cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7ns4pk2
title: Data from: Adaptive phenotypic plasticity contributes to divergence between lake and river populations of an East African cichlid fish

description: Adaptive phenotypic plasticity and fixed genotypic differences have long
 been considered opposing strategies in adaptation. More recently, these
 mechanisms have been proposed to act complementarily and under certain
 conditions jointly facilitate evolution, speciation and even adaptive
 radiations. Here we investigate the relative contributions of adaptive
 phenotypic plasticity vs. local adaptation to fitness, using an emerging
 model system for studying early phases of adaptive divergence, the
 generalist cichlid fish species Astatotilapia burtoni. We tested direct
 fitness consequences of morphological divergence between lake and river
 populations in nature by performing two transplant experiments in Lake
 Tanganyika. In the first experiment we used wild-caught juvenile lake and
 river individuals, while in the second experiment we used F1 crosses
 between lake and river fish bred in a common garden setup. By tracking the
 survival and growth of translocated individuals in enclosures in the lake
 over several weeks, we revealed local adaptation evidenced by faster
 growth of the wild-caught resident population in the first experiment. On
 the other hand, we did not find difference in growth between different
 types of F1 crosses in the second experiment, suggesting a substantial
 contribution of adaptive phenotypic plasticity to increased immigrant
 fitness. Our findings highlight the value of formally comparing fitness of
 wild-caught and common-garden-reared individuals and emphasize the
 necessity of considering adaptive phenotypic plasticity in the study of
 adaptive divergence.
description: Individual measurement
 data from transplant experiement 1 using wild-caught Astatotilapia burtoni
 transplanted to the lake habitatSL - standard length, TL
 - total length, W -weight, m- male, f - female, ? - unknown, KaL - Kalambo
 lake, Ka2 - Kalambo river upstreamexperiement1.txtIndividual measurement data from transplant experiment 2 using F1 crosses between lake and stream Astatotilapia burtoni transplanted to the lake habitatSL- standard length, TL - total length, W - weight, m- male, f - female, ? - unknown, KaL x KaL - pure lake cross, Ka2 x KaL - hybrid, Ka2 x Ka2 - pure river crossexperiment2.txt
DOI: 10.5061/dryad.q6n3mn0d
title: Data from: Testing the role of phenotypic plasticity for local adaptation: growth and development in time-constrained Rana temporaria populations

description: Phenotypic plasticity can be important for local adaptation, since it
 enables individuals to survive in a novel environment until genetic
 changes have been accumulated by genetic accommodation. By analyzing the
 relationship between development rate and growth rate, it can be
 determined if plasticity in life history traits is caused by changed
 physiology or behaviour. We extended this to examine if plasticity had
 been aiding local adaptation, by investigating if the plastic response had
 been fixed in locally adapted populations. Tadpoles from island
 populations of Rana temporaria, locally adapted to different pool drying
 regimes, were monitored in a common garden. Individual differences in
 development rate were caused by different foraging efficiency. However,
 developmental plasticity was physiologically mediated by trading off
 growth against development rate. Surprisingly, plasticity has not aided
 local adaptation to time-stressed environments, since local adaptation was
 not caused by genetic assimilation but on selection on the standing
 genetic variation in development time.
description: Dryad
 entrySee ReadMe
 file
DOI: 10.5061/dryad.r21q1
title: Data from: Interactions among bacterial strains and fluke genotypes shape virulence of co-infection

