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The Pacific cod Gadus macrocephalus is a demersal, economically important fish in the family Gadidae. Population genetic differentiation of Pacific cod was examined across its northwestern Pacific range by screening variation of eight microsatellite loci in the present study. All four populations exhibited high genetic diversity. Pairwise fixation index (Fst) suggested a moderate to high level of genetic differentiation among populations. Population of the Yellow Sea (YS) showed higher genetic difference compared to the other three populations based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE, which implied restricted gene flow among them. Wilcoxon signed rank tests suggested no significant heterozygosity excess and no recent genetic bottleneck events were detected. Microsatellite DNA is an effective molecular marker for detecting the phylogeographic pattern of Pacific cod, and these Pacific cod populations should be three management units.

Amentotaxus argotaenia (Hance) Pilg. is a threatened conifer with a wide distribution range from North to Central Vietnam due to habitat loss and over-exploitation. To provide information for its conservation and sustainable management, in the present study, genetic diversity and population genetic structure for 200 trees from eight populations, representing the natural distribution range of this species were estimated using nuclear microsatellites. The results showed a moderate genetic diversity of A. argotaenia (HO = 0.331, HE = 0.358). Significant heterozygosity deficits were detected in three populations in the Northeast area. Genetic differentiation was low in the same distribution area and high in different areas. However, the gene flow among the studied populations was relatively high (Nm = 1.17). Habitat fragmentation, geographical distance and high mountain range can be the major factors that reduce gene exchange between different areas. Various clustering analyses distinguished three major genetic groups related to the three distribution areas of this species in Vietnam. Based on the study results, we propose that some populations could be prioritized for in situ conservation due to their high genetic diversity with high allelic richness or private alleles, meanwhile other populations should be collected for ex situ conservation as genetic resources in the future.

KEY MESSAGE : Genetic diversity and population structure in the US Upland cotton was established and core sets of allelic richness were identified for developing association mapping populations in cotton. Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete cultivars without the yield drag typically associated with wild accessions. A set of 381 accessions comprising 378 Upland (Gossypium hirsutum L.) and 3 G. barbadense L. accessions of the United States cotton belt were genotyped using 120 genome-wide SSR markers to establish the genetic diversity and population structure in tetraploid cotton. These accessions represent more than 100 years of Upland cotton breeding in the United States. Genetic diversity analysis identified a total of 546 alleles across 141 marker loci. Twenty-two percent of the alleles in Upland accessions were unique, specific to a single accession. Population structure analysis revealed extensive admixture and identified five subgroups corresponding to Southeastern, Midsouth, Southwest, and Western zones of cotton growing areas in the United States, with the three accessions of G. barbadense forming a separate cluster. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between G. hirsutum accessions was 0.195 indicating low levels of genetic diversity in Upland cotton germplasm pool. The results from both population structure and phylogenetic analysis were in agreement with pedigree information, although there were a few exceptions. Further, core sets of different sizes representing different levels of allelic richness in Upland cotton were identified. Establishment of genetic diversity, population structure, and identification of core sets from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in Upland cotton.

Blue honeysuckle (Lonicera caerulea L.) is a promising berry crop producing edible early-ripening berries with a valuable chemical composition. We evaluated the genetic diversity of native L. caerulea populations from the western (Baltic states) and eastern (the Russian Far East and Japan) edges of the Eurasian range using inter-simple sequence repeat (ISSR) and chloroplast DNA (psbA-trnH and trnL-trnF) markers. The genetic relationships of populations and genotypes were analyzed using principal coordinate and cluster analyses (neighbor joining and Bayesian clustering). Sampling was carried out in two disjunct areas of this circumpolar species and the analyses showed clustering of individuals and populations according to geographic origin. The analysis of genetic structure based on ISSR markers showed that the studied populations of L. caerulea were highly differentiated. However, sequence analysis of two chloroplast DNA (cpDNA) regions revealed no phylogeographic structure among the populations. We also found that the eastern populations of blue honeysuckle had significantly greater genetic diversity parameters than the populations from the Baltic region. This finding correlates with the endangered status of blue honeysuckle in the Baltic states.

We aimed to reveal the dispersal and gene flow of the local wild boar (Sus scrofa) population and find their genetic boundary in Fukushima Prefecture. After the nuclear incident in 2011, the land was considered a difficult-to-return zone, and the increase in the number of wild boars was pronounced. To provide an effective management strategy for the wild boar population, we used multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and clarified the genetic structure of wild boars. We obtained 328 single-nucleotide polymorphisms from 179 samples. STRUCTURE analysis showed that the most likely number of population cluster was K = 2. Molecular analysis of variance showed significant genetic differences between groups of wild boars inhabiting in the east and west across the Abukuma River. The migration rate from the eastern population to the western population is higher than in the reverse case based on BayesAss analysis. Our study indicates that both the Abukuma River and anthropogenic urbanization along the river may affect the migration of wild boars and the population in western was established mainly by the migration from other neighboring prefectures.

Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual-based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real-world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.

In the pre-alpine region of Europe numbers and sizes of populations of the clonal lake shore plant Ranunculus reptans have declined because of the regulation of lake water levels. We investigated genetic variation among and within 17 populations of different size (cover 1-10 000 m2) in R. reptans with RAPD (random amplified polymorphic DNA) profiles. We sampled 127 rosettes in 14 populations at Lake Constance and three populations at or near Lake Como. There was significant genetic variation between plants from the two lake regions (5.9%, analysis of molecular variance [AMOVA], P < 0.001), among populations within lake regions (20.4%, P < 0.001), and within populations (73.7%, P < 0.001). Under the assumptions of Wright's island model the variation among populations corresponds to a gene flow of Nem = 0.70. Within the 14 Lake Constance populations we detected significant genetic variation among subpopulations separated by only a few metres (4.0% of the within-population variation; P < 0.05). Molecular variance was 24% smaller in small populations covering <100 m2area than in larger ones (P < 0.03), indicating that samples from large populations were genetically more variable than samples representing comparable areas of smaller populations. We conclude that gene flow among populations is very limited and that genetic drift has caused reduced genetic variability of smaller populations. Conservation of genetic variability in R. reptans requires persistence of large and also of small populations (because of population differentiation), and it could be enhanced by increasing the size of small populations (to counter genetic drift).

Background Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. Results In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. Conclusions This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

We investigated the distribution of genetic variation and the relationship between population size and genetic variation in the rare plant Gentianella germanica using RAPD (random amplified polymorphic DNA) profiles. Plants for the analysis were grown from seeds sampled from 72 parent plants in 11 G. germanica populations of different size (40-5000 fruiting individuals). In large populations, seeds were sampled from parents in two spatially distinct subpopulations comparable in area to the total area covered by small populations. Analysis of molecular variance revealed significant genetic variation among populations (P 0.001), while genetic variation among subpopulations was marginally significant (P 0.06). Average molecular variance within subpopulations in large populations did not differ significantly from whole-population values. There was a positive correlation between genetic variation and population size (P 0.01). Genetic variation was also positively correlated with the number of seeds per plant in the field (P 0.02) and the number of flowers per planted seed in a common garden experiment (P 0.051). We conclude that gene flow among natural populations is very limited and that reduced plant fitness in small populations of G. germanica most likely has genetic causes. Management should aim to increase the size of small populations to minimize further loss of genetic variation. Because a large proportion of genetic variation is among populations, even small populations are worth preserving

Background Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. Results Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11  C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant “Isolation by Distance” between populations. Conclusions Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.