Knowledge Of Genetic Diversity Research Articles

Genetic diversity is considered important but interpreted narrowly in country reports to the Convention on Biological Diversity: Current actions and indicators are insufficient

International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on progress. However, the CBD and similar policy agreements have often neglected genetic diversity. This is a critical gap because genetic diversity underlies adaptation to environmental change and ecosystem resilience. Here we aim to inform future policy, monitoring, and reporting efforts focused on limiting biodiversity loss by conducting the largest yet evaluation of how Parties to the CBD report on genetic diversity. A large, globally representative sample of 114 CBD National Reports was examined to assess reported actions, progress, values and indicators related to genetic diversity. Although the importance of genetic diversity is recognized by most Parties to the CBD, genetic diversity targets mainly addressed variation within crops and livestock (a small fraction of all species). Reported actions to conserve genetic diversity primarily concerned ex situ facilities and legislation, rather than monitoring and in situ intervention. The most commonly reported status indicators are not well correlated to maintaining genetic diversity. Lastly, few reports mentioned genetic monitoring using DNA data, indigenous use and knowledge of genetic diversity, or development of strategies to conserve genetic diversity. We make several recommendations for the post-2020 CBD Biodiversity Framework, and similar efforts such as IPBES, to improve awareness, assessment, and monitoring of genetic diversity, and facilitate consistent and complete reporting in the future.

Analysis of a Novel Bacteriophage vB_AchrS_AchV4 Highlights the Diversity of Achromobacter Viruses.

Achromobacter spp. are ubiquitous in nature and are increasingly being recognized as emerging nosocomial pathogens. Nevertheless, to date, only 30 complete genome sequences of Achromobacter phages are available in GenBank, and nearly all of those phages were isolated on Achromobacter xylosoxidans. Here, we report the isolation and characterization of bacteriophage vB_AchrS_AchV4. To the best of our knowledge, vB_AchrS_AchV4 is the first virus isolated from Achromobacter spanius. Both vB_AchrS_AchV4 and its host, Achromobacter spanius RL_4, were isolated in Lithuania. VB_AchrS_AchV4 is a siphovirus, since it has an isometric head (64 ± 3.2 nm in diameter) and a non-contractile flexible tail (232 ± 5.4). The genome of vB_AchrS_AchV4 is a linear dsDNA molecule of 59,489 bp with a G+C content of 62.8%. It contains no tRNA genes, yet it includes 82 protein-coding genes, of which 27 have no homologues in phages. Using bioinformatics approaches, 36 vB_AchrS_AchV4 genes were given a putative function. A further four were annotated based on the results of LC–MS/MS. Comparative analyses revealed that vB_AchrS_AchV4 is a singleton siphovirus with no close relatives among known tailed phages. In summary, this work not only describes a novel and unique phage, but also advances our knowledge of genetic diversity and evolution of Achromobacter bacteriophages.

Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

Spatial genetic structure of terrestrial orchid Cymbidium faberi in the Qinling Mountains revealed by microsatellite loci

Knowledge of genetic diversity and population structure is essential for species conservation and understanding the species evolutionary processes. Cymbidium faberi is a terrestrial orchid listed in Appendix of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), with northernmost distribution in the Qinling Mountains of China. However, few studies have investigated the genetic variation of C. faberi in the Qinling Mountains. Using 12 microsatellite markers, we examined genetic diversity and spatial genetic structure of 284 C. faberi samples collected from 15 locations in the Qinling Mountains. We found that mean allelic richness AR and expected heterozygosity HE were 3.439 and 0.396, respectively. The level of genetic differentiation between populations varied from low to high (FST = 0.0038–0.2586). Also, an increase in genetic distance with geographic distance has been observed (mantel r = 0.846, P < 0.01). Additionally, both STRUCTURE and discriminant analysis of principal components (DAPC) revealed a significant genetic differentiation in C. faberi. Our results suggest that restricted seed and pollen dispersal may account for the genetic differentiation among populations of C. faberi in the Qinling Mountains; these findings may provide helpful references for understanding the diversity of orchids and developing proper measures to conserve this orchid species.

Genetic Diversity of Cattle Bred in Territory of the Tyumen Region, Russia.

