FST Values Research Articles

An assemblage-level comparison of genetic diversity and population genetic structure between island and mainland ant populations.

Island biotas provide unparalleled opportunities to examine evolutionary processes. Founder effects and bottlenecks, e.g., typically decrease genetic diversity in island populations, while selection for reduced dispersal can increase population structure. Given that support for these generalities mostly comes from single-species analyses, assemblage-level comparisons are needed to clarify how (i) colonization affects the gene pools of interacting insular organisms, and (ii) patterns of genetic differentiation vary within assemblages of organisms. Here, we use genome-wide sequence data from ultraconserved elements (UCEs) to compare the genetic diversity and population structure of mainland and island populations of nine ant species in coastal southern California. As expected, island populations (from Santa Cruz Island) had lower expected heterozygosity and Watterson's theta compared to mainland populations (from the Lompoc Valley). Island populations, however, exhibited smaller genetic distances among samples, indicating less population subdivision. Within the focal assemblage, pairwise Fst values revealed pronounced interspecific variation in mainland-island differentiation, which increases with gyne body size. Our results reveal population differences across an assemblage of interacting species and illuminate general patterns of insularization in ants. Compared to single-species studies, our analysis of nine conspecific population pairs from the same island-mainland system offers a powerful approach to studying fundamental evolutionary processes.

Genetic Diversity and Profile of Red Algae Pterocladiella capillacea (Gelidiales, Rhodophyta) along the Coast of China

Red algae Pterocladiella capillacea off the coast of China were investigated for genetic diversity. With 176 samples categorized into six populations based on concatenated rbcL and cox1 sequences, the results rang warning bells for the genetic diversity of Pterocladiella capillacea along the Chinese coastline: (1) a good diversity of haplotype (Hd > 0.5) in Naozhou and Hui’an populations situated along the southern coast of China, but highest in the former; (2) less nucleotide diversity in each of the six populations (Pi < 0.005); (3) genetic differentiation occurred between the north population in Changdao and the two southern grown populations in Nan’ao, and Naozhou. To identify molecular markers, an MP phylogenetic tree was used to illustrate genetic profiles in detail, with 161 concatenated sequences clustered into four branches: Changdao (north), Nan’ao (south), Naozhou (south), and the remaining regions (middle). The Fst value for each of Changdao, Nan’ao, and Naozhou was greater than 0.5, which denotes that these three populations are genetically different to those growing in the middle coast. Moreover, a 30-haplotype-based median-joining network corroborated this genetic differentiation, though variations between all the investigated populations were not very high due to the relatively smaller values of genetic distance between the six (Dxy < 0.01). Overall, red algae P. capillacea in Chinese coastal seawater showed a higher haplotype diversity and lower nucleotide diversity. Such a genetic profile indicates that both natural random genetic drift and interference from human activities have possibly affected the distribution of gene frequencies in red algae P. capillacea along the Chinese coastline.

Plasmodium vivax populations in the western Greater Mekong Subregion evaluated using a genetic barcode.

An improved understanding of the Plasmodium vivax populations in the Great Mekong Subregion (GMS) is needed to monitor the progress of malaria elimination. This study aimed to use a P. vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics and explore the gene flow among P. vivax parasite populations in the western GMS (China, Myanmar and Thailand). A total of 315 P. vivax patient samples collected in 2011 and 2018 from four regions of the western GMS were genotyped for 42 SNPs using the high-throughput MassARRAY SNP genotyping technology. Population genetic analysis was conducted to estimate the genetic diversity, effective population size, and population structure among the P. vivax populations. Overall, 291 samples were successfully genotyped at 39 SNPs. A significant difference was observed in the proportion of polyclonal infections among the five P. vivax populations (P = 0.0012, Pearson Chi-square test, χ2 = 18.1), with western Myanmar having the highest proportion (96.2%, 50/52) in 2018. Likewise, the average complexity of infection was also highest in western Myanmar (1.31) and lowest in northeast Myanmar (1.01) in 2018. The older samples from western China in 2011 had the highest pairwise nucleotide diversity (π, 0.388 ± 0.046), expected heterozygosity (He, 0.363 ± 0.02), and the largest effective population size. In comparison, in the neighboring northeast Myanmar, the more recent samples in 2018 showed the lowest values (π, 0.224 ± 0.036; He, 0.220 ± 0.026). Furthermore, the 2018 northeast Myanmar parasites showed high and moderate genetic differentiation from other populations with FST values of 0.162-0.252, whereas genetic differentiation among other populations was relatively low (FST ≤ 0.059). Principal component analysis, phylogeny, and STRUCTURE analysis showed that the P. vivax population in northeast Myanmar in 2018 substantially diverged from other populations. Although the 42 SNP barcode is a valuable tool for tracking parasite origins of worldwide parasite populations, a more extended barcode with additional SNPs is needed to distinguish the more related parasite populations in the western GMS.

