Introgressive hybridization as a mechanism for species rescue

A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas

The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.

Patterns of admixture and introgression in a mosaic Mytilus galloprovincialis and Mytilus edulis hybrid zone in SW England

The study of hybrid zones offers important insights into speciation. Earlier studies on hybrid populations of the marine mussel species Mytilus edulis and Mytilus galloprovincialis in SW England provided evidence of admixture but were constrained by the limited number of molecular markers available. We use 57 ancestry-informative SNPs, most of which have been mapped genetically, to provide evidence of distinctive differences between admixed populations in SW England and asymmetrical introgression from M. edulis to M. galloprovincialis. We combine the genetic study with analysis of phenotypic traits of potential ecological and adaptive significance. We demonstrate that hybrid individuals have brown mantle edges unlike the white or purple in the parental species, suggesting allelic or non-allelic genomic interactions. We report differences in gonad development stage between the species consistent with a prezygotic barrier between the species. By incorporating results from publications dating back to 1980, we confirm the long-term stability of the hybrid zone despite higher viability of M. galloprovincialis. This stability coincides with a dramatic change in temperature of UK coastal waters and suggests that these hybrid populations might be resisting the effects of global warming. However, a single SNP locus associated with the Notch transmembrane signalling protein shows a markedly different pattern of variation to the others and might be associated with adaptation of M. galloprovincialis to colder northern temperatures.

Genetic divergences and hybridization within the Sebastes inermis complex

The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow.

Evidence of introgression, ecological divergence and adaptation in Asterias sea stars

Hybrid zones are important windows into the evolutionary dynamics of populations, revealing how processes like introgression and adaptation structure population genomic variation. Importantly, they are useful for understanding speciation and how species respond to their environments. Here, we investigate two closely related sea star species, Asterias rubens and A. forbesi, distributed along rocky European and North American coastlines of the North Atlantic, and use genome-wide molecular markers to infer the distribution of genomic variation within and between species in this group. Using genomic data and environmental niche modelling, we document hybridization occurring between northern New England and the southern Canadian Maritimes. We investigate the factors that maintain this hybrid zone, as well as the environmental variables that putatively drive selection within and between species. We find that the two species differ in their environmental niche breadth; Asterias forbesi displays a relatively narrow environmental niche while conversely, A. rubens has a wider niche breadth. Species distribution models accurately predict hybrids to occur within environmental niche overlap, thereby suggesting environmental selection plays an important role in the maintenance of the hybrid zone. Our results imply that the distribution of genomic variation in North Atlantic sea stars is influenced by the environment, which will be crucial to consider as the climate changes.

Cryopreservation and Its Application in Aquaculture

Aquaculture is the major aquatic animal production segment. Problems like inbreeding depression, genetic drift, introgressive hybridization, etc. have been influencing the production of quality seeds negatively. Cryopreservation serves as a way-out for these problems and a possible answer to produce quality seeds and genetically improved varieties. It has been considered as a major strategy for conservation of fish genetic resources. Cryopreservation of fish gametes has been in vogue since 1953 and the technology is well studied and validated for many species. So far the milt of 200 fish species has been cryopreserved successfully. In this chapter, the importance of aquaculture in overcoming malnutrition, genetic issues affecting quality seed production, cryopreservation protocol employed for various fish species, problems faced in cryopreserving fish eggs and embryos and future of cryopreservation in aquaculture have been discussed.

Species cohesion of an extremophyte (Carex angustisquama, Cyperaceae) in solfatara fields maintained under interspecific natural hybridization

BACKGROUND AND AIMS

Hybridization is the main driver of plant diversification, and gene flow via hybridization has multifaceted effects on plant evolution. Carex angustisquama is an extremophyte that grows on soils heavily acidified by volcanism. Despite its habitat distinct from that of other species, this species is known to form interspecific hybrids, implying interspecific gene flow. It is crucial to verify the extent and direction of interspecific gene flow between C. angustisquama and closely related species to understand the evolutionary process of an extremophyte in solfatara fields.

METHODS

In this study, expressed sequence tag-simple sequence repeat markers were utilized to infer the extent and direction of interspecific gene flow between C. angustisquama and closely related species.

KEY RESULTS

Bayesian clustering and simulation analyses revealed that all individuals of the three hybrid species were classified into the first hybrid generation or first backcross to C. angustisquama; therefore, current interspecific gene flow is limited. Moreover, in the Bayesian inference of historical gene flow based on multispecies samples, the model that assumed no interspecific gene flow was the most strongly supported across all species pairs, including phylogenetically close but ecologically distinctive species pairs.

