Degree Of Population Subdivision Research Articles

Determinants of marital behaviour in five Apennine communities of Central Italy inferred by surname analysis, repeated pairs and kinship estimates

The work makes use of surname analysis, repeated pairs and kinship estimates in 11,009 marriage records celebrated in five communities of the Italian Central Apennine (Celano, Lecce dei Marsi, Ortucchio, Roio, Villavallelonga) from 1802 to 1965 with the objective to deepen knowledge of the relative influence of several determinants on their marital behaviour. These towns are part of the same geographic and economic environment: the slopes of the ancient Fucino Lake. This work further elaborates the results from previous studies on the bio-demographic model of the region. The data were analyzed according to three periods of approximately 50 years. Results show the highest inbreeding coefficients in the pastoral towns of Roio and Villavallelonga. Repeated pair analysis highlights a certain degree of population subdivision which declined in time in Celano, Lecce dei Marsi and Ortucchio. The highest and increasing values of RP-RPr in time in Roio suggest a general reduction in genetic heterogeneity. This is possibly due to the celebration of marriages among families selected on the economic basis of pastoralism, as this town historically has had a leading tradition of sheep-farming. Villavallelonga, excluding isonymous marriages, shows an increase in repeated pair unions in time, thus revealing a substructure with marriages among preferred lineages. This is in line with previous results on consanguineous marriages which indicated the tendency of avoiding unions between close relatives in this small geographic isolate. This study demonstrates the influence of geographical (altitude) and social factors (pastoralism) on the marital structures of the investigated populations.

Mating system analyses of tropical populations of the black mangrove, Avicennia germinans (L.) L. (Avicenniaceae)

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Population and Conservation Genetics of Crawfish Frogs,Lithobates areolatus, at Their Northeastern Range Limit

Abstract Crawfish Frogs (Lithobates areolatus) are a North American ranid, considered near threatened globally with populations in decline throughout their range. We studied populations of Crawfish Frogs on local and regional scales at their northeastern range limit to (1) assess the level of genetic diversity within populations, (2) estimate fine-scale genetic structure, and (3) estimate genetic differentiation between populations at the regional level. We used 10 microsatellite loci to genotype frogs collected from three regional sites in Indiana separated by 50–172 km and at one of these sites within a network of three breeding ponds <1 km apart. Heterozygosity estimates revealed high levels of diversity within these populations (mean HO: 0.54–0.67 per site), which is encouraging for future management. The degree of population subdivision was low at the regional level (FST = 0.071 for sites within 172 km). Genetic differentiation was related to geographic distance between sampling sites, as predicted b...

The Genetic Structure of Anophelines (Culicidae: Diptera): RAPD Versus Allozymes

The genetic structure of the species related to genus Anopheles was studied using both allozymes and RAPDs (random amplified polymorphic DNA). More accurate genetic diversity and differentiation could be detected with RAPD markers than with allozyme profiles. The degree of population subdivision was also much greater for RAPDs than for allozymes. The dendrograms produced by each of these markers differed significantly. We believe that RAPDs represent more recent mutational changes and an accurate picture of genetic relatedness than allozymes which represent ancestral genomic qualities of species. Also the mutational rates of the genes or their allelic profiles can be recorded more accurately with RAPD procedure than with allozyme electrophoresis which tends to miss certain nucleotide sequences in the non-coding regions of the genome.

CONTRASTING PATTERNS OF SPATIAL GENETIC STRUCTURE IN SYMPATRIC ROCK-DWELLING CICHLID FISHES

The cichlid fish of Lake Tanganyika in Eastern Africa are a celebrated example of both ecological and species diversification. Because population subdivision is likely to play an important role in the speciation process, understanding how habitat features interact with species' demographic, behavioral and ecological attributes to influence gene flow and population divergence may help explain the causes of high species richness in this and other systems. Here, we test the roles of isolation-by-habitat and isolation-by-distance in generating fine-scale population genetic structure in three sympatric species of habitat-restricted cichlids in Lake Tanganyika. Using multilocus microsatellite genotypes, we contrast patterns of population differentiation in these habitat specialists along a mosaic coastline of both favorable and unfavorable habitat. Despite their close phylogenetic relationship and shared habitat affinity, these species show striking differences in their pattern of genetic subdivision within the same geographical region, suggesting substantially different patterns of gene flow. In particular, two trophically specialized species exhibit much more restricted gene flow over sandy habitat than a trophically opportunistic species. This result suggests that ecological and behavioral traits have a strong influence on the scale and degree of population subdivision, a finding that has potentially important implications for understanding differential propensities for diversification among lineages and phylogenetic patterns of diversity.