Evidence for human-caused founder effect in populations of Solanum jamesii at archaeological sites: II. Genetic sequencing establishes ancient transport across the Southwest USA.

The domestication of wild plant species can begin with gathering and transport of propagules by Indigenous peoples. The effect on genomic composition, especially in clonal, self-incompatible perennials would be instantaneous and drastic with respect to new, anthropogenic populations subsequently established. Reductions in genetic diversity and mating capability would be symptomatic and the presence of unique alleles and genetic sequences would reveal the origins and ancestry of populations associated with archaeological sites. The current distribution of the Four Corners potato, Solanum jamesii Torr. in the Southwestern USA, may thus reflect the early stages of a domestication process that began with tuber transport. Herein genetic sequencing (GBS) data are used to further examine the hypothesis of domestication in this culturally significant species by sampling 25 archaeological and non-archaeological populations. Archaeological populations from Utah, Colorado and northern Arizona have lower levels of polymorphic loci, unique alleles, and heterozygosity than non-archaeological populations from the Mogollon region of central Arizona and New Mexico. Principle components analysis, Fst values, and structure analysis revealed that genetic relationships among archaeological populations did not correspond to geographic proximity. Populations in Escalante, Utah were related to those on the Mogollon Rim (400 km south) and had multiple origins and significant disjunctions with those populations in Bears Ears, Chaco Canyon, and Mesa Verde sites. Movement of tubers from the Mogollon region may have occurred many times and in multiple directions during the past, resulting in the complex genetic patterns seen in populations from across the Four Corners region.

Integrating wing morphometrics and mitochondrial DNA analysis to assess the filaria vector Mansonia uniformis (Diptera: Culicidae) populations in Thailand.

Mansonia uniformis (Diptera: Culicidae) is recognized as a vector of Brugia malayi and has been reported to transmit Wuchereria bancrofti, both causing lymphatic filariasis in humans. This study employed geometric morphometrics (GM) to investigate wing shape variation and analyzed genetic diversity through cytochrome c oxidase subunit 1 (COI) gene analyses in Ma. uniformis populations across Thailand. Wing GM analyses indicated significant differences in wing shape based on Mahalanobis distances among nearly all population pairs (p < 0.05), with no significant correlation between wing shape and geographic distance (r = 0.210, p > 0.05). Genetic analyses identified 63 haplotypes and 49 polymorphic sites, with the overall population exhibiting a nucleotide diversity of 0.006 (± 0.001) and a haplotype diversity of 0.912 (± 0.017). Deviations from neutrality, as indicated by Tajima's D and Fu's FS tests for the overall Ma. uniformis populations in Thailand, were statistically significant and negative, suggesting population expansion (both p < 0.05). Analysis of molecular variance revealed no significant genetic structure when all populations were categorized based on collection sites and geographic regions. However, significant differences in FST values were observed between some populations. These findings enhance our understanding of the geographical and genetic factors influencing Ma. uniformis populations, which are crucial for developing effective control strategies in Thailand.

Classification accuracy of machine learning algorithms for Chinese local cattle breeds using genomic markers.

Accurate breed classification is required for the conservation and utilization of farm animal genetic resources. Traditional classification methods mainly rely on phenotypic characterization. However, it is difficult to distinguish between the highly similar breeds due to the challenges in qualifying the phenotypic character. Machine learning algorithms show unique advantages in breed classification using genomic information. To evaluate the classification methods for Chinese cattle breeds, this study utilized genomic SNP data from 213 individuals across seven Chinese local breeds and compared the classification accuracies of three feature selection methods (FST value sorting and screening, mRMR, and Relief-F) and three machine learning algorithms (Random Forest, Support Vector Machine, and Naive Bayes). Results showed that: 1) using the FST method to screen more than 1500 SNPs, or using the mRMR algorithm to screen more than 1000 SNPs, the SVM classification algorithm can achieve more than 99.47% classification accuracy; 2) the most effective algorithm was SVM, followed by NB, while the best SNP selection method was FST and mRMR, followed by Relief-F; 3) species misclassification often occurs between breeds with high similarity. This study demonstrates that machine learning classification models combined with genomic data are effective methods for the classification of local cattle breeds, providing a technical basis for the rapid and accurate classification of cattle breeds in China.