description: Most studies of virulence of infection focus on pairwise host-parasite
 interactions. However, hosts are almost universally co-infected by several
 parasite strains and/or genotypes of the same or different species. While
 theory predicts that co infection favours more virulent parasite genotypes
 through intensified competition for host resources, knowledge of effects
 of genotype by genotype (G×G) interactions between unrelated parasite
 species on virulence of co infection is limited. Here we tested such
 relationship by challenging rainbow trout with replicated bacterial
 strains and fluke genotypes both singly and in all possible pairwise
 combinations. We found that virulence (host mortality) was higher in co
 infections compared to single-infections. Importantly, we also found that
 the overall virulence was dependent on the genetic identity of the
 co-infecting partners so that the outcome of co infection could not be
 predicted from the respective virulence of single infections. Our results
 imply that G×G interactions among co infecting parasites may significantly
 affect host health, add to variance in parasite fitness and thus influence
 evolutionary dynamics and ecology of disease in unexpected ways.
description: Louhi et al. Original
 dataOriginal data from the
 experimental exposure of fish to Flavobacterium columnare and Diplostomum
 pseudospathaceum. The data present survival times (hours) and numbers of
 Diplostomum in the eye lenses for fish in single flavobacterial infections
 (strains 1-6), single Diplostomum infections (genotypes a-e), and in all
 pairwise co-infection combinations of the strains and
 genotypes.
DOI: 10.5061/dryad.8ph59
title: Data from: High rate of translocation-based gene birth on the Drosophila Y chromosome

description: The Y chromosome is a unique genetic environment defined by a lack of
 recombination and male-limited inheritance. The Drosophila Y chromosome
 has been gradually acquiring genes from the rest of the genome, with only
 seven Y-linked genes being gained over the past 63 million years (0.12
 gene gains per million years). Using a next-generation sequencing
 (NGS)-powered genomic scan, we show that gene transfers to the Y
 chromosome are much more common than previously suspected: at least 25
 have arisen across three Drosophila species over the past 5.4 million
 years (1.67 per million years for each lineage). The gene transfer rate is
 significantly lower in Drosophila melanogaster than in the Drosophila
 simulans clade, primarily due to Y-linked retrotranspositions being
 significantly more common in the latter. Despite all Y-linked gene
 transfers being evolutionarily recent (&lt;1 million years old), only
 three showed evidence for purifying selection (ω ≤ 0.14). Thus, although
 the resulting Y-linked functional gene acquisition rate (0.25 new genes
 per million years) is double the longer-term estimate, the fate of most
 new Y-linked genes is defined by rapid degeneration and pseudogenization.
 Our results show that Y-linked gene traffic, and the molecular mechanisms
 governing these transfers, can diverge rapidly between species, revealing
 the Drosophila Y chromosome to be more dynamic than previously
 appreciated. Our analytical method provides a powerful means to identify
 Y-linked gene transfers and will help illuminate the evolutionary dynamics
 of the Y chromosome in Drosophila and other species.
description: Extract reads from bam
 file based on presence of specific allelePython script that reads
 from bam file based on presence of alleles in text file (text file with
 three columns: 1. Chromsome, 2. Position, 3. alllele [A, T, C, G]).
 Returns a bam file with extracted reads. See script for more details.
 example: python get_male_spec_reads.py -b bam.file -s
 snp.fileget_male_spec_reads.pyPipeline for determining Y-linked gene transfers. R script.R script used to determine incipient Y-linked transfers using male/female pairs from two D. melanogaster strains. All data are publicly available. See supplementary materials for full description of pipeline, and description of data used in pipeline.Detect_tranlocated_regions_Dmel_noY_noU_StdDist.rUse polymorphism data to determine age of Y-linked transferR script for determining the age of a Y-linked transfers and perform statistical tests comparing age distribution of non-genic and genic transfers. See supplementary materials for more details, including description of datasets used.Polymorphism_based_age_estimation_noY_noU_MS.r
DOI: 10.5061/dryad.106
title: Data from: Reassessment of Homology of Morphological Characters in Tetractinellid Sponges Based on Molecular Data

description: We compared four approaches for analyzing three data sets derived from
 staphylinoid beetles, a superfamily whose known species diversity is
 roughly comparable to that of vertebrates. One data set is derived from
 adult morphology and the two molecular data sets are from 12S ribosomal
 RNA and cytochrome b mitochondrial DNA. We found that taxonomic congruence
 following conditional data combination, herein called compatible evidence
 (CE), resolved more nodes compatible with an initial conservative
 hypothesis than did total evidence (TE), conditional data combination
 (CDC), or taxonomic congruence (TC). CE sets a base of nodes obtained by
 CDC analysis and then investigates what further agreement may arise in a
 universe where these nodes are accepted as given. We suggest that CE75-75
 may be appropriate for future studies that aim to both generate a
 well-corroborated tree and investigate conflicts between data sets,
 partitions, and characters. CE75-75 is a 75% bootstrap consensus CDC tree
 followed by combinable-component consensus of a 75% bootstrap consensus of
 each homogeneous set of partitions having hierarchical structure.
description: Chombard et al Data
 Matrix9HNEXUS.txt
DOI: 10.5061/dryad.3vc108b
title: Data from: Scale-dependent home range optimality for a solitary omnivore