Genetic variation and population structure of interleukin genes among seven ethnic populations from Karnataka, India

The extent of genetic variation and the degree of genetic differentiation among seven ethnic populations from Karnataka, India (Bunt, Havyak, Iyengar, Lingayath, Smartha, Vaishya, Vokkaliga), was investigated using four single nucleotide polymorphisms (SNPs: IL-1A 4845, IL-1B 3954, IL-1B 511 and IL-1RA 2018) of the interleukin gene cluster. Allele frequencies varied by threefold among these populations, which also differed for gene diversity and heterozygosity levels. The average degree of population subdivision among these castes was low (F(ST) = 0.02). However, pair-wise interpopulation differentiation ranged from 0-7%, indicating no detectable differentiation to moderate differentiation between specific populations. The results of phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data on these ethnic groups. Variation in the allele frequencies, as well as differentiation, may be attributed to differential selection and demographic factors including consanguinity among the ethnic groups. Information on the distribution of functionally relevant polymorphisms among ethnic populations may be important towards developing community medicine and public health policies.

Population genetics of the mangrove salt marsh snake, Nerodia clarkii compressicauda, in a linear, fragmented habitat

The mangrove salt marsh snake (Nerodia clarkii compressicauda) occupies a unique and disappearing habitat in much of coastal southern Florida. Given extensive habitat fragmentation and high predation pressure in open spaces, it seems likely that populations of N. c. compressicauda consist of isolated groups of related individuals. To assess the degree of population subdivision in this species we genotyped a total of 125 individuals from seven locations along the Florida coast at four microsatellite loci. Overall heterozygosity was moderate (57.7%) and somewhat lower than that seen in other snake species. Population subdivision was particularly pronounced with 19 of 21 sample pair-wise ΦST values significantly different from zero and ranging from 0.064 to 0.343 (P ≤ 0.05). About 11 of 39 alleles were private alleles that also tended to be in high frequency in the populations where they occurred (average frequency ~27%). The correlation of genetic and geographic distances was highly significant and positive (r 2 = 0.8733 and P < 0.001) with ΦST increasing by ~0.01 for every 10 km of separation. Overall, salt marsh snake populations appear to be fractured into isolated neighborhoods on the order of 50–80 km. In spite of its apparent local abundance, we believe that N. c. compressicauda is in need of conservation protection. The combination of extremely low dispersal, narrow habitat requirements, and most importantly, extensive habitat alteration resulting from coastal real estate development may mean that N. c. compressicauda is highly susceptible to population extirpation and potentially extinction.

The gene pool of the Belgorod oblast population: I. Differentiation of all district populations based on anthroponymic data

The gene pool of the entire population of all the 21 raions (districts) of the Belgorod oblast (region) has been studied using anthroponymic data. Considerable geographic variations of the number of surnames and the degree of population subdivision (0.00003 < f(r)* < 0.00125) in the 21 districts have been demonstrated. Districts with low population subdivision levels are mainly located in the central and southwestern raions of the Belgorod oblast, contain an urbanized area (city), and border on Ukraine (they are characterized by a considerable Ukrainian immigration). Urbanization significantly affects the population structure of the Belgorod oblast. In urbanized districts, rural populations lack the relationships between the population size, number of surnames, and population subdivision level (f(r)).

Genetic diversity and structure in the rare Colorado endemic plant Physaria bellii Mulligan (Brassicaceae)

Physaria bellii (Brassicaceae) is a rare, outcrossing perennial endemic to shale and sandstone outcrops along the Front Range of northern Colorado, USA. This species is locally abundant, but ranked G2/S2—imperiled because of threats to its habitat and a small number of populations—according to NatureServe’s standardized ranking system. Leaf tissue from ten populations was analyzed with ISSR (Inter-Simple Sequence Repeat) markers to discern the amount of genetic diversity and degree of population subdivision in P. bellii. Genetic diversity was moderate (0.22) and a moderately high degree of population structure was found (FST calculated using two algorithms ranged from 0.17 to 0.24). An AMOVA partitioned most of the variation among individuals within populations (76%), and the remainder among populations (24%). Results from a Principal Coordinates analysis were consistent with the geographic distribution of populations. A Mantel test of the correlation between genetic and geographic distances was highly significant (P < 0.001). The pattern of variation thus appears to be distributed along a gradient, and efforts to conserve this species should involve preserving enough populations so that gene flow between populations is not interrupted.