Improving the genetic potential of animals using genomic technologies is an effective way to solve problems in domestic breeding of dairy breeds. The aim of the current study is to analyze the genetic diversity of Holstein cattle bred in the Tyumen Region using microsatellite markers. The blood samples of 241 Holstein cow were collected for genomic analysis. Genetic identification was performed using COrDIS kits. The resulting data indicated the presence of genetic diversity in the studied sample of dairy cattle bred at the Tyumen Region for a number of indicators. The number of alleles at 15 microsatellite loci in the tested breeds varied from 5 to 14. Eighteen unique allelic variants can be breed-specific markers for genetic identification of dairy cattle. The recorded data showed a high level of animal genetic variability. A high level of polymorphism (Ае 3.32) was detected in 47% of the loci under research. High values of the observed heterozygosity up to 0.91 at the Eth3 locus and of the polymorphism up to 0.77 at the Tgla53 locus were detected. In the results, 7% erroneous entries in the progeny pedigree was detected. The results of the current study contribute to the knowledge of genetic diversity of dairy cattle in the Tyumen region, Russia, and also paved the way to seek new relationships between allelic variants of microsatellite loci with the productive traits of animals.

Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers.

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Exploration of Plasmodium vivax merozoite surface proteins 1 and 7 genetic diversity in Brazilian Amazon and Rio de Janeiro Atlantic Forest.

Plasmodium vivax merozoite surface proteins (PvMSP) 1 and 7 are considered vaccine targets. Genetic diversity knowledge is crucial to assess their potential as immunogens and to provide insights about population structure in different epidemiological contexts. Here, we investigate the variability of pvmsp-142, pvmsp-7E, and pvmsp-7F genes in 227 samples from the Brazilian Amazon (BA) and Rio de Janeiro Atlantic Forest (AF). pvmsp-142 has 63 polymorphisms - 57 nonsynonymous - generating a nucleotide diversity of π=0.009 in AF, and π=0.018 in BA. In pvmsp-7E, 134 polymorphisms - 103 nonsynonymous - generate the nucleotide diversity of π=0.027 in AF, and π=0.042 in BA. The pvmsp-7F has only two SNPs - A610G and A1054T -, with nucleotide diversity of π=0.0004 in AF, and π=0.0007 in BA. The haplotype diversity of pvmsp-142, pvmsp-7E, and pvmsp-7F genes is 0.997, 1.00, and 0.649, respectively. None of the pvmsp-142 or pvmsp-7E sequences are identical to the Salvador 1 strain's sequence. Conversely, most of pvmsp-7F sequences (94/48%) are identical to Sal-1. We evaluated eight B-cell epitopes in pvmsp-7E, four of them showed higher nucleotide diversity compared to pvmsp-7E's epitopes. Positive selection was detected in pvmsp-142, pvmsp-7E central region, and pvmsp-7F with Tajima's D. In pvmsp-7E, the significant nucleotide and haplotype diversities with low genetic differentiation, could be indicative of balancing selection. The genetic differentiation of pvmsp-142 (0.315) and pvmsp-7F (0.354) genes between AF and BA regions is significant, which is not the case for pvmsp-7E (0.193). We conclude that pvmsp-142 and pvmsp-7E have great genetic diversity even in AF region, an enclosure area with deficient transmission levels of P. vivax zoonotic malaria. In both Brazilian regions, pvmsp-119, pvmsp-7E, and pvmsp-7F are conserved, most likely due to their roles in parasite survival, and could be considered potential targets for a "blood-stage vaccine".

Genetic diversity and population structure of endangered plant species Anagallis foemina Mill. [Lysimachia foemina (Mill.) U. Manns & Anderb.

Anagallis foemina L. [syn. Lysimachia foemina (Mill.) U. Manns & Anderb.] is an annual, segetal weed from the family Primulaceae, recognized as a very rare and endangered species in many European countries. The rare occurrence of this species is associated with the specificity of the habitats in which it occurs. Knowledge of genetic diversity within and between rare species populations is a crucial step for investigating the causes of extinction as well as developing effective conservation strategies. The current study undertakes the assessment of the genetic variation and population structure of Anagallis foemina L. specimens collected in south-eastern Poland, Volhynian Polesie and West Volhynian Upland based on inter-simple sequence repeats (ISSR) polymorphism. Twenty ISSR primers amplified 374 DNA fragments, of which 79% were polymorphic. The polymorphic information content values ranged from 0.230 to 0.430 with an average of 0.344. An average genetic similarity calculated based on Dice algorithm between all analysed samples was 0.635 (0.28–1.00). The AMOVA study found a significant difference (Φpt = 0.88, P = 0.001) between Anagallis L. genotypes gathered in Volhynian Polesie (VP) and West Volhynian Upland (VU). Analysis indicated, that 89% of the variation existed among groups and 11% within groups. UPGMA analyses grouped A. foemina samples into 2 clearly separated clusters. The plants of the same geographic origin were grouped together. Principal coordinates analysis (PCoA) as well as STRUCTURE also grouped samples in consistence with the collection site, indicating close genetic affinity of plants from the same location. The observed results are typical for fragmented and isolated populations of rare species. Isolation of a small population leads to a decrease in internal genetic variation and to an increase of variation among them. In that case, the conservation of populations from each regional cluster is important to preserve biodiversity.

Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA

Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I–IV). The goal of the present study was to use Bayesian phylogenetic inference to expand our understanding of the spatial, temporal, and host patterns of PRV-1 from the waters of the northeast Pacific. To that end, we determined the coding genome sequences of fourteen PRV-1 samples that were selected to improve our knowledge of genetic diversity across a broader temporal, geographic, and host range, including the first reported genome sequences from the northwest Atlantic (Eastern Canada). Nucleotide and amino acid sequences of the concatenated genomes and their individual segments revealed that established sequences from the northeast Pacific were monophyletic in all analyses. Bayesian inference phylogenetic trees of S1 sequences using BEAST and MrBayes also found that sequences from the northeast Pacific grouped separately from sequences from other areas. One PRV-1 sample (WCAN_BC17_AS_2017) from an escaped Atlantic salmon, collected in British Columbia but derived from Icelandic broodstock, grouped with other S1 sequences from Iceland. Our concatenated genome and S1 analysis demonstrated that PRV-1 from the northeast Pacific is genetically distinct but descended from PRV-1 from the North Atlantic. However, the analyses were inconclusive as to the timing and exact source of introduction into the northeast Pacific, either from eastern North America or from European waters of the North Atlantic. There was no evidence that PRV-1 was evolving differently between free-ranging Pacific Salmon and farmed Atlantic Salmon. The northeast Pacific PRV-1 sequences fall within genogroup II based on the classification of Garseth, Ekrem, and Biering (Garseth, A. H., Ekrem, T., and Biering, E. (2013) ‘Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon’, PLoS One, 8: e82202.), which also includes North Atlantic sequences from Eastern Canada, Iceland, and Norway. The additional full-genome sequences herein strengthen our understanding of phylogeographical patterns related to the northeast Pacific, but a more balanced representation of full PRV-1 genomes from across its range, as well additional sequencing of archived samples, is still needed to better understand global relationships including potential transmission links among regions.

The diversity of powdery mildew resistance gene loci among wheat germplasm in Southwest China

Knowledge of genetic diversity and genes conferring disease resistance is essential for the effective use of wheat germplasm resistant to powdery mildew in breeding programs in southwest China. In this study, a collection of 140 common wheat varieties was evaluated for their resistance to powdery mildew in four different environments. Thirty-six varieties (25.71%) showed resistance in all four environments, and most of these varieties originated from the Guizhou Province. This collection was also scanned for molecular markers closely linked to the powdery mildew resistance genes. Most of the wheat varieties (79.86%) carried the resistance Pm30 gene locus. Genotyping by sequencing (GBS) was used to screen our collection against the whole genome. Finally, 6864 informative SNP markers were used to construct a consensus tree with 1000 bootstraps, which showed two groups based on their origins and the presence of the Pm21 gene locus. Our results provide useful information for breeding wheat resistant to powdery mildew in China, and they will likely contribute to the identification of new resistance genes in the future.

Inter-Simple Sequence Repeat (ISSR) Polymorphism of Tuberculosis Patients from Mile Four Hospital, Abakaliki, Nigeria

