Genetic Structure Of Fragmented Populations Research Articles

Kinship and Breeding Site Philopatry Drive Fine-Scale Genetic Structure in Fragmented Populations of the Gopher Frog (Rana capito) in North Carolina

The Gopher Frog (Rana capito) is a threatened species native to the southeastern longleaf pine ecosystem. Although once much more widespread across the southeastern United States, they now occur in North Carolina at only a handful of disjunct sites in the Coastal Plain and Sandhills regions of the state. The long-term persistence of these populations is thus a concern, as is a loss of genetic variation over time. We used mitochondrial and microsatellite markers to better understand the spatial structure of genetic variation and levels of genetic variability across these remaining populations in order to inform conservation and management decisions. Eight unique mitochondrial haplotypes were found, but these were all genetically similar to one another. Levels of genetic diversity based on the microsatellite analyses were similar across populations, but inbreeding coefficients in two populations were significant, suggesting a potential vulnerability to inbreeding depression. All disjunct populations showed significant genetic differentiation, which was not related to geographic distance. Conversely, within populations, the genetic relatedness of individuals between ponds decreased as distance between ponds increased. This kinship pattern is likely driven by strong breeding philopatry (individuals returning to the same ponds across years) and indicates that conservation actions at the scale of <1 km would primarily affect kin groups of Gopher Frogs, whereas conservation actions at scales ‡1.5 km would be needed to capture more distantly related individuals. Management efforts should thus focus on local metapopulation dynamics by maintaining multiple breeding ponds at each location, and by enhancing connectivity between these breeding ponds.

Mind the gap: genetic distance increases with habitat gap size in Florida scrub jays

Habitat gap size has been negatively linked to movement probability in several species occupying fragmented landscapes. How these effects on movement behaviour in turn affect the genetic structure of fragmented populations at local scales is less well known. We tested, and confirmed, the hypothesis that genetic differentiation among adjacent populations of Florida scrub jays--an endangered bird species with poor dispersal abilities and a high degree of habitat specialization--increases with the width of habitat gaps separating them. This relationship was not an artefact of simple isolation-by-distance, as genetic distance was not correlated with the Euclidean distance between geographical centroids of the adjacent populations. Our results suggest that gap size affects movement behaviour even at remarkably local spatial scales, producing direct consequences on the genetic structure of fragmented populations. This finding shows that conserving genetic continuity for specialist species within fragmented habitat requires maintenance or restoration of preserve networks in which habitat gaps do not exceed a species-specific threshold distance.

Genetic structure in fragmented populations of Solanum lycocarpum A. St.-Hil. with distinct anthropogenic histories in a Cerrado region of Brazil

Solanum lycocarpum is a woody tree widely distributed in the Cerrado that reaches high population densities in disturbed environments. We examined the genetic diversity and population differentiation of six S. lycocarpum populations with different degrees of human disturbance in order to determine if they are negatively affected by anthropogenic activity. Three populations located in southern and three located in southeastern regions of Goiás State, Central Brazil, were genotyped with five microsatellite markers. The population located in a protected area had higher number of alleles (26) than the remaining populations (19 to 21 alleles). It indicates that extensive and continuous areas of preserved native vegetation contribute positively to the conservation of genetic diversity, even with S. lycocarpum that easily adapts to disturbed environments. The three southeastern populations, although fragmented, had preserved native vegetation and were not significantly different from each other (θp = 0.002). All other population pairs compared were significantly divergent (θp varied from 0.03 to 0.11 between pairs, P < 0.05). We found three distinct sets of allele frequencies. The three southeastern populations shared similar gene pools, as well as the two disturbed southern populations, which are secondary vegetation. The southern population located in protected area had the most dissimilar gene pool. In conclusion, populations showing a higher degree of human disturbance tends to show a larger population differentiation than expected from the isolation by distance model, which in the current scenario of the Cerrado destruction points out to a threat to the long-term conservation of the species.

Genetic structure in fragmented populations of Hippophae rhamnoides ssp. sinensis in China investigated by ISSR and cpSSR markers

Hippophae rhamnoides ssp. sinensis is an ecologically and economically important species that has been widely used as a pioneer plant in China. In this study, we employed both nuclear ISSR and maternal cpSSR markers to survey the genetic diversity and structure of populations of ssp. sinensis representing three different landscapes, the northwestern desert and grassland region, the alpine vegetation region of the Qinghai-Tibetan Plateau, and the northeastern humid forest region. In all, 12 natural populations with a scattered distribution in the area were studied. The genetic diversities of populations were found to be uneven, and the total genetic diversity was low on the basis of both types of marker. Mantel tests based on both individual Euclidean distance matrices and population genetic distance (measured by Φpt) matrices showed that the two marker systems detected similar trends with respect to genetic distances between populations. The analysis of molecular variance (AMOVA) revealed significant differentiation among populations and among regions for both types of marker. Although the detected pattern of isolation-by-distance among all sampled populations confirmed the earlier colonization pathway, the low level of gene flow and the lack of isolation by distance within each region suggested the presence of an additional dispersal barrier. UPGMA dendrograms and PCA plots also revealed clear clustering and significant regional differentiation. Our results indicate that the genetic structure of ssp. sinensis has been affected by habitat fragmentation and restricted population sizes. We propose that the biology of reproduction and ecology have played determinant roles in the development of the regional structure of populations. The genetic information obtained will help to establish conservation strategies and programs for sustainable management of H. rhamnoides ssp. sinensis.

Genetic structure of fragmented populations of a threatened endemic percid of the Rhône river: Zingel asper.