CONCLUSIONS

Our results revealed that interspecific gene flow between C. angustisquama and its related species has been limited both currently and historically. Moreover, our results of Bayesian inference of historical gene flow indicated that extrinsic, rather than intrinsic, factors probably act as isolating barriers between Carex species, with hybrid breakdown via microhabitat segregation being the probable potential barrier. Overall, our findings provide insights into the evolutionary process of an extremophyte in solfatara fields and offer an important example of the mechanisms of diversification of the speciose genus Carex.

How will mosquitoes adapt to climate warming?

The potential for adaptive evolution to enable species persistence under a changing climate is one of the most important questions for understanding impacts of future climate change. Climate adaptation may be particularly likely for short-lived ectotherms, including many pest, pathogen, and vector species. For these taxa, estimating climate adaptive potential is critical for accurate predictive modeling and public health preparedness. Here, we demonstrate how a simple theoretical framework used in conservation biology-evolutionary rescue models-can be used to investigate the potential for climate adaptation in these taxa, using mosquito thermal adaptation as a focal case. Synthesizing current evidence, we find that short mosquito generation times, high population growth rates, and strong temperature-imposed selection favor thermal adaptation. However, knowledge gaps about the extent of phenotypic and genotypic variation in thermal tolerance within mosquito populations, the environmental sensitivity of selection, and the role of phenotypic plasticity constrain our ability to make more precise estimates. We describe how common garden and selection experiments can be used to fill these data gaps. Lastly, we investigate the consequences of mosquito climate adaptation on disease transmission using Aedes aegypti-transmitted dengue virus in Northern Brazil as a case study. The approach outlined here can be applied to any disease vector or pest species and type of environmental change.

Morphological ghosts of introgression in Darwin's finch populations

Many species of plants, animals, and microorganisms exchange genes well after the point of evolutionary divergence at which taxonomists recognize them as species. Genomes contain signatures of past gene exchange and, in some cases, they reveal a legacy of lineages that no longer exist. But genomic data are not available for many organisms, and particularly problematic for reconstructing and interpreting evolutionary history are communities that have been depleted by extinctions. For these, morphology may substitute for genes, as exemplified by the history of Darwin's finches on the Galápagos islands of Floreana and San Cristóbal. Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris in 1835. The populations became extinct in the next few decades, partly due to destruction of Opuntia cactus by introduced goats, whereas Geospiza fortis has persisted to the present. We used measurements of large samples of G. fortis collected for museums in the period 1891 to 1906 to test for unusually large variances and skewed distributions of beak and body size resulting from introgression. We found strong evidence of hybridization on Floreana but not on San Cristóbal. The skew is in the direction of the absent G. magnirostris We estimate introgression influenced 6% of the frequency distribution that was eroded by selection after G. magnirostris became extinct on these islands. The genetic residuum of an extinct species in an extant one has implications for its future evolution, as well as for a conservation program of reintroductions in extinction-depleted communities.

Evolutionary Rescue of an Environmental Pseudomonas otitidis in Response to Anthropogenic Perturbation

Anthropogenic perturbations introduce novel selective pressures to natural environments, impacting the genomic variability of organisms and thus altering the evolutionary trajectory of populations. Water overexploitation for agricultural purposes and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction along with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis over a 13-year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response to perturbation of this lineage. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which points to the occurrence of an evolutionary rescue event. Loss of genomic and nucleotide variation alongside an increment in mean and variance of Tajima’s D, characteristic of sudden population expansions, support this observation. In addition, a significant increase in recombination rate (R/θ) was observed, pointing to horizontal gene transfer playing a role in population recovery. Furthermore, the gain of phosphorylation, DNA recombination, small-molecule metabolism and transport and loss of biosynthetic and regulatory genes suggest a functional shift in response to the environmental perturbation. Despite subsequent sampling events in the studied site, no pseudomonad was found until the lagoon completely dried in 2017. We speculate about the causes of P. otitidis final decline or possible extinction. Overall our results are evidence of adaptive responses at the genomic level of bacterial populations in a heavily exploited aquifer.