Genetic differentiation of Indian camel (Camelus dromedarius) breeds using random oligonucleotide primers

SummaryThe camel population in India is facing a severe decline which demands that immediate steps are taken to ensure its conservation. Characterisation is an integral part of the conservation program. The Polymerase Chain Reaction-Randomly Amplified Polymorphic DNA profile of unrelated camels of the Bikaneri (29), Jaisalmeri (30) and Kachchhi (18) breeds were analyzed. Reproducible polymorphic bands with varying frequencies among the three breeds of camel were obtained with five oligonucleotide primers. A total of 75 bands were amplified, of which 27 (36%) were polymorphic. The probability of obtaining identical fingerprints was observed to be the lowest in primer GC-10 (5.7%) followed by OP-08 (8.7%), GT-10 (11.3%), G-2 (15.5%) and G-1 (80%). Breed informative bands were amplified. The maximum genetic variability was observed in the Bikaneri (0.80±0.05) followed by the Kachchhi (0.84±0.06) and the Jaisalmeri (0.87±0.05) breeds. The inter-breed genetic distance estimates indicated a closer relationship in the Bikaneri-Kachchhi camels, (0.075), followed by the Jaisalmeri-Kachchhi (0.106) and Bikaneri-Jaisalmeri (0.132) breeds. A similar genetic relationship was observed when the degree of population subdivision was measured between the Bikaneri-Kachchhi (0.529), Jaisalmeri-Kachchhi (0.558) and Bikaneri-Jaisalmeri (0.566) breeds.

The effects of 20 years of highway presence on the genetic structure of Rana dalmatina populations

:Habitat destruction and fragmentation caused by highways can negatively affect animal populations, but a better understanding of the effects of highways on population genetic structure is still needed to improve conservation plans in urbanized landscapes. We investigated the degree of genetic variability and differentiation within and among seven Rana dalmatina populations located far from highly trafficked roads (non-fragmented populations) and four populations sampled on both sides of a major highway (fragmented populations). The degree of population subdivision was significantly higher among fragmented (Fst = 0.238) as compared to non-fragmented populations (Fst = 0.022). Furthermore, in the four fragmented populations, significantly lower allelic richness as compared to non-fragmented populations was observed. Together with potential high levels of road mortality leading to smaller population size, these results suggest that separation by highways not only has reduced the genetic diversity and polymorphism in local populations over two decades, but also has resulted in a higher degree of population differentiation, most likely due to genetic drift.

Joint Effects of Self-Fertilization and Population Structure on Mutation Load, Inbreeding Depression and Heterosis

Both the spatial distribution of organisms and their mode of reproduction have important effects on the change in allele frequencies within populations. In this article, we study the combined effect of population structure and the rate of partial selfing of organisms on the efficiency of selection against recurrent deleterious mutations. Assuming an island model of population structure and weak selection, we express the mutation load, the within- and between-deme inbreeding depression, and heterosis as functions of the frequency of deleterious mutants in the metapopulation; we then use a diffusion model to calculate an expression for the equilibrium probability distribution of this frequency of deleterious mutants. This allows us to derive approximations for the average mutant frequency, mutation load, inbreeding depression, and heterosis, the simplest ones being Equations 35-39 in the text. We find that population structure can help to purge recessive deleterious mutations and reduce the load for some parameter values (in particular when the dominance coefficient of these mutations is <0.2-0.3), but that this effect is reversed when the selfing rate is above a given value. Conversely, within-deme inbreeding depression always decreases, while heterosis always increases, with the degree of population subdivision, for all selfing rates.

Genetic diversity and structure of urban populations ofPierisbutterflies assessed using amplified fragment length polymorphism

Conservation programs in urban ecosystems need to determine the genetic background in populations of urban dwellers. We examined the genetic diversity and structure of Pieris rapae and P. melete using AFLP markers, and compared them between species and between urban and rural environments. As a result: (i). in both species, there was no reduction in genetic diversity within urban populations by direct comparison of diversity measurements, although the analysis of molecular variance suggested significant reductions in the variance within seasonal subpopulations in urban populations; (ii). P. rapae retained greater genetic diversity within species and populations; (iii). populations of both species showed significant genetic differentiation, and P. melete was more strongly subdivided; (iv). in both species, geographically close populations did not cluster with one another in the upgma analysis; (v). there was no genetic isolation due to geographical distance in either species; (vi). the genetic composition of seasonal subpopulations differed in urban populations of both species, and the genetic distances among subpopulations were correlated with seasonal differences in P. rapae and with temporal differences in P. melete. These results indicate that the genetic diversity in urban populations of both species was reduced at times, but was maintained by dispersal from genetically differentiated populations. Differences in the ability and mode of dispersal in the two species may be reflected in the degree of population subdivision and patterns of seasonal change in the genetic composition.

