Genetic Structure Of Wild Populations Research Articles

ボノボ野生個体群の広域的な遺伝子構造：ミトコンドリアDNAタイプの多様性と分布（予報）

ボノボ野生個体群の広域的な遺伝子構造：ミトコンドリアDNAタイプの多様性と分布（予報）

Genetic diversity and genetic structure in wild populations of Mexican oregano (Lippia graveolens H.B.K.) and its relationship with the chemical composition of the essential oil

Mexican oregano is an aromatic plant traditionally harvested from wild populations by rural communities; however, there is little information about population genetics aspects of this species. Moreover, considering that the variation in essential oil production of aromatic plants has been attributed to several environmental as well as genetic factors, in this study we estimated the genetic diversity and genetic structure from 14 wild populations of L. graveolens located in four different bioclimatic regions in southeastern Mexico using AFLP markers. The overall genetic diversity of L. graveolens described as the percentage of polymorphic loci (PPL = 60.9 %) and Nei’s gene diversity (H j = 0.17) was moderate, but not associated with the bioclimatic conditions. Genetic variation was analyzed at chemotype and population levels. Regarding chemotypes, thymol had the highest genetic diversity (PPL = 82.8 % and H j = 0.22). PCoA revealed that chemotypes exhibit a certain level of genetic differentiation. Maximum parsimony dendrogram showed a grouping of individuals with a predominant chemotype. Bayesian analyses revealed a low, but significant differentiation among chemotypes (θ ΙΙ = 0.008). Regarding populations, gene diversity showed significant differences (F 13,1204 = 22.8, P < 0.001); populations dominated by individuals from the thymol chemotype showed the highest gene diversity (H j = 0.31–0.25), while populations with exclusively sesquiterpene chemotype showed the lowest value (H j = 0.058). Cluster and Bayesian analyses (θ ΙΙ = 0.027) revealed a low level of genetic differentiation among populations. Correlation analysis showed a significant association between the distance matrices based on the genetic markers (AFLP) and chemical compounds of essential oil (r = 0.06, P < 0.001). Our results suggest an important genetic influence on the observed chemical profiles. Nevertheless, other biotic and abiotic environmental pressures also play an important role in determining the chemotype and structure found in this aromatic species.

Genetic diversity and population structure of bocachico Prochilodus magdalenae (Pisces, Prochilodontidae) in the Magdalena River basin and its tributaries, Colombia

Prochilodus magdalenae is an endemic freshwater fish that occurs in the Magdalena, Sinú and Atrato hydrographic basins. It has an important economic role and is a food resource for the artisanal fishing communities. Its socioeconomic importance contrasts with the current status of its fisheries, where stocks are being depleted. Considering its importance and lack of information on its genetic structure, we used seven microsatellite markers to assess the genetic structure of wild populations of P. magdalenae. The genetic diversity was assessed and the population genetic structure was estimated through Fst, analysis of molecular variance and Bayesian analysis. A total of 290 alleles were found in all loci throughout all population. The high polymorphism contrasts with the levels of observed heterozygosity (Ho = 0.276), which are the lowest values recorded for the family. We found three populations of bocachico coexisting throughout the studied system, contradicting the hypothesis that freshwater migratory fish form panmictic populations. These results on the genetic structure of P. magdalenae constitute tools for a better understanding of the behavior and biology of this species, contributing to fish management and conservation programs.

Description of microsatellite markers in four mullids based on the development and cross-species amplification of 18 new markers in red mullet (Mullus barbatus)

Abstract We investigated the transferability and characterized the genetic diversity of 18 microsatellite markers newly developed for the red mullet ( Mullus barbatus ) in populations of four different species of the Mullidae family: the striped red mullet ( Mullus surmuletus ), the golden-banded goatfish ( Upeneus moluccensis ), the West African goatfish ( Pseudupeneus prayensis ) and the yellow goatfish ( Mulloidichthys martinicus ). Results indicate that the loci are polymorphic to different extent in M. surmuletus (94%), U . moluccensis (83%), P . prayensis (78%), and M . martinicus (67%). The high rates of successful cross-amplification of microsatellite loci among Mullidae species will offer excellent opportunities to investigate the genetic structure of wild populations, to explore their conservation genetics and fisheries management and to study any future interaction and introgression between them.