Patterns of introgression vary within an avian hybrid zone

Background

Exploring hybrid zone dynamics at different spatial scales allows for better understanding of local factors that influence hybrid zone structure. In this study, we tested hypotheses about drivers of introgression at two spatial scales within the Saltmarsh Sparrow (Ammospiza caudacuta) and Nelson’s Sparrow (A. nelsoni) hybrid zone. Specifically, we evaluated the influence of neutral demographic processes (relative species abundance), natural selection (exogenous environmental factors and genetic incompatibilities), and sexual selection (assortative mating) in this mosaic hybrid zone. By intensively sampling adults (n = 218) and chicks (n = 326) at two geographically proximate locations in the center of the hybrid zone, we determined patterns of introgression on a fine scale across sites of differing habitat. We made broadscale comparisons of patterns from the center with those of prior studies in the southern edge of the hybrid zone.

Results

A panel of fixed SNPs (135) identified from ddRAD sequencing was used to calculate a hybrid index and determine genotypic composition/admixture level of the populations. Another panel of polymorphic SNPs (589) was used to assign paternity and reconstruct mating pairs to test for sexual selection. On a broad-scale, patterns of introgression were not explained by random mating within marshes. We found high rates of back-crossing and similarly low rates of recent-generation (F1/F2) hybrids in the center and south of the zone. Offspring genotypic proportions did not meet those expected from random mating within the parental genotypic distribution. Additionally, we observed half as many F1/F2 hybrid female adults than nestlings, while respective male groups showed no difference, in support of Haldane’s Rule. The observed proportion of interspecific mating was lower than expected when accounting for mate availability, indicating assortative mating was limiting widespread hybridization. On a fine spatial scale, we found variation in the relative influence of neutral and selective forces between inland and coastal habitats, with the smaller, inland marsh influenced primarily by neutral demographic processes, and the expansive, coastal marsh experiencing higher selective pressures in the form of natural (exogenous and endogenous) and sexual selection.

Conclusions

Multiple drivers of introgression, including neutral and selective pressures (exogenous, endogenous, and sexual selection), are structuring this hybrid zone, and their relative influence is site and context-dependent.

Genetic relationships and hybridization among three western Atlantic sparid species: sheepshead (Archosargus probatocephalus), sea bream (A. rhomboidalis) and pinfish (Lagodon rhomboides)

Three species of sparids in the western Atlantic, sheepshead (Archosargus probatocephalus), sea bream (A. rhomboidalis), and pinfish (Lagodon rhomboides), share overlapping habitats, spawning seasons, and spawning grounds, providing opportunities for interaction among these species. Three regions of mitochondrial DNA and three nuclear DNA intron sequences were used to construct the genetic relationships among these species. The results showed that these species are closely related, suggesting the presence of soft polytomy with sheepshead and western Atlantic sea bream as sister species. However, western Atlantic sea bream and pinfish are equally divergent from sheepshead. We used a suite of 18 microsatellite markers to verify the occurrence of hybridization, identify the parental types, and evaluate the filial-generation status of 36 individuals morphologically identified as hybrids from the Indian River Lagoon system, in Florida. The 36 putative hybrids were analyzed with a reference group of 172 western Atlantic sea bream, 232 pinfish, and 157 sheepsheads and were all genetically determined to be F1 of sheepshead and western Atlantic sea bream with very little indication or no introgressive hybridization among the 172 reference specimens of western Atlantic sea bream. Hybridization was asymmetric, with western Atlantic sea bream males crossing with sheepshead females. Hybrids were first observed in the Indian River Lagoon in 2005, after the western Atlantic sea bream had become common there, in the 1990s. Their occurrence could be associated with unique features of the Indian River Lagoon that bring the two species together or with recent anthropogenic changes in this system. Further study is needed to determine the causes and long-term effects of the recurrent production of F1 hybrids and the degree of their sterility in the Indian River Lagoon.

Abiotic genetic adaptation in the Fagaceae

Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.

