Bayesian Clustering Analysis Research Articles

Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle (Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers.

Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.

Continuous affect responses to a large diverse set of unfamiliar music: Bayesian time-series and cluster analyses.

Continuous affect responses to a large diverse set of unfamiliar music: Bayesian time-series and cluster analyses.

Genetic Diversity of <i>Juniperus communis</i> L. in Eurasia and Alaska, Inferred from Nuclear Microsatellites Markers

The structure of genetic variation of the common juniper (Juniperus communis L.), a widespread wind-pollinated golarctic shrub of Cupressaceae was surveyed. We used 7 microsatellite markers including three new to genotype samples from 23 Eurasian populations and one from North America (Alaska). The geographical patterns are interpreted jointly with our previously available chloroplast DNA data. High genetic diversity was revealed with highest values in the same northern populations (Sweden, Estonia, Mezen, Polar Urals, Yamal, Kolyma, as well as in the Alps) as previously identified at cpDNA analysis. Nuclear markers exhibited a lower level interpopulation differentiation (FST = 9.8%) than chloroplast markers (FST = 76%). Bayesian cluster analysis showed that the optimal number of genetic groups (K) was two. All the 24 populations of J. communis were divided into the East group (north-east and Far East of Russia, Alaska and Himalayan) and the West group (Europe, Ural and Siberia). In the Alpine and Mountain Shoria populations, genotypes from different genetic groups are combined.

Lahaul-Zanskar-Sham Valley Corridor in Indian Trans Himalayan Region Facilitates Dispersal and Gene Flow in Himalayan Ibex.

Wildlife corridors that connect mosaic habitats in heterogeneous mountainous landscapes can be of high significance as they facilitate the genetic and demographic stability of free-ranging populations. Peripheral populations of widespread species are usually ignored in conservation planning. However, these populations retain locally common alleles and are genetic reservoir under the changing climatic conditions. Capra sibirica has widespread distribution, and its southern peripheral population is distributed in the Indian trans-Himalayan region (ITR). In the present study, we studied the spatial distribution and genetic make-up of Himalayan ibex from the ITR following the landscape genetics approach. We obtained 16 haplotypes at the mitochondrial d-loop region and found a stable demography in the past with a recent decline. With 10 nuclear microsatellites, we ascertained 111 unique individuals assigned into two clusters following Bayesian and non-Bayesian clustering analysis with several admixed individuals. We also recorded 25 first-generation migrants that reflected relatively high dispersal and gene-flow across the range. We identified a 19,835 sq.km suitable area with 13,311 sq.km in Ladakh and 6524 sq.km in Lahaul-Spiti. We identified a novel movement corridor for Himalayan ibex across the Lahaul-Zanskar-Sham valley (L-Z-SV) that displayed a fairly good conductance with low genetic divergence among the samples collected on the L-Z-SV corridor. We propose declaring a protected area in the Lahaul and Kargil districts to prioritize dedicated conservation efforts for the Himalayan ibex and other sympatric ungulates that impart a major role in the diet of large carnivore and balancing ecosystem services in the trans-Himalayan region.

Landscape genetics identifies barriers to Natterjack toad metapopulation dispersal

Habitat fragmentation and loss reduce population size and connectivity, which imperils populations. Functional connectivity is key for species persistence in human-modified landscapes. To inform species conservation management, we investigated spatial genetic structure, gene flow and inferred dispersal between twelve breeding sites of the Natterjack toad (Bufo calamita); regionally Red-Listed as Endangered in Ireland. Spatial genetic structure was determined using both Bayesian and non-Bayesian clustering analysis of 13 polymorphic microsatellite loci genotyping 247 individuals. We tested the influence of geographic distance, climate, habitat, geographical features, and anthropogenic pressure on pairwise genetic distances between breeding sites using Isolation-by-distance and Isolation-by-resistance based on least-cost path and circuit theory models of functional connectivity. There was clear spatial structuring with genetic distances increasing with geographic distance. Gene flow was best explained by Isolation-by-resistance models with coniferous forestry plantations, bog, marsh, moor and heath, scrub, anthropogenic presence (Human Influence Index) and rivers (riparian density) identified as habitats with high resistance to gene flow while metapopulation connectivity was enhanced by coastal habitats (beaches, sand dunes and salt marshes) and coastal grassland. Despite substantial declines in census numbers over the past 15 years and its regional status as Endangered, the Natterjack toad population in Ireland retains high genetic diversity. If declines continue, maintaining habitat connectivity to prevent genetic erosion by management of coastal grasslands, pond construction and assisted migration through translocation will be increasingly important.

