Studies Of Population Differentiation Research Articles

Role of Provenance Trials in the Study of Population Differentiation

Wide distribution of many Linnean species across climatic, edaphic and biotic barriers may be either due to a wide ecological amplitude of the species as such, or to the presence of a number of distinct local populations, well adapted to the respective ecoclimates. These populations may show continuous variation along an envirormental gradient (ecocline) or discontinuous variation (ecotypes). The morphological or physiological adaptive characters are genetically fixed. Although a number of genecological techniques have been developed in the recent past, to differentiate such ecologic populations, the provenance trial technique has gained much importance. In the present communication the technique as well as some important results obtained through its use, both within and outside India, have been briefly discussed.

Variabilidad genética del pez Lutjanus guttatus (Perciformes: Lutjanidae) mediante el uso de microsatélites en Costa Rica

Introduction: The rose spotted snapper (Lutjanus guttatus) is a highly consumed marine fish and of commercial interest in Costa Rica, under a strong fishing pressure that can affect the genetic diversity of the population creating problems related to inbreeding depression. Objective: To evaluate the genetic diversity of the spotted snapper (Lutjanus guttatus) population in Costa Rica using microsatellites. Methodology: Samples were collected from two locations (Golfo Dulce and Golfo de Nicoya) in 2019, and 44 individuals from each site were studied. DNA extraction and amplification of 10 microsatellites by PCR were carried out for subsequent genotyping for genetic diversity and population structure analysis. Results: The genetic diversity parameters show a high polymorphism, associated to a high number of alleles per locus, but low levels of observed heterozygosity in comparison to the expected heterozygosity (Ho = 0,774 and 0,800 and He = 0,948 and 0,954 for Gulf of Nicoya and Gulf Dulce, respectively). The study of population differentiation indicates that there is not enough evidence to ensure the two populations are different (FST = 0,00264, p > 0.05). The significant deviation from Hardy-Weinberg Equilibrium obtained indicated the possible presence of organisms in the population that does not come from the wild. Conclusions: The rose spotted snapper in Costa Rica shows high levels of genetic diversity, without evidence of differentiation in genetic subpopulations, that should be considered as a single panmictic population for fishery management purposes. The possible mix of individuals of a distinct origin found in the wild suggests the presence of organisms that come from a stock enhancement program or from commercial aquaculture carried out in the region. The use of genetic markers is recommended to keep track of the genetic characteristics of the wild population, to follow-up stock enhancement programs, and eventually, asses their effect.

Honorary Lifetime Membership Award: Ellen D. Ketterson.

Honorary Lifetime Membership Award: Ellen D. Ketterson.

A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs.

Dramatic phenotypic differences between domestic pigs and wild boars (Sus scrofa) provide opportunities to investigate molecular mechanisms underlying the formation of complex traits, including morphology, physiology and behaviour. Most studies comparing domestic pigs and wild boars have focused on variations in DNA sequences and mRNA expression, but not on epigenetic changes. Here, we present a genome‐wide comparative study on H3K27ac enhancer activities and the corresponding mRNA profiling in the brain and liver tissues of adult Bama Xiang pigs (BMXs) and Chinese wild boars (CWBs). We identified a total of 1,29,487 potential regulatory elements, among which 11,241 H3K27ac peaks showed differential activity between CWBs and BMXs in at least one tissue. These peaks were overrepresented by binding motifs of FOXA1, JunB, ATF3 and BATF, and overlapped with differentially expressed genes that are involved in female mating behaviour, response to growth factors and hormones, and lipid metabolism. We also identified 4118 nonredundant super‐enhancers from ChIP‐Seq data on H3K27ac. Notably, we identified differentially active peaks located close to or within candidate genes, including TBX19, MSTN, AHR and P2RY1, which were identified in DNA sequence‐based population differentiation studies. This study generates a valuable dataset on H3K27ac profiles of the brain and liver from domestic pigs and wild boars, which helps gain insights into the changes in enhancer activities from wild boars to domestic pigs.