Conservation through the lens of (mal)adaptation: Concepts and meta-analysis

Evolutionary approaches are gaining popularity in conservation science, with diverse strategies applied in efforts to support adaptive population outcomes. Yet conservation strategies differ in the type of adaptive outcomes they promote as conservation goals. For instance, strategies based on genetic or demographic rescue implicitly target adaptive population states whereas strategies utilizing transgenerational plasticity or evolutionary rescue implicitly target adaptive processes. These two goals are somewhat polar: adaptive state strategies optimize current population fitness, which should reduce phenotypic and/or genetic variance, reducing adaptability in changing or uncertain environments; adaptive process strategies increase genetic variance, causing maladaptation in the short term, but increase adaptability over the long term. Maladaptation refers to suboptimal population fitness, adaptation refers to optimal population fitness, and (mal)adaptation refers to the continuum of fitness variation from maladaptation to adaptation. Here, we present a conceptual classification for conservation that implicitly considers (mal)adaptation in the short-term and long-term outcomes of conservation strategies. We describe cases of how (mal)adaptation is implicated in traditional conservation strategies, as well as strategies that have potential as a conservation tool but are relatively underutilized. We use a meta-analysis of a small number of available studies to evaluate whether the different conservation strategies employed are better suited toward increasing population fitness across multiple generations. We found weakly increasing adaptation over time for transgenerational plasticity, genetic rescue, and evolutionary rescue. Demographic rescue was generally maladaptive, both immediately after conservation intervention and after several generations. Interspecific hybridization was adaptive only in the F1 generation, but then rapidly leads to maladaptation. Management decisions that are made to support the process of adaptation must adequately account for (mal)adaptation as a potential outcome and even as a tool to bolster adaptive capacity to changing conditions.

Body condition (Wr ) and reproductive potential of bighead and silver carp hybrids: Postzygotic selection in the Mississippi River Basin

Invasive bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are reproductively isolated in their native range, but form a bimodal, multigenerational hybrid swarm within the Mississippi River Basin (MRB). Despite observed F1 hybrid superiority in experimental settings, effects of postzygotic selection on bighead and silver carp hybrids have not been tested in a natural system. Individual parent and hybrid genotypes were resolved at 57 species-specific loci and used to evaluate postzygotic selection for body condition (Wr ) and female reproductive potential (presence of spawning stage gonads and gonadosomatic index [GSI]) in the MRB during 2009-2011. Body condition in the Marseilles Reach, Illinois River declined with a decrease in species-specific allele frequency from 1.0 to 0.4 for each species and early generation hybrids (F1, F2, and first-generation backcross) had lower mean Wr than late generation hybrids (2nd+ generation backcrosses) and parentals. Proportions of stage IV and stage V (spawning stage) female gonads differed between bighead and silver carp, but not among parentals and their early and late generation hybrids within the MRB. Mean GSI values did not differ between parentals and hybrids. Because reproductive potential did not differ between hybrids and parentals, our results suggest that early generation hybrids occur in low frequency either as a factor of poor condition (Wr ) and postreproductive survival, infrequent reproductive encounters by parental bighead and silver carp, or selection pressures acting on juvenile or immature life stages. Our results suggest that a combination of genetic and environmental factors may contribute to the postzygotic success of bighead and silver carp hybrids in the Mississippi River Basin.

Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus)

Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.

Cryptic Biological Invasions: a General Model of Hybridization

The dispersal of non-native genes due to hybridization is a form of cryptic invasion with growing concern in evolution and conservation. This includes the spread of transgenic genes and antibiotic resistance. To investigate how genes and phenotypes are transmitted, we developed a general model that, for the first time, considers concurrently: multiple loci, quantitative and qualitative gene expression, assortative mating, dominance/recessivity inheritance and density-dependent demographic effects. Selection acting on alleles or genotypes can also be incorporated. Our results reveal that the conclusions about how hybridization threatens a species can be biased if they are based on single-gene models, while considering two or more genes can correct this bias. We also show that demography can amplify or balance the genetic effects, evidencing the need of jointly incorporating both processes. By implementing our model in a real case, we show that mallard ducks introduced in New Zealand benefit from hybridization to replace native grey-ducks. Total displacement can take a few generations and occurs by interspecific competition and by competition between hybrids and natives, demonstrating how hybridization may facilitate biological invasions. We argue that our general model represents a powerful tool for the study of a wide range of biological and societal questions.

Females drive asymmetrical introgression from rare to common species in Darwin's tree finches

The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger-bodied C. pauper to the common, smaller-bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex-specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species-specific.

Evolution and the duration of a doomed population

Many populations are doomed to extinction, but little is known about how evolution contributes to their longevity. We address this by modeling an asexual population consisting of genotypes whose abundances change independently according to a system of continuous branching diffusions. Each genotype is characterized by its initial abundance, growth rate, and reproductive variance. The latter two components determine the genotype's "risk function" which describes its per capita probability of extinction at any time. We derive the probability distribution of extinction times for a polymorphic population, which can be expressed in terms of genotypic risk functions. We use this to explore how spontaneous mutation, abrupt environmental change, or population supplementation and removal affect the time to extinction. Results suggest that evolution based on new mutations does little to alter the time to extinction. Abrupt environmental changes that affect all genotypes can have more substantial impact, but, curiously, a beneficial change does more to extend the lifetime of thriving than threatened populations of the same initial abundance. Our results can be used to design policies that meet specific conservation goals or management strategies that speed the elimination of agricultural pests or human pathogens.

