中华猕猴桃和美味猕猴桃自然居群遗传结构及其种间杂交渐渗

 利用9对SSR引物对中华猕猴桃（Actinidia chinensis）和美味猕猴桃（A. deliciosa）两近缘种的5个同域分布复合体和各自1个非同域分布居群进行了遗传多样性、居群遗传结构的分析以及种间杂交渐渗的探讨。结果表明：1）两物种共有等位基因比例高达81.13%,物种特有等位基因较少（中华猕猴桃：13.27%,美味猕猴桃：5.61%）,但共享等位基因表型频率在两近缘种间存在差异,而且与各同域复合体中两物种样本的交错程度或间距存在关联;2）两种猕猴桃均具有极高遗传多样性,美味猕猴桃的遗传多样性（H_o＝0 .749, PIC＝0.818）都略高于中华猕猴桃（H_o＝0.686,PIC＝0.799）;3）两猕 猴桃物种均具有较低的Nei’s居群遗传分化度,但AMOVA分析结果揭示种内异域居群间（F_ST=0.091 5）和同域复合体种间（F_ST=0.111 5）均存在一定程度的遗传分化;中华猕猴桃居群遗传分化（G_ST=0.086; F_ST=0.212 1）高于美味猕猴桃（G_ST= 0.080;F_ST=0.142 0）;4）同域分布复合体两物种间的遗传分化（G_ST=0.020）低于物种内异域居群间的遗传分化（中华猕猴桃：G_ST=0.086; 美味猕猴桃：G_ST=0.080）,同域复合体物种间的基因流（N_m＝7.89 -29.75）远远高于 同种异域居群间（中华猕猴桃：N_m =2.663; 美味猕猴桃：N_m=2.880）; 5）居群UPGMA聚类揭示在同一地域的居群优先聚类,个体聚类结果显示多数个体聚在各自居群组内,但各地理居群并不按地理距离的远近聚类,这与Mantel相关性检测所揭示的居群间遗传距离与地理距离没有显著性相关的结果一致。进一步分析表明两种猕猴桃的遗传多样性和居群遗传结构不仅受其广域分布、远交、晚期分化等生活史特性的影响,同时还与猕猴桃的染色体基数高 (x=29)、倍性复杂和种间杂交等因素密切相关,其中两种猕猴桃的共享祖先多态性和同域分布种间杂交基因渗透对两猕猴桃的居群遗传结构产生了重要影响。     

Population differentiation in plethodontid salamanders: divergence of allozymes and sexual compatibility among populations of Desmognathus imitator and D. ochrophaeus (Gaudata: Plethodontidae)

Plethodontid salamanders of the genus Desmognathus exhibit varying levels of genetic differentiation among and within both allopatric and sympatric taxa. This provides excellent opportunities to study population differentiation and speciation. Two morphologically similar species in this genus, D. imitator and D. ochrophaeus, are genetically well-differentiated from one another and occur in sympatry with no evidence of hybridization and introgression. We report that the degree of sexual isolation between these two species is very high, regardless of whether the populations under comparison are allopatric or sympatric with one another. Neither reinforcement nor reproductive character displacement are required to explain the evolution of sexual incompatibility in sympatry. Sexual behaviour apparently diverges while populations are allopatric with one another. Preliminary study indicates that D. imitator consists of populations among which there may be significant sexual isolation in the absence of detectable genetic differentiation.     

