Genomic toolboxes for conservation biologists

Conservation genetics is expanding its research horizon with a genomic approach, by incorporating the modern techniques of next-generation sequencing (NGS). Application of NGS overcomes many limitations of conservation genetics. First, NGS allows for genome-wide screening of markers, which may lead to a more representative estimation of genetic variation within and between populations. Second, NGS allows for distinction between neutral and non-neutral markers. By screening populations on thousands of single nucleotide polymorphism markers, signals of selection can be found for some markers. Variation in these markers will give insight into functional rather than neutral genetic variation. Third, NGS facilitates the study of gene expression. Conservation genomics will increase our insight in how the environment and genes interact to affect phenotype and fitness. In addition, the NGS approach opens a way to study processes such as inbreeding depression and local adaptation mechanistically. Conservation genetics programs are directed to a fundamental understanding of the processes involved in conservation genetics and should preferably be started in species for which large databases on ecology, demography and genetics are available. Here, we describe and illustrate the connection between the application of NGS technologies and the research questions in conservation. The perspectives of conservation genomics programs are also discussed

Mendelian Inheritance Pattern and High Mutation Rates of Microsatellite Alleles in the Diatom Pseudo-nitzchia multistriata

The diatom Pseudo-nitzschia multistriata exhibits a diplontic life cycle composed of an extensive phase of vegetative cell division and a brief phase of sexual reproduction. To explore genotypic stability, we genotyped seven polymorphic microsatellite loci in 26 monoclonal strains over 3–16 months in a culture maintenance regime. Moreover, to assess inheritance patterns of the microsatellite alleles, we genotyped 246 F1 strains resulting from four mating experiments between parental strains of know genotype. Results generally conformed expectations according to Mendelian inheritance patterns, but deviations were detected indicating mutations during sexual reproduction. A total of forty-two mutations were detected in the clonal cultures over time. Microsatellites with more core-repeats accumulated mutations faster. The mutation rate varied significantly across loci and strains. A binomial mass function and a computer simulation showed that the mutation rate was significantly higher during the first months of culture (μ≈3×10-3 per locus per cell division) and decreased to μ≈1×10-3 in the strains kept for 16 months. Our results suggest that genetic mutations acquired in both the vegetative phase and sexual reproduction add to the allelic diversity of microsatellites, and hence to the genotypic variation present in a natural population

Darwin’s wind hypothesis: does it work for plant dispersal in fragmented habitats?

Using the wind-dispersed plant Mycelis muralis, we examined how landscape fragmentation affects variation in seed traits contributing to dispersal. Inverse terminal velocity (Vt−1) of field-collected achenes was used as a proxy for individual seed dispersal ability. We related this measure to different metrics of landscape connectivity, at two spatial scales: in a detailed analysis of eight landscapes in Spain and along a latitudinal gradient using 29 landscapes across three European regions. In the highly patchy Spanish landscapes, seed Vt−1 increased significantly with increasing connectivity. A common garden experiment suggested that differences in Vt−1 may be in part genetically based. The Vt−1 was also found to increase with landscape occupancy, a coarser measure of connectivity, on a much broader (European) scale. Finally, Vt−1 was found to increase along a south–north latitudinal gradient. Our results for M. muralis are consistent with ‘Darwin’s wind dispersal hypothesis’ that high cost of dispersal may select for lower dispersal ability in fragmented landscapes, as well as with the ‘leading edge hypothesis’ that most recently colonized populations harbour more dispersive phenotypes.

Belowground DNA-based techniques: untangling the network of plant root interactions

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Population Genetics of Franciscana Dolphins (Pontoporia blainvillei): Introducing a New Population from the Southern Edge of Their Distribution

