BUSCADOR RECOLECTA

Sperm DNA fragmentation data Total DNA fragmentation index (tDFI) and high DNA stainability (HDS) results obtained by Sperm Chromatin Structure Assay (SCSA). ALL DATA.xlsx, Sperm competition, a prevalent evolutionary process in which the spermatozoa of two or more males compete for the fertilization of the same ovum, leads to morphological and physiological adaptations, including increases in energetic metabolism that may serve to propel sperm faster but that may have negative effects on DNA integrity. Sperm DNA damage is associated with reduced rates of fertilization, embryo and foetal loss, offspring mortality, and mutations leading to genetic disease. We tested whether high levels of sperm competition affect sperm DNA integrity. We evaluated sperm DNA integrity in 18 species of rodents that differ in their levels of sperm competition using the sperm chromatin structure assay (SCSA). DNA integrity was assessed upon sperm collection, in response to incubation under capacitating or non-capacitating conditions, and after exposure to physical and chemical stressors. Sperm DNA was very resistant to physical and chemical stressors, whereas incubation in non-capacitating and capacitating conditions resulted in only a small increase in sperm DNA damage. Importantly, levels of sperm competition were positively associated with sperm DNA fragmentation across rodent species. This is the first evidence showing that high levels of sperm competition lead to an important cost in the form of increased sperm DNA damage., Peer reviewed

borneo dataset Includes liana and tree species, DBH and host used by lianas across 120 sample plots in primary and logged forest, Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the ‘health’ and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more abundant, had higher species richness and different species compositions in logged than in primary forests. Logged forests showed heavier liana loads disparately affecting slow-growth tree species, which could exacerbate the loss of timber value and carbon storage already associated to logging. Moreover, simulation scenarios of host tree local species loss indicated that logging might decrease the robustness of liana-tree interaction networks if heavily infested trees (i.e. the most connected ones) are more likely to disappear. This effect is partially mitigated in the short term by the colonization of host trees by a greater diversity of liana species within logged forests, yet this might not compensate for the loss of preferred tree hosts in the long term. As a consequence, species interaction networks may show a lagged response to disturbance, which may trigger sudden collapses in species richness and ecosystem function in response to additional disturbances, representing a new type of “extinction debt”., Peer reviewed

Phased DNA sequences and aminoacids This file contains all the phased sequences used in the study, with heterozygous gaps resolved. Fasta containing aminoacids translations are also provided for markers used in MK tests. Phased_DNA_sequences_and_amino_acids.zip Informations about individuals This file contains for each individual included in the study its identifier, its color form/morph, the locality where it was sampled and its sex. Individual_information.xlsx, Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits five plumage color variants that can be grouped into three color forms which occupy discrete geographic regions in the lowlands of Réunion and a fourth form which comprises two color morphs (grey and brown), occurs at high elevation, and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of seven candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin and SLC24A5. Of these seven genes, two (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied may beare involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other non-model species., Peer reviewed

157k_362Loci_align_9plus Nexus file of 362 UCE loci from a minimum of nine individuals, with at least three informative sites. The total alignment is over 157,000 bp. ML tree of Mitogenomes plus UCE outgroups Mitochondrial tree, generated through Maximum Likelihood. Mitogene_Tree_DCSPrior Mitogenome BEAST xml file from this publication. FcC_info FasConCat data partitioning text file. FcC_supermatrix FasConCat supermatrix fasta file. 28ConpleteGeneTrees Subset of 28 UCE loci from complete data matrix. NJst_362LociSpTree Species tree from NJst. 157kUCEs BEAST xml file for 362 UCE loci dataset. 157k_38subsets Zipped folder containing each of the 38 data partitions selected from the k-means algorithm., Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. Results: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace’s line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. Conclusions: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7–12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species., Peer reviewed

list of the samples used in the phylogeny Gives for each sample used in the phylogeny, its ID number, species, subspecies, country and locality of capture, and the Genbank access number of the sequence used. list_of_samples_phylogeny.xlsx CytB sequences psittacula krameri Gives the cytB sequences that were used in the phylogeny. CytB_sequences_psittacula_krameri.xlsx microsatellite data set Gives the microsatellite profiles of each individuals used in the population genetics analyses. msat_data_set_psittacula_krameri.xlsx traditional morphometric measurements Gives the raw morphological measurements taken on individuals from the native and invasive ranges and used in the traditional morphometric analysis. morphometric_data_traditional_psittacula_krameri.xlsx geometric morphometric data Gives the morphological variables taken on individuals from the native and invasive ranges and used in the geometric morphometric analysis. morphometric_data_geometric_psittacula_krameri.xlsx, The Ring-necked parakeet (Psittacula krameri), native of Asia and Africa, is a very successful invasive species in Europe: it has been present there for over 50 years. A recent study showed that European invasive populations occupy a colder climatic niche than in their native range but the establishment of this tropical species in temperate regions remains unexplained. Two main hypotheses may explain the success of Ring-necked parakeet in Europe: admixture between individuals from different origins and/or rapid adaptation to new environmental conditions. In this study, we investigated with molecular data the origin of European populations of Ring-necked parakeets to assess whether these populations result from admixture between individuals from different source populations. We also investigated the morphology of individuals from European populations and from the native range to assess whether the invasive populations have morphologically diverged from their source and could have become adapted to European conditions. We found evidence of admixture in some of the European populations but not all of them. Admixture between individuals from different origins within European populations thus cannot explain alone their invasive success. Conversely, we found that the morphology of the individuals from European populations has diverged from the morphology of native individuals, in a similar direction. Rapid adaptation to European environmental conditions via phenotypic plasticity or natural selection could thus be a factor explaining the invasive success of Ring-necked parakeets in Europe., Peer reviewed

