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Correlated evolution of categorical characters under a simple model. 简单模型下分类特征的相关演化。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-22 DOI: 10.1093/evolut/qpae166
Michael C Grundler

I describe a simple model for quantifying the strength of association between two categorical characters evolving on a phylogenetic tree. The model can be used to estimate a correlation statistic that asks whether or not the two characters tend to change at the same time (positive correlation) or at different times (no correlation). This is different than asking if changes in one character are associated with a particular state in another character, which has been the focus of most prior tests for phylogenetic correlation in categorical characters. Analyses of simulated data indicate that positive correlations can be accurately estimated over a range of different tree sizes and phylogenetic signals.

我描述了一个简单的模型,用于量化在系统发生树上演化的两个分类特征之间的关联强度。该模型可用于估算相关性统计量,即这两个特征是否倾向于同时发生变化(正相关)或在不同时间发生变化(无相关)。这与询问一个特征的变化是否与另一个特征的特定状态相关不同,后者是之前大多数分类特征系统发育相关性检验的重点。对模拟数据的分析表明,在不同的树大小和系统发育信号范围内,都可以准确地估计出正相关性。
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引用次数: 0
Selection on sporulation strategies in a metapopulation can lead to coexistence. 元种群中孢子策略的选择可导致共存。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-22 DOI: 10.1093/evolut/qpae161
Stephen R Proulx, Taom Sakal, Zach Reitz, Kelly Thomasson

In constant environments the coexistence of similar species or genotypes is generally limited. In a metapopulation context, however, types that utilize the same resource but are distributed along a competition-colonization trade-off, can coexist. Much thought in this area focuses on a generic trade-off between within-deme competitive ability and between-deme dispersal ability. We point out that the sporulation program in yeasts and other microbes can create a natural trade-off such that strains which initiate sporulation at higher rates suffer in terms of within-deme competition but benefit in terms of between deme dispersal. We develop metapopulation models where the within- deme behavior follows chemostat dynamics. We first show that the rate of sporulation determines the colonization ability of the strain, with colonization ability increasing with sporulation rate up to a point. Metapopulation stability of a single strain exists in a defined range of sporulation rates. We then use pairwise invasability plots to show that coexistence of strains with different sporulation rates generally occurs, but that the set of sporulation rates that can potentially coexist is smaller than the set that allows for stable metapopulations. We extend our pairwise results to show how a continuous set of strains can coexist and verify our conclusions with numerical calculations and stochastic simulations. Our results show that stable variation in sporulation rates is expected under a wide range of ecological conditions.

在恒定的环境中,相似物种或基因型的共存通常是有限的。然而,在元种群环境中,利用相同资源但分布在竞争-殖民化权衡中的类型可以共存。这方面的许多想法都集中在种内竞争能力和种间扩散能力之间的一般权衡上。我们指出,酵母菌和其他微生物的孢子繁殖程序会产生一种自然的权衡,即孢子繁殖率较高的菌株会在菌丝内竞争中受损,但在菌丝间扩散中受益。我们建立了元种群模型,其中种群内的行为遵循恒温器动力学。我们首先证明,孢子繁殖率决定了菌株的定殖能力,定殖能力随着孢子繁殖率的增加而增加,直至达到一个点。单一菌株的种群稳定性存在于确定的孢子繁殖率范围内。然后,我们使用配对入侵图来表明,具有不同孢子繁殖率的菌株一般会共存,但可能共存的孢子繁殖率集合小于允许稳定元种群的集合。我们扩展了成对结果,以说明连续的菌株集如何共存,并通过数值计算和随机模拟验证了我们的结论。我们的结果表明,在广泛的生态条件下,孢子繁殖率的稳定变化是可以预期的。
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引用次数: 0
Hill-Robertson interference may bias the inference of fitness effects of new mutations in highly selfing species. 在高度自交的物种中,希尔-罗伯逊干扰可能会使新突变对适应性影响的推断产生偏差。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-20 DOI: 10.1093/evolut/qpae168
Austin Daigle, Parul Johri

