Using genotype simulations and Bayesian analyses to identify individuals of hybrid origin in Australian bass: lessons for fisheries management

Simulated genotypes, Bayesian analyses and molecular genetic data were used to detect individuals of hybrid origin and hybrid introgression between the Australian bass ( Macquaria novemaculeata ), a species extensively stocked in Australia, and estuary perch ( Macquaria colonorum ). Based on this analytical framework, 93% of the hybrids up to three generations later could be distinguished from the Australian bass. Individuals of hybrid origin were identified in all three rivers sampled. In addition, this study verified the fertility of hybrids between Australian bass and estuary perch as determined through genomic introgression. This study exemplifies an analytical procedure that has implications for identifying suitable individuals for use in breeding and restocking programmes for other species.     

Effects of barotrauma and mitigation methods on released Australian bass Macquaria novemaculeata

The effects of barotrauma on the short-term mortality and physical condition of Australian bass Macquaria novemaculeata were investigated after being: (1) conventionally angled and released during two tournaments in deep impoundments and (2) released untreated or subjected to venting or recompression during a manipulative experiment. All fish were released into two 20 m deep bathy-cages and monitored for 3 days. Of 238 M. novemaculeata angled during the tournaments, 43 (18·1%) had clinical signs of barotrauma or were vented and five of these later died (11·6% mortality). Catch histories varied significantly between both barotrauma and non-barotrauma fish and tournaments, but only hook ingestion significantly influenced mortality (P < 0·05). During the manipulative experiment, venting significantly influenced mortality (13·3%) compared to no treatment or recompression (no deaths). Magnetic resonance images and dissections of barotrauma fish indicated large variation among clinical signs. On the basis of these results, wherever possible M. novemaculeata suffering barotrauma should be immediately released with no treatment. Fish that are unable to resubmerge should be recompressed, while those held in live wells and released in shallow water should be vented.     

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata . Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics ( AMOVA ) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (Φ_ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata , culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.     

Genetic population structure of the catadromous Perciform: Macquaria novemaculeata (Percichthyidae)

Genetic population structure in the catadromous Australian bass Macquaria novemaculeata was investigated using samples from four locations spanning 600 km along the eastern Australian coastline. Both allozymes and mtDNA control region sequences were examined. Population subdivision estimates based on allozymes revealed low levels of population structuring ( G_st =0·043, P <0·05). However, mtDNA indicated moderate levels of geographic population structure ( G_st =0·146, P <0·0l). Phylogenetic analysis of mtDNA control region sequences (mean sequence divergence 1·9%) indicated little phylogeographic structuring. Results suggested that genotypic variation within each river population, while being affected primarily by genetic drift, was also prevented from more significant divergence by homogenizing levels of gene flow—synonymous with a one-dimensional stepping-stone model of population structure. The catadromous life history of Macquaria novemaculeata was considered to be influential on the pattern of population structure displayed. Results were compared to the few population genetic studies involving catadromous fishes, indicating that catadromy alone is unlikely to be a good predictor of population structure. A more comprehensive suite of biological characteristics than simple life-history traits must be considered fully to allow reliable predictive models of population structure to be formulated.     

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.     

Generalist niche, specialist strategy: the diet of an Australian percichthyid

Dietary analysis revealed that an impoundment population of Australian bass Macquaria novemaculeata holds a generalist niche, but one arising from persistent individual specialization and interindividual variation. This 'individual specialist' strategy appeared adaptive, but the strength of individual specialization was largely independent of variation in diet composition, except during blooms of Daphnia sp. Diet composition and dietary overlap showed only moderate ontogenetic variation, and niche breadth showed no relationship with ontogeny. Macquaria novemaculeata showed an asymmetric predator and prey size distribution, consistent with many aquatic predators, with positive relationships between fish size and average, maximum and minimum prey size. There was no asymmetry in the relative size-based niche breadths of individuals, however, which indicates that the niche is a fixed 'window' of relative prey sizes. The difference in the dietary niche and prey-size relationships of M. novemaculeata at the population and individual levels highlights the necessity of assessing the niche at both these levels.     

