Pairwise FST Comparisons Research Articles

Distribution and genetic diversity of cobitid species in Iran (Teleostei: Cobitidae)

Several species of Cobitis have been reported within Iran, but only four are recognized as valid. The geographical distribution and genetic diversity of these species are not well-known. Two new populations of C. saniae and C. avicennae were reported herein based on their morphological and phylogenetic characters from the Mahabad River, a tributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkheh drainage, respectively. The genetic diversity and genetic structure of populations of C. saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of the mitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan, and Georgia were used. A moderate to high level haplotype diversity and low nucleotide diversity were found in most of the populations of all three species. The AMOVA test and pairwise FST comparison revealed significant genetic structure and genetic distance between the Urmia Lake basin and other C. saniae populations. The results highlight the importance of conserving these species and their habitats, particularly in the Urmia Lake basin, where significant genetic differentiation was observed.

Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli

The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.

Genetic Analysis Reveals Substantial Proportion of Non-targeted Tilapias among Farmed Stocks in Kilosa and Kibaha, Tanzania

Nile tilapia farmers in Tanzania have been complaining about slow growth and low yields. Since some farmers obtain their seeds from unreliable sources, they may potentially be dealing with various non-targeted tilapias that require different environments and treatments to enhance growth and yields. Thus, this study analysed fragments (600 base pairs) of the cytochrome oxidase subunit I gene (COI) from 74 farmed tilapias in Kilosa and Kibaha, Tanzania to determine the presence of non-targeted tilapias. An additional 42 samples from the Magadu Fish Farm, Mindu dam, and Lake Victoria were included for comparison. The findings revealed that non-targeted tilapias accounted for 22.22–31.41% of the farmed stock, supporting the hypothesis that farmers are unknowingly dealing with a variety of non-targeted tilapias. Furthermore, pairwise FST comparison indicated genetic relatedness among the farmed fish, suggesting the sharing of fingerlings from the same broodstock or collection from the same wild locality. Therefore, farmers are advised to ensure they source seeds from certified hatcheries to minimize the risk of stocking non-targeted species. Additionally, due to the observed low genetic diversity in Kilosa samples, it is recommended that the country should establish a national breeding program for tilapia to provide farmers with access to high-quality seeds.

Population genetics of the hound needlefish Tylosurus crocodilus (Belonidae) indicate high connectivity in Tanzanian coastal waters

ABSTRACT The hound needlefish Tylosurus crocodilus (Belonidae) is a highly demanded fish in the local markets of Tanzania, but the growing coastal population threatens its sustainability. As belonids are highly migratory fishes utilising various parts of the seascape, increased fishing pressure may disrupt connectivity patterns on different spatiotemporal scales and disaggregate populations. Using the COI gene, this study assessed the genetic population structure, connectivity patterns, and historical demography of T. crocodilus collected in seven sites spread along Tanzanian coastal waters. Results showed fourteen haplotypes with low overall nucleotide and haplotype diversity. Pairwise FST comparisons revealed no significant differences among the sampled sites, except for the northernmost site (Tanga) and an island in the south (Songosongo). Analysis of molecular variance (AMOVA) revealed a non-significant genetic structure among populations (FST = 0.01782), suggesting the fishery across Tanzanian waters exploits the same population. Moreover, there was no correlative relationship between genetic and pairwise geographic distances, rejecting the isolation by distance hypothesis. However, neutrality tests and mismatch distribution analysis revealed that recent demographic expansion might exist. Empirical evidence of panmixia suggests high genetic connectivity. In combination with low genetic diversity, management should be directed to actions that prevent genetic diversity loss and the effect of genetic drift on populations.

Applying genomic approaches to delineate conservation strategies using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula as a model

Effective conservation actions to counteract the current decline of populations and species require a deep knowledge on their genetic structure. We used Single Nucleotide Polymorphisms (SNPs) to infer the population structure of the highly threatened freshwater pearl mussel Margaritifera margaritifera in the Iberian Peninsula. A total of 130 individuals were collected from 26 locations belonging to 16 basins. We obtained 31,692 SNPs through Genotyping by Sequencing (GBS) and used this dataset to infer population structure. Genetic diversity given as observed heterozygosity was low. Pairwise FST comparisons revealed low levels of genetic differentiation among geographically close populations. Up to 3 major genetic lineages were determined: Atlantic, Cantabrian and Douro. This structure suggests a close co-evolutionary process with brown trout (Salmo trutta), the primordial fish host of this mussel in the studied area. Some sub-basins showed some genetic structuring, whereas in others no intrapopulation differentiation was found. Our results confirm that genetic conservation units do not match individual basins, and that knowledge about the genetic structure is necessary before planning recovery plans that may involve relocation or restocking. The same reasoning should be applied to strictly freshwater species that are sessile or have restricted dispersal abilities and are currently imperiled worldwide.

