们需要可以探索有丝分裂核相互作用的遗传模型:结果:我们在来自不同生态位点的 15 个分离酵母菌之间系统地交换了 mtDNA,从而产生了 225 个独特的线粒体-核基因型。表型分析证实,线粒体与核基因型之间对环境敏感的相互作用导致了生长差异。同一支系或不同支系的菌株之间的 mtDNA 交换同样可能表现出线粒体核外显性,尽管外显效应的大小随遗传距离的增加而增加。当菌株在类似隔离生境的培养基中生长时,具有原始mtDNA的菌株比具有合成有丝分裂核组合的菌株更适合生长:结论:这项研究表明,有丝分裂核相互作用的自然变异有助于形成适合度景观。线粒体-核基因型共同适应的多个实例表明,对有丝分裂核相互作用的选择可能在帮助酵母菌适应新环境和促进共同进化方面发挥作用。
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引用次数: 0
Floral signals evolve in a predictable way under artificial and pollinator selection in Brassica rapa. 在人工和传粉昆虫的选择下,甘蓝型油菜的花信号以可预测的方式进化。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-24 DOI: 10.1186/s12862-020-01692-7
Pengjuan Zu, Florian P Schiestl, Daniel Gervasi, Xin Li, Daniel Runcie, Frédéric Guillaume

Background: Angiosperms employ an astonishing variety of visual and olfactory floral signals that are generally thought to evolve under natural selection. Those morphological and chemical traits can form highly correlated sets of traits. It is not always clear which of these are used by pollinators as primary targets of selection and which would be indirectly selected by being linked to those primary targets. Quantitative genetics tools for predicting multiple traits response to selection have been developed since long and have advanced our understanding of evolution of genetically correlated traits in various biological systems. We use these tools to predict the evolutionary trajectories of floral traits and understand the selection pressures acting on them.

Results: We used data from an artificial selection and a pollinator (bumblebee, hoverfly) evolution experiment with fast cycling Brassica rapa plants to predict evolutionary changes of 12 floral volatiles and 4 morphological floral traits in response to selection. Using the observed selection gradients and the genetic variance-covariance matrix (G-matrix) of the traits, we showed that the observed responses of most floral traits including volatiles were predicted in the right direction in both artificial- and bumblebee-selection experiment. Genetic covariance had a mix of constraining and facilitating effects on evolutionary responses. We further revealed that G-matrices also evolved in the selection processes.

Conclusions: Overall, our integrative study shows that floral signals, especially volatiles, evolve under selection in a mostly predictable way, at least during short term evolution. Evolutionary constraints stemming from genetic covariance affected traits evolutionary trajectories and thus it is important to include genetic covariance for predicting the evolutionary changes of a comprehensive suite of traits. Other processes such as resource limitation and selfing also need to be considered for a better understanding of floral trait evolution.

背景:被子植物利用各种各样的视觉和嗅觉花信号,这些信号通常被认为是在自然选择下进化而来的。这些形态和化学特征可以形成高度相关的特征集。目前尚不清楚哪些被传粉昆虫用作主要选择目标,哪些将通过与这些主要目标联系而被间接选择。长期以来,用于预测多个性状对选择的反应的定量遗传学工具已经开发出来,并促进了我们对各种生物系统中遗传相关性状进化的理解。我们使用这些工具来预测花性状的进化轨迹,并了解作用在它们身上的选择压力。结果:我们使用来自人工选择和快速循环的芸苔属植物的传粉昆虫(大黄蜂、气垫苍蝇)进化实验的数据,预测了12种花挥发物和4种形态花性状对选择的进化变化。利用观察到的选择梯度和性状的遗传方差协方差矩阵(G-matrix),我们发现在人工和大黄蜂选择实验中,包括挥发物在内的大多数花性状的观察到的反应都是朝着正确的方向预测的。遗传协方差对进化反应既有制约作用,也有促进作用。我们进一步揭示了G-矩阵也在选择过程中进化。结论:总的来说,我们的综合研究表明,花信号,尤其是挥发物,在选择下以一种最可预测的方式进化,至少在短期进化中是这样。源自遗传协方差的进化约束影响了性状的进化轨迹,因此,包括遗传协方差对于预测一组综合性状的进化变化很重要。为了更好地理解花的性状进化,还需要考虑其他过程,如资源限制和自交。
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引用次数: 0
Phenotypic coupling of sleep and starvation resistance evolves in D. melanogaster. 黑腹蝇中睡眠和耐饥饿性的表型耦合进化
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-22 DOI: 10.1186/s12862-020-01691-8
Didem P Sarikaya, Julie Cridland, Adam Tarakji, Hayley Sheehy, Sophia Davis, Ashley Kochummen, Ryan Hatmaker, Nossin Khan, Joanna Chiu, David J Begun