Impacts of human-induced environmental disturbances on hybridization between two ecologically differentiated Californian oak species

Natural hybridization, which can be involved in local adaptation and in speciation processes, has been linked to different sources of anthropogenic disturbance. Here, we use genotypic data to study range-wide patterns of genetic admixture between the serpentine-soil specialist leather oak (Quercus durata) and the widespread Californian scrub oak (Quercus berberidifolia). First, we estimated hybridization rates and the direction of gene flow. Second, we tested the hypothesis that genetic admixture increases with different sources of environmental disturbance, namely anthropogenic destruction of natural habitats and wildfire frequency estimated from long-term records of fire occurrence. Our analyses indicate considerable rates of hybridization (> 25%), asymmetric gene flow from Q. durata into Q. berberidifolia, and a higher occurrence of hybrids in areas where both species live in close parapatry. In accordance with the environmental disturbance hypothesis, we found that genetic admixture increases with wildfire frequency, but we did not find a significant effect of other sources of human-induced habitat alteration (urbanization, land clearing for agriculture) or a suite of ecological factors (climate, elevation, soil type). Our findings highlight that wildfires constitute an important source of environmental disturbance, promoting hybridization between two ecologically well-differentiated native species.

Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure

Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously. A third group, "slope," has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.

Hybridization and hybrid speciation under global change

Contents 1170 I. 1170 II. 1172 III. 1175 IV. 1180 V. 1183 1184 References 1184 SUMMARY: An unintended consequence of global change is an increase in opportunities for hybridization among previously isolated lineages. Here we illustrate how global change can facilitate the breakdown of reproductive barriers and the formation of hybrids, drawing on the flora of the British Isles for insight. Although global change may ameliorate some of the barriers preventing hybrid establishment, for example by providing new ecological niches for hybrids, it will have limited effects on environment-independent post-zygotic barriers. For example, genic incompatibilities and differences in chromosome numbers and structure within hybrid genomes are unlikely to be affected by global change. We thus speculate that global change will have a larger effect on eroding pre-zygotic barriers (eco-geographical isolation and phenology) than post-zygotic barriers, shifting the relative importance of these two classes of reproductive barriers from what is usually seen in naturally produced hybrids where pre-zygotic barriers are the largest contributors to reproductive isolation. Although the long-term fate of neo-hybrids is still to be determined, the massive impact of global change on the dynamics and distribution of biodiversity generates an unprecedented opportunity to study large numbers of unpredicted, and often replicated, hybridization 'experiments', allowing us to peer into the birth and death of evolutionary lineages.

Adaptive introgression as a resource for management and genetic conservation in a changing climate

Current rates of climate change require organisms to respond through migration, phenotypic plasticity, or genetic changes via adaptation. We focused on questions regarding species' and populations' ability to respond to climate change through adaptation. Specifically, the role adaptive introgression, movement of genetic material from the genome of 1 species into the genome of another through repeated interbreeding, may play in increasing species' ability to respond to a changing climate. Such interspecific gene flow may mediate extinction risk or consequences of limited adaptive potential that result from standing genetic variation and mutation alone, enabling a quicker demographic recovery in response to changing environments. Despite the near dismissal of the potential benefits of hybridization by conservation practitioners, we examined a number of case studies across different taxa that suggest gene flow between sympatric or parapatric sister species or within species that exhibit strong ecotypic differentiation may represent an underutilized management option to conserve evolutionary potential in a changing environment. This will be particularly true where advanced-generation hybrids exhibit adaptive traits outside the parental phenotypic range, a phenomenon known as transgressive segregation. The ideas presented in this essay are meant to provoke discussion regarding how we maintain evolutionary potential, the conservation value of natural hybrid zones, and consideration of their important role in adaptation to climate.