Asymmetric introgression reveals the genetic architecture of a plumage trait

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

Population genetic diversity in an Iraqi population and gene flow across the Arabian Peninsula

Y-STRs have emerged as important forensic and population genetic markers for human identification and population differentiation studies. Therefore, population databases for these markers have been developed for almost all major populations around the world. The Iraqi population encompasses several ethnic groups that need to be genetically characterised and evaluated for possible substructures. Previous studies on the Iraqi population based on Y-STR markers were limited by a restricted number of markers. A larger database for Iraqi Arab population needed to be developed to help study and compare the population with other Middle Eastern populations. Twenty-three Y-STR loci included in the PowerPlex Y23 (Promega, Madison, WI, USA) were typed in 254 males from the Iraqi Arab population. Global and regional Y-STR analysis demonstrated regional genetic continuity among the populations of Iraq, the Arabian Peninsula and the Middle East. The Iraqi Arab haplotypes were used to allocate samples to their most likely haplogroups using Athey’s Haplogroup Predictor tool. Prediction indicated predominance (36.6%) of haplogroup J1 in Iraqi Arabs. The migration rate between other populations and the Iraqis was inferred using coalescence theory in the Migrate-n program. Y-STR data were used to test different out-of-Africa migration models as well as more recent migrations within the Arabian Peninsula. The migration models demonstrated that gene flow to Iraq began from East Africa, with the Levantine corridor the most probable passageway out of Africa. The data presented here will enrich our understanding of genetic diversity in the region and introduce a PowerPlex Y23 database to the forensic community.

A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea.

Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step toward developing pan-genomic resources for Atlantic cod.

Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation.

Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.

Identifying QTL–allele system of seed protein content in Chinese soybean landraces for population differentiation studies and optimal cross predictions

Soybean originated in ancient China has been quickly extended globally as a major protein and oil crop. The QTL–allele constitution of seed protein content (SPC) in the Chinese soybean landrace population (CSLRP) was studied using a representative sample composed of 365 accessions tested under multiple environments and analysed under the novel restricted two-stage multi-locus genome-wide association study (RTM-GWAS) procedure based on 29,121 SNPLDB (single nucleotide polymorphism linkage disequilibrium blocks) markers. The SPC varied from 37.51 to 50.46% among accessions, for which 89 QTLs, each with 2–9 alleles in a total of 255 alleles were identified, accounting for 83.16% of the phenotypic variation covering most of the genetic variation (h2 = 84.31%). The QTL–alleles of the 365 landraces were organized into a 255 × 365 QTL–allele matrix as the compact form of SPC genetic constitution in CSLRP. Of the 89 QTLs, 53 showed significantly differentiated allele frequency distribution patterns among geographic eco-regions (sub-populations). There were 32.09% alleles not common among sub-populations but found only in some sub-populations; new allele(s) emerged on some loci in some respective sub-populations, with Eco-region III showing less but Eco-region VI more emergence. The QTL–allele matrix was also used for prediction of optimal crosses for breeding purpose to reach a 99th percentile potential of up to 54.81%, more than the highest accession (50.46%). From the 89 QTLs, 59 SPC candidate genes involving biological processes, cellular components and molecular functions were annotated. Among them, Glyma18g13574 and Glyma20g21370 were inferred as two of the major SPC genes in the whole genome.

Characterization of SNP markers for the painted bunting (Passerina ciris) and their relevance in population differentiation and genome evolution studies

We developed nuclear single nucleotide polymorphism (SNP) markers for the Painted Bunting (Passerina ciris) using next-generation sequencing genotyping on the Illumina HiSeq4000 platform. Following the best-RAD approach, we sequenced 96 individuals from five breeding populations occurring in the United States. We assessed the discerning power of 105,000 SNPs and confirmed the quality of these markers in population differentiation studies. We detected outlier SNPs within or near protein coding genes, including sequences coding for olfactory receptors which may relate to migratory navigation. Finally, we provide a novel list of 33 primer pairs flanking SNPs to link individuals to regional populations and improve our understanding of the evolution of this migratory songbird.

Phenetic similarity of European golden jackal (Canis aureus moreoticus) populations from southeastern Europe based on craniometric data

AbstractThis study describes the craniometrical population pattern of the European golden jackal (

Genetic polymorphism and evolutionary differentiation of Eastern Chinese Han: a comprehensive and comparative analysis on KIRs