Background: One hypothesis for the function of sleep is that it serves as a mechanism to conserve energy. Recent studies have suggested that increased sleep can be an adaptive mechanism to improve survival under food deprivation in Drosophila melanogaster. To test the generality of this hypothesis, we compared sleep and its plastic response to starvation in a temperate and tropical population of Drosophila melanogaster.

Results: We found that flies from the temperate population were more starvation resistant, and hypothesized that they would engage in behaviors that are considered to conserve energy, including increased sleep and reduced movement. Surprisingly, temperate flies slept less and moved more when they were awake compared to tropical flies, both under fed and starved conditions, therefore sleep did not correlate with population-level differences in starvation resistance. In contrast, total sleep and percent change in sleep when starved were strongly positively correlated with starvation resistance within the tropical population, but not within the temperate population. Thus, we observe unexpectedly complex relationships between starvation and sleep that vary both within and across populations. These observations falsify the simple hypothesis of a straightforward relationship between sleep and energy conservation. We also tested the hypothesis that starvation is correlated with metabolic phenotypes by investigating stored lipid and carbohydrate levels, and found that stored metabolites partially contributed towards variation starvation resistance.

Conclusions: Our findings demonstrate that the function of sleep under starvation can rapidly evolve on short timescales and raise new questions about the physiological correlates of sleep and the extent to which variation in sleep is shaped by natural selection.

背景:关于睡眠功能的一个假设是,睡眠是一种保存能量的机制。最近的研究表明,增加睡眠可能是黑腹果蝇在食物匮乏条件下提高存活率的一种适应机制。为了验证这一假设的普遍性,我们比较了温带和热带黑腹果蝇种群的睡眠及其对饥饿的可塑性反应:结果:我们发现温带种群的果蝇更耐受饥饿,并假设它们会采取被认为是节约能量的行为,包括增加睡眠和减少运动。令人惊讶的是,与热带苍蝇相比,温带苍蝇在清醒时睡眠更少、运动更多,无论是在喂食还是饥饿条件下,因此睡眠与抗饥饿性的种群水平差异无关。相反,在热带种群中,总睡眠时间和饥饿时睡眠时间变化的百分比与耐饥饿性呈强烈的正相关,而在温带种群中则不然。因此,我们观察到饥饿与睡眠之间存在意想不到的复杂关系,这种关系在种群内部和种群之间都存在差异。这些观察结果推翻了睡眠与能量守恒之间存在直接关系的简单假设。我们还通过调查储存的脂质和碳水化合物水平,检验了饥饿与代谢表型相关的假说,发现储存的代谢物部分导致了抗饥饿能力的变化:我们的研究结果表明,饥饿状态下的睡眠功能可以在短时间内迅速进化,并对睡眠的生理相关性以及自然选择在多大程度上塑造了睡眠的变异提出了新的问题。
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引用次数: 0
Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses. Iniistius trivittatus 的完整线粒体基因组以及在箭鱼 rRNA 和 tRNA 基因之间观察到的两个插入基因的独特变异。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-21 DOI: 10.1186/s12862-020-01683-8
Dong Liu, Yuanyuan Zhang, Ming Zhang, Jinquan Yang, Wenqiao Tang

Background: The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species.

Results: We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments.