REINFORCEMENT OF STICKLEBACK MATE PREFERENCES: SYMPATRY BREEDS CONTEMPT

Detailed studies of reproductive isolation and how it varies among populations can provide valuable insight into the mechanisms of speciation. Here we investigate how the strength of premating isolation varies between sympatric and allopatric populations of threespine sticklebacks to test a prediction of the hypothesis of reinforcement: that interspecific mate discrimination should be stronger in sympatry than in allopatry. In conducting such tests, it is important to control for ecological character displacement between sympatric species because ecological character divergence may strengthen prezygotic isolation as a by-product. We control for ecological character displacement by comparing mate preferences of females from a sympatric population (benthics) with mate preferences of females from two allopatric populations that most closely resemble the sympatric benthic females in ecology and morphology. No-choice mating trials indicate that sympatric benthic females mate less readily with heterospecific (limnetic) than conspecific (benthic) males, whereas two different populations of allopatric females resembling benthics show no such discrimination. These differences demonstrate reproductive character displacement of benthic female mate choice. Previous studies have established that hybridization between sympatric species occurred in the past in the wild and that hybrid offspring have lower fitness than either parental species, thus providing conditions under which natural selection would favor individuals that do not hybridize. Results are therefore consistent with the hypothesis that female mate preferences have evolved as a response to reduced hybrid fitness (reinforcement), although direct effects of sympatry or a biased extinction process could also produce the pattern. Males of the other sympatric species (limnetics) showed a preference for smaller females, in contrast to the inferred ancestral preference for larger females, suggesting reproductive character displacement of limnetic male mate preferences as well.     

Introgression versus immigration in hybridizing high-dispersal echinoderms

Phylogeographic studies designed to estimate rates and patterns of genetic differentiation within species often reveal unexpected and graphically striking cases of allele or haplotype sharing between species (introgression) via hybridization and backcrossing. Does introgression between species significantly influence population genetic structure relative to more conventional sources of differentiation (drift) and similarity (dispersal) among populations within species? Here we use mtDNA sequences from four species in two genera of sea urchins and sea stars to quantify the relative magnitude of gene flow across oceans and across species boundaries in the context of the trans-Arctic interchange of marine organisms between the Pacific and Atlantic oceans. In spite of the much smaller distances between sympatric congeners, rates of gene flow between sympatric species via heterospecific gamete interactions were small and significantly lower than gene flow across oceans via dispersal of planktonic larvae. We conclude that, in these cases at least, larvae are more effective than gametes as vectors of gene flow.     

Comparison of gene flow among species that occur within the same geographic locations versus gene flow among populations within species reveals introgression among several Elymus species

One of the challenges in evolutionary biology is to understand the evolution of speciation with incomplete reproductive isolation as many taxa have continued gene flow both during and after speciation. Comparison of population structure between sympatric and allopatric populations can reveal specific introgression and determine if introgression occurs in a unidirectional or bidirectional manner. Simple sequence repeat markers were used to characterize sympatric and allopatric population structure of plant species, Elymus alaskanus (Scribn. and Merr.) Löve, E. caninus L., E. fibrosus (Schrenk) Tzvel., and E. mutabilis (Drobov) Tzvelev. Our results showed that genetic diversity (H_E) at species level is E. caninus (0.5355) > E. alaskanus (0.4511) > E. fibrosus (0.3924) > E. mutabilis (0.3764), suggesting that E. caninus and E. alaskanus are more variable than E. fibrosus and E. mutabilis. Gene flow between species that occurs within the same geographic locations versus gene flow between populations within species was compared to provide evidence of introgression. Our results indicated that gene flow between species that occur within the same geographic location is higher than that between populations within species, suggesting that gene flow resulting from introgressive hybridization might have occurred among the sympatric populations of these species, and may play an important role in partitioning of genetic diversity among and within populations. The migration rate from E. fibrosus to E. mutabilis is highest (0.2631) among the four species studied. Asymmetrical rates of gene flow among four species were also observed. The findings highlight the complex evolution of these four Elymus species.     

A population genomic analysis of species boundaries: neutral processes, adaptive divergence and introgression between two hybridizing plant species

Little is known about the nature of species boundaries between closely related plant species and about the extent of introgression as a consequence of hybridization upon secondary contact. To address these topics we analyzed genome-wide differentiation between two closely related Silene species, Silene latifolia and S. dioica , and assessed the strength of introgression in sympatry. More than 300 AFLP markers were genotyped in three allopatric and three sympatric populations of each species. Outlier analyses were performed separately for sympatric and allopatric populations. Both positive and negative outlier loci were found, indicating that divergent and balancing selection, respectively, have shaped patterns of divergence between the two species. Sympatric populations of the two species were found to be less differentiated genetically than allopatric populations, indicating that hybridization has led to gene introgression. We conclude that differentiation between S. latifolia and S. dioica has been shaped by a combination of introgression and selection. These results challenge the view that species differentiation is a genome-wide phenomenon, and instead support the idea that genomes can be porous and that species differentiation has a genic basis.     

