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Euphorbia nicaeensis AFLP data matrix AFLP genotypes for E. nicaeensis individuals in 40 plots. "Open" refers to plots of non-facilitated individuals, while "Facilit" refers to plots of individuals growing under Juniperus sabina shrubs. Rows correspond to individual plants, while columns are the 112 loci genotyped. This is a tab-delimited text file. Euphorbia.nicaeensis.AFLP.data.txt, Plant facilitation is a positive interaction where a nurse or nurse plant community alters the local conditions, improving the life-time fitness of other beneficiary plants. In stressful environments, a common consequence is the formation of discrete vegetation patches under nurse plants, surrounded by open space. The consequences of such spatial patterns have been studied mostly at the community level. At the population level, facilitation causes a distribution of beneficiary individuals that could have intra-specific genetic consequences. The spatial patchiness and the increase in local aggregation can potentially affect the population fine-scale genetic structure. In addition, marked microenvironmental differences under nurses versus outside could lead to plastic phenotypic variation between facilitated and non-facilitated individuals, as for example reproductive asynchrony, potentially producing assortative mating. This study tests the hypothesis that plant facilitation can have genetic consequences for the population of a beneficiary plant (Euphorbia nicaeensis) by affecting its spatial genetic structure and mating patterns between subpopulations of facilitated and non-facilitated individuals. Facilitation in this system creates an aggregated distribution of beneficiary individuals compared to a minority of non-facilitated individuals that grow on the open ground. Facilitation also leads to slight phenological differences mediated by strong microenvironmental differences created by nurses compared to the open ground. Yet a molecular analysis showed that, although there is fine scale spatial genetic structure in this system, there is no evidence that it is caused by facilitation. Numerical simulations further showed that spatial genetic patterns in the population are little influenced by the phenological mismatch observed in the field. Synthesis. Facilitation leads to the strong spatial aggregation of beneficiary plants and desynchronizes their flowering phenology, but the magnitude of these effects is not enough to have local genetic consequences in our study system. Facilitation seems thus to have a homogenizing role by allowing the persistence of a diverse gene pool in populations in harsh environments, rather than fomenting genetic differentiation. Further information on other systems where facilitation produces stronger spatial or phenological effects on facilitated plants is needed to fill the large knowledge gap we have on the genetic effects of facilitation., Peer reviewed

Gabon_dryad_fish_data Data description: Date – MM/DD/YYYY ; Reef – Gabon ; STATION – Rig1……Rig10 ; Latitude – Decimal degrees, WGS 1984 ; Longitude - Decimal degrees, WGS 1984 ; Depth_m- depth in meters ; Depth_stratum - DIVER – AMF = Alan Friedlander ; TRANSECT = A, B, C, D ; Taxon – lowest possible scientific name ; num_m^2 – numerical abundance in number per meter squared ; g_m^2 – biomass in grams per meter squared, The marine biodiversity of Gabon, West Africa has not been well studied and is largely unknown. Our examination of marine communities associated with oil platforms in Gabon is the first scientific investigation of these structures and highlights the unique ecosystems associated with them. A number of species previously unknown to Gabonese waters were recorded during our surveys on these platforms. Clear distinctions in benthic communities were observed between older, larger platforms in the north and newer platforms to the south or closer to shore. The former were dominated by a solitary cup coral, Tubastraea sp., whereas the latter were dominated by the barnacle Megabalanus tintinnabulum, but with more diverse benthic assemblages compared to the northerly platforms. Previous work documented the presence of limited zooxanthellated scleractinian corals on natural rocky substrate in Gabon but none were recorded on platforms. Total estimated fish biomass on these platforms exceeded one ton at some locations and was dominated by barracuda (Sphyraena spp.), jacks (Carangids), and rainbow runner (Elagatis bipinnulata). Thirty-four percent of fish species observed on these platforms are new records for Gabon and 6% are new to tropical West Africa. Fish assemblages closely associated with platforms had distinct amphi-Atlantic affinities and platforms likely extend the distribution of these species into coastal West Africa. At least one potential invasive species, the snowflake coral (Carijoa riisei), was observed on the platforms. Oil platforms may act as stepping stones, increasing regional biodiversity and production but they may also be vectors for invasive species. Gabon is a world leader in terrestrial conservation with a network of protected areas covering >10% of the country. Oil exploration and biodiversity conservation currently co-exist in terrestrial and freshwater ecosystems in Gabon. Efforts to increase marine protection in Gabon may benefit by including oil platforms in the marine protected area design process., Peer reviewed