The accurate estimation of the distribution of fitness effects (DFE) of new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed for DFE inference using the site frequency spectrum of putatively neutral and selected sites, their applicability in species with diverse life history traits and complex demographic scenarios is not well understood. Selfing is common among eukaryotic species and can lead to decreased effective recombination rates, increasing the effects of selection at linked sites, including interference between selected alleles. We employ forward simulations to investigate the limitations of current DFE estimation approaches in the presence of selfing and other model violations, such as linkage, departures from semidominance, population structure, and uneven sampling. We find that distortions of the site frequency spectrum due to Hill-Robertson interference in highly selfing populations lead to mis-inference of the deleterious DFE of new mutations. Specifically, when inferring the distribution of selection coefficients, there is an overestimation of nearly neutral and strongly deleterious mutations and an underestimation of mildly deleterious mutations when interference between selected alleles is pervasive. In addition, the presence of cryptic population structure with low rates of migration and uneven sampling across subpopulations leads to the false inference of a deleterious DFE skewed towards effectively neutral/mildly deleterious mutations. Finally, the proportion of adaptive substitutions estimated at high rates of selfing is substantially overestimated. Our observations apply broadly to species and genomic regions with little/no recombination and where interference might be pervasive.

准确估计新突变的适合度效应(DFE)分布对种群遗传推断至关重要,但仍然是一项具有挑战性的任务。虽然利用假定中性位点和选择位点的位点频谱推断 DFE 的方法层出不穷,但这些方法在具有不同生活史特征和复杂人口统计学情景的物种中的适用性还不甚明了。自交在真核生物物种中很常见,会导致有效重组率下降,增加连接位点的选择效应,包括被选择等位基因之间的干扰。我们采用正向模拟研究了当前 DFE 估计方法在自交和其他违反模型情况下的局限性,如连锁、偏离半显性、种群结构和不均匀采样。我们发现,在高度自交的种群中,由于希尔-罗伯逊干扰导致的位点频谱失真会导致对新突变的有害 DFE 的错误推断。具体来说,在推断选择系数的分布时,当被选等位基因之间的干扰普遍存在时,会高估近中性突变和强致畸突变,低估轻度致畸突变。此外,低迁移率的隐性种群结构以及亚种群间取样的不均衡也会导致错误推断,即有害的 DFE 偏向于有效中性/轻度有害突变。最后,在高自交率下估计的适应性替换比例被大大高估。我们的观察结果广泛适用于重组较少/没有重组以及干扰可能普遍存在的物种和基因组区域。
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引用次数: 0
Brain-body co-evolution in incipient versus established primate species - evaluating Simpson's "most important distinction". 初生灵长类物种与成熟灵长类物种的脑体共同进化--评估辛普森的 "最重要区别"。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-19 DOI: 10.1093/evolut/qpae167
Folmer Bokma, Masahito Tsuboi, Nils Chr Stenseth

Are differences between species the long-term consequence of microevolution within species, or does speciation involve fundamentally different processes? We analyzed brain and body sizes of present-day primate species using a novel phylogenetic comparative method that decomposes the phenotypic covariance of these traits into speciational and anagenetic components. We estimated that approximately half of speciation events are accompanied by accelerated phenotypic change. Equivalent in magnitude to approximately 7 million years of gradual microevolution, such speciational changes in brain and body size account for about 58% of the phenotypic variation among extant species. Interestingly, speciational changes in brain and body size appear significantly less correlated (r≈0.83) than gradual, microevolutionary changes in these same traits (r≈0.97). This indicates that the strong allometric constraint that dictates microevolution in brain and body sizes is relaxed at speciation events. These results suggest that phenotypic evolution is not only accelerated during speciation, but also involves events that seldomly occur at microevolutionary timescales.