Andean bear Tremarctos ornatus natural history and conservation

ABSTRACT A wealth of information has been generated for the Andean bear Tremarctos ornatus during the past four decades, and a thorough review of the species' natural history, ecology and conservation is provided here. The Andean bear is the only remaining bear species in South America. Evolutionarily, it is the youngest of all ursids and the only remnant taxon within the subfamily Tremarctinae. The species is distributed throughout the Andes mountain range from Venezuela to Bolivia, but the limits of its current and past range are uncertain. The species is polyestrous, capable of delayed implantation and a facultative seasonal breeder. Genetic information is scarce, and species‐specific markers need to be developed for a more appropriate assessment of the genetic structure of wild populations. Andean bears inhabit a wide variety of habitats across the Andes including different forest types and high‐elevation grasslands. They are omnivorous with a frugivorous/folivorous emphasis that is reflected by adaptations of the typical tremarctine mandible. Andean bears are vulnerable to extinction due to land conversion and poaching. Efforts have been made to protect them, but threats have not been reduced significantly. Therefore, the species is expected to move faster towards extinction than any other carnivore in the region.

Genetic Structure in Wild Populations of Ayu Plecoglossus altivelis in Korea and Japan

We investigated the genetic structure of Korean and Japanese ayu Plecoglossus altivelis populations by examining 669 individuals from 14 populations using three microsatellite loci. Genetic variation did not differ significantly among the populations examined in terms of allelic number and heterozygosity. Korean populations were genetically close to each other, implying that persistent gene flow has occurred in these populations. This suggests that eastern populations in Korea form a single large population and all of the Korean populations are distinct from the Japanese populations. Pairwise population <TEX>$F_{ST}$</TEX> estimates, principal component analyses, and a neighbor-joining tree showed that genetic separation between the southern and pooled eastern coast populations was probably influenced by restricted gene flow. Hierarchical analysis of molecular variance (AMOVA) revealed a weak but significant genetic structure among three ayu groups (eastern and southern coasts of Korea and the Japan coast), and no genetic variation within groups. The estimated genetic population structure and potential applications of microsatellite markers may aid in the proper management of ayu populations.

Isolation and characterization of microsatellite loci in Santalum lanceolatum and Santalum leptocladum (Santalaceae)

Microsatellite primers were developed for the first time in the native Australian sandalwood species Santalum lanceolatum. • Using an enrichment cloning protocol, five novel polymorphic codominant loci were developed and characterized in S. lanceolatum and S. leptocladum. In addition to these, three existing microsatellite loci from other sandalwood species were successfully amplified and characterized for S. lanceolatum and S. leptocladum. Among the eight loci, allelic diversity ranged from 4 to 29. • Primers will be useful for studies of clonality, genetic diversity and spatial genetic structure in wild populations. When coupled with other molecular techniques will help investigate the relationship between S. lanceolatum and S. leptocladum, species of commercial and conservation interest.

Microsatellite variation and population genetic structure of a neotropical endangered Bryconinae species Brycon insignis Steindachner, 1877: implications for its conservation and sustainable management

Piabanha (Brycon insignis) is a freshwater fish species from the drainages in Southeastern Brazil. During the 1950s, it was an important economic and food resource for local populations, but dramatic and continuous environmental degradation seriously jeopardized the B. insignis populations in the region. Microsatellite markers were used to assess the genetic structure of wild populations of B. insignis and compare the genetic variability and integrity of the wild populations with a captive population. Samples of DNA from 208 specimens from geographically isolated populations were analyzed. Population genetic structure was investigated using F ST, R ST estimates as well as AMOVA. All five loci used in this study were polymorphic with observed heterozygosity ranging from 0.77 (± 0.15) to 0.88 (± 0.07) in the wild population and 0.90 (± 0.09) in the captive population and the allelic richness average were 7.56 (± 0.27) and 5.80 (± 1.02), respectively. Overall genetic differences were significantly partitioned among populations (F ST = 0.072, p = 0.034). Evidence of a genetic bottleneck was found in some of the wild populations, but especially in the captive population. The results showed that genetic variability still can be found in B. insignis populations which are currently structured possibly due to anthropic actions. The implications of these findings for the management and conservation of B. insignis populations are discussed.

Neutral markers mirror small-scale quantitative genetic differentiation in an avian island population

We still know remarkably little about the extent to which neutral markers can provide a biologically relevant description of population structure. In the present study, we address this question, and quantify microsatellite differentiation among a small, structured island population of great tits (Parus major), and a large mainland population 150 km away. Although only a few kilometres apart, we found small but statistically significant levels of differentiation between the eastern and the western part of the island. On the other hand, there was no differentiation between the western part of the island and the mainland population, whereas the eastern part and the mainland did differ significantly. This initially counterintuitive result provides powerful support for the hypothesis that the large genetic difference in clutch size between both parts of the island found earlier is maintained by different levels of gene flow into both parts of the island, and illustrates the capac! ity of microsatellites to provide a meaningful description of population structure. Importantly, because the level of microsatellite differentiation is very low, we were unable to infer any population structure without grouping individuals a priori. Hence, these low levels of differentiation in neutral markers could easily remain undetected, or incorrectly be dismissed as biologically irrelevant. Thus, although microsatellites can provide a powerful tool to study genetic structure in wild populations, they should be used in conjunction with a range of other sources of information, rather than as a replacement.