Rodent DRB Alleles from Asia Dataset of MHC class II DRB exon 2 allele sequences from rodents sampling in Thailand, Laos and Cambodia. The name of alleles include the species ID: Bain for Bandicota indica ; Basa for Bandicota savilei ; Bebe for Berylmys berdmorei ; Bebo for Berylmys bowersi ; Leed for Leopoldamys edwardsi ; Muca for Mus caroli ; Muce for Mus cervicolor ; Muco for Mus cookii ; Raex for Rattus exulans ; Rasa for Rattus sakaratensis ; Rata for Rattus tanezumi ; RaR3 for Rattus tanezumi mitochondrial lineage R3 454 raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 1 This FASTA file contains 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv. 454_Reads_DRB_Asia_Run1.fasta 454 quality scores of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 1 This file contains the quality scores for the 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv. 454_Reads_DRB_Asia_Run1.qual.txt 454 reads of the MHC class II DRB exon 2 gene from rodents including a correction for the reverse tags - Run 1 This FASTA file contains 91,467 raw sequences produced using 454 GS-FLX pyrosequencing (first run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The reverse tags forming a homopolymer GG with the "454-Adaptor" sequence were truncated. This file contains the raw sequences corrected (addition of a G at the end of the reads) for the concerned tags. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run1.csv. 454_Reads_DRB_Asia_Run1_G_add_in_Rev_Tags.fasta Information concerning the samples multiplexed in the 454 Run 1 This SESAME software formatted file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name, the population name and the ploidy level for each of the 864 samples multiplexed in the 454 pyrosequencing run 1. 454_Reads_DRB_Asia_Run1.csv 454 raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2 This FASTA file contains 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run2.csv. 454_Reads_DRB_Asia_Run2.fasta 454 quality scores of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2 This file contains the quality scores for the 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 864 multiplexed samples and associated tags are provided in the following file: 454_Reads_DRB_Asia_Run2.csv. 454_Reads_DRB_Asia_Run2.qual Information concerning the samples multiplexed in the 454 Run 2 This SESAME software formatted file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name, the population name and the ploidy level for each of the 864 samples multiplexed in the 454 pyrosequencing run 2. 454_Reads_DRB_Asia_Run2.csv 454 standard flowgram format (SFF) file of the raw sequences of the MHC class II DRB exon 2 gene from rodents - Run 2 This SFF file contains the encoded results of each flowgram for the 272,975 raw sequences produced using 454 GS-FLX Titanium pyrosequencing (second run). The 864 multiplexed amplicons were tagged using both forward and reverse primers. Note: The SFF file for the run 1 is not available (not provide by the sequencing company). 454_Reads_DRB_Asia_Run2.sff, Genes of the major histocompatibility complex (MHC) encode proteins that recognize foreign antigens and are thus crucial for immune response. In a population of a single host species, parasite-mediated selection drives MHC allelic diversity. However, in a community-wide context, species interactions may modulate selection regimes because the prevalence of a given parasite in a given host may depend on its prevalence in other hosts. By combining network analysis with immunogenetics, we show that host species infected by similar parasites harbour similar alleles with similar frequencies. We further show, using a Bayesian approach, that the probability of mutual occurrence of a functional allele and a parasite in a given host individual is nonrandom and depends on other host–parasite interactions, driving co-evolution within subgroups of parasite species and functional alleles. Therefore, indirect effects among hosts and parasites can shape host MHC diversity, scaling it from the population to the community level., Peer reviewed

Survey results and feeding experiment data All fish and benthos (algae and invertebrate) survey data and results from feeding assays. All data collected in the field. data_Verges_Tomas_etalJEcol.xlsx, A striking example of climate-mediated range shifts in marine systems is the intrusion of tropical species into temperate areas worldwide, but we know very little about the ecological consequences of these range expansions. In the Mediterranean Sea, the range expansion of tropical rabbitfishes that first entered the basin via the Suez Canal provides a good example of how tropical herbivorous fish can impact the structure of rocky bottoms in temperate seas. Two species of rabbitfishes have now become a dominant component of total fish biomass in the southernmost part of the eastern Mediterranean. Experimental evidence shows these species can profoundly transform benthic communities, turning algal forests into ‘barrens’, but the specific mechanisms that facilitate this shift have not been established. We surveyed ~1000 km of coastline in the eastern Mediterranean and identified two clearly distinct areas, a warmer group of regions with abundant tropical rabbitfish and a colder group of regions where these consumers were absent/ extremely rare. In regions with abundant rabbitfish, canopy algae were 65% less abundant, there was a 60% reduction of overall benthic biomass (algae and invertebrates) and a 40% decrease in total species richness. Video-recorded feeding experiments showed that the extensive barrens characteristic of regions with abundant rabbitfish were not due to greater rates of herbivory by these tropical consumers, but rather by functional differences among the herbivores. Temperate herbivorous fish displayed the greatest macroalgae consumption rates overall, but they fed exclusively on established adult macroalgae. In contrast, in regions with abundant rabbitfishes, these consumers fed complementarily on both established macroalgae and on the epilithic algal matrix, which typically contains macroalgal recruits. Synthesis: Range-shifting tropical rabbitfish can severely reduce the biomass and biodiversity of temperate reefs at a scale of hundreds of kilometres. A shift from macroalgal dominance to barrens is mediated by the addition of functionally diverse herbivores that characterise tropical reefs. This work highlights the importance of assessing the functional traits of range-shifting species to determine potential mechanisms of impact on ecological communities., Peer reviewed