Differential effects of climate and species interactions on range limits at a hybrid zone: potential direct and indirect impacts of climate change

The relative contributions of climate versus interspecific interactions in shaping species distributions have important implications for closely related species at contact zones. When hybridization occurs within a contact zone, these factors regulate hybrid zone location and movement. While a hybrid zone's position may depend on both climate and interactions between the hybridizing species, little is known about how these factors interact to affect hybrid zone dynamics. Here, we utilize SDM (species distribution modeling) both to characterize the factors affecting the current location of a moving North American avian hybrid zone and to predict potential direct and indirect effects of climate change on future distributions. We focus on two passerine species that hybridize where their ranges meet, the Black‐capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee. Our contemporary climate models predict the occurrence of climatically suitable habitat extending beyond the hybrid zone for P. atricapillus only, suggesting that interspecific interactions primarily regulate this range boundary in P. atricapillus, while climatic factors regulate P. carolinensis. Year 2050 climate models predict a drastic northward shift in suitable habitat for P. carolinensis. Because of the greater importance of interspecific interactions for regulating the southern range limit of P. atricapillus, these climate‐mediated shifts in the distribution of P. carolinensis may indirectly lead to a range retraction in P. atricapillus. Together, our results highlight the ways climate change can both directly and indirectly affect species distributions and hybrid zone location. In addition, our study lends support to the longstanding hypothesis that abiotic factors regulate species' poleward range limits, while biotic factors shape equatorial range limits.

Wide prevalence of hybridization in two sympatric grasshopper species may be shaped by their relative abundances

BACKGROUND

Hybridization between species is of conservation concern as it might threaten the genetic integrity of species. Anthropogenic factors can alter hybridization dynamics by introducing new potentially hybridizing species or by diminishing barriers to hybridization. This may even affect sympatric species pairs through environmental change, which so far has received little attention. We studied hybridization prevalence and the underlying behavioral mechanisms in two sympatric grasshopper species, a rare specialist (Chorthippus montanus) and a common generalist (Chorthippus parallelus). We conducted a mate choice experiment with constant intraspecific density and varying heterospecific density, i.e. varying relative frequency of both species.

RESULTS

Mate choice was frequency-dependent in both species with a higher risk of cross-mating with increasing heterospecific frequency, while conspecific mating increased linearly with increasing conspecific density. This illustrates that reproductive barriers could be altered by environmental change, if the relative frequency of species pairs is affected. Moreover, we performed a microsatellite analysis to detect hybridization in twelve syntopic populations (and four allotopic populations). Hybrids were detected in nearly all syntopic populations with hybridization rates reaching up to 8.9 %. Genetic diversity increased for both species when hybrids were included in the data set, but only in the common species a positive correlation between hybridization rate and genetic diversity was detected.

CONCLUSION

Our study illustrates that the relative frequency of the two species strongly determines the effectiveness of reproductive barriers and that even the more choosy species (Ch. montanus) may face a higher risk of hybridization if population size decreases and its relative frequency becomes low compared to its sister species. The asymmetric mate preferences of both species may lead to quasi-unidirectional gene flow caused by unidirectional backcrossing. This might explain why genetic diversity increased only in the common species, but not in the rare one. Altogether, the hybridization rate was much higher than expected for a widely sympatric species pair.

Variable mating behaviors and the maintenance of tropical biodiversity

Current theoretical studies on mechanisms promoting species co-existence in diverse communities assume that species are fixed in their mating behavior. Each species is a discrete evolutionary unit, even though most empirical evidence indicates that inter-specific gene flow occurs in plant and animal groups. Here, in a data-driven meta-community model of species co-existence, we allow mating behavior to respond to local species composition and abundance. While individuals primarily out-cross, species maintain a diminished capacity for selfing and hybridization. Mate choice is treated as a variable behavior, which responds to intrinsic traits determining mate choice and the density and availability of sympatric inter-fertile individuals. When mate choice is strongly limited, even low survivorship of selfed offspring can prevent extinction of rare species. With increasing mate choice, low hybridization success rates maintain community level diversity for extended periods of time. In high diversity tropical tree communities, competition among sympatric congeneric species is negligible, because direct spatial proximity with close relatives is infrequent. Therefore, the genomic donorship presents little cost. By incorporating variable mating behavior into evolutionary models of diversification, we also discuss how participation in a syngameon may be selectively advantageous. We view this behavior as a genomic mutualism, where maintenance of genomic structure and diminished inter-fertility, allows each species in the syngameon to benefit from a greater effective population size during episodes of selective disadvantage. Rare species would play a particularly important role in these syngameons as they are more likely to produce heterospecific crosses and transgressive phenotypes. We propose that inter-specific gene flow can play a critical role by allowing genomic mutualists to avoid extinction and gain local adaptations.