description: Spatial and temporal heterogeneity are fundamental mechanisms structuring
 home ranges. Under optimality, an individual should structure their space
 use economically to maximize fitness. We evaluated support for three
 hypotheses related to range optimality in American black bears (Ursus
 americanus), predicting (1) range location on a landscape will correspond
 with high vegetation productivity, (2) increasing forest fragmentation
 will result in larger ranges, and (3) increasing proportion of forest
 and/or mean vegetation productivity will result in smaller ranges. We used
 black bear radio telemetry data from Michigan (2009-2015), Missouri
 (2010-2016) and Mississippi (2008-2017), USA. Annual space use excluded
 winter, and we separated seasonal space use into spring, summer, and fall.
 We collected data from 143 bears (80 females, 63 males), resulting in 97
 annual and 538 seasonal ranges. We used generalized linear mixed models to
 evaluate productivity (estimated through Normalized Difference Vegetation
 Index, NDVI) selection, and range size (km2) variation between
 individuals. At the annual scale, black bears consistently selected areas
 with greater vegetation productivity than the surrounding landscape; yet
 selection weakened and was more variable seasonally. Opposite to our
 prediction, we found that increasing fragmentation consistently resulted
 in smaller ranges; non-forested land covers and forest edges might provide
 greater abundance or more diverse foods for bears. Ranges with a greater
 proportion of forest were smaller, likely reflecting an increase in food
 and cover which could reduce movements, yet there was no support for more
 productive ranges also being smaller as expected from an area minimizing
 strategy. Black bears displayed a scale-dependent space use strategy: at
 larger spatial and temporal scales, productivity acted as the strongest
 limiting factor and energy maximizing was the dominant strategy, while an
 area minimizing strategy was exhibited seasonally. We revealed consistent,
 scale-dependent responses by black bears to environmental conditions,
 demonstrating the intrinsic plasticity of this adaptable omnivore.
description: Black bear home range
 datasetHome range data from
 black bears in MI, MO, and MS (USA) from 2008-2017. Data includes bear ID,
 range area, state, season, year, and other environmental variables. For
 details about the variables please refer to the manuscript. If more info
 needed contact M. Gantchoff.final
 submission.zip
DOI: 10.5061/dryad.4h0k1
title: Data from: Three hundred years of low non-paternity in a human population

description: When cuckoldry is frequent we can expect fathers to withhold investment in
 offspring that may not be theirs. Human paternal investment can be
 substantial and is in line with observations from tens of thousands of
 conceptions that suggest that cuckoldry is rare in humans. The generality
 of this claim seems to be in question as the rate of cuckoldry varies
 across populations and studies have mostly been on Western populations.
 Two additional factors complicate our conclusions, (1) current estimates
 of the rate of cuckoldry in humans may not reflect our past behaviour as
 adultery can be concealed by the use of contraceptives; and (2) it is
 difficult to obtain samples that are random with respect to their
 paternity certainty. Studies that combine genealogies with Y-chromosome
 haplotyping are able to circumvent some of these problems by probing into
 humans’ historical behaviour. Here we use this approach to investigate
 1273 conceptions over a period of 330 years in 23 families of the
 Afrikaner population in South Africa. We use haplotype frequency and
 diversity and coalescent simulations to show that the male population did
 not undergo a severe bottleneck and that paternity exclusion rates are
 high for this population. The rate of cuckoldry in this Western population
 was 0.9% (95% confidence interval 0.4–1.5%), and we argue that given the
 current data on historical populations we have to conclude that, at least
 for Western human populations, cuckoldry rate is probably in the range of
 1%.
description: Supplementary Material
 for “Three hundred years of low non-paternity in a human
 population”This document contains
 Supplementary Table 1 "Genealogically linked surnames
 genotyped", Supplementary Figure 1 "A histogram of father's
 age at birth of their sons", the R code for calculating exclusion
 probabilities and the References for the supplementary
 material.Supplementary Material
 Heredity.docxSuplementary Table S2
 for “Three hundred years of low non-paternity in a human
 population”This files contains
 Supplementary Table 2 "Unique YSTR haplotypes found in this
 study".Suplementary Table S2 YSTR
 haplotypes.xlsx
DOI: 10.5061/dryad.51p4f
title: Data from: How persistent are the impacts of logging roads on Central African forest vegetation?

