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Ecological and genetic studies of the sand skink (Plestiodon reynoldsi) in central and south Florida/Research to Benefit the conservation of the Florida Sand Skink
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With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
We studied a fossorial endemic lizard (the sand skink, Plestiodon reynoldsi) to determine habitat structural and vegetation associations in altered habitats at micro-, local, and macroscales. Lizards were present in each of the structural categories and vegetation types we studied, although active orange groves negatively influenced distribution and relative density (determined as the proportion of coverboards within a sampling plot containing signs of sand skink presence). Conversely, relative densities were highest in forested habitats, which contain structural features similar to natural habitats. Sand skinks readily used the two soil types at our site, although the greatest densities were in sampling plots containing both types. We conclude that conditions are suitable for sand skink habitation within a variety of habitats with different structures, including those altered by humans. However, in all cases the underlying soil was also loose and dry, making fossorial locomotion possible for this species. Three lines of evidence suggest that populations in altered habitats were resident, rather than transient: (1) sand skinks are still present in altered habitats more than 35 skink generations after alteration occurred; (2) there was no relationship between sand skink density and distance to natural habitat; and (3) a very small portion of our site (<2%) consisted of natural habitat, which is most likely too small to be a long-term source population to nearby altered habitats. Our results indicate that although P. reynoldsi is often considered habitat-specific, this notion may be due to focusing sampling efforts on natural rather than disturbed habitats. Therefore, relying on preconceived notions of habitat associations may not be sufficient to understand the ecological relationships and local-scale distribution of this threatened species. Using such misinformation may lead to the design and implementation of inadequate conservation plans that ignore altered habitats in which focal species occur.
A recent study showed that populations of the threatened Florida Sand Skink had limited loss of genetic diversity over the past 60 yr as a consequence of anthropogenic fragmentation. This study assumed that 60 yr represents 30–37 generations for the Florida Sand Skink, but a new evaluation of mark–recapture data shows that 60 yr represents only about 15 generations. This result suggests that too little time may have passed to observe the full genetic consequences of contemporary anthropogenic fragmentation in the Florida Sand Skink and reinforces similar results from other species. We suggest that snapshots of existing genetic variability in fragmented populations are limited in their ability to predict the evolutionary fate of a species unless life-history attributes of the organism are taken into account.
Many reptile species are declining, yet there is little information on the current distribution and conservation status of most species, let alone how this may change with future development of natural habitats. We studied the distribution, habitat associations, and conservation status of Florida Sand Skinks (Plestiodon reynoldsi), a fossorial sand-swimming lizard endemic to Florida, USA. We used data collected between 1912 and 2006 to map the distribution of occurrences of this species and used Geographic Information System (GIS) data layers to determine the habitats in which it occurs. We found that Florida Sand Skinks occupy many different habitat types throughout their range, including human-altered areas used for agriculture. However, Florida Sand Skinks appear to be absent from urban areas. Between 1974 and 2004, the amount of natural habitat available to support populations declined by 17.8% (5.9% per decade), and this trend is predicted to continue until at least the year 2060. Projections of future development of natural and disturbed habitats show linear increases during this same time, and will further fragment the remaining natural habitats. This makes protection of habitat for this species an immediate and real concern. Florida Sand Skinks (and other sympatric species) are rapidly losing habitat due to urbanization, and much of the remaining natural habitat outside of protected areas could be lost during the next several decades.
Dry, sandy scrub habitats of the Florida peninsula represent naturally fragmented remnants of xeric ecosystems that were widespread during the Pliocene and early Pleistocene. This habitat is characterized by high endemism, and distribution of genetic and evolutionary diversity among scrub "islands" is of compelling interest because Florida scrub is rapidly disappearing under human development. We compare range-wide diversity in mitochondrial cytochrome b sequences for three scrub-associated lizards with contrasting levels of habitat specificity. All species show strong geographic partitioning of genetic diversity, supporting the hypothesis that scrub fauna is highly restricted by vicariant separations. The mole skink (Eumeces egregius), the least habitat specific, has the lowest phylogeographic structure among the lizards (φ st = 0.631). The mtDNA geneology for E. egregius is not entirely concordant with the five recognized subspecies and supports a link between populations in central Florida (E. e. lividus) and the Florida Keys (E.e. egregius) rather than a previously proposed affiliation between northern and southern populations. The Florida scrub lizard (Sceloporus woodi) is the most habitat specific of the lizards and has the strongest phylogeographic structure (φ st = 0.876). The sand skink (Neoseps reynoldsi) falls between the mole skink and scrub lizard in terms of habitat specificity and phylogeographic structure (φ st = 0.667). For all three species, networks of mtDNA haplotypes coalesce on two central ridges that contain the oldest scrub. The geographic structure and deep evolutionary lineages observed in these species have strong implications for conservation, including strategies for translocation, reserve design, and management of landscape connectivity.