The genetic structure of endangered populations in the Cranberry Fritillary, Boloria aquilonaris (Lepidoptera, Nymphalidae): RAPDs vs allozymes.

The genetic population structure of the Cranberry Fritillary Boloria aquilonaris was studied using both RAPDs (random amplified polymorphic DNA) and allozymes. In Belgium, B. aquilonaris has a naturally fragmented distribution that has been accentuated due to human activity during the last century. The genetic population structure of this butterfly was analysed at the regional (several Ardenne uplands) and at the landscape level (several populations within an Ardenne upland). Both population genetic markers confirmed results from a previous CMR study at the landscape scale. At the regional scale however, important incongruences were observed between RAPDs and allozymes. The average gene diversity for the RAPD data was twice that of the allozyme data. The degree of population subdivision was also much greater for RAPDs than for allozymes. The UPGMA clusters produced by each of these markers differed significantly. We believe that, given the higher rate of mutation of RAPDs and the greater number of loci assayed by this method, RAPDs reveal a more accurate and recent population genetic structure than allozymes.

Genetic similarity as a measure for connectivity between fragmented populations of the moor frog (Rana arvalis).

Genetic differentiation among populations of the moor frog (Rana arvalis) was tested on a spatial scale where some dispersal between populations is expected to occur, in a landscape in The Netherlands that has become fragmented fairly recently, in the 1930s. Five microsatellite loci were used, with 2-8 alleles per locus. FIS was 0.049 across loci, and most populations were in HW equilibrium. The degree of population subdivision was low (FST=0.052). A significant positive correlation between genetic distance and geographical distance was found, indicating a limitation in dispersal among populations due to distance. To test the impact of the landscape mosaic on the connectivity between patches, distance measures were corrected for relative amounts of habitat types with known positive or negative influence on moor frog dispersal. Notably, the resistance variable for the fraction of negative linear elements (roads and railways) gave a higher explanatory value than geographical distance itself. Therefore, it is particularly the number of barriers (roads and railways) between populations that emerges as a factor that reduces exchange between populations. It is concluded that genetic techniques show promise in determining the influence of landscape connectivity on animal dispersal.

Mitochondrial and nuclear DNA analysis of population subdivision among young-of-the-year Spanish mackerel ( Scomberomorus maculatus ) from the western Atlantic and Gulf of Mexico

The degree of population subdivision among collections of young-of-the-year (YOY) Spanish mackerel Scomberomorus maculatus sampled from along the Atlantic coast of the United States (Atlantic) and Gulf of Mexico (Gulf) was examined. Young-of-the-year were collected from spawning areas to minimize possible mixing among putative spawning stocks that may occur at later life history stages along migratory pathways or at over-wintering grounds. Restriction fragment length polymorphism (RFLP) analysis of the mitochondrial DNA (mtDNA) ND4 region and a nuclear actin intron was conducted. Collections in each of two years were analyzed to minimize bias associated with sampling at a single point in space or time. Substantial variation was detected at ND4 (haplotype diversity=0.81) and at the actin intron locus (gene diversity=0.21). Significant differences in gene diversity or allele frequencies were not detected among temporal samples at any of three locations. A homogeneous distribution of genetic variance among samples from widely spaced geographic regions was consistent with the hypothesis that Spanish mackerel comprise a single intermingling genetic stock. Power analysis showed that the mitochondrial analysis from this study was much more likely to detect population subdivision than analysis of the nuclear actin locus, despite lower mtDNA sample size.

