Discordant introgression in a rapidly expanding hybrid swarm

Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone

Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range‐limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species’ ranges, whereas putative cases of adaptive introgression had exceptionally wide clines with centers shifted toward one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per‐generation dispersal between 200 and 400 m, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range‐limited species.

Biological and trophic consequences of genetic introgression between endemic and invasive Barbus fishes

Genetic introgression with native species is recognized as a detrimental impact resulting from biological invasions involving taxonomically similar invaders. Whilst the underlying genetic mechanisms are increasingly understood, the ecological consequences of introgression are relatively less studied, despite their utility for increasing knowledge on how invasion impacts can manifest. Here, the ecological consequences of genetic introgression from an invasive congener were tested using the endemic barbel populations of central Italy, where the invader was the European barbel Barbus barbus. Four populations of native Barbus species (B. plebejus and B. tyberinus) were studied: two purebred and two completely introgressed with alien B. barbus. Across the four populations, differences in their biological traits (growth, body condition and population demographic structure) and trophic ecology (gut content analysis and stable isotope analysis) were tested. While all populations had similar body condition and were dominated by fish up to 2 years of age, the introgressed fish had substantially greater lengths at the same age, with maximum lengths 410–460 mm in hybrids versus 340–360 mm in native purebred barbel. The population characterized by the highest number of introgressed B. barbus alleles (81 %) had the largest trophic niche and a substantially lower trophic position than the other populations through its exploitation of a wider range of resources (e.g. small fishes and plants). These results attest that the genetic introgression of an invasive congener with native species can result in substantial ecological consequences, including the potential for cascading effects.

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.

Hybridization and rapid differentiation after secondary contact between the native green anole (Anolis carolinensis) and the introduced green anole (Anolis porcatus)

In allopatric species, reproductive isolation evolves through the accumulation of genetic incompatibilities. The degree of divergence required for complete reproductive isolation is highly variable across taxa, which makes the outcome of secondary contact between allopatric species unpredictable. Since before the Pliocene, two species of Anolis lizards, Anolis carolinensis and Anolis porcatus, have been allopatric, yet this period of independent evolution has not led to substantial species-specific morphological differentiation, and therefore, they might not be reproductively isolated. In this study, we determined the genetic consequences of localized, secondary contact between the native green anole, A. carolinensis, and the introduced Cuban green anole, A. porcatus, in South Miami. Using 18 microsatellite markers, we found that the South Miami population formed a genetic cluster distinct from both parental species. Mitochondrial DNA revealed maternal A. porcatus ancestry for 35% of the individuals sampled from this population, indicating a high degree of cytonuclear discordance. Thus, hybridization with A. porcatus, not just population structure within A. carolinensis, may be responsible for the genetic distinctiveness of this population. Using tree-based maximum-likelihood analysis, we found support for a more recent, secondary introduction of A. porcatus to Florida. Evidence that ~33% of the nuclear DNA resulted from a secondary introduction supports the hybrid origin of the green anole population in South Miami. We used multiple lines of evidence and multiple genetic markers to reconstruct otherwise cryptic patterns of species introduction and hybridization. Genetic evidence for a lack of reproductive isolation, as well as morphological similarities between the two species, supports revising the taxonomy of A. carolinensis to include A. porcatus from western Cuba. Future studies should target the current geographic extent of introgression originating from the past injection of genetic material from Cuban green anoles and determine the consequences for the evolutionary trajectory of green anole populations in southern Florida.

Rapid movement and instability of an invasive hybrid swarm

Unstable hybrid swarms that arise following the introduction of non‐native species can overwhelm native congeners, yet the stability of invasive hybrid swarms has not been well documented over time. Here, we examine genetic variation and clinal stability across a recently formed hybrid swarm involving native blacktail shiner (Cyprinella venusta) and non‐native red shiner (C. lutrensis) in the Upper Coosa River basin, which is widely considered to be a global hot spot of aquatic biodiversity. Examination of phenotypic, multilocus genotypic, and mitochondrial haplotype variability between 2005 and 2011 revealed that the proportion of hybrids has increased over time, with more than a third of all sampled individuals exhibiting admixture in the final year of sampling. Comparisons of clines over time indicated that the hybrid swarm has been rapidly progressing upstream, but at a declining and slower pace than rates estimated from historical collection records. Clinal comparisons also showed that the hybrid swarm has been expanding and contracting over time. Additionally, we documented the presence of red shiner and hybrids farther downstream than prior studies have detected, which suggests that congeners in the Coosa River basin, including all remaining populations of the threatened blue shiner (Cyprinella caerulea), are at greater risk than previously thought.

Biogeography of "Cyprinella lutrensis": intensive genetic sampling from the Pecos River 'melting pot' reveals a dynamic history and phylogenetic complexity

Thorough sampling is necessary to delineate lineage diversity for polytypic "species" such as Cyprinella lutrensis. We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study emphasized the Pecos River due to its complex geological history and potential to harbor multiple lineages. We used geometric-morphometric, morphometric, and meristic analyses to test for phenotypic divergence and combined nucDNA with mtDNA to test for cytonuclear disequilibrium and combined our sequences with published data to conduct a phylogenetic re-assessment of the entire C. lutrensis clade. We detected five co-occurring mtDNA lineages in the Pecos River, but no evidence for cytonuclear disequilibrium or phenotypic divergence. Recognized species were interspersed amongst divergent lineages of "C. lutrensis". Allopatric divergence among drainages isolated in the Late Miocene and Pliocene apparently produced several recognized species and major divisions within "C. lutrensis". Pleistocene re-expansion and subsequent re-fragmentation of a centralized lineage founded younger, divergent lineages throughout the Rio Grande basin and Edwards Plateau. There is also evidence of recent introductions to the Rio Grande, Pecos and South Canadian Rivers. Nonetheless, deeply divergent lineages have coexisted since the Pleistocene.