Populations rarely show immediate genetic responses to habitat fragmentation, even in taxa that possess suites of traits known
to increase their vulnerability to extinction. Thus conservation geneticists must consider the time scale over which contemporary
evolutionary processes operate to accurately portray the effects of habitat isolation. Here, we examine the genetic impacts
of fragmentation on the Florida sand skink Plestiodonreynoldsi, a sand swimming lizard that is highly adapted to the upland scrub habitat of central Florida. We studied fragments located
on the southern Lake Wales Ridge, where human activity in the latter half of the 20th century has modified the natural patchiness
of the landscape. Based on a relaxed molecular clock method, we estimate that sand skinks have persisted in this region for
approximately 1.5million years and that the time frame of human disturbance is equivalent to fewer than 30 skink generations.
Using genotypes from eight microsatellite loci, we screened for molecular signatures of this disturbance by assessing congruence
between population structure, as inferred from spatially-informed Bayesian assignment tests, and the current geography of
scrub fragments. We also tested for potential intrapopulation genetic effects of inbreeding in isolated populations by comparing
the average pairwise relatedness of individuals within fragments of different areas and isolation. Our results indicate that
although some patches show a higher degree of relatedness than expected under random mating, the genetic effects of recent
isolation are not evident in this part of the species’ range. We argue that this result is an artefact of a time-lag in the
response to disturbance, and that species-typical demographic features may explain the genetic inertia observed in these populations.
Florida scrub habitat is a naturally fire maintained habitat that is highly
endangered because of high demand for land for agriculture and real estate. Maintenance
of remaining patches of Florida scrub habitat requires active management. We
experimentally investigated the effects of clearcutting and burning on sand skink
populations in three patches of sand pine scrub. Each patch included a clearcut plot, a
burned plot, and an undisturbed plot. Treatment plot boundaries were drawn in 1995
such that each plot was no different from any other plot in sand skink densities. The
responses of sand skink and other herpetofauna populations were monitored over the
following five-year period (1996-2000) immediately following clearcutting and burning.
Initially sand skink captures in the burned and clearcut plots were lower than in
the undisturbed plots. Over the five-year period, sand skink captures significantly
increased in the clearcut plots. No clear trend occurred in the burned plots, although
fluctuations from year to year were significant. After treatment, number of sand skink
captures differed among treatment plots within each site. The treatments also did not
affect sand skink distributions within the sites in the same way among the sites. The
distribution of sand skinks within the three sites appeared to be influenced by an
interaction between treatment plot and microhabitat characteristics. Sand skink presence
has been related previously to low soil compaction, large soil particle size, low soil
moisture, low soil temperature, large amounts of loose sand and bare ground, and low
average understory vegetation. The treatment plot in which the sand skinks were found
in the greatest numbers may have been more a function of the microhabitat characteristics
rather than the treatment. Analysis of the distribution of individuals also indicated that
sand skink distribution was clumped, especially near the centers of the three sites.
Analysis of herpetofaunal data from the experimental sites indicated that toward
the end of the study, the number of species captured appeared to be converging among
the undisturbed, clearcut, and burned plots. Diversity estimates, however, which
incorporate number of individuals as well as number of species, indicated that the burned
and undisturbed plots had greater herpetofaunal diversity than the clearcut plots.
Comparisons were made with other studies performed in north central Florida (Ocala
National Forest) and southern Florida.
