cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7h44j0zqw
title: Autosomal suppression and fitness costs of an old driving X chromosome in Drosophila testacea

description: Driving X chromosomes (XDs) are meiotic drivers that bias their own
 transmission through males by killing Y-bearing gametes. These chromosomes
 can in theory spread rapidly in populations and cause extinction, but many
 are found as balanced polymorphisms or as “cryptic” XDs shut down by drive
 suppressors. The relative likelihood of these outcomes, as well as the
 evolutionary pathways through which they come about, are not
 well-understood. An XD was recently discovered in the mycophagous fly,
 Drosophila testacea, presenting the opportunity to compare this XD with
 the well-studied XD of its sister species, Drosophila neotestacea.
 Comparing features of independently evolved XDs in young sister species is
 a promising avenue towards understanding how XDs and their counter acting
 forces change over time. In contrast to the XD of D. neotestacea, we find
 that the XD of D. testacea is old, with its origin predating the radiation
 of three species: D. testacea, D. neotestacea, and their shared sister
 species, Drosophila orientacea. Motivated by the suggestion that older XDs
 should be more deleterious to carriers, we assessed the effect of the XD
 on both male and female fertility. Unlike what is known from D.
 neotestacea, we found a strong fitness cost in females homozygous for the
 XD in D. testacea: a large proportion of homozygous females failed to
 produce offspring after being housed with males for several days. Our male
 fertility experiments show that while XD male fertility is lower under
 sperm depleting conditions, XD males have comparable fertility to males
 carrying a standard X chromosome under a free mating regime, which may
 better approximate conditions in wild populations of D. testacea. Lastly,
 we demonstrate the presence of autosomal suppression of X chromosome
 drive. Our results provide support for a model of XD evolution where the
 dynamics of young XDs are governed by fitness consequences in males,
 whereas in older XD systems, both suppression and fitness consequences in
 females likely supersede male fitness costs.
DOI: 10.5061/dryad.5dv41ns33
title: Substrate quality and not dominant plant community determines the vertical distribution and C assimilation of enchytraeids in peatlands

description: Peatlands are important carbon (C) stores as a result of acidity,
 waterlogging conditions and low temperatures slowing decomposition rates.
 However, climate change is predicted to bring not only changes in abiotic
 conditions, but also the replacement of peat-forming vegetation, such as
 Sphagnum mosses, with vascular plants. In these systems, enchytraeid worms
 represent the dominant mesofaunal group, and previous climate change
 manipulations have shown that their abundances and vertical distribution
 are strongly influenced by temperature and moisture gradients, with
 important implications for C cycling. Therefore, determining their
 behavioural responses to changes in both abiotic and biotic factors is
 crucial to quantify their contribution to decomposition processes. We
 investigated the importance of vertical edaphic gradients (soil moisture
 and labile C) on enchytraeids total numbers, vertical distribution and
 feeding activities by inverting intact soil cores and hence, reversing
 both substrate quality but leaving the microclimatic gradients intact.
 This manipulative experiment was set-up in two different peatland areas,
 one dominated by heather (Erica mackaiana) and another by mosses (Sphagnum
 sp.) to determine the influence of different plant functional growth forms
 on these responses. Our results showed that most enchytraeid species were
 “stayers” (i.e. in the “Upturned cores”, they remained in the same layer
 where they are “Normally” located), and hence, their vertical distribution
 was more dependent on substrate quality than a change in microclimate.
 This response was more evident under drier conditions (i.e. the highest
 locations of the height gradient at the heather site) than at the wettest
 locations (i.e. the bottom of the slope and under mosses) due to more
 pronounced vertical gradients in substrate quality. Furthermore,
 radiocarbon measurements on enchytraeid tissues showed that to avoid
 competition among the growing populations for the limited labile resources
 present in the top layers, enchytraeids selected older C sources. These
 findings indicate that future climate change scenarios will not only bring
 important changes in the abiotic conditions (temperature and moisture) and
 biotic properties of peatlands (both vegetation composition and
 below-ground soil biota community structure and vertical distribution),
 but also alterations in the feeding preferences of key decomposers that
 could result in the mobilisation of previously unavailable C pools.
DOI: 10.5061/dryad.brv15dv5w
title: Data from: A novel phenotype combining primary ovarian insufficiency growth retardation and pilomatricomas with MCM8 mutation