Genomic replacement of native Cobitis lutheri with introduced C. tetralineata through a hybrid swarm following the artificial connection of river systems

River connections via artificial canals will bring about secondary contacts between previously isolated fish species. Here, we present a genetic consequence of such a secondary contact between Cobitis fish species, C. lutheri in the Dongjin River, and C. tetralineata in the Seomjin River in Korea. The construction of water canals about 80 years ago has unidirectionally introduced C. tetralineata into the native habitat of C. lutheri, and then these species have hybridized in the main stream section of the Dongjin River. According to the divergence population genetic analyses of DNA sequence data, the two species diverged about 3.3 million years ago, which is interestingly coincident with the unprecedented paleoceanographic change that caused isolations of the paleo-river systems in northeast Asia due to sea-level changes around the late Pliocene. Multilocus genotypic data of nine microsatellites and three nuclear loci revealed an extensively admixed structure in the hybrid zone with a high proportion of various post-F1 hybrids. Surprisingly, pure native C. lutheri was absent in the hybrid zone in contrast to the 7% of pure C. tetralineata. Such a biased proportion must have resulted from the dominant influence of continually introducing C. tetralineata on the native C. lutheri which has no supply of natives from other tributaries to the hybrid zone due to numerous low-head dams. In addition, mating experiments indicated that there is no discernible reproductive isolation between them. All the results suggest that the gene pool of native C. lutheri is being rapidly replaced by that of continually introducing C. tetralineata through a hybrid swarm for the last 80 years, which will ultimately lead to the genomic extinction of natives in this hybrid zone.

Speciation in fishes

The field of speciation has seen much renewed interest in the past few years, with theoretical and empirical advances that have moved it from a descriptive field to a predictive and testable one. The goal of this review is to provide a general background on research on speciation as it pertains to fishes. Three major components to the question are first discussed: the spatial, ecological and sexual factors that influence speciation mechanisms. We then move to the latest developments in the field of speciation genomics. Affordable and rapidly available, massively parallel sequencing data allow speciation studies to converge into a single comprehensive line of investigation, where the focus has shifted to the search for speciation genes and genomic islands of speciation. We argue that fish present a very diverse array of scenarios, making them an ideal model to study speciation processes.

Invasion genetics of vendace (Coregonus albula (L.)) in the Inari-Pasvik watercourse: revealing the origin and expansion pattern of a rapid colonization event

Species invasions can have wide-ranging biological and socio-economic effects and are generally unwanted by legislation. Identification of the source population as well as the ecology and genetics of both the invader population and the receiving community is of crucial importance. The rapid invasion of a small coregonid fish vendace (Coregonus albula) in a major northern European subarctic watercourse has resulted in a labile ecological situation in the receiving community. The ecological impact of the invasion has been thoroughly documented, but the genetics of the invasion remains to be explored. We analyzed the genetic diversity and divergence patterns among the two possible source populations from southern Finnish Lapland and three colonists populations within the Inari-Pasvik watercourse using ten microsatellite loci in order to (i) identify the most likely source of the invasion, (ii) reveal the dispersal pattern and genetic structure of the secondary expansion, and (iii) to investigate whether the initial introduction and the secondary expansion were associated with founder effects. We revealed that repeated translocation of vendace from Lake Sinettäjärvi into a tributary lake of L. Inari in 1964–1966 is the most plausible source for the invasion. Both the initial introduction and the secondary expansion were found not to be associated with significant founder effects. The secondary expansion followed a stepping stone pattern and the source and colonist populations of this expansion have undergone rapid genetic divergence within a period of 15–35 years (ca. 8–17 generations). The rapid divergence may be contributed to lack of gene flow among the source and colonist populations due to the extensive hydroelectric damming in the watercourse. Multiple introductions and substantial genetic variation in combination with the boom-and-bust population development of the species thus likely counteracted the founder effects as well as fueled the rapid establishment and expansion of this species within the Inari-Pasvik watercourse.

Exposure to an environmental estrogen breaks down sexual isolation between native and invasive species

Environmental change can increase the likelihood of interspecific hybridization by altering properties of mate recognition and discrimination between sympatric congeners. We examined how exposure to an environmentally widespread endocrine-disrupting chemical (EDC), bisphenol A (BPA), affected visual communication signals and behavioral isolation between an introduced freshwater fish and a native congener (genus: Cyprinella). Exposure to BPA induced changes in the expression of male secondary traits as well as male and female mate choice, leading to an overall reduction in prezygotic isolation between congeners. Changes in female mate discrimination were not tightly linked to changes in male phenotypic traits, suggesting that EDC exposure may alter female choice thresholds independently of the effects of exposure on males. These findings indicate that environmental exposure to EDCs can lead to population declines via the erosion of species boundaries and by promoting the establishment and spread of non-native species via hybridization.