Abstract.—Despite the recent popularity of prescribed burns in the southeast USA, little research is available on the effects ofprescribed fire on herpetofauna in the western coastal plain (Gulf Coast, USA). We assessed the effects of a restorationprescribed burn on herpetofauna and composed an inventory of amphibians and reptiles on the Grand Bay NationalEstuarine Research Reserve (GBNERR) and surrounding Grand Bay National Wildlife Refuge (GBNWR), Jackson County,Mississippi. We used visual encounter surveys (VES), minnow traps, and polyvinyl chloride (PVC) tubes to sampleherpetofauna. We recorded 429 individuals and 29 species from January-June, 2004. We found greater numbers ofherpetofauna in burned than unburned stands, while species diversity indices were equal between burn treatments. Ourresults provide the first herpetological survey of the reserve, providing a baseline for monitoring herpetofauna population andcommunity trends.
Current efforts to reconstruct the tree of life and histories of multigene families demand the inference of phylogenies consisting of thousands of gene sequences. However, for such large data sets even a moderate exploration of the tree space needed to identify the optimal tree is virtually impossible. For these cases the neighbor-joining (NJ) method is frequently used because of its demonstrated accuracy for smaller data sets and its computational speed. As data sets grow, however, the fraction of the tree space examined by the NJ algorithm becomes minuscule. Here, we report the results of our computer simulation for examining the accuracy of NJ trees for inferring very large phylogenies. First we present a likelihood method for the simultaneous estimation of all pairwise distances by using biologically realistic models of nucleotide substitution. Use of this method corrects up to 60% of NJ tree errors. Our simulation results show that the accuracy of NJ trees decline only by ≈5% when the number of sequences used increases from 32 to 4,096 (128 times) even in the presence of extensive variation in the evolutionary rate among lineages or significant biases in the nucleotide composition and transition/transversion ratio. Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies.
• phylogenetics
• molecular evolution
• distance estimation
• tree of life
• maximum likelihood
We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).
Molecular genetic analyses show that introduced populations undergoing biological invasions often bring together individuals from genetically disparate native-range source populations, which can elevate genotypic variation if these individuals interbreed. Differential admixture among multiple native-range sources explains mitochondrial haplotypic diversity within and differentiation among invasive populations of the lizard Anolis sagrei. Our examination of microsatellite variation supports the hypothesis that lizards from disparate native-range sources, identified using mtDNA haplotypes, form genetically admixed introduced populations. Furthermore, within-population genotypic diversity increases with the number of sources and among-population genotypic differentiation reflects disparity in their native-range sources. If adaptive genetic variation is similarly restructured, then the ability of invasive species to adapt to new conditions may be enhanced.
Savannas and barrens were major components of the historic North American landscape before it was extensively altered by agricultural and urban development during the past century. Rock outcrop plant communities and serpentine barrens are of interest because they are refugia for endemic species adapted to extreme environmental conditions. Many of these communities have been reduced to less than one per cent of their original area and are imperiled ecosystems. This book provides a coherent, readable summary of the technical information available on savannas, barrens and rock outcrop plant communities. It is organized by region into four parts: eastern south-eastern region, central/midwest region, western/south-western region, and northern region. Written by internationally recognized regional specialists, each chapter includes a description of the climate, geology, soils associated with the community, and information about its historic and current vegetation.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
Experimental plots were burned every year (1E), every 2yr (2E), or every 7yr (7E); the control plot (CE) has not burned for 20yr. Amphibians and reptiles of 27 species were captured. Severe cold in December 1983 may have caused a large decline in herpetofauna in 1984. Both Shannon-Weiner and Simpson's diversity indexes indicated that plot 2E had the lowest diversity each year. Greatest diversity was found on 1E or 7E. The 2yr fire periodicity produced a dense layer of grasses and herbaceous plants that was not readily occupied by sandhill herpetofauna. The most abundant reptile was 6-lined racerunner Cnemidophorus sexlineatus (33% of all captures). The highest density of racerunners was found on 1E, while lizards on 7E showed the greatest philopatric tendencies (especially in 1983, the year 7E was burned). -from Author