Repeated unidirectional introgression of nuclear and mitochondrial DNA between four congeneric Tanganyikan cichlids

With an increasing number of reported cases of hybridization and introgression, interspecific gene flow between animals has recently become a widely accepted and broadly studied phenomenon. In this study, we examine patterns of hybridization and introgression in Ophthalmotilapia spp., a genus of cichlid fish from Lake Tanganyika, using mitochondrial and nuclear DNA from all four species in the genus and including specimens from over 800 km of shoreline. These four species have very different, partially overlapping distribution ranges, thus allowing us to study in detail patterns of gene flow between sympatric and allopatric populations of the different species. We show that a significant proportion of individuals of the lake-wide distributed O. nasuta carry mitochondrial and/or nuclear DNA typical of other Ophthalmotilapia species. Strikingly, all such individuals were found in populations living in sympatry with each of the other Ophthalmotilapia species, strongly suggesting that this pattern originated by repeated and independent episodes of genetic exchange in different parts of the lake, with unidirectional introgression occurring into O. nasuta. Our analysis rejects the hypotheses that unidirectional introgression is caused by natural selection favoring heterospecific DNA, by skewed abundances of Ophthalmotilapia species or by hybridization events occurring during a putative spatial expansion in O. nasuta. Instead, cytonuclear incompatibilities or asymmetric behavioral reproductive isolation seem to have driven repeated, unidirectional introgression of nuclear and mitochondrial DNA into O. nasuta in different parts of the lake.     

SIMULATING RANGE EXPANSION: MALE SPECIES RECOGNITION AND LOSS OF PREMATING ISOLATION IN DAMSELFLIES

Prolonged periods of allopatry might result in loss of the ability to discriminate against other formerly sympatric species, and can lead to heterospecific matings and hybridization upon secondary contact. Loss of premating isolation during prolonged allopatry can operate in the opposite direction of reinforcement, but has until now been little explored. We investigated how premating isolation between two closely related damselfly species, Calopteryx splendens and C. virgo , might be affected by the expected future northward range expansion of C. splendens into the allopatric zone of C. virgo in northern Scandinavia. We simulated the expected secondary contact by presenting C. splendens females to C. virgo males in the northern allopatric populations in Finland. Premating isolation toward C. splendens in northern allopatric populations was compared to sympatric populations in southern Finland and southern Sweden. Male courtship responses of C. virgo toward conspecific females showed limited geographic variation, however, courtship attempts toward heterospecific C. splendens females increased significantly from sympatry to allopatry. Our results suggest that allopatric C. virgo males have partly lost their ability to discriminate against heterospecific females. Reduced premating isolation in allopatry might lead to increased heterospecific matings between taxa that are currently expanding and shifting their ranges in response to climate change.     

Population genetics of a polyploid: is there hybridization between lineages of Hyla versicolor?

Several studies have demonstrated that polyploid species can form recurrently from their progenitors, but few studies have evaluated gene flow between the resultant polyploid lineages. Here we examine the possibility of hybridization between lineages of the tetraploid common gray treefrog (Hyla versicolor). We utilize a polymerase chain reaction (PCR) cloning approach to estimate the genotypes of tetraploid individuals and measure genetic differentiation between (1) sympatric populations of two lineages and (2) allopatric populations of a single lineage. We find that allele frequencies in sympatric populations of two lineages do not differ, suggesting that frogs of these two lineages hybridize in areas where they co-occur.     