Genetic structure of a hybrid zone between two violets,Viola rossii Hemsl. and V. bissetii Maxim.: dominance of F1 individuals in a narrow contact range

The genetic composition of a hybrid zone can provide insight into the evolution of diversification in plants. We carried out morphological and amplified fragment length polymorphism analyses to investigate the genetic composition of a hybrid zone between two violets, Viola bissetii Hemsl. and Viola rossii Maxim. Our aim was to clarify the formation and maintenance of hybrids between these Viola species. We found that most hybrid individuals (V. bissetii × V. rossii) were of the F₁ generation, with a few of the F₂ generation. We found no backcrosses. The scarcity of post‐F₁ hybrids indicates that a species barrier is established between the parental species. The F₁‐dominated hybrid zone occupied only a narrow, intermediate ecotone between the parental habitats, suggesting that selection by environmental factors against hybrids may help to maintain the current conditions in this hybrid zone.     

Morphological variation in the catadromous Australian bass, from seven geographically distinct riverine drainages

The Australian bass Macquaria novemaculeata is a catadromous species restricted to coastal drainages of south-eastern Australia and recently has undergone reductions in population numbers. Morphometric variation among bass from seven distinct drainages was used to test for the presence of stock structuring. Males and females were treated separately. For both male and female bass, significant heterogeneity in morphology among sample locales was revealed by univariate statistics and discriminant function analysis, with morphological variation found to differ in a clinal pattern. The demonstration of population-specific morphological traits among bass from different river drainages may indicate that inter-populational movement is restricted and that each sample locale constitutes a separate stock of bass.     

Morphological Variation in Wild Marmosets (Callithrix penicillata and C. geoffroyi) and Their Hybrids

Evolutionary theory and observation predict wider phenotypic variation in hybrids than parental species. Emergent phenotypic novelty in hybrids may in turn drive new adaptations or speciation by breaking parental phenotypic constraints. Primate hybridization is often documented through genetic evidence, but knowledge about the primate hybrid phenotype remains limited due to a small number of available studies on hybrid primate morphology. Here, we examine pelage and morphometric variation in two Brazilian marmoset species (Callithrix penicillata and C. geoffroyi) and their hybrids. Hybrids were sampled in an anthropogenic hybrid zone in the municipality of Viçosa, Minas Gerais state, Brazil. We analyzed hybrid facial and body pelage color variation, and compared 13 morphometric measures between hybrids and parental species. Five different hybrid facial morphotypes were observed, varying from intermediate to parental-like. Hybrid facial morphotypes were biased towards C. penicillata, suggesting that the pelage of this species may be dominant to that of C. geoffroyi in this context, and indicating that mate preference, and therefore gene flow/introgression, may be biased towards C. penicillata within the hybrid zone. Hybrid morphometric features were on average intermediate to parental species traits, but transgressive hybrids were also observed, suggesting that morphometric variation for the studied traits is consistent with Rieseberg’s complementary allele model. Finally, we observed a decoupling of facial patterning and size/shape in hybrids, relative to parent phenotypes, suggesting that an important factor driving phenotypic novelty within the Viçosa marmoset hybrid zone might be the loosening of evolutionary constraints on phenotypic trait integration.     

Rare and asymmetrical hybridization of the endemic Barbus carpathicus with its widespread congener Barbus barbus

In endemic species that co-occur with widespread congeners, hybridization can lead to an influx of novel and beneficial genetic variation, but high rates of introgression may cause genetic swamping of the endemic species and have detrimental effects on its survival potential. This study examines hybridization between sympatric populations of the Carpathian barbel Barbus carpathicus , a recently discovered cryptic species with a restricted range, and the widespread common barbel Barbus barbus . Based on six diagnostic allozyme loci, a microsatellite locus and mtDNA, hybrids were found to be present at multiple localities within the Vistula River drainage (Baltic Sea) as well as in the Tisza River system of the Danube River drainage (Black Sea). However, the numbers of hybrids were very low; four individuals of 230 fish sampled from the Vistula drainage. Bayesian assessment of their nuclear genotypes suggested that two hybrids in the Vistula drainage and nine in the Tisza system were F₁ generation, and one in the Vistula drainage and one in the Tisza system were backcrosses (BC) to B. barbus , while no F₂ or BC to B. carpathicus were detected. No hybrid carried B. carpathicus mtDNA and cytonuclear linkage disequilibria showed significant positive associations between hybrid genotypes and B. barbus mtDNA, suggesting unidirectionality in the interspecific mating with a disproportionate contribution of B. barbus mothers. Despite geographically broad occurrence of hybrids, these data provide evidence of strong constraints on hybridization in the native breeding habitats and the lack of introgression towards B. carpathicus .     