description: Context: Primary Ovarian insufficiency (POI) affects 1% of women under 40
 years and leads most often to definitive infertility with adverse health
 outcomes. Very recently, genes involved in DNA repair have been shown to
 cause POI. Objective: To identify the cause of a familial POI in a
 consanguineous Turkish family. Design: Exome sequencing was performed in
 the proposita and her mother. Chromosomal breaks were studied in
 lymphoblastoid cell lines treated with Mitomycin (MMC). Setting and
 patients: The proposita presented intra-uterine and post-natal growth
 retardation, multiple pilomatricomas in childhood and primary amenorrhea.
 She was treated with growth hormone (GH) from 14 to 18 years. Results: We
 identified a novel nonsense mutation in exon 9 of the minichromosome
 maintenance complex component 8 gene (MCM8) NM_001281522.1:
 c.925C&gt;T/p.R309* yielding a truncated protein devoid of the 531
 C-terminal residues. The mutation was homozygous in the daughter and
 heterozygous in the mother. MMC induced DNA breaks and aberrant metaphases
 in the patient’s lymphoblastoid cells. The mother’s cells had intermediate
 but significantly higher chromosomal breaks compared to a control.
 Conclusion: We describe a novel phenotype of syndromic POI related to a
 novel truncating MCM8 mutation. We show for the first time that
 spontaneous tumors (pilomatricomas) are associated with MCM8 genetic
 defect making the screening of this gene necessary before starting GH
 therapy in POI with short stature, especially in a familial or
 consanguineous context. Appropriate familial monitoring in the long term
 is necessary and fertility preservation should be considered in
 heterozygous siblings to avoid rapid follicular atresia.
description: Supplemental materials for associated paper.
DOI: 10.5061/dryad.05qfttdzv
title: Genetic variation in an ephemeral mudflat species: the role of the soil seed bank and dispersal in river and secondary anthropogenic habitats

description: Many ephemeral mudflat species, which rely on a soil seed bank to build up
 the next generation, are endangered in their natural habitat due to the
 widespread regulation of rivers. The aim of the present study was to
 elucidate the role of the soil seed bank and dispersal for the maintenance
 of genetic diversity in populations of near-natural river habitats and
 anthropogenic habitats created by traditional fish farming practices using
 Cyperus fuscus as a model. Using microsatellite markers, we found no
 difference in genetic diversity levels between soil seed bank and
 above-ground population and only moderate differentiation between the two
 fractions. One possible interpretation is the difference in short-term
 selection during germination under specific conditions (glasshouse versus
 field) resulting in an ecological filtering of genotypes out of the
 reservoir in the soil. River populations harboured significantly more
 genetic diversity than populations from the anthropogenic pond types. We
 suggest that altered levels and patterns of dispersal together with
 stronger selection pressures and historical bottlenecks in anthropogenic
 habitats are responsible for the observed reduction in genetic diversity.
 Dispersal is also supposed to largely prohibit genetic structure across
 Europe, although there is a gradient in private allelic richness from
 southern Europe and Anatolia (high values) to northern, especially
 north-western, Europe (low values), which probably relates to postglacial
 expansion out of southern and/or eastern refugia.
description: Data are in GenAlEx format. Missing values:
 0
DOI: 10.5061/dryad.ns1rn8pp4
title: Space invaders: searching for invasive Smallmouth Bass (Micropterus dolomieu) in a renowned Atlantic Salmon (Salmo salar) river

description: Humans have the ability to permanently alter aquatic ecosystems and the
 introduction of species is often the most serious alteration. 
 Non-native Smallmouth Bass (Micropterus dolomieu) were identified in
 Miramichi Lake c. 2008, which is a headwater tributary to the Southwest
 Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose
 salmon population is dwindling.  A containment programme managed
 by the Department of Fisheries and Oceans, Canada (DFO) was implemented in
 2009 to confine Smallmouth Bass (SMB) to the lake.  We utilized
 environmental DNA (eDNA) as a detection tool to establish the potential
 escape of SMB into the Southwest Miramichi River.  We sampled at
 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake
 Brook), which flows into the main stem Southwest Miramichi River, and the
 main stem Southwest Miramichi River between August and October
 2017.  We observed n=6 positive detections located in the lake,
 Lake Brook, and the main stem Southwest Miramichi downstream of the
 lake.  No detections were observed upstream of the confluence of
 Lake Brook and the main stem Southwest Miramichi.  The spatial
 pattern of positive eDNA detections downstream of the lake suggests the
 presence of individual fish versus lake-sourced DNA in the outlet stream
 discharging to the main river.  Smallmouth Bass were later
 confirmed by visual observation during a snorkeling campaign, and
 angling.  Our results, both eDNA and visual confirmation,
 definitively show Smallmouth Bass now occupy the main stem of the
 Southwest Miramichi. 
description: See paper for methods
description: These data are exact results from qPCR.
DOI: 10.5061/dryad.9p8cz8wcb
title: Population‐level variation of digestive physiology costs of mounting an immune response in damselflies

