Levels Of Genetic Differentiation Research Articles

A study on the genetic diversity and subpopulation structure of three Bulgarian mountainous sheep breeds, based on genotyping of microsatellite markers

Traditional domestic breeds of domestic animals are part of the “living” wealth of the world, part of the disappearing biodiversity and a valuable local gene pool. Nowadays, they are increasingly included in the category of “rare and disappearing” breeds. Therefore, the purpose of this study was to reveal the genetic diversity and population structure of three Bulgarian mountainous sheep breeds (Rhodopean Tsigai, RT; Middle Rhodopean sheep, MRS; and Karakachan sheep, KS). A total of 113 unrelated individuals (two flocks of each breed) from different regions of the country were investigated based on 11 STR (short tandem repeat) markers. The obtained results showed a total of 116 alleles in the three sheep breeds. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 8.21, 4.72, and 0.79. The largest number of alleles were found in the population of MRS (9.18 ± 0.76), followed by RT (8.27 ± 0.64) and KS (7.18 ± 0.47). The largest polymorphism was found in INRA005 and INRA06 loci with 11 and 10 alleles, respectively, and the smallest polymorphic loci were noted for the locus McM042 and INRA172 with only 6 alleles. The observed heterozygosity showed the highest value in KS (0.79 ± 0.04), followed by RT (0.76 ± 0.02) and MRS (0.73 ± 0.04). The range of expected heterozygosity was from 0.77 ± 0.02 in MRS to 0.75 ± 0.03 in KS. The fixation index FST, estimated by analysis of molecular variance (AMOVA), was 0.2090, indicating moderate levels of genetic differentiation among the populations. The FST between the investigated breeds indicated a moderate value of 0.216, and the analysis of variance (ANOVA) data showed only 1% variation among the populations, whereas 99% was due to variation within breeds. The results by the STRUCTURE analysis revealed that all breeds were heterogeneous and formed three distinct clusters. The results of the genetic diversity and structure analysis of the investigated breeds provide useful information for assessing the genetic diversity of other Bulgarian autochthonous sheep breeds, serving as a cornerstone for designing effective conservation management strategies.

Genetic Diversity and Phylogeography of Taenioides cirratus in Five Geographical Populations Based on Mitochondrial COI and Cytb Gene Sequences

The genetic diversity of Taenioides cirratus was investigated on the basis of mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) gene sequences. A total of 159 specimens collected from the Chaohu Lake (CL), Nansihu Lake (NL), Taihu Lake (TL), Pearl River (PR), and Nandu River (NR) were sequenced. The total length of the sequence was 2485 bp with 412 polymorphic sites. A total of 73 haplotypes were identified, with Hap1 being the most widely distributed. The PR and NR populations showed high genetic diversity, while the CL population showed low genetic diversity. TL and NL showed high haplotype diversity but low nucleotide diversity. The analysis of molecular variance demonstrated that the sequence variations were mainly occurred among populations. T. cirratus populations are declining, and rare alleles are present at low frequencies, as analysed using a neutral test and a mismatched distribution analysis. There was a relatively high level of genetic differentiation among the populations of the Yangtze River basin (including NL), PR, and NR (Fst > 0.15). The two similar phylogenetic trees constructed by the maximum likelihood (ML) and Bayesian inference (BI) methods presented three major lineages, of which lineage II contains haplotypes from PR and NR, lineage III contains haplotypes from CL, NL, TL, and PR, whereas lineage I contains only a portion of haplotypes from NR. Based on the neutral test, mismatch analysis, and Bayesian Skyline Plot (BSP), geological and climatic events were inferred to have played an important role in the historical dynamics of T. cirratus population. Hap1, Hap25, and Hap58 were inferred as possible ancestral haplotypes by network analysis. Our study offers an essential foundation for resource preservation and additional taxonomic clarification of T. cirratus.

