Genetic Distance Estimates Research Articles

Genetic resources of African mahogany in Brazil: genomic diversity and structure of forest plantations

BackgroundAfrican mahogany species (Khaya sp.) have been introduced to Brazil gaining increasing economic interest over the last years, as they produce high quality wood for industrial applications. To this date, however, the knowledge available on the genetic basis of African mahogany plantations in Brazil is limited, which has driven this study to examine the extent of genetic diversity and structure of three cultivated species (Khaya grandifoliola, Khaya senegalensis and Khaya ivorensis) and their prospects for forest breeding.ResultsIn total, 115 individuals were genotyped (48 of K. grandifoliola, 34 of K. senegalensis and 33 of K. ivorensis) for 3,330 filtered neutral loci obtained from genotyping-by-sequencing for the three species. The number of SNPs varied from 2,951 in K. ivorensis to 4,754 in K. senegalensis. Multiloci clustering, principal component analysis, Bayesian structure and network analyses showed a clear genetic separation among the three species. Structure analysis also showed internal structure within each species, highlighting genetic subgroups that could be sampled for selecting distinct genotypes for further breeding, although the genetic distances are moderate to low.ConclusionIn our study, SNP markers efficiently assessed the genomic diversity of African mahogany forest plantations in Brazil. Our genetic data clearly separated the three Khaya species. Moreover, pairwise estimates of genetic distances among individuals within each species showed considerable genetic divergence among individuals. By genotyping 115 pre-selected individuals with desirable growth traits, allowed us not only to recommend superior genotypes but also to identify genetically distinct individuals for use in breeding crosses.

Molecular Data Confirm Interspecific Limits of Four Alloxysta and One Phaenoglyphis Species of Parasitic Wasps within the Subfamily Charipinae (Cynipoidea: Figitidae).

The hymenopteran subfamily Charipinae (Cynipoidea: Figitidae) consist of a group of parasitic wasps that are exclusive hyperparasitoids of Hemipteran. The species boundaries in Charipinae have historically been unclear. While diagnostic morphological features have been established for the stepwise separation of species, it is recommended to confirm those limits using molecular data. Here, we focus on the genera Alloxysta Förster, 1869 and Phaenoglyphis Förster, 1869, both of which contain species that are hyperparasitoids of aphids. We sequenced three genes (mitochondrial COI and 16S rDNA, and nuclear ITS2 rDNA) from specimens that were identified as belonging to five species: Alloxysta brevis (Thomson, 1862), A. castanea (Hartig, 1841), A. ramulifera (Thomson, 1862), A. victrix (Westwood, 1833), and Phaenoglyphis villosa (Hartig, 1841). The phylogeny resulting from concatenating these genes supported the species status of the five morphologically identified taxa, with P. villosa nested within Alloxysta. Our study thus indicates that these molecular markers can successfully distinguish charipine species, and also indicates that the genera Alloxysta and Phaenoglyphis may be more closely related than previously hypothesized. We also present the first estimates of genetic distances for these species. Future studies that include more species, loci, and/or genomic data will complement our research and help determine species relationships within the Charipinae subfamily.

Differentiated adaptative genetic architecture and language-related demographical history in South China inferred from 619 genomes from 56 populations

