Basic Population Genetic Parameters Research Articles

Population genetics of the endangered Clanwilliam sandfish Labeo seeberi: considerations for conservation management

The Cape Fold Ecoregion (CFE) is one of southern Africa’s unique aquatic ecoregions and its freshwater fish fauna is characterized by high levels of endemism. As with many other Mediterranean-type ecosystems, the region is also a hotspot for threatened and range-restricted freshwater fish. Many of the CFE’s endemic species are at risk for extinction, with declines in population sizes and distribution ranges. The Clanwilliam sandfish Labeo seeberi is an example of such a species and is considered one of South Africa’s most endangered large migratory cyprinids. This species is endemic to the Olifants/Doring river system in the CFE and has been subject to a major population decline, mainly as a result of invasive alien fish and adverse climate events. Little is known of the genetics of the Clanwilliam sandfish, thus this study aimed to provide basic population genetic parameters to inform future conservation interventions. Both microsatellite and mitochondrial DNA (mtDNA) markers were used to assess populations from three sites within the Olifants/Doring river system. Genetic diversity was moderate to low and did not reflect the drastic decline expected on the basis of previous relative abundance data. This is likely due to a lag effect between ecological/life history demographics (due to juvenile recruitment failures) and population genetic composition. Furthermore, there was limited genetic differentiation between the sampling locations, suggesting a single breeding population, but mtDNA haplotype distribution and slight divergence of the smaller populations does suggest that the population might have become recently fragmented. The results show that the effective population size of the current breeding population might still be sufficient to maintain evolutionary potential in the short term, which could act as a buffer until conservation strategies focusing on protecting breeding animals and maximizing juvenile survival can restore population numbers.

Population genetic SNP analysis of marble and brown trout in a hybridization zone of the Adriatic watershed in Slovenia

Marble trout (Salmo marmoratus) is an extensively managed salmonid taxon threatened by historical introductions of non-native brown trout (Salmo trutta) of different origins into habitats in the northern part of its distribution, namely the Po river system and the Slovenian part of the Adriatic watershed. Hybridization between marble trout and brown trout results in fertile offspring, creating an extensive zone of genetic mixing, with varying amount of introgression. A rehabilitation programme for marble trout has been undertaken in Slovenia for two decades, dependent upon eight non-introgressed marble trout populations inhabiting isolated streams in the upper Soča river valley. MtDNA and a new marker system based on nuclear DNA, designed for identification of trouts and their hybrids in the genus Salmo, were used to determine the extent of introgressive hybridization between marble and brown trout across a large area of the Adriatic watershed in Slovenia. Individual admixture coefficients, the posterior probability of each individual belonging to one or other of the parental species and user-defined categories of admixture were determined along with basic population genetic parameters, revealing variable intensity and patterns of individual introgression throughout the zone of hybridization. In most of the populations analysed, hybridization of native marble trout with the introduced Atlantic lineage of brown trout was observed. In the upper Soča river system a high proportion of genetically non-introgressed (pure) marble trout was found, enabling selection of these fish for supplementary material in the reintroduction programme. Conclusions regarding management of marble trout in Slovenia can be inferred from the patterns observed in the present study: (1) transfer of pure populations to fishless or fished-out streams is recommended, (2) to sustain genetic diversity of the species, non-introgressed individuals sorted out from the zone of hybridization should be used to produce juveniles for supplementation stocking in fish farms, and (3) extension of the marble trout repopulation programme to highly introgressed populations in small unmanaged streams, which represent a potential source for downstream genetic ‘contamination’.

Population genetic study of the raccoon dog (<i>Nyctereutes procyonoides</i>) in South Korea using newly developed 12 microsatellite markers

