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opencc-zeroDec 2015View details →

Data from: Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data

Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LiDAR and SONAR data sets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from southeastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genomewide SNP markers, we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LiDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.

Data from: Contrasting impacts of land use change on phylogenetic and functional diversity of tropical forest birds

1.Biodiversity conservation strategies increasingly target maintaining evolutionary history and the resilience of ecosystem function, not just species richness (SR). This has led to the emergence of two metrics commonly proposed as tools for decision making: phylogenetic diversity (PD) and functional diversity (FD). Yet the extent to which they are interchangeable remains poorly understood. 2.We explore shifts in and relationships between FD and PD of bird communities across a disturbance gradient in Borneo, from old-growth tropical forest to oil palm plantation. 3.We show a marked decline in PD, and an increase in phylogenetic mean nearest taxon distance (MNTD) from forest to oil palm, in line with declining SR across the gradient. However, phylogenetic mean pairwise distance (MPD) is constrained by forest logging more than by conversion to oil palm, taking account of SR. 4.The decline in FD across the gradient is less severe than in PD, with all metrics indicating relatively high trait diversity in oil palm despite low SR, although functional redundancy is much reduced. Accounting for SR, levels of functional over- or under-dispersion of bird communities are strongly coupled to habitat disturbance level rather than to any equivalent phylogenetic metric. 5.Policy Implications. We suggest that while phylogenetic diversity (PD) is an improvement on species richness as a proxy for functional diversity (FD), conservation decisions based on PD alone cannot reliably safeguard maximal FD. Thus, PD and FD are related but still complementary. Priority setting exercises should use these metrics in combination to identify conservation targets.

Data from: Heat tolerance in Drosophila subobscura along a latitudinal gradient: contrasting patterns between plastic and genetic responses

Susceptibility to global warming relies on how thermal tolerances respond to increasing temperatures through plasticity or evolution. Climatic adaptation can be assessed examining the geographic variation in thermal-related traits. We studied latitudinal patterns in heat tolerance in Drosophila subobscura reared at two temperatures. We used four static stressful temperatures to estimate the thermal death time curves (TDT), and two ramping assays with fast and slow heating rates. TDT curves allow estimating the critical thermal maximum CTmax, by extrapolating to the temperature that would knockdown the flies almost 'instantaneously', and the thermal sensitivity to increasing stressful temperatures. We found a positive latitudinal cline for CTmax, but no clinal pattern for knockdown temperatures estimated from the ramping assays. Although high-latitude populations were more tolerant to an acute heat stress, they were also more sensitive to prolonged exposure to less stressful temperatures, supporting a trade-off between acute and chronic heat tolerances. Conversely, developmental plasticity did not affect CTmax but increased the tolerance to chronic heat exposition. The patterns observed from the TDT curves help to understand why the relationship between heat tolerance and latitude depends on the methodology used and, therefore, these curves provide a more complete and reliable measurement of heat tolerance.

Data from: Contrasting responses of male and female foraging effort to year-round wind conditions

1. There is growing interest in the effects of wind on wild animals, given evidence that wind speeds are increasing and becoming more variable in some regions, particularly at temperate latitudes. Wind may alter movement patterns or foraging ability, with consequences for energy budgets and, ultimately, demographic rates. 2. These effects are expected to vary among individuals due to intrinsic factors such as sex, age or feeding proficiency. Furthermore, this variation is predicted to become more marked as wind conditions deteriorate, which may have profound consequences for population dynamics as the climate changes. However, the interaction between wind and intrinsic effects has not been comprehensively tested. 3. In many species, in particular those showing sexual size dimorphism, males and females vary in foraging performance. Here, we undertook year-round deployments of data loggers to test for interactions between sex and wind speed and direction on foraging effort in adult European shags Phalacrocorax aristotelis, a pursuit-diving seabird in which males are c. 18% heavier. 4. We found that foraging time was lower at high wind speeds but higher during easterly (onshore) winds. Furthermore, there was an interaction between sex and wind conditions on foraging effort, such that females foraged for longer than males when winds were of greater strength (9% difference at high wind speeds vs. 1% at low wind speeds) and when winds were easterly compared with westerly (7% and 4% difference, respectively). 5. The results supported our prediction that sex-specific differences in foraging effort would become more marked as wind conditions worsen. Since foraging time is linked to demographic rates in this species, our findings are likely to have important consequences for population dynamics by amplifying sex-specific differences in survival rates.

opencc-zeroDec 2012View details →

Data from: Foliar nutrient concentrations and resorption efficiency in plants of contrasting nutrient-acquisition strategies along a 2-million year dune chronosequence