description: 1. Trade‐offs are often predicted to occur between energetically costly
 activities, such as somatic growth and eliciting immune responses to
 parasites. Although parasitism frequently reduces growth via lowered
 consumption, it remains unclear if the energetic demands of generating
 immune responses also affect the digestive physiological processes
 necessary for growth. Moreover, as local environmental conditions affect
 energetic investment towards growth and immune responses, the extent of
 any digestive–immune response trade‐offs may vary among populations and
 not be fixed at the species‐level. 2. To test these ideas,
 melanisation – a general innate immune
 response – was first induced in damselfly larvae
 (Enallagma vesperum) from two populations. The study then quantified
 growth and consumption rates, assimilation and production efficiencies,
 and daily metabolic rates to determine if digestive–immune response
 trade‐offs were present and, if so, whether they differed between
 populations. 3. There was no evidence of any trade‐offs between immune
 responses and digestive physiology components in either population.
 However, the results did show that populations differentially allocated
 energy towards different digestive physiology components after an immune
 response was elicited: one population increased their relative consumption
 and daily metabolic rates, while the other population had lower
 assimilation efficiencies and consumption rates. 4. Although researchers
 lack a mechanistic understanding of the observed population‐level
 differences, these results suggest that accounting for population‐level
 variation in digestive physiology and immune responses is critical to
 inferences about how immunological defences to parasitism may affect the
 ability for organisms to both acquire and utilise resources.E
description: Two CSV files that include the dry/wet mass regression values
 (DryMass_1.0.csv) and obtained values from the feeding trials and immune
 challenge (Assimilation_2.1.csv).
DOI: 10.5061/dryad.7pvmcvdps
title: Functional trait table for mixed-species flocking birds in the Western Andes of Colombia

description: These data represent functional traits relevant to the foraging ecology
 and habitat preferences of mixed-species flock joining bird species from
 the Western Andes of Colombia. We collected these data based on published
 data for the species from the Handbook of the Birds Alive online database
 (del Hoyo et al. 2020), supplemented with additional natural history
 references were available, with the objective of calculating the
 functional richness contained in mixed-species flock compositions sampled
 across a patch size gradient of subtropical forest fragments in the
 Serriania de los Paraguas, Valle del Cauca department, Colombia. We
 tabulated foraging data from 99 bird species observed at least once in a
 mixed-species flock, including body mass, nest type and clutch size,
 relative use of four different diet categories, use of different
 foraging attack maneuvers, foraging substrates, and elevational strata
 within the forest. We used these data in Jones and Robinson (2020) to
 calculate the Functional Richness and Functional Dispersion indices for
 each flock composition.
description: These data were collected from the <em>Handbook of the
 Birds Alive</em> online database, based on published material. We
 supplemented this with taxon-specific natural history resources where
 possible; references for each species are listed in the last column of the
 data set. Formal references for each source are listed in the
 supplementary materials to Jones and Robinson (2020). For each species, we
 recorded the largest body mass available where multiple body masses were
 listed. We classified the nest type into cavity, cup, and dome. Relative
 dietary preferences were quantified on a scale from 0 (no consumption) to
 3 (major portion of the diet); these categories were not mutually
 exclusive. Use of foraging attack maneuvers, foraging substrates,
 vegetation stratum within the forest, and habitat category (forest
 interior, forest edge, secondary forest, open habitat) were classified as
 used (1) or not used (0). Foraging attack maneuver use classifications
 follow the Robinson and Remsen (1990) categorization scheme.
description: We removed the nest type and clutch size data prior to
 calculating functional diversity indices for the Jones and Robinson (2020)
 publication.
DOI: 10.5061/dryad.0gb5mkkxm
title: Small mammal species richness and turnover along elevational gradient in Yulong Mountain, Yunnan, Southwest China

description: Understanding the species diversity patterns along elevational gradients
 is critical for biodiversity conservation in mountainous regions. We
 examined the elevational patterns of species richness and turnover, and
 evaluated the effects of spatial and environmental factors on non-volant
 small mammals (hereafter ‘small mammal’) predicted a priori by alternative
 hypotheses [Mid-domain effect (MDE), species area relationship (SAR),
 energy, environmental stability and habitat complexity)] proposed to
 explain the variation of diversity. We designed a standardized sampling
 scheme to trap small mammals at ten elevational bands across the entire
 elevational gradient on Yulong Mountain, Southwest China. A total of 1808
 small mammals representing 23 species were trapped. We observed the
 hump-shaped distribution pattern of the overall species richness along
 elevational gradient. Insectivores, rodents, large-ranged species and
 endemic species richness showed the general hump-shaped pattern but peaked
 at different elevations, whereas the small-ranged species and endemic
 species favored the decreasing richness pattern. The MDE and the energy
 hypothesis were supported, whereas little support was found for the SAR,
 the environmental stability hypothesis and the habitat complexity.
 However, the primary driver(s) for richness patterns differed among the
 partitioning groups, with NDVI (the normalized difference vegetation
 index) and MDE were the most important variables for the total richness
 pattern. Species turnover for all small mammal groups increased with
 elevation, and it supported a decrease of community similarity with
 elevational distance. Our results emphasized for increased conservation
 efforts in the higher elevation regions of the Yulong Mountain.
description: A total of ten elevational sampling bands were establishedand
 along the Yulong Mountain from 2550 to 4250 m. We trapped small mammals
 using standardized techniques, and recorded the ecological variables
 (i.e.the temperature, humidity data and plant species richness) from
 each sampling site.
description: This dataset contains a copy of the data files used for this
 paper.
DOI: 10.15468/dl.sufmd8
title: Occurrence Download

