Conserving adaptive genetic diversity in dynamic landscapes

Genetic variation supplies the raw material for adaptation, evolution and survival of populations and has therefore been a key focus of conservation biology ever since its foundation (Soulé 1985). In previous decades, the neutral component of genetic diversity (generated by mutation and shaped by drift) has been the subject of intense scientific research, fuelled by the increasing availability of molecular markers. On the other hand, the adaptive component of genetic diversity, which is shaped by the action of natural selection, has long remained elusive and difficult to assess, especially at small spatial or temporal scales (Ouborg et al. 2010). Fortunately, new technological and methodological developments now make it possible to identify loci in the genome that are influenced by selection, and thus to get a more complete view of genetic diversity. One article featured in this issue of Molecular Ecology is a good example of this recent breakthrough. Richter-Boix et al. (2011) examined a network of moor frog populations breeding in contrasting habitats in order to understand how landscape features influence patterns of genetic variation. They combined information from both neutral markers and loci putatively under selection to quantify the relative roles of selection and isolation in the evolution of fine-scale local adaptations in these populations. This study nicely illustrates how data on polymorphisms of neutral and adaptive loci can now be judiciously synthesized to help identify the best strategies for preserving adaptive variation, and more generally to enlighten conservation and population-management plans.     

Early assessment of the impact of alien species: differential consequences of an invasive crayfish on adult and larval amphibians

Aim Early assessment of the impact of invasive alien species is crucial to set up timely management, but often the impact is evident when it is too late for action. We evaluated relationships between the alien crayfish, Procambarus clarkii, the distribution of native amphibians, and the abundance of their larvae. We assessed whether considering measures of reproductive success provide a more prompt measure of impact than considering just species distribution. Location One hundred and twenty‐five wetlands in Northern Italy, in an area recently invaded by P. clarkii. Methods We surveyed wetlands to assess the presence of breeding activity of amphibians and the distribution of P. clarkii. We measured the abundance of amphibian larvae before metamorphosis through pipe sampling. We built models analysing the relationships between amphibian and crayfish distribution, while taking into account spatial autocorrelation and environmental features. Analyses were performed at both the species level (generalized linear models and spatial eigenvector mapping) and community level (constrained redundancy analysis). Results In terms of breeding site distribution, only two amphibians (Lissotriton vulgaris and Hyla intermedia) were negatively associated with P. clarkii, while the relationships between other the species and P. clarkii were positive or not significant. However, larval abundance for all amphibian species was negatively associated with the alien crayfish. Analyses performed at community and single species levels yielded consistent results. Main conclusions Procambarus clarkii impacts amphibians through different processes. Newts probably avoid invaded wetlands for breeding. Other species attempt breeding in wetlands with crayfish, but suffer very low success. Considering distribution data alone would not provide a correct picture of the impact of this alien species; measures of reproductive success may allow a more accurate assessment of the impact.     

Characterization of the transcripts and protein isoforms for cytoplasmic polyadenylation element binding protein-3 (CPEB3) in the mouse retina

Background  

Cytoplasmic polyadenylation element binding proteins (CPEBs) regulate translation by binding to regulatory motifs of defined mRNA targets. This translational mechanism has been shown to play a critical role in oocyte maturation, early development, and memory formation in the hippocampus. Little is known about the presence or functions of CPEBs in the retina. The purpose of the current study is to investigate the alternative splicing isoforms of a particular CPEB, CPEB3, based on current databases, and to characterize the expression of CPEB3 in the retina.     

Bergmann's rule in amphibians: combining demographic and ecological parameters to explain body size variation among populations in the common toad Bufo bufo