Conclusions: This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

背景介绍鲈形目(Labridae)鲈科在世界上有519个物种。与摄食相关的颌的功能进化导致了物种的分化,咽颌器独立进化,但腕足动物的进化机制仍未解决。有丝分裂基因组数据可用于推断腕足动物的遗传多样性和研究其进化历史,但迄今为止该科仅有8个完整的有丝分裂基因组被测序。在此,我们测序了三疣梭子鱼(Iniistius trivittatus)的完整有丝分裂基因组,以研究濑鱼物种间的遗传分化:结果:我们采用一种新的 PCR 策略对笛鲷的有丝分裂基因组进行了测序。有丝分裂基因组全长 16,820 bp,包括 13 个蛋白质编码基因、2 个核糖体 RNA(rRNA)基因、22 个转运 RNA(tRNA)基因和一个控制区。与八个已知的线粒体基因组相比,在 12S rRNA - tRNAVal - 16S rRNA 的基因间区域发现了两个额外的非编码区(长度分别为 121 和 107 bp),即所谓的插入区。据推测,这两个罕见插入片段来自与 tRNA 相关的逆转录酶。与细胞色素 b 基因相比,这两个插入序列在种内水平上高度保守,但它们表现出显著的变异和较低的相似性(结论:本研究发现了更多局限于尖嘴鱼种的有丝分裂基因组插入序列。有插入基因的 rRNA 基因可能经历了适应摄食模式的选择性压力。这些知识有助于更好地理解濑鱼形态进化的分子机制。
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引用次数: 0
Fossil-calibrated molecular phylogeny of atlantid heteropods (Gastropoda, Pterotracheoidea). 经化石校正的异足目(腹足纲,翼足目)分子系统发育。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-21 DOI: 10.1186/s12862-020-01682-9
Deborah Wall-Palmer, Arie W Janssen, Erica Goetze, Le Qin Choo, Lisette Mekkes, Katja T C A Peijnenburg

Background: The aragonite shelled, planktonic gastropod family Atlantidae (shelled heteropods) is likely to be one of the first groups to be impacted by imminent ocean changes, including ocean warming and ocean acidification. With a fossil record spanning at least 100 Ma, atlantids have experienced and survived global-scale ocean changes and extinction events in the past. However, the diversification patterns and tempo of evolution in this family are largely unknown.

Results: Based on a concatenated maximum likelihood phylogeny of three genes (cytochrome c oxidase subunit 1 mitochondrial DNA, 28S and 18S ribosomal rRNA) we show that the three extant genera of the family Atlantidae, Atlanta, Protatlanta and Oxygyrus, form monophyletic groups. The genus Atlanta is split into two groups, one exhibiting smaller, well ornamented shells, and the other having larger, less ornamented shells. The fossil record, in combination with a fossil-calibrated phylogeny, suggests that large scale atlantid extinction was accompanied by considerable and rapid diversification over the last 25 Ma, potentially driven by vicariance events.

Conclusions: Now confronted with a rapidly changing modern ocean, the ability of atlantids to survive past global change crises gives some optimism that they may be able to persist through the Anthropocene.

背景:有文石壳的浮游腹足类亚特兰特科(有壳异足类)很可能是最先受到迫在眉睫的海洋变化(包括海洋变暖和海洋酸化)影响的类群之一。亚特兰蒂斯科的化石记录至少跨越了 100 个万年前,它们在过去经历了全球规模的海洋变化和物种灭绝事件,并幸存了下来。然而,该科动物的多样化模式和进化速度在很大程度上还不为人所知:结果:基于三个基因(细胞色素 c 氧化酶亚单位 1 线粒体 DNA、28S 和 18S 核糖体 rRNA)的最大似然法系统发生分析表明,亚特兰特科现存的三个属:亚特兰特属(Atlanta)、原亚特兰特属(Protatlanta)和 Oxygyrus 属(Oxygyrus)形成了单系群。亚特兰大属分为两组,一组的贝壳较小、装饰精美,另一组的贝壳较大、装饰较少。化石记录与经化石校准的系统发育相结合,表明在过去的 25 Ma 期间,伴随着大规模的亚特兰蒂斯类灭绝的是相当大的快速多样化,这可能是由沧海桑田事件驱动的:现在,面对瞬息万变的现代海洋,蝠鲼能够在过去的全球变化危机中幸存下来,这让人乐观地认为,它们或许能够在人类世继续生存下去。
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引用次数: 0
Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity. 微生物杂交后代的减数分裂重组及其对致病性的影响。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-17 DOI: 10.1186/s12862-020-01689-2
Britta Bueker, Marco Alexandre Guerreiro, Michael E Hood, Andreas Brachmann, Sven Rahmann, Dominik Begerow