Breeding structure of Glossina pallidipes populations evaluated by mitochondrial variation

Mitochondrial DNA diversity was studied at four loci in six natural populations of the tsetse fly Glossina pallidipes from Zimbabwe, Mozambique, Kenya, and Ethiopia. Single-locus diversity varied from 0.39 at 12S to 0.65 at COII. A total of 32 haplotypes was found with a mean of 6.4 +/- 2.9 per locus. To study breeding structure, diversity at two loci, COII and 16S2, was evaluated in 18 populations sampled from an area of approximately 1,611,000 km2 and in three laboratory cultures. Twenty-six haplotypes were detected at the two loci and mean haplotype diversity over all natural populations was 0.63. A high degree of population subdivision was detected within and among the Ethiopian and Kenya populations. The Zimbabwe and Zambia populations showed much less variation and differentiation than the northern populations. A population in Mozambique showed high levels of haplotype variation and affinities closest to populations in eastern Kenya, some 1700 km to the north. Analysis of variance of haplotype frequencies showed that 51.5% of the total lay within populations, 13% among populations within five nested groups, and 35.5% among the five groups. Wright's FST was 0.485, Nei's GST was 0.33, and Weir and Cunningham's theta = 0.45. Ecological data show that G. pallidipes is highly vagile. The large amount of genetic differentiation may be explained by genetic drift that occurred in scattered, relict populations during the rinderpest panzootic of the late 19th and early 20th centuries.

Species Limits and Phylogenetic Relationships among Populations of Peromyscus furvus

We examined electrophoretic variation at 33 presumptive protein-coding loci for seven populations of Peromyscus furvus to determine population structure and test hypotheses of species boundaries. Protein electrophoresis revealed few fixed differences among populations and no diagnostic fixed alleles. Phenetic analysis of biochemical data support the hypothesis that P. furvus is a single phylogenetic entity. Populations from Jalapa, Veracruz, Mexico, and Puerto de la Soledad, Oaxaca, Mexico, were the most divergent. Polymorphic characters were subjected to parsimony analyses using presence-absence and frequency coding. Parsimony analyses showed that populations formerly recognized as P. angustirostris, P. furvus , and P. latirostris were not monophyletic groups within P. furvus (sensu lato). However, a high degree of population subdivision was detected. Working within the framework of the phylogenetic species concept, we concluded that populations of P. furvus represent one monophyletic species.

Unusually fine–scale genetic structuring found in rapidly speciating Malawi cichlid fishes

Mechanisms behind the explosive radiation of over 500 cichlid fish species from a single founding population in Lake Malawi during the last 700 000 years are poorly understood. Recent studies have suggested that the degree of population subdivision among the habitat patches within the lake may be responsible, but the evidence has been circumstantial: lack of a dispersal stage in haplochromine cichlids; genetic and colour variation among populations separated by large-scale geographical barriers; and fluctuating lake levels. One reason for the rapidity of speciation in these fishes may be that population subdivision is on a much finer scale than previously thought. Here we quantify the level of population subdivision and estimate migration at a scale of 700-1400 m, in order to investigate whether cichlid populations are sufficiently isolated from each other for allopatric divergence and perhaps speciation to take place. Using six microsatellite loci, we demonstrate the existence of highly significant genetic differentiation between subpopulations on adjacent headlands in each of four rock-dwelling haplochromine cichlid species. Our results suggest that these fish populations are divided into thousands of subunits among which genetic divergence is currently occurring, and that this may provide unprecedented opportunities for allopatric speciation.

The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations.

Levels of neutral genetic diversity in populations subdivided into two demes were studied by multilocus stochastic simulations. The model includes deleterious mutations at loci throughout the genome, causing 'background selection', as well as a single locus at which a polymorphism is maintained, either by frequency-dependent selection or by local selective differences. These balanced polymorphisms induce long coalescence times at linked neutral loci, so that sequence diversity at these loci is enhanced at statistical equilibrium. We study how equilibrium neutral diversity levels are affected by the degree of population subdivision, the presence or absence of background selection, and the level of inbreeding of the population. The simulation results are compared with approximate analytical formulae, assuming the infinite sites neutral model. We discuss how balancing selection can be distinguished from local selection, by determining whether peaks of diversity in the region of the polymorphic locus are seen within or between demes. The width of such diversity peaks is shown to depend on the total species population size, rather than local deme sizes. We show that, with population subdivision, local selection enhances between-deme diversity even at neutral sites distant from the polymorphic locus, producing higher FST values than with no selection; very high values can be generated at sites close to a selected locus. Background selection also increases FST, mainly because of decreased diversity within populations, which implies that its effects may be distinguishable from those of local selection. Both effects are stronger in selfing than outcrossing populations. Linkage disequilibrium between neutral sites is generated by both balancing and local selection, especially in selfing populations, because of linkage disequilibrium between the neutral sites and the selectively maintained alleles. We discuss how these theoretical results can be related to data on genetic diversity within and between local populations of a species.