Research advances in animal distant hybridization

Distant hybridization refers to crosses between two different species or higher-ranking taxa that enables interspecific genome transfer and leads to changes in phenotypes and genotypes of the resulting progeny. If progeny derived from distant hybridization are bisexual and fertile, they can form a hybrid lineage through self-mating, with major implications for evolutionary biology, genetics, and breeding. Here, we review and summarize the published literature, and present our results on fish distant hybridization. Relevant problems involving distant hybridization between orders, families, subfamilies, genera, and species of animals are introduced and discussed, with an additional focus on fish distant hybrid lineages, genetic variation, patterns, and applications. Our review serves as a useful reference for evolutionary biology research and animal genetic breeding.     

Geographic variation in hybridization across a reinforcement contact zone of chorus frogs (Pseudacris)

Reinforcement contact zones, which are secondary contact zones where species are diverging in reproductive behaviors due to selection against hybridization, represent natural laboratories for studying speciation‐in‐action. Here, we examined replicate localities across the entire reinforcement contact zone between North American chorus frogs Pseudacris feriarum and P. nigrita to investigate geographic variation in hybridization frequencies and to assess whether reinforcement may have contributed to increased genetic divergence within species. Previous work indicated these species have undergone reproductive character displacement (RCD) in male acoustic signals and female preferences due to reinforcement. We also examined acoustic signal variation across the contact zone to assess whether signal characteristics reliably predict hybrid index and to elucidate whether the degree of RCD predicts hybridization rate. Using microsatellites, mitochondrial sequences, and acoustic signal information from >1,000 individuals across >50 localities and ten sympatric focal regions, we demonstrate: (1) hybridization occurs and (2) varies substantially across the geographic range of the contact zone, (3) hybridization is asymmetric and in the direction predicted from observed patterns of asymmetric RCD, (4) in one species, genetic distance is higher between conspecific localities where one or both have been reinforced than between nonreinforced localities, after controlling for geographic distance, (5) acoustic signal characters strongly predict hybrid index, and (6) the degree of RCD does not strongly predict admixture levels. By showing that hybridization occurs in all sympatric localities, this study provides the fifth and final line of evidence that reproductive character displacement is due to reinforcement in the chorus frog contact zone. Furthermore, this work suggests that the dual action of cascade reinforcement and partial geographic isolation is promoting genetic diversification within one of the reinforced species.     

Novel colour polymorphisms in a hybrid zone of Mandarina (Gastropoda: Pulmonata)

A hybrid zone of the land snails Mandarina mandarina and Mandarina chichijimana in the oceanic Bonin Islands was studied morphologically and genetically to show the potential of hybridization as a source of morphological novelties. These species are clearly distinguishable on the basis of allozymes, colour polymorphisms, shell form and genital morphology, but exhibit a hybrid zone from the northeast to southwest of Chichijima island. There is a cline in the frequency of the colour patterns characteristic of each of the species, and specimens with intermediate colour pattern on the shells appear in the hybrid zone. Not only specimens with colour patterns that are overlapping of the patterns of the two species, but also specimens with unique colour patterns appear in the hybrid populations. These unique colour patterns are not found in the pure populations of both species or other Mandarina species in Chichijima Islands, and it is suggested that these are produced by the hybridization. Because of the appearance of many types of unique colour patterns, variability of the colour polymorphism in the hybrid populations are remarkably higher than that in the pure populations. This result suggests that the novel morphology is produced by the hybridization between species with distinctive morphology. This reveals the importance of hybridization as a source of morphological variation, diversity and evolutionary novelty.     

An ecomorphological framework for the coexistence of two cyprinid fish and their hybrids in a novel environment

Niche variation between hybrid taxa and their parental species has been deemed imperative to the persistence of hybrid populations in nature. However, the ecological factors promoting hybrid establishment remain poorly understood. Through the application of a multidisciplinary approach integrating genetics, morphometry, life‐history, and trophic ecology, we studied the hybrids of roach (Rutilus rutilus L.) and bream (Abramis brama L.), and their parental species inhabiting an Irish lake. The roach × bream hybrid exhibited a body shape intermediate of that of the parental species. Diet analyses depicted the hybrid as a generalist, feeding on all prey items consumed by either parental species. Stable isotope data confirm the trophic niche breadth of hybrids. A significant correlation between body shape and diet was detected, suggesting that the intermediate phenotype of hybrids might play a role in their feeding abilities, resulting in the utilization of a broader trophic spectrum than the parental species. Growth and age class structure analyses also yielded a scenario that is consistent with the ecological success of hybrids. Genetic analyses suggest that the majority of hybrids result from first‐generation crosses between the parental species; however, a potentially significant proportion of back‐crosses with bream were also detected. The recent introduction of roach and bream into Irish waters, as well as the climatic and ecological features of the colonized habitats, can explain the remarkable success of the roach × bream hybrid in Ireland. The adaptive significance of hybridization and its demographic consequences for the parental species are discussed. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 768–783.     