Sixty years of anthropogenic pressure: a spatio‐temporal genetic analysis of brown trout populations subject to stocking and population declines

Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with nonlocal strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation by distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation by distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analysing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.

Isolation and characterization of nine microsatellite loci from the pike‐perch, Sander lucioperca (Linnaeus, 1758)

In order to facilitate studies on the genetic structure of wild populations as well as to monitor genetic changes in cultured stocks, nine polymorphic microsatellite loci were isolated from pike-perch (Sander lucioperca). Single loci allele numbers varied between two (loci MSL-3 and MSL-7) and six (loci MSL-1 and MSL-2), and observed heterozygosities ranged from 0.36 (locus MSL-2) to 1.00 (locus MSL-9) in a test panel of 25 individuals. Only one pair of loci (MSL-5 and MSL-8) displayed significant linkage disequilibrium after sequential Bonferroni corrections. Hardy-Weinberg tests revealed significant excesses of heterozygotes at three loci (MSL-1, MSL-7, and MSL-9).

Population structure and diversity in sexual and asexual populations of the pathogenic fungus Melampsora lini.

Many pathogens undergo both sexual and asexual reproduction to varying degrees, yet the ecological, genetic and evolutionary consequences of different reproductive strategies remain poorly understood. Here we investigate the population genetic structure of wild populations of the plant pathogen Melampsora lini on its host Linum marginale, using amplified fragment length polymorphism (AFLP) markers, two genes underlying pathogen virulence, and phenotypic variation in virulence. In Australia, M. lini occurs as two genetically and geographically divergent lineages (AA and AB), one of which is completely asexual (AB), and the other able to reproduce both clonally and sexually (AA). To quantify the genetic and evolutionary consequences of these different life histories, we sampled five populations in each of two biogeographical regions. Analysis of AFLP data obtained for 275 isolates revealed largely disjunct geographical distributions for the two different lineages, low genetic diversity within lineages, and strong genetic structure among populations within each region. We also detected significant divergence among populations for both Avr genes and virulence phenotypes, although generally these values were lower than those obtained with AFLP markers. Furthermore, isolates belonging to lineage AA collectively harboured significantly higher genotypic and phenotypic diversity than lineage AB isolates. Together these results illustrate the important roles of reproductive modes and geographical structure in the generation and maintenance of virulence diversity in populations of M. lini.

The impact of local extinction on genetic structure of wild populations of lima beans (Phaseolus lunatus) in the Central Valley of Costa Rica: consequences for the conservation of plant genetic resources

Plant populations may experience local extinction and at the same time new populations may appear in nearby suitable locations. Species may also colonize the same site on multiple occasions. Here, we examined the impact of local extinction and recolonization on the genetic structure of wild populations of lima beans (Phaseolus lunatus) in the Central Valley of Costa Rica. We compared genetic diversity from the samples taken from the populations before and after extinction at 13 locations using microsatellite markers. Locations were classified according to the occurrence of extinction episodes during the previous five years into three groups: 1) populations that experienced extinction for more than one year, and were later recolonized (recolonized), 2) populations that did not experience local extinction (control), and 3) populations that did not experience local extinction during the study, but were cut to experimentally simulate extinction (experimental). Our data did not show a clear tendency in variation in allele frequencies, expected heterozygosity, and effective number of alleles within and between groups of populations. However, we found that the level of genetic differentiation between samples collected at different times at the same location was different in the three groups of populations. Recolonized locations showed the highest level of genetic differentiation (mean F(st) = 0.2769), followed by control locations (mean F(st) = 0.0576) and experimental locations (mean F(st) = 0.0189). Similar findings were observed for Neis genetic distance between samples (d(ij) = 0.1786, 0.0400, and 0.0037, respectively). Our results indicate that genetic change in lima beans depends on the duration and frequency of local extinction episodes. These findings also showed that control populations are not in equilibrium. Implications of these results for the establishment of conservation strategies of genetic resources of lima beans are discussed.

The genetic structure of endangered indigenous populations of the amago salmon, Oncorhynchus masou ishikawae, in Japan

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise FST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the 1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure of wild populations in the main channel of the River Koza.

Isolation and characterization of 149 novel microsatellite DNA markers for striped bass, Morone saxatilis, and cross‐species amplification in white bass, Morone chrysops, and their hybrid

AbstractTo support detailed genetic analysis of striped bass (Morone saxatilis) and white bass (Morone chrysops), we isolated 153 microsatellite loci from repeat‐enriched striped bass DNA libraries. Of these, 147 markers amplified in striped bass (average 4.7 alleles per locus) and 133 in white bass (average 2.2 alleles per locus). One hundred twenty‐two markers amplified in their hybrid. Development of new microsatellite markers will facilitate evaluations of genetic structure in wild populations and will support pedigree analysis and linkage mapping for selective breeding.