Killer cell immunoglobulin-like receptor genes, namely KIRs, cluster together within the 160 kb genomic DNA region. In this study, we used PCR-SSP approach and successfully identified the genotype of 17 KIR genes in 123 independent healthy donors residing in the Jiangsu province, China. All individuals were positive at the 7 genes. The observed carrier gene frequencies (OFs) of remaining 10 KIRs ranged from 14.63% (KIR2DS3) to 95.93% (KIR3DL1). We found 27 distinct genotypes excluding KIR1D. The most frequent occurred in 63 individuals (51.22%). The linkage disequilibrium analysis signified 29 positive and 6 negative relations in 45 pairwise comparisons. To study population differentiation, we drew a Heatmap based on the data of KIRs from 59 populations and conducted Hierarchical Clustering by Euclidean distances. We next validated our results by estimating pairwise DA distances and illustrating a Neighbor-Joining tree, as well as a MDS plot covering 3 additional Chinese Han groups. The phylogenetic reconstruction and cluster analysis strongly indicated a genetically close relationship between Eastern and Jilin Hans. In conclusion, the present study provided a meritorious resource of KIR genotyping for population genetics, and could be helpful to uncover the genetic mechanism of KIRs in immune disease in the future.

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush).

The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists.

Genetic diversity and population structure analysis of Qinghai-Tibetan plateau schizothoracine fish (Gymnocypris dobula) based on mtDNA D-loop sequences

Gymnocypris dobula is a commercially important fishery species and mostly distributed in the freshwater of Tibetan plateau. In this study, genetic diversity and intraspecific population differentiation were examined by using mitochondrial DNA D-loop sequences in 97 individuals sampled from three localities (Pali, Lasa and Yanghu) in the Tibetan plateau. Two hundred and fourteen polymorphic sites and 50 haplotypes were defined among the three localities. Genetic diversity analysis showed that the highest genetic diversity level was found in Pali population. Phylogenetic relationships analysis results indicated that closer phylogenetic relationships were found between the Yanghu and Lasa populations. Genetic population differentiation analysis indicated that the majority of variation (84.91%) was attributed to variations among populations and the largest differentiation was found between Pali and Lasa localities (Fst = 0.874, Nm = 0.036). Moreover, the historical demographic events were assessed by implementing the mismatch distribution analysis, Fajima's D test and Fu's Fs test. The results indicated that the Pali population had undergone a demographic expansion, possibly within the last 0.163 MYA (Million Years Ago). Our study firstly identified the population genetic structure of the G. dobula, which could be helpful for artificial breeding, fishery stock identification and resource conservation for this species.

Host Defense Skin Peptides Vary with Color Pattern in the Highly Polymorphic Red-Eyed Treefrog

Patterns of phenotypic variation across a geographic range provide important insights into evolutionary processes underlying diversification and speciation. Most evolutionary studies use putatively neutral markers to examine evolutionary diversification. However, functional phenotypes such as gene-encoded host-defense polypeptides (HDPs) could provide key insights into the processes of population differentiation, yet they are rarely included in population analyses. The red-eyed treefrog, Agalychnis callidryas (Cope, 1862), exhibits regional variation in multiple traits, including color pattern and body size across a narrow geographic range. This treefrog produces bioactive peptides exuded onto the skin surface, presumably for pathogen and predator defense. However, the geographic patterns of variation in peptides and the factors that mediate intraspecific peptide variation across the range of this species remain untested. Here, we examine the roles of phylogenetic history, geographic barriers, geographic distance, and color-pattern variation as determinants of skin peptide diversity in 54 individuals among 11 populations across Costa Rica and Panama. Each of the five distinct Agalychnis color morphs are represented in our sample. We performed peptide mass fingerprinting and compared mass spectral data from skin peptide secretions to quantify divergence in peptide profiles among individuals, both within and among regions. We used two metrics to estimate genetic variation: genetic distance estimated from microsatellites and patristic distance estimated from mtDNA haplotype diversity. Matrix correspondence tests revealed that skin peptide variation is best predicted by differences in leg color pattern across all regions. In addition, we found that flank color pattern and phylogeny also explain differences in peptide diversity. Patterns of peptide differentiation and phylogenetic topology were incongruent in two regions, indicating a possible role of localized selection on peptide variation. Skin peptide profiles are useful in population differentiation studies of a polymorphic species as well as studies of selection and phenotype covariation among closely related species. Our results highlight the use of skin peptides as characters for future studies of population differentiation and contribute to our understanding of biogeography in Central America.

