Genetic divergence in nuclear genomes between populations of <Emphasis Type="Italic">Fagus crenata</Emphasis> along the Japan Sea and Pacific sides of Japan

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species’ range. Although population differentiation was very low (F _ST = 0.027; R _ST = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H _E = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.     

Identification of candidate AFLP markers for shell color of the Pacific oyster (Crassostrea gigas) under artificial selection

The shell color of the Pacific oyster (Crassostrea gigas) is a desirable trait, but only a few genetic studies on shell color have been documented. Through successive selective breeding, four shell color variants of white (W), gold (G), black (B) and purple (P) C. gigas have been developed. The amplified fragment length polymorphism (AFLP) technique was used to scan the genomes of the four variants with different shell colors and one wild population (C) to identify candidate markers for shell polymorphism. Fifteen AFLP primer combinations were used, 1079 loci were scored as polymorphic loci, and the percentage of polymorphic bands was 95.5%. In the gold, white, black, purple and wild populations, the percentages of polymorphic loci were estimated to be 90.5% (G), 90.0% (W), 91.1% (B), 95.3% (P) and 93.2% (C); the expected heterozygosity values were 0.3115 (G), 0.3044 (W), 0.3102 (B), 0.3285 (P) and 0.3105 (C). The white shell variant was observed to have slightly lower genetic diversity than others, with a F_ST value of 0.1483. These results indicated that the four different shell color variants had high genetic diversity and that the genetic differentiation of populations mostly results from genetic diversity of individuals within populations. Furthermore, 11 outlier loci were considered candidate markers for shell color. This work provides new insights on relationships among color variants of C. gigas.     

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

Selective breeding often produces an improvement in phenotype. Much of the phenotypic change within a species is a consequence of genetic variation. However, there is growing evidence for phenotypic change even in the absence of DNA sequence polymorphisms, termed epigenetic variation. This study’s goal was to investigate the genetic and epigenetic variation in the mass selection populations of the Pacific oyster (Crassostrea gigas), determine if any correlation exists between the genetic and epigenetic variations. This can serve as a first step in investigating the potential role epigenetic variations have in selective breeding. Amplified fragment length polymorphism analysis and methylation-sensitive amplified polymorphism methodology were used to monitor genetic and epigenetic variation in two populations (the base stock and the third selected generation) from a mass selection line in the Pacific oyster. The correlation between genetic and epigenetic variation was evaluated by Co-Inertia Analysis. The genetic difference was mainly found in the gene frequency shift revealed by the F _ST value (0.0151, P < 0.01) and no significant reduction in genetic diversity was detected. The percentage of methylation in C. gigas was 26.4 %. No significant difference was observed on the average state of methylation, but a few bands showed different frequencies between the two populations. Co-Inertia Analysis revealed a significant association between the genetic and epigenetic profiles (P < 0.01).     

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic diversity of 0.38 among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise G_ST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese, Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and G_ST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow.     

PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia

Haruan (Channa striatus) is in great demand in the Malaysian domestic fish market. In the present study, mtDNA cyt b was used to investigate genetic variation of C. striatus among populations in Peninsular Malaysia. The overall population of C. striatus demonstrated a high level of haplotype diversity (h) and a low-to-moderate level of nucleotide diversity (π). Analysis of molecular variance (AMOVA) results showed a significantly different genetic differentiation among 6 populations (F_ST = 0.37566, P = 0.01). Gene flow (Nm) was high and ranged from 0.32469 to infinity (∞). No significant relationship between genetic distance and geographic distance was detected. A UPGMA tree based on the distance matrix of net interpopulation nucleotide divergence (d_A) and haplotype network of mtDNA cyt b revealed that C. striatus is divided into 2 major clades. The neutrality and mismatch distribution tests for all populations suggested that C. striatus in the study areas had undergone population expansion. The estimated time of population expansion in the mtDNA cyt b of C. striatus populations occurred 0.72-6.19 million years ago. Genetic diversity of mtDNA cyt b and population structure among Haruan populations in Peninsular Malaysia will be useful in fisheries management for standardization for Good Agriculture Practices (GAP) in fish-farming technology, as well as providing the basis for Good Manufacturing Practices (GMP).     

