In a manner analogous to the use of atom collisions in the study of particle physics, admixture between divergent populations or species (i.e., genome collisions) can shed light on the fundamental nature of biological groups (e.g., species) and the genetic basis of barriers to gene flow between them (Buerkle & Lexer, 2008). And like atom collisions, which can result in both fusion and emission of novel particles, collisions between divergent genomes can both erode and create biological diversity. For example, whereas demographic or genetic swamping can result in loss of biodiversity, hybrid speciation can lead to gains. From a conservation standpoint, a better understanding of the causes and prevalence of these outcomes is necessary to identify and protect processes that maintain biodiversity and promote adaptive evolution. But the role of admixture in generating novelty becomes especially contentious when one of the hybridizing populations is a narrow endemic or critically endangered. In a From the Cover article in this issue of Molecular Ecology , Ebersbach et al. (2020) analzyed the evolutionary outcomes and conservation implications of hybridization between a critically endangered South American poison frog, Oophaga lehmanni (Myers & Daly, 1976), and its congener, O. anchicayensis (Posso‐Terranova & Andres, 2018). Using trait data, reduced‐representation genome sequences, and statistical population genomics, Ebersbach et al. (2020) identified three poison frog populations of hybrid origin. Frogs from these populations exhibit novel color pattern phenotypes and genomes that are mosaics of ancestry segments inherited from O. lehmanni and O. anchicayensis . Historical demographic inferences suggest that these admixed populations did not originate through recent, human‐mediated translocations associated with the pet trade, but rather are of older origin and have persisted through time as isolated, admixed entities (i.e., taxa). This study highlights the role of admixture and subsequent evolution of hybrid genomes in the genesis of biodiversity, and adds support to the idea that divergence via admixture may be a somewhat common facet of the evolutionary process.

Many early studies in ecological genetics focused on color pattern variation, and specifically on the evolutionary processes that maintain color polymorphisms in natural populations (Ford, 1977). This emphasis has continued to the present day, and we now know more about the genetic basis and evolution of color and color patterns than most other traits (e.g., Martin & Orgogozo, 2013). Color pattern polymorphisms often exhibit relatively simple, modular genetic architectures (e.g., Lindtke et al., 2017; Van Belleghem et al., 2017), and adaptive introgression of color pattern loci has been documented in multiple species (e.g., Dasmahapatra, Walters, & Briscoe, 2012). Harlequin poison frogs (genus Oophaga ) exhibit particularly striking levels of variation in color and color patterns (i.e., spots and stripes), with different morphs being found at large and small (e.g., a few kilometers) spatial scales (Ebersbach et al., 2020) (Figure 1). Past work suggests that the frog's patchy distribution, drift, and natural and sexual selection likely contribute to the geographic mosaic of color pattern morphs, but the possible contribution of hybridization to this phenotypic diversity had not been thoroughly investigated until now.

Ebersbach et al. (2020) take a population genomics approach to show that hybridization between O. lehmanni and O. anchicayensis gave rise to a series of admixed populations that exhibit novel color patterns (i.e., a novel combination of orange and red spots and stripes) (Figure 1). Specifically, principal components analysis (PCA) of 49 morphological variables (including color patterns), shows that the populations are phenotypically distinct from both parental species. Population genomic analyses with PCA‐based methods and Bayesian admixture models (i.e., ADMIXTURE, fast STRUCTURE and introgress ) confirm the hybrid origin of this series of populations. The genomic analyses suggest the admixed populations comprise late‐generation hybrids (i.e., F_n ), with a near or complete absence of early‐generation hybrids (e.g., F₁, BC₁, or F₂), and thus, that most matings are between hybrids with low rates of contemporary gene flow into the admixed populations. Bayesian genomic cline analysis further shows that the genomes of the hybrids are made up of a mosaic of ancestry segments originating from each species (i.e., segments of chromosomes from each species) (Gompert & Buerkle, 2011). For some regions of the genome, most of the hybrid frogs have ancestry segments from O. lehmanni (positive α outliers for genomic clines), whereas for other regions of the genome, most of the frogs have ancestry from O. anchicayensis (negative α outliers). Other genomic regions show evidence of restricted introgression, with ancestry segments confined mostly to alternative genomic backgrounds, and perhaps to different admixed populations (β outliers). Although these analyses do not directly demonstrate that the genomic mosaic of ancestry in the hybrids is responsible for the novel color patterns observed in the hybrid frog populations, this is certainly a plausible hypothesis and one put forward by the authors (Ebersbach et al., 2020).