There is, for planning, regulatory, or facilities management purposes an increased demand for thematic maps depicting land use and land cover (LU/LC). The Southwest Florida Water Management District is currently in the process of developing LU/LC maps as part of its GIS database development effort. Presented here is a description of automated sample generation methods developed at the District using GIS techniques, results of statistical evaluation of these sample data, and the field experiences and person-hour requirements associated with the accuracy assessment of the LU/LC data. -from Authors
Factors influencing the distribution and abundance of black-tailed prairie dog (Cynomys ludovicianus) colonies are of interest to rangeland managers because of the significant influence prairie dogs can exert on both livestock and biodiversity. We examined the influence of 4 prescribed burns and one wildfire on the rate and direction of prairie dog colony expansion in shortgrass steppe of southeastern Colorado. Our study was conducted during 2 years with below-average precipitation, when prairie dog colonies were expanding throughout the study area. Under these dry conditions, the rate of black-tailed prairie dog colony expansion into burned grassland (mean X=2.6 ha·100-m perimeter-1·y-1; range=0.8-5.9 ha·100-m perimeter-1·y-1; N=5 colonies) was marginally greater than the expansion rate into unburned grassland (mean X=1.3 ha·100-m perimeter-1·y-1; range=0.2-4.9 ha·100-m perimeter-1·y-1; N=23 colonies; P=0.066). For 3 colonies that were burned on only a portion of their perimeter, we documented consistently high rates of expansion into the adjacent burned grassland (38%-42% of available burned habitat colonized) but variable expansion rates into the adjacent unburned grassland (2%-39% of available unburned habitat colonized). While our results provide evidence that burning can increase colony expansion rate even under conditions of low vegetative structure, this effect was minor at the scale of the overall colony complex because some unburned colonies were also able to expand at high rates. This result highlights the need to evaluate effects of fire on colony expansion during above-average rainfall years, when expansion into unburned grassland may be considerably lower.
A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.
Over a 12-year period (1992-2003), we examined the impact of prescribed burning and hardwood removal on a population of nine-banded armadillos (Dasypus novemcinctus) located at Tall Timbers Research Station just north of Tallahassee, Florida. Although these armadillos are often found in close proximity to humans, there currently are no data on how they are affected by human impacts on the environment. Responses to annual burns between 1992-1997 indicated that in some years armadillos, particularly adults, avoided areas that had been burned, but effects were inconsistent and relatively weak. In contrast, hardwood removal during 1998-2000 coincided with a significant decline in population numbers that continued through 2003. However, interpretation of hardwood removal effects was complicated by the occurrence of a severe drought during the same time period. Comparisons between animals in logged and unlogged parts of the study area during the period of hardwood removal revealed few differences, suggesting drought was an important influence. However, because our population continued to decline after the drought ended, it seems likely that hardwood removal generated more persistent effects that were temporarily masked by the drought. We observed armadillos frequently in logged areas, probably because few other habitat choices were available. Armadillos weighed less during and after hardwood removal than prior to it. Although adult reproductive behavior appeared largely unaffected by logging, numbers of juveniles captured and recruited declined significantly with the onset of hardwood removal. There was no evidence that the disturbance from logging caused increases in distances moved by animals that remained in the study area. Our results may have broader implications for predicting how armadillo populations in Latin America will be affected by similar land management practices.
We characterized microsatellite loci for the sand skink ( Neoseps reynoldsi ) for future studies of genetic structure in this threatened taxon. We screened a partial genomic library enriched for microsatellites, designed primers for eight loci and assessed these markers for polymorph- ism across 11 populations in central Florida. Preliminary analyses indicate deviations from Hardy-Weinberg expectations for most loci, suggesting population genetic structure across the sampled populations; therefore, understanding genetic connectivity is critical for main- taining genetic variation in this species.