Population genetics and phylogeography of North American Merlins (Falco columbarius) in thepost‐DDT era

In North America, the population genetic structure of many raptor species has been shaped by patterns of post‐glacial population expansion and anthropogenic forces, such as the widespread use of the organochlorine pesticide dichlorodiphenyltrichloroethane (DDT) during the mid‐20th century. While common themes of post‐glacial avian population expansion have emerged, little is known about the genetic impacts of DDT on raptor species that experienced a population bottleneck but were not the focus of conservation efforts. We investigated how the combination of post‐Pleistocene environmental change and the DDT‐era population bottleneck have influenced the contemporary population structure of MerlinsFalco columbariusin North America. We genotyped migrating Merlins across North America (n = 272) at 23 polymorphic microsatellite loci and generated sequence data for a 569‐base‐pair segment of the mitochondrial control region. We used hierarchical analysis of molecular variance, pairwiseFST/STcomparisons and Bayesian clustering analyses to assess genetic differentiation between individuals from eastern and western North America, distinct migratory flyways, and three recognized North American subspecies. Across all analyses, we found low or no population differentiation, suggesting that North American Merlins largely comprise one panmictic population showing evidence of a post‐glacial population expansion with little genetic differentiation detected between regions. Furthermore, we did not detect a contemporary signal of a genetic bottleneck that could have resulted from the DDT‐era population decline with the markers used in this study. Consistent with other avian species, we found a correlation between allele length variation at a microsatellite isolated from the 3′ untranslated region of theADCYAP1gene and migratory versus sedentary characteristics in Merlin subspecies. We detected two common mitochondrial control region haplotypes in the geographical regions sampled, a unique pattern among other widespread North American raptor species. This study furthers our understanding of the genetic and demographic history of Merlins in North America and can inform future genomic studies of this species.

Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds.

As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ Ho ≤ .34; .30 ≤ He ≤ .35; 1.7 × 10-3 ≤ π ≤ 3.1 × 10-3) and the levels of inbreeding were negligible (.005 ≤ FIS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75Mb in Serra da Estrela to 61,29Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.

Inconsistency between morphological diversity and genetic structuring: proposal for one species of Undaria in Japan

Abstract Genetic structure analyses have yielded some examples of inconsistencies between genetic and morphological information. Here, eleven nuclear microsatellite markers and mitochondrial haplotypes were used to examine the genetic structure and gene flow among Japanese Undaria pinnatifida populations and the congeneric species U. undarioides and U. peterseniana. Undaria pinnatifida was subdivided into four “Groups” of populations based on Bayesian clustering analysis, Neighbor-net analysis and Principal coordinate analysis (PCoA). Undaria undarioides samples formed a unique Group. In contrast, U. peterseniana samples either grouped with a mixture of U. pinnatifida and U. undarioides clusters or were included within one of the U. pinnatifida clusters. More significantly, Groups of populations shared alleles with geographically adjacent Groups even between different morphospecies. No clear differences between the inter-and intra-specific genetic divergence were observed in either nuclear or mitochondrial markers. As a result, U. undarioides and U. peterseniana were synonymized with U. pinnatifida. Isolation-by-distance suggested the significance of geographical isolation for maintaining the observed divergence.