Large‐scale patterns of body size variation are described by well‐known generalizations such as Bergmann’s rule; the generality and underlying causes of these patterns have been much debated. Intraspecific extension of this rule was tested in various ectotherms, and evidence was found for both Bergmann and converse Bergmann clines. In this study, we explored spatial patterns of variation in a widespread amphibian, the Common toad (Bufo bufo), along a 2240 km latitudinal gradient across Europe. We tested for covariation of adult body size, age and growth parameters with latitude, altitude, length of activity period and mean temperature during this period using both original and literature data. We selected 13 European populations, representing a latitudinal range from 43 to 63°N and altitudinal range from 15 to 1850 m a.s.l. The length of activity period (12–33 weeks) and T_mean (6.6–15.6°C) significantly decreased as latitude and altitude of these populations increased. Mean body size decreased as latitude increased (not with altitude), and increased with T_mean (not with length of activity period). Mean and minimal adult age increased with latitude and altitude, longevity increased with altitude only. Age increased as length of activity period decreased (not with T_mean). The growth coefficient (0.32–0.92 in males, 0.18–0.74 in females, available for six populations) decreased as altitude increased, and increased as both length of activity period and T_mean increased; latitudinal trend was non‐significant. Our analysis shows that B. bufo clearly exhibited a converse Bergmann cline along latitudinal gradient, but not along altitudinal gradient; the main effect of elevation was on age. The effects of ecological conditions also differed: body size increased with T_mean, while age parameters were related to the length of activity period. This study highlights that, to identify causal factors underlying general ecogeographical rules, we have to take into account different phases of the life cycle, co‐variation among life history traits and ecological factors acting on each of these traits. In amphibians with complex life cycles, lack of appropriate demographical or ecological data may affect our understanding of the variety of observed body size patterns.     

Elevational gradient and human effects on butterfly species richness in the French Alps

We examined how butterfly species richness is affected by human impact and elevation, and how species ranges are distributed along the elevational gradient (200–2700 m) in the Isère Department (French Alps). A total of 35,724 butterfly observations gathered in summer (May–September) between 1995 and 2015 were analyzed. The number of estimated species per 100‐m elevational band was fitted to the elevational gradient using a generalized additive model. Estimations were also performed on a 500 m × 500 m grid at low altitude (200–500 m) to test for the human impact on species richness using generalized least squares regression models. Each species elevational range was plotted against the elevational gradient. Butterfly richness along the elevational gradient first increased (200–500 m) to reach a maximum of 150 species at 700 m and then remained nearly constant till a sharp decrease after 1900 m, suggesting that after some temperature threshold, only few specialized species can survive. At low elevation, urbanization and arable lands had a strongly negative impact on butterfly diversity, which was buffered by a positive effect of permanent crops. Butterfly diversity is exceptionally high (185 species) in this alpine department that represents less than 5% of the French territory and yet holds more than 70% of all the Rhopalocera species recorded in France. Both climate and habitat shape the distribution of species, with a negative effect of anthropization at low altitude and strong climatic constraints at high altitude.     

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato

Background  

Tomato (Solanum lycopersicon) and potato (S. tuberosum) are two economically important crop species, the genomes of which are currently being sequenced. This study presents a first genome-wide analysis of these two species, based on two large collections of BAC end sequences representing approximately 19% of the tomato genome and 10% of the potato genome.     

Replication levels,false presences and the estimation of the presence/absence from eDNA metabarcoding data

Environmental DNA (eDNA) metabarcoding is increasingly used to study the present and past biodiversity. eDNA analyses often rely on amplification of very small quantities or degraded DNA. To avoid missing detection of taxa that are actually present (false negatives), multiple extractions and amplifications of the same samples are often performed. However, the level of replication needed for reliable estimates of the presence/absence patterns remains an unaddressed topic. Furthermore, degraded DNA and PCR/sequencing errors might produce false positives. We used simulations and empirical data to evaluate the level of replication required for accurate detection of targeted taxa in different contexts and to assess the performance of methods used to reduce the risk of false detections. Furthermore, we evaluated whether statistical approaches developed to estimate occupancy in the presence of observational errors can successfully estimate true prevalence, detection probability and false‐positive rates. Replications reduced the rate of false negatives; the optimal level of replication was strongly dependent on the detection probability of taxa. Occupancy models successfully estimated true prevalence, detection probability and false‐positive rates, but their performance increased with the number of replicates. At least eight PCR replicates should be performed if detection probability is not high, such as in ancient DNA studies. Multiple DNA extractions from the same sample yielded consistent results; in some cases, collecting multiple samples from the same locality allowed detecting more species. The optimal level of replication for accurate species detection strongly varies among studies and could be explicitly estimated to improve the reliability of results.