Tuberculosis (TB) is a serious health issue in Ebonyi State and Nigeria at large. The knowledge of genetic diversity and population structure of TB patients in Ebonyi State is still inadequate. Therefore, this work tends to assess the genetic diversity and population structure in association with tuberculosis population using Inter-simple sequence repeat (ISSR) markers. A total of 25 samples were collected, in which 21 were from TB patients and 4 from NTB patients as controls. DNA extraction was done using Cetyltrimethylammonium bromide (CTAB) method followed by Polymerase chain reaction (PCR) with ISSR primers. Analyses of dendrogram, principal component analysis, genetic diversity and population structure were computed with the scored matrix data. Six ISSR markers were polymorphic. The polymorphic information content (PIC) values ranged from 0.2635 to 0.8158 with a mean of 0.6156. The genetic diversity ranged from 0.1504 to 0.8352 with a mean of 0.6156, while the major allele frequency ranged from 0.2800 to 0.9200 with a mean of 0.5018. The allele count ranged from 1 to 23, while the frequency ranged from 0.0400 to 0.9200. The values of number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (H) and Shannon's information index (I) from the entire population were 2.000±0.000, 1.8562±0.1011, 0.4595±0.0330 and 0.6517±0.0350, respectively while that of the six ISSR markers ranges from 1.3200-2.0000, 1.1184-1.9091, 0.0456-0.4571 and 0.1388-0.6611, respectively. From the six ISSR marker data, the number of polymorphic loci (NPL) and percentage polymorphic loci (PPL) ranged from 2 to 25 and 32% to 100% respectively. A dendrogram of the 25 TB and non- NTB clustered them into nine major groups. This study revealed high diversity among TB patientsatgene loci also probed, but did not show any clear association between TB susceptibility and the gene loci.

Chloroplast microsatellites reveal genetic diversity and population structure in natural populations of Himalayan Cedar (Cedrus deodara (Roxb.) G. Don) in India

Abstract Himalayan cedar (Cedrus deodara) is one of the most important temperate timber species of Western Himalayas and is considered to be among the endangered conifer species in the region. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Ten polymorphic chloroplast microsatellites (cpSSR) were used to study genetic diversity and population structure in twenty one natural populations of C. deodara throughout its entire distribution range in Western Himalayas. When alleles at each of the 10 loci were jointly analysed, 254 different haplotypes were identified among 1050 individuals. The cpSSRs indicate that C. deodara forests maintain a moderately high level of genetic diversity (mean h = 0.79 ). AMOVA analysis showed that most of the diversity in C. deodara occurs within populations. Bayesian analysis for population structure (BAPS) revealed spatial structuration of the variation (22 % of the total variation) and substructuring captured nineteen genetic clusters in the entire divisions of the populations. Most of the populations were clustered independently with minor admixtures. The distribution of genetic diversity and sub-structuring of C. deodara may be due to restricted gene flow due to geographic isolation, genetic drift, and natural selection. These findings indicated existence of genetically distinct and different high diversity and low diversity clusters, which are potential groups of populations that require attention for their conservation and management. The results are interpreted in context of future conservation plans for C. deodara.

Identification of polymorphic SSR markers in elite genotypes of pearl millet and diversity analysis

Abstract Pearl millet is a climate-resilient crop of marginal agro-ecologies and semi-arid tropics of Asia and Africa. With substantial nutritional qualities crop requires low inputs and is capable of giving economic returns. Development of high-yielding hybrids is an important breeding objective for pearl millet worldwide. The knowledge of genetic diversity is a prerequisite for developing superior hybrids. In the current study, attempts were made to evaluate the diversity of 17 important Indian pearl millet inbred genotypes and one popular hybrid 9444 using fluorescent labeled SSR markers. A total of 342 polymorphic alleles with an average of 4.62 alleles per primer were produced from 74 SSR markers. Polymorphic information content (PIC) ranged from 0.10 to 0.89 with an average of 0.55. A very low level of heterozygosity was detected in genotypes. The average genetic dissimilarity detected between pairs of inbred lines was 0.66. Genetic dissimilarity estimates calculated among the inbred lines varied from 0.108 (AIMP-03 and AIMP-08) to a maximum of 0.851(AIMP-03/AIMP-08 and 81B). The results indicated that sufficient genetic variability is available in studied genotypes which can be exploited through heterosis breeding to develop hybrids. The study also presents a suit of SSR markers that could be effectively used for genetic diversity analysis in pearl millet.

Forest genomics: Advancing climate adaptation, forest health, productivity, and conservation.

Forest ecosystems provide important ecological services and resources, from habitat for biodiversity to the production of environmentally friendly products, and play a key role in the global carbon cycle. Humanity is counting on forests to sequester and store a substantial portion of the anthropogenic carbon dioxide produced globally. However, the unprecedented rate of climate change, deforestation, and accidental importation of invasive insects and diseases are threatening the health and productivity of forests, and their capacity to provide these services. Knowledge of genetic diversity, local adaptation, and genetic control of key traits is required to predict the adaptive capacity of tree populations, inform forest management and conservation decisions, and improve breeding for productive trees that will withstand the challenges of the 21st century. Genomic approaches have well accelerated the generation of knowledge of the genetic and evolutionary underpinnings of nonmodel tree species, and advanced their applications to address these challenges. This special issue of Evolutionary Applications features 14 papers that demonstrate the value of a wide range of genomic approaches that can be used to better understand the biology of forest trees, including species that are widespread and managed for timber production, and others that are threatened or endangered, or serve important ecological roles. We highlight some of the major advances, ranging from understanding the evolution of genomes since the period when gymnosperms separated from angiosperms 300 million years ago to using genomic selection to accelerate breeding for tree health and productivity. We also discuss some of the challenges and future directions for applying genomic tools to address long‐standing questions about forest trees.