More generally, shuffling of parental allele combinations in admixed populations can readily create genetically distinct populations and phenotypic novelties (e.g., Elgvin et al., 2017; Rieseberg et al., 2003). This occurs because recombination and independent assortment in hybrids break up parental ancestry segments (i.e., chromosomes with parental gene combinations), and generate new gene combinations with alleles from each of the hybridizing lineages. These new gene combinations can result in transgressive phenotypes, that is, phenotypes beyond the range observed in either species. Whereas individuals with transgressive phenotypes can be observed in early‐generation hybrids, entire populations exhibiting novel gene combinations and phenotypes can become established if gene flow between the admixed population and parental species declines or ceases. In such cases, recombination erodes the size of ancestry segments, and ancestry segments begin to fix by genetic drift or selection in a process known as genome stabilization (Buerkle & Rieseberg, 2008) (Figure 2). This can include selection against developmental incompatibilities or for adaptation to a novel biotic or abiotic environment (Schumer et al., 2018). The outcome of this process is a population or species of hybrid origin that is genetically divergent, and often phenotypically distinct, from each of the parental species.

Past debates have considered whether or not populations arising through the process of hybridization and genome stabilization represent hybrid species, with the prevailing notion being that hybrid species must exhibit near complete reproductive isolation from the parent taxa and that reproductive isolation must have evolved as a direct consequence of hybridization (e.g., Schumer, Rosenthal, & Andolfatto, 2014). However, even in cases where other processes facilitate reproductive isolation after admixture, or when reproductive isolation and genome stabilization are incomplete, the outcome is nevertheless a genetically distinct population or group. This is especially true when the genomes of the hybrids include non‐trivial contributions from each species (e.g., more than 10%), as the admixed population would necessarily differ, at least genetically and almost certainly in ecologically relevant phenotypes, from any non‐admixed population. There is increasing evidence that such distinct, stabilized (or semi‐stabilized hybrid populations) might not be uncommon and could represent a non‐negligible component of biological diversity (regardless of taxonomic status or decisive evidence of hybrid speciation per se) (e.g., Ebersbach et al., 2020; Elgvin et al., 2017; Gompert et al., 2014; Gross & Rieseberg, 2005; Schumer et al., 2018). Such results are consistent with verbal models that suggest repeated bouts of geographic isolation and admixture can fuel adaptive radiations (Seehausen, 2004). This has implications for conservation efforts and policy, especially in cases like Oophaga where one or both hybridizing taxa are endangered (Ebersbach et al., 2020).

Hybridization can unlock novel phenotypes not found in either parental population and increase the adaptive capacity of populations in changing environments (Hamilton & Miller, 2016). Despite this, a heavy focus on the “purity” of species prevails in government policy. A 2015 review of conservation policies in the U.S. and Canada found that only 16% provided guidelines for management of hybrids, and of these, 46% denied protection for individuals of hybrid origin (Jackiw, Mandil, & Hager, 2015). More importantly within the context of hybrid origins, the large majority of hybrid policies (77%) made no attempt to distinguish between levels of hybridization (i.e. F₁ hybrids vs. backcrosses or early vs. late‐generation hybrids) (Jackiw et al., 2015). This lack of nuance leaves policy administrators with few means for differentiating between the evolutionary potential of stable, late‐generation hybrid populations (as in Oophaga; Ebersbach et al., 2020) vs. cases of ongoing, maladaptive genetic swamping. Furthermore, in cases where admixture is a frequent driver of diversification, yet species‐level divergence remains low (e.g., Gompert et al., 2014), conservation policy may under‐protect the biological diversity of entire taxa (vonHoldt, Brzeski, Wilcove, & Rutledge, 2018). Hybridization is a nuanced process, and requires equally nuanced treatment in conservation policy.

Our ability to detect complex patterns of admixture and gene flow between populations is better than ever before (e.g., Ebersbach et al., 2020). Whereas early genetic analyses based on a limited number of markers (i.e. microsatellites) were lacking in power, whole and partial genome methods have revealed that admixture is both a frequent and widespread evolutionary process (vonHoldt et al., 2018). This opens the door for using admixture as a tool to deepen our understanding of the genomic processes underlying speciation and diversification. As the study of atom collisions enabled the discovery of fundamental properties of particle physics, so the study of admixture (genome collisions) may elucidate how fundamental evolutionary processes mold and maintain biological diversity.