物种之间的差异是物种内部微进化的长期结果,还是物种形成涉及根本不同的过程?我们使用一种新的系统发育比较方法分析了现今灵长类物种的大脑和身体大小,该方法将这些性状的表型协方差分解为物种和遗传两部分。我们估计,大约有一半的物种起源事件伴随着加速的表型变化。大脑和身体大小的这种物种变化约占现存物种表型变异的58%,相当于大约700万年的微进化。有趣的是,大脑和身体大小的物种变化相关性(r≈0.83)明显低于这些相同特征的微进化渐变相关性(r≈0.97)。这表明,决定大脑和身体大小微进化的强大的等距约束在物种分化事件中被放松了。这些结果表明,表型进化不仅在物种演化过程中加速,而且还涉及很少发生在微进化时间尺度上的事件。
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引用次数: 0
Weak integration allows novel fin shapes and spurs locomotor diversity in reef fishes. 弱整合允许珊瑚礁鱼类形成新颖的鳍形,并刺激其运动多样性。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-19 DOI: 10.1093/evolut/qpae165
Darien R Satterfield, Bernice Yin, Sky Jung, Samantha Hodges-Lisk, Dylan K Wainwright, Michael D Burns, Peter C Wainwright

In complex functional systems composed of many traits, selection for specialized function can induce trait evolution by acting directly on individual components within the system, or indirectly through networks of trait integration. However, strong integration can also hinder diversification into regions of trait space that are not aligned with axes of covariation among traits. As a result, non-independence among traits may limit capacity for functional expansion. We explore this dynamic in the evolution of fin shapes in 106 species from 38 families of coral reef fishes, a polyphyletic assemblage that shows exceptional diversity in locomotor function. Despite strong shared developmental pathways and expectations of a strong match between form and function, we find that species that share swimming mode show substantial disparity in fin shape, and preferred swimming mode is a poor predictor of fin shape. The evolution of fin shape is weakly integrated across the four functionally dominant fins in swimming (the pectoral, caudal, dorsal, and anal fins) and integration is weakened as derived swimming modes evolve. The weak integration among fins in the ancestral locomotor condition provides a primary axis of diversification while allowing for substantial off-axis diversification via independent trait responses to selection. However, the evolution of novel locomotor modes coincides with a loss of integrated axes of covariation among fins. Our study highlights the need for additional work on the functional consequences of fin shape in fishes and impact of evolutionary integration on functions other than locomotion.

在由许多性状组成的复杂功能系统中,对特化功能的选择可以通过直接作用于系统中的单个成分,或通过性状整合网络间接地引起性状进化。然而,强大的整合也会阻碍向性状空间中与性状间协变轴不一致的区域进行多样化。因此,性状之间的非独立性可能会限制功能扩展的能力。我们从珊瑚礁鱼类 38 个科 106 个物种的鳍状进化中探讨了这种动态变化,珊瑚礁鱼类是一个多谱系的集合体,在运动功能方面表现出特殊的多样性。尽管有很强的共同发育途径,而且人们期望鳍的形状与功能之间有很强的匹配性,但我们发现,具有相同游泳模式的物种在鳍的形状上表现出很大的差异,而且偏好的游泳模式对鳍形状的预测很差。鳍形状的进化在游泳中占主导地位的四种鳍(胸鳍、尾鳍、背鳍和臀鳍)之间的整合程度很弱,而且随着衍生游泳模式的进化,整合程度也在减弱。在祖先的运动条件下,鳍之间的弱整合提供了一个主要的多样化轴,同时通过对选择的独立性状反应,允许大量的轴外多样化。然而,新型运动模式的进化与鳍间共变综合轴的丧失相吻合。我们的研究突出表明,有必要就鱼类鳍状的功能后果以及进化整合对运动以外功能的影响开展更多的工作。
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引用次数: 0
Juvenile and total reproductive values for sexual reproduction under any genetic system. 任何遗传系统下有性生殖的幼年生殖值和总生殖值。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-18 DOI: 10.1093/evolut/qpae163
Petri Rautiala, Jussi Lehtonen