Behavioral asymmetries in a moving hybrid zone

Three narrow hybrid zones exist between hermit and Townsend'swarblers in the Pacific Northwest. Character transition curvessuggest that these zones are moving and that Townsend's warblershave a selective advantage over hermit warblers. This studycompares year-to-year return rates, male persistence on territories,pairing success, pairing patterns, and territory quality of hermitand Townsend's warblers and their hybrids in the WashingtonCascades hybrid zone. There was no difference in the year-to-yearreturn rate between the parental species. Townsend's males weremore successful in maintaining territories and attracting matesthan hermit males. Among mated pairs there were few hermit malescompared to females, independently supporting the inferiorityof hermit males in competition for territories or female mate choicefor Townsend's-like males. I found no difference in the qualityof hermit and Townsend's territories; however, in poor habitatsTownsend's males were more successful at attracting mates, suggestingfemale preference for Townsend's-like males. In high-qualityhabitats, there was no difference in pairing success betweenthe parental species. The fitness of hybrids relative to parentalsaffects the width and movement of the zone. Hybrids were intermediatein their ability to maintain territories and to attract mates, whichshould increase the width of the zone and accelerate its movement.Fewer hybrid males returned to from one year to the next, andamong mated pairs there were few hybrid females relative tomales, suggesting hybrid inferiority, which should narrow thehybrid zone and slow its movement.     

Genotype‐environment associations support a mosaic hybrid zone between two tidal marsh birds

Local environmental features can shape hybrid zone dynamics when hybrids are bounded by ecotones or when patchily distributed habitat types lead to a corresponding mosaic of genotypes. We investigated the role of marsh‐level characteristics in shaping a hybrid zone between two recently diverged avian taxa – Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) sparrows. These species occupy different niches where allopatric, with caudacutus restricted to coastal marshes and nelsoni found in a broader array of wetland and grassland habitats and co‐occur in tidal marshes in sympatry. We determined the influence of habitat types on the distribution of pure and hybrid sparrows and assessed the degree of overlap in the ecological niche of each taxon. To do this, we sampled and genotyped 305 sparrows from 34 marshes across the hybrid zone and from adjacent regions. We used linear regression to test for associations between marsh characteristics and the distribution of pure and admixed sparrows. We found a positive correlation between genotype and environmental variables with a patchy distribution of genotypes and habitats across the hybrid zone. Ecological niche models suggest that the hybrid niche was more similar to that of A. nelsoni and habitat suitability was influenced strongly by distance from coastline. Our results support a mosaic model of hybrid zone maintenance, suggesting a role for local environmental features in shaping the distribution and frequency of pure species and hybrids across space.     

Plant hybrid zones as centers of biodiversity: the herbivore community of two endemic Tasmanian eucalypts

We found the hybrid zone between Eucalyptus amygdalina and Eucalyptus risdonii to be a center of insect and fungal species richness and abundance. Of 40 taxa examined, 73% were significantly more abundant in the hybrid zone than in pure zones, 25% showed on significant differences, and 2% were most abundant on a pure host species. The average hybrid tree supported 53% more insect and fungal species, and relative abundances were, on average, 4 times greater on hybrids than on either eucalypt species growing in pure stands. Hybrids may act as refugia for rare species: 5 of 40 species were largely restricted to the hybrid zone. Also, 50% of the species coexisted only in the hybrid zone, making for mique species assemblages. Although hybrids support more species and greater abundances, all hybrids are not equal: 68% of the 40 taxa examined were significantly more abundant on one hybrid phenotype than another. While herbivore concentrations on F1 type intermediates were rare, concentrations were common on phenotypes resembling backcrosses either to E. amygdalina or E. risdonii. For specialist herbivores, the hybrid phenotype most heavily utilized appears to be determined by its phenotypic affinity to its host species. Generalists exhibit an overall greater abundance on hybrids, but are less likely to utilize one hybrid phenotype over another. Mechanistic explanations for these distributions are numerous and probably species specific, but are likely to include: increased genetic susceptibility of hybrids due to hybrid breakdown; increased stress in the hybrid zone resulting in greater plant susceptibility; and a greater diversity of resources in the hybrid zone which could support more species. Seed capsule production by hybrids and their parental species is negatively correlated with herbivory. However, it is difficult to determine whether herbivores cause this pattern as hybrids may have inherently lower sexual reproduction. Laws enacted to protect rare and endangered species do not include hybrids. We argue that a re-examination of our current hybrid policy is warranted. Plant hybrid zones are centers of plant evolution and speciation, sources of economically important plants and potential biocontrol agents, and, as our study suggests, also provide essential habitats for phytophagous communities.     

