Does natural selection promote population divergence? A comparative analysis of population structure using amplified fragment length polymorphism markers and quantitative traits

Divergent natural selection is considered an important force in plant evolution leading to phenotypic differentiation between populations exploiting different environments. Extending an earlier greenhouse study of population differentiation in the selfing annual plant Senecio vulgaris, we estimated the degree of population divergence in several quantitative traits related to growth and life history and compared these estimates with those based on presumably neutral molecular markers (amplified fragment length polymorphisms; AFLPs). This approach allowed us to disentangle the effects of divergent selection from that of other evolutionary forces (e.g. genetic drift). Five populations were examined from each of two habitat types (ruderal and agricultural habitats). We found a high proportion of total genetic variance to be among populations, both for AFLP markers (phiST = 0.49) and for quantitative traits (range of QST: 0.26-0.77). There was a strong correlation between molecular and quantitative genetic differentiation between pairs of populations (Mantel's r = 0.59). However, estimates of population differentiation in several quantitative traits exceeded the neutral expectation (estimated from AFLP data), suggesting that divergent selection contributed to phenotypic differentiation, especially between populations from ruderal and agricultural habitats. Estimates of within-population variation in AFLP markers and quantitative genetic were poorly correlated, indicating that molecular marker data may be of limited value to predict the evolutionary potential of populations of S. vulgaris.     

Genetic diversity of the endangered Faucaria tigrina (Aizoaceae) through ISSR “fingerprinting” using automated fragment detection

Faucaria tigrina (Haw.) Schwantes is a rare, threatened succulent found exclusively on the outskirts of Grahamstown, Eastern Cape, South Africa. There are three extant populations of the species; two large ones (approximately 300 and 620 adults) separated by under two kilometres, and a third very much smaller one slightly further away. Genetic theory expects that smaller, isolated populations face a loss in genetic variation through inbreeding and genetic drift and that as declining genetic variation is linked to a loss in fitness, this species may face extinction in the long term. This study used the ISSR-PCR genetic methods linked to an automated detection platform to determine if these populations are genetically distinct, and whether they are genetically depauperate. Two ISSR primers were used, and the automated detection system identified a total of 572 ISSR loci. An UPGMA clustering analysis showed each population to be genetically distinct, and that the genetic diversity of each population does not appear to be particularly low. F. tigrina is separable from the related Faucaria britteniae L. Bolus using the ISSR method, suggesting that this method may be appropriate for systematic studies in the Aizoaceae, which comprises many genera with closely related species.     

Genetic diversity and population genetic structure of three endemic species of Mammillaria (Cactaceae) from the Tehuacán Valley in central México

Biodiversity and Conservation - Mammillaria hernandezii, M. dixanthocentron and M. lanata are endemic and threatened cactus species that inhabit the Tehuacán Valley, an arid zone in southern...     

Preliminary analysis of the genetic diversity and population structure of mortiño (Vaccinium floribundum Kunth)

Mortiño (Vaccinium floribundum Kunth) is a deciduous perennial shrub endemic to the high Andes of South America. Despite a rich ethnobotanic history among indigenous communities, mortiño remains a wild species vulnerable to extinction from the ongoing fragmentation of its natural habitat. This study assessed the degree of genetic diversity and population structure of Ecuadorian V. floribundum as a preliminary step towards the establishment of effective conservation and sustainable-agriculture strategies. Mortiño individuals (126 in total) sampled from 3 regions in the northern highlands of Ecuador were characterized using 11 heterologous SSR markers originally developed for Vaccinium corymbosum. Expected heterozygosity (He = 0.49) revealed a moderate degree of genetic diversity for Ecuadorian mortiño, and pairwise F statistics between sampling regions (0.019≤ Fst ≤0.041) demonstrated low-to-moderate population differentiation. Population structure analysis clustered mortiño germplasm into 3 groups, each representing the 3 distinct regions from where samples were collected. The geographic patterning of genetic diversity for V. floribundum could be explained by an isolation-by-distance model, where physical barriers along the Andean highlands reduce genetic exchange between distanced populations. To confirm the latter, this study should extend to a wider sampling range, covering other regions along the Andean alley where the species is found.     