description: A dataset containing 9710 records in GBIF matching the query:
SELECT
 '423' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 115.12824358810933
 AND decimalLongitude &lt;= 125.87556979961315
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 9710 records were derived from 130 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002163-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2ngf1vhjk
title: Lack of sibling avoidance during mate selection in the butterfly Bicyclus anynana

description: Species susceptible to inbreeding depression are hypothesized to combat
 this problem through a number of different mechanisms, including kin
 recognition. For species with kin recognition, it is unknown if filial
 recognition is innate or due to prior juvenile experience with siblings.
 Here, we first test for the presence of kin recognition, and then test
 these two hypotheses for the development of filial recognition, in the
 butterfly Bicyclus anynana, a species that suffers from
 inbreeding depression when forcibly inbred but recovers within a few
 generations when allowed to breed freely. We evaluate whether the rapid
 recovery from inbreeding depression is associated with either innate or
 learned filial recognition. First, we determined whether females innately
 prefer unrelated males over sibling males using females reared in
 isolation and then given a choice between an unrelated and a sibling male.
 Then, we determined if females raised with siblings learned to detect and
 avoid mating with siblings as adults when provided a choice between an
 unrelated male and a sibling male. Finally, we determined if females
 raised with siblings could learn to detect and avoid mating with familiar
 siblings when given a choice between familiar and unfamiliar siblings. We
 found that females mated randomly in all three choice combinations.
 Observed male behavior also did not influence female mating outcome. Our
 results suggest that adult females do not innately avoid or learn to avoid
 siblings during mate selection, and that filial detection may not be as
 critical to reproductive fitness in B. anynana as
 previously thought.
description: This is the behavioral data for the manuscript Lack of sibling
 avoidance during mate selection in the butterfly Bicyclus anynana. This
 data was used to show that females did not have innate or learned
 avoidance of siblings during mate selection.
DOI: 10.5061/dryad.s1rn8pk4b
title: Extensive in situ radiation of feather lice on tinamous

description: Tinamous host the highest generic diversity of lice of any group of birds,
 as well as hosting representatives of all four avian feather louse
 ecomorphs. Although the generic diversity of tinamou feather lice is well
 documented, few attempts have been made to reconstruct the phylogenetic
 relationships among these lice. To test whether tinamou feather lice form
 a monophyletic group as a whole, we used whole genome sequencing to
 estimate a higher-level phylogeny of tinamou feather lice, together with a
 broad diversity of other avian feather louse groups. In total, we analyzed
 sequences from over 1000 genes for 48 genera of avian lice using both
 concatenated and coalescent approaches to estimate the phylogeny of this
 diverse group of avian feather lice. Although the body louse ecomorph of
 tinamou feather lice formed a monophyletic group, they did not strictly
 form a monophyletic group together with the other three ecomorphs of
 tinamou feather lice. In particular, a clade comprised of several feather
 louse genera, mainly from South America, are nested phylogenetically
 within tinamou lice, which also have their main center of diversity in
 South America. These results suggest in situ radiation of these parasites
 in South America.
description: <strong>The concatentated data matrix created using
 SequenceMatrix.</strong>
 tinamou_concat_nexus_naked.phy
 <strong>Tinamou Louse IQ Tree consensus tree
 file.</strong>
 tinamou_concat_nexus_naked.phy.contree
 <strong>Gene tree files from nuclear data, all trees were
 estimated in RAxML.</strong>
 gene_trees.zip <strong>Tinamou Louse
 gene alignment files</strong>
 gene_alignements.zip <strong>ASTRAL
 output tree</strong>
 Tinamou_ASTRAL.tree <strong>Maximum
 likelihood tree RAxML output</strong>
 RAxML_bipartitions.tinamou_concatenated.tree
 <strong>Maximum likelihood tree with partitions RAxML
 output and PartitionFinder best scheme output</strong>
 RAxML_bipartitions.Tinamou_concat_with_partitions.tree
 Tinamou_partitions_best_scheme.txt
 <strong>Maximum likelihood tree after Degen recoding
 analysis RAxML output</strong>
 RAxML_bipartitions.tinamou_recoding.tree