Over a 12-year period (1992–2003), we examined the impact of prescribed burning and hardwood removal on a population of nine-banded armadillos (Dasypus novemcinctus) located at Tall Timbers Research Station just north of Tallahassee, Florida. Although these armadillos are often found in close proximity to humans, there currently are no data on how they are affected by human impacts on the environment. Responses to annual burns between 1992–1997 indicated that in some years armadillos, particularly adults, avoided areas that had been burned, but effects were inconsistent and relatively weak. In contrast, hardwood removal during 1998–2000 coincided with a significant decline in population numbers that continued through 2003. However, interpretation of hardwood removal effects was complicated by the occurrence of a severe drought during the same time period. Comparisons between animals in logged and unlogged parts of the study area during the period of hardwood removal revealed few differences, suggesting drought was an important influence. However, because our population continued to decline after the drought ended, it seems likely that hardwood removal generated more persistent effects that were temporarily masked by the drought. We observed armadillos frequently in logged areas, probably because few other habitat choices were available. Armadillos weighed less during and after hardwood removal than prior to it. Although adult reproductive behavior appeared largely unaffected by logging, numbers of juveniles captured and recruited declined significantly with the onset of hardwood removal. There was no evidence that the disturbance from logging caused increases in distances moved by animals that remained in the study area. Our results may have broader implications for predicting how armadillo populations in Latin America will be affected by similar land management practices.
FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as arlequin, tcs and mrbayes. The toolbox is expected to grow on the basis of requests for particular services and converters in the future. FaBox is freely available at http://www.birc.au.dk/fabox.
We analyzed 16 years of mark-recapture data to investigate whether a wildfire influenced survival of an arboreal ambush-forager (broad-headed snake [Hoplocephalus bungaroides]) and a terrestrial active forager (small-eyed snake Cryptophis nigrescens). We predicted that wildfire would cause direct mortality and reduce subsequent survival of both snake species. Contrary to this prediction, wildfire did not affect abundance of broad-headed snakes, but abundance of small-eyed snakes decreased by 48% after the wildfire. Estimated annual survival of small-eyed snakes was 37% lower after fire (s=0.47, SE=0.07) than before fire (s=0.74, SE=0.05). Prescribed burning may be a suitable tool for creating open habitat mosaics for the endangered broad-headed snake.
Fire alters the abundance and diversity of many species, but its effects on amphibians are poorly known. We tested whether prescribed burning affected amphibian abundance and diversity within the Francis Marion National Forest, South Carolina, by monitoring assemblages at 15 temporary ponds with five different burn histories: 0, 1, 3, 5, and 12 years after burns. We also monitored terrestrial and aquatic environmental variables likely to influence amphibian diversity, such as leaf-litter depth, pond water chemistry, and distance to neighboring ponds. Fire had significant negative effects. Immediate effects ( burning during the study ) explained 12.8% and 10.8% of the variation in anuran and amphibian abundance, respectively, whereas short-term effects explained 31.8% and 24.6% of variation in amphibian species richness and evenness, respectively. Species richness increased and evenness decreased with time since burn, primarily because salamanders were rarely encountered at sites burned within 2 years. These sites had the shallowest leaf litter and highest soil temperature variances. Environmental factors unrelated to burning also significantly influenced amphibian diversity. Water chemistry explained 31.1% of variation in species richness, 32.2% of evenness, and>25% of anuran, salamander, and total amphibian abundances. Salamanders were most sensitive to water chemistry factors, particularly pH. Our results suggest that decreasing the frequency of prescribed burns from the current 2–3 years to 3–7 years will better maintain diverse amphibian and plant assemblages. Substituting growing-season burns for the current practice of winter and spring burns would avoid repeatedly interrupting amphibian breeding and would maintain the desired longleaf pine community.
Genetic data are useful for estimating the genealogical relationship or relatedness between individuals of unknown ancestry. We present a computer program, ml-relate that calculates maximum likelihood estimates of relatedness and relationship. ml-relate is designed for microsatellite data and can accommodate null alleles. It uses simulation to determine which relationships are consistent with genotype data and to compare putative relationships with alternatives. ml-relate runs on the Microsoft Windows operating system and is available from http://www.montana.edu/kalinowski.
GENALEX is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include AMOVA, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and TWOGENER. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, GENALEX 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
This paper reviews the necessary considerations and available techniques for assessing the accuracy of remotely sensed data. Included in this review are the classification system, the sampling scheme, the sample size, spatial autocorrelation, and the assessment techniques. All analysis is based on the use of an error matrix or contingency table. Example matrices and results of the analysis are presented. Future trends including the need for assessment of other spatial data are also discussed.
Thesis (M.S.)--University of South Florida, 2001. Includes bibliographical references (leaves 64-71).
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.
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