GENETIC DIVERSITY AND POPULATION STRUCTURE OF COMMON BEAN GENOTYPES USING MORPHOLOGICAL TRAITS AND SSR

The objectives of this study were to estimate the performance of the common bean (Phaseolus vulgaris L.) genotypes under water-stress conditions, and their genetic diversity. White bean surpassed the others for relative water content, root/shoot ratio and leaf area under water-stress condition. Scatter plot indicates a strong association of yield with pod numbers plant-1, branch number and harvest index. A total of 69 polymorphic were obtained, applying 26 SSR primers on 14 genotypes. Major allele frequency was 0.601, and the average value of PIC was 0.407. The highest value of gene diversity (0.745) and PIC (0.704) were recorded for BMd-23 marker. Molecular variance among population indicated 25%, while 47% was realized within populations. Structure analysis divided the common bean genotypes into three groups (DeltaK value =3). Chity and Boschbohnen were identified to have a mixed ancestor while all the others were pure at their populations. A dendrogram and PCoA analyses are accordingly indicated three groups of the genotypes based on SSR marker data. STRUCTURE, UPGMA and PCoA analysis revealed the presence of two separated gene pools of Andean and Mesoamerican common beans, with a high level of genetic differentiation (FST value=0.250). Both phenotypic and molecular genetic outcomes here would accelerate future improvement programs.

Dispersive currents explain patterns of population connectivity in an ecologically and economically important fish.

How to identify the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents coupled with high levels of dispersal and gene flow can decrease the utility of modern population genetic tools. To address this challenge, we used RAD-Seq to genotype 959 yellow perch (Perca flavescens), a species with an ~40-day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. We also developed a novel, integrative approach that couples detailed biophysical models with eco-genetic agent-based models to generate "predictive" values of genetic differentiation. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations (F ST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that were derived from periods of time when there were strong and highly dispersive currents. Thus, these highly dispersive currents are driving the patterns of population connectivity in the main basin. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent (F ST = 0.11). By integrating biophysical and eco-genetic models with genome-wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems.

Tufted Puffins exhibit low levels of genetic differentiation among breeding colonies in North America

Abstract Tufted Puffins (Fratercula cirrhata) are experiencing population declines in some parts of their distribution, making this a species of increased conservation interest. Genetic data will help to identify Tufted Puffin populations of conservation importance and provide an important tool for developing conservation management plans. This species is broadly distributed across the North Pacific Ocean but little is known about the extent of genetic variation and differentiation across their range. In this study, we examine mitochondrial DNA (mtDNA), 8 microsatellite loci and 1,260 single nucleotide polymorphisms (SNPs) to determine the extent of gene flow among 7 breeding colonies (Oregon to the western Aleutians) in the North American breeding range of the species and identify potential barriers to dispersal. Our results show that most breeding colonies form a single genetic cluster, and mtDNA data show substantial historical gene flow among populations. For the microsatellite dataset, all FST comparisons that include St. Lazaria, in southeast Alaska, except Oregon, which had a small sample size, were significant as were comparisons between Triangle Island and the two westernmost sampling sites of Buldir and Aiktak. For the SNP dataset, FST comparisons were low and nonsignificant, further suggesting that breeding colonies form a single panmictic population. Individuals were more closely related to individuals from the same colony, and we found a weak relationship between genetic and geographic distance. This suggests that dispersal among colonies is high, likely facilitated by an overlap in wintering ranges among colonies. The high connectivity among breeding colonies indicates that Tufted Puffins form a single conservation unit, although future genetic studies should incorporate a whole genome sequencing approach to assessing how functional genetic diversity varies across their distribution.

Reduced genetic diversity and restricted gene flow of broadcast-spawning coral Galaxea fascicularis in the South China Sea reveals potential degradation under environmental change

Under the dual effects of climate change and anthropogenic activities, coral reefs in the South China Sea (SCS) are at serious risk of degradation. Galaxea fascicularis is a widely distributed species in the SCS, and the study of its genetics, survival, and adaptability is conducive to further understanding the future characteristics of coral reefs in the SCS. In this study, 146 G. fascicularis samples were selected from 9 survey stations across 12 latitudes in the SCS, and 8 pairs of microsatellite markers were used to characterize their genetic diversity and structure. The results showed moderate genetic diversity index values (Ar = 3.444–4.147, He = 0.634–0.782, Ho = 0.367–0.586). The AMOVA results and pairwise FST values showed a moderate level of genetic differentiation (ΦST = 0.119, P < 0.05) among G. fascicularis populations in the SCS, whereas its genetic structure showed high genetic differentiation (FST = 0.062–0.225) among relatively high-latitude populations (n = 3) and low genetic differentiation (FST = 0.012–0.064) in low-latitude populations (n = 6). The living environment of relatively high-latitude populations is disturbed by high-intensity human activities, leading to the specialization of local populations. Mantel test results showed a significant positive correlation between genetic differentiation among G. fascicularis populations and sea surface temperature (SST) variance (R2 = 0.4885; Mantel test, p = 0.010 < 0.05) in addition to geographical distance (R2 = 0.1134; Mantel, test p = 0.040 < 0.05), indicating that SST and geographical isolation were primary factors affecting the genetic structure of this species in the SCS. The lower genetic diversity and limited gene flow of G. fascicularis indicate limited genetic adaptation, and corresponding vulnerability may be more pronounced under future environmental changes. These findings provide a theoretical basis for the conservation and restoration of coral reefs in the SCS.