类似于在粒子物理学研究中使用原子碰撞，分散种群或物种之间的混合（即基因组碰撞）可以阐明生物群体（例如物种）的基本性质和屏障的遗传基础使它们之间的基因流动（Buerkle＆Lexer，2008）。就像原子碰撞会导致新粒子的融合和发射一样，发散基因组之间的碰撞也会侵蚀并产生生物多样性。例如，人口或遗传沼泽可能导致生物多样性的丧失，而杂交物种则可以带来收益。从保护的角度来看，有必要更好地了解这些结果的原因和普遍性，以识别和保护维持生物多样性并促进适应性进化的过程。但是，当杂交种群之一是狭end的地方性或极度濒临灭绝的物种时，混合剂在产生新颖性中的作用就特别有争议。在本期《分子生态学》的封面文章中，Ebersbach等人。（2020年）分析了濒临灭绝的南美毒蛙Oophaga lehmanni（Myers＆Daly，1976）和其同类动物O. anchicayensis（Posso-Terranova＆Andres，2018）之间杂交的进化结果和保护意义。使用性状数据，减少表示的基因组序列和统计种群基因组学，Ebersbach等。（2020）确定了三个混合来源的毒蛙种群。从这些人口青蛙呈现新颖的彩色图案的表型和从遗传祖先段的马赛克基因组O. lehmanni和O. anchicayensis。历史上的人口统计学推论表明，这些混杂的种群并非起源于与宠物贸易有关的最近的，人类介导的易位，而是起源于较旧的种群，并作为孤立的，混杂的实体（即，分类群）而持续存在。这项研究突出了混合基因组的混合作用及其后续进化在​​生物多样性起源中的作用，并为以下观点提供了支持：通过混合产生的差异可能是进化过程中一个常见的方面。

生态遗传学的许多早期研究都集中在颜色模式的变化上，特别是在维持自然种群颜色多态性的进化过程中（Ford，1977）。这种强调一直持续到今天，我们现在比大多数其他性状更了解颜色和颜色模式的遗传基础以及进化（例如，Martin＆Orgogozo，2013年）。彩色模式多态性通常表现出相对简单的模块化遗传结构（例如Lindtke等人，2017 ; Van Belleghem等人，2017），并且彩色模式基因座的适应性基因渗入已在多种物种（例如Dasmahapatra，Walters， ＆Briscoe，2012）。丑角毒蛙（属Oophaga）表现出特别惊人的颜色和颜色模式变化（即斑点和条纹），在大小空间（例如几千米）上都发现了不同的形态（Ebersbach等，2020）（图1 ）。过去的工作表明，青蛙的斑块状分布，漂移，自然和有性选择可能有助于颜色图案形态的地理镶嵌，但是迄今为止，尚未充分研究杂交对这种表型多样性的可能贡献。

Ebersbach等。（2020）取群体基因组学的方法来显示之间的杂交O. lehmanni和O. anchicayensis产生了一系列表现出新颖的彩色图案混合种群的（即，一个新的橙色和红色的斑点和条纹的组合）（图1 ）。具体来说，对49个形态变量（包括颜色模式）的主成分分析（PCA）表明，这些种群在表型上与两个亲代物种都不同。使用基于PCA的方法和贝叶斯混合模型（即ADMIXTURE，快速结构和渐渗）进行种群基因组分析）确认这一系列人口的混合血统。基因组分析表明，混合种群包括后代杂种（即F _n ），几乎或完全没有前代杂种（例如F ₁，BC ₁或F ₂），因此大多数交配杂种之间的当代基因流到混合的人口中的比率低。贝叶斯基因组谱分析进一步表明，杂种的基因组由起源于每个物种的祖先片段（即来自每个物种的染色体片段）的镶嵌组成（Gompert＆Buerkle，2011）。对于基因组的某些区域，大多数杂种蛙都有雷曼氏酵母的祖先片段。（基因组谱系的阳性α离群值），而对于基因组其他区域，大多数青蛙的血统都来自O. anchicayensis（阴性α离群值）。其他基因组区域显示出基因渗入受限的证据，祖先段主要限于其他基因组背景，并且可能限于不同的混合种群（β离群值）。尽管这些分析未直接证明杂种中的祖先的基因组镶嵌是导致杂种蛙种群中观察到的新颖颜色模式的原因，但这无疑是一个合理的假设，也是作者提出的一种假设（Ebersbach等，2020）。

