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opencc-by-4.0Feb 2022View details →

Genetic and phenotypic diversity of banana-infecting Fusarium strains

Genetic and phenotypic diversity of banana-infecting Fusarium strains. Dataset1 contains molecular diagnosis and pathogenicity assays of Fusarium isolates. Dataset2 describes the sequenced isolates used in the study.

FIGURE 6 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran

FIGURE 6. STRUCTURE analysis of L. rigidum populations (A: the relationship between k and Delta k; the grouping based on k=18 (top) and k=17 (below) (The population code is according to Table 1).

FIGURE 3 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran

FIGURE 3. TCS Network of L. rigidum studied populations based on ISSR data (The population code is according to Table 1) (Numbers of branches reveal number of different loci among studied populations).

FIGURE 5 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran

FIGURE 5. NeighborNet diagram of L. rigidum studied populations based on SCoT data (The population code is according to Table 1).

FIGURE 2 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran

FIGURE 2. UPGMA dendrogram of L. rigidum specimens showing genetic differences of the studied populations based on ISSR data (The population code is according to Table 1).

FIGURE 4 in Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud.) in Iran

FIGURE 4. STRUCTURE analysis of L. rigidum populations (A: the relationship between k and Delta k; the grouping based on k=18 (top) and k=3 (below) (The population code is according to Table 1).

FIGURE 4 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers

FIGURE 4. PCA plot of Salicornia persica populations based on morphological characters. Numbers are according to Table 1.

FIGURE 3 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers

FIGURE 3. PCoA plot of populations in Salicornia persica based on SCoT molecular markers, (Population numbers are according to Table 1.)

FIGURE 2 in Comparative study and genetic diversity of Salicornia persica (Chenopodiaceae) using SCOT molecular markers

FIGURE 2. WARD tree of populations in Salicornia persica based on SCoT molecular markers, (Population numbers are according to Table 1.)

opencc-zeroApr 2022View details →

Genetic diversity and relatedness among African Painted dogs in North America

African painted dogs (Lycaon pictus, APD) are highly endangered, with fewer than 7,000 remaining in nature. Captive breeding programs can preserve a genetically diverse population and provide a source of individuals for re-introductions. However, most programs are initiated from few founders and suffer from low genetic diversity and inbreeding. The aims of this study were to use molecular markers to assess genetic variation, inbreeding, and relatedness among APDs in the North American captive population, to use these data to realign studbook records, and to compare these data to wild populations and to the European captive population to facilitate development of a global management plan. We sequenced mitochondrial and major histocompatibility (MHC) class II loci, and genotyped 14 microsatellite loci from 109 APDs from 34 institutions in North America. We identified three likely studbook errors and resolved ten cases of uncertain paternity. Overall, microsatellite heterozygosity was higher than reported in Europe, but effective population size estimates were lower. Mitochondrial sequence variation was extremely limited, and there were fewer MHC haplotypes than in Europe or the wild. Although the population did not show evidence of significant inbreeding overall, several individuals shared high relatedness values, which should be incorporated into future breeding programs.

opencc-zeroApr 2022View details →

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

Reduced genetic diversity of freshwater amphipods in rivers with increased levels of anthropogenic organic micropollutants

Anthropogenic chemicals in freshwater environments contribute majorly to ecosystem degradation and biodiversity decline. In particular, anthropogenic organic micropollutants (AOM), a diverse group of compounds including pesticides, pharmaceuticals, and industrial chemicals, can significantly impact freshwater organisms. AOM were found to impact the genetic diversity of freshwater species, however, the degree to which AOM cause changes in population genetic structure and allelic richness of freshwater macroinvertebrates remains poorly understood. Here, the impact of AOM on the genetic diversity of the common amphipod Gammarus pulex (Linnaeus, 1758) (clade E) was investigated on a regional scale. The site-specific AOM levels and their toxic potentials were determined in water and G. pulex tissue sample extracts for 34 sites along six rivers impacted by wastewater effluents and agricultural run-off in central Germany. Population genetic parameters were determined for G. pulex from the sampling sites by genotyping 16 microsatellite loci. Genetic differentiation among G. pulex from the studied rivers was strongly associated with geographic distance between sites, but also with differences in site-specific concentrations of AOM. Thus, genetic diversity parameters of G. pulex were found to be related to site-specific AOM levels; allelic richness was significantly negatively correlated to levels of AOM in G. pulex tissue (p < 0.003) and was reduced by up to 22% at sites with increased levels of AOM. This was seen despite a positive relationship between allelic richness and the presence of waste-water effluent. In addition, the inbreeding coefficient of G. pulex from sites with toxic AOM levels was up to 2.5 times higher than in G. pulex from more pristine sites. These results indicate that AOM levels commonly found in European rivers significantly contribute to changes in the genetic diversity of an ecologically relevant indicator species.

