Responses of a native and a recent invader snail to warming and dry conditions: the case of the lower Ebro River

Aquatic habitats have been highly modified by human actions that reduce their native diversity and create conditions suitable for tolerant alien species. Pomacea maculata was detected in 2009 in both the alluvial plain and the final stretch of the Ebro River. Since then, a permanent population has stabilized in the littoral area of the river where the water level fluctuates according to the river discharge. Melanopsis tricarinata is an endemic snail species highly affected by the reduction in its natural habitat. Currently, the two species do not share the same reaches in the river, but the possibility exists, as the distribution of the P. maculata is constantly increasing. This study aims to analyse the diets and to assess the responses of both snails to global change. The diet of both species was analysed in the field and their responses to water warming and dryness compared under laboratory conditions. This study includes the calculation of future river water temperatures based on air temperature projections. In addition, based on water discharge management scenarios, the study estimated the increase in dry river bed area. The diet of both snail species was similar and based on Cladophora. P. maculata better resisted high temperatures and dry conditions than M. tricarinata. The projections of water temperatures showed an increase in daily temperatures, especially in summer. The hydraulic model suggested that a relevant increase in dry river bed areas will occur. Overall, these results provide insight into the global change factors that could favour P. maculata spread in the river and the reduction in suitable habitat for M. tricarinata and will be useful for future decisions of water discharge management

Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA

There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and specieswide genetic diversity among other signs of genomic erosion. We analyze ancient (N¼10), historical (N¼245), and contemporary (N¼172) samples with microsatellite and mitogenome data to reconstruct the species’ demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. Results: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. Conclusions: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species

Searching for DNA in museum specimens: a comparison of sources in a mammal species

The number of genetic studies that use preserved specimens as sources of DNA has been steadily increasing during the last few years. Therefore, selecting the sources that are more likely to provide a suitable amount of DNA of enough quality to be amplified and at the min- imum cost to the original specimen is an important step for future research. We have com- pared different types of tissue (hides vs. bones) from museum specimens of Iberian lynx and multiple alternative sources within each type (skin, footpad, footpad powder, claw, diaphy- sis, maxilloturbinal bone, mastoid process and canine) for DNA yield and probability of amplification of both mitochondrial and nuclear targets. Our results show that bone samples yield more and better DNA than hides, particularly from sources from skull, such as mastoid process and canines. However, claws offer an amplification success as high as bone sources, which makes them the preferred DNA source when no skeletal pieces have been preserved. Most importantly, these recommended sources can be sampled incurring minimal damage to the specimens while amplifying at a high success rate for both mitochondrial and microsatel- lite markers.Peer reviewe

The relevance of environment vs. composition on dissolved organic matter degradation in freshwaters

Dissolved organic matter (DOM) composition exerts a direct control on its degradation and subsequent persistence in aquatic ecosystems. Yet, under certain conditions, the degradation patterns of DOM cannot be solely explained by its composition, highlighting the relevance of environmental conditions for DOM degradation. Here, we experimentally assessed the relative influence of composition vs. environment on DOM degradation by performing degradation bioassays using three contrasting DOM sources inoculated with a standardized bacterial inoculum under five distinct environments. The DOM degradation kinetics modeled using reactivity continuum models showed that composition was more important than environment in determining the bulk DOM decay patterns. Changes in DOM composition resulted from the interaction between DOM source and environment. The role of environment was stronger on shaping the bacterial community composition, but the intrinsic nature of the DOM source exerted stronger control on the DOM degradation function

Delineating the Continuum of Dissolved Organic Matter in Temperate River Networks

The origin and reactivity of dissolved organic matter (DOM) have received attention for decades due to the key role DOM plays in global carbon cycling and the ecology of aquatic systems. However, DOM dynamics in river networks remain unresolved, hampered by the lack of data integrating the spatial and temporal dimensions inherent to riverine ecosystems. Here we examine the longitudinal patterns of dissolved organic carbon (DOC) concentration and DOM chemical diversity along a temperate river network under different hydrological conditions, encompassing small headwater streams to the river mouth and base flow to storm events. We show that, during nonstorm conditions, the concentration of DOC and the chemical diversity of DOM exhibit their maxima in the middle section of the network, depicting a bell-shaped pattern along the river continuum. In contrast, DOM shows a homogeneous longitudinal pattern during storm events, with highly concentrated and diverse DOM along the river network. We posit that these emerging patterns result from changes in the relative influence of catchment versus in-stream biogeochemical processes along the river continuum and that the degree of influence is modulated by river network hydrology. Based on these findings we put forward the "Bending DOM Concept," a new conceptual framework around which testable hypotheses on the spatiotemporal dynamics of DOM and the functioning of temperate river networks may be formulated

Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

[Background] Demographic bottlenecks erode genetic diversity and may increase endangered species’ extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus.[Results] The Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels.[Conclusions] Species-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.Funding for this project was provided by the Spanish Dirección General de Investigación Científica y Técnica (CGL2010–21540/BOS and CGL2013–47755-P), project "Adaptive variation in declining species: Survey of MHC variation in Eurasian lynx populations at the western edge of its range" funded by the internal EBD proposal call “Microproyectos” financed by the Spanish Ministry of Economy and Competitiveness, through the Severo Ochoa Program for Centres of Excellence in R + D + I (SEV-2012-0262), and project 2014/15/B/NZ8/00212 funded by the National Science Center, Poland. Elena Marmesat received a JAE predoctoral grant from CSIC (Spanish National Research Council). We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).Peer reviewe