Population data and microsatellite genotype matrix of Disocorea humilis Population data and microsatellite genotype matrix of Disocorea humilis, The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary., Peer reviewed

Metadata Dataset used in this manuscript: results of the experiment and field measures. Abbreviations: 0, 120, 480 h (weight): concentration of oligopeptides at 0, 120 and 480 hours of the experiment. Data are corrected by the weight of each feather piece. metadata_RuizRodriguezetal.pdf, 1.Mechanisms guaranteeing reliability of messages are essential in understanding the underlying information and evolution of signals. Microorganisms may degrade signalling traits and therefore, influence the transmitted information and evolution of these characters. The role of microorganisms in animal signalling has, however, rarely been investigated. 2.Here, we explore a possible role for feather-degrading bacteria driving the design of ornamental throat feathers in male spotless starlings (Sturnus unicolor). We estimated length, bacterial load, degradation status, and susceptibility to degradation by keratinolytic bacteria in those feathers, compared to non-ornamental adjacent feathers in males, as well as to throat feathers in females. In addition, the volume of the uropygial gland and its secretion was measured, and the secretion extracted. We also experimentally evaluated the capacity of each secretion to inhibit growth of a keratinolytic bacterium. 3.The apical part of male ornamental throat feathers harboured more bacteria and degraded more quickly than the basal part; these patterns were not detected in female throat feathers or in non-ornamental male feathers. Moreover, degradation status of male and female throat feathers did not differ, but was positively associated with feather bacterial density. Finally, the size of the uropygial gland in both males and females predicted volume and the inhibitory capacity of secretion against feather-degrading bacteria. Only in males was uropygial gland size negatively associated with the level of feather degradation. 4.All results indicate differential susceptibility of different parts of throat feathers to keratinolytic bacterial attack, which supports the possibility that throat feathers in starlings reflect individual ability to combat feather-degrading bacteria honestly. This is further supported by the relationship detected between antimicrobial properties of uropygial secretion and the level of feather degradation. 5.Our results suggest that selection pressures exerted by feather-degrading bacteria on hosts may promote evolution of particular morphologies of secondary sexual traits with different susceptibility to bacterial degradation that reliably inform of their bacterial load. Those results will help to understand the evolution of ornamental signals., Peer reviewed

Supplementary Material The file includes two figures and three tables. Supplementary Material.pdf, Genetic constraints can block many mutational pathways to optimal genotypes in real fitness landscapes, yet the extent to which this can limit evolution remains to be determined. Interestingly, mutator bacteria elevate only specific types of mutations, and therefore could be very sensitive to genetic constraints. Testing this possibility is not only clinically relevant, but can also inform about the general impact of genetic constraints in adaptation. Here, we evolved 576 populations of two mutator and one wild-type Escherichia coli to doubling concentrations of the antibiotic cefotaxime. All strains carried TEM-1, a β-lactamase enzyme well known by its low availability of mutational pathways. Crucially, one of the mutators does not elevate any of the relevant first-step mutations known to improve cefatoximase activity. Despite this, both mutators displayed a similar ability to evolve more than 1000-fold resistance. Initial adaptation proceeded in parallel through general multi-drug resistance mechanisms. High-level resistance, in contrast, was achieved through divergent paths; with the a priori inferior mutator exploiting alternative mutational pathways in PBP3, the target of the antibiotic. These results have implications for mutator management in clinical infections and, more generally, illustrate that limits to natural selection in real organisms are alleviated by the existence of multiple loci contributing to fitness., Peer reviewed