What Maintains the Central North Pacific Genetic Discontinuity in Pacific Herring?

Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (Φ_ST  = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (Φ_ST  = 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (Φ_ST  = 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.     

Population genetic characterization of the endangered silver skipper,Leptalina unicolor (Lepidoptera: Hesperiidae), using novel microsatellite markers and mitochondrial DNA gene sequences

The silver stripped skipper, Leptalina unicolor, is listed as an endangered species with a paucity of leftover populations in Korea. Prior population genetic analysis is essential for the establishment of effective conservation strategies. In the present study, we investigated the genetic diversity and the relationships of L. unicolor populations in Korea using 12 newly developed L. unicolor-specific microsatellite markers and two mitochondrial DNA (mtDNA) sequences (a total of 1283 bp from COI and CytB). Due to the endangered status and rarity, a total of 33 individuals from two localities in Gangwon-do Province (Seohwa and Girin) and one in Gyeongsangnam-do Province (Danjang) were sampled. The concatenated mtDNA sequences revealed very low genetic diversity in each population, with only one to three independent haplotypes per population. F_ST, principal coordinate analysis, and independent structural analysis of the concatenated mtDNA sequences and the 12 microsatellite loci developed in this study showed that each L. unicolor population in Korea is nearly completely isolated, although inbreeding has not yet occurred. Long-term conservation habitat recovery that increases the available population appears to be important in the prevention of genetic drift and inbreeding, which occur in small isolated populations and reduce the viability of populations under fluctuating environmental conditions.     

Genetic variation within the sand-fixation species Caragana microphylla (Leguminosae) in Horqin sandy land detected by inter-simple sequence repeats analysis

Caragana microphylla is the most dominant and constructive shrub species in the Horqin sandy land in the northeast of China. We evaluated it's the level of genetic variation within and among populations sampled from two different populations types in Horqin sandy land by using inter-simple sequence repeat polymorphism (ISSR) molecular markers. The results showed that eight ISSR primers generated 106 bands, of which 87 were polymorphic. At the species level, genetic diversity was relatively high (P = 82.08%, h = 0.2831, I = 0.4233). Genetic variation in natural populations (h = 0.2152, I = 0.3169) was more than that in plantation populations (h = 0.2021, I = 0.3040). Based on Nei's G_ST value, more genetic differentiation among plantation populations was detected (G_ST = 0.7787). Six populations of C. microphylla clustered into two clades. These results have important implications for restoring and managing the degraded ecosystem in arid and semi-arid areas.     

Risso’s dolphins (<Emphasis Type="Italic">Grampus griseus</Emphasis>) in UK waters are differentiated from a population in the Mediterranean Sea and genetically less diverse

The Risso’s dolphin (Grampus griseus) has a worldwide distribution, but little is known about their population genetic structure. Local coastal populations are never known to be abundant, and are sometimes under anthropogenic impact. Therefore the question of regional differentiation by genetic drift and overall diversity levels is of conservation interest. Here we present preliminary data that clearly indicate genetic differentiation and lower genetic diversity of a population sampled in UK waters (primarily from the Western Isles, Scotland) compared to a Mediterranean sample. Significant differentiation was found in comparison with a sample from the Mediterranean for both microsatellite DNA markers (F _ST = 0.0296) and mtDNA sequence data (F _ST = 0.260; ϕ _ST = 0.542). Allelic diversity was lower in the UK for nearly all loci.     

Multiple ice‐age refugia in Pacific cod,Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (F_ST = 0.028, r² = 0.33) and mtDNA (F_ST = 0.027, r² = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.     

AFLP markers suggest low population genetic differentiation of the black rockfish Sebastes schlegelii

AFLP markers were used to investigate the population genetic differentiation among populations of Sebastes schlegelii from China and Japan. A total of 405 bands were amplified for 180 individuals from 9 populations by 3 pairs of selective primers. S. schlegelii exhibited high Nei's gene diversity with an average value of 0.29 for all populations. No significant genealogical branches or clusters corresponding to sampling localities were detected by UPGMA tree. The results of AMOVA analysis and pairwise F_ST values showed no genetic divergence among different geographic populations. The result of STRUCTURE demonstrated all populations of S. schlegelii examined in the study shared one single gene pool.     