Due to anthropogenic factors, the franciscana dolphin, Pontoporia blainvillei, is the most threatened small cetacean on the Atlantic coast of South America. Four Franciscana Management Areas have been proposed: Espiritu Santo to Rio de Janeiro (FMA I), São Paulo to Santa Catarina (FMA II), Rio Grande do Sul to Uruguay (FMA III), and Argentina (FMA IV). Further genetic studies distinguished additional populations within these FMAs. We analyzed the population structure, phylogeography, and demographic history in the southernmost portion of the species range. From the analysis of mitochondrial DNA control region sequences, 5 novel haplotypes were found, totalizing 60 haplotypes for the entire distribution range. The haplotype network did not show an apparent phylogeographical signal for the southern FMAs. Two populations were identified: Monte Hermoso (MH) and Necochea (NC)+Claromecó (CL)+Río Negro (RN). The low levels of genetic variability, the relative constant size over time, and the low levels of gene flow may indicate that MH has been colonized by a few maternal lineages and became isolated from geographically close populations. The apparent increase in NC+CL+RN size would be consistent with the higher genetic variability found, since genetic diversity is generally higher in older and expanding populations. Additionally, RN may have experienced a recent split from CL and NC; current high levels of gene flow may be occurring between the latter ones. FMA IV would comprise four franciscana dolphin populations: Samborombón West+Samborombón South, Cabo San Antonio+Buenos Aires East, NC+CL+Buenos Aires Southwest+RN and MH. Results achieved in this study need to be taken into account in order to ensure the long-term survival of the species.Fil: Gariboldi, María Constanza. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; ArgentinaFil: Tunez, Juan Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Luján; ArgentinaFil: Dejean, Cristina Beatriz. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; Argentina. Universidad de Buenos Aires. Facultad de Filosofía y Letras. Instituto de Ciencias Antropológicas. Sección Antropología Biológica; ArgentinaFil: Failla, Mauricio. Fundación Cethus; ArgentinaFil: Vitullo, Alfredo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; ArgentinaFil: Negri, Maria Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales ; ArgentinaFil: Cappozzo, Humberto Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Maimónides. Área de Investigaciones Biomédicas y Biotecnológicas. Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y de Diagnóstico; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales ; Argentin

Assessing the vulnerability of freshwater crayfish to climate change

Aim: Climate change is a major threat to the persistence of biodiversity. Global assessments highlight the most climate vulnerable species and geographic regions based on species traits and measures of exposure to climate change. Yet the majority of climate change vulnerability assessments have focused on terrestrial and marine vertebrates and largely ignored the less well‐known freshwater species and invertebrates. We present the first global analysis of 574 species of freshwater crayfish (Families: Astacidae, Parastacidae and Cambaridae) using IUCN's trait‐based vulnerability assessment protocol. Location Global. Methods: We collected species‐specific information on sensitivity (eight traits), adaptive capacity (four traits) and exposure (five traits) to climate change and combined those dimensions to assess overall species vulnerability. Results: Our results predicted that 87% of freshwater crayfish species are highly sensitive to climate change (primarily due to habitat specialization), 35% have low adaptive capacity and 57% are highly exposed (based on an ensemble mean of four general circulation models for a moderate Intergovernmental Panel on Climate Change (IPCC) scenario, RCP6.0). Combining sensitivity, low adaptive capacity and exposure, we assessed 87 species (15%) as vulnerable to climate change. These species are distributed globally with high concentrations in the south‐eastern USA (36 species), south‐eastern Australia (21 species) and Mexico (10 species), reflecting global patterns of crayfish species richness. Of the 91 species listed as threatened by climate change in the IUCN Red List, we predicted 18 species to be climate change vulnerable. Main conclusions: We identified hotspots of species vulnerable to climate change that require further conservation attention. The IUCN trait‐based protocol can help identify data gaps and key traits that should be investigated further and thus can help overcome knowledge shortfalls on the effects of climate change. Our study provides key insights for the application of climate change vulnerability assessment to data‐poor invertebrates, which remain underrepresented in global conservation priorities

Gene diversity and demographic turnover in central and peripheral populations of the perennial herb Gypsophila fastigiata

Within-population gene diversity (H-S) was estimated (using allozyme markers) for 16 populations of the perennial, outcrossing plant, Gypsophila fastigiata, on the Baltic island of Oland. The populations were characterized by data on extent, density, life-stages, and habitat diversity. Populations were classed as central or peripheral in relation to the distribution of ''alvar" (habitats with shallow, calcareous soils on limestone bedrock) on southern Oland. Three minimal adequate models were used to explain H-S and the proportions of juveniles and dead adults. In the first model, H-S was significantly lower in peripheral populations and there were no significant additional effects of other explanatory variables. The lower diversity in peripheral populations can be explained by a combination of genetic drift (in populations that vary in size in response to habitat fragmentation) and lower levels of interpopulation gene flow than in central populations. In the two life-stage models, peripheral populations had significantly larger proportions of both juveniles and dead adults indicating a greater demographic turnover than in the central populations. There were also significant effects of H-S and species diversity on the proportion of juveniles. The central or peripheral position of populations is the strop est predictor of both within-population gene diversity and life-stage dynamics in Oland G. fastigiata