High genetic diversity in anguillid glass eels across three Southeast Asian countries revealed through mitochondrial DNA D-loop sequences, with notes on population structure

Understanding the genetic diversity and population structure of anguillid eels is crucial for effective management. In this study, we used the mitochondrial DNA (mtDNA) D-loop marker to identify anguillid glass eels and assessed their genetic diversity across six sampling sites spanning three Southeast Asian countries. We also examined the population structures of Anguilla marmorata and A. celebesensis. We validated nine distinct species and subspecies of anguillid eels from 465 specimens collected in Indonesia (n = 246), the Philippines (n = 119), and Vietnam (n = 100). High gene diversities were observed across the species, ranging from 0.979 (A. celebesensis) to 1.000 (A. bicolor bicolor, A. marmorata, and A. interioris). Correspondingly, nucleotide diversity values were relatively low, varying from 0.036 (A. marmorata) to 0.057 (A. interioris). A. marmorata (n = 162) displayed a broad distribution, being observed across all six sites, with a significant yet low average fixation index of 0.05755. Pairwise comparisons of FST values between Cimandiri and other locations (except for Cagayan) were relatively high and statistically significant (p < 0.01), indicating significant genetic differentiation of Cimandiri samples compared to most locations in this study. On the other hand, A. celebesensis (n = 110), exhibited a non-significant and low fixation index (0.007), indicating no genetic differentiation in samples from Poso and Poigar Rivers, Indonesia. Our findings highlight the essential need for coordinated management strategies among regions that share common stocks. Additionally, this study underscores the efficacy of the mtDNA D-loop in precisely identifying glass eel species/subspecies and elucidating the genetic diversity and population structure of tropical anguillid eels.

Clinal variation in quantitative traits but not in evolutionary potential along elevational and latitudinal gradients in the widespread Anthyllis vulneraria.

Strong elevational and latitudinal gradients allow the study of genetic differentiation in response to similar environmental changes. However, it is uncertain whether the environmental changes along the two types of gradients result in similar genetically based changes in quantitative traits. Peripheral arctic and alpine populations are thought to have less evolutionary potential than more central populations do. We studied quantitative traits of the widespread Anthyllis vulneraria in a common garden. Plants originated from 20 populations along a 2000-m elevational gradient from the lowlands to the elevational limit of the species in the Alps, and from 20 populations along a 2400-km latitudinal gradient from the center of the distribution of the species in Central Europe to its northern distributional margin. Most traits showed similar clinal variations with elevation and latitude of origin, and the magnitude of all measured traits in relation to mean annual temperature was similar. Higher QST values than FST values in several traits indicated diversifying selection, but for others QST was smaller than FST. Genetic diversity of quantitative traits and neutral molecular markers was not correlated. Plasticity in response to favorable conditions declined with elevation and less strongly with latitude of origin, but the evolvability of traits did not. The clinal variation suggests adaptive differentiation of quantitative traits along the two gradients. The evolutionary potential of peripheral populations is not necessarily reduced, but lower plasticity may threaten their survival under rapidly changing climatic conditions.

Genetic diversity of Rhombomys opimus and Meriones meridianus with potential divergence of plague resistance in the Junggar Basin plague focus based on RT1-Db1*exon1

In the Junggar Basin plague focus, Rhombomys opimus and Meriones meridianus live together, and their parasitic fleas have a similar community structure. However, R. opimus has significantly higher positive rates of Yersinia pestis and anti-F1 antibody compared with M. meridianus. In this study, Y. pestis- and antiF1 antibody-negative R. opimus and M. penicilliger were collected in Qitai county, Fukang city and Mulei county of the eastern part of the Junggar Basin. The genomic DNA was extracted from their spleen tissues, and RT1-Db1*exon1 was amplified through PCR procedure and then sequenced. Sequence analysis was performed and molecular diversity parameters were calculated and compared. The results showed that there were significant differences in nucleotide composition, amino acid composition, number and distribution of single nucleotide polymorphism (SNP) sites and number of haplotypes between R. opimus and M. penicilliger. The nucleotide diversity (π) for R. opimus was 0.00420 ± 0.00139, the haplotype diversity (h) was 0.833 ± 0.086, and the average number of nucleotide differences (K) was 2.02564. The π for M. penicilliger was 0.06569 ± 0.02524, and the h was 1.000 ± 0.045, and the K was 10.4444. The fixation index (FST) value between R. opimus and M. penicilliger was 0.9207. Furthermore, the FST value within R. opimus (0.0275) was significantly lower than that within M. penicilliger (0.2106), indicating a greater genetic variation of M. penicilliger compared with R. opimus. In conclusion, the genetic diversity analysis based on RT1-Db1*exon1 showed that M. penicilliger had higher gene polymorphism and greater genetic differentiation compared with R. opimus in the Junggar Basin plague focus, which might be associated with the low infection rate of Y. pestis.