Reproductive value (RV) is the expected contribution of genes by an individual or class of individuals to the gene pool in the distant future, and it plays a crucial role in understanding adaptation in long-term evolution. Class RVs are linked to the genetic system and to life history: for diploid genetics, Grafen derived expressions for relative RVs of female and male juveniles, and for the absolute RVs of all females and of all males. Subsequently, Gardner presented a derivation for relative RVs of juvenile females and males under haplodiploidy. Here we generalise these results to any genetic system for biparental sexual reproduction, such that RV is explicitly linked to parameters of the genetic system and life history. The earlier results by Grafen and Gardner arise as special cases. Finally, we derive expressions for absolute juvenile and total reproductive values of both sexes under any genetic system.

生殖价值(RV)是个体或个体类别在遥远未来对基因库的预期贡献,在理解长期进化中的适应性方面起着至关重要的作用。类生殖力值与遗传系统和生活史有关:对于二倍体遗传学,格拉芬推导出了雌性和雄性幼体的相对生殖力值表达式,以及所有雌性和所有雄性的绝对生殖力值表达式。随后,加德纳(Gardner)提出了单倍体情况下雌性和雄性幼体相对 RV 的推导。在这里,我们将这些结果推广到任何双亲有性生殖的遗传系统,这样 RV 就与遗传系统和生活史参数明确相关。格拉芬和加德纳的早期结果是特例。最后,我们推导出在任何遗传系统下雌雄个体的绝对幼年生殖值和总生殖值的表达式。
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引用次数: 0
Correction to: Making sense of recent models of the "sheltering" hypothesis for recombination arrest between sex chromosomes. 更正:理解性染色体间重组抑制的 "庇护 "假说的最新模型。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-16 DOI: 10.1093/evolut/qpae153
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引用次数: 0
Whole-genome sequencing confirms multiple species of Galapagos giant tortoises. 全基因组测序证实加拉帕戈斯巨龟有多个物种。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-16 DOI: 10.1093/evolut/qpae164
Stephen J Gaughran, Rachel Gray, Alexander Ochoa, Menna Jones, Nicole Fusco, Joshua M Miller, Nikos Poulakakis, Kevin de Queiroz, Adalgisa Caccone, Evelyn L Jensen
<p><p>Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with most analyses supporting 13 species. There is mixed support for the species status of taxa living on the same island, with some methods delimiting them as separate species and others suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. Our study provides insight into the complex process of speciation on islands, which is urgently needed given the threatened status of island species around the world. Las tortugas gigantes de las Galápagos son endémicas del Archipiélago de Galápagos, donde se encuentran como poblaciones aisladas. Aunque estas poblaciones se consideran distinguibles en