Reinforcement generates reproductive isolation between neighbouring conspecific populations of spadefoot toads

Reproductive character displacement is the adaptive evolution of traits that minimize deleterious reproductive interactions between species. When arising from selection to avoid hybridization, this process is referred to as reinforcement. Reproductive character displacement generates divergence not only between interacting species, but also between conspecific populations that are sympatric with heterospecifics versus those that are allopatric. Consequently, such conspecific populations can become reproductively isolated. We compared female mate preferences in, and evaluated gene flow between, neighbouring populations of spadefoot toads that did and did not occur with heterospecifics (mixed- and pure-species populations, respectively). We found that in mixed-species populations females significantly preferred conspecifics. Such females also tended to prefer a conspecific call character that was dissimilar from heterospecifics. By contrast, females from pure-species populations did not discriminate conspecific from heterospecific calls. They also preferred a more exaggerated conspecific call character that resembles heterospecific males. Moreover, gene flow was significantly reduced between mixed- and pure-species population types. Thus, character displacement (and, more specifically, reinforcement) may initiate reproductive isolation between conspecific populations that differ in interactions with heterospecifics.     

Reinforcement shapes clines in female mate discrimination in Drosophila subquinaria

Reinforcement of species boundaries may alter mate recognition in a way that also affects patterns of mate preference among conspecific populations. In the fly Drosophila subquinaria, females sympatric with the closely related species D. recens reject mating with heterospecific males as well as with conspecific males from allopatric populations. Here, we assess geographic variation in behavioral isolation within and among populations of D. subquinaria and use cline theory to understand patterns of selection on reinforced discrimination and its consequences for sexual isolation within species. We find that selection has fixed rejection of D. recens males in sympatry, while significant genetic variation in this behavior occurs within allopatric populations. In conspecific matings sexual isolation is also asymmetric and stronger in populations that are sympatric with D. recens. The clines in behavioral discrimination within and between species are similar in shape and are maintained by strong selection in the face of gene flow, and we show that some of their genetic basis may be either shared or linked. Thus, while reinforcement can drive extremely strong phenotypic divergence, the long‐term consequences for incipient speciation depend on gene flow, genetic linkage of discrimination traits, and the cost of these behaviors in allopatry.     

Sympatric serpentine endemic Monardella (Lamiaceae) species maintain habitat differences despite hybridization

Ecological differentiation and genetic isolation are thought to be critical in facilitating coexistence between related species, but the relative importance of these phenomena and the interactions between them are not well understood. Here, we examine divergence in abiotic habitat affinity and the extent of hybridization and introgression between two rare species of Monardella (Lamiaceae) that are both restricted to the same serpentine soil exposure in California. Although broadly sympatric, they are found in microhabitats that differ consistently in soil chemistry, slope, rockiness and vegetation. We identify one active hybrid zone at a site with intermediate soil and above‐ground characteristics, and we document admixture patterns indicative of extensive and asymmetric introgression from one species into the other. We find that genetic distance among heterospecific populations is related to geographic distance, such that the extent of apparent introgression is partly explained by the spatial proximity to the hybrid zone. Our work shows that plant species can maintain morphological and ecological integrity in the face of weak genetic isolation, intermediate habitats can facilitate the establishment of hybrids, and that the degree of apparent introgression a population experiences is related to its geographic location rather than its local habitat characteristics.     

Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry have received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites, we examined hybridization between sympatric populations of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to test whether the frequency of hybridization and pattern of introgression have been impacted by the construction of a dam that isolated formerly anadromous populations of both species in a landlocked freshwater reservoir. The frequency of hybridization and pattern of introgression differed markedly between anadromous and landlocked populations. The rangewide frequency of hybridization among anadromous populations was generally 0–8%, whereas all landlocked individuals were hybrids. Although neutral introgression was observed among anadromous hybrids, directional introgression leading to increased prevalence of alewife genotypes was detected among landlocked hybrids. We demonstrate that habitat alteration can lead to hybrid swarm formation between divergent species that naturally occur sympatrically, and provide empirical evidence that reinforcement does not always sustain reproductive isolation under such circumstances.     

