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Concept: Genetic diversity

161

Systematic influenza virus surveillance has been carried out in India since 2004 and has revealed the cocirculation of type B lineages. The genetic diversity of influenza B viruses was observed when full-genome analysis was performed. In 2010, the cocirculation of multiple genotypes was observed.

Concepts: DNA, Gene, Genetics, Evolution, Virus, Influenza, Genetic diversity, Influenzavirus B

156

The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives.

Concepts: Gene, Biodiversity, Conservation biology, Allele, Evolution, Biology, Genetic diversity, Lathyrus sativus

27

Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using Start Codon Targetted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21 % polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 to 7.50. The percentage of polymorphic loci (Pp) ranging from 25 % to 56.82 %, Nei’s gene diversity (h) from 0.08 to 0.15 with mean Nei’s gene diversity of 0.28, and Shannon’s information index (I) values ranging between from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37 % of variation within the populations, whereas 56.63 % variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance.

Concepts: DNA, Gene, Genetics, Evolution, Biology, Population genetics, Genetic diversity, Dendrobium

26

Abstract Genetic variation and population structure of northern snakehead (Channa argus) from eight locations in China were investigated using mitochondrial DNA control region and adjacent regions sequences. Sequence analysis showed that there were 105 haplotypes in 260 individuals, 48 unique haplotypes and 57 shared haplotypes, but no common haplotype shared by all populations. As a whole, the haplotype diversity was high (h = 0.989), while the nucleotide diversity was low (π = 0.00482). AMOVA analysis detected significant genetic differentiation among all eight populations (FST = 0.328, p < 0.01) and 66.17% of the total variance was resulted from intra-population differentiation. UPGMA analysis indicated that the eight populations could be divided into four major clusters, which was consistent with that the eight sampled locations were belonged to four isolated river systems. The neutrality and mismatch distribution tests suggested that the eight populations of C. argus in the sampling locations underwent recent population expansion. Among the eight populations, the Erhai Lake population may represent a unique genetic resource and therefore needs to be conserved.

Concepts: DNA, Genetics, Biology, Mitochondrion, Population genetics, Genetic diversity, Channa, Channidae

26

In this study the genetic diversity of local freshwater leeches (Hirudinaria spp.) was inferred using mtDNA COI gene analysis and compared with the gross external variations of 26 freshwater leech specimens obtained from the wild and leech farms. Based on a neighbor-joining tree generated from 516 COI base sequences, four distinct clades of Hirudinaria were seen with interspecific genetic divergence in the range of 7.6-14.5%. The external morphological variations based on the presence of stripes, location of gonopores, and anus separated the samples into four morphologically distinct groups matching the four clades obtained from the molecular data. Two black stripes at the ventral region were observed only in specimens found clustered with clades that contained the GenBank-reported H. manillensis, whereas the brown or dark green coloration without stripes on the ventral region was seen in samples that clustered with H. javanica and H. bpling clades.

Concepts: DNA, Gene, Genetics, Color, Population genetics, Green, Genetic diversity, Leech

25

The loss of genetic diversity, due to exposure to chemical contamination (genetic erosion), is a major threat to population viability. Genetic erosion is the loss of genetic variation: the loss of alleles determining the value of a specific trait or set of traits. Almost a third of the known amphibian species is considered to be endangered and a decrease of genetic variability can push them to the verge of extinction. This review indicates that loss of genetic variation due to chemical contamination has effects on: 1) fitness, 2) environmental plasticity, 3) co-tolerance mechanisms, 4) trade-off mechanisms, and 5) tolerance to pathogens in amphibian populations.

Concepts: Gene, Biodiversity, Conservation biology, Evolution, Species, Population genetics, Amphibian, Genetic diversity

23

Inter simple sequence repeat (ISSR) and simple sequence repeat (SSR) markers were used to assess the genetic diversity of 36 pineapple accessions that were introduced from 10 countries/regions. Thirteen ISSR primers amplified 96 bands, of which 91 (93.65%) were polymorphic, whereas 20 SSR primers amplified 73 bands, of which 70 (96.50%) were polymorphic. Nei’s gene diversity (h = 0.28), Shannon’s information index (I = 0.43), and polymorphism information content (PIC = 0.29) generated using the SSR primers were higher than that with ISSR primers (h =  0.23, I = 0.37, PIC = 0.24), thereby suggesting that the SSR system is more efficient than the ISSR system in assessing genetic diversity in various pineapple accessions. Mean genetic similarities were 0.74, 0.61, and 0.69, as determined using ISSR, SSR, and combined ISSR/SSR, respectively. These results suggest that the genetic diversity among pineapple accessions is very high. We clustered the 36 pineapple accessions into three or five groups on the basis of the phylogenetic trees constructed based on the results of ISSR, SSR, and combined ISSR/SSR analyses using the unweighted pair-group with arithmetic averaging (UPGMA) method. The results of principal components analysis (PCA) also supported the UPGMA clustering. These results will be useful not only for the scientific conservation and management of pineapple germplasm but also for the improvement of the current pineapple breeding strategies.

Concepts: Genetics, Evolution, Arithmetic mean, Computational phylogenetics, Genetic diversity, Ananas, Bromeliaceae, Pineapple

18

The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5-10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.

Concepts: Biology, Climate, Climate change, Population genetics, Change, Global warming, Genetic diversity, Species distribution

17

We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8.4%. Using a joint model including both host and viral effects, we estimate a total of 30% heritability, indicating that most of the host effects are reflected in viral sequence variation.

Concepts: HIV, Gene, Genetics, Evolution, Human genome, Mathematics, Genome, Genetic diversity

13

Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a ‘hump’ in diversity across the range studied (-9.4 to -43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.

Concepts: Biodiversity, Evolution, Biology, Earth, Biome, Genetic diversity, Equator, Biogeography