Genetic diversity of Iranian Chrysanthemum morifolium cultivars using morphological traits and sequence-related amplified polymorphism (SRAP) markers

Knowledge of genetic diversity and relatedness of cultivars; is essential for a successful breeding scheme. The present study was conducted to assess the genetic diversity of 30 Iranian Chrysanthemum morifolium cultivars using sequence-related amplified polymorphism (SRAP) molecular markers and morphological traits. For this purpose, 30 cultivars were planted in a completely randomized block design with three replications at the Research Farm of Isfahan University of Technology in 2015. The evaluation of morphological traits during the two consecutive years showed a wide range of variations among different cultivars. The results obtained by the analysis of variance also revealed the significant effects of cultivar, environment and cultivar × environment interaction on all studied traits. Correlation analysis of variables further showed that flowering durability was affected by plant morphology. Results of cluster analysis based on the phenotypic data divided the cultivars into six groups. Molecular analysis using SRAP markers produced a total of 213 identifiable fragments with an average of 21.3 polymorphic bands per combination. The polymorphic information content (PIC) value was 0.46. Along with the Bayesian structure analysis which showed that the highest value of the maximum delta log likelihood (ΔK) was K = 3, cluster analysis also grouped the cultivars into three main clusters. The high value of admixture revealed ancestral relationships between the studied cultivars. Overall, our findings revealed the potential of SRAP markers and morphological traits for the analysis of genetic diversity in Chrysanthemum. This can be, in turn, used in selecting the desired parents in the hybrid breeding programs as well as developing superior cultivars for ornamental applications.

Evaluation of genetic diversity of parental lines for development of heterotic groups in hybrid rice (Oryza sativa L.)

Knowledge of genetic diversity and potential heterotic relationships among parental lines is of significant importance in hybrid rice breeding programs. In the present study, in order to understand the genetic diversity among 96 parental lines, they were characterized for their diversity with respect to their morphological traits (n = 12) and molecular markers using a set of 50 SSR markers. Morphological diversity was estimated using Mahalanobis D2 statistics in terms of generalized group distance. Based on morphological diversity analysis, the 96 lines were grouped into 5 major and 13 monogenotypic clusters. In molecular marker analysis, the parental lines were consistently clustered into B (Maintainer group) and R (Restorer group) groups based on distance and model based approaches. Strong correspondence was observed between the pedigree of parental lines with molecular genotyping based grouping than morphological trait based grouping. From the results of the present investigation, it is evident that the available diversity among the two groups i.e., maintainer group (B) and restorer group (R) is sufficient for developing heterotic hybrids, but within the maintainer and restorer groups, the diversity is limited, the diversity among restorers was moderate, while it was low among the maintainers and hence efforts are needed for broadening their genetic base of parental lines for development and adoption of high-yielding hybrids.

Phylogeography, genetic diversity, and connectivity of brown bear populations in Central Asia.