Gene flow across a climatic barrier between hybridizing avian species, California and Gambel's quail (Callipepla californica and C. gambelii)

Allopatric species commonly interbreed in a restricted margin between their ranges. The particular factors that permit interbreeding between species determine the extent of hybridization and its significance for evolution and conservation. Using California quail and Gambel's quail (Callipepla californica and C. gambelii) that naturally hybridize in a narrow region between relatively mesic and xeric environments, I assessed the exchange of genetic and phenotypic traits in relation to vegetative and climatic features (temperature and precipitation) that characterize the area of range overlap, and I examined genetic and phenotypic traits within the hybrid zone over a five-year period in relation to variation in precipitation. Using microsatellite markers, this study reveals that genetic, plumage, and morphometric traits are tightly associated with vegetation, rainfall, and temperature profiles through the abrupt transition from one parental species to the other across the hybrid zone. Results show that the hybrid zone has remained clinal, stationary, and bounded over the five-year study period. There was no evidence of introgression outside the narrow hybrid zone. Interannual climatic fluctuations are associated with internal hybrid zone dynamics but did not alter the shape and position of the zone. A transect through the hybrid zone revealed rapid and episodic genetic mixing within the zone. Possible long-term consequences of this restricted hybridization for the evolution of the two parental species are discussed in the light of changing environments.     

Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area

Instances of hybridization between endemic and alien species pose a threat to species integrity but also provide us with an opportunity to study the dynamics of gene flow between two species as they first meet. Here, we used variation at 22 highly differentiated microsatellite loci and one mitochondrial DNA (mtDNA) marker in a sample of 735 individuals, to investigate the genetic consequences of an introduction of Japanese sika deer ( Cervus nippon ) for native red deer ( C. elaphus ) on the Kintyre Peninsula in Scotland. We investigated population structure, estimated null-allele frequency and assigned individual hybrid scores using a Bayesian clustering algorithm implemented in structure 2.2. The dataset clearly divided into two clusters and generally, introgression into red and sika was low. However at one site, West Loch Awe, 43% of individuals were hybrids. MtDNA introgression indicated that hybridization was occurring between red-deer hinds and sika-deer stags. We argue that the pattern of differential introgression across the study area is primarily due to the rarity of hybridization events between the two species and the limited time the two species have been in contact (< 120 years). This contrasts with the causes of classic mosaic hybrid zones (selection induced by habitat variability). Currently, it seems possible that, in time, the level of hybridization found at West Loch Awe could also be found across the whole of the peninsula.     

Genetic relationships among Hylocereus and Selenicereus vine cacti (Cactaceae): evidence from hybridization and cytological studies

BACKGROUND AND AIMS: Hylocereus and Selenicereus are native to tropical and sub-tropical America. Based on its taxonomic status and crossability relations it was postulated that H. megalanthus (syn. S. megalanthus) is an allotetraploid (2n = 4x = 44) derived from natural hybridization between two closely related diploid taxa. The present work aimed at elucidating the genetic relationships between species of the two genera. METHODS: Crosses were performed and the putative hybrids were analysed by chromosome counts and morphological traits. The ploidy level of hybrids was confirmed by fluorescent in situ hybridization (FISH) of rDNA sites. Genomic in situ hybridization (GISH) was used in an attempt to identify the putative diploid genome donors of H. megalanthus and an artificial interploid hybrid. KEY RESULTS: Reciprocal crosses among four diploid Hylocereus species (H. costaricensis, H. monacanthus (syn. H. polyrhizus), H. undatus and Hylocereus sp.) yielded viable diploid hybrids, with regular chromosome pairing. Reciprocal crosses between these Hylocereus spp. and H. megalanthus yielded viable triploid, pentaploid, hexaploid and aneuploid hybrids. Morphological and phenological traits confirm the hybrid origin. In situ detection of rDNA sites was in accord with the ploidy status of the species and hybrid studied. GISH results indicated that overall sequence composition of H. megalanthus is similar to that of H. ocamponis and S. grandiflorus. High sequence similarity was also found between the parental genomes of H. monacanthus and H. megalanthus in one triploid hybrid. CONCLUSIONS: The ease of obtaining partially fertile F1 hybrids and the relative sequence similarity (in GISH study) suggest close genetic relationships among the taxa analysed.     