Mutation and haplotype analyses of the Werner’s syndrome gene based on its genomic structure: genetic epidemiology in the Japanese population

The correlation between mutations in the Werner’s syndrome (WRN) gene and the haplotypes of surrounding markers was studied in Japanese patients. We have elucidated the genomic structure of WRN helicase, and found five additional mutations, designated mutations 6–10. Mutations 4 and 6 were found to be the two major mutations in this population; these mutations comprised 50.8% and 17.5%, respectively, of the total in a sample of 126 apparently unrelated chromosomes. Almost all the patients homozygous for mutation 4 shared a haplotype around the WRN gene, consistent with the view that they are derived from a single ancestor. This important advantage demonstrated in the identification of the WRN gene suggests that the Japanese present a unique population for the cloning of other disease genes. The conserved haplotype was observed across 19 loci, extending a distance estimated to be more than 1.4 Mbp around the WRN gene. This haplotype is rare among random Japanese individuals. Unexpectedly, all the nine patients homozygous for mutation 6 shared a haplotype that was identical to this haplotype at 18 of these 19 markers. These results suggest that mutations 4 and 6 arose independently in almost identical rare haplotypes. The remaining mutations (1, 5, 7, 8, 9, and 10) occurred rarely, and were each associated with different haplotypes. Received: 16 December 1996 / Accepted: 16 February 1997     

Genetic variation and structure in natural and reintroduced populations of the endangered legume,Pyne’s ground plum (Astragalus bibullatus)

Conservation Genetics - Rare species with limited geographic distributions and small census populations are particularly susceptible to genetic drift and inbreeding. Assessing genetic variation...     

Seasonal variation in genetic population structure of sábalo (Prochilodus lineatus) in the Lower Uruguay River

Prochilodus lineatus is a highly migratory fish species that sustains the most important commercial fishery of Paraná-Paraguay basin. Migratory patterns are poorly known and only few population genetic studies are available for this species in the Upper Paraná. To assess genetic population structure, we genotyped a sample of 93 individuals from the Lower Uruguay River close to Gualeguaychú city (Entre Ríos, Argentina) at three different times, July 2008 (Winter), September 2008 (Spring) and May 2009 (Fall). All individuals were genotyped for 12 microsatellite loci previously found to be informative to assess populations of P. lineatus. Our results show seasonal variation of the genetic sub-structuring at this locality that may be related to the presence of different migratory stocks throughout the year. The Fall sample includes an additional genetic cluster of individuals not detected in Winter and Spring, suggesting that this species should be considered a mixed stock fishery.     

Analysis of mating system and genetic structure in the endangered,amphicarpic plant,Lewton’s polygala (<Emphasis Type="Italic">Polygala lewtonii)</Emphasis>

Polygala lewtonii is a federally endangered, amphicarpic plant with a mixed mating system and three types of flowers: (1) aboveground, chasmogamous flowers (i.e., open-pollinated; CH), (2) aboveground, cleistogamous flowers (i.e., closed, selfing; CL) and (3) CL flowers on belowground stems (amphicarpy). Aboveground seeds are ant-dispersed, whereas belowground seeds are spaced across the length of the rhizome. Here, we collected individuals of P. lewtonii at both range-wide and fine geographic scales and genotyped them at 11 microsatellite loci. We analyzed patterns of genetic diversity and structure to understand: (1) the predominant mating system (selfing or outcrossing), (2) the movement of pollen and seeds across the landscape, and (3) the optimal strategy to conserve the full range of genetic variation. P. lewtonii reproduces predominantly by selfing or bi-parental inbreeding, but reproduction occurred through each of the three flower types. Some individuals produced by selfing/inbreeding were tightly clustered spatially, and were likely produced either by belowground flowers or by aboveground flowers with limited seed dispersal. Other selfed/inbred individuals were spatially separated (maximum of 15 m), and were likely produced by aboveground flowers followed by seed dispersal by ants. Fine-scale patterns of genetic structure indicate that some gene flow is occurring among aboveground CH flowers but both pollen and outcrossed seeds are moving limited distances (maximum of 0.5 km). Because genetic variation is structured at a fine spatial scale, protecting many populations is necessary to fully conserve the genetic variation in P. lewtonii. Conservation seed banking, if accompanied by research on seed germination requirements, may also contribute to the effective protection of genetic variation in P. lewtonii.     