Population structure and genetic diversity of Stipa grandis P. Smirn,a dominant species in the typical steppe of northern China

Random amplified polymorphic DNA (RAPD) markers were used to characterize genetic heterogeneity within and among five populations of Stipa grandis in the Xilingol Plateau. Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were comparatively high in the five populations, and the Population GSM was found to have the highest genetic diversity among all populations. An analysis of molecular variance indicated that the majority of variation existed within populations (74.12%), and that there was significant differentiation among populations (Φ_ST = 25.88%, P < 0.001). Genetic distance (Φ_ST) ranged from 0.198 to 0.310 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the Φ_ST values, gene flow (Nm) was estimated and was found to vary from 0.556 to 1.013 between pair-wise populations and 0.7412 among populations. The results of UPGMA cluster analysis and nonmetric multi-dimensional scaling analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of S. grandis in northern China and will be useful for conservation managers to work out an effective strategy to protect this important species.     

Weak population genetic differentiation in the most numerous Arctic seabird,the little auk

Quantifying patterns of genetic diversity and differentiation among populations of Arctic birds is fundamental for understanding past and ongoing population processes in the Arctic. However, the genetic differentiation of many important Arctic species remains uninvestigated. Here, phylogeography and population genetics were examined in the worldwide population of a small seabird, the little auk (dovekie, Alle alle)—the most numerous avian species of the Arctic ecosystem. Blood samples or feathers were collected from 328 little auks (325 from the nominate subspecies and 3 from the A. a. polaris) in nine main breeding aggregations in the northern Atlantic and one location from the Pacific Ocean. The mtDNA haplotypes of the two subspecies were not segregated into separate groups. Also, no genetic structure was found within the nominate race based on microsatellite markers. The level of genetic differentiation among populations was low yet significant (mean F _ST = 0.005). Some pairwise F _ST comparisons revealed significant differences, including those involving the most distant Pacific colony as well as among some Atlantic populations. Weak population differentiation following the model of isolation by distance in the little auk is similar to the patterns reported in other high-Arctic bird species, indicating that a lack of distinct genetic structure is a common phenomenon in the Arctic avifauna.     

Mitochondrial DNA variation and population genetic structure in the small yellow croaker at the coast of Yellow Sea and East China Sea

Small yellow croaker is one of the most important fishery species in China. The mass–scale artificial propagation of this fish species was initially developed in 2015 with the aim of facilitating the fish production stock enhancement and aquaculture programs in the future. In the present study, the wild broodfish and its corresponding progeny along with three other wild populations were sampled and subjected to sequence analysis of the mitochondrial cytochrome c oxidase subunit I gene. The genetic diversity and population genetic structure were evaluated with a total sample size of 141 individuals representing the populations of the Yellow Sea (Qingdao and Lvsi populations) and the East China Sea (Xiangshan and Ningde populations). The wild populations were characterized by high haplotype diversity (0.925–0.976) and low nucleotide diversity (0.376%–0.560%). The hierarchical analysis of molecular variance (AMOVA) analysis and the values of pairwise Ф-statistics (Ф_ST) indicated non-significant genetic differentiation among the four wild populations. The hatchery stock XSH exhibited lower indices of genetic diversity compared with the wild populations that could be attributed to the small effective population size. The findings of the present study have valuable insight to the sustainable management and utilization of this resource.     

Genetic diversity of the black mangrove (Avicennia germinans L.) in Colombia

This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (F_RT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (F_ST = 0.10 for the Caribbean coast and F_ST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast.     

Multi-Gene Analysis Reveals a Lack of Genetic Divergence between Calanus agulhensis and C. sinicus (Copepoda; Calanoida)