Genetic origin and differentiation of ten paddy field–farmed Cyprinus carpio strains in China

The common carp Cyprinus carpio has three subspecies, C. c. haematopterus, C. c. rubrofuscus, and C. c. carpio, and is also the main aquaculture species kept in paddy fields, known as paddy field carp (PFC). Many aquaculture strains of PFC have been developed worldwide. However, the contributions of each subspecies to the genetic material of many strains remain poorly understood. Moreover, the levels of genetic differentiation among these strains were defectively investigated due to limited sample coverage and molecular loci in previous reports. In this study, we collected 10 PFC strains in China, and used two mitochondrial loci (cytochrome b oxidase and the control region) and six microsatellite loci to trace their genetic origin and assess genetic differentiation among these strains. A constructed haplotype network provided evidence that PFC strains contained matrilineal genetic material from two common carp subspecies, C. c. haematopterus and C. c. rubrofuscus. The matrilineal genetic origin of cultivated strains could be traced to C. c. rubrofuscus in most cases. Genetic diversity calculations and Bayesian cluster analysis found that the Ruyuan Shili carp showed lower genetic diversity than the other strains and harbored simplex genetic resources, which was likely a result of inbreeding, intensive selection or a lack of systematic selection. Analysis of molecular variance and pairwise FST comparisons revealed statistically significant genetic differentiation among the analyzed PFC strains, and between populations within Heibei carp and Jinbei carp strains, suggesting that different PFC strains or localities may possess endemic genetic properties. Taken together, the present study provides important implications for the management of PFC, and could assist in improving monitoring programs for this historically significant aquaculture species.

Effect of chronic radiation on the flax (Linum usitatissimum L.) genome grown for six consecutive generations in the radioactive Chernobyl area.

The growth of plants under chronic radiation stress in the Chernobyl area may cause changes in the genome of plants. To assess the extent of genetic and epigenetic changes in nuclear DNA, seeds of the annual crop flax (Linum usitatissimum L.) of the Kyivskyi variety, sown 21 years after the accident and grown for six generations in radioactive (RAD) and remediated (REM) fields were analysed. Flaxseed used for sowing first generation, which served as a reference (REF), was also analysed. The AFLP (Amplified Fragment Length Polymorphism) revealed a higher number of specific EcoRI-MseI loci (3.4-fold) in pooled flaxseed samples harvested from the RAD field compared with the REM field, indicating a link between the mutation process in the flax genome and the ongoing adaptation process. MSAP (Methylation-Sensitive Amplified Polymorphism) detecting EcoRI-MspI and EcoRI-HpaII loci in flax nuclear DNA genome showed no significant differences in methylation level, reaching about 33% in each of the groups studied. On the other hand, significant changes in the DNA methylation pattern of flaxseed samples harvested from the RAD field compared with controls were detected. Pairwise FST comparison revealed within both, EcoRI-MspI and transformed methylation-Sensitive data sets more than a 3-fold increase of genetic divergence in the RAD field compared with both controls. These results indicate that the nuclear genome of flax exposed to chronic radiation for six generations has more mutations and uses DNA methylation as one of the adaptation mechanisms for sustainability under adverse conditions.

Population Genetics Reveals That the Western Tianshan Mountains Populations of Agrilus mali (Coleoptera: Buprestidae) May Have Not been Recently Introduced.