The Crested Auklet, Aethia cristatella (Alcidae, Charadriiformes), does not vary geographically in genetics, morphology or vocalizations

The study of population differentiation is essential for understanding species evolution and ecology. Despite a large amount of published works in this area of study, the prediction of population structure in a number of animal species and, particularly, in seabirds remains difficult. The Crested Auklet (Aethia cristatella) is a small, planktivorous seabird species that breeds in colonies on islands and along the coastline of the North Pacific. Despite their vast breeding area and huge population numbers, the phenotypic features of adult birds from different colonies and genetic population variability have not been studied yet. Here we conducted a combined study of population differentiation in the Crested Auklet, using both phenotypic and genetic features. Data were collected at nine points across the species’ distribution range from 1988 to 2012. We analyzed population variability of the mitochondrial control region fragment, microsatellites, two types of vocalizations (barks and trumpet calls), morphometric and ornamentation measurements. However, we did not detect any obvious cues to different populations, either in genetic, morphometric or acoustic variables. Crested Auklets from different geographic areas do not express any genetic differences. We surmise that the absence of population separation in Crested Auklet can be explained by an important ecological characteristic of the species: these birds are pelagic during non-breeding season; therefore, young birds likely migrate far away from their natal colonies during their first year of life and do not often return to breed at their native colony.

Iris atrofusca genetic and phenotypic variation, the role of habitat-specific selection in this variation structuring, and conservation implications using quasi in situ guidelines

Knowing the extent and structure of genetic variation in an endangered species is essential for establishing efficient conservation practices. However, the proper use of this information requires understanding the role of habitat-specific selection in genetic structuring. We present a study of population differentiation in an endangered species that utilizes guidelines of recently a proposedquasi in situconservation approach, i.e. taking into account the scale and spatial pattern of local adaptation since if local adaptation is important, the introduced genotypes must be matched to the local biotic/abiotic conditions. Following this approach, we examined the extent and structure of genetic (AFLP) and phenotypic variation and tested for adaptive significance of this variation in critically endangeredIris atrofuscagrowing in Israel and Jordan. From these results we propose a sampling design that would (i) preserve species adaptive potential and (ii) insure environmental match of the plant material for relocation, reintroduction or enhancement.

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

Given the low intraspecific chloroplast diversity detected in northern red oak (Quercus rubra L.), more powerful genetic tools are necessary to accurately characterize Q. rubra chloroplast diversity and structure. We report the sequencing, assembly, and annotation of the chloroplast genome of northern red oak via pyrosequencing and a combination of de novo and reference-guided assembly (RGA). Chloroplast DNA from 16 individuals was separated into four MID-tagged pools for a Genome Sequencer 20 quarter-run (Roche Life Sciences, Indianapolis, IN, USA). A four-step assembly method was used to generate the Q. rubra chloroplast consensus sequence: (1) reads were assembled de novo into contigs, (2) de novo contigs were aligned to a reference genome and merged to produce a consensus sequence, (3) the consensus sequence was aligned to the reference sequence and gaps between contigs were filled with reference sequence to generate a "pseudoreference", and (4) reads were mapped to the pseudoreference using RGA to generate the draft chloroplast genome. One hundred percent of the pseudoreference sequence was covered with a minimum coverage of 2× and an average coverage of 43.75×. The 161,304-bp Q. rubra chloroplast genome draft sequence contained 137 genes and one rps19 pseudogene. The sequence was compared to that of Quercus robur and Q. nigra with 951 and 186 insertion/deletion or SNP polymorphisms detected, respectively. A total of 51 intraspecific polymorphisms were detected among four northern red oak individuals. The fully sequenced and annotated Q. rubra chloroplast genome containing locations of interspecific and intraspecific polymorphisms will be essential for studying population differentiation, phylogeography, and evolutionary history of this species as well as meeting management goals such as monitoring reintroduced populations, tracking wood products, and certifying seed lots and forests.

Microsatellite primers in the foundation tree species Pinus edulis and P. monophylla (Pinaceae).

• Premise of the study: Microsatellite primers were developed in the foundational tree species Pinus edulis to investigate population differentiation of P. edulis and hybridization among closely related species.• Methods and Results: Using a hybridization protocol, primer sets for 11 microsatellite loci were developed using megagametophyte tissue from P. edulis and scored for polymorphism in three populations of P. edulis and a single P. monophylla population. The primers amplified simple and compound di-, tri-, and pentanucleotide repeats with two to 18 alleles per locus.• Conclusions: These results demonstrate the utility of the described primers for studies of population differentiation within and among P. edulis populations as well as across putative hybrid zones where P. edulis may coexist with sister species.

StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations

Statistical Analysis of Mixed-Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed-ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise FST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed-ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high-throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.