Background: Hybridization is a central mechanism in evolution, producing new species or introducing important genetic variation into existing species. In plant-pathogenic fungi, adaptation and specialization to exploit a host species are key determinants of evolutionary success. Here, we performed experimental crosses between the two pathogenic Microbotryum species, M. lychnidis-dioicae and M. silenes-acaulis that are specialized to different hosts. The resulting offspring were analyzed on phenotypic and genomic levels to describe genomic characteristics of hybrid offspring and genetic factors likely involved in host-specialization.

Results: Genomic analyses of interspecific fungal hybrids revealed that individuals were most viable if the majority of loci were inherited from one species. Interestingly, species-specific loci were strictly controlled by the species' origin of the mating type locus. Moreover we detected signs of crossing over and chromosome duplications in the genomes of the analyzed hybrids. In Microbotryum, mitochondrial DNA was found to be uniparentally inherited from the a2 mating type. Genome comparison revealed that most gene families are shared and the majority of genes are conserved between the two species, indicating very similar biological features, including infection and pathogenicity processes. Moreover, we detected 211 candidate genes that were retained under host-driven selection of backcrossed lines. These genes and might therefore either play a crucial role in host specialization or be linked to genes that are essential for specialization.

Conclusion: The combination of genome analyses with experimental selection and hybridization is a promising way to investigate host-pathogen interactions. This study manifests genetic factors of host specialization that are required for successful biotrophic infection of the post-zygotic stage, but also demonstrates the strong influence of intra-genomic conflicts or instabilities on the viability of hybrids in the haploid host-independent stage.

背景:杂交是生物进化的核心机制,可产生新物种或为现有物种引入重要的遗传变异。在植物病原真菌中,利用宿主物种的适应性和专一性是决定进化成功与否的关键因素。在这里,我们进行了两种致病性微囊菌(M. lychnidis-dioicae和M. silenes-acaulis)之间的杂交实验,这两种致病性微囊菌专门利用不同的寄主。对杂交后代的表型和基因组水平进行了分析,以描述杂交后代的基因组特征以及可能参与寄主专化的遗传因素:结果:对种间真菌杂交种的基因组分析表明,如果大多数基因位点都遗传自一个物种,那么个体的生存能力最强。有趣的是,物种特异性基因座受到交配型基因座的物种起源的严格控制。此外,我们还在分析的杂交种基因组中发现了杂交和染色体重复的迹象。在微囊藻中,我们发现线粒体 DNA 是由 a2 交配型单亲遗传的。基因组比较显示,两个物种之间共享大多数基因家族,而且大多数基因是保守的,这表明两个物种的生物学特征非常相似,包括感染和致病过程。此外,我们还发现了 211 个候选基因,这些基因在宿主驱动的回交系选择中被保留下来。因此,这些基因可能在宿主特化过程中发挥了关键作用,或者与特化所必需的基因有关:结论:将基因组分析与实验选择和杂交结合起来,是研究宿主与病原体相互作用的一种很有前途的方法。这项研究表明,宿主特化的遗传因素是后合子阶段成功的生物营养感染所必需的,同时也证明了基因组内的冲突或不稳定对单倍体宿主独立阶段杂交种的生存能力有很大影响。
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引用次数: 0
Genotypic similarities among the parthenogenetic Darevskia rock lizards with different hybrid origins. 不同杂交来源孤雌达氏岩蜥蜴基因型的相似性。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-16 DOI: 10.1186/s12862-020-01690-9
David Tarkhnishvili, Alexey Yanchukov, Mehmet Kürşat Şahin, Mariam Gabelaia, Marine Murtskhvaladze, Kamil Candan, Eduard Galoyan, Marine Arakelyan, Giorgi Iankoshvili, Yusuf Kumlutaş, Çetin Ilgaz, Ferhat Matur, Faruk Çolak, Meriç Erdolu, Sofiko Kurdadze, Natia Barateli, Cort L Anderson

Background: The majority of parthenogenetic vertebrates derive from hybridization between sexually reproducing species, but the exact number of hybridization events ancestral to currently extant clonal lineages is difficult to determine. Usually, we do not know whether the parental species are able to contribute their genes to the parthenogenetic vertebrate lineages after the initial hybridization. In this paper, we address the hypothesis, whether some genotypes of seven phenotypically distinct parthenogenetic rock lizards (genus Darevskia) could have resulted from back-crosses of parthenogens with their presumed parental species. We also tried to identify, as precise as possible, the ancestral populations of all seven parthenogens.