Agrilus mali Matsumura is a wood-boring beetle that aggressively attacks species of the genus Malus, that has recently caused serious damage to the wild apple tree M. sieversii (Lebed.) in the western Tianshan Mountains in Xinjiang. It was first detected there in the early 1990s and spread rapidly, being thus considered a regional invasive pest. To explore the possible outbreak mechanism of the local population and characterize the genetic differentiation of A. mali across different regions of China, we used three mitochondrial genes (COI, COII, and CytB) to investigate the genetic diversity and genetic structure of 17 A. mali populations containing 205 individuals collected from five Chinese provinces. Among them, nine populations were from the western Tianshan Mountains. Ultimately, of the 136 pairwise F st comparisons, 99 showed high genetic differentiation among overall populations, and Tianshan populations exhibited significant differentiation with most of the non-Tianshan populations. Furthermore, A. mali populations represented relatively abundant haplotypes (54 haplotypes). Nine populations from the Tianshan Mountains showed 32 haplotypes (26 of which were unique), displaying relatively high genetic diversity. Additionally, the Mantel test revealed population genetic differentiation among either overall populations or the Tianshan Mountains populations, likely caused by geographical isolation. Phylogenic relationships showed that all populations clustered into three clades, and Tianshan Mountains populations, including CY, occupied one of the three clades. These results suggest that A. mali in the western Tianshan region has possibly been present in the area for a long period, and may not have been introduced recently. Highly frequent gene flows within Tianshan populations are possibly caused by human activities and may enhance the adaptability of A. mali along the western Tianshan Mountains, leading to periodic outbreaks. These findings enhance our understanding of jewel beetle population genetics and provide valuable information for pest management.

Linkage disequilibrium and population structure in a core collection of Brassica napus (L.).

Estimation of genetic diversity in rapeseed is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed germplasm using 8,502 single nucleotide polymorphism (SNP) markers. We divided the germplasm collection into five subpopulations (P1 to P5) according to geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Admixture model based structure analysis, principal component and neighbor-joining tree analysis placed all subpopulations into three distinct clusters. Admixed genotype constituted 29.24% of total genotypes, while remaining 70.76% belongs to identified clusters. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb); relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. The findings regarding LD pattern and population structure will help to utilize the collection as an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.

Genetic population structure of summer flounder Paralichthys dentatus using microsatellite DNA analysis

Summer flounder Paralichthys dentatus supports one of the most valuable commercial and recreational fisheries along the Atlantic Coast of the U.S. However, in recent decades the management of this species has proven to be one of the most contentious for any exploited marine resource in the region. A coastwide catch quota is imposed annually for summer flounder of which 60% is allocated to the commercial fishery and 40% to the recreational fishery. The allocation is further divided among the individual coastal states from North Carolina to Massachusetts based on their landings in the 1980s. This process, based on political jurisdictions, does not consider the species’ biological stock structure. Previous genetic studies (allozyme, mtDNA, and SNPs) provided contradictory results regarding the possible population structure of summer. To address this issue, we used DNA microsatellite analysis at 9 loci to define the coastwide population structure of summer flounder. In total, 1182 specimens were analyzed from 18 collection sites. Most collections were from the Continental Shelf during the fall-winter spawning season. These were supplemented with additional samples from inshore waters from North Carolina to Florida, and inshore sites which support significant recreational fisheries at Nantucket Shoals, Massachusetts and Fire Island, New York. The overall level of genetic differentiation in pairwise comparisons between collections was very low, mean FST= 0.001. There was no evidence of genetic differentiation between collections from north and south of Cape Hatteras. Our microsatellite results are consistent with an earlier SNP study which failed to find significant allelic heterogeneity among coastwide collections of summer flounder. However, a subset of pairwise FST comparisons between some collections proved statistically significant. Furthermore, in STRUCTURE analysis we found evidence of two genetic clusters within the species’ northern landings area, however, this finding was not supported by DPAC analysis. We conclude that summer flounder most likely constitute a single population along their entire Atlantic Coast distribution.

Historical Connectivity and Demography of the Ferocious Reef Crab, Eriphia ferox (Crustacea; Eriphiidae), Demonstrate That Taoyuan Algal Reef Is an Essential Population Source Along the East Taiwan Strait