Genetic variability of the postharvest pathogen Gilbertella persicaria: identification of randomly amplified polymorphic DNA (RAPD) markers correlating with (+) and (–) mating types

Random amplified polymorphic DNA (RAPD) and isoenzyme polymorphisms among 16 isolates of the postharvest pathogen Gilbertella persicaria were examined. Six different 10-bp primers were used to determine the extent of intraspecific genetic variability. Nine composite amplification types were identified. RAPD markers were obtained which correlated with the mating types of the G. persicaria isolates. The variability of the isoenzyme patterns was very low and no correlation was found between the isoenzyme markers and the mating abilities. When 80 single carbon substrates were tested in utilization assays, most of them were utilized uniformly by the 16 G. persicaria strains. However, some compounds elicited differences between the isolates representing the two mating types. -Alanine (0.2%) has little effect on the germination of the sporangiospores of the (+) isolates, but inhibited the germination of (–) sporangiospores. Glycerol-1-monoacetate supported the growth of both mating types, but at concentrations higher than 4% this was accompanied with a compact (colonial) growth for plus mating type isolates only.     

Bryophyte diaspore bank: a genetic memory? Genetic structure and genetic diversity of surface populations and diaspore bank in the liverwort Mannia fragrans (Aytoniaceae)

Propagule banks are assumed to be able to store considerable genetic variability. Bryophyte populations are expected to rely more heavily on stored propagules than those of seed plants due to the vulnerability of the haploid gametophyte. This reliance has important implications for the genetic structure and evolutionary potential of surface populations. A liverwort, Mannia fragrans, was used to test whether the bryophyte diaspore bank functions as a "genetic memory." If a diaspore bank is capable of conserving genetic variability over generations, the levels of genetic diversity in the soil are expected to be similar or higher than at the surface. Surface and diaspore bank constituents of two populations of M. fragrans were investigated. Genetic structure and diversity measured as unbiased heterozygosity were analyzed using three ISSR markers. Similar genetic diversities were found in the soil (H(s) = 0.067) and at the surface (H(s)= 0.082). However, more haplotypes and specific haplotype lineages were present in soil samples. The results suggest that the bryophyte diaspore bank has an important role in accumulating genetic variability over generations and seasons. It is postulated that the role of the diaspore bank as a "genetic memory" is especially important in species of temporarily available habitats that have long-lived spores and genetically variable populations.     

Isozyme polymorphism and genetic structure of the population of Sorbus torminalis (L.) Crantz from the Bytyń Forest (Poland)

Dormant buds collected from 35 wild service trees (Sorbus torminalis) in the Bytyń Forest were tested with horizontal gel electrophoresis to assess the genetic structure of the population. Among 16 investigated isozyme loci, seven loci (ADH-A, 6PGD-A, GDH-B, ME-A, SOD-A, PGM-A, PGM-B) proved to be polymorphic, whereas the other nine loci (SDH-A, SDH-B, DIA-C, DIA-D, FLE-A, FLE-B, GOT-B, IDH-A, IDH-B) were monomorphic. The number of alleles per polymorphic locus ranged from two to three, with a mean of 2.29. The average observed and expected heterozygosities were 0.2665 and 0.3462, respectively. The combined FIS value over all polymorphic loci was 0.2179, which reflects a substantial deficit of heterozygotes. Two polymorphic loci (SOD-A, PGM-A) were identified in S. torminalis for the first time.     

Genetic structure of Himalayan marmot (Marmota himalayana) population alongside the Qinghai–Tibet Railway

In order to verify the effect of social behavior and geographical isolation on the genetic structure of the Himalayan marmot (Marmota himalayana) population, we examined the genetic diversity of Himalayan marmots alongside the Qinghai–Tibet Railway using microsatellite markers. Eight microsatellite loci were used to examine 120 animals of 4 populations: Ulan (U), Delhi (D), Tuotuohe (T) and Ando (A). The results show that: (1) Himalayan marmots alongside the Qinghai–Tibet Railway are highly genetically diversified. The allele number (Na), effective allele number (Ne), observed heterozygosity (Ho), Nei’s expected heterozygosity (He) and polymorphism information content (PIC) of the total Himalayan marmot population were 4.75, 3.0332, 0.6990, 0.6672, 0.6102, respectively. (2) Himalayan marmots may be able to avoid inbreeding by a mechanism that will prevent the genetic diversity reduction caused by their social lifestyle. Heterozygote excess was observed at most loci. The inbreeding coefficients within the subpopulation (F_IS), in the total population (F_IT), the differentiation index of population (F_ST), and the gene flow (Nm) were ?0.2265, ?0.0477, 0.1458, and 1.4646, respectively. (3) The genetic differentiation of the Himalayan marmot population was in accordance with Wright’s “isolation by distance” theory. The Mantel test indicates that the correlation between genetic distance and geographic distance was significant (P < 0.05, r = 0.698). (4) Each of the four geographical populations had moderate differentiation. Both geographic distance and isolation could affect the population genetic structure of the Himalayan marmot. The maximum gene flow (3.5915), the smallest genetic differentiation index (0.0651), the lowest genetic distance (0.0700) and the highest genetic identity (0.9526) were all between the Ulan population and Delhi populations. (5) The cluster analysis, based on Nei’s standard genetic distance, showed that the populations of Delhi and Ulan were first merged in a cluster, and then Tuotuohe population was merged in the clustering. The Ando population was the last element in the clustering.     