Results: We analysed partial mtDNA sequences and microsatellite genotypes of all seven parthenogens and their presumed ansectral species, sampled across the entire geographic range of parthenogenesis in this group. Our results confirm the previous designation of the parental species, but further specify the maternal populations that are likely ancestral to different parthenogenetic lineages. Contrary to the expectation of independent hybrid origins of the unisexual taxa, we found that genotypes at multiple loci were shared frequently between different parthenogenetic species. The highest proportions of shared genotypes were detected between (i) D. sapphirina and D. bendimahiensis and (ii) D. dahli and D. armeniaca, and less often between other parthenogens. In case (ii), genotypes at the remaining loci were notably distinct.

Conclusions: We suggest that both observations (i-ii) can be explained by two parthenogenetic forms tracing their origin to a single initial hybridization event. In case (ii), however, occasional gene exchange between the unisexual and the parental bisexual species could have taken place after the onset of parthenogenetic reproduction. Indeed, backcrossed polyploid hybrids are relatively frequent in Darevskia, although no direct evidence of recent gene flow has been previously documented. Our results further suggest that parthenogens are losing heterozygosity as a result of allelic conversion, hence their fitness is expected to decline over time as genetic diversity declines. Backcrosses with the parental species could be a rescue mechanism which might prevent this decline, and therefore increase the persistance of unisexual forms.

背景:大多数孤雌生殖脊椎动物来自有性繁殖物种之间的杂交,但是祖先到目前存在的克隆谱系的杂交事件的确切数量很难确定。通常,我们不知道亲本物种在初始杂交后是否能够将它们的基因贡献给孤雌生殖的脊椎动物谱系。在本文中,我们提出了一个假设,即7种表型不同的孤雌岩蜥蜴(Darevskia属)的某些基因型是否可能是由孤雌雌蜥蜴与其假定的亲本物种的回交产生的。我们还试图尽可能精确地确定所有七个孤雌生殖的祖先种群。结果:我们分析了所有7个孤雌生殖及其推测的旁种的部分mtDNA序列和微卫星基因型,在该群体的整个孤雌生殖地理范围内取样。我们的研究结果证实了先前对亲本物种的指定,但进一步明确了母系种群可能是不同孤雌生殖谱系的祖先。与单性分类群独立杂交起源的预期相反,我们发现多个位点的基因型在不同的孤雌生殖物种之间经常共享。共有基因型的比例最高的是(i)萨菲绿瓢虫与本迪马伊瓢虫,(ii)达丽瓢虫与亚美尼亚瓢虫,其他孤雌瓢虫之间的比例较低。在病例(ii)中,其余位点的基因型明显不同。结论:我们认为这两种观察结果(i-ii)都可以用两种孤雌生殖形式来解释,它们的起源可以追溯到单一的初始杂交事件。然而,在情况(ii)中,单性物种和亲本双性物种之间偶尔的基因交换可能在孤雌生殖开始后发生。事实上,回交的多倍体杂交品种在达列夫斯基相对频繁,尽管之前没有直接证据证明最近的基因流动。我们的研究结果进一步表明,孤雌生殖由于等位基因转换而失去杂合性,因此随着遗传多样性的下降,它们的适合度预计会随着时间的推移而下降。与亲本物种回交可能是一种拯救机制,可以防止这种衰退,从而增加单性形式的持久性。
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引用次数: 10
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species. 多模型海景基因组学确定了在同域海洋物种中选择的不同环境驱动因素。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-16 DOI: 10.1186/s12862-020-01679-4
Erica S Nielsen, Romina Henriques, Maria Beger, Robert J Toonen, Sophie von der Heyden

Background: As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis).

Results: Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus.

Conclusion: The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.