Isolation and characterization of microsatellite markers from the sweet passion fruit (Passiflora alata Curtis: Passifloraceae)

Abstract Passiflora alata is one of the commercialized species of the passion vines, grown for its edible fruits. It is found in South America, mainly Paraguay, Argentina, Peru and Brazil. The development of a set of microsatellite markers was proposed to provide tools for analysing both genetic structure of wild populations and the reproductive system of the species, which are poorly understood. Seven markers were developed from a P. alata‐genomic library enriched for simple sequence repeats (SSR). Twelve individuals were genotyped, and the levels of the expected heterozygosity (HE) did show that those markers could be used to develop P. alata genetic studies.

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.

Genetic variation in horticulturally important traits of fifteen wild lingonberry Vaccinium vitis-idaea L. populations

Plant breeding of lingonberry (Vaccinium vitis-idaea L.) is still in its infancy. In order to optimize sampling strategy to broaden the genetic base and to improve horticulturally important traits, we need more information about the genetic structure of wild populations. In a field study, seeds were collected from thirteen widely spaced lingonberry populations in Sweden, from one in Estonia and from one in Japan. The resulting seedlings were subsequently transferred into a field with a randomized design and were investigated regarding horticulturally important traits (growth, flowering, phenology and cropping performance). Common for all traits was that the amount of variation (mean for 17 traits: 21.8% ± 11.2) was smaller among populations than within populations. In spite of this low variation, the study revealed significant genetic variation (p<0.05) among populations in nearly all traits investigated. Significant correlations were found between several traits: between plant width and plant height (r=0.516, p<0.001),between plant height and total fruit yield (r=0.253, p<0.001),between number of rhizome-derived daughter plants and total fruit yield (r=–0.189, p<0.001) and between the beginning of spring flowering and the duration of repeat flowering (r=–0.354, p<0.001). Many traits were associated with the latitude of the sample location, e.g. duration of flowering (r=–0.620, p<0.05) and total fruit yield (r=–0.580, p<0.05). Populations collected from southern latitudes (56°–60°N) in general showed better values than the northern populations for horticulturally important traits. The Japanese population, which belongs to the subspecies minus, differed in many traits from all the other populations which belong to the subspecies vitis-idaea.

Population genetic structure in penaeid prawns

Genetic data are available for 27 species of penaeid prawn. Collected largely for fisheries purposes, they include information on several species of importance to aquaculture. Most studies used allozymes, but a small number have used mtDNA, random amplified polymorphic DNAs (RAPDs) and/or microsatellites. The DNA-based markers have revealed far greater levels of variation compared with the allozyme data. However, in the few cases for which joint information is available, the mtDNA and microsatellite information tended to confirm the spatial patterns of variation detected by allozymes. These revealed little genetic variation over long distances (thousands of kilometres) for many species, but relatively major shifts in gene, or genotype, frequencies over relatively short distances (hundreds of kilometres). Much of the genetic structure in wild populations appears to reflect historical events on large biogeographical scales, rather than resulting from patterns of present-day dispersal. Genetic variation in cultured stocks is generally less than in wild ones, the extent of the reduction being dependent upon broodstock management procedures. There is no conclusive evidence that aquaculture escapees have altered the genetic constitution of wild stocks of Penaeus monodon in Thailand. Nevertheless, the occurrence of strong patterns of geographic variation in wild stocks suggests that more detailed planning will be required to maintain this diversity, and to determine how best to capture its benefits for aquaculture.

Genetic variability of Colletotrichum lindemuthianum in wild populations of common bean

The genetic structure of wild populations of Colletotrichum lindemuthianum was evaluated for virulence and molecular markers. Forty‐five isolates were collected from five wild common bean populations located in their South‐Andean centre of origin. The five pathogen populations were monomorphic in their ITS regions, but 45 polymorphic markers were identified using RAPDs. Polymorphism for virulence was also observed; 15 pathotypes were characterized on an international set of 12 differentials. A molecular variance analysis (AMOVA) showed that a very large part of the total genetic variation was within populations. Statistical analysis showed that there was a weak though significant differentiation among the five populations for the RAPD and virulence markers. A positive and significant correlation was found between geographic distance and the distances from RAPD and virulence data, suggesting migration between adjacent populations along the Argentinian transect. Our results suggest that the Andean wild isolates of C. lindemuthianum do not reflect all the putative diversity found in the isolates from cultivated common bean.