POLLEN-TUBE COMPETITION,SIRING SUCCESS,AND CONSISTENT ASYMMETRIC HYBRIDIZATION IN LOUISIANA IRISES

Postpollination mechanisms can play an important role in limiting natural hybridization in plants. Reciprocal hand pollination experiments were performed to study these mechanisms in two species of Louisiana iris: Iris brevicaulis and I. fulva. Relative pollen-tube growth rates changed significantly through time, with I. fulva tubes increasingly outperforming I. brevicaulis tubes in both conspecific and heterospecific styles. However, this pattern of change in relative performance was a poor predictor of siring success: the majority of seeds sired by both maternal species was conspecific rather than hybrid. Experimental crosses and field studies show consistent asymmetric hybridization in Louisiana irises, with I. fulva being a more successful father and a more selective mother than both I. brevicaulis and a third species, I. hexagona. The cause of this pattern is not yet clear, but the pattern itself is unusual. Typically, short-styled species tend to be less successful in reciprocal crosses than long-styled relatives, but I. fulva has shorter styles than either I. brevicaulis or I. hexagona. The effects of pollen-tube competition, differential fertilization, and selective abortion in causing this pattern of asymmetric hybridization is discussed.     

A karyological analysis of the artificial hybridization between Clarias gariepinus (Burchell, 1822) and Heterobranchus longifilis Valenciennes, 1840 (Pisces; Clariidae)

A karyological analysis of an artificial hybridization (reciprocal crosses) between two African clariid catfish, Clarias gariepinus (Burchell, 1822) and Heterobranchus longifilis Valenciennes, 1840, was performed. C. gariepinus has a standard karyotype of 2 n = 56, while H. longifilis has 2 n = 52. The hybrids revealed an intermediate karyotype (2 n = 54), and it appears as if they have totalized the haploid chromosome number of both parental species, excluding gynogenesis or androgenesis. The hybrid karyotype is considered as aneuploid, although the hybrids proved to be fertile. No variation was found in the hybrids karyotypes.     

Developmental trajectories and breakdown in F1 interpopulation hybrids of Tribolium castaneum

When hybrid inviability is an indirect by‐product of local adaptation, we expect its degree of severity between pairs of populations to vary and to be sensitive to the environment. While complete reciprocal hybrid inviability is the outcome of the gradual process of local adaptation, it is not representative of the process of accumulation of incompatibility. In the flour beetle, Tribolium castaneum, some pairs of populations exhibit complete, reciprocal F1 hybrid incompatibility while other pairs are fully or partially compatible. We characterize this naturally occurring variation in the degree and timing of expression of the hybrid incompatible phenotype to better understand the number of genes or developmental processes contributing to speciation. We assessed the morphological and developmental variation in four Tribolium castaneum populations and their 12 possible F1 hybrids at each life‐history stage from egg to adult. We find that the rate of hybrid larval development is affected in all interpopulation crosses, including those eventually producing viable, fertile adults. Hybrid incompatibility manifests early in development as changes in the duration of instars and diminished success in the transition between instars are relative to the parent populations. Parent populations with similar developmental profiles may produce hybrids with disrupted development. The degree and timing of expression of hybrid inviability depends upon populations crossed, direction of the cross, and environment in which hybrids are raised. Our findings suggest that the coordinated expression of genes involved in transitional periods of development is the underlying cause of hybrid incompatibility in this species.     

Melanization plasticity of Drosophila kikkawai,Drosophila leontia and reciprocal hybrids under different temperatures

Drosophila (Sophophora) kikkawai, Burla, 1954 and Drosophila (Sophophora) leontia, Tsacas & David 1978 are closely related sibling species, the former being cosmopolitan and the latter is restricted to tropical localities. We investigated the influence of introgressive hybridization on phenotypic diversity of the two sibling species in the present study. How hybridization supports the relative abundance of pure species according to latitudinal cline is the aim of this study because hybrids show a tendency to acquire geographical location of their parent species in equal or greater abundance. How hybridization supports the plasticity for melanization of hybrids is not explored yet. The two species can cross and generate hybrids. For this, we crossed true breeding strains of both species to obtain the hybrids i.e. dark female (♀) of D. kikkawai (D. k) with males (♂) of D. leontia (D. l) in cross I and light ♀ of D. k with ♂ of D. l in cross II along with their reciprocal crosses. Finally, we studied the plasticity of both species and their hybrids at 6 growth temperatures (14, 17, 21, 25, 28 and 31 °C). We found that there is no plasticity for melanization in true breeding darker and lighter strain of D. kikkawai as well as D. leontia whereas hybrids of both species showed high phenotypic plasticity. Significant differences in slope values across temperatures in parental and hybrid lines suggest plastic effects. Phenotypic variation in abdominal melanization in hybrids can be interpreted as a result of gene introgression with D. kikkawai. We conclude that introgressive hybridization might be an important, although underestimated, mechanism shaping species distribution and adaptation.     

Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

Many salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery‐reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts of inadvertent gene flow via straying from hatchery releases on wild populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16 years (1996–2012). Both microsatellites and SNPs revealed congruent population genetic structuring, indicating that introgression changed the genetic make‐up of wild populations by increasing genetic diversity and reducing genetic divergence. However, the degree of genetic introgression varied among studied populations, being higher in the eastern part and lower in the western part of Estonia, which most likely reflects the history of past stocking activities. Using kernel smoothing and permutation testing, we detected considerable heterogeneity in introgression patterns across the genome, with a large number of regions exhibiting nonrandom introgression widely dispersed across the genome. We also observed substantial variation in nonrandom introgression patterns within populations, as the majority of genomic regions showing elevated or reduced introgression were not consistently detected among temporal samples. This suggests that recombination, selection and stochastic processes may contribute to complex nonrandom introgression patterns. Our results suggest that (i) some genomic regions in Atlantic salmon are more vulnerable to introgressive hybridization, while others show greater resistance to unidirectional gene flow; and (ii) the hybridization of previously separated populations leads to complex and dynamic nonrandom introgression patterns that most likely have functional consequences for indigenous populations.     

Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality

When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced‐generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.     

Origin of gynodioecy in Limnanthes: evidence from ecogeographic patterns of variation

Summary Evidence for hybrid origin of gene-cytoplasmic gynodioecy in Limnanthes douglasii is presented in terms of the parapatric distributions of putative parental taxa and the increased levels of genetic variation in gynodioecious populations. Attempts to produce gynodioecy through artificial hybridization between different accessions apparently failed due to the limited number of parental combinations used in making hybrids. Further studies are proposed on the hybrid origin model and on selective forces determining the fate of gynodioecy with its contributions to higher levels of hybridity and genetic variation.     

Patterns of hybridization in plants

Hybridization plays an important role in the evolution of many taxonomic groups, but large-scale phylogenetic patterns of hybridization are poorly known. Here, we investigate patterns of hybridization in vascular plants. Our dataset included 282 families, 3212 genera and ≈37,000 species accounts from eight regional floras covering continental Europe, two island regions, and parts of North America and Australia. Interspecific hybrids were common in the wild, occurring in 40% of families and 16% of genera, with an overall frequency of 0.09 hybrids per nonhybrid species. Taxon species richness explained a large amount of variation in the number of hybrids, but taxon bias (study effort) did not. We accounted for species richness in calculating hybridization propensities, and found that both families and genera differed in hybridization propensity. Hybridization propensity of a given group was generally consistent across regions (with the exception of Hawaii), suggesting that hybridization behavior may be determined more by intrinsic properties of a group than by environmental conditions. We found evidence of a strong phylogenetic signal (λ=0.93) in hybridization propensity as hybrids were not uniformly distributed across orders of vascular plants. Characterization of the hybridization behavior of groups should lead to increased predictive power regarding their traits and evolutionary trajectories, and will allow comparative tests of the traits driving differences in hybridization propensity.     

Interspecific differentiation and intraspecific substructure in two closely related clupeids with extensive hybridization, Alosa alosa and Alosa fallax

In this study, the evolutionary relationships within and among populations of European shads, Alosa alosa and Alosa fallax , was investigated. Screening of allelic variation across eight allozyme loci and sequencing 448 bp of the mtDNA cytochrome b gene in 14 rivers throughout the range of the species supported that the two taxa were independent lineages (1·3% net nucleotide divergence) despite extensive hybridization. Genetic diversity and structure was considerably higher in A. fallax than A. alosa and the former species revealed evidence of distinct lineages in the Mediterranean and Atlantic basins. A Bayesian clustering approach combined with gill raker counts verified that individuals of the two species could be assigned to their parent group with relatively high confidence. Evaluation of hybridization in the Lima and Mondego Rivers in Portugal provided evidence that introgression is extensive but is not currently obscuring (through hybrid swarming) the diagnosability of the two species.     

Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context

Hybridization can profoundly affect the genomic composition and phenotypes of closely related species, and provides an opportunity to identify mechanisms that maintain reproductive isolation between species. Recent evidence suggests that hybridization outcomes within a species pair can vary across locations. However, we still do not know how variable outcomes of hybridization are across geographic replicates, and what mechanisms drive that variation. In this study, we described hybridization outcomes across 27 locations in the North Fork Shoshone River basin (Wyoming, USA) where native Yellowstone cutthroat trout and introduced rainbow trout co‐occur. We used genomic data and hierarchical Bayesian models to precisely identify ancestry of hybrid individuals. Hybridization outcomes varied across locations. In some locations, only rainbow trout and advanced backcrossed hybrids towards rainbow trout were present, while trout in other locations had a broader range of ancestry, including both parental species and first‐generation hybrids. Later‐generation intermediate hybrids were rare relative to backcrossed hybrids and rainbow trout individuals. Using an individual‐based simulation, we found that outcomes of hybridization in the North Fork Shoshone River basin deviate substantially from what we would expect under null expectations of random mating and no selection against hybrids. Since this deviation implies that some mechanisms of reproductive isolation function to maintain parental taxa and a diversity of hybrid types, we then modelled hybridization outcomes as a function of environmental variables and stocking history that are likely to affect prezygotic barriers to hybridization. Variables associated with history of fish stocking were the strongest predictors of hybridization outcomes, followed by environmental variables that might affect overlap in spawning time and location.     

Homoploid hybrid speciation and genome evolution via chromosome sorting

Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as support for homoploid hybrid speciation (HHS), a process by which a new reproductively isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However, convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendants. We show that meiotic segregation, operating in the hybrid lineage, resulted in the formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrate that during the heterozygous stage of the hybrid species formation, recombination was limited between rearranged chromosomes of different parental origin, representing evidence that the reproductive isolation was a direct consequence of hybridization.     

Birds rarely hybridize: A citizen science approach to estimating rates of hybridization in the wild*

The rate of hybridization among taxa is a central consideration in any discussion of speciation, but rates of hybridization are difficult to estimate in most wild populations of animals. We used a successful citizen science dataset, eBird, to estimate the rates of hybridization for wild birds in the United States. We calculated the frequency at which hybrid individuals belonging to different species, families, and orders of birds were observed. Between 1 January 2010 and 31 December 2018, a total of 334,770,194 species records were reported to eBird within the United States. Of this total, 212,875 or 0.064% were reported as hybrids. This estimate is higher than the rate of hybridization (0.00167%) reported by Mayr based on impressions from a career studying museum specimens. However, if the 10 most influential hybrid species are removed from the eBird dataset, the rate of hybridization decreases substantially to about 0.009%. We conclude that the rate of hybridization for individuals in most bird species is extremely low, even though the potential for birds to produce fertile offspring through hybrid crosses is high. These findings indicate that there is strong prezygotic selection working in most avian species.     

Differential selection to avoid hybridization in two toad species

Abstract.— The fitness consequences of hybridization critically affect the speciation process. When hybridization is costly, selection favors the evolution of prezygotic isolating mechanisms (e.g., mating behaviors) that reduce heter-ospecific matings and, consequently, enhance reproductive isolation between species (a process termed reinforcement). If, however, selection to avoid hybridization differs between species, reinforcement may be impeded. Here, we examined both the frequency and fitness effects of hybridization between plains spadefoot toads ( Spea bombifrons ) and New Mexico spadefoot toads ( S. multiplicata ). Hybridization was most frequent in smaller breeding ponds that tend to be ephemeral, and heterospecific pairs consisted almost entirely of S. bombifrons females and S. multiplicata males. Moreover, in controlled experimental crosses, hybrid offspring from crosses in which S. multiplicata was maternal had significantly lower survival and longer development time than pure S. multiplicata offspring. By contrast, hybrid offspring from crosses in which S. bombifrons was maternal outperformed pure S. bombifrons offspring by reaching metamorphosis faster. These data suggest that, although S. multiplicata females are under selection to avoid hybridization, selection might favor those S. bombifrons females that hybridize with S. multiplicata if their breeding pond is highly ephemeral. Generally, the strength of selection to avoid hybridization may differ for hybridizing species, possibly impeding reinforcement.