Population structure and genetic diversity of the endangered fish black shinner Pseudopungtungia nigra (Cyprinidae) in Korea: a wild and restoration population

The black shinner Pseudopungtungia nigra Mori, 1935 is an endangered fish endemic to Korea. It lives in the narrow basin of the Geumgang River, Mangyeonggang River, and Ungcheoncheon Stream, which flow into the West Sea of Korea. One population of P. nigra in Ungcheoncheon Stream has been locally exterminated once; it is now inhabiting the upper reaches of the dam through a restoration program. Efforts to identify and understand the genetic structure of these populations are important for conservation planning. Here, we analyzed genetic diversity using 21 microsatellite markers for 9 populations. The mean number of alleles ranged from 4.4 to 8.1, mean allelic richness ranged from 4.6 to 7.8, mean observed heterozygosity ranged from 0.519 to 0.702, and mean expected heterozygosity ranged from 0.540 to 0.763. All groups had recent and historical bottlenecks (P < 0.05, M-ratio < 0.68). Three groups [YD (2019), OC and UC] had significant inbreeding index values, suggesting that they were engaged in inbreeding. We observed a moderate level of genetic differentiation between MG and the rest of the population (FST = 0.135 to 0.168, P < 0.05). The genetic structure exhibited a fitting constant K = 2, along with separation between MG and the remaining populations. With respect to genetic flow, YD (2019), OC, CG, and ND shifted to the UC population (0.263 to 0.278). The genetic flow of each population was transferred only within the population; there was no gene flow among populations, except for the Ungcheoncheon Stream population. This study shows that the Ungcheoncheon Stream population needs conservation efforts to increase its genetic diversity, and the Geumgang River populations needs a conservation plan that considers the possibility of conservation and evolution through gene exchange among the populations.

Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data

Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species’ significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.

Population genetics of Nelumbo lutea (American lotus) near its northwestern range limit

Nelumbo lutea Wild. (American lotus) has a broad and changing geographical distribution that is influenced by human transplanting and changes to climate, hydrology, and habitat. Populations vary from extensive stands where the species appears to be an effective colonizer, to sites where the species has declined or appears to have been extirpated. Previous studies in apparently stable populations from central and southern United States revealed low genetic diversity within and between populations. In this study, we assess genetic diversity at the northern edge of N. lutea’s range where it is often imperiled. A total of 489 individuals in 25 populations collected in Upper Mississippi River regions in Minnesota and Wisconsin were amplified in 12 microsatellite loci. Ten microsatellite loci indicated significant deviation from Hardy-Weinberg principal and were utilized for further analysis. Generally, genetic diversity was low compared to the genetic studies from southern North America. Despite low levels of genetic differentiation (Fst range; 0.003–0.059), structure and UPGMA analysis indicated the possibility of two distinct clusters and slight admixture in some populations. Initial low genetic diversity in populations was likely caused by founder effect if few individuals were established at each site. Limited migration and clonal growth contribute to the continued low diversity. We provide recommendations and research suggestions for the conservation of this species.

Low levels of genetic differentiation and structure in red fox populations in Eastern Canada and implications for Arctic fox rabies propagation potential.

Rabies is a lethal zoonosis present in most parts of the world which can be transmitted to humans through the bite from an infected mammalian reservoir host. The Arctic rabies virus variant (ARVV) persists mainly in populations of Arctic foxes (Vulpes lagopus), and to a lesser extent in red fox populations (Vulpes vulpes). Red foxes are thought to be responsible for sporadic southward movement waves of the ARVV outside the enzootic area of northern Canada. In this study, we wanted to investigate whether red foxes displayed notable levels of genetic structure across the Quebec-Labrador Peninsula, which includes portions of the provinces of Quebec and Newfoundland-Labrador in Canada, and is a region with a history of southward ARVV movement waves. We combined two datasets that were collected and genotyped using different protocols, totalling 675 red fox individuals across the whole region and genotyped across 13 microsatellite markers. We found two genetic clusters across the region, reflecting a latitudinal gradient, and characterized by low genetic differentiation. We also observed weak but significant isolation by distance, which seems to be marginally more important for females than for males. These findings suggest a general lack of resistance to movement in red fox populations across the Quebec-Labrador Peninsula, regardless of sex. Implications of these findings include additional support for the hypothesis of long-distance southward ARVV propagation through its red fox reservoir host.