1. Long-term pedogenesis leads to important changes in the availability of soil nutrients, especially nitrogen (N) and phosphorus (P). Changes in the availability of micronutrients can also occur, but are less well understood. We explored whether changes in leaf nutrient concentrations and resorption were consistent with a shift from N to P limitation of plant productivity with soil age along a >2-million year dune chronosequence in south-western Australia. We also compared these traits among plants of contrasting nutrient-acquisition strategies, focusing on N, P and micronutrients. 2. The range in leaf [P] for individual species along the chronosequence was exceptionally large for both green (103–3000 μg P g-1) and senesced (19–5600 μg P g-1) leaves, almost equalling that found globally. From the youngest to the oldest soil, cover-weighted mean leaf [P] declined from 1840 to 228 μg P g-1, while P-resorption efficiency increased from 0% to 79%. All species converged towards a highly conservative P-use strategy on the oldest soils. 3. Declines in cover-weighted mean leaf [N] with soil age were less strong than for leaf [P], ranging from 13.4 mg N g-1 on the youngest soil to 9.5 mg N g-1 on the oldest soil. However, mean leaf N-resorption efficiency was greatest (45%) on the youngest, N-poor soils. Leaf N:P ratio increased from 8 on the youngest soil to 42 on the oldest soil. 4. Leaf zinc (Zn) concentrations were low across all chronosequence stages, but mean Zn-resorption efficiency was greatest (55–74%) on the youngest calcareous dunes, reflecting low Zn availability at high pH. 5. N2-fixing species had high leaf [N] compared with other species. Non-mycorrhizal species had very low leaf [P] and accumulated Mn across all soils. We surmise that this reflects Mn solubilisation by organic acids released for P acquisition. 6. Synthesis. Our results show community-wide variation in leaf nutrient concentrations and resorption that is consistent with a shift from N to P limitation during long-term ecosystem development. High Zn resorption on young calcareous dunes supports the possibility of micronutrient co-limitation. High leaf [Mn] on older dunes suggests the importance of carboxylate release for P acquisition. Our results show a strong effect of soil nutrient availability on nutrient-use efficiency, and reveal considerable differences among plants of contrasting nutrient-acquisition strategies.

Data from: Contrasting ecological roles of non-native ungulates in a novel ecosystem

Conservation has long focused on preserving or restoring pristine ecosystems. However, understanding and managing novel ecosystems has grown in importance as they outnumber pristine ecosystems worldwide. While non-native species may be neutral or detrimental in pristine ecosystems, it is possible that even notorious invaders could play beneficial or mixed roles in novel ecosystems. We examined the effects of two long-established non-native species – Philippine deer (Rusa marianna) and feral pigs (Sus scrofa) – in Guam, Micronesia, where native vertebrate frugivores are functionally absent leaving forests devoid of seed dispersers. We compared the roles of deer and pigs on seedling survival, seed dispersal, and plant community structure in limestone karst forests. Deer, even at low abundances, had pronounced negative impacts on forest communities by decreasing seedling and vine abundance. In contrast, pigs showed no such relationship, and more seeds were found in pig scats than deer scats, suggesting that pigs provide an ecosystem function – seed dispersal – that has been lost from Guam. Our study presents a surprising discrepancy between the roles of two non-native species that are traditionally managed as a single entity, suggesting that ecological function, rather than identity as a non-native, may be more important to consider in managing novel systems.

opencc-zeroDec 2012View details →

Data from: Dispersal in a patchy landscape reveals contrasting determinants of infection in a wild avian malaria system

1. Understanding exactly when, where and how hosts become infected with parasites is critical to understanding host-parasite coevolution. However, for host-parasite systems in which hosts or parasites are mobile (for example vector-borne diseases), the spatial location of infection, and the relative importance of parasite exposure at successive host life-history stages, are often uncertain. 2. Here, using a six-year longitudinal dataset from a spatially referenced population of blue tits, we test the extent to which infection by avian malaria parasites is determined by conditions experienced at natal or breeding sites, as well as by postnatal dispersal between the two. 3. We show that the location and timing of infection differs markedly between two sympatric malaria parasite species. For one species (P. circumflexum), our analyses indicate that infection occurs after birds have settled on breeding territories, and because the distribution of this parasite is temporally stable, hosts could in principle alter their exposure and potentially avoid infection through postnatal dispersal. Conversely, the spatial distribution of another parasite species (P. relictum) is unpredictable, and infection probability is positively associated with postnatal dispersal distance, potentially indicating that infection occurs during this major dispersal event. 4. These findings suggest that hosts in this population may be subject to divergent selection pressures from these two parasites, potentially acting at different life-history stages. Because this implies parasite species-specific predictions for many coevolutionary processes, they also illustrate the complexity of predicting such processes in multi-parasite systems.