Genomic insights into the critically endangered King Island scrubtit.

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.

Haemonchus contortus, an obligatory haematophagus worm infection in small ruminants: Population genetics and genetic diversity

Haemonchus contortus, a stomach worm, is prevalent in ruminants worldwide. They particularly hamper profitable small ruminant production. Here, we estimate the genetic variation of H. contortus collected from slaughtered goats and sheep from various geographic zones of Bangladesh using multiple genes. To perform this, adult parasites were isolated from the abomasum of slaughtered animals (sheep and goats). Among them, 79 male H. contortus were identified by microscopy. Following the extraction of DNA, ITS-2 and cox1 genes were amplified and subsequently considered for sequencing. After alignment and editing, sequences were analyzed to find out sequence variation, diversity pattern of genes, and population genetics of isolates. Among the sequence data, the analyses identified 19 genotypes of ITS-2 and 77 haplotypes of cox1 genes. The diversity of nucleotides was 0.0103 for ITS-2 and 0.029 for cox1 gene. The dendogram constructed by the genotype and haplotype sequences of H. contortus revealed that two populations were circulating in Bangladesh without any demarcation of host and geographic regions. Analysis of population genetics demonstrated a high flow of genes (89.2 %) within the population of the worm in Bangladesh. The Fst value showed very little amount of genetic difference among the worm populations of Bangladesh but marked genetic variation between different continents. The findings are expected to help explain the risks of anthelmintic resistance and the transmission pattern of the parasite, and also provide a control strategy against H. contortus.

Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines

BackgroundThe adaptive divergence of Aedes aegypti populations to heterogeneous environments can be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines.MethodsWe used the Pool-Seq double digestion restriction-site association DNA sequencing (ddRAD-Seq) approach to generate a high number of single nucleotide polymorphisms (SNPs), with the aim to determine local adaptation and compare the population structure with 11 microsatellite markers. A total of 217 Ae. aegypti individuals from seven female and seven male populations collected from Metropolitan Manila were used in the assays.ResultsWe detected 65,473 SNPs across the populations, of which 76 were non-neutral SNPs. Of these non-neutral SNPs, the multivariate regression test associated 50 with eight landscape variables (e.g. open space, forest, etc.) and 29 with five climate variables (e.g. air temperature, humidity, etc.) (P-value range 0.005–0.045) in female and male populations separately. Male and female populations exhibited contrasting spatial divergence, with males exhibiting greater divergence than females, most likely reflecting the different dispersal abilities of male and female mosquitoes. In the comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of the neutral SNPs, indicating that the neutral SNPs generated via pool ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales.ConclusionsOverall, our study demonstrates the utility of pool ddRAD-Seq for examining genetic differences in Ae. aegypti populations in areas at fine-spatial scales that could inform vector control programs such as Wolbachia-infected mosquito mass-release programs. This in turn would provide information on mosquito population dispersal patterns and the potential barriers to mosquito movement within and around the release area. In addition, the potential of environmental adaptability observed in Ae. aegypti could help population control efforts.Graphical

A First Look at Genetic Diversity of Metapenaeus ensis Populations in Tam Giang – Cau Hai Lagoon, Vietnam

This study investigates the genetic diversity and population structure of the greasyback shrimp, Metapenaeus ensis (De Haan, 1844), within the Tam Giang – Cau Hai lagoon, Vietnam, by analyzing mtCOI genes from 91 individuals collected across four populations in nine sampling locations. High genetic diversity was found, with 34 unique haplotypes and 38 genetic variations identified. Most genetic variation occurred within populations (AMOVA), suggesting high gene flow. Low and non-significant Fst values and close genetic distances confirmed minimal differentiation among populations. These findings provide the first insights into M. ensis population genetics in this lagoon, informing conservation and management efforts. Understanding genetic diversity is crucial for sustainable management and conservation of marine species. This research aids in understanding population resilience, potential impacts of overfishing, and may assist in developing sustainable harvest strategies of this economically important shrimp species.

Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals

The primary objective of Sustainable Development Goal target 2.5 established by the United Nations is to ensure the preservation of genetic diversity in domesticated animals. The ICAR-National Bureau of Animal Genetic Resources in India has been actively engaged in the conservation of cattle and buffalo bull semen for long-term storage. This present study aimed to assess the genetic diversity present in the conserved cattle bull semen, which would aid in determining the most suitable strategy for future conservation management. A total of 192 bull semen belonging to 19 cattle breeds were selected to evaluate genetic diversity using 17 pairs of FAO recommended microsatellite primers. Total 267 alleles were detected across all the samples which indicates substantial amount of allelic variation is being maintained in conserved bulls. Further, all cattle bulls semen conserved showed higher observed heterozygosity than expected heterozygosity which indicates excess genetic diversity in all the populations. The FST, F IT and FIS value across the loci and population is 0.146 ± 0.009, 0.054 ± 0.038, and − 0.105 ± 0.035, respectively, which suggests lack of inbreeding in conserved cattle bull semen. This study has established genetic diversity in conserved cattle semen samples to achieve sustainable development goals. In addition, it provides compelling evidence that the current approach for conserving cattle bull semen is heading in the correct direction.

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

BackgroundGenome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.ResultsThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.ConclusionsThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study.

Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.

A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data.

Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an Fst of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an Fst value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.

An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing

In recent years, probabilistic genotyping software has been adapted for the analysis of massively parallel sequencing (MPS) forensic data. Likelihood ratios (LR) are based on allele frequencies selected from populations of interest. This study provides an outline of sequence-based (SB) allele frequencies for autosomal short tandem repeats (aSTRs) and identity single nucleotide polymorphisms (iSNPs) in 371 individuals from Southern Norway. 27 aSTRs and 94 iSNPs were previously analysed with the ForenSeq™ DNA Signature Prep Kit (Verogen). The number of alleles with frequencies less than 0.05 for sequenced-based alleles was 4.6 times higher than for length-based alleles. Consistent with previous studies, it was observed that sequence-based data (both with and without flanks) exhibited higher allele diversity compared to length-based (LB) data; random match probabilities were lower for SB alleles confirming their advantage to discriminate between individuals. Two alleles in markers D22S1045 and Penta D were observed with SNPs in the 3´ flanking region, which have not been reported before. Also, a novel SNP with a minor allele frequency (MAF) of 0.001, was found in marker TH01. The impact of the sample size on minor allele frequency (MAF) values was studied in 88 iSNPs from Southern Norway (n = 371). The findings were then compared to a larger Norwegian population dataset (n = 15,769). The results showed that the smaller Southern Norway dataset provided similar results, and it was a representative sample. Population structure was analyzed for regions within Southern Norway; FST estimates for aSTR and iSNPs did not indicate any genetic structure. Finally, we investigated the genetic differences between Southern Norway and two other populations: Northern Norway and Denmark. Allele frequencies between these populations were compared, and we found no significant frequency differences (p-values > 0.0001). We also calculated the pairwise FST values per marker and comparisons between Southern and Northern Norway showed small differences. In contrast, the comparisons between Southern Norway and Denmark showed higher FST values for some markers, possibly driven by distinct alleles that were present in only one of the populations. In summary, we propose that allele frequencies from each population considered in this study could be used interchangeably to calculate genotype probabilities.

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology.

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

Milk protein polymorphisms and casein haplotypes in Blanco Orejinegro cattle of Colombia

The aim was to determine the genetic variation in the CSN1S1, CSN2, CSN1S2, CSN3 and LGB genes in Blanco Orejinegro cattle. 419 animals from 15 herds were genotyped with GGP Bovine 150 K (n= 70) and 50 K (n= 349) chips. Information was obtained from 43 SNPs in the mentioned genes and protein variants *B, *C and *D of αS1-CN; *A1, *A2, *B, *H2 and *F of β-CN; *A and *D of αS2-CN, *A, *A1, *B, *I and *H of κ-CN and *A, *B, *C, *D, *E, *F and *H of β-LG were reconstructed. Allele and genotypic frequencies were estimated for SNPs and for protein variants; Hardy-Weinberg equilibrium and FST values were evaluated for each of the SNPs under different structuring criteria. LD values and haplotypic frequencies were estimated for caseins. The most frequent variants were CSN1S1*B (0.804), CSN2*A2 (0.509), CSN1S2*A (0.997), CSN3*A (0.679) and β-LG*B (0.657). None of the variants showed deviations from HWE, but the CSN2*A2 allele showed a slight increasing trend over time. The FST values were low (0.035) regardless of the structuring criteria. Twenty-eight CSN1S1-CSN2-CSN1S2-CSN3 haplotypes were found, 22 of them with frequencies &lt;5%; the three most frequent were BB-A1A2-AA-AA-AA-AA (16.6%), BB-A1A2-AA-AA-AA-AB (14.1%) and BB-A2A2-AA-AA-AA (10.1%). A good potential of BON cattle to produce high quality milk with functional value was reported.