Genetic analyses of the host-pathogen system Turnip yellows virus (TuYV)—rapeseed (Brassica napus L.) and development of molecular markers for TuYV-resistance

The aphid transmitted Turnip yellows virus (TuYV) has become a serious pathogen in many rapeseed (Brassica napus L.) growing areas. Three-years’ field trials were carried out to get detailed information on the genetics of TuYV resistance derived from the resynthesised B. napus line ‘R54’ and to develop closely linked markers. F₁ plants and segregating doubled-haploid (DH) populations derived from crosses to susceptible cultivars were analysed using artificial inoculation with virus-bearing aphids, followed by DAS-ELISA. Assuming a threshold of E ₄₀₅ = 0.1 in ELISA carried out in December, the results led to the conclusion that pre-winter inhibition of TuYV is inherited in a monogenic dominant manner. However, the virus titre in most resistant lines increased during the growing period, indicating that the resistance is incomplete and that the level of the virus titre is influenced by environmental factors. Bulked-segregant marker analysis for this resistance locus identified two closely linked SSR markers along with six closely linked and three co-segregating AFLP markers. Two AFLP markers were converted into co-dominant STS markers, facilitating efficient marker-based selection for TuYV resistance. Effective markers are particularly valuable with respect to breeding for TuYV resistance, because artificial inoculation procedures using virus-bearing aphids are extremely difficult to integrate into practical rapeseed breeding programs.     

Low genetic diversity and lack of population structure in the endangered Galápagos penguin (<Emphasis Type="Italic">Spheniscus mendiculus</Emphasis>)

Long-term monitoring of the endangered Galápagos penguin (Spheniscus mendiculus) has indicated poor reproductive periods and severe population fluctuations in association with El Niño – Southern Oscillation events. An earlier mark and recapture study indicated that adults exhibit some degree of breeding-site and mate fidelity, and that juveniles potentially move more frequently than adults; however, the extent to which migrants and gene flow occur between islands within the Galápagos archipelago is largely unknown. This study tested the hypothesis that geographic isolation and adult breeding philopatry has led to a degree of genetic differentiation between island subpopulations within the archipelago. We examined the genetic diversity within and among different subpopulations and the extent to which gene flow occurs between island subpopulations. Estimates of allelic richness and gene diversity were not significantly different between subpopulations. Tests to detect genetic heterogeneity failed to reject the H ₀ of no difference in allele frequencies for chi-square (P = 0.28) and Fisher’s exact test (P = 0.19). All pairwise values of the F _ST variant θ were not significant, while a power analysis revealed a >99% probability of detecting a biologically true F _ST of 0.05. Migration estimates in BAYESASS+ suggest symmetrical gene flow throughout the species’ distribution. Our results indicate a low level of genetic diversity throughout the population and a seemingly high level of gene flow between subpopulations. We argue that the Galápagos penguin should be managed as one panmictic population and we discuss the risk of disease threats in the archipelago.     

Genetic diversity and population structure of North America’s rarest heron, the reddish egret (Egretta rufescens)