Knowledge of genetic diversity and population structure is critical for conservation and management planning at the population level within a species’ range. Many brown bear populations in Central Asia are small and geographically isolated, yet their phylogeographic relationships, genetic diversity, and contemporary connectivity are poorly understood. To address this knowledge gap, we collected brown bear samples from the Gobi Desert (n = 2360), Altai, Sayan, Khentii, and Ikh Khyangan mountains of Mongolia (n = 79), and Deosai National Park in the Himalayan Mountain Range of Pakistan (n = 5) and generated 927 base pairs of mitochondrial DNA (mtDNA) sequence data and genotypes at 13 nuclear DNA microsatellite loci. We documented high levels of mtDNA and nDNA diversity in the brown bear populations of northern Mongolia (Altai, Sayan, Buteeliin nuruu and Khentii), but substantially lower diversity in brown bear populations in the Gobi Desert and Himalayas of Pakistan. We detected 3 brown bear mtDNA phylogeographic groups among bears of the region, with clade 3a1 in Sayan, Khentii, and Buteeliin nuruu mountains, clade 3b in Altai, Sayan, Buteeliin nuruu, Khentii, and Ikh Khyangan, and clade 6 in Gobi and Pakistan. Our results also clarified the phylogenetic relationships and divergence times with other brown bear mtDNA clades around the world. The nDNA genetic structure analyses revealed distinctiveness of Gobi bears and different population subdivisions compared to mtDNA results. For example, genetic distance for nDNA microsatellite loci between the bears in Gobi and Altai (FST = 0.147) was less than that of the Gobi and Pakistan (FST = 0.308) suggesting more recent male-mediated nuclear gene flow between Gobi and Altai than between Gobi and the Pakistan bears. Our results provide valuable information for conservation and management of bears in this understudied region of Central Asia and highlight the need for special protection and additional research on Gobi brown bears.

Assessment of genetic diversity and mating system of Acacia cyclops restoration and remnant populations

Acacia cyclops, or Ngaamarur, is a common coastal shrub or small tree of the southwest of Western Australia and South Australia used for restoration in these landscapes and elsewhere. Knowledge of genetic diversity and mating systems of restoration populations is often lacking but can help inform likely restoration success. We compared genetic diversity and mating system parameters at three restoration populations of A. cyclops to nearby remnant reference populations. Mean levels of genetic diversity in restoration populations (Na = 1.806, Ne = 1.560, He = 0.270, Ho = 0.359) were not significantly different from those in the reference populations (Na = 1.833, Ne = 1.574, He = 0.269, Ho = 0.352) suggesting diverse seed collections were made for restoration. Allelic genetic divergence among restoration and reference populations was low (DST ≤ 0.04) suggesting that seeds were of local provenance. Mating system parameters were similar among restoration (tm = 0.989, tm–ts = 0.010, rpm = 0.392) and reference populations (tm = 0.868, tm–ts = 0.039, rpm = 0.410), suggesting functionality of the mating system and restitution of generalist insect pollinator services in restored populations at 7, 10, and 12 years after planting. Lower levels of heterozygosity in progeny compared to adults suggest post‐germination or late‐acting selection against inbred seedlings. Evidence for selection and seedling attrition further emphasizes the benefits of collections from many individuals in well‐connected outcrossed source populations. Overall, results suggest available local genetic diversity was captured and restoration populations have mating systems equivalent to those of reference populations.

Genetic diversity and connectivity in fragmented populations of Rhinanthus minor in two regions with contrasting land-use

Knowledge of genetic diversity and connectivity within and between populations of specialist meadow plants is crucial to developing effective conservation strategies at the landscape-scale. This study investigated levels of genetic diversity within, and gene flow between populations of a key annual species, Rhinanthus minor in protected meadows and landscape matrix sites in two contrasting regions. Possible barriers to gene flow were also analysed. Leaf material from 714 individuals in an extensively managed upland region and an intensively managed lowland region of the UK was genotyped using microsatellite markers. Genetic diversity was similar in the two regions (He = 0.48 and 0.44). FST values indicated population differentiation in both regions but the estimate was higher in the lowland (FST = 0.28) than in the upland region (FST = 0.19); evidence of global structure was revealed in a spatial principal components analysis but a maximum likelihood population effects model did not identify significant predictors of population differentiation after testing the effects of Euclidean geographic distance, land cover and elevation. Conservation strategies should aim to maintain large populations in meadows to enhance genetic diversity. At the same time the focus should be on existing and additional species-rich grassland fragments, particularly in areas of intensive land-use, if genetic connectivity is to be retained.

Phylogenetic Diversity of Orientia tsutsugamushi Isolates in Patients with Scrub Typhus in Bengaluru, India

AbstractScrub typhus has re-emerged as an important cause of acute febrile illness in India. There is a dearth of information on strain diversity of Orientia tsutsugamushi from Karnataka, India, hence the present study sought to address this issue. One hundred clinically suspected cases of scrub typhus/rickettsiosis (as per the DHR-ICMR guidelines) were included. Nested-polymerase chain reaction (PCR) for 56-kDa gene and phylogenetic analysis was performed. PCR was positive in 22 cases and phylogenetic analysis showed the presence of different strains, with predominance of clustering (57%) with Gilliam-type for the first time in Karnataka. Knowledge of genetic diversity has implications in development of diagnostics and vaccine.