BackgroundThe underrepresentation of human genomic resources from Southern Chinese populations limited their health equality in the precision medicine era and complete understanding of their genetic formation, admixture, and adaptive features. Besides, linguistical and genetic evidence supported the controversial hypothesis of their origin processes. One hotspot case was from the Chinese Guangxi Pinghua Han people (GPH), whose language was significantly similar to Southern Chinese dialects but whose uniparental gene pool was phylogenetically associated with the indigenous Tai-Kadai (TK) people. Here, we analyzed genome-wide SNP data in 619 people from four language families and 56 geographically different populations, in which 261 people from 21 geographically distinct populations were first reported here.ResultsWe identified significant population stratification among ethnolinguistically diverse Guangxi populations, suggesting their differentiated genetic origin and admixture processes. GPH shared more alleles related to Zhuang than Southern Han Chinese but received more northern ancestry relative to Zhuang. Admixture models and estimates of genetic distances showed that GPH had a close genetic relationship with geographically close TK compared to Northern Han Chinese, supporting their admixture origin hypothesis. Further admixture time and demographic history reconstruction supported GPH was formed via admixture between Northern Han Chinese and Southern TK people. We identified robust signatures associated with lipid metabolisms, such as fatty acid desaturases (FADS) and medically relevant loci associated with Mendelian disorder (GJB2) and complex diseases. We also explored the shared and unique selection signatures of ethnically different but linguistically related Guangxi lineages and found some shared signals related to immune and malaria resistance.ConclusionsOur genetic analysis illuminated the language-related fine-scale genetic structure and provided robust genetic evidence to support the admixture hypothesis that can explain the pattern of observed genetic diversity and formation of GPH. This work presented one comprehensive analysis focused on the population history and demographical adaptative process, which provided genetic evidence for personal health management and disease risk prediction models from Guangxi people. Further large-scale whole-genome sequencing projects would provide the entire landscape of southern Chinese genomic diversity and their contributions to human health and disease traits.

A new HaCV-EBHSV recombinant lagovirus circulating in European brown hares (Lepus europaeus) from Catalonia, Spain

In 2020/2021, several European brown hare syndrome virus (EBHSV) outbreaks were recorded in European hares (Lepus europaeus) from Catalonia, Spain. Recombination analysis combined with phylogenetic reconstruction and estimation of genetic distances of the complete coding sequences revealed that 5 strains were recombinants. The recombination breakpoint is located within the non-structural protein 2C-like RNA helicase (nucleotide position ~ 1889). For the genomic fragment upstream of the breakpoint, a non-pathogenic EBHSV-related strain (hare calicivirus, HaCV; GII.2) was the most closely related sequence; for the rest of the genome, the most similar strains were the European brown hare syndrome virus (EBHSV) strains recovered from the same 2020/2021 outbreaks, suggesting a recent origin. While the functional impact of the atypical recombination breakpoint remains undetermined, the novel recombinant strain was detected in different European brown hare populations from Catalonia, located 20–100 km apart, and seems to have caused a fatal disease both in juvenile and adult animals, confirming its viability and ability to spread and establish infection. This is the first report of a recombination event involving HaCV and EBHSV and, despite the recombination with a non-pathogenic strain, it appears to be associated with mortality in European brown hares, which warrants close monitoring.

Breeding design in wheat by combining the QTL information in a GWAS panel with a general genetic map and computer simulation

A large amount of genome-wide association study (GWAS) panels together with quantitative-trait locus (QTL) information associated with breeding-targeted traits have been described in wheat (Triticum aestivum L.). However, the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge. In this study, we first report a general genetic map which was constructed from 44 published linkage maps. It permits the estimation of genetic distances between any two genetic loci with physical map positions, thereby unifying the linkage relationships between QTL, genes, and genomic markers from multiple genetic populations. Second, we describe QTL mapping in a wheat GWAS panel of 688 accessions, identifying 77 QTL associated with 12 yield and grain-quality traits. Because these QTL have known physical map positions, they could be mapped onto the general map. Finally, we present a design approach to wheat breeding by using known QTL information and computer simulation. Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype, trait correlations in simulated progeny populations, and genetic gain of selected progenies. It is possible to simultaneously improve yield and grain quality by suitable parental selection, progeny population size, and progeny selection scheme. Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment, increasing predictability and efficiency in wheat breeding.