Data from: Lack of evolution in a leaf beetle that lives on two contrasting host plants

The interactions between plant-eating insects and their hosts have shaped both the insects and the plants, driving evolution of plant defenses and insect specialization. The leaf beetle Trirhabda eriodictyonis (Chrysomelidae) lives on two shrubs with differing defenses: Eriodictyon crassifolium has hairy leaves, whereas E. trichocalyx has resinous leaves. We tested whether these beetles have differentiated onto the two host plants, and if not, whether the beetles prefer the better host plant and prefer mates who are from that host plant. In feeding tests, adult beetles strongly preferred eating E. trichocalyx regardless of which host they came from. In addition, females laid more eggs if they ate E. trichocalyx than E. crassifolium. So, E. trichocalyx is generally the better host. However, beetle mate preference was not in line with food choice. Males did not prefer to mate with females from E. trichocalyx. Females from E. crassifolium did prefer males from E. trichocalyx over males from E. crassifolium, but did not lay more eggs as a result of these matings. We conclude that the beetle populations we studied have not differentiated based on their host plants and may not have even adapted to the better host. Although to humans these host plant defenses differ dramatically, signs that they have caused evolution in the beetles are lacking. The case of T. eriodictyonis stands counter to many other studies that have seen the differentiation of ecotypes and/or adaptive coordination of an herbivore's life cycle based on host plant differences.

opencc-zeroDec 2018View details →

Data from: Recent decadal drought reverts warming–triggered growth enhancement in contrasting climates in the southern Andes treeline

Aims: Rising temperature and declining summer precipitation due to the 1970s-climate shift in southern South America have reduced forest productivity at dry sites. Here, we worked with the most widespread Southern Hemisphere treeline species, Nothofagus pumilio, across contrasting climatic conditions and determined whether rising atmospheric CO2 concentrations as well as warmer and drier climatic conditions provoked by the 70s-climatic shift have been causing systematic changes in treeline growth rates and intrinsic water-use efficiency (iWUE).Location: 36–54° S, southern Andes. Time period: 1950–2010. Major taxa studied: Nothofagus pumilio. Methods: We worked at five disparate climatic treeline locations, spanning 18 degrees of latitude; at each location, we sampled trees at four different elevations, including treeline elevation. We quantified the variation of annual tree-ring width (TRW) as a function of climate, elevation, tree age, size, annual CO2 concentrations, and location, using linear mixed-effects models and interpreted TRW trends in relation to iWUE and isotope (δ13C and δ18O) signalling. Results: Across locations, the patterns of treeline growth occurring in the 1980–2010 period exhibited a clear and significant negative trend, in contrast to the previous 1950–1980 period. We found an increase of iWUE and δ18O across time and locations. Given that an increase in δ18O indicates a decrease in stomatal conductance, we assert that drought-induced stomatal closure appears to be causing the reduction in growth. Main conclusions: We show unequivocal evidence that warmer and drier summer conditions translated into a decrease of growth rates along the elevational treeline of the southern Andes, reverting previous growth improvements linked to climate warming. An improvement in iWUE at all locations is most likely explained by decreased stomatal conductance given the rising δ18O signal. An iWUE–growth decoupling may act as an ecological strategy to respond to drought.

Data from: Do neophobia and dietary wariness explain ecological flexibility? An analysis with two seed-eating birds of contrasting habits

The neophobia threshold hypothesis (NTH) suggests that the acquisition and maintenance of a high behavioral and ecological flexibility in the evolutionary and adaptive history of a species is the consequence of lower levels of neophobia towards new micro-habitats and of dietary wariness of novel foods. To test this idea we assessed the degree of neophobia and dietary wariness in two seed-eating bird species with contrasting degrees of ecological flexibility that inhabit the central Monte desert (Argentina): a grass-seed specialist, the many-colored chaco-finch, and a generalist feeder, the rufous-collared sparrow. We expected that both species would exhibit neophobia and wariness when faced with new foraging opportunities but that the rufous-collared sparrow would be less neophobic and less wary than the specialized many-colored chaco-finch. Experimental indicators of neophobia and dietary wariness included willingness to eat near novel objects and willingness to eat novel seeds, respectively. Both species showed similar levels of reluctance to novelty, although the sparrow could be slightly more reluctant than the finch. Contrary to our predictions, the sparrow was neither less hesitant nor faster or greedier than the finch. This experimental evidence does not support a negative relationship between neophobia/wariness and ecological flexibility in these two seed-eating birds and it coincides with the growing evidence that challenges the NTH. Some of our results provide support for the dangerous niche hypothesis, especially as the rufous-collared sparrow, that feeds on more diverse and potentially dangerous food, showed higher levels of neophobia in some cases. Although the idea of neophobia and wariness being plausible causes of ecological specialization sounds attractive, the current situation calls for further research so that the causes of ecological flexibility in granivorous birds can be better understood.

