Diversity2014, 6(4), 665-680; doi:10.3390/d6040665 - published 20 October 2014 Show/Hide Abstract
Abstract: Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.
Diversity2014, 6(4), 652-664; doi:10.3390/d6040652 - published 15 October 2014 Show/Hide Abstract
Abstract: Chinese privet (Ligustrum sinense) was the most prevalent invasive shrub in the forestlands of Eastern Texas in 2006. We analyzed extensive field data collected by the Forest Inventory and Analysis Program of the U.S. Forest Service to quantify the range expansion of Chinese privet from 2006 to 2011. Our results indicated the presence of Chinese privet on sampled plots increased during this period. Chinese privet spread extensively in the north. Results of logistic regression, which classified 73% of the field plots correctly with regard to species presence and absence, indicated probability of invasion was correlated positively with elevation, adjacency (within 300 m) to water bodies, and site productivity, and was correlated negatively with stand age, site preparation (including clearing, slash burning, chopping, disking, bedding, and other practices clearly intended to prepare a site for regeneration), artificial regeneration (which refers to planting or direct seeding that results in at least 50% of the stand being comprised of stocked trees), and distance to the nearest road. Habitats most at risk to further invasion (likelihood of invasion > 40%) under current conditions occurred primarily in Northeast Texas. Practicing site preparation and artificial regeneration reduced the estimated probabilities of further invasion.
Diversity2014, 6(4), 633-651; doi:10.3390/d6040633 - published 29 September 2014 Show/Hide Abstract
Abstract: The Salix alba L. (white willow)—Salix fragilis L. (crack willow) complex includes closely related polyploid species, mainly tetraploid (2n= 4x= 76), which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome behavior of these pure willow trees, genetic analysis of their naturally occurring interspecific polyploid hybrids is still very difficult. A two-way pseudo-testcross strategy was exploited using single-dose AFLP markers in order to assess the main inheritance patterns of tetraploid biotypes (disomy vs. tetrasomy) in segregating populations stemmed from S. alba × S. fragilis crosses and reciprocals. In addition, a genomic in situ hybridization (GISH) technology was implemented in willow to shed some light on the genome structure of S. alba and S. fragilis species, and their hybrids (allopolyploidy vs. autopolyploidy). The frequency of S. alba-specific molecular markers was almost double compared to that of S. fragilis-specific ones, suggesting the phylogenetic hypothesis of S. fragilis as derivative species from S. alba-like progenitors. Cytogenetic observations at pro-metaphase revealed about half of the chromosome complements being less contracted than the remaining ones, supporting an allopolyploid origin of both S. alba and S. fragilis. Both genetic segregation and genomic hybridization data are consistent with an allotetraploid nature of the Salix species. In particular, the vast majority of the AFLP markers were inherited according to disomic patterns in S. alba × S. fragilis populations and reciprocals. Moreover, in all S. alba against S. fragilis hybridizations and reciprocals, GISH signals were observed only on the contracted chromosomes whereas the non-contracted chromosomes were never hybridized. In conclusion, half of the chromosomes of the pure species S. alba and S. fragilis are closely related and they could share a common diploid ancestor, while the rest of chromosomes are morphologically differentiated in either S. alba or S. fragilis and they should derive from distinct diploid ancestors.
Diversity2014, 6(3), 597-632; doi:10.3390/d6030597 - published 18 September 2014 Show/Hide Abstract
Abstract: Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates) and cyprinodontiforms (among fishes) appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.
Diversity2014, 6(3), 579-596; doi:10.3390/d6030579 - published 5 September 2014 Show/Hide Abstract
Abstract: Media constantly refer of unscrupulous producers that adulterate, alter or replace premium products in food chains with the goal to maximize illegally profits. Food traceability is a central issue for the identification of improper labeling of processed food and feed and there are rules aimed to protect consumers and producers against fraudulent substitution of quality products in food chain, but the tools available are not always appropriate. DNA-based markers proved very effective for fresh and processed food molecular authentication. In this review, we illustrate potential and limits of different DNA markers focusing on low, medium and high-throughput markers, in order to monitor the genetic identity of food components in meat, fish and plants net-chains.
Diversity2014, 6(3), 567-578; doi:10.3390/d6030567 - published 29 August 2014 Show/Hide Abstract
Abstract: TheWestern Ghats is a global biodiversity hotspot and home to diverse and unique assemblages of amphibians. Several rivers originate from these mountains and hydropower is being tapped from them. The impacts of hydrological regulation of riparian ecosystems to wildlife and its habitat are poorly documented, and in particular the fate of frog populations is unknown. We examined the effects of dams on riparian frog communities in the Thamirabarani catchment in southern Western Ghats. We used nocturnal visual encounter surveys constrained for time, to document the species richness of frogs below and above the dam, and also at control sites in the same catchment. While we did not find differences in species richness below and above the dams, the frog community composition was significantly altered as a likely consequence of altered flow regime. The frog species compositions in control sites were similar to above-dam sites. Below-dam sites had a distinctly different species composition. Select endemic frog species appeared to be adversely impacted due to the dams. Below-dam sites had a greater proportion of generalist and widely distributed species. Dams in the Western Ghats appeared to adversely impact population of endemic species, particularly those belonging to the genus Nyctibatrachus that shows specialization for intact streams.