The east Taiwan Strait is largely fringed by sandy and muddy habitats. However, a massive algal reef made of crustose coralline algae has been found along the coast off Taoyuan city in northwestern Taiwan. The porous structure of Taoyuan Algal Reef harbors high abundance and diversity in marine organisms, including the ferocious reef crab, Eriphia ferox. Such a pivotal geographic location and unique ecological features make Taoyuan Algal Reef a potential stepping stone connecting biotic reefs in the east Taiwan Strait, South China Sea to the south, and even the high latitude of Japan to the north. In this study, we examined the population connectivity and historical demography of E. ferox by analyzing mitochondrial cytochrome oxidase I (COI) fragments of 317 individuals sampled from 21 localities in the northwestern Pacific. Our analyses of haplotype network and pairwise FST comparisons revealed a lack of phylogeographical structure among E. ferox populations, implying the existence of a migration corridor connecting the South and East China Seas through the east Taiwan Strait. Multiple lines of evidence, including significant values in neutrality tests, unimodally shaped mismatch distributions, and Bayesian skyline plots elucidated the rapid population growth of E. ferox following the sea-level rise after Last Glacial Maximum (ca. 2–10 Ka). Such demographic expansion in E. ferox coincided with the time when Taoyuan Algal Reef started to build up around 7,500 years ago. Coalescent migration analyses further indicated that the large and continuous E. ferox population exclusively found in Datan Algal Reef, the heart of Taoyuan Algal Reef, was a source population exporting migrants both northward and southward to the adjacent populations. The bidirectional gene flow should be attributed to larval dispersal by ocean currents and secondary contact due to historical population expansion. Instead of serving as a stepping stone, our results support that Taoyuan Algal Reef is an essential population source for biotic reef-associated species along the east Taiwan Strait, and highlight the importance of conserving such a unique ecosystem currently threatened by anthropogenic development.

Deep genetic structure of a ground-herb along contrasting environments of seasonally dry understories in Amazonia and Cerrado as revealed from targeted genomic sequencing

AbstractCentral South America primarily comprises seasonally dry tropical domains, where a sharp rainy season defines phenological and yearly growth patterns. Here we examine if the genetic structure of the understorey ground-herb Chamaecostus subsessilis species complex, from South American seasonally dry forests, is defined by intrinsic contrasting environments of the Cerrado and southern Amazonia. We analysed a dataset of c. 20 kb of sequence data from targeted capture high-throughput sequencing using PCR-generated probes. We used an admixture model and population pairwise FST comparisons to interpret genetic structure. We also used a Bayesian coalescent approach with a relaxed clock to estimate divergence times between populations and haplotypes. Genetic structure reflects separate populations from Amazonia and from the Cerrado, whereas a haplotype-based phylogenetic tree provides further spatiotemporal evidence of this strong phylogeographical structure. Spatial arrangements among genetic lineages of the C. subsessilis species complex reveal that intraspecific evolution in Central South America seasonally dry understories is closely linked to environmental gradients.

Genetic Differentiation for Gene Diversity among Pearl Millet (Pennisetum glaucum (L.) R. Br.) Landraces As Revealed by SSR Markers

Pearl millet (Pennisetum glaucum) is one the most important crops in Burkina Faso. Knowledge of the genetic parameters of different pearl millet landraces grown in Burkina Faso is of great importance for improvement and breeding programs of pearl millet. In this study, 20 pairs of SSR markers were used to compare and analyze the genetic diversity of 86 landrace populations. Results show a total of 67 alleles detected and each locus varies between 2 and 6 with an average of 4 alleles per marker. The probability to having two different alleles per locus was 0.61. The values of genetic diversity parameters of pearl millet populations from the northern region of the country were higher than those from the others regions. The analysis indicates that, over time, alleles are lost and new alleles are added. Analysis of molecular variance showed genetic variation was primarily a function of differences in cultivated populations. Most pairwise FST comparisons between provenances were at a statistically significant level. Our study will provide a scientific basis for the effective management and utilization of germplasm resources of pearl millet populations.

Population Genetic Structure and Phylogeography of Co-Distributed Pachymeniopsis Species (Rhodophyta) along the Coast of Korea and Japan