Data from: Biotic and climatic velocity identify contrasting areas of vulnerability to climate change

Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation. The most commonly used of such metrics is the velocity of climate change, which estimates the speed at which species must migrate over the earth's surface to maintain constant climatic conditions. However, "analog-based" velocities, which represent the actual distance to where analogous climates will be found in the future, may provide contrasting results to the more common form of velocity based on local climate gradients. Additionally, whereas climatic velocity reflects the exposure of organisms to climate change, resultant biotic effects are dependent on the sensitivity of individual species as reflected in part by their climatic niche width. This has motivated development of biotic velocity, a metric which uses data on projected species range shifts to estimate the velocity at which species must move to track their climatic niche. We calculated climatic and biotic velocity for the Western Hemisphere for 1961–2100, and applied the results to example ecological and conservation planning questions, to demonstrate the potential of such analog-based metrics to provide information on broad-scale patterns of exposure and sensitivity. Geographic patterns of biotic velocity for 2954 species of birds, mammals, and amphibians differed from climatic velocity in north temperate and boreal regions. However, both biotic and climatic velocities were greatest at low latitudes, implying that threats to equatorial species arise from both the future magnitude of climatic velocities and the narrow climatic tolerances of species in these regions, which currently experience low seasonal and interannual climatic variability. Biotic and climatic velocity, by approximating lower and upper bounds on migration rates, can inform conservation of species and locally-adapted populations, respectively, and in combination with backward velocity, a function of distance to a source of colonizers adapted to a site's future climate, can facilitate conservation of diversity at multiple scales in the face of climate change.

Data from: Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes

The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it is necessary to first understand how environmental factors affect their expression and success. We used otolith 87Sr/86Sr in adult Chinook salmon (Oncorhynchus tshawytcha) returning to the Stanislaus River in the California Central Valley (USA) to reconstruct the sizes at which they outmigrated as juveniles in a wetter (2000) and drier (2003) year. We compared rotary screw trap-derived estimates of outmigrant timing, abundance and size with those reconstructed in the adults from the same cohort. This allowed us to estimate the relative survival and contribution of migratory phenotypes (fry, parr, smolts) to the adult spawning population under different flow regimes. Juvenile abundance and outmigration behavior varied with hydroclimatic regime, while downstream survival appeared to be driven by size- and time-selective mortality. Although fry survival is generally assumed to be negligible in this system, >20% of the adult spawners from outmigration year 2000 had outmigrated as fry. In both years, all three phenotypes contributed to the spawning population, however their relative proportions differed, reflecting greater fry contributions in the wetter year (23% vs. 10%) and greater smolt contributions in the drier year (13% vs. 44%). These data demonstrate that the expression and success of migratory phenotypes vary with hydrologic regime, emphasizing the importance of maintaining diversity in a changing climate.

opencc-zeroAug 2019View details →

Data from: Plasticity through canalization: the contrasting effect of temperature on trait size and growth in Drosophila

In most ectotherms, a reduction in developmental temperature leads to an increase in body size, a phenomenon known as the temperature size rule (TSR). In Drosophila melanogaster, temperature affects body size primarily by affecting critical size, the point in development when larvae initiate the hormonal cascade that stops growth and starts metamorphosis. However, while the thermal plasticity of critical size can explain the effect of temperature on overall body size, it cannot entirely account for the effect of temperature on the size of individual traits, which vary in their thermal sensitivity. Specifically, the legs and male genitalia show reduced thermal plasticity for size, while the wings show elevated thermal plasticity, relative to overall body size. Here, we show that these differences in thermal plasticity among traits reflect, in part, differences in the effect of temperature on the rates of cell proliferation during trait growth. Counterintuitively, the elevated thermal plasticity of the wings is due to canalization in the rate of cell proliferation across temperatures. The opposite is true for the legs. These data reveal that environmental canalization at one level of organization may explain plasticity at another, and vice versa.