Genetic evidence of the unique identity of the West African Mangrove Oyster (Crassostrea tulipa) from the Gulf of Guinea

This research enabled the genetic identification of the West African mangrove oysters, Crassostrea tulipa, as well as establishing the evolutionary relationship between it and other Crassostrea species. Essentially, the study assisted in clearing up a long-standing confusion over this species’ synonymy with C. gasar. Also, the population structure of 60 C. tulipa individuals, from three different ecotypes, was analyzed using the mitochondrial cytochrome oxidase I (COI) genes as a marker. Results provided the first genetic sequences for C. tulipa and deposited in the GeneBank. Optimal and consensus bootstrap Neighbor-Joining trees distinctively differentiated C. tulipa from other Crassostrea species and consistently formed a different clade with C. gasar, with no bootstrap value from either NJ, MPT, or UPG trees supporting their similarity. C. tulipa sequences occurred as different haplotypes from other Crassostrea sp, with a mutation value as high as 288 and a haplotype diversity of 0.893 between C. tulipa and C. gasar sequences. High estimates of genetic distance (1.40–1.55) and patristic divergence were recorded between C. tulipa and C. gasar, in the same range as with seven other species. The study thus reveals the unique identity of C. tulipa as genetically distinct from C. gasar and other Crassostrea species. Based on the population structure analyses from the neutrality test, a low to high haplotype diversity h (0.000–0.963) and low nucleotide diversity π (0.00–0.378) were obtained. A negative mean Tajima’s D (−0.65247), and a positive Fu’s Fs (3.194), suggest rare variations or low-frequency polymorphisms. In addition to serving as the basis for phylogeny, the identification of C. tulipa and the recent data on its population structure also serve as the basis for conservation efforts and hatchery-based aquaculture.

Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes.

Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.

Differentiation of three sheep breeds which have a genetic relationship by body sizes

Sumatera Composite (SC) sheep and Barbados Black Belly cross (BC) sheep are two sheep that have half the genetics of Sumatera local (SL) sheep. Populations with partially the same genetic composition are sometimes difficult to distinguish. Based on female body size sheep, an analysis was carried out to distinguish the three breed sheep that have genetic relationship. The research was conducted using SC, BC and SL ewe measured in body weight and 8 body sizes. Analysis of variance and canonical discriminant analysis, Mahalanobis distance, plotting canonical and dendogram were performed by SAS software ver. 9.0. Body weight and all body sizes of SC and BC sheep were significantly different from SL sheep. Canonical discriminant analysis successfully could differentiate among the three sheep breeds that have genetic relationship. The results of genetic distance estimation showed that SC sheep had genetic closeness to BC sheep compared to SL sheep. The size of the skull length, body weight and chest girth were the breed differentiation variable in this study.

Genetic distance and phylogenetic relationships of some Echinostoma species (E. malayanum, E. revolutum, E. miyagawai) and Hypoderaeum conoideum (family Echinostomatidae) inferred from partial 28S rDNA sequence analysis

Echinostomiasis is a neglected disease caused by the intestinal flukes (family Echinostomatidae, suborder Echinostomata) and is common in communities in Asian countries, such as India, Indonesia, the Philippines, China, Malaysia, Singapore, Korea, Japan, Thailand, Laos, Cambodia and Vietnam. The genetic markers from the nuclear ribosomal transcription units are commonly used in genetic studies and phylogenetic analyses. A portion of the 28S rDNA sequence (domains D1–D3, of 1062–1067 bp for the final use) was obtained from the zoonotic Echinostoma malayanum (strain E/Amala-EMI3-TH), E. revolutum (strain Erevo-MSD15-TH), E. miyagawai (Emiya-RED11-TH), and Hypoderaeum conoideum (Hcono-RED42-TH) species; and used to perform an alignment for genetic distance estimation and phylogenetic analysis. The alignment was performed using 62 strains of 42 species from 19 genera of the family Echinostomatidae, including Echinoparyphium, Echinostoma, Artyfechinostomum, Patagifer, Neoacanthoparyphium, Hypoderaeum, Echinoparyphium, Drepanocephalus, Euparyphium, Chaunocephalus, Neopetasiger, Ribeiroia, Cathaemasia, Rhopalias, Isthmiophora, Petasiger, Moliniella, Pegosomum, and Schistosoma (family Schistosomatidae). The genetic distance estimation among 16 strains/10 species has shown a low intra-specific divergence level between strains within the same species, such as E. miyagawai (0–0.10%), E. revolutum (0.10–0.50%), and H. conoideum (0–0.10%), while between strains within the same genus it was higher (normally over 1.0%) and among strains/species between genera it was the highest (3.06–4.12%). The 28S rDNA sequence analysis and phylogenetic relationship well supported the Echinostoma/ Artyfechinostomum malayanum intergeneric taxonomy and the topology indicated clear, well-supported positions of member species in different genera in the family Echinostomatidae of the suborder Echinostomata. More sensu lato samples of the genera, are required for sequencing, particularly those of zoonotic species in the five genera: Artyfechinostomum, Echinostoma, Hypoderaeum, Echinoparyphium, and Isthmiophora. The resultant mitochondrial and nuclear data obtained from these species will be a good source to use to clearly assess the taxonomic and generic relationships.

Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances.

A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. ITS2 genetic distances were estimated comparatively by using both conventional DNA substitution models and RNA-specific models, which were performed in the PHASE package. Our results showed that the existence of the CBC substitution inflated the ITS2 genetic distances to different extents, and the deviation could be 180% higher if the relative ratio of substitution rate in ITS2 secondary structure stems was threefold higher than that in the loops. However, the CBC effect was minor if that ratio was below two, indicating that the DNA model is still applicable in recent lineages in which few CBCs occur. We thus provide a general empirical threshold to take account of CBC before ITS2 phylogenetic analyses.

Genetic diversity and population structure of four Nigerian indigenous cattle breeds.

A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (Ho) and expected (He) heterozygosity, polymorphism information content (PIC), test of Hardy-Weinberg equilibrium, and genetic diversity; pairwise Nei's genetic distance, Wright's F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean Ho and He were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, FST, were significantly different (p < 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N'Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.

Genetic Diversity among Single, Double, And Triple Cross Hybrids in Beit Alpha Cucumber (Cucumis sativus)

Genetic variation was investigated in fifteen single, eighteen three-way, and nine double hybrid crosses and their parents along with nine elite commercial cucumber hybrids. Six lines (NS5, NS9, NS17, NS29, NS31, and NS33) were used to develop these cross hybrids. Based on AFLP and SSR analysis, the studied cucumber genotypes have a narrow genetic base. The results also showed genetic differentiation compared to commercial varieties. Out of 1352 bands produced from 12 AFLP primer pairs, only 47 were polymorphic. Similarly, out of 26 SSR primers, only one primer was polymorphic. The highest heterozygosity index (0.6044), polymorphic information content value (0.5392), and marker Index (0.6044) were observed with M-CTT_E-AAG AFLP primer combination, while the highest effective multiplex ratio (2.8246) and resolving power (4.8421) were observed with M-CTC_E-AGC AFLP primer combination. Genetic distance estimation revealed clear distinctiveness of the studied genotypes with the control varieties. The cluster analysis by UPGMA showed two main clusters covering 84% of the studied genotypes grouped. This research shows that double and three-way hybrid crosses can be used in cucumber hybrid breeding.

DNA barcoding identification of Greek freshwater fishes.

Biodiversity is a key factor for the functioning and efficiency of an ecosystem. Greece, though covering a relatively small surface area, hosts a great deal of species diversity. This is especially true for freshwater fishes. In recent years, the traditional methods of species identification have been supplemented by the use of molecular markers. The present study therefore aims to extensively produce DNA barcodes for Greek freshwater fish species and investigate thoroughly if the presently accepted species classification is in agreement with molecular data. A 624-bases long fragment of the COI gene was sequenced, from 406 freshwater fish specimens belonging to 24 genera and originating from 18 lake and river sites. These sequences were used along with 596 sequences from the same genera, recovered from BOLD, for the construction of phylogenetic trees and the estimation of genetic distances between individuals. In total, 1002 sequences belonging to 72 species were analyzed. The method was found to be effective for 55 of 72 studied species. 17 closely related species with low interspecific genetic distances were observed, for which further study is proposed. It should also be noted that, in four cases, cryptic diversity was observed, where groups originally identified as one species exhibited genetic distance great enough to be separated into discrete species. Region specific haplotypes were also detected within populations of 14 species, giving the possibility to identify even the geographic origin of a species. Our findings are discussed in the light of the rich history of the Balkan peninsula and provide a significant steppingstone for the further study of Greek and European freshwater fish biodiversity.