The raccoon dog (Nyctereutes procyonoides) is distributed from southeastern Siberia to northern Vietnam, including Korea and Japan, as well as Europe. In Korea, most of its predators and competitors are extinct, which has resulted in rapid growth of the raccoon dog population. This population increase has raised concerns about its role in the ecosystem and the zoonotic transfer of various contagious diseases, and thus an effective method of raccoon dog population control in Korea is required. To investigate the genetic diversity and structure of raccoon dog populations, 12 polymorphic microsatellite loci were identified and characterized. These novel microsatellite markers were employed to obtain basic population genetic parameters for 104 N. procyonoides specimens from five locations in South Korea. The mean allele number of 12 loci across samples was 8.7, and the number of alleles per locus ranged 2-13. Mean expected and observed heterozygosities were 0.723 and 0.619, respectively. Genetic differentiation, estimated by pairwise FST, was significant for all population pairs excepting Seoul/Gyeonggi and Gangwon pair, with a moderate level of genetic differentiation for all the population pairs (mean FST = 0.054), but little differentiation between Seoul/Gyeonggi and Gangwon (FST = 0.024). Bayesian-based clustering analysis predicted that Korean raccoon dog population is composed of four distinct genetic subpopulations. These genetic information and structure of raccoon dog will be very useful to prevent spreading infectious diseases.

Genetic population structure of the malaria vector Anopheles baimaii in north-east India using mitochondrial DNA

BackgroundAnopheles baimaii is a primary vector of human malaria in the forest settings of Southeast Asia including the north-eastern region of India. Here, the genetic population structure and the basic population genetic parameters of An. baimaii in north-east India were estimated using DNA sequences of the mitochondrial cytochrome oxidase sub unit II (COII) gene.MethodsAnopheles baimaii were collected from 26 geo-referenced locations across the seven north-east Indian states and the COII gene was sequenced from 176 individuals across these sites. Fifty-seven COII sequences of An. baimaii from six locations in Bangladesh, Myanmar and Thailand from a previous study were added to this dataset. Altogether, 233 sequences were grouped into eight population groups, to facilitate analyses of genetic diversity, population structure and population history.ResultsA star-shaped median joining haplotype network, unimodal mismatch distribution and significantly negative neutrality tests indicated population expansion in An. baimaii with the start of expansion estimated to be ~0.243 million years before present (MYBP) in north-east India. The populations of An. baimaii from north-east India had the highest haplotype and nucleotide diversity with all other populations having a subset of this diversity, likely as the result of range expansion from north-east India. The north-east Indian populations were genetically distinct from those in Bangladesh, Myanmar and Thailand, indicating that mountains, such as the Arakan mountain range between north-east India and Myanmar, are a significant barrier to gene flow. Within north-east India, there was no genetic differentiation among populations with the exception of the Central 2 population in the Barail hills area that was significantly differentiated from other populations.ConclusionsThe high genetic distinctiveness of the Central 2 population in the Barail hills area of the north-east India should be confirmed and its epidemiological significance further investigated. The lack of genetic population structure in the other north-east Indian populations likely reflects large population sizes of An. baimaii that, historically, were able to disperse through continuous forest habitats in the north-east India. Additional markers and analytical approaches are required to determine if recent deforestation is now preventing ongoing gene flow. Until such information is acquired, An. baimaii in north-east India should be treated as a single unit for the implementation of vector control measures.

Isolation and characterization of 12 microsatellite loci from Korean water deer (Hydropotes inermis argyropus) for population structure analysis in South Korea

The main goals of this study were to isolate microsatellites markers of Korean water deer (Hydropotes inermis argyropus) and understand the genetic status of the species in South Korea. Twelve new microsatellite loci were isolated and characterized to establish basic population genetic parameters for 45 H. i. argyropus specimens in South Korea. There were no significant regional or genetic structure differences between the mid-eastern and southwestern populations in South Korea according to the population genetic analyses. The number of alleles per locus ranged from two to 13 with an average of 6.08. Mean expected (H E) and observed heterozygosity (H O) were 0.622 and 0.533, respectively. Microsatellite variability was also not significant between the two regions (F ST=0.012). These new markers should facilitate the future population genetics studies of Korean water deer and other closely related species.

Patterns of Genetic Variation Within and Between Gibbon Species

Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5–6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ∼60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.

How do population genetic parameters affect germination of the heterocarpic species Atriplex tatarica (Amaranthaceae)?