Progeny selections of coffee cultivar 'Mundo Novo' with potential for the specialty coffee market

Coffee is one of the most popular beverages in the world with a global market worth over <inline-formula><tex-math id="Z-20230106103009">\begin{document}${\$\text{USD}} $\end{document}</tex-math><alternatives><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="BPR-2023-0001_Z-20230106103009.jpg"/><graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="BPR-2023-0001_Z-20230106103009.png"/></alternatives></inline-formula> 100 billion. In Brazil, the Arabica coffee (<italic>Coffea arabica</italic>) cultivar 'Mundo Novo' is one of the most planted cultivars due to its high yield, growth vigor and stability. However, this traditional cultivar is generally not considered a good production source for specialty coffee. Exploring intra-cultivar variation and selecting 'Mundo Novo' progenies with superior sensory quality may provide a viable option for coffee producers targeting the rapidly expanding specialty coffee market. The present study analyzed cup quality attributes, agronomic characteristics and genetic identities of 14 genotypes selected from the putative progenies of 'Mundo Novo' and assessed their potential as specialty coffee in Brazil. Beverage quality was assessed using chemical and sensory analysis according to the methodology proposed by the Specialty Coffee Association (SCA) in six selected genotypes. High sensory quality, with sensory scores above 80 points was observed which qualified them in the very good and excellent quality categories. Genetic identities of the 14 selections were verified using 96 SNP markers, based on 57 reference cultivars from the coffee collection of EPAMIG (<italic>Empresa de Pesquisa Agropecuária de Minas Gerais</italic>), Brazil. Multivariant and Bayesian clustering analysis generated consistent results and confirmed that all the 14 selections were progenies of 'Mundo Novo'. Among them, the top three genotypes (SGAB 1, SGAB 7 and SGAB 8) were selected as promising genotypes, either for future genetic improvement or for direct use in the production of specialty coffee

Склонность к риску и устойчивость к стрессу как факторы принадлежности к профессиональным и досуговым группам и их ассоциация с шестью генами-кандидатами

The search for sensations is a complex set of behavioral responses that are significant features of a person's personality. The purpose of this study was to identify differences in the occurrence of allelic variants of the OXTR, HTR2A, HTR2C, CRHR1, BDNF, AR genes in two groups of men practicing risky behavior (racers and paratroopers) compared with the control sample; identification of differences in the frequencies of polymorphic variants of candidate genes in riders and paratroopers. Materials and methods. The materials for this article were collected (buccal epithelium or saliva) in the period from 2017 to 2021 in the Moscow, Smolensk, Nizhny Novgorod regions and the city of Togliatti during the stages of the Russian Cup in auto racing (racers – 55 people), in the Republic of Kabardino- Balkaria at the mountaineering base "Bezengi" (paratroopers – 84 people), as well as the village of Bogovarovo, Kostroma Region (control sample: men and women – 214 people). Genotyping of the samples was carried out using PCR-RFLP and fragment analysis. With the help of population genetic analysis, the studied samples were characterized by a number of parameters (frequency of genotypes and alleles, expected heterozygosity). The similarity/difference of the samples in the genetic structure of the six genetic loci used was assessed using the G-test, Ney genetic distances and principal coordinates method, as well as analysis of molecular variability (FST) and Bayesian cluster analysis. Results. Some difference in the genetic structure of the sample of paratroopers from the control for all six loci, and racers from the control sample for the part of the loci used was shown. Discussion. The results obtained revealed the following: 1. persons practicing risky behavior are generally characterized by a certain genetic profile, in particular, according to the polymorphisms tested in our study; 2. individuals who demonstrate a willingness to take risks as part of their professional activities differ from those who prefer risky hobbies in terms of the combination of polymorphisms tested in our study, and are genetically predisposed to greater mental resistance to stress, conscientiousness and diligence, conscientiousness and extraversion.