description: 1. Logging roads can trigger tropical forest degradation by reducing the
 integrity of the ecosystem and providing access for encroachment.
 Therefore, road-management is crucial in reconciling selective logging and
 biodiversity conservation. Most logging roads are abandoned after timber
 harvesting, however little is known about their long-term impacts on
 forest vegetation and accessibility, especially in Central Africa. 2. In
 11 logging concessions in the Congo Basin we field-sampled a
 chronosequence of roads that, judged by satellite images, had been
 abandoned between 1985 and 2015. We assessed recovery of timber resources,
 tree diversity and above-ground biomass in three zones: the road track,
 the road edge (where forest had been cleared during road construction) and
 the adjacent logged forest. 3. The density of commercial timber species ≤
 15 cm DBH was almost three times higher in the road track (327 individuals
 ha-1) and edge (278) than in the logged adjacent forest (111). Over time,
 tree species diversity converged to a comparable level between roads and
 adjacent forests, along with decreasing soil compaction and increasing
 canopy closure. 4. The average width of forest clearing for road
 construction was 20 m, covering a total 0.76% of the forest area inside
 concessions. After 15 years following abandonment, road tracks had
 recovered 24 Mg ha-1 of above-ground woody biomass, which was 6% of that
 in the adjacent forest, while road edges had accumulated 167 Mg ha-1
 (42%). Ten years after abandonment, roads were no longer penetrable by
 poachers on motorcycles. Exotic herb species were fully replaced by
 dominant Marantaceae that have even higher abundance in the adjacent
 forest. 5. Synthesis and applications. Our evidence of vegetation recovery
 suggests that logging roads are mostly transient elements in forest
 landscapes. However, given the slow recovery of biomass on abandoned road
 tracks, we advocate both reducing the width of forest clearing for road
 construction and reopening old logging roads for future harvests, rather
 than building new roads in intact forests. Road edges seem suitable for
 post-logging silviculture which needs to be assisted by removing dominant
 herbs during the early years after abandonment while the road track is
 still accessible
description: Full plot analysis
 dataCharacterization of the
 location, environmental parameters, list of recorded species and full
 vegetation inventories for each 5x5 m sampling plot on and along abandoned
 logging roads in Central Africa.Kleinschroth_etal_dataset.zip
DOI: 10.5061/dryad.ns657
title: Data from: The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally

description: The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming
 family Marasmiaceae, but it has never been observed to produce a fruiting
 body, which calls to question its capacity for sexual reproduction. In
 this study, we identified potential A (HD1 and HD2) and B (pheromone
 precursors and pheromone receptors) mating genes in M. roreri. A PCR-based
 method was subsequently devised to determine the mating type for a set of
 47 isolates from across the geographic range of the fungus. We developed
 and generated an 11-marker microsatellite set and conducted association
 and linkage disequilibrium (standardized index of association, IAs)
 analyses. We also performed an ancestral reconstruction analysis to show
 that the ancestor of M. roreri is predicted to be heterothallic and
 tetrapolar, which together with sliding window analyses support that the A
 and B mating loci are likely unlinked and follow a tetrapolar organization
 within the genome. The A locus is composed of a pair of HD1 and HD2 genes,
 whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and
 receptor, STE3_Mr4. Two A and B alleles but only two mating types were
 identified. Association analyses divided isolates into two well-defined
 genetically distinct groups that correlate with their mating type; IAs
 values show high linkage disequilibrium as is expected in clonal
 reproduction. Interestingly, both mating types were found in South
 American isolates but only one mating type was found in Central American
 isolates, supporting a prior hypothesis of clonal dissemination throughout
 Central America after a single or very few introductions of the fungus
 from South America.
description: Microsatellite binary
 data of Moniliophthora roreri isolatesThese microsatellite
 data was used to perform association and linkage disequilibrium analysis
 in forty isolates of M. roreri. There are in total forty alleles found in
 eleven microsatellite markers tested.Microsatellite
 data_M_roreri_JDiazV_MCAime.xlsxGBlocks alignment of ITS
 sequences of Marasmiineae speciesThis files contains the
 GBlocks alignment used to perform the phylogenetic and ancestral
 reconstruction state of species within the most representative families in
 the Marasmiineae.GBlocks alignment ITS for
 phylogeny.fastaGblocks alignment of
 STE3 pheromone receptors of M. roreriThis file contains the
 GBlocks alignment of all the STE3 receptors from M. roreri and related
 species to perform the phylogenetic analysis described in the
 paper.Gblocks alignment of pheromone
 receptors.fasta
DOI: 10.5061/dryad.t3cd2
title: Data from: Virus adaptation to quantitative plant resistance: erosion or breakdown?