Applying genomics to metapopulation management in North American insurance populations of southern sable antelope (Hippotragus niger niger) and addra gazelle (Nanger dama ruficollis)

Insurance populations can provide a short-term safeguard for at-risk species. The goal for all insurance populations should be to maintain a high welfare, genetically diverse, self-sustaining population that is available for eventual reintroduction of animals back into the wild when it is safe to do so. However, many insurance populations in zoos are not meeting sustainability goals, and there is a need for larger conservation centers and sanctuaries, a greater focus on threatened species, and metapopulation management between independently managed populations. Within North America, privately-owned ranches frequently maintain large populations of threatened ungulates that are presently managed independently from AZA-accredited zoos. Using a large set of single nucleotide polymorphisms, we generated empirical kinship and genetic distance estimates for AZA and private ranch populations of southern sable antelope ( Hippotragus niger niger ) and critically endangered addra gazelle ( Nanger dama ruficollis ). We used stochastic population models to project population mean kinship ( mk ) and founder genome equivalents (FGE) over time with and without genetic metapopulation management, using empirical kinships and genetic distances to guide transfers. Mean kinship-guided transfers were consistently beneficial for all study populations, for both species. Genetic distance-guided transfers, however, resulted in modest population mk increases for AZA populations, but predicted remarkable decreases in population mk for ranch populations. Although predicted benefits varied depending on management approach, our results show that a metapopulation management plan, whether mutually beneficial or altruistic, best supports species conservation by mitigating the loss of genetic diversity, minimizing the possibility of inbreeding, and yielding genetically diverse animals.

Estimation of genetic distances among various genotypes of blackgram (Vigna mungo (L.) Hepper) using D2 statistics

The genetic distance assessment of forty blackgram genotypes was conducted employing Mahalanobis’ D2 statistics considering ten quantitative characters. All the studied genotypes were grouped in ten discrete clusters, among which cluster I was indeed the largest with thirteen genotypes followed by cluster V with eight genotypes, cluster IV with seven genotypes and cluster II with five genotypes. Cluster IX was digenotypic, other clusters III, VI, VII, VIII and X were all solitary. Cluster IV and IX had the greatest inter-cluster gap followed by cluster VIII and IX, clusters VII and IX, clusters II and IX, clusters III and IX, clusters V and IV, clusters IX and Cluster X and between cluster VI and IX, implying that a successful breeding programme can be begun by selecting diverse lines to improve productivity and other yield-related traits. In the current investigation, cluster X, cluster VI, cluster IV and cluster VIII were considered divergent enough and found to be the best. Hence, genotypes from these clusters viz., TU 94-2 from cluster IX, PU 31 from cluster VI, IPU 94-1 from cluster IV and LBG 623 from cluster VIII can be used in the crossing programme for additional genetic enhancement. Cluster IX had the highest mean score for traits viz., the number of clusters per plant, the number of pods per plant, pod length, test weight and grain yield per plant. The number of pods per plant provided the most to genetic diversity succeeded by the number of clusters per plant, days to maturity, plant height, pod length and test weight. As a result, in a crossing programme, selecting and utilising genotypes based on these traits will be more rewarding. Furthermore, taking into account the genotype disposition in various clusters, one can perform different possible crosses to produce heterotic hybrids or transgressive segregants, based on the nature of gene action regulating the traits. Key words: Blackgram, Genetic distance, Genetic divergence, D2, Vigna mungo

Heterosis and Genetic Diversity of Yield and Its Some Components in F1 of Sunflower Inbred Lines