Hybridization facilitates evolutionary rescue

The resilience of populations to rapid environmental degradation is a major concern for biodiversity conservation. When environments deteriorate to lethal levels, species must evolve to adapt to the new conditions to avoid extinction. Here, we test the hypothesis that evolutionary rescue may be enabled by hybridization, because hybridization increases genetic variability. Using experimental evolution, we show that interspecific hybrid populations of Saccharomyces yeast adapt to grow in more highly degraded environments than intraspecific and parental crosses, resulting in survival rates far exceeding those of their ancestors. We conclude that hybridization can increase evolutionary responsiveness and that taxa able to exchange genes with distant relatives may better survive rapid environmental change.

Hybridization in a warmer world

Climate change is profoundly affecting the evolutionary trajectory of individual species and ecological communities, in part through the creation of novel species assemblages. How climate change will influence competitive interactions has been an active area of research. Far less attention, however, has been given to altered reproductive interactions. Yet, reproductive interactions between formerly isolated species are inevitable as populations shift geographically and temporally as a result of climate change, potentially resulting in introgression, speciation, or even extinction. The susceptibility of hybridization rates to anthropogenic disturbance was first recognized in the 1930s. To date, work on anthropogenically mediated hybridization has focused primarily on either physical habitat disturbance or species invasion. Here, I review recent literature on hybridization to identify how ecological responses to climate change will increase the likelihood of hybridization via the dissolution of species barriers maintained by habitat, time, or behavior. Using this literature, I identify several cases where novel hybrid zones have recently formed, likely as a result of changing climate. Future research should focus on identifying areas and taxonomic groups where reproductive species interactions are most likely to be influenced by climate change. Furthermore, a better understanding of the evolutionary consequences of climate-mediated secondary contact is urgently needed. Paradoxically, hybridization is both a major conservation concern and an important source of novel genetic and phenotypic variation. Hybridization may therefore both contribute to increasing rates of extinction and stimulate the creation of novel phenotypes that will speed adaptation to novel climates. Predicting which result will occur following secondary contact will be an important contribution to conservation for many species.

Hybrid speciation in a marine mammal: the clymene dolphin (Stenella clymene)

Natural hybridization may result in the exchange of genetic material between divergent lineages and even the formation of new taxa. Many of the Neo-Darwinian architects argued that, particularly for animal clades, natural hybridization was maladaptive. Recent evidence, however, has falsified this hypothesis, instead indicating that this process may lead to increased biodiversity through the formation of new species. Although such cases of hybrid speciation have been described in plants, fish and insects, they are considered exceptionally rare in mammals. Here we present evidence for a marine mammal, Stenella clymene, arising through natural hybridization. We found phylogenetic discordance between mitochondrial and nuclear markers, which, coupled with a pattern of transgressive segregation seen in the morphometric variation of some characters, support a case of hybrid speciation. S. clymene is currently genetically differentiated from its putative parental species, Stenella coerueloalba and Stenella longisrostris, although low levels of introgressive hybridization may be occurring. Although non-reticulate forms of evolution, such as incomplete lineage sorting, could explain our genetic results, we consider that the genetic and morphological evidence taken together argue more convincingly towards a case of hybrid speciation. We anticipate that our study will bring attention to this important aspect of reticulate evolution in non-model mammal species. The study of speciation through hybridization is an excellent opportunity to understand the mechanisms leading to speciation in the context of gene flow.

Climate-Driven Reshuffling of Species and Genes: Potential Conservation Roles for Species Translocations and Recombinant Hybrid Genotypes

Comprising 50%-75% of the world's fauna, insects are a prominent part of biodiversity in communities and ecosystems globally. Biodiversity across all levels of biological classifications is fundamentally based on genetic diversity. However, the integration of genomics and phylogenetics into conservation management may not be as rapid as climate change. The genetics of hybrid introgression as a source of novel variation for ecological divergence and evolutionary speciation (and resilience) may generate adaptive potential and diversity fast enough to respond to locally-altered environmental conditions. Major plant and herbivore hybrid zones with associated communities deserve conservation consideration. This review addresses functional genetics across multi-trophic-level interactions including "invasive species" in various ecosystems as they may become disrupted in different ways by rapid climate change. "Invasive genes" (into new species and populations) need to be recognized for their positive creative potential and addressed in conservation programs. "Genetic rescue" via hybrid translocations may provide needed adaptive flexibility for rapid adaptation to environmental change. While concerns persist for some conservationists, this review emphasizes the positive aspects of hybrids and hybridization. Specific implications of natural genetic introgression are addressed with a few examples from butterflies, including transgressive phenotypes and climate-driven homoploid recombinant hybrid speciation. Some specific examples illustrate these points using the swallowtail butterflies (Papilionidae) with their long-term historical data base (phylogeographical diversity changes) and recent (3-decade) climate-driven temporal and genetic divergence in recombinant homoploid hybrids and relatively recent hybrid speciation of Papilio appalachiensis in North America. Climate-induced "reshuffling" (recombinations) of species composition, genotypes, and genomes may become increasingly ecologically and evolutionarily predictable, but future conservation management programs are more likely to remain constrained by human behavior than by lack of academic knowledge.