description: Adaptation of populations to new environments is frequently costly due to
 trade-offs between life history traits, and consequently, parasites are
 expected to be locally adapted to sympatric hosts. Also, during adaptation
 to the host, an increase of parasite fitness could have direct
 consequences on its aggressiveness (i.e. the quantity of damages caused to
 the host by the virus). These two phenomena have been observed in the
 context of pathogen adaptation to host qualitative and monogenic
 resistances. However, the ability of pathogens to adapt to quantitative
 polygenic plant resistances and the consequences of these potential
 adaptations on other pathogen life history traits remain to be evaluated.
 Using Potato virus Y and two pepper genotypes (one susceptible and one
 with quantitative resistance), experimental evolutions showed that
 adaptation to a quantitative resistance was possible and resulted in
 resistance breakdown. This adaptation was associated to a fitness cost on
 the susceptible cultivar, but had no consequence neither in terms of
 aggressiveness, which could be explained by a high tolerance level, nor in
 terms of aphid transmission efficiency. It results that quantitative
 resistances are not necessarily durable but management strategies mixing
 susceptible and resistant cultivars in space and/or in time should be
 useful to preserve their efficiency.
description: DATA_JEB-2012-00203
DOI: 10.5061/dryad.34fv6
title: Data from: Effect of the landscape matrix on gene flow in a coastal amphibian metapopulation

description: Functional connectivity is crucial for the persistence of a
 metapopulation, because migration among subpopulations enables
 recolonization and counteracts genetic drift, which is especially
 important in small subpopulations. We studied the degree and drivers of
 connectivity among occupied patches of a coastal dune metapopulation of
 the Natterjack Toad (Epidalea calamita Laurenti), on the basis of
 microsatellite variation. As spatial landscape heterogeneity is expected
 to influence dispersal and genetic structure, we analyzed which landscape
 features affect functional connectivity and to what extent. Sixty
 different landscape resistance scenarios as well as the
 isolation-by-distance model were compared using two landscape genetics
 approaches. We identified three subpopulations with unidirectional levels
 of gene flow among the two most geographically separated subpopulations,
 while inferred gene flow into the geographically intermediate
 subpopulation was limited. Urbanization and vegetation height negatively
 affected connectivity. Low estimates of genetic diversity and effective
 population size indicate that conservation measures in the smallest and
 most isolated subpopulation are required.
description: Genotypes Natterjack
 ToadThe data file contains
 two spread sheets. The first shows the total dataset, with in the first
 column the sample codes, in the second the spawn string code when
 individuals were sampled from the same spawn string, in the third the name
 of the subpopulation, in the fourth the site number, and in the fith and
 sixth column the X and Y coordinates, respectively (Lambert-72
 coordinates). The next 11 columns represent the different microsatellite
 markers. Alleles are separated by a forward slash. Missing genotypes are
 indicated with 'NA'. The second spread sheet contains the
 dataset without full siblings except one per family, that was used for the
 landscape genetic analyses.Dryad_NatterjackToad.xlsx