Fall season 2020, six inbred lines of sunflower were crossed by half-diallel crosses to obtain 15 single hybrids. The genotypes (parents and first-generation hybrids -F1) were planted in randomized comlete block design (RCBD) with three replications in a field/Babylon Governorate during the spring season 2021. The study aimed to estimate Heterosis of the first generation hybrids from the mean of the parents for the traits; stem diameter, head diameter, number of seeds per head, weight of 100 seeds, seed yield and oil yield per plant. Furthermore, estimation of genetic distance among genotypes using cluster analysis. The results of the analysis of variance showed that there were significant differences at the probability level (0.01) for all the studied traits of the parents and the first generation hybrids. The two hybrids (I×Q) and (Q×C) were distinguished a high significant positive heterosis for most of the traits measured. The cluster analysis showed that the two genotypes that include hybrids (Q×C) and (Q×F) had the highest Euclidean distance (175.92 and 183.66) respectively. This indicated to high degree of genetic diversity between the two hybrids and the rest of the studied hybrids, which it positively reflected on the performance of the hybrids for the studied traits. The results of Principal Component Analysis (PCA) and Dendrogram showed that (Q) genotype was far from the rest of the genotypes and isolated to a single group, whereas the remaining genotypes separated into groups to two separed branches, especially the two genotypes (C( and )Q). The reason may be due to the distinguish genetic difference of these interested genotypes which have the ablility to transfer from parents to the its progenies, which resulted from a presence of the clear genetic distance between them, while, other genotypes lacks the of this genetic variation case.

Population structure and genetic relatedness of Sri Lankan Jaffna Local sheep with major South Indian breeds

Jaffna Local is an endangered indigenous sheep population in the island country of Sri Lanka. The present study was aimed at assessing genetic diversity of Jaffna Local sheep and its relationship with major South Indian breeds. A total of 320 sheep were genotyped at 19 short tandem repeat marker loci and sequenced for mitochondrial DNA (mtDNA) control region to assess population structure, genetic admixture and phylogeography. The results revealed Jaffna Local sheep having relatively low diversity and high estimated inbreeding coefficient as compared to major South Indian breeds. The results of genetic distance estimations, AMOVA and Bayesian analysis clearly indicated relatively closer genetic relationship of Jaffna Local sheep with Southern Tamil Nadu sheep breeds (Vembur, Kilakarisal) and Mandya as compared to other South Indian breeds. Analysis of mtDNA control region revealed 16 haplotypes in Jaffna Local sheep, of which four were observed to be singletons and specific to this breed. The maternal lineages of all the Jaffna Local and South Indian sheep belonged to haplogroup A (HPG-A). Sequence mismatch analysis revealed uni-modal distribution in Jaffna Local sheep indicating haplotype expansion. Considering Jaffna Local sheep is the only defined breed of Sri Lanka, it is imperative to implement selective breeding program in the native tract to prevent genetic dilution and foster conservation of this important indigenous genetic resource of Sri Lanka.

Alignment-free methods for polyploid genomes: Quick and reliable genetic distance estimation.

Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic data sets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyse publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems or those with only poor-quality sequence data available.

Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene.

Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree‐based methods (NJ, ML, and bPTP) and distance‐based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p‐distances had similar results. Mean K2P distances and p‐distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.

Microsatellite markers in the study of polymorphism of domestic pig breeds (Sus scrofa domesticus)

Using 13 tetra- and 7 dinucleotide microsatellites, we studied the polymorphism of 6 breeds of pigs - Belarusian large white (BLW), Belarusian meat (BM), Belarusian black motley (BBM), Landrace (LR), Yorkshire (YR) and Duroc (DR), which are bred in Belarus. A high level of genetic polymorphism is shown for all breeds, with the exception of the DR breed. For 6 breeds, a low level of inbreeding is shown. Alleles peculiar only to these breeds were found in the gene pools of all the studied breeds. This fact confirms the importance of preserving local breeds for maintaining polymorphism in domestic pigs as a whole. Estimation of genetic distances reveals a significant contribution of the commercial European breeds of Landrace and Yorkshire, however, the evolutionary paths of all three native breeds differ.