cuanto a morfología, comportamiento y genética, la divergencia reciente de estos taxones hace que su estatus como especies sea controvertido. Aquí aplicamos métodos de coalescencia de especies múltiples con datos de resecuenciación de genomas completos de 38 tortugas de los 13 taxones existentes para evaluar el sustento de la delimitación de estos taxones como especies. En contraste con estudios previos basados únicamente en el tiempo de divergencia, encontramos evidencia sólida para rechazar la hipótesis de que todas las tortugas gigantes de las Galápagos pertenecen a una sola especie. En cambio, una interpretación conservadora de los resultados basados en modelos y divergencia indica que estos taxones forman un complejo de especies que consiste de un mínimo de 9 especies, con la mayoría de los análisis respaldando la existencia de 13 especies. Hay sustento mixto para designar como especies a los taxones que habitan la misma isla, con algunos métodos delimitándolos como especies y otros sugiriendo la existencia de poblaciones múltiples de una sola especie por isla. Estos resultados dejan en claro que los taxones de tortugas gigantes de las Galápagos representan diferentes etapas del proceso de especiación, con algunos taxones más avanzados en ese proceso evolutivo que otros. Nuestro estudio ofrece una perspectiva sobre el com
加拉帕戈斯巨龟是加拉帕戈斯群岛的特有物种,在那里它们以孤立的种群存在。虽然人们普遍认为这些种群在形态、行为和遗传学方面是可以区分的,但最近这些类群的分化使得它们的物种地位备受争议。在本文中,我们将多物种凝聚法应用于物种划分,对所有 13 个现存类群中 38 种龟的全基因组重测序数据进行了评估,以支持将这些类群划分为物种。与以往仅基于分化时间的研究不同,我们发现了强有力的证据来否定所有加拉帕戈斯巨龟都属于单一物种的假设。相反,对基于模型和基于分化的结果的保守解释表明,这些类群形成了一个至少由 9 个物种组成的物种复合体,大多数分析支持 13 个物种。对于生活在同一岛屿上的分类群的物种地位,支持的意见不一,有些方法将它们划定为独立的物种,有些方法则认为每个岛屿上有多个单一物种的种群。这些结果清楚地表明,加拉帕戈斯巨龟类群代表了物种演化过程中的不同阶段,有些类群比其他类群在演化过程中走得更远。我们的研究有助于深入了解岛屿物种变异的复杂过程,鉴于全球岛屿物种濒临灭绝的现状,我们迫切需要了解这一过程。加拉帕戈斯巨龟是加拉帕戈斯群岛的特有物种,以孤立种群的形式出现在群岛上。尽管这些种群在形态、行为和遗传学方面被认为是可以区分的,但最近这些类群的分化使得它们的物种地位备受争议。在本文中,我们采用多物种凝聚法,对 13 个现存类群中 38 只海龟的全基因组重测序数据进行了分析,以评估将这些类群划分为物种的支持度。与之前仅基于分化时间的研究不同,我们发现了强有力的证据来否定所有加拉帕戈斯巨龟都属于单一物种的假说。相反,基于模式和分化的保守解释表明,这些类群形成了一个至少由 9 个物种组成的物种复合体,大多数分析支持存在 13 个物种。将栖息在同一岛屿上的分类群指定为物种的支持率不一,一些方法将它们划定为物种,而另一些方法则认为每个岛屿上存在单一物种的多个种群。这些结果清楚地表明,加拉帕戈斯巨龟类群代表了物种演化过程的不同阶段,有些类群比其他类群在演化过程中走得更远。我们的研究有助于深入了解岛屿物种演化的复杂过程,鉴于岛屿物种在全球范围内受到的威胁,我们迫切需要了解这一过程。
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引用次数: 0
Convergent evolution in shape in European lineages of gobies. 欧洲虾虎鱼品系形状的趋同进化。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-10 DOI: 10.1093/evolut/qpae162
Jasna Vukić, Kristina Beatrix Bílá, Tereza Soukupová, Marcelo Kovačić, Radek Šanda, Lukáš Kratochvíl