Origin and genetic variability of populations of the invasive plant Rumex alpinus L. in the Giant (Krkonoše) Mountains.

Monk's rhubarb, Rumex alpinus L. (R. alpinus), is a perennial plant native to the mountains of Central and Southern Europe. Currently, the distribution of R. alpinus has been partly affected by its utilization as a vegetable and a medicinal herb. In the mountains of the Czech Republic, it is considered an invasive plant, probably introduced into the Krkonoše Mountains by colonists from the Alps. This study's main aim was to verify whether R. alpinus was introduced into the Krkonoše Mountains by alpine colonists or whether it was anthropogenically introduced from the Carpathians. Furthermore, the genetic structure of native and introduced populations of R. alpinus was determined. For the evaluation of genetic structure, 417 samples of R. alpinus were collected from the Alps, Carpathians, Balkan, Pyrenees, and Czech Mountains. In total, 12 simple sequence repeat (SSR) markers were applied. The results of AMOVA showed a high 60% variation within populations, 27% variation among groups, and 13% among the population within groups. The overall unbiased gene diversity was high (^ĥ = 0.55). The higher level of genetic differentiation among populations (FST = 0.35; p < .01) indicated restricted gene flow between populations. Compared to native populations, limited genetic variability was observed in the nonnative populations. It was concluded that local adaptation, low gene exchange, and genetic drift affected the genetic diversity of nonnative R. alpinus. The results support a genetic link between Alpine and Czech genotypes of R. alpinus, while the Carpathians genotypes corresponded to the Balkan genotype.

Genetic Diversity and Genetic Structure of Phascolosoma esculenta Populations in Southeastern China Based on 16S rRNA Gene Sequences

Here, we investigated the population genetic structure and genetic diversity of the endemic Chinese oceanic sipuncula Phascolosoma esculenta by using partial mitochondrial DNA 16S rRNA sequences. In total, 80 samples were collected from Xiangshan, Wenling, Ningde, and Zhanjiang, which are four muddy intertidal zones of southeastern China. Results showed that of the 80 16S rRNA gene fragments, 5 were 1010 bp in length, 73 were 1011 bp in length, and 2 were 1012 bp in length. The A+T content (67.7%) was signifi cantly higher than the C+G content (32.3%), thus exhibiting obvious AT biases. In addition, 27 different haplotypes were defi ned by 33 polymorphic sites, giving an overall haplotype diversity of 0.908 and a nucleotide diversity of 0.00247. The topological structure of the haplotype neighbor-joining tree was extremely simple, without any obvious geographical structures within the four groupings. The genetic distances among populations ranged from 0.0022 to 0.0031, and those within populations ranged from 0.002 to 0.0028. The results of AMOVA revealed a low level of genetic differentiation among the four populations. A neutral test and mismatch analysis indicated a recent population expansion for P. esculenta.

Geological events and climate change drive diversification and speciation of mute cicadas in eastern continental Asia

The poor mobility of nymphs living underground, usually for many years, and the weak flying ability of adults make cicadas unique for evolutionary biology and bio-geographical study. Cicadas of the genus Karenia are unusual in Cicadidae in lacking the timbals that produce sound. Population differentiation, genetic structure, dispersal and evolutionary history of the eastern Asian mute cicada Karenia caelatata were investigated based on morphological, acoustic and molecular data. The results reveal a high level of genetic differentiation in this species. Six independent clades with nearly unique sets of haplotypes corresponding to geographically isolated populations are recognized. Genetic and geographic distances are significantly correlated among lineages. The phenotypic differentiation is generally consistent with the high levels of genetic divergence across populations. Results of ecological niche modeling suggest that the potential distribution range of this mountain-habitat specialist during the Last Glacial Maximum was broader than its current range, indicating this species had benefited from the climate change during the early Pleistocene in southern China. Geological events such as orogeny in Southwest China and Pleistocene climate oscillations have driven the differentiation and divergence of this species, and basins, plains and rivers function as natural “barriers” to block the gene flow. Besides significant genetic divergence being found among clades, the populations occurring in the Wuyi Mountains and the Hengduan Mountains are significantly different in the calling song structure from other populations. This may have resulted from significant population differentiation and subsequent adaptation of related populations. We conclude that ecological differences in habitats, coupled with geographical isolation, have driven population divergence and allopatric speciation. This study provides a plausible example of incipient speciation in Cicadidae and improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this unusual cicada species. It informs future studies on population differentiation, speciation and phylogeography of other mountain-habitat insects in the East Asian continent.

Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye.

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r2 was between 0.45 and 0.2 and became flat when r2 was 0.05. The average LD decay for the entire genome was 30 kb when r2=0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.

Genetic structure of an endangered species Ormosia henryi in southern China, and implications for conservation

BackgroundThe evergreen broadleaved forest (EBLF) is an iconic vegetation type of East Asia, and it contributes fundamentally to biodiversity-based ecosystem functioning and services. However, the native habitat of EBLFs keeps on decreasing due to anthropogenic activities. Ormosia henryi is a valuable rare woody species in EBLFs that is particularly sensitive to habitat loss. In this study, ten natural populations of O. henryi in southern China were sampled, and then genotyping by sequencing (GBS) was applied to elucidate the standing genetic variation and population structure of this endangered species.ResultsIn ten O. henryi populations, 64,158 high-quality SNPs were generated by GBS. Based on these markers, a relatively low level of genetic diversity was found with the expected heterozygosity (He) ranging from 0.2371 to 0.2901. Pairwise FST between populations varied from 0.0213 to 0.1652, indicating a moderate level of genetic differentiation. However, contemporary gene flow between populations were rare. Assignment test and principal component analysis (PCA) both supported that O. henryi populations in southern China could be divided into four genetic groups, and prominent genetic admixture was found in those populations located in southern Jiangxi Province. Mantel tests and multiple matrix regression with randomization (MMRR) analyses suggested that isolation by distance (IBD) could be the possible reason for describing the current population genetic structure. In addition, the effective population size (Ne) of O. henryi was extremely small, and showed a continuous declining trend since the Last Glacial Period.ConclusionsOur results indicate that the endangered status of O. henryi is seriously underestimated. Artificial conservation measures should be applied as soon as possible to prevent O. henryi from the fate of extinction. Further studies are needed to elucidate the mechanism that leading to the continuous loss of genetic diversity in O. henryi and help to develop a better conservation strategy.

Genetic diversity among sea snakes of the genus Hydrophis (Elapidae, Reptilia) in the Persian Gulf and Gulf of Oman.

Sea snakes of the genus Hydrophis are important components of animal diversity in Iranian waters of the Persian Gulf and Gulf of Oman. Ten species of Hydrophis have been identified from the these waters and, in this study, genetic structure of seven species was compared with other populations in the eastern Indian Ocean and the West Pacific. We found that six species (H.platurus, H.cyanocinctus, H.spiralis, H.schistosus, H.gracilis, and H.lapemiodes) show high genetic similarity with conspecific populations in the Indian Ocean and Australia. However, H.curtus from southern Iran shows a high level of genetic differentiation from conspecific populations in Sri Lanka and Indonesia (0.6% and 6% genetic distance from Sri Lankan samples for 16S and COI gene fragments, respectively). Variation between Iranian and Southeast Asian populations may reflect new genetic lineages and suggest the need of further morphological evaluations to re-evaluate their taxonomic position.

Genetic structure and phylogeography of the endemic species broadbanded velvetchin Hapalogenys analis in the Northwest Pacific

In recent years, due to high-intensity fishing pressure and environmental pollution, some economically important fish species in the waters of the Northwest Pacific have shown a miniaturization trend as well as a sharp decline in fishery resources. Broadbanded velvetchin Hapalogenys analis is an economically important fish species that is widely distributed in the Northwest Pacific Ocean. To improve the understanding regarding its genetic structure and systematic geographic patterns, 87 mitochondrial control region sequences in four geographically distinct populations in the marginal sea of the Northwest Pacific Ocean were identified and analyzed. Thus, 67 haplotypes were detected in 812-base pair homologous sequences, and the haplotypes were identified as predominantly singletons. Further, genetic diversity and genetic structure analysis revealed that the Chinese and Japanese populations of H. analis had different genetic patterns as well as high levels of genetic differentiation. Furthermore, the population of H. analis expanded in the late Pleistocene and middle Pleistocene. We also identified biogeographical barriers, Pleistocene geological events, ocean circulation, habitat, and life history characteristics as the factors that influenced the population genetic structure and systematic geographical pattern of the broadbanded velvetchin species. This study provides information that can be applied in the conservation, sustainable utilization, and genetic diversity maintenance of H. analis.