Evolutionary rescue beyond the models

Laboratory model systems and mathematical models have shed considerable light on the fundamental properties and processes of evolutionary rescue. But it remains to determine the extent to which these model-based findings can help biologists predict when evolution will fail or succeed in rescuing natural populations that are facing novel conditions that threaten their persistence. In this article, we present a prospectus for transferring our basic understanding of evolutionary rescue to wild and other non-laboratory populations. Current experimental and theoretical results emphasize how the interplay between inheritance processes and absolute fitness in changed environments drive population dynamics and determine prospects of extinction. We discuss the challenge of inferring these elements of the evolutionary rescue process in field and natural settings. Addressing this challenge will contribute to a more comprehensive understanding of population persistence that combines processes of evolutionary rescue with developmental and ecological mechanisms.

Natural Interactions between S. haematobium and S. guineensis in the Republic of Benin

Schistosomiasis is a parasitic disease which affects millions of people around the world, particularly in Africa. In this continent, different species are able to interbreed, like Schistosoma haematobium and Schistosoma guineensis, two schistosome species infecting humans. The Republic of Benin is known to harbor S. haematobium, but its geographical situation in between Nigeria, Mali, and Burkina Faso, where S. guineensis was found, raises the question about the possible presence of S. haematobium/S. guineensis hybrids in this country. We conducted morphological analyses on schistosome eggs and molecular analyses on schistosome larvae (high resolution melting (HRM) analysis and gene sequencing) in order to detect any natural interaction between these two species of schistosomes. The morphological results showed the presence of three egg morphotypes (S. haematobium, S. guineensis, and intermediate). Three genotypes were detected by ITS2 rDNA HRM analysis: S. haematobium, S. guineensis, and hybrid, and their percentages confirmed the results of the morphological analysis. However, sequencing of the CO1 mtDNA gene showed that all the samples from Benin belonged to S. haematobium. Our results provide the first evidence of introgression of S. guineensis genes in S. haematobium in Benin.

Families of transposable elements, population structure and the origin of species

Background

Eukaryotic genomes harbor diverse families of repetitive DNA derived from transposable elements (TEs) that are able to replicate and insert into genomic DNA. The biological role of TEs remains unclear, although they have profound mutagenic impact on eukaryotic genomes and the origin of repetitive families often correlates with speciation events. We present a new hypothesis to explain the observed correlations based on classical concepts of population genetics.

Presentation of the hypothesis

The main thesis presented in this paper is that the TE-derived repetitive families originate primarily by genetic drift in small populations derived mostly by subdivisions of large populations into subpopulations. We outline the potential impact of the emerging repetitive families on genetic diversification of different subpopulations, and discuss implications of such diversification for the origin of new species.

Testing the hypothesis

Several testable predictions of the hypothesis are examined. First, we focus on the prediction that the number of diverse families of TEs fixed in a representative genome of a particular species positively correlates with the cumulative number of subpopulations (demes) in the historical metapopulation from which the species has emerged. Furthermore, we present evidence indicating that human AluYa5 and AluYb8 families might have originated in separate proto-human subpopulations. We also revisit prior evidence linking the origin of repetitive families to mammalian phylogeny and present additional evidence linking repetitive families to speciation based on mammalian taxonomy. Finally, we discuss evidence that mammalian orders represented by the largest numbers of species may be subject to relatively recent population subdivisions and speciation events.

Implications of the hypothesis

The hypothesis implies that subdivision of a population into small subpopulations is the major step in the origin of new families of TEs as well as of new species. The origin of new subpopulations is likely to be driven by the availability of new biological niches, consistent with the hypothesis of punctuated equilibria. The hypothesis also has implications for the ongoing debate on the role of genetic drift in genome evolution.

Reviewers

This article was reviewed by Eugene Koonin, Juergen Brosius and I. King Jordan.