Genotype-by-environment interaction and the fitness of plant hybrids in the wild

Natural hybrid zones between related species illustrate processes that contribute to genetic differentiation and species formation. A common viewpoint is that hybrids are essentially unfit, but they exist in a stable tension zone where selection against them is balanced by gene flow between the parent species. An alternative idea is that selection depends on the environment, for example, by favoring opposite traits in the two parental habitats or favoring hybrids within a bounded region. To determine whether selection of hybrids is environment dependent, we crossed plants of naturally hybridizing Ipomopsis aggregata and I. tenuituba in the Colorado Rocky Mountains and reciprocally planted the seed offspring into a suite of natural environments across the hybrid zone. All types of crosses produced similar numbers and weights of seeds. However, survival of the offspring after 5 years differed markedly among cross types. On average, the F1 hybrids had survival and growth rates as high as the average for their parents. But hybrid survival depended strongly on the direction of a cross, that is, on which species served as the maternal parent. This fitness difference between reciprocal hybrids appeared only in the parental environments, suggesting cytonuclear gene interactions that are environment specific. These results indicate that complex genotype-by-environment interactions can contribute to the evolutionary outcome of hybridization.     

Identification of hemiclonal reproduction in three species of Hexagrammos marine reef fishes

Natural hybrids between the boreal species Hexagrammos octogrammus and two temperate species Hexagrammos agrammus and Hexagrammos otakii were observed frequently in southern Hokkaido, Japan. Previous studies revealed that H. octogrammus is a maternal ancestor of both hybrids; the hybrids are all fertile females and they frequently breed with paternal species. Although such rampant hybridization occurs, species boundaries have been maintained in the hybrid zone. Possible explanations for the absence of introgressions, despite the frequent backcrossing, might include clonal reproduction: parthenogenesis, gynogenesis and hybridogenesis. The natural hybrids produced haploid eggs that contained only the H. octogrammus genome (maternal ancestor) with discarded paternal genome and generated F₁‐hybrid type offspring by fertilization with the haploid sperm of H. agrammus or H. otakii (paternal ancestor). This reproductive mode was found in an artificial backcross hybrid between the natural hybrid and a male of the paternal ancestor. These findings indicate that the natural hybrids adopt hybridogenesis with high possibility and produce successive generations through hybridogenesis by backcrossing with the paternal ancestor. These hybrids of Hexagrammos represent the first hybridogenetic system found from marine fishes that widely inhabit the North Pacific Ocean. In contrast with other hybridogenetic systems, these Hexagrammos hybrids coexist with all three ancestral species in the hybrid zone. The coexistence mechanism is also discussed.     

Distribution of Phoxinus eos,Phoxinus neogaeus,and Their Asexually-Reproducing Hybrids (Pisces: Cyprinidae) in Algonquin Provincial Park,Ontario

Hybrid Phoxinus are one of the few asexually reproducing vertebrates species. The distribution of hybrid Phoxinus among lakes in Algonquin Park, Ontario, was evaluated relative to the distribution of parental species and relative to physiochemical lake characteristics. No association between the distribution of hybrids and the distribution of parental species was found, suggesting that the hybrids can successfully coexist with either parental species. In addition, we found no association between hybrid distribution and the physiochemical characteristics of lakes, suggesting that the hybrids are generalists with respect to the ecological niches available in Algonquin Park. There was a difference between the physiochemical characteristics of lakes with and without the parental species P. neogaeus. The lakes containing P. neogaeus were lower elevation than the lakes containing the other parental species, P. eos. The difference in distribution between the parental species may therefore be due to different dispersal abilities, to later arrival following post-glacial dispersal, or to differences in ecology. These results suggest that asexual reproduction is a successful strategy for hybrid Phoxinus in Algonquin Park because these sperm-dependent asexual hybrids are able to survive and persist regardless of which parental species is present, and regardless of the physiochemical characteristics of their habitat.     