Data from: Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands

The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.

opencc-zeroJun 2019View details →

Data from: Seasonality in spatial distribution: climate and land use have contrasting effects on the species richness of breeding and wintering birds

Aim: Many studies have examined large-scale distributions of various taxa and their drivers, emphasizing the importance of climate, topography, and land-use. Most studies have dealt with distributions over a single season or annually without considering seasonality. However, animal distributions and their drivers can differ among seasons because many animals migrate to suitable climates and areas with abundant prey resources. We aim to clarify seasonality in bird distributions and their drivers. Location: Japan. Methods: We examined the effects of climate (annual mean temperature, snow depth), topography (elevation), and land use (extent of surrounding habitat) on bird species richness, in the breeding and wintering seasons separately, using nationwide data (254 forest and 43 grassland sites, respectively). We separately analyzed the species richness of all species, residents, short-, and long-distance migrants in forests and grasslands. Results: In the breeding season, the annual mean temperature negatively affected all groups (except for forest and grassland residents), and the extent of surrounding habitat positively affected many groups. By contrast, in the wintering season, temperature positively affected all groups (except for forest residents), and the extent of surrounding habitat positively affected only grassland long-distance migrants. In both seasons, the species richness of forest and grassland residents was high in regions of moderate and high temperature, respectively. Moreover, snow depth negatively affected all forest groups in the wintering season. Mapping expected species richness suggested that regions with different climates served as habitats for different groups during different seasons. Main conclusions: All regions were important bird habitats depending on the season, reflecting the contrasting effects of temperature across seasons. In the breeding season, surrounding land-use was also an important driver. To understand the seasonal role that each region and environment plays in maintaining species/communities, a large-scale study considering both environmental seasonality and species distribution is needed.

opencc-zeroDec 2017View details →

Data from: Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence and long-distance dispersal in North American palms

Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genome-wide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognised species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genome-wide divergence mediated by multiple effectors.

Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities

Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near-pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near-pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near-pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near-pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near-pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche-based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β-diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.

opencc-zeroDec 2018View details →

Data from: Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

Understanding the genetic basis of local adaptation has long been the focus of evolutionary biology. Recently there has been increased interest in deciphering the evolutionary role of Daphnia's plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences within and between four European Daphnia galeata populations. To distinguish neutral from adaptive differentiation, we corrected for phylogenetic differentiation of Daphnia populations. We also applied a "transcriptome scan" approach to investigate the role of natural selection in shaping divergent expression profiles among populations. Furthermore, a SNP analysis allowed inferring population structure and the distribution of genetic variation. Using sequence information, the transcripts were annotated using a comparative genomics approach. In total, ~33% of 32903 transcripts were differentially expressed between populations. Among 10280 differentially expressed transcripts, 5209 transcripts deviated from neutral expectations and were likely involved in local adaptation. The population divergence at the sequence level was higher than at the gene expression level by several orders of magnitude and revealed very distinct clusters according to population origin. Our analysis revealed the respective roles of genetic drift and selection in the four Daphnia populations. This study is a first attempt to understand the genetic background of adaptation to environmental changes in a key species of aquatic ecosystems in absence of any laboratory induced stressor.

Data from: Contrasting habitat and landscape effects on the fitness of a long-lived grassland plant under forest encroachment: do they provide evidence for extinction debt?

1. Habitat loss, fragmentation and transformation threaten the persistence of many species worldwide. Population and individual fitness are often compromised in small, degraded and isolated habitats, but extinction can be a slow process and extinction debts are common. 2. Long-lived species are prone to persist as remnant populations in low quality habitats for a long time, but the population and individual-level mechanisms of extinction debt remain poorly explored so far. 3. We here investigate the mechanisms involved in the long-term persistence of the common grassland specialist, long-lived, clonal plant Aphyllanthes monspeliensis L. (Asparagaceae). after forest encroachment into semi-natural Mediterranean calcareous grasslands in Catalonia (NE Iberian Peninsula). For this purpose we assess vegetative (aboveground and belowground) and reproductive plant performance indicators and their habitat and landscape (current and historical) drivers. 4. We confirm the existence of an extinction debt for this species, since current plant frequency is related to historical but not current connectivity, and we also find a positive effect of historical connectivity on seed set. In addition, current tree cover negatively affects individual size and aboveground/belowground biomass ratio, and biotic soil acidification leads to a reduction in the flowering probability of individuals and stems. 5. However, we also find that current connectivity negatively affects flowering and that tree cover enhances seed set. The forestation process, thus, also exerts a positive effect on some fitness traits, probably by providing a moister environment. 6. Synthesis. Habitat loss and deterioration result in a decreased vegetative performance of Aphyllanthes monspeliensis, a grassland specialist, but show contrasting effects on its reproductive performance. However, further forest encroachment would increase light competition and soil acidification, threatening its persistence and promoting the payment of the extinction debt if no conservation measures are taken.