更普遍地讲，混和种群中父母等位基因组合的改组可以很容易地产生遗传上不同的种群和表型新颖性（例如Elgvin等人，2017 ; Rieseberg等人，2003）。发生这种情况是因为杂种中的重组和独立分类破坏了亲代谱系片段（即具有亲代基因组合的染色体），并从每个杂交谱系中产生了具有等位基因的新基因组合。这些新的基因组合可能会导致海侵性表型，即超出任何一个物种中观察到的范围的表型。在早期的杂种中可以观察到具有海侵性表型的个体，而如果混合种群与亲本物种之间的基因流减少或停止，则展现出新基因组合和表型的整个种群都可以建立。在这种情况下，重组会侵蚀祖先片段的大小，而祖先片段开始通过遗传漂移或选择而被固定，称为基因组稳定化（Buerkle＆Rieseberg，2008）（图2）。这可以包括针对发育不相容性的选择或针对新型生物或非生物环境的适应性选择（Schumer等人，2018）。该过程的结果是杂交起源的种群或物种，其在遗传上与每个亲本物种不同，并且通常在表型上不同。

过去的辩论曾考虑过杂交和基因组稳定过程中产生的种群是否代表杂种，普遍的观点是杂种必须表现出与亲本分类单元近乎完全的生殖分离，并且生殖分离必定是直接后果。 （例如，舒默（Schumer），罗森塔尔（Rosenthal）和安道尔法托（Andolfatto），2014年）。但是，即使在其他过程促进混合后的生殖分离或生殖分离和基因组稳定不完全的情况下，结果仍然是遗传上不同的种群或群体。当杂种的基因组包括每个物种的非平凡贡献（例如，超过10％）时，尤其如此，因为混合种群必然至少在遗传上和几乎肯定在生态上相关的表型上与任何非混合人口。越来越多的证据表明，这种独特的，稳定的（或半稳定的杂交种群）可能并不少见，并且可能代表着生物多样性不可忽略的组成部分（无论分类地位或杂交物种本身的决定性证据）（例如，埃伯斯巴赫等2020 ; Elgvin et al。，2017 ; Gompert等，2014；Gross＆Rieseberg，2005；舒默等人，2018）。这样的结果与言语模型相一致，言语模型表明反复的地理隔离和掺混可以激发适应性辐射（Seehausen，2004）。这对保护工作和政策产生了影响，尤其是在像Oophaga这样的一个或两个杂交类群都濒临灭绝的情况下（Ebersbach等，2020）。

杂交可以解锁在任何父母群体中均未发现的新表型，并增加人们在不断变化的环境中的适应能力（Hamilton＆Miller，2016）。尽管如此，政府政策仍然高度重视物种的“纯度”。2015年对美国和加拿大的保护政策进行的审查发现，只有16％的人为杂种的管理提供了指导原则，其中46％拒绝保护对杂种来源的个体的保护（Jackiw，Mandil和Hager，2015年）。更重要的是，在杂交起源的背景下，绝大多数的杂交政策（77％）都没有试图区分杂交水平（即F ₁杂交与回交杂交或早期与后代杂交）（Jackiw等人。 ，2015）。这种细微差别的缺乏使政策管理者几乎没有办法区分稳定的，后代杂交种群的进化潜力（如在Oophaga； Ebersbach等人，2020年）与持续的，适应不良的基因沼泽案例。此外，如果混和物经常成为多样化的驱动力，但物种水平的差异仍然很低（例如，Gompert等人，2014年），则保护政策可能会保护整个类群的生物多样性（vonHoldt，Brzeski，Wilcov， ＆Rutledge，2018年）。杂交是一个细微的过程，在保护政策中需要同样细微的处理。

我们检测种群之间混合物和基因流的复杂模式的能力比以往任何时候都更好（例如，Ebersbach等人，2020年）。尽管基于有限数量的标记物（即微卫星）的早期遗传分析缺乏能力，但全基因组和部分基因组方法显示混合是一个既频繁又普遍的进化过程（vonHoldt et al。，2018）。这为使用混合物作为一种工具打开了大门，使我们加深了对物种形成和多样化基础基因组过程的了解。由于对原子碰撞的研究使人们能够发现粒子物理学的基本特性，因此对混合物（基因组碰撞）的研究可以阐明基本的进化过程如何塑造和维持生物多样性。