The heterocarpic species Atriplex tatarica produces two types of seeds. In this study, how basic population genetic parameters correlate with seed germinability under various experimental conditions was tested. Population genetic diversity was ascertained in eight populations of A. tatarica by assessing patterns of variation at nine allozyme loci. Germinability of both seed types from all sampled populations was determined by a common laboratory experiment under different salinity levels. Basic population genetic parameters, i.e. percentage of polymorphic loci, average number of alleles per locus and observed heterozygosity were correlated with observed population germination characteristics. Atriplex tatarica possesses a remarkable heterocarpy, i.e. one type of seed is non-dormant and the other shows different dormancy levels in relation to experimental conditions. Significant negative correlations have been detected between germination of both seed types and the coefficient of inbreeding, and a significant negative correlation between germination of dormant seeds and other population genetic parameters, i.e. percentage of polymorphic loci and average number of alleles per polymorphic locus. Moreover, populations from the region characterized by a shorter growing season manifested higher germinability, i.e. had lower dormancy, than those from the lower-latitude one. In general, germination of non-dormant seeds is probably not under strong genetic control. Hence, they germinate as soon as conditions are favourable, thus ensuring survival in the short term, but populations risk local extinction if conditions become adverse (i.e. a high-risk strategy). In contrast, germination of the dormant type of seeds is under stronger genetic control and is significantly correlated with basic population genetic parameters. These seeds ensure long-term reproduction and survival in the field by protracted germination, albeit in low quantities (i.e. A. tatarica also adopts a low-risk strategy).

Genetic Diversity and Gene Flow in Yellowstone Basin Pronghorn (Antilocapra Americana)

Yellowstone National Park's northern range is home to a geographically isolated population of pronghorn (Antilocapra americana) greatly reduced from historic levels of abundance. The genetic consequences of demographic declines in this population over the past 150 years are unknown, and the rates of genetic exchange among this and other populations in the Yellowstone basin are also unknown. We used 18 nuclear DNA microsatellite loci and noninvasively collected fecal samples from 73 individuals to quantify basic population genetic parameters and gene flow within and among the Yellowstone pronghorn population, a new population in the Paradise Valley, and a large population near Livingston, MT. Evidence for a genetic bottleneck in Yellowstone was strong based on several tests of heterozygote excess (Wilcoxon tests P≤ 0.033) and the relative ratio of allele richness to allele size range (M =0.283). However, mean population heterozygosity was high (HO = 0.665), and no indications of inbreeding were detected. Gene flow from elsewhere in the Yellowstone basin to Yellowstone National Park is extremely low. However, emigration from Yellowstone to the Paradise Valley population is high (26.7%), reinforcing conclusions based on behavioral data that this new population was founded by Yellowstone individuals. Despite years of population decline and genetic isolation, Yellowstone pronghorn appear to retain substantial genetic diversity.

Isolation and characterization of microsatellite loci from the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae)

AbstractWe report the isolation and development of 81 novel primers for amplifying microsatellite loci in the Rhagoletis pomonella sibling species complex, and the sequencing, characterization and analysis of basic population genetic parameters for nine of these genes. We also report the successful cross‐species amplification of several of these loci. The R. pomonella sibling species complex is a textbook example of genetic differentiation in sympatry via host‐plant shifting. Microsatellite markers can be useful for mapping host‐plant‐associated adaptations in Rhagoletis that generate reproductive isolation and facilitate speciation, as well as for resolving the genetic structure and evolutionary history of fly populations.

Tissue enzyme loci for routine genotyping in Norway pout ( Trisopterus esmarkii Nilsson, 1855): Electrophoresis conditions, tissue manifestations, allele designations and basic population genetic parameters

In order to find polymorphic tissue enzymes and suitable buffer systems for use in population genetic studies of Norway pout ( Trisopterus esmarkii ), a pilot study was performed using 30 individual specimens from one location. A set of potentially useful genetic markers was established, based on electrophoretic analysis of 22 different tissue enzymes in three different buffer systems. The initial analyses revealed 31 putative loci, from which eight were considered to be reliable in routine scoring. Here, a total of 1797 specimens of Norway pout, from 23 individual locations in the fjords and coastal waters of Norway, were scored for these eight loci. Variant alleles were found at all loci. At least five of the loci were polymorphic by the 0.99 criterion ( LDH-2 *, GPI-1 *, GPI-2 *, G3PDH-2 *, IDHP-2 *) and one locus also by the 0.95 criterion ( LDH-2 *). The frequency of polymorphic loci were P 0.99 ≥ 0.625 and P 0.95 = 0.125. The average heterozygosity over all loci based on Hardy-Weinberg expectation...