The global distribution of the reddish egret is characterized by disjunct colonies occurring from the Pacific side of Northwest Mexico to the Caribbean. We examined distantly isolated colonies of reddish egret to determine global population genetic structure. We used seven polymorphic microsatellites to accomplish five goals: (1) to assess range wide population differentiation among reddish egret (Egretta rufescens) populations, (2) identify extent of gene flow, (3) determine any historical occurrence of bottlenecks, (4) assess genetic differentiation between color morphs, (5) clarify subspecies status of E. r. dickeyi, a completely dark morph population located in and around the Baja California peninsula, Mexico. Genetic differentiation was dramatic (global Fst = 0.161) throughout the reddish egrets range extending from Baja California, Mexico to Great Inagua, Bahamas. Differentiation occurred among three distinct regions (Fst = 0.238) but not among colonies/islands within regions suggesting regional philopatry. Genetic diversity (alleles per locus, and heterozygosity) in Baja California Sur, Mexico and Great Inagua, Bahamas populations is lower than in the Texas/Mexico population due to minimal dispersal between regions and smaller population sizes. Dark and white color morphs when present within the same region showed no differentiation. Patterns of recent population bottlenecks are not evident in each of the three regional populations. With evidence of limited gene flow in addition to low genetic diversity and prospects of habitat loss we recommend that reddish egrets be managed as three distinct or evolutionary significant units.     

Genetic structure of an isolated group of the indigenous population of northern Siberia, the Nganasans (Tavginians) of Ta?mir

Demographic data of genetic interest were studied in presently living population in comparison with preseding generations of Nganasans. Decrease of sex ratio in the whole population has been revealed along with the reduction of reproductive and, possibly, effective size. The number and variance of livebirths per female were 7.29 and 9.86 respectively. Crow' index of the opportunity for selection (I) and its components (Im and If) were estimated. I was found to be 1.17, whereas Im and If--1.56 and 0.18 respectively. Linear pattern of settling in the past as well as the type of migration between adjoining subpopulations depended on culture and economy of arctic reindeer hunters as well as landscape character.     

Variation in the genetic structure of Peromyscus populations. I. Genetic heterozygosity—its relationship to adaptive divergence

The genetic structure of nine Peromyscus maniculatus nebrascensis demes from southeastern Wyoming was determined by analyzing allozymes encoded by 23 genetic loci with polyacrylamide gel electrophoresis. Genetic variability is extremely high for two genetic parameters; the proportion of loci heterozygous per individual averaged 0.16, and the proportion of loci polymorphic per deme averaged 0.41. Previous estimates of genetic heterozygosity for species within the genus Peromyscus have a mean of 0.06. The results of the present study suggest that genetic heterozygosity is considerably higher within P. maniculatus demes than within demes of other species in the genus. Geographic range is correlated with heterozygosity among Peromyscus species, as is adaptive divergence into broad-niched species. These correlates suggest that high heterozygosity may reflect an adaptation to a variable environment.     

Genetic structure of Himalayan marmot (Marmota himalayana) population alongside the Qinghai–Tibet Railway

In order to verify the effect of social behavior and geographical isolation on the genetic structure of the Himalayan marmot (Marmota himalayana) population, we examined the genetic diversity of Himalayan marmots alongside the Qinghai–Tibet Railway using microsatellite markers. Eight microsatellite loci were used to examine 120 animals of 4 populations: Ulan (U), Delhi (D), Tuotuohe (T) and Ando (A). The results show that: (1) Himalayan marmots alongside the Qinghai–Tibet Railway are highly genetically diversified. The allele number (Na), effective allele number (Ne), observed heterozygosity (Ho), Nei’s expected heterozygosity (He) and polymorphism information content (PIC) of the total Himalayan marmot population were 4.75, 3.0332, 0.6990, 0.6672, 0.6102, respectively. (2) Himalayan marmots may be able to avoid inbreeding by a mechanism that will prevent the genetic diversity reduction caused by their social lifestyle. Heterozygote excess was observed at most loci. The inbreeding coefficients within the subpopulation (F_IS), in the total population (F_IT), the differentiation index of population (F_ST), and the gene flow (Nm) were ?0.2265, ?0.0477, 0.1458, and 1.4646, respectively. (3) The genetic differentiation of the Himalayan marmot population was in accordance with Wright’s “isolation by distance” theory. The Mantel test indicates that the correlation between genetic distance and geographic distance was significant (P < 0.05, r = 0.698). (4) Each of the four geographical populations had moderate differentiation. Both geographic distance and isolation could affect the population genetic structure of the Himalayan marmot. The maximum gene flow (3.5915), the smallest genetic differentiation index (0.0651), the lowest genetic distance (0.0700) and the highest genetic identity (0.9526) were all between the Ulan population and Delhi populations. (5) The cluster analysis, based on Nei’s standard genetic distance, showed that the populations of Delhi and Ulan were first merged in a cluster, and then Tuotuohe population was merged in the clustering. The Ando population was the last element in the clustering.