Assessing genetic diversity and population structure for prioritizing conservation of the critically endangered Great Indian Bustard (Aredotis nigriceps)

The critically endangered Great Indian Bustard Ardeotis nigriceps (GIB) is on the verge of imminent extinction, and exists as fragmented populations with 100–150 birds in India and a few in neighbouring Pakistan. Rajasthan holds the largest population of ∼128 birds, Gujarat has ∼5, and Maharashtra-Karnataka-Andhra Pradesh having ∼10 birds. Their range and abundance have reduced by 90% within last 50 years, primarily due to hunting, habitat loss to agriculture and industry, and power-line collisions. Conservation agencies are implementing habitat protection/restoration and conservation breeding as insurance against extinction and for future reintroductions/supplementation. To guide these ongoing in-situ and ex-situ conservation measures, we examined patterns of genetic diversity, population structure, bottlenecks and dispersal using microsatellite and mitochondrial markers. Analyses of 73 individual GIB revealed low mt-DNA (h=0.554, π = 0.001) and microsatellite diversity (Ho=0.32). Bayesian clustering analysis identified three genetic populations. Migration between these populations was low and asymmetric, highest being from Rajasthan into Maharashtra (9%) and Madhya Pradesh (4%), perhaps due to extreme habitat fragmentation and small numbers. Rajasthan population encompassed the maximum genetic diversity, that along with its large size and availability of breeders, made it ideal for sourcing founders for conservation breeding. However, the presence of private alleles in other populations implies that additional sourcing of birds from Andhra Pradesh and Gujarat may be required to capture the extant gene pool of GIB in captive founder population.

DArTSeq SNP-based genetic diversity and population structure studies among taro [(Colocasia esculenta (L.) Schott] accessions sourced from Nigeria and Vanuatu.

Taro is a valuable staple food crop among resource-poor rural people in countries such as Nigeria and Ghana, among others. Characterization of genetic diversity is a prerequisite for proper management of breeding programs and conservation of genetic resources. Two hundred seventy one taro accessions obtained from Nigeria and Vanuatu were genotyped using DArTseq-based SNP markers with the objectives of investigating the genetic diversity and population structure. In the analysis, 10,391 SNP markers were filtered from the sequence and used. The analysis revealed higher transition than transversion types of SNPs in the ratio of 1.43:1. The polymorphism ranged from 0.26 to 0.29 for the markers, indicating moderate genetic diversity. A model-based Bayesian clustering analysis of taro accessions yielded five subgroups and revealed the admixture situation in 19.19% of all accessions in the study. Vanuatu taro accessions exhibited more genetic diversity than Nigerian taro accessions. The population diversity estimate (PhiPt) was relatively higher (0.52) for accessions originating from Vanuatu than for Nigerian accessions. Analysis of molecular variance (AMOVA) revealed that most variation existed among individuals within a population at 52%. Nei's genetic distance showed that relatedness is based on geographical proximity. Collection of taro genetic resources should give more emphasis to within regions to utilize diversity in taro breeding program. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in taro. The genotypic markers provided in this study are useful for association mapping studies.

An isolated population reveals greater genetic structuring of the Australian dingo

The Australian dingo is a recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed 34 microsatellite markers using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual level. The broader southern Australia sample (n = 1138) comprised mostly hybrid animals, with 30% considered pure dingoes. All western Victorian individuals (n = 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and low genetic diversity on all measures tested. Based upon our characterisation of this unusual mainland population, we advise against assuming homogeneity of dingoes across the continent.

Unveiling a hotspot of genetic diversity in southern Italy for the endangered Hermann’s tortoise Testudo hermanni

BackgroundHotspots of intraspecific genetic diversity represent invaluable resources for species to cope with environmental changes, and their identification is increasingly recognized as a major goal of conservation ecology research. However, even for iconic and endangered species, conservation strategies are often planned without thorough information on the geographic patterns of genetic variation. Here, we investigated the spatial patterns of genetic variation of the endangered Hermann’s tortoise Testudo hermanni in the Italian Peninsula by genotyping 174 individuals at 7 microsatellite loci, with the aim to contribute to planning effective conservation strategies.ResultsOrdination-based and Bayesian clustering analyses consistently identified three main genetic clusters, one spread in the central and northern part of the peninsula, and two restricted to southern Italy and Sicily, respectively. The highest levels of genetic diversity were found in populations of the southern cluster and, in particular, at the northern edges of its distribution (He > 0.6, Ar > 2.8 ), that correspond to areas of putative secondary contact and admixture between distinct lineages. Our results clearly identify a hotspot of genetic diversity for the Hermann’s tortoise in southern Italy.ConclusionWe inferred the evolutionary history and the spatial patterns of genetic variation of the Hermann’s tortoise in the Italian Peninsula. We identified three main genetic clusters along the peninsula and a hotspot of intraspecific diversity in southern Italy. Our results underline the urgent need for conservation actions to warrant the long-term persistence of viable tortoise populations in this area. Furthrmore, these data add further evidence to the role of southern Italy as a biodiversity hotspot for temperate fauna, claiming for higher consideration of this area in large scale conservation programs.

Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau

BackgroundMountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth. Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region.ResultsCombining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species.ConclusionOur study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.

CHARACTERIZATION OF MOLECULAR GENETIC MARKERS IN SPHENISCUS BANDED PENGUINS FOR THE IDENTIFICATION OF A STRANDED JUVENILE INDIVIDUAL IN CENTRAL AMERICA

Abstract. – In this study, the mitochondrial Cytochrome C Oxidase 1 gene, three nuclear microsatellite markers, and the MHC class II DRβ1 exon 2 were assessed for species-specific differences that would allow diagnostic identification of Spheniscus mendiculus, S. humboldti, and S. magellanicus specimens. Analyses of reference samples for these species revealed that genetic variation at these markers showed species-specific haplotypes and alleles that can provide positive evidence for species identification. Bayesian cluster analyses demonstrated high probability of assignment (&gt;99%) for individual samples to their corresponding species. The set of nuclear and mitochondrial markers studied proved useful for the identification of a juvenile penguin stranded on the Pacific Ocean shores of El Salvador as a Magellanic penguin. The negative consequences of accidental captures of Magellanic penguins by fishermen and the relocation of wildlife through human intervention are discussed.

A naive Bayesian method to chase mantle plumes in global tomography models

SUMMARY This study provides a quantitative approach to search for mantle plumes in global seismic tomography models without any preconceived notions about the associated mantle velocity anomalies, other than the assumption that the plumes are not significantly deflected horizontally by more than 6°, anywhere in the mantle. We design identification tests with a reasonable detection threshold while keeping false alarms at a level lower than 5 per cent. This is based on a naive Bayesian clustering analysis, which is possible thanks to the varimax principal component analysis that provides components of the tomography models that are much more independent than the original number of depth slices in the models. We find that using such independent components greatly reduces detection errors compared to using an arbitrary number of depth slices due to correlations between the different slices. We detect a wide range of behaviour of the seismic velocity profiles underneath the hotspots investigated in this study. Moreover, we retrieve locations away from hotspots that have similar seismic velocity profile signatures to those underneath some hotspots. Hence, it is not possible to obtain a unique definition of seismic velocity anomalies that are associated with hotspots and thus care needs to be taken when searching for mantle plumes beneath hotspots using prior assumptions about the velocity anomalies that might be associated with them. On the other hand, we establish a probability distribution of the seismic velocity profiles that is specific to a sublist of hotspots. Overall, the mantle plume zones identified in our analysis do not appear to surround the Africa and Pacific large low shear velocity provinces (LLSVPs), but are rather within them. This rules out the idea that LLSVPs correspond to compact, dense piles with mantle plumes rising from their edges. Instead, our analysis suggests two possible options that either the LLSVPs: (1) correspond to bundles of thermochemical mantle plumes or (2) are made up of compact piles topped by a bundle of plumes.

