cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bcc2fqzhn
title: Mixed-species groups of herbivorous reef fish show variable responses to ecosystem perturbations in the Lakshadweep Islands, India

description: This dataset contains data on mixed-species groups of herbivorous reef
 fish and local species composition in the Lakshadweep Islands, India.
 Herbivorous reef fish provide a vital function in reef ecosystems by
 removing algae and making space available to coral recruits. The high
 abundance of herbivores in the reefs of the Lakshadweep islands has
 potentially aided in reef recovery and helped avoid a phase shift to an
 algal-dominated system, despite most areas having suffered massive coral
 losses. Mixed-species grouping in herbivores could potentially benefit
 both the participant species and the reef ecosystem by improving foraging
 efficiency. We examined the grouping propensity and species richness for
 three types of herbivore groups after a mass-bleaching event in 2010 and a
 mass recruitment event in 2015. The species richness and number of
 parrotfish groups, as well as the grouping propensity of common species,
 declined starkly across years, indicating that these groups may have
 formed in response to the mass-bleaching event, slowly diminishing as the
 reefs recovered. Conversely, large surgeonfish, which varied in richness
 and propensity across islands and aspect, are likely influenced by local
 processes. Small surgeonfish only increased in species richness and number
 in 2015, which may have been in response to the recruitment event. Thus,
 herbivorous fish may respond differently to local ecosystem perturbations
 and play different roles in reef recovery.
description: The Lakshadweep islands, located 200-400 km off the west coast of
 India, are an archipelago of atolls and small islands, located on the
 Laccadives-Chagos ridge. This study was carried out within the lagoon and
 in the reef areas of three of islands within the archipelago, namely
 Kavaratti, Kadmat, and Agatti. Mixed-species groups were sampled between
 the months of October-April over the course of three field seasons;
 2012-2013, 2013-2014, and 2014-2015. A total of 45 sites were sampled
 during each year of the study: 15 at each island, with 5 each in the
 lagoon and in reefs on the eastern and western aspects of the islands. The
 depth of the sites in the reef ranged from 12-18 meters, and sites in the
 lagoon ranged between 0.5 to 2 meters. Sampling was conducted using SCUBA
 in the reef and by snorkelling within the lagoon, between 8 a.m. to 2
 p.m.  Groups were sampled using a 60-minute random-walk at the three study
 islands.  The local species pool of fish was sampled by visual census
 using timed belt transects.
DOI: 10.5061/dryad.kkwh70s86
title: Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site

description: The data in this archive are the results of a study on the impact of heavy
 metals (HMs) on the soil microbiota of an urban Superfund site in Alabama.
 HMs are known to modify bacterial communities both in the laboratory and
 in situ. Consequently, soils in HM-contaminated sites such as the U.S.
 Environmental Protection Agency (EPA) Superfund sites are predicted to
 have altered ecosystem functioning, with potential ramifications for the
 health of organisms, including humans, that live nearby. Further, several
 studies have shown that heavy metal-resistant (HMR) bacteria often also
 display antimicrobial resistance (AMR), and therefore HM-contaminated
 soils could potentially act as reservoirs that could disseminate AMR genes
 into human-associated pathogenic bacteria. To explore this possibility,
 topsoil samples were collected from six public locations in the zip code
 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in
 six public areas in the neighboring zip code, 35214. 35027 soils had
 significantly elevated levels of the HMs As, Mn, Pb, and Zn, and
 sequencing of the V4 region of the bacterial 16S rRNA gene revealed that
 elevated HM concentrations correlated with reduced microbial diversity and
 altered community structure. While there was no difference between zip
 codes in the proportion of total culturable HMR bacteria, bacterial
 isolates with HMR almost always also exhibited AMR. Metagenomes inferred
 using PICRUSt2 also predicted significantly higher mean relative
 frequencies in 35207 for several AMR genes related to both specific and
 broad-spectrum AMR phenotypes. Together, these results support the
 hypothesis that chronic HM pollution alters the soil bacterial community
 structure in ecologically meaningful ways and may also select for bacteria
 with increased potential to contribute to AMR in human disease.
description: Full methods are contained in our publication "Heavy Metal
 Pollution Impacts Soil Bacterial Community Structure and Antimicrobial
 Resistance at the Birmingham 35th Avenue Superfund Site" in
 Microbiology Spectrum. Briefly, we collected soils from replicate
 locations in two zip codes in North Birmingham, Alabama. One zip code
 contains the heavy-metal-polluted 35th Avenue Superfund Site, and the
 second is demographically comparable but outside of the Superfund borders.
 Using a mixture of culture-based and next generation sequencing
 approaches, we characterized the microbial communities and their levels of
 heavy metal and antibiotic resistance in both zip codes to test the
 hypothesis that chronic anthropogenic metal contamination selects for
 antimicrobial resistance in environmental bacterial populations.
description: All of