Evidence of reinforcement of premating isolation between two species of the genus Ochthebius (Coleoptera: Hydraenidae)

The increase in premating reproductive isolation between recently diverged and potentially interbreeding taxa resulting from selection against hybridization (reinforcement) is one of the most contentious issues in evolutionary biology. After many years of debate, its plausibility under various conditions has been shown by theoretical studies and some cases have been documented. At present, interest is arising about the frequency and importance of reinforcement in nature. Ochthebius quadricollis and Ochthebius sp. A are two hydraenid beetles inhabiting marine rock pools in the Mediterranean basin. By molecular analysis of a contact zone between the two species along the Italian Tyrrhenian coast, full reproductive isolation between the two species was evidenced. However, the finding of introgressed specimens at some diagnostic loci suggested that gene flow occurred in the past but then ceased. In this article, by analyzing species composition of mating couples collected in sympatric localities, we show the existence of strong assortative mating between the two species in nature. In laboratory multiple-choice mating trials, sympatric populations showed greater assortative mating than allopatric populations. Reinforcement is suggested as the most parsimonious hypothesis to explain the evolution of discriminative mate recognition systems occurring among O. quadricollis and Ochthebius sp. A under sympatric, but not allopatric, populations.     

Hybridization in the recent past

The question we address in this article is how hybridization in the recent past can be detected in recently evolved species. Such species may not have evolved genetic incompatibilities and may hybridize with little or no fitness loss. Hybridization can be recognized by relatively small genetic differences between sympatric populations because sympatric populations have the opportunity to interbreed whereas allopatric populations do not. Using microsatellite DNA data from Darwin's finches in the Galapagos archipelago, we compare sympatric and allopatric genetic distances in pairs of Geospiza and Camarhynchus species. In agreement with the hybridization hypothesis, we found a statistically strong tendency for a species to be more similar genetically to a sympatric relative than to allopatric populations of that relative. Hybridization has been studied directly on two islands, but it is evidently more widespread in the archipelago. We argue that introgressive hybridization may have been a persistent feature of the adaptive radiation through most of its history, facilitating evolutionary diversification and occasionally affecting both the speed and direction of evolution.     

Searching for the genetic footprint of ancient and recent hybridization

Determining the long‐term consequences of hybridization remains a central quest for evolutionary biologists. A particular challenge is to establish whether and to what extent widespread hybridization results in gene flow (introgression) between parental taxa. In this issue of Molecular Ecology, Jordan et al. ( 2018 ) search for evidence of gene flow between two closely related species of Geum (Rosaceae), which hybridize readily in contemporary populations and where hybrid swarms have been recorded for at least 200 years (Ruhsam, Hollingsworth, & Ennos, 2013 ). The authors find mixed evidence of ancient introgression when analysing allopatric populations. Intriguingly, when analysing populations of a region where the two species occur either mixed in the same population or in close proximity, and where hybrids are presently common, Jordan and colleagues find that the majority of randomly sampled individuals analysed (92/96) show no evidence of introgression (defined as individuals with admixture coefficients of <1%). The few individuals identified as hybrids are shown to likely be F1 or early‐generation backcrosses, indicating that even in sympatric regions, hybridization does not penetrate beyond a few generations. Based on their findings, Geum seems to be an example of little to no introgression despite contemporary hybridization.     

Phenotypic divergence but not genetic distance predicts assortative mating among species of a cichlid fish radiation

The hypothesis of ecological divergence giving rise to premating isolation in the face of gene flow is controversial. However, this may be an important mechanism to explain the rapid multiplication of species during adaptive radiation following the colonization of a new environment when geographical barriers to gene flow are largely absent but underutilized niche space is abundant. Using cichlid fish, we tested the prediction of ecological speciation that the strength of premating isolation among species is predicted by phenotypic rather than genetic distance. We conducted mate choice experiments between three closely related, sympatric species of a recent radiation in Lake Mweru (Zambia/DRC) that differ in habitat use and phenotype, and a distantly related population from Lake Bangweulu that resembles one of the species in Lake Mweru. We found significant assortative mating among all closely related, sympatric species that differed phenotypically, but none between the distantly related allopatric populations of more similar phenotype. Phenotypic distance between species was a good predictor of the strength of premating isolation, suggesting that assortative mating can evolve rapidly in association with ecological divergence during adaptive radiation. Our data also reveals that distantly related allopatric populations that have not diverged phenotypically, may hybridize when coming into secondary contact, e.g. upon river capture because of diversion of drainage systems.     

Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance

Determining which reproductive isolating barriers arise first between geographically isolated lineages is critical to understanding allopatric speciation. We examined behavioral isolation among four recently diverged allopatric species in the orangethroat darter clade (Etheostoma: Ceasia). We also examined behavioral isolation between each Ceasia species and the sympatric rainbow darter Etheostoma caeruleum. We asked (1) is behavioral isolation present between allopatric Ceasia species, and how does this compare to behavioral isolation with E. caeruleum, (2) does male color distance and/or genetic distance predict behavioral isolation between species, and (3) what are the relative contributions of female choice, male choice, and male competition to behavioral isolation? We found that behavioral isolation, genetic differentiation, and male color pattern differentiation were present between allopatric Ceasia species. Males, but not females, discerned between conspecific and heterospecific mates. Males also directed more aggression toward conspecific rival males. The high levels of behavioral isolation among Ceasia species showed no obvious pattern with genetic distance or male color distance. However, when the E. caeruleum was included in the analysis, an association between male aggression and male color distance was apparent. We discuss the possibility that reinforcement between Ceasia and E. caeruleum is driving behavioral isolation among allopatric Ceasia species.     

Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions

Secondary contact in close relatives can result in hybridization and the admixture of previously isolated gene pools. However, after an initial period of hybridization, reproductive isolation can evolve through different processes and lead to the interruption of gene flow and the completion of the speciation process. Omocestus minutissimus and O. uhagonii are two closely related grasshoppers with partially overlapping distributions in the Central System mountains of the Iberian Peninsula. To analyse spatial patterns of historical and/or contemporary hybridization between these two taxa and understand how species boundaries are maintained in the region of secondary contact, we sampled sympatric and allopatric populations of the two species and obtained genome‐wide single nucleotide polymorphism data using a restriction site‐associated DNA sequencing approach. We used Bayesian clustering analyses to test the hypothesis of contemporary hybridization in sympatric populations and employed a suite of phylogenomic approaches and a coalescent‐based simulation framework to evaluate alternative hypothetical scenarios of interspecific gene flow. Our analyses rejected the hypothesis of contemporary hybridization but revealed past introgression in the area where the distributions of the two species overlap. Overall, these results point to a scenario of historical gene flow after secondary contact followed by the evolution of reproductive isolation that currently prevents hybridization among sympatric populations.     

DIVERSIFICATION OF CONSPECIFIC SIGNALS IN SYMPATRY: GEOGRAPHIC OVERLAP DRIVES MULTIDIMENSIONAL REPRODUCTIVE CHARACTER DISPLACEMENT IN FROGS

Theoretical models suggest that geographic overlap with different heterospecific assemblages can promote divergence of mate recognition systems among conspecific populations. Divergence occurs when different traits undergo reproductive character displacement across populations within a contact zone. Here, I tested this hypothesis by assessing patterns of acoustic signal divergence in two- and three-species assemblages of chorus frogs ( Pseudacris ), focusing in particular on P. feriarum and P. nigrita . In addition, I tested one criterion for reinforcement, by examining the evolution of female P. feriarum preferences in the contact zone. Patterns of signal evolution indicated that in each of the four sympatric populations studied, only the rarer species displaced substantially ( P. feriarum in three cases and P. nigrita in one instance). Moreover, the three displaced P. feriarum populations diverged in different signal traits across the contact zone, evolving in directions that increased the energetic cost of calling relative to the allopatric call, and in ways that maximized differences from the particular heterospecific assemblage present. Consistent with reinforcement, divergence of female preferences in sympatry was estimated to reduce their propensity to hybridize by 60%. Together, signal and preference data suggest that interactions between species can promote diversification within species, potentially contributing to reproductive isolation among conspecific populations.