Genetic diversity and population structure of the antimalarial plant Cryptolepis sanguinolenta in Ghana

Cryptolepis sanguinolenta is an important medicinal plant used in the treatment of malaria in Ghana. Overharvesting, destruction of entire plant populations and poor seed viability have resulted in a substantial decrease in wild populations thereby threatening its long-term potential and survivability. In this study, fifteen polymorphic microsatellite loci were used to evaluate the genetic diversity and population structure of 179 C. sanguinolenta individuals among eight subpopulations in Ghana. The subpopulations were separated by a distance of 8.3 – 233.3 km. Our results indicated relatively high levels of genetic diversity (Ho= 0.41; He=0.61) and high gene flow (Nm=7.06), an indication of greater stability and adaptability within the ecosystem, limited genetic differentiation (mean FST=0.05; highest FST=0.1), which suggested insignificant differentiation among the subpopulations. The high levels of gene flow resulting from the wind-dispersed seeds might have contributed to the limited genetic differentiation among the subpopulations. The Bayesian cluster analysis revealed the presence of a population structure (K=2). A lack of isolation by distance (r=0.012; P=0.34) indicated an increase in the genetic similarity among the subpopulations as the geographic distance between them decreased. This study described the genetic diversity and population structure in the current C. sanguinolenta accessions and laid a foundation for future breeding efforts.

Is Lutjanus argentimaculatus genetically connected along the Arabian Sea and Bay of Bengal? A study using microsatellite markers

The mangrove red snapper, Lutjanus argentimaculatus, is a marine fish of key economic and cultural importance in the Indo-Pacific region. It is now considered much more of an important aquaculture species than capture fisheries. The present study aimed to reveal the genetic structure of this candidate species from the Arabian Sea and Bay of Bengal using microsatellite markers. Twelve microsatellite markers used for genetic stock characterization and 384 samples collected from six different locations were used for the study. Genetic characterization using microsatellite markers suggested a single unit stock of red snapper in the sampling region with sufficient gene flow between populations to restrict the genetic structuring. Genetic differentiation co-efficient analysis suggested lack of structuring between populations. However, Bayesian cluster analysis performed in STRUCTURE revealed some evidence of sub-structuring between the Arabian Sea and Bay of Bengal populations. Hierarchical AMOVA analysis, Principal Coordinate Analysis (PCoA) and isolation by distance analysis offered some support to the above findings. The inability of microsatellites to detect population differentiation in this instance suggests the need for more powerful markers, like SNPs, to reveal the sub-structuring before appropriate management practices can be developed for the mangrove red snapper in Indian waters.

Host Plant Variation and Lack of Genetic Differentiation in Populations of Dione (Agraulis) dodona Lamas & Farfán (Lepidoptera: Nymphalidae).

Simple SummaryIn this study, we analyzed the population genetics of Dione (A.) dodona Lamas and Farfán (Nymphalidae), a recently described butterfly from xerophytic environments of the western slopes of the Central Andes, associated with Malesherbia tenuifolia (Passifloraceae). Searches for additional host-plant species were carried out throughout its known distribution. In total, seven species of Malesherbia have been reported as host plants for D. (A.) dodona, extending its distribution as far north as 50 km. We obtained samples of the last larval instar in six localities on different host-plant species that have disjointed distributions. We inferred the genetic diversity and structure between populations by using microsatellites and mitochondrial COI markers. The results showed a weak genetic differentiation between the evaluated populations, suggesting a continuum of gene flow through high dispersal, along with the disjoint occurrence of the host plants.Dione (Agraulis) dodona (Nymphalidae: Heliconiinae) is a butterfly restricted to the western slopes of the Andes of Peru and Chile and is associated with Malesherbia tenuifolia in xerophytic environments. In this study, we found six additional species of host plants for D. (A.) dodona belonging to the genus Malesherbia (Passifloraceae). We used mitochondrial DNA sequences (COI) and microsatellites to screen genetic variation and investigate population structure in six geographic disjointed populations of D. (A.) dodona associated with distinct Malesherbia species. The PCoA analysis based on allele frequencies evidenced a lack of differentiation among populations and a low FST. The Bayesian cluster analyses revealed the existence of three genetically distinct groups, but almost all individuals present an admixture ancestry. An absence of isolation by distance pattern was observed. Possible scenarios are discussed: a bottleneck or recent colonization from interconnected populations from the south, and ongoing gene flow among local populations by high dispersal through a landscape formed of isolated populations of Malesherbia.