Quercus robur tree genotypes. Genotypes and geographic coordinates for adult Quercus robur trees (n = 135) growing in a 20 km long valley and 684 acorns from 72 mother trees at 20 microsatellite loci. Samples come form 10 distinct oak populations. genotypes.xlsx Phenological data for Quercus oak trees. Data on flowering phenology for oak individual trees in 10 populations for two study years. phenology_data.xlsx, Low-latitudinal range margins of temperate and boreal plant species typically consist of scattered populations that persist locally in microrefugia. It remains poorly understood how their refugial habitats affect patterns of gene flow and connectivity, key components for their long-term viability and evolution. We examine landscape-scale patterns of historical and contemporary gene flow in refugial populations of the widespread European forest tree Pedunculate oak (Quercus robur) at the species' southwestern range margin. We sampled all adult trees (n = 135) growing in a 20 km long valley and genotyped 724 acorns from 72 mother trees at 17 microsatellite loci. The ten oak stands that we identified were highly differentiated and formed four distinct genetic clusters, despite sporadic historical dispersal being detectable. By far most contemporary pollination occurred within stands, either between local mates (85.6%) or through selfing (6.8%). Pollen exchange between stands (2.6%) was remarkably rare given their relative proximity and was complemented by long-distance pollen immigration (4.4%) and hybridization with the locally abundant Quercus pyrenaica (0.6%). The frequency of between-stand mating events decreased with increasing size and spatial isolation of stands. Overall, our results reveal outstandingly little long-distance gene flow for a wind-pollinated tree species. We argue that the distinct landscape characteristics of oaks' refugial habitats, with a combination of a rugged topography, dense vegetation and humid microclimate, are likely to increase plant survival but to hamper effective long-distance pollen dispersal. Moreover, local mating might be favoured by high tree compatibility resulting from genetic purging in these long-term relict populations., Peer reviewed

Dataset_JAppEcol_ALA, Due to reductions in winter food resources, newly sown cereal seeds have become a key component of many bird species' diets, but these seeds are often treated with pesticides that may cause toxic effects. To complete an appropriate risk assessment, data on treated seed toxicity need to be combined with information about the risk of exposure of birds in the field and the factors that modulate such exposure. We studied the abundance of pesticide-treated seeds available for birds in the field, the pesticides and their concentrations in treated seeds, and the bird species observed in the field that were feeding on these pesticide-treated seeds. The exposure of red-legged partridge to treated winter cereal seeds was characterized through the analysis of crop and gizzard contents of hunted individuals (n = 189). Moreover, we measured the contribution of cereal seeds in the autumn–winter diet of partridges in order to assess the potential risk of exposure to pesticide-treated seeds. Density of treated seeds on the soil surface after sowing (11·3 ± 1·2 seeds m−2 in the centre of field and 43·4 ± 5·5 seeds m−2 in the headlands) was enough to provide, in an area between 6 and 50 m2, doses of six active ingredients above those indicating acute (i.e. a dose capable of killing 50% of individuals of a sensitive species) and / or chronic (no observed effect level) toxicity. Up to 30 bird species were observed consuming treated cereal seeds in recently sown fields. Corn bunting was identified as an appropriate focal passerine species for the risk assessment of pesticide-treated seeds. We found that treated seeds were an important route of pesticide ingestion for red-legged partridge; pesticide residues (six fungicides and two insecticides) were found in 32·3% of crops and gizzards. Cereal seeds represented more than half (53·4 ± 4·3%) of total biomass consumed by partridges from October to February. Synthesis and applications. The field exposure data combined with previous studies about the toxicity to partridges of using pesticide-treated seeds point to an unacceptable risk of this practice to farmland birds. Our results suggest that the prophylactic use of pesticide-coated seeds should be avoided, with the approval of this treatment considered on a case-by-case basis and accompanied with specific measures to minimize risks of adverse effects on avian communities., Peer reviewed

