Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennant i) in California ...occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatellite loci from 275 contemporary and 21 historical fisher samples (1880–1920) to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European) bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19 th and early 20 th centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement.
Many empirical studies estimating effective population size apply the temporal method that provides an estimate of the variance effective size through the amount of temporal allele frequency change ...under the assumption that the study population is completely isolated. This assumption is frequently violated, and the magnitude of the resulting bias is generally unknown. We studied how gene flow affects estimates of effective size obtained by the temporal method when sampling from a population system and provide analytical expressions for the expected estimate under an island model of migration. We show that the temporal method tends to systematically underestimate both local and global effective size when populations are connected by gene flow, and the bias is sometimes dramatic. The problem is particularly likely to occur when sampling from a subdivided population where high levels of gene flow obscure identification of subpopulation boundaries. In such situations, sampling in a manner that prevents biased estimates can be difficult. This phenomenon might partially explain the frequently reported unexpectedly low effective population sizes of marine populations that have raised concern regarding the genetic vulnerability of even exceptionally large populations.
We analyzed 13 microsatellite loci to estimate gene flow among westslope cutthroat trout, Oncorhynchus clarkii lewisi, populations and determine the invasion pattern of hybrids between native O. c. ...lewisi and introduced rainbow trout, Oncorhynchus mykiss, in streams of the upper Flathead River system, Montana (USA) and British Columbia (Canada). Fourteen of 31 sites lacked evidence of O. mykiss introgression, and gene flow among these nonhybridized O. c. lewisi populations was low, as indicated by significant allele frequency divergence among populations (θ
ST
= 0.076, ρ
ST
= 0.094, P < 0.001). Among hybridized sites, O. mykiss admixture declined with upstream distance from a site containing a hybrid swarm with a predominant (92%) O. mykiss genetic contribution. The spatial distribution of hybrid genotypes at seven diagnostic microsatellite loci revealed that O. mykiss invasion is facilitated by both long distance dispersal from this hybrid swarm and stepping-stone dispersal between hybridized populations. This study provides an example of how increased straying rates in the invasive taxon can contribute to the spread of extinction by hybridization and suggests that eradicating sources of introgression may be a useful conservation strategy for protecting species threatened with genomic extinction.
A great deal of effort is spent protecting geographically peripheral populations of widespread species. We consider under what conditions it is appropriate to expend resources to protect these ...populations. The conservation value of peripheral populations depends upon their genetic divergence from other conspecific populations. Peripheral populations are expected to diverge from central populations as a result of the interwoven effects of isolation, genetic drift, and natural selection. Available empirical evidence suggests that peripheral populations are often genetically and morphologically divergent from central populations. The long-term conservation of species is likely to depend upon the protection of genetically distinct populations. In addition, peripheral populations are potentially important sites of future speciation events. Under some circumstances, conservation of peripheral populations may be beneficial to the protection of the evolutionary process and the environmental systems that are likely to generate future evolutionary diversity.
Genetic connectivity results from the dispersal and reproduction of individuals across landscapes. Mammalian populations frequently exhibit sex‐biased dispersal, but this factor has rarely been ...addressed in individual‐based landscape genetics research. In this study, we evaluate the effects of sex‐biased dispersal and landscape heterogeneity on genetic connectivity in a small and isolated population of fisher (Pekania pennanti). We genotyped 247 fisher samples collected across the southern Sierra Nevada Mountains of California. We tested for genetic evidence of sex‐biased dispersal using sex‐specific population structure and spatial autocorrelation analyses, and sex‐biased dispersal tests of the assignment index, FST, and FIS. We developed resistance surfaces for eight landscape features hypothesized to affect gene flow and optimized each resistance surface independently by sex. Using multiple regression of distance matrices and an information‐theoretic model selection approach, we fit models of genetic distance to landscape resistance distance separately by sex and geographic region. We found genetic evidence of sex‐biased dispersal with significant differences in FST, FIS, and spatial autocorrelation between sexes. Optimal resistance values differed by sex, and model variables, fit, and parameter estimates varied substantially both between sexes and between geographic regions. We found a stronger relationship between landscape features and genetic distance for females, the philopatric sex, than the more widely dispersing males. Our results show that landscape features influencing gene flow differed by both sex and regional heterogeneity. Conducting analyses by sex and by region allowed for the identification of landscape genetics relationships not discernible when analyzed together. Our results show that failing to account for these factors can confound results and obscure relationships between landscape features and gene flow.
Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary ...throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.
In the face of continuing habitat fragmentation and isolation, the optimal level of connectivity between populations has become a central issue in conservation biology. A common rule of thumb holds ...that one migrant per generation into a subpopulation is sufficient to minimize the loss of polymorphism and heterozygosity within subpopulations while allowing for divergence in allele frequencies among subpopulations. The one-migrant-per-generation rule is based on numerous simplifying assumptions that may not hold in natural populations. We examine the conceptual and theoretical basis of the rule and consider both genetic and nongenetic factors that influence the desired level of connectivity among subpopulations. We conclude that one migrant per generation is a desirable minimum, but it may be inadequate for many natural populations. We suggest that a minimum of 1 and a maximum of 10 migrants per generation would be an appropriate general rule of thumb for genetic purposes, bearing in mind that factors other than genetics may further influence the ideal level of connectivity.
We present a conceptual framework for choosing native plant material to be used in restoration projects on the basis of ecological genetics. We evaluate both the likelihood of rapid establishment of ...plants and the probability of long‐term persistence of restored or later successional communities. In addition, we consider the possible harmful effects of restoration projects on nearby ecosystems and their native resident populations. Two attributes of the site to be restored play an important role in determining which genetic source will be most appropriate: (1) degree of disturbance and (2) size of the disturbance. Local plants or plants from environments that “match” the habitat to be restored are best suited to restore sites where degree of disturbance has been low. Hybrids or “mixtures” of genotypes from different sources may provide the best strategy for restoring highly disturbed sites to which local plants are not adapted. Cultivars that have been modified by intentional or inadvertent selection have serious drawbacks. Nevertheless, cultivars may be appropriate when the goal is rapid recovery of small sites that are highly disturbed.
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