During their radiation, certain groups of animals evolved significant phenotypic disparity (morphological diversity), enabling them to thrive in diverse environments. Adaptations to the same type of environment can lead to convergent evolution in function and morphology. However, well-documented examples in repeated adaptations of teleost fishes to different habitats, which are not primarily related to trophic specialization, are still scarce. Gobies are a remarkable fish group, exhibiting a great species diversity, morphological variability, and extraordinary ability to colonize very different environments. A variety of lifestyles and body forms evolved also in European lineages of gobies. We conducted two-dimensional geometric morphometric and phylomorphospace analyses in European lineages of gobies and evaluated the extent of convergent evolution in shape associated with adaptation to various habitats. Our analyses revealed the change in shape along the nektonic-cryptobenthic axis, from very slender head and body to stout body and wide head. We showed convergent evolution related to mode of locomotion in the given habitat in four ecological groups: nektonic, hyperbenthic, cryptobenthic and freshwater gobies. Gobies, therefore, emerge as a highly diversified lineage with unique lifestyle variations, offering invaluable insights into filling of ecomorphological space and mechanisms of adaptation to various aquatic environments with distinct locomotion requirements.

在辐射过程中,某些动物群体进化出显著的表型差异(形态多样性),使它们能够在不同的环境中繁衍生息。对同类环境的适应会导致功能和形态的趋同进化。然而,有据可查的远摄鱼类对不同生境的重复适应(主要与营养特化无关)的例子仍然很少。虾虎鱼是一个非凡的鱼类群体,表现出物种多样性、形态多变性以及在非常不同的环境中定居的非凡能力。欧洲虾虎鱼种系中也演化出了多种生活方式和身体形态。我们对欧洲虾虎鱼品系进行了二维几何形态计量学和系统形态空间分析,并评估了与适应不同生境相关的形态趋同进化程度。我们的分析表明,鰕虎鱼的形状沿着浮游生物-隐栖生物轴发生变化,从头部和身体非常细长到身体粗壮、头部宽大。我们发现在四个生态类群中,与特定生境中的运动模式有关的趋同进化:底栖虾虎鱼、超底栖虾虎鱼、隐底栖虾虎鱼和淡水虾虎鱼。因此,虾虎鱼是一个具有独特生活方式变异的高度多样化品系,它为我们提供了宝贵的洞察力,帮助我们了解对具有不同运动要求的各种水生环境的适应机制。
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引用次数: 0
Asymmetrical hybridization and environmental factors influence the spatial genetic structure of a killifish hybrid zone. 非对称杂交和环境因素影响鳉鱼杂交区的空间遗传结构。
IF 3.1 2区 环境科学与生态学 Q2 ECOLOGY Pub Date : 2024-11-08 DOI: 10.1093/evolut/qpae160
Andrew L Hardy, Michelle R Gaither, Katie E Lotterhos, Samuel Greaves, Kyra Jean Cipolla, Emily V Kerns, Andres Prieto Trujillo, Matthew R Gilg

Hybridization offers insight into speciation and the forces that maintain barriers to reproduction, and hybrid zones provide excellent opportunities to test how environment shapes barriers to reproduction and hybrid fitness. A hybrid zone between the killifish, Fundulus heteroclitus and F. grandis, had been identified in northeastern Florida, although the spatial structure and parameters that affect the distribution of the two species remain unknown. The present study aimed to determine the fine-scale spatial genetic patterns of the hybrid zone to test the hypothesis that species ranges are influenced by changes in dominant vegetation, and to determine how differences in reproductive barriers between the two species influence the observed patterns. The area of overlap between the two species spanned ~37 km and showed a mosaic pattern of hybridization, suggesting the spatial structure of the hybrid zone is largely influenced by the environment. Environmental association analysis, however, suggested that while dominant vegetation had a significant influence on the spatial structure of the hybrid zone, a combination of environmental factors was driving the observed patterns. Hybridization tended to be rare at sites where F. heteroclitus was the more abundant species, suggesting that differences in preference for conspecifics can lead to differences in rates of introgression into parental taxa and likely result in a range-shift as opposed to adaptation in the face of climate change.

杂交可以让人们深入了解物种演化和维持繁殖障碍的力量,而杂交区则为检验环境如何形成繁殖障碍和杂交适应性提供了绝佳的机会。在佛罗里达州东北部发现了鳉鱼(Fundulus heteroclitus和F. grandis)的杂交区,但影响这两个物种分布的空间结构和参数仍然未知。本研究旨在确定杂交区的精细尺度空间遗传模式,以验证物种范围受优势植被变化影响的假设,并确定两个物种之间的繁殖障碍差异如何影响观察到的模式。两个物种的重叠区域长约 37 千米,并呈现出马赛克杂交模式,这表明杂交区的空间结构在很大程度上受环境影响。然而,环境关联分析表明,虽然优势植被对杂交区的空间结构有显著影响,但环境因素的综合作用也推动了观察到的杂交模式。在异尖吻鲈物种较多的地点,杂交往往很少发生,这表明对同种异体的偏好不同会导致亲本类群的引入率不同,很可能导致范围转移,而不是适应气候变化。
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引用次数: 0
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Evolution
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