Inferring phylogeographic patterns of macroalgal species is essential for understanding the population structure and for the conservation of macroalgal species. In this study, the phylogeographic patterns of two co-distributed macroalgal species along the coast of Korea and Japan, Pachymeniopsis lanceolata and Pachymeniopsis elliptica, were analyzed. Pachymeniopsis lanceolata (215 specimens from 36 sites) and P. elliptica (138 specimens from 24 sites), using the plastid rbcL gene, are characterized by fifteen and six haplotypes, respectively. Mitochondrial COI-5P gene sequences revealed a low variation for both species. An analysis of molecular variance (AMOVA), pairwise FST comparisons, and haplotype networks based on the rbcL data suggest a weak genetic differentiation of both species. The shared haplotypes (P. lanceolata: LR01; P. elliptica: ER01) found in the entire sampling range indicate that these two Pachymeniopsis species can disperse over long distances along the coast of Korea and Japan. Despite the similar phylogeographic pattern, our results suggest that P. lanceolata has a higher genetic diversity, with a wider distribution along the Korean Peninsula than P. elliptica. Moreover, it is adapted to low sea surface temperatures and survived in more of the available habitats during periods of climatic change, whereas P. elliptica is less adaptable and more susceptible to environmental disturbance. This phylogeographic study provides a rationale for the conservation of the wild Pachymeniopsis population.

Genetic diversity and contemporary population genetic structure of Avicennia marina from Mozambique

The aim of this study was to determine the genetic diversity and population genetic structure of Avicennia marina, an important mangrove tree species with a wide distribution. Samples were collected from four sampling localities, characterised by different environmental conditions, situated along the coast of Mozambique within southern Africa: Pemba-Metuge, Bons Sinais Estuary, Costa do Sol and Inhaca Island. We used five species-specific polymorphic microsatellite loci for screening 20 samples from each of the sampling localities. The overall level of polymorphism observed was relatively high with 3–22 alleles detected at each locus. AMOVA showed the highest level of variation, 96.6 %, was located within populations. Pairwise FST comparisons were non-significant between sampling localities. No isolation by distance was detected. Structure results suggested the presence of one population after independent clustering of all samples. The results showed high levels of gene flow for A. marina along the coast of Mozambique and suggested the absence of barriers to gene flow. The results and information from this study will inform strategies for the conservation of A. marina. We discuss the importance of preserving the mangrove forest, supported by our own result, by managing and reducing anthropogenic activities that can damage the genetic diversity within these localities that are under high pressure due to urban growth. This will positively contribute to how and where effort and resources should be focused on for its conservation and sustainable management and utilisation.

Prioritising source populations for supplementing genetic diversity of reintroduced southern brown bandicoots Isoodon obesulus obesulus

Reintroduction programs can benefit from optimisation of source populations to maximise genetic diversity. Here, we report an approach to guide genetic supplementation of founder individuals to maximise genetic diversity in a reintroduction program for a nationally threatened Australian ground-dwelling marsupial, the southern brown bandicoot (eastern subspecies), Isoodon obesulus obesulus. Following local extinction ~ 100 years earlier, founding individuals were reintroduced to Booderee National Park in south-eastern Australia over three years from the nearest viable wild population, approximately 250 km to the south. To assess and manage risks associated with low genetic diversity, we measured genetic diversity of the reintroduced population relative to the diversity across the subspecies’ range. The genetic diversity of the initial founder population was comparable with other sampled populations; most likely because the source population had high genetic diversity relative to other locations. We simulated scenarios of supplementation of the founder population from alternative candidate sources. We identified populations in the Melbourne region of Victoria as those that would yield the greatest increase in genetic diversity in the Booderee population. The simulated increase in diversity resulting from supplementation was accurately predicted by the pairwise FST comparison between the candidate and recipient population, but not diversity of the supplementation source itself. Genetic diversity is an important consideration in reintroductions; our study enables managers to make informed decisions to maximise the long-term persistence and genetic diversity of reintroduced populations.

Comparative analysis of genetic diversity of rice (Oryza sativa L.) varieties cultivated in different periods in China