The discrimination and taxonomic identification of marine species continues to pose a challenge despite the growing number of diagnostic metrics and approaches. This study examined the genetic relationship between two sibling species of the genus Calanus (Crustacea; Copepoda; Calanidae), C. agulhensis and C. sinicus, using a multi-gene analysis. DNA sequences were determined for portions of the mitochondrial cytochrome c oxidase I (mtCOI); nuclear citrate synthase (CS), and large subunit (28S) rRNA genes for specimens collected from the Sea of Japan and North East (NE) Pacific Ocean for C. sinicus and from the Benguela Current and Agulhas Bank, off South Africa, for C. agulhensis. For mtCOI, C. sinicus and C. agulhensis showed similar levels of haplotype diversity (H_d = 0.695 and 0.660, respectively) and nucleotide diversity (π = 0.003 and 0.002, respectively). Pairwise F_ST distances for mtCOI were significant only between C. agulhensis collected from the Agulhas and two C. sinicus populations: the Sea of Japan (F_ST = 0.152, p<0.01) and NE Pacific (F_ST = 0.228, p<0.005). Between the species, F_ST distances were low for both mtCOI (F_ST = 0.083, p = 0.003) and CS (F_ST = 0.050, p = 0.021). Large subunit (28S) rRNA showed no variation between the species. Our results provide evidence of the lack of genetic distinction of C. sinicus and C. agulhensis, raise questions of whether C. agulhensis warrants status as a distinct species, and indicate the clear need for more intensive and extensive ecological and genetic analysis.     

Genetic diversity and population structure of the endangered conifer Taxus wallichiana var. mairei (Taxaceae) revealed by Simple Sequence Repeat (SSR) markers

Taxus wallichiana var. mairei is an endangered conifer with important medicinal value in southern China. Nuclear SSR markers were employed to assess genetic diversity and structure of 13 geographically disjunct populations. The present study revealed a moderate genetic diversity (H_E = 0.538) and low genetic differentiation (F_ST = 0.159). And most populations encountered in severe inbreeding and bottleneck effect. No significant genetic structure was detected by IBD and Structure analysis, which was supported by AMOVA analysis. The present results could be ascribed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. However, the 13 studied populations were divided into four clusters based on the UPGMA dendrogram; these clusters were almost congruent with their geographical distributions. Vital areas such as southern mountains of Sichuan basin, Nanling Mts. and the margin of this yew's distribution range had a high priority for conservation.     

Population Structure of the Giant Garter Snake, Thamnophis gigas

The giant garter snake, Thamnophis gigas, is a threatened species endemic to California’s Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F_ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F_ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas.     

Genetic diversity of Stipa grandis P.Smirn populations across the species’ range in the Inner Mongolia Plateau of China

In order to investigate the genetic diversity of dominant species under the background of climate change and grassland utilization in the Inner Mongolia Plateau of China, we sampled seven Stipa grandis populations along an increasing aridity gradient in the present study. The Nei’s gene diversity of populations (He) was estimated to be 0.15 and the percentage of polymorphic loci (PPL) was 49.28%. The genetic differentiation among populations (Φ_ST) was 0.2431. There was a significant relationship between genetic distance and geographic distance among the S. grandis populations by Mantel's test. The genetic diversity was significantly correlated with longitude and annual mean precipitation, which suggested that a combination of climatic factors affected the genetic diversity. The populations in the marginal habitat should be paid more attention because of their low genetic diversity and its significance for conservation of the whole species.     

Genetic homogeneity between Korean and Japanese populations of the broad-leaved evergreen tree Machilus thunbergii (Lauraceae): A massive post-glacial immigration through the Korea Strait or something else?

The warm-temperate vegetation of Korea, currently limited to southern coastal areas, shifted during the Last Glacial Maximum (LGM) towards glacial refugia, putatively located in southern Japan. We hypothesized two scenarios of post-glacial re-colonization of warm-temperate species in relation to current levels of genetic diversity within their populations. If extant Korean populations originated from a single source (a single glacial refugium), we expect significantly lower levels of genetic diversity relative to those from Japan due to founder effects. Alternatively, if they were derived from multiple source populations, levels of genetic diversity within Korean populations will not be significantly reduced compared to those of Japanese ones. To test which of these scenarios is more likely, we investigated the patterns of genetic diversity in 14 populations (seven from southern Korea and seven from southern Japan) of the broad-leaved evergreen tree Machilus thunbergii, employing 11 allozyme loci. High levels of genetic variation in M. thunbergii were found both in southern Korea and southern Japan, with a considerable genetic homogeneity not only between the two regions but also between populations within the two regions. These results suggest a pattern of re-colonization after the LGM fitting the second scenario (immigration from multiple refugia), probably through multiple waves and/or with large founder populations.