The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.

Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h(2) ) in a suite of measurements that define corallite architecture, and could partition additive and nonadditive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h(2) estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h(2) were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.

Estimation of mating systems in Short and Tall ecomorphs of the coral Favia fragum.

We used 15 microsatellite markers to estimate the selfing rate (s), outcrossing rate (t(O) ) and hybridization between partially sympatric ecomorphs (t(H) ) of the coral Favia fragum. Genotyping of progeny arrays revealed complete self-fertilization in the Tall ecomorph and low outcrossing (t(O) + t(H) < 1%) in the Short ecomorph. Further, all larvae could be assigned with high probability to the same population as their parental dam, indicating no hybridization between ecomorphs (t(H) = 0). Despite low ecological estimates of outcrossing, Q values from highly structured adult populations indicated that 9% of the adult samples were the products of outcrossing, and an additional 11% were hybrids. Reproductive isolation appears to have a strong geographical component, as we did not detect hybrids at a second site where the two ecomorphs were distributed in complete microallopatry. Adult estimates of gene flow within ecomorphs may be positively biased by ecomorph-specific patterns of inbreeding depression, but cryptic gene flow between ecomorphs is most likely explained by undetected outcrossing and the fact that hybrid lineages persist after repeated generations of self-fertilization. Our microsatellite data show that phenotypic differences between ecomorphs are maintained in sympatry despite evidence for hybridization.

Fifteen new microsatellite markers for the reef coral Favia fragum and a new Symbiodinium microsatellite.

Sixteen new microsatellite loci were isolated from the Tropical Atlantic coral Favia fragum. One locus amplified with pure zooxanthellae DNA template, revealing a symbiont (Symbiodinium) origin. We genotyped 48 short and 45 tall ecomorphs of F. fragum from the Bocas del Toro region of Panama. For 15 host loci, allelic diversity ranged from three to 23 with an average of 5.75 alleles per locus. Analysis of genotypic data revealed significant heterozygote deficits at all loci and linkage disequilibrium between loci, as did a previous study of the two ecomorphs with allozymes. We found evidence for null alleles at four of the host loci in the form of locus-specific polymerase chain reaction failure; however, extreme inbreeding via self-fertilization is likely to explain the large departures from Hardy-Weinberg equilibrium.

High genetic diversity and no inbreeding in the endangered copper redhorse, Moxostoma hubbsi (Catostomidae, Pisces): the positive sides of a long generation time.

The evolutionary potential of a species is determined by its genetic diversity. Thus, management plans should integrate genetic concerns into active conservation efforts. The copper redhorse (Moxostoma hubbsi) is an endangered species, with an endemic distribution limited to the Richelieu River and a short section of the St Lawrence River in Quebec, Canada. The population, gradually fragmented since 1849, is characterized by a decline in population size and a lack of recruitment. A total of 269 samples were collected between 1984 and 2004 and genotyped using 22 microsatellite loci, which indicated that these fish comprise a single population, with a global F(ST) value of only 0.0038. Despite a small census size ( approximately 500), a high degree of genetic diversity was observed compared to common values for freshwater fishes (average number of 12.5 alleles/locus and average HO of 0.77 +/- 0.08). No difference was observed between expected and observed pairwise values of relatedness (r(xy): -0.00013 +/- 0.11737), suggesting an outbred population. Long-term Ne was estimated at 4476 whereas contemporary Ne values ranged from 107 to 568, suggesting a pronounced yet gradual demographic decline of the population, as no bottleneck could be detected for the recent past. By means of simulations, we estimated Ne would need to remain at more than approximately 400 to retain 90% of the genetic diversity over 100 years. Overall, these observations corroborate other recent empirical studies confirming that long generation times may act as a buffering effect contributing to a reduction in the pace of genetic diversity erosion in threatened species.

Consequences of unequal population size, asymmetric gene flow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis).

Unravelling relationships between dispersal and population structure requires considering the impacts of assumption violations of indirect gene flow models in a given system. We combined temporal, individual and coalescent-based analyses of microsatellite DNA variation to explore the general hypothesis that unequal effective population size (Ne), asymmetric gene flow (m) and nonrandom (sex-biased) individual dispersal had an important effect on spatiotemporal population structuring in lake-dwelling brook charr (Salvelinus fontinalis). This integrative examination shed light on the dichotomous structuring observed between an outlet and three tributary-spawning populations and their potential for adaptive divergence. It revealed further that finer tributary population structuring incongruent with drainage structure has been shaped by asymmetric m from one population with a large Ne towards two populations of smaller Ne. Gene flow among the tributaries was also mediated mainly by male-biased dispersal. However, longer distance dispersal from tributaries to the outflow was female-biased. Spatially dependent sex-biased dispersal may have contributed therefore to gene flow at different levels of population structuring. Our results demonstrate how dispersal and population structure may interrelate to produce spatial variation in intraspecific diversity, and are therefore relevant for conservation programmes seeking to define conservation units or predict recolonization rates of extirpated populations.