Zingel asper is an endemic percid of the Rhône basin considered to be critically endangered. This species was continuously distributed throughout the Rhône in 1900, but today only occupies 17% of its initial area. In the present study, five microsatellite loci were used to assess the level of genetic variability within and among populations localized in different sub-basins. Contrasting results were obtained for the three main populations from the Rhône. A reduced allelic diversity was observed for the two populations displaying the lowest patch sizes (length of the river system occupied); of these, a recent genetic bottleneck was detected for the population showing a particularly low density. However, the third population was characterized by a relatively large spatial extent, high local fish concentrations and an allelic diversity that was twice as high and associated with an equilibrium between mutation and drift. Thus, this population shows an apparently better evolutionary potential for long-term survival. Since 1930, a marked fragmentation of the whole Rhône system has appeared, related to the development of dams, and we assume that the significant genetic differentiation detected between the populations could mainly reflect the impact of this fragmentation. The high turnover of the Z. asper populations, and the major role of dispersal in population persistence (highlighted in a recent population dynamics study), indeed suggest that the differentiation observed could mainly have arisen from habitat fragmentation in recent history.

Polymorphic microsatellites for the study of fragmented populations of Pitcairnia geyskesii L. B. Smith (Bromeliaceae), a specific saxicolous species of inselbergs in French Guiana

Abstract Pitcairnia geyskesii is a saxicolous bromeliad endemic to the granitic inselbergs of French Guiana and Surinam. Seven polymorphic microsatellite markers were characterized to investigate the polymorphism among individuals sampled on five inselbergs in French Guiana. The total number of alleles per locus varied from four to 14. Mean observed heterozygosities at each microsatellite locus ranged from 0.114 to 0.629. This set of microsatellites offers an efficient tool for more detailed investigations on the genetic structure of fragmented populations living on such a singular and insular habitat within tropical rainforest.

Hierarchical genetic structure in fragmented populations of the Little Pocket Mouse (Perognathus longimembris) in Southern California

The geographic genetic structure, based onsequence variation of an 810 base pair fragmentof the mitochondrial cytochrome b gene,is described for populations of five subspeciesof the Little Pocket Mouse, Perognathuslongimembris, from Southern California. Oneof these, P. l. pacificus (Pacific PocketMouse), is listed as Endangered by the U.S.Federal Government. Sixty-two uniquehaplotypes were recovered from 99 individualssampled. Phylogenetic analyses of thesevariants do not identify regionallyreciprocally monophyletic lineages concordantwith the current subspecies designations, butmost haplotypes group by subspecies in networksgenerated by either statistical parsimony ormolecular variance parsimony. Moreover, asubstantial proportion of the total pool ofhaplotype variation is attributed to thesesubspecies, or to local populations withingeographic segments of each, indicating theirrelative evolutionary independence. The pooledextant populations of the endangered PacificPocket Mouse exhibit the same levels ofnucleotide and haplotype diversity as other,presumptively less-impacted populations ofadjacent subspecies, although the sample fromDana Point, Orange County, has markedly lowhaplotype diversity in comparison to allothers. These populations also show a geneticsignature of population expansion rather thanone of decline. Both pieces of evidence are atodds with current empirical populationestimates, which reinforces the fact thatpresent-day patterns of genetic diversity arethe product of coalescent history and will notnecessarily reflect recent anthropogenic, orother, perturbations. Comparison of haplotypevariation within and among extant populationsof the Pacific Pocket Mouse with those obtainedfrom museum samples collected more than 70years ago suggests that the pattern ofpopulation differentiation and diversity was inplace before the post-World War II exponentialurbanization of Southern California.

Microsatellite diversity and genetic structure of fragmented populations of the rare, fire-dependent shrub Grevillea macleayana.

Recent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self-compatible and have limited seed dispersal. However, long-lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species, Grevillea macleayana (Proteaceae), that occurs in many small populations, is self-compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long-lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found that G. macleayana may have relatively low within-population diversity (3.2-4.2 alleles/locus; Hexp = 0.420-0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation-drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire-shaped distribution, may have restricted long-distance gene flow in the past.

Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK.

The relationships among 207 squirrels from 12 locations in the UK and three in mainland Europe were examined using mitochondrial DNA (mtDNA) control region sequence. Twenty-six haplotypes were detected, many of which were population specific. Eighty per cent of the populations analysed contained two or more haplotypes. Hierarchical analysis of molecular variance showed the majority of genetic variation to be partitioned among populations. Genetic diversity varied considerably within the UK, and conformed to no obvious geographical trend. The populations in Argyll and Spadeadam Forest showed the highest levels of variation in the UK. However, the greatest genetic diversity was seen in Bavaria, southern Germany where six unique alleles were detected in a sample of 10 individuals. Phylogenetic analysis revealed no evolutionary divergence between UK and mainland European haplotypes. We conclude that, within the UK, the genetic patterns observed are most likely to be explained by the effects of genetic drift which has occurred since the isolation of populations during the past few hundred years, hence we cannot detect any underlying phylogeographic pattern. Therefore, the use of larger, geographically distinct populations within the UK for augmentation of small isolated populations is unlikely to pose problems of genetic incompatibility. Further, the role that demographic factors may have in complicating the application of current genetically based management unit criteria is likely to need further attention.

Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera.

We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited less stability in allelic composition across sites and stages. The number of alleles per hectare (ha) of forest was similar when continuous forest plots were compared to plots from fragmented forest for all three stages. This pattern also held for the number of unique multilocus adult and sapling genotypes, but the number of unique seedling genotypes per ha of fragmented forest greatly exceeded expectations based on continuous forest data, probably due to the concentration of seeds into remnant forest patches by foraging bats. Significant inbreeding and genetic differentiation were most often associated with the fragmented forest and the seedlings. Finally, principal component analysis reaffirmed that a bottleneck, acting in concert with pre-existing genetic structure in the adults, had led to enhanced and rapid divergence in the seedlings following deforestation, a result that is of central interest for landscape management.