Subspecies limits based on morphometry and mitochondrial DNA genomics in a polytypic species, the common grackle, Quiscalus quiscula

Abstract Nearctic migratory songbirds have demonstrated low levels of genetic differentiation and weak phylogeographical structure in mitochondrial DNA lineages compared with resident species. The common grackle, Quiscalus quiscula, is a widespread, partially migratory, North American icterid composed of three currently recognized subspecies. In this study, mensural characters (external and skeletal measurements) and the complete mitochondrial genome together with two mitochondrial genes, Cytb and ND2, were used to investigate subspecific differentiation and demographic history of the common grackle. The results showed substantial variation in body size among subspecies, mostly distributed between the ‘Florida grackle’, Quiscalus quiscula quiscula, and the two other subspecies. Analysis of mitochondrial DNA indicated low levels of genetic variation, but we found distinct haplotypes in Florida that form a clade in the phylogenetic tree. This suggests that the nominate subspecies in Florida is a distinct evolutionary unit. The sharing of haplotypes among the other subspecies (Quiscalus quiscula versicolor and Quiscalus quiscula stonei) in the north suggests high levels of gene flow, making the status of these two subspecies equivocal. Gene flow between nominate Q. q. quiscula, Q. q. versicolor and putative Q. q. stonei is probably attributable to historical changes in distribution and abundance following climate change events. We therefore recognize only two subspecies in the common grackle complex.

Genetic Diversity and Population Structure in Solanum nigrum Based on Single-Nucleotide Polymorphism (SNP) Markers

Solanum nigrum is a noxious weed in agricultural ecosystem that limits many crops’ production. The aim of the present study was to understand the level of genetic diversity and population structure of S. nigrum in China. A specific-locus amplified fragment (SLAF) sequencing method was conducted to detect single-nucleotide polymorphisms (SNPs) in the genomes of S. nigrum from 66 populations in China. A total of 616,533 high-quality SNPs were identified from 189,840 SLAFs, with an average sequencing depth of 10.59× fold and a Q30 value of 93% and a GC content of 42.78%. It showed a considerable amount of genetic diversity and genetic variability of S. nigrum among samples. The genetic differentiation of S. nigrum indicated that there was a low level of genetic differentiation (Fst &lt; 0.1000) among geographical populations. A cluster analysis showed that populations of S. nigrum were divided into two subgroups, with some samples from adjacent position roughly clustered together, which showed some correlation between geographic origins. A population structure analysis suggested the 66 S. nigrum samples could have originated from three different genetic clusters. The Xinjiang site was the only location where all genetic clusters were found, which suggested these populations were genetically diverse. These results showed that there was a high degree of genetic diversity and low difference among the different geographical populations of S. nigrum. The results from the genetic structure of the SNP markers indicated that wide genetic variability exists among the population of S. nigrum in China, which may contribute to the adaptation and infestation of this weed species.

Geographic isolation and long-distance gene flow influence the genetic structure of the blue fan palm Brahea armata (Arecaceae)

The formation of the Baja California Peninsula (BCP) has impacted the microevolutionary dynamics of different species in ways that depend on biological traits such as dispersal capacity. Plants with relatively low levels of vagility have exhibited high genetic divergence between the BCP and Continental mainland. Brahea armata (Arecaceae) is a palm species inhabiting the northern part of the BCP and Sonora; its distribution occurs in isolated oases of vegetation. We aimed to evaluate the influence of the formation of the BCP on the genetic structure of B. armata using nuclear microsatellites and chloroplast markers (cpDNA) to compare patterns of genetic diversity and structure with previous published studies. Because gene flow through seeds is usually more limited compared to pollen flow, we expect to find stronger genetic structure at (cpDNA) than at nuclear markers. Moreover, larger genetic structure might also be explained by the smaller effective population size of cpDNA. We analyzed six microsatellite markers and two cpDNA regions. The main results indicated high levels of genetic differentiation among isolated populations located in the BCP, while low genetic differentiation was found between southern populations of the BCP and Sonora, suggesting long distance gene flow. In contrast, chloroplast markers indicated high levels of genetic structure between BCP and Sonora populations, suggesting asymmetrical gene flow between pollen (measured by nuclear microsatellites) and seed (cpDNA markers). This study provides valuable information on genetic diversity of B. armata that can be relevant for conservation and management; and develops microsatellites markers that can be transferred to other Brahea species.