背景:随着全球变化和人为压力的持续增加,保护和管理越来越需要考虑物种适应新环境条件的潜力。因此,有必要描述作用于生态系统的主要选择力量,以及这些力量如何影响种群和物种的进化潜力。使用多模型的海洋基因组学方法,我们比较了三种具有不同生态和生活史的南部非洲同域海洋无脊椎动物的假设环境驱动因素:海胆(Parechinus angulosus),普通岸蟹(Cyclograpsus punctatus)和颗粒帽贝(Scutellastra granularis)。结果:利用Pool-seq、限制性限制位点相关DNA测序(RAD-seq)和7种异常值检测方法,我们沿着强大的生物地理梯度描述了人群之间的基因组差异。在3个物种中,只有S. granularis表现出明显的距离隔离和环境隔离效应。相比之下,海表盐度(SSS)和气温变化幅度与马尾鱼和鳗鲡基因组变异的相关性更强。3个物种之间的基因组结构也存在差异,在东海岸和西海岸的两个集群中,有离群位点对S. granularis和P. angulosus有贡献,而对C. punctatus没有贡献。结论:不同物种的进化潜力不同,表明物种特有的栖息地需求和对环境胁迫的响应可能比区域内的强环境梯度更能预测物种的进化模式。我们还发现了异常值检测方法之间的巨大差异,从而提供了一种新的多模型方法来识别作用于物种的主要环境选择力。总的来说,这项工作强调了如何将比较方法添加到海景基因组学(包括多个模型和物种)中来阐明生态系统对全球变化的复杂进化反应。
{"title":"Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species.","authors":"Erica S Nielsen,&nbsp;Romina Henriques,&nbsp;Maria Beger,&nbsp;Robert J Toonen,&nbsp;Sophie von der Heyden","doi":"10.1186/s12862-020-01679-4","DOIUrl":"https://doi.org/10.1186/s12862-020-01679-4","url":null,"abstract":"<p><strong>Background: </strong>As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis).</p><p><strong>Results: </strong>Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus.</p><p><strong>Conclusion: </strong>The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":"20 1","pages":"121"},"PeriodicalIF":3.4,"publicationDate":"2020-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12862-020-01679-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38389370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories. 家鼠(小家鼠)系统发育的进一步解决通过整合的隔离与迁移的历史。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-09-15 DOI: 10.1186/s12862-020-01666-9
Megan Phifer-Rixey, Bettina Harr, Jody Hey

Background: The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange.

Results: Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short.

Conclusions: Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.

家鼠的三个主要亚种,家鼠(Mus musculus castaneus)、家鼠(musculus domesticus)和家鼠(musculus musus musus),估计在350-500KYA之间发生了分化。由于它们相对较近的分化、亚种之间持续的基因流动以及复杂的人口统计历史,对它们进化历史细节的研究变得复杂。以往的研究在一定程度上受限于所调查的基因座数量和/或所使用方法的范围。在这里,我们采用了一种方法(IMa3),该方法提供了种群系统发育的估计,同时允许复杂的基因交换历史。结果:结果有力地支持了一种拓扑结构,即家兔是家兔和家兔的姐妹。此外,我们还发现了所有亚种对之间基因流动的证据,但这种基因流动主要局限于m.m. musculus到m.m. domesticus之间。其他关键参数的估计依赖于对家鼠的世代时间和突变率的假设。然而,我们的研究结果支持了前人的研究结果,即castaneus的有效种群大小Ne大于其他两个亚种,三个亚种在130 - 420KYA之间开始分化,并且分化时间间隔较短。结论:基因组数据的人口统计学和系统发育联合分析为家鼠的分化史提供了更清晰的图景。
{"title":"Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories.","authors":"Megan Phifer-Rixey, Bettina Harr, Jody Hey","doi":"10.1186/s12862-020-01666-9","DOIUrl":"10.1186/s12862-020-01666-9","url":null,"abstract":"<p><strong>Background: </strong>The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange.</p><p><strong>Results: </strong>Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, N<sub>e,</sub> of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short.</p><p><strong>Conclusions: </strong>Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":"20 1","pages":"120"},"PeriodicalIF":3.4,"publicationDate":"2020-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38480469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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BMC Evolutionary Biology
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