Genetic assessment of the effects of streamscape succession on coho salmon Oncorhynchus kisutch colonization in recently deglaciated streams.

Measures of genetic diversity within and among populations and historical geomorphological data on stream landscapes were used in model simulations based on approximate Bayesian computation (ABC) to examine hypotheses of the relative importance of stream features (geomorphology and age) associated with colonization events and gene flow for coho salmon Oncorhynchus kisutch breeding in recently deglaciated streams (50-240 years b.p.) in Glacier Bay National Park (GBNP), Alaska. Population estimates of genetic diversity including heterozygosity and allelic richness declined significantly and monotonically from the oldest and largest to youngest and smallest GBNP streams. Interpopulation variance in allele frequency increased with increasing distance between streams (r = 0·435, P < 0·01) and was inversely related to stream age (r = -0·281, P < 0·01). The most supported model of colonization involved ongoing or recent (<10 generations before sampling) colonization originating from large populations outside Glacier Bay proper into all other GBNP streams sampled. Results here show that sustained gene flow from large source populations is important to recently established O. kisutch metapopulations. Studies that document how genetic and demographic characteristics of newly founded populations vary associated with successional changes in stream habitat are of particular importance to and have significant implications for, restoration of declining or repatriation of extirpated populations in other regions of the species' native range.

Colonizing the world in spite of reduced MHC variation.

The major histocompatibility complex (MHC), which harbours the most polymorphic vertebrate genes, plays a critical role in the host-pathogen coevolutionary arms race. However, the extent to which MHC diversity determines disease susceptibility and long-term persistence of populations is currently under debate, as recent studies have demonstrated that low MHC variability does not necessarily hamper population viability. However, these studies typically assayed small and decimated populations in species with restricted distribution, thereby making inferences about the evolutionary potential of these populations difficult. Here, we show that MHC impoverishment has not constrained the ecological radiation and flourishing of falcons (Aves: Falconidae) worldwide. We found two remarkably different patterns of MHC variation within the genus Falco. Whereas MHC variation in kestrels (the basal group within the genus) is very high, falcons exhibit ancestrally low intra- and interspecific MHC variability. This pattern is not due to the inadvertent survey of paralogous genes or pseudogenes. Further, patterns of variation in mitochondrial or other nuclear genes do not indicate a generalized low level of genome-wide variability among falcons. Although a relative contribution of genetic drift cannot be completely ruled out, we propose the falcons went through an evolutionary transition, driven and maintained by natural selection, from primarily highly variable towards low polymorphic and slow-evolving MHC genes with a very specific immune function. This study highlights that the importance of MHC diversity cannot be generalized among vertebrates, and hints at the evolution of compensatory immune mechanisms in falcons to cope with emerging and continuously evolving pathogens.

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska.

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Microsatellite analyses of the trout of northwest Mexico.

The trout of northwest Mexico represent an undescribed group of fish considered part of the Oncorhynchus mykiss (Pacific trout) complex of species and subspecies. Recent genetic studies have shown these fish to have important genetic diversity and a unique evolutionary history when compared to coastal rainbow trout. Increased levels of allelic diversity have been found in this species at the southern extent of its range. In this study we describe the trout in the Sierra Madre Occidental from the rios Yaqui, Mayo, Casas Grandes and de Bavispe, and their relationship to the more southern distribution of Mexican golden trout (O. chrysogaster) using 11 microsatellite loci. Microsatellite allelic diversity in Mexican trout was high with a mean of 6.6 alleles/locus, average heterozygosity = 0.35, and a mean Fst = 0.43 for all loci combined. Microsatellite data were congruent with previously published mtDNA results showing unique panmictic population structure in the Rio Yaqui trout that differs from Pacific coastal trout and Mexican golden trout. These data also add support for the theory of headwaters transfer of trout across the Continental Divide from tributaries of the Rio de Bavispe into the Rio Casas Grandes. Rio Mayo trout share a close genetic relationship to trout in Rio Yaqui, but sample sizes from the Rio Mayo prevent significant comparisons in this study. Microsatellite analyses show significant allelic frequency differences between Rio Yaqui trout and O. chrysogaster in Sinaloa and Durango Mexico, adding further support for a unique evolutionary status for this group of northwestern Mexican trout.

Inheritance of nuclear DNA markers in gynogenetic haploid pink salmon.

We describe the inheritance of 460 PCR-based loci in the polyploid-derived pink salmon (Oncorhynchus gorbuscha) genome using gynogenetic haploid embryos. We detected a length polymorphism in a growth hormone gene (GH-2) intron that is caused by an 81 bp insertion homologous to the 3' end of the salmonid short interspersed repetitive element (SINE) SmaI. Such insertion polymorphisms within species bring into question the use of SINEs as phylogenetic markers. We confirmed that a microsatellite locus encodes a PCR-null allele that is responsible for an apparent deficit of heterozygotes in a population sample from Prince William Sound. Another set of microsatellite primers amplified alleles of the same molecular weight from both loci of a duplicated pair. In our analysis of several PCR-based multilocus techniques, we failed to detect evidence of comigrating fragments produced by duplicated loci. Segregation analysis of PCR-based markers using gynogenetic haploid embryos ensures that the interpretation of molecular variation is not complicated by heterozygosity, diploidy, or gene duplication. We urge investigators to test the inheritance of polymorphisms in salmonids prior to using them to measure genetic variation.