Hybridization and low genetic diversity in the endangered Alabama Red-Bellied Turtle (Pseudemys alabamensis)

Pseudemys alabamensis is one of the most endangered freshwater turtle species in the United States due to its restricted geographic distribution in coastal Alabama and Mississippi. Populations of P. alabamensis are geographically isolated from one another by land and salt water, which could act as barriers to gene flow. It is currently unknown how differentiated these isolated populations are from one another and whether they have experienced reductions in population size. Previous work found morphological differences between Alabama and Mississippi populations, suggesting that they may be evolutionarily distinct. Other Pseudemys turtles such as P. concinna and P. floridana occur naturally within the same geographic area as P. alabamensis and are known to hybridize with each other. These more abundant species could threaten the unique genetic identity of P. alabamensis through introgression. In order to evaluate the endangered status of P. alabamensis and the level of hybridization with other species, we used mitochondrial and nuclear microsatellite markers to assess genetic variation within and among populations of P. alabamensis throughout its range and estimate admixture with co-occurring Pseudemys species. In P. alabamensis, we found no variation in mitochondrial DNA and observed an excess of homozygosity in the microsatellite data. Our results indicate evidence of genetic differentiation between Alabama and Mississippi populations of P. alabamensis, and low estimated breeding sizes and inbreeding for two populations (Fowl River, Alabama and Biloxi, Mississippi). Our results also support admixture of P. alabamensis with P. concinna/P. floridana. Based on our results, P. alabamensis is highly endangered throughout its range and threatened by both low population sizes and hybridization. In order to improve the species' chances of survival, focus should be placed on habitat preservation, maintenance of genetic diversity within both Mississippi and Alabama populations, and regular population monitoring activities such as nest surveillance and estimates of recruitment.

Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae)

The Atlantic and Amazon rainforests have a shared but unclear past, with intermittent connections resulting from historical climate change. We investigate these connections by studying the phylogeography and climatic niche of the disjunct distributed frog Lithobates palmipes. We sequenced two fragments of mitochondrial DNA from Atlantic Forest (AtF) and Amazonia (AmF) individuals and evaluated how genetic diversity is distributed in space and whether past demographic changes occurred. Also, we evaluated the existence of past suitable connections between biomes for L. palmipes through ecological niche models (ENM) and tested for niche divergence. The AtF group is nested within the AmF group and closely related to individuals from eastern Amazonia, a pattern recovered in many species that used northeast connection routes. We found evidence of recurrent use of connections in different directions and time during the Pleistocene, resulting in genetic structure between biomes, with no signal of demographic change and evidence of niche divergence across both genetic groups. ENMs indicated suitable areas connecting forests throughout northeastern Brazil during the Pleistocene. Mitochondrial lineages do not match biomes exactly. One lineage is composed of AtF populations and eastern Amazonia individuals. The other is composed of western Amazonia individuals, suggesting an effect of past climatic heterogeneity within the Amazonia forest. This is the first evidence that this route drove genetic and ecological diversity for amphibians recently, a group with habits and ecological requirements different from other vertebrates that have been shown to use this putative corridor.

Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program

Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species' range (64,519 km2). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumour disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for "resistance" alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012-2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures.

opencc-zeroDec 2011View details →

Data from: Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear.

In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a "yardstick" to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this dataset to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed along a species range.

opencc-zeroJul 2022View details →

Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex

Fusarium is associated with a number of wilt, blight, scab and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of Fusarium incarnatum-equiseti species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on inter-simple sequence repeat polymerase chain reaction (ISSR-PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intra-population genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.

opennotspecifiedNov 2017View details →

Lophuromys stanley: is member of the L. flavopunctatus species complex and was named during partial revision of the L. aguilus species complex. It is characterized by craniometric and genetic character-istics; its skull proportions are similar to L. laticeps, and molecularly, it is similar to L. margarettae and L. zena (cytochrome-b). Lophuromys stanleyi is one of four endemic species in the Rwenzori Mountains diversity hotspot. Monotypic. Distribution. Rwenzori Mts, E DR Congo and SW Uganda. Descriptive notes. Head-body 113-126 mm, tail 40-80 mm, ear 16-19 mm, hindfoot 22-24 mm; weight 36-55 g. The Rwenzori Brush-furred Rat has a speckled pelage similar to other speciesin the L. flavopunctatus species complex. Tail is short, 50-60% of head-body length. Habitat. Poorly known, but type specimen was collected at an elevation of 3700 m. Food and Feeding. No information. Breeding. No information. Activity patterns. No information. in Muridae

Lophuromys stanley: is member of the L. flavopunctatus species complex and was named during partial revision of the L. aguilus species complex. It is characterized by craniometric and genetic character-istics; its skull proportions are similar to L. laticeps, and molecularly, it is similar to L. margarettae and L. zena (cytochrome-b). Lophuromys stanleyi is one of four endemic species in the Rwenzori Mountains diversity hotspot. Monotypic. Distribution. Rwenzori Mts, E DR Congo and SW Uganda. Descriptive notes. Head-body 113-126 mm, tail 40-80 mm, ear 16-19 mm, hindfoot 22-24 mm; weight 36-55 g. The Rwenzori Brush-furred Rat has a speckled pelage similar to other speciesin the L. flavopunctatus species complex. Tail is short, 50-60% of head-body length. Habitat. Poorly known, but type specimen was collected at an elevation of 3700 m. Food and Feeding. No information. Breeding. No information. Activity patterns. No information.

opennotspecifiedJul 2022View details →

FIGURE 4 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers

FIGURE 4: WARD tree of SCoT data revealing species delimitation in the Delphinium sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.