A microsatellite study in the Łęgucki Młyn/Popielno hybrid zone reveals no genetic differentiation between two chromosome races of the common shrew (Sorex araneus)

This study investigated a chromosome hybrid zone between two chromosomal races of the common shrew (Sorex araneus). Gene flow and genetic structure of the hybrid zone, located in the northeast of Poland, were studied using seven polymorphic autosomal microsatellite loci (L9, L14, L33, L45, L67, L68, L97) and a Y-linked microsatellite locus (L8Y). Seventy-five animals (46 of the Łęgucki Młyn race and 29 of the Popielno race) from nine different localities were examined and the data were analyzed using hierarchical AMOVA and F-statistic. The studied microsatellite loci and races (divided into nine geographical populations) were characterized by observed heterozygosity (HO), expected heterozygosities within (HS), and between (HT) populations, inbreeding coefficient (FIS), fixation index (FST), and average allelic richness (A). We found that genetic structuring within and between the two chromosome races were weak and non-significant. This finding and unconstrained gene flow between the races indicates a high level of migration within the Łęgucki Młyn/Popielno hybrid zone, suggesting that evolutionarily important genetic structuring does not occur in interracial zones where races which are not genetically distinct come into contact

Reintroduction of the European Capercaillie from the Capercaillie Breeding Centre in Wisła Forest District: Genetic Assessments of Captive and Reintroduced Populations.

The Western capercaillie (Tetrao urogallus) is a specific bird species, which, despite its very broad distribution and large global population size, is highly endangered in many Western and Central European countries. According to the species situation, in many countries (including Poland), breeding and reintroduction programmes have been started. One of the most complex and large-scale reintroduction programmes was started in Bory Dolnośląskie Forest, and the Capercaillie Breeding Centre in Wisła Forest District was used as one of the sources of individuals for reintroduction. As genetic tools provide essential knowledge about species biodiversity, which is crucially important during the breeding process and reintroduction, both captive and reintroduced grouse populations were genetically analysed. We were particularly interested in genetic diversity of the individuals in both populations and the genetic relationship between them, as well as between them and other capercaillie representatives from their current range. To fulfil these goals we determined nine microsatellite loci along with a fragment of the mitochondrial control region. Genetic diversity parameters were moderate to high compared to populations from other Central and Western European countries. Both populations were clustered into three distinct genetic clades based on microsatellites. Phylogenetic analysis placed all mitochondrial haplotypes we revealed in the Eurasian clade. The present results will play an important role as they will help to preserve and maximize genetic diversity in captive populations, and will provide a basis for future monitoring of the reintroduction process

Phylogeny of Amazona barbadensis and the Yellow-headed Amazon complex (Aves: Psittacidae): a new look at South American parrot evolution.

The Yellow-shouldered Amazon (Amazona barbadensis) is the sole parrot of the genus Amazona that inhabits only dry forests. Its population has been dropping; therefore it has been the topic of many studies and conservation efforts. However, the phylogenetic relationship of this species to potential relatives classified within the Yellow-Headed Amazon (YHA) complex are still not clear. Therefore, we used more extensive data sets, including the newly sequenced mitochondrial genome of A. barbadensis, to conduct phylogenetic analyses. Various combinations of genes and many phylogenetic approaches showed that A. barbadensis clustered significantly with A. ochrocephala ochrocephala from Colombia and Venezuela, which created the Northern South American (NSA) lineage, clearly separated from two other lineages within the YHA complex, the Central (CA) and South American (SA). Tree topology tests and exclusion of rapidly evolving sites provided support for a NSA+SA grouping. We propose an evolutionary scenario for the YHA complex and its colonization of the American mainland. The NSA lineage likely represents the most ancestral lineage, which derived from Lesser Antillean Amazons and colonized the northern coast of Venezuela about a million years ago. Then, Central America was colonized through the Isthmus of Panama, which led to the emergence of the CA lineage. The southward expansion to South America and the origin of the SA lineage happened almost simultaneously. However, more intensive or prolonged gene flow or migrations have led to much weaker geographic differentiation of genetic markers in the SA than in the CA lineage

Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach

Abstract The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best

Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis.

The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated

Frequency of the mtDNA haplotypes among CBC-WFD founders’ population and BDF reintroduced population.

<p>Frequency of the mtDNA haplotypes among CBC-WFD founders’ population and BDF reintroduced population.</p

Divergence time in million years estimated by two methods for analysed data sets.

2<p>based on Ribas et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone.0097228-Ribas1" target="_blank">[14]</a> and modified data set;</p>3<p>based on Rusello and Amato <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone.0097228-Russello1" target="_blank">[7]</a> and modified data set;</p>4<p>similar to the set³ but including also cytochrome <i>b</i>.</p

Localization of the Bory Dolnośląskie Forest, Capercaillie Breeding Centre Wisła Forestry District (CBC-WFD) and base population localities for founder individuals (with its number) in CBC-WFD– 1. Czantoria Mountain (1 individual), 2. Ujsoły (2 ind.), 3.Tatry Mountains (1 ind.), 4. Turbacz Mountain (6 ind.), 5. Lielcycy Forestry (7 ind.)

<p>Localization of the Bory Dolnośląskie Forest, Capercaillie Breeding Centre Wisła Forestry District (CBC-WFD) and base population localities for founder individuals (with its number) in CBC-WFD– 1. Czantoria Mountain (1 individual), 2. Ujsoły (2 ind.), 3.Tatry Mountains (1 ind.), 4. Turbacz Mountain (6 ind.), 5. Lielcycy Forestry (7 ind.)</p

Relationships between three main Yellow-headed <i>Amazona</i> lineages and their support values obtained for different methods and analysed data sets.

1<p>based on Ribas et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone.0097228-Ribas1" target="_blank">[14]</a> data set;</p>2<p>based on Ribas et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone.0097228-Ribas1" target="_blank">[14]</a> and modified data set;</p>3<p>based on Rusello and Amato <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone.0097228-Russello1" target="_blank">[7]</a> and modified data set;</p>4<p>similar to the set³ but including also cytochrome <i>b</i>;</p><p>*the clade contains also <i>A. arausiaca</i> and <i>A. versicolor</i>; LR-ELW - Local Rearrangements–Expected Likelihood Weights method; boot – bootstrap method; aLRT - the approximate likelihood ratio test based on a Shimodaira-Hasegawa-like procedure.</p><p>C –Central American lineage, S – South American lineage, NS – Northern South American lineage including <i>A. barbadensis</i> and its relative <i>A. ochrocephala ochrocephala</i>.</p

The Bayesian tree for the YHA complex and Lesser Antillean Amazons, LA (A) as well as all taxa (B) based on 12s+16s+cox³ data set.

<p>Asterisks at the end of some names indicate samples that were also used in further analysis based on the cytochrome oxidase data set (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone-0097228-g005" target="_blank">Figure 5</a>). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone-0097228-g001" target="_blank">Figure 1</a> for other explanations and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097228#pone.0097228.s004" target="_blank">Table S2</a> for more details.</p