Characterization of a contemporaneous hybrid zone between two darter species (Etheostoma bison and E. caeruleum) in the Buffalo River System

Hybrid zones have long intrigued evolutionary biologists and provide a natural laboratory to explore the evolution of reproductive isolation (speciation). Molecular characterization of hybrid zone dynamics can provide insight into the strength of reproductive isolation as well as the underlying evolutionary processes shaping gene flow. Approximately one-third of darter species naturally hybridize making this species-rich North American freshwater teleost fish clade an ideal system to investigate the extent and direction of hybridization. The objective of this study was to use diagnostic microsatellite markers to calculate genetic hybrid index scores of two syntopic, but distantly related darter species, Etheostoma bison and Etheostoma caeruleum. A combination of hybrid index scores, assignment tests, and mitochondrial haplotype profiles uncovered mixed ancestry in approximately 6 % of sampled adult individuals, supporting contemporaneous hybridization that was previously undocumented in E. bison. Moreover, hybrids were not limited to the F₁ generation, but encompassed the entire suite of hybrid categories (F₁, F₂ and backcross hybrids). The low number of hybrids assigned to each hybrid category represents a bimodal hybrid zone, suggesting reproductive isolation is strong (but incomplete) and also advocates for the ability of hybrids to produce second-generation hybrids and backcross into both parental species, mediating introgression across species boundaries. To this end, cytonuclear profiles of the sampled parental species and hybrids were consistent with bidirectional gene flow, although there was an overall trend of asymmetric hybridization between E. caeruleum females and E. bison males. The spatiotemporal variation in hybridization rates and resulting cytonuclear patterns expanded on in this study provide a comparative genetic framework on which future studies can begin to elucidate the underlying processes that not only generate a mosaic hybrid zone, but maintain the distinctness of species in the face of gene flow.     

Near absence of hybridization between sauger and introduced walleye despite massive releases

We analyzed 11 microsatellite loci to determine the genetic population structure of saugers and to describe the amount and pattern of hybridization with widely introduced walleyes in the upper Missouri River drainage. We detected significant genetic differentiation among saugers spawning upstream and downstream of the confluence of the Bighorn and Yellowstone Rivers. Samples from upstream of the confluence had significantly lower heterozygosity and allelic richness. We suspect this reflects isolation at the periphery of the species’ range and possibly genetic drift resulting from recent population contractions due to dams, diversions, and water development. We detected only eighteen hybrids out of 925 individuals analyzed. Hybridization appeared recent, as nearly 50% of the hybrids showed significant evidence for having a non-hybrid ancestor within two generations. All but one hybrid were detected in the Yellowstone River drainage, despite a substantially higher rate of walleye stocking in the Missouri River drainage, suggesting conditions in the Yellowstone may be more conducive to hybridization. Rarity of hybridization is unexpected, given both massive walleye releases and previous findings of more frequent hybridization in the study area. Introgression of walleye genes into native saugers does not appear to be an immediate threat.     

Genetic structure of hybrid zones between Silene latifolia and Silene dioica (Caryophyllaceae): evidence for introgressive hybridization

Natural hybrid zones provide a valuable tool to study introgressive hybridization, because they can contain a wide variety of genotypes that result from many generations of recombination. Here we used molecular markers and morphological variation to describe the structure of two natural hybrid zones between Silene latifolia and Silene dioica in the Swiss Alps. Populations in both hybrid zones consisted of few intermediate hybrids and were dominated by backcross hybrids. The latter were also found in the parental populations at the margins of the hybrid zones. Out of 209 amplified fragment length polymorphism (AFLP) markers scored in 390 individuals, only 7 (3.3%) were species specific. These results indicate that introgression between S. dioica and S. latifolia is extensive, and that hybrid zones act as bridges to gene flow between these two species. Analysis of linkage disequilibrium identified few populations in which hybridization is ongoing, whereas in most populations linkage disequilibrium has eroded. Where hybridization is ongoing, strong changes in species-specific marker frequencies and morphological traits were observed. Plastid introgression into the hybrid zone was found to be bidirectional, but only the S. latifolia plastid haplotype was found in a nuclear S. dioica background. This unidirectional plastid introgression from S. latifolia into S. dioica is most likely due to pollen-flow from S. dioica onto S. latifolia, and results in plastid capture. Comparisons between the molecular and the morphological hybrid indices revealed that morphology in this study system is useful for identifying hybrids, but not for detailed analysis of hybrid zone structure.