host_distribution, Feather mites (Astigmata: Analgoidea and Pterolichoidea) are among the most abundant and commonly occurring bird ectosymbionts. Basic questions on the ecology and evolution of feather mites remain unanswered because feather mite species identification is often only possible for adult males, and it is laborious even for specialized taxonomists, thus precluding large-scale identifications. Here, we tested DNA barcoding as a useful molecular tool to identify feather mites from passerine birds. Three hundred and sixty-one specimens of 72 species of feather mites from 68 species of European passerine birds from Russia and Spain were barcoded. The accuracy of barcoding and minibarcoding was tested. Moreover, threshold choice (a controversial issue in barcoding studies) was also explored in a new way, by calculating through simulations the effect of sampling effort (in species number and species composition) on threshold calculations. We found one 200-bp minibarcode region that showed the same accuracy as the full-length barcode (602 bp) and was surrounded by conserved regions potentially useful for group-specific degenerate primers. Species identification accuracy was perfect (100%) but decreased when singletons or species of the Proctophyllodes pinnatus group were included. In fact, barcoding confirmed previous taxonomic issues within the P. pinnatus group. Following an integrative taxonomy approach, we compared our barcode study with previous taxonomic knowledge on feather mites, discovering three new putative cryptic species and validating three previous morphologically different (but still undescribed) new species., Peer reviewed

Fig2A_cpDNA_Platycodoneae NEXUS and tre files with the analysis settings used in MrBayes inferred from the concatenated chloroplast dataset (psbJ-petA, trnL-trnF, petB-petD) for the Platycodoneae Fig2B_ITS_platycodoneae NEXUS and tre files with the analysis settings used in MrBayes inferred from the nuclear ribosomal dataset (ITS) for Platycodoneae Fig2C_ITS_4cpdna NEXUS and tre files with the analysis settings used in MrBayes inferred from the combined nuclear and chloroplast dataset (ITS, psbJ-petA, trnL-trnF, petB-petD, trnS-trnG) for Platycodoneae Nested-dating approach analysis Script (.xml) and tre files for the "Nested analyses" of all three linked datasets: Platycodoneae, C. eminii and C. canariensis Nested Analysis.zip Figure S1 Nexus and .tre files for the single-gene analyses of the Platycodoneae dataset. Figure S2 Nexus and .tre files for the single-gene analyses of the Canarina dataset, Transoceanic distributions have attracted the interest of scientists for centuries. Less attention has been paid to the evolutionary origins of ‘continent-wide’ disjunctions, in which related taxa are distributed across isolated regions within the same continent. A prime example is the ‘Rand Flora’ pattern, which shows sister taxa disjunctly distributed in the continental margins of Africa. Here, we explore the evolutionary origins of this pattern using the genus Canarina, with three species: C. canariensis, associated with the Canarian laurisilva, and C. eminii and C. abyssinica, endemic to the Afromontane region in East Africa, as case study. We infer phylogenetic relationships, divergence times and the history of migration events within Canarina using Bayesian inference on a large sample of chloroplast and nuclear sequences. Ecological niche modelling was employed to infer the climatic niche of Canarina through time. Dating was performed with a novel nested approach to solve the problem of using deep time calibration points within a molecular dataset comprising both above-species and population-level sampling. Results show C. abyssinica as sister to a clade formed by disjunct C. eminii and C. canariensis. Miocene divergences were inferred among species, whereas infraspecific divergences fell within the Pleistocene–Holocene periods. Although C. eminii and C. canariensis showed a strong genetic geographic structure, among-population divergences were older in the former than in the latter. Our results suggest that Canarina originated in East Africa and later migrated across North Africa, with vicariance and aridification-driven extinction explaining the 7000 km/7 million year divergence between the Canarian and East African endemics., Peer reviewed

All data for Transgenerational Effects manuscript All data for the manuscript in an Excel file. Details can be found in the first spreadsheet and ESM. DRYAD Transgenerational_effects_Drosophila.xlsx, The consequences of sexual interactions extend beyond the simple production of offspring. These interactions typically entail direct effects on female fitness, but may also impact the life histories of later generations. Evaluating the cross-generational effects of sexual interactions provides insights into the dynamics of sexual selection and conflict. Such studies can elucidate whether offspring fitness optima diverge across sexes upon heightened levels of sexual interaction among parents. Here, we found that, in Drosophila melanogaster, components of reproductive success in females, but not males, were contingent on the nature of sexual interactions experienced by their mothers. In particular, maternal sexual interactions with non-sires enhanced female fecundity in the following generation. This highlights the importance of non-sire influences of sexual interactions on the expression of offspring life histories., Peer reviewed