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1.
The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.  相似文献   

2.
Range expansion and contraction has occurred in the history of most species and can seriously impact patterns of genetic diversity. Historical data about range change are rare and generally appropriate for studies at large scales, whereas the individual pollen and seed dispersal events that form the basis of geneflow and colonization generally occur at a local scale. In this study, we investigated range change in Fagus sylvatica on Mont Ventoux, France, using historical data from 1838 to the present and approximate Bayesian computation (ABC) analyses of genetic data. From the historical data, we identified a population minimum in 1845 and located remnant populations at least 200 years old. The ABC analysis selected a demographic scenario with three populations, corresponding to two remnant populations and one area of recent expansion. It also identified expansion from a smaller ancestral population but did not find that this expansion followed a population bottleneck, as suggested by the historical data. Despite a strong support to the selected scenario for our data set, the ABC approach showed a low power to discriminate among scenarios on average and a low ability to accurately estimate effective population sizes and divergence dates, probably due to the temporal scale of the study. This study provides an unusual opportunity to test ABC analysis in a system with a well-documented demographic history and identify discrepancies between the results of historical, classical population genetic and ABC analyses. The results also provide valuable insights into genetic processes at work at a fine spatial and temporal scale in range change and colonization.  相似文献   

3.
Low levels of genetic variation are thought to contribute significantly to the higher extinction rates of endemic island populations compared to their mainland counterparts. We used six microsatellite loci to compare the genetic structure of the endangered silver rice rat (Oryzomys argentatus) population in Saddlebunch Key, Florida to the mainland population of the closely related marsh rice rat (Oryzomys palustris natator) in Everglades National Park. Allelic richness and gene diversity are significantly lower in Saddlebunch Key than in the larger mainland population, and the two populations are significantly differentiated as measured by both F-statistics and Bayesian clustering methods. These findings support the classification of the Keys population as a “distinct vertebrate population” by the U.S. Fish and Wildlife Service. Current gene diversity (H E) is higher than expected under mutation-drift equilibrium in Saddlebunch Key, indicating a genetic bottleneck. The Keys population also exhibits a mode shift in its allele frequency distribution which suggests a very recent bottleneck has occurred and is consistent with reports of recent population declines. Although habitat loss and exotic species pose a more immediate and serious threat to silver rice rats, the continued loss of genetic variation may contribute to their long-term extinction risk due to inbreeding or by lowering the population’s ability to adapt to future environmental changes. The protection of habitat and the removal of introduced predators and competitors may help increase the population size of silver rice rats and lower their risk of extinction, both from a demographic and a genetic perspective.  相似文献   

4.
The “Weak Garden of Eden” model for the origin and dispersal of modern humans (Harpendinget al., 1993) posits that modern humans spread into separate regions from a restricted source, around 100 ka (thousand years ago), then passed through population bottlenecks. Around 50 ka, dramatic growth occurred within dispersed populations that were genetically isolated from each other. Population growth began earliest in Africa and later in Eurasia and is hypothesized to have been caused by the invention and spread of a more efficient Later Stone Age/Upper Paleolithic technology, which developed in equatorial Africa.Climatic and geological evidence suggest an alternative hypothesis for Late Pleistocene population bottlenecks and releases. The last glacial period was preceded by one thousand years of the coldest temperatures of the Later Pleistocene (∼71–70 ka), apparently caused by the eruption of Toba, Sumatra. Toba was the largest known explosive eruption of the Quaternary. Toba's volcanic winter could have decimated most modern human populations, especially outside of isolated tropical refugia. Release from the bottleneck could have occurred either at the end of this hypercold phase, or 10,000 years later, at the transition from cold oxygen isotope stage 4 to warmer stage 3. The largest populations surviving through the bottleneck should have been found in the largest tropical refugia, and thus in equatorial Africa. High genetic diversity in modern Africans may thus reflect a less severe bottleneck rather than earlier population growth.Volcanic winter may have reduced populations to levels low enough for founder effects, genetic drift and local adaptations to produce rapid population differentiation. If Toba caused the bottlenecks, then modern human races may have differentiated abruptly, only 70 thousand years ago.  相似文献   

5.
The increasing abundance of human genetic data has shown that the geographical patterns of worldwide genetic diversity are best explained by human expansion out of Africa. This expansion is modelled well by prolonged migration from a single origin in Africa with multiple subsequent serial founding events. We discuss a new simulation model for the serial founder effect out of Africa and compare it with results from previous studies. Unlike previous models, we distinguish colonization events from the continued exchange of people between occupied territories as a result of mating. We conduct a search through parameter space to estimate the range of parameter values that best explain key statistics from published data on worldwide variation in microsatellites. The range of parameters we use is chosen to be compatible with an out-of-Africa migration at 50-60Kyr ago and archaeo-ethno-demographic information. In addition to a colonization rate of 0.09-0.18, for an acceptable fit to the published microsatellite data, incorporation into existing models of exchange between neighbouring populations is essential, but at a very low rate. A linear decay of genetic diversity with geographical distance from the origin of expansion could apply to any species, especially if it moved recently into new geographical niches.  相似文献   

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