Pre- and postcopulatory trait measures Sheet 1: Data. Sheet 2: Variable descriptions Episodes sexsel_DRYADdata.xlsx, When females mate polyandrously, male reproductive success depends both on the male's ability to attain matings and his ability to outcompete rival males in the fertilization of ova post copulation. Increased investment in ejaculate components may trade-off with investment in precopulatory traits due to resource allocation. Alternatively, pre- and postcopulatory traits could be positively related if individuals can afford to invest heavily in traits advantageous at both episodes of selection. There is empirical evidence for both positive and negative associations between pre- and postcopulatory episodes, but little is known about the genetic basis of these correlations. In this study, we measured morphological, chemical, and behavioural precopulatory male traits and investigated their relationship with measures of male fitness (male mating success, remating inhibition and offensive sperm competitiveness) across 40 isofemale lines of Drosophila melanogaster. We found significant variation among isofemale lines, indicating a genetic basis for most of the traits investigated. However, we found weak evidence for genetic correlations between precopulatory traits and our indices of male fitness. Moreover, pre-and postcopulatory episodes of selection were uncorrelated, suggesting selection may act independently at the different episodes to maximise male reproductive success., Peer reviewed

Female mating frequency, P2 and Egg-adult Viability data Sheet 1: Female lifetime mating frequency, Sheet 2: Description of variables contained in Sheet 1. Sheet 3: Focal male P2 and egg-to adult viability data, Sheet 4: Description of variables contained in Sheet 3. sexy-good sperm.xlsx, Polyandry is widespread despite its costs. The sexually selected sperm hypotheses (‘sexy’ and ‘good’ sperm) posit that sperm competition plays a role in the evolution of polyandry. Two poorly studied assumptions of these hypotheses are the presence of additive genetic variance in polyandry and sperm competitiveness. Using a quantitative genetic breeding design in a natural population of Drosophila melanogaster, we first established the potential for polyandry to respond to selection. We then investigated whether polyandry can evolve through sexually selected sperm processes. We measured lifetime polyandry and offensive sperm competitiveness (P2) while controlling for sampling variance due to male x male x female interactions. We also measured additive genetic variance in egg-to-adult viability and controlled for its effect on P2 estimates. Female lifetime polyandry showed significant and substantial additive genetic variance and evolvability. In contrast, we found little genetic variance or evolvability in P2 or egg-to-adult viability. Additive genetic variance in polyandry highlights its potential to respond to selection. However, the low levels of genetic variance in sperm competitiveness suggest the evolution of polyandry may not be driven by sexy sperm or good sperm processes., Peer reviewed

Data for field experiment This is the field data for the manuscript “Condition-dependent trade-offs between sexual traits, body condition and immunity: the effect of novel habitats”. Data was collected by MIC and CC. All methods are described in the associated manuscript. Column headings are described in the excel spreadsheet. Field experiment.xlsx Data from mesocosm experiment This is the mesocosm data for the manuscript “Condition-dependent trade-offs between sexual traits, body condition and immunity: the effect of novel habitats” Data was collected by MIC and CC. All methods are described in the associated manuscript. Column headings are described in the excel spreadsheet. mesocosm experiment.xlsx, Background: The optimal allocation of resources to sexual signals and other life history traits is usually dependent on an individual's condition, while variation in the expression of sexual traits across environments depends on the combined effects of local adaptation, mean condition, and phenotypic responses to environment-specific cues that affect resource allocation. A clear contrast can often be drawn between natural habitats and novel habitats, such as forest plantations and urban areas. In some species, males seem to change their sexual signals in these novel environments, but why this occurs and how it affects signal reliability is still poorly understood. Results: The relative size of sexual traits and level of immune responses were significantly lower for male palmate newts Lissotriton helveticus caught in pine and eucalyptus plantations compared to those caught in native forests, but there was no habitat-dependent difference in body condition (n= 18 sites, 382 males). The reliability with which sexual traits signalled body condition and immune responses was the same in all three habitats. Finally, we conducted a mesocosm experiment in which males were maintained in pine, eucalypt or oak infused water for 21 days. Males in plantation-like water (pine or eucalypt) showed significantly lower immune responses but no change in body condition. This matches the pattern seen for field-caught males. Unlike field-caught males, however, there was no relationship between water type and relative sexual trait size. Conclusions: Pine and eucalyptus plantations are likely to be detrimental to male palmate newt because they are associated with reduced immune function and smaller sexual traits. This could be because ecological aspects of these novel habitats, such as high water turbidity or changes in male-male competition, drive selection for reduced investment into sexual traits. However, it is more probable that there are differences in the ease of acquisition, hence optimal allocation, of resources among habitats. Our mesocosm experiment also provides some evidence that water toxicity is a causal factor. Our findings offer insights into how plantations affect amphibian life histories, and how novel habitats might generate long-term selection for new resource allocation strategies in native species., Peer reviewed