Understanding the genetic diversity of various rice (Oryza sativa L.) cultivars cultivated over time in China is of great significance for the selection of parent materials for targeted rice breeding and the cultivation of new desirable varieties. In this study, 36 pairs of SSR markers were used to compare and analyze the genetic diversity of 1610 rice varieties bred in China from the 1980s to the 2010s. A total of 1568 allelic mutations were detected, with each locus varying having from 16 to 115, with an average of 44 per marker. The average gene diversity index and the polymorphism information content (PIC) of each locus were 0.8403 and 0.8243, respectively. The genetic diversity parameter values of japonica (Oryza sativa L. subsp. japonica Kato) rice varieties were higher than those of indica (Oryza sativa L. subsp. indica Kato) varieties. Over time, original unique alleles are lost, and new unique alleles are added. The total number of alleles, the number of unique alleles, and the number of varieties with unique alleles tend to increase over decades of breeding. In all ages, indica rice contained the largest number of unique alleles (19) in the 2000s, and japonica rice contained the largest number of unique alleles (11) in the 2010s. The trends of gene diversity index and PIC values increased first and then decreased. Gene diversity indices and PIC for indica rice reached their maximums (0.698 and 0.664 respectively) in the 1990s and japonica rice reached its highest values for these diversity metrics (0.791 and 0.766 respectively) in the 2000s. Analysis of molecular variance showed that genetic variation was primarily derived from differences of varieties that were bred during a given period. Most of the pair-wise Fst comparisons between different periods were at a statistically significant level. Cluster analysis shows distinctions in the genetic relationship of varieties bred in the twentieth century and the twenty-first century, but the genetic relationship between the varieties is relatively close when comparing within the twentieth or twenty-firs century, respectively. Our study will provide a scientific basis for the effective protection and efficient use of rice germplasm resources.

Population genetics of Penaeus semisulcatus from Persian Gulf and Oman Sea using newly developed DNA microsatellite markers

A population genetics study on Penaeus semisulcatus from Persian Gulf was performed to assist in the selection of suitable broodstocks for future breeding programs. Eight novel microsatellite loci were developed to study population genetics structure of P. semisulcatus in three population sites, Persian Gulf and Oman Sea (Jask, Hormoz and Kuhestak). There were incidences of heterozygosity deficiency and significant deviations from Hardy Weinberg equilibrium (HWE) at most loci (p<0.001). However, four loci (loci E2 and B9 – Hormoz; loci C6 – Kuhestak; and loci H9 – Jask) found to be in HWE. Micro-Checker analysis revealed null alleles in the three microsatellite loci (B5, C6 and C9). Pairwise Fst comparison based on allelic and genotypic frequencies indicated that the three populations were significantly differentiated from each other (p<0.05). High levels of pairwise Fst (0.106) and low levels of Nm (2.103) observed between Hormoz and Jask populations indicated restricted gene flow between the two populations. On the other hand, low levels of pairwise Fst (0.016) and high levels of Nm (15.876) observed between Hormoz and Kuhestak populations indicated high gene flow between these populations. In this study, the assignment test was examined in order to find gene flow connectivity between the three populations. Overall, results revealed high gene flow between Hormoz and Kuhestak and restricted genetic flow between Jask and both Hormoz and Kuhestak populations, providing new input for selection of genetically-suitable broodstocks.

No Population Genetic Structure of Skipjack Tuna (Katsuwonus pelamis) in the Tropical Western and Central Pacific Assessed Using Single Nucleotide Polymorphisms

Skipjack tuna (Katsuwonus pelamis) has historically been considered panmictic at the ocean basin scale because of the species’ life history and substantial absolute population size. However, recent advances in population genomics have enabled scientists to demonstrate population structure in other species that were likewise traditionally assumed to be panmictic. Accordingly, we used DArTseq, a proprietary platform of reduced-representation genome sequencing developed by Diversity Arrays Technology (DArTech) to genotype 222 skipjack tuna from 9 sample groups collected across 6 exclusive economic zones (EEZs) and over 6 years in the tropical Western and Central Pacific Ocean. This is one of the most fine-scale population genetics assessments of skipjack tuna to date. We found several statistically significant pairwise FST comparisons using purportedly neutral loci, but very little indication of structure based on observed and expected heterozygosity, effective population size, a Mantel test, AMOVA, numerous genetic clustering and population assignment tests, and exploration of correlation with oceanographic features. Significant pairwise FST values were often shallow and resulted in uncertainty about their biological significance. Furthermore, a test of the hypothesis that the geographic and temporal distribution of the potentially adaptive genetic diversity may depict cryptic fine scale structure using two different outlier detection methods, could not reject panmixia based on estimates of fixation indices and two clustering software. Our results support the presence of a single population of skipjack tuna in the tropical Western and Central Pacific Ocean, but highly recommend the expansion of the study area, in latitude, longitude, and seasonality, before drawing any global conclusions.

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

BackgroundA sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers.ResultsAll the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance.ConclusionsTo maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest (Fst > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.