Experience from Lipizzan horse and salmonid species endemic to the Adriatic river systemExamples for the application of molecular markers for preservation of biodiversity and management of animal genetic resources

Management of breeding- and free-living populations, traditionally based on phenotypic traits, relays more and more on availability of reliable information about the basic population genetic parameters as heterozygosity, mean number of alleles per locus, percentage of polymorphic loci, population structuring, genetic distances and others. Therefore, the application of molecular markers, revealing a great deal of phenotypically hidden information, becomes inevitable for population analysis. Conservation geneticists use this information for implementation of appropriate management policies. Application of molecular markers in Lipizzan horse breed, which is an example for a pedigreed breeding population, and in two endangered salmonid fish populations in Slovenia, are presented. In the Lipizzan horse breed, an insight in the population structure, overall heterozygosity, relationship between population parameters and phenotypic traits and reliability of pedigree data was gained by using molecular markers. Marble trout and Adriatic grayling were selected as examples for free-living populations, seriously endangered by human activity in the past. Development of informative molecular markers, their application and suggestions for appropriate conservation actions are described.

Experience from Lipizzan horse and salmonid species endemic to the Adriatic river system: Examples for the application of molecular markers for preservation of biodiversity and management of animal genetic resources

Management of breeding- and free-living populations, traditionally based on phenotypic traits, relays more and more on availability of reliable information about the basic population genetic parameters as heterozygosity, mean number of alleles per locus, percentage of polymorphic loci, population structuring, genetic distances and others. Therefore, the application of molecular markers, revealing a great deal of phenotypically hidden information, becomes inevitable for population analysis. Conservation geneticists use this information for implementation of appropriate management policies. Application of molecular markers in Lipizzan horse breed, which is an example for a pedigreed breeding population, and in two endangered salmonid fish populations in Slovenia, are presented. In the Lipizzan horse breed, an insight in the population structure, overall heterozygosity, relationship between population parameters and phenotypic traits and reliability of pedigree data was gained by using molecular markers. Marble trout and Adriatic grayling were selected as examples for free-living populations, seriously endangered by human activity in the past. Development of informative molecular markers, their application and suggestions for appropriate conservation actions are described.

Understanding the genetic architecture of a quantitative trait in gymnosperms by genotyping haploid megagametophytes

The gymnosperms are a group of plants characterized by a haploid female gametophyte (megagametophyte). With the function of bearing the female gametes and nourishing the developing embryo, the megagametophyte has provided a simple way to understand the genetics of gymnosperm species using biochemical or genetic markers. In this paper, a quantitative genetic approach is proposed to study the genetic architecture of a quantitative trait in gymnosperms by taking advantage of the megagametophyte and the concept of average effect of a gene. Average effect describes the value associated with an allele carried by an individual and transmitted to its offspring. Through the genetic dissection of the average effect and genetic variance associated with a gamete carrying candidate genes, this approach can provide estimates of basic population genetic parameters, such as additive, dominant and epistatic effects, allelic frequencies and linkage disequilibrium. The candidate genes, known through their major mutant phenotype, have been reported in gymnosperms. An example for a candidate gene affecting lignin biosynthesis was applied to demonstrate the statistical procedures of the approach and its advantage. The conditions upon which the approach can be effectively used are discussed.

Estimation of heterozygosity for single-probe multilocus DNA fingerprints.

In spite of the increasing application of DNA fingerprinting to natural populations and to the genetic identification of humans, explicit methods for estimation of basic population genetic parameters from DNA fingerprinting data have not been developed. Contributing to this omission is the inability to determine, for multilocus fingerprinting probes, relatively important genetic information, such as the number of loci, the number of alleles, and the distribution of these alleles into specific loci. One of the most useful genetic parameters that could be derived from such data would be the average heterozygosity, which has traditionally been employed to measure the level of genetic variation within populations and to compare genetic variation among different loci. We derive here explicit formulas for both the estimation of average heterozygosity at multiple hypervariable loci and a maximum value for this estimate. These estimates are based upon the DNA restriction-pattern matrices that are typical for fingerprinting studies of humans and natural populations. For several empirical data sets from our laboratory, estimates of average and maximal heterozygosity are shown to be relatively close to each other. Furthermore, variances of these statistics based on simulation studies are relatively small. These observations, as well as consideration of the effect of missing alleles and alternate numbers of loci, suggest that the average heterozygosity can be accurately estimated using phenotypic DNA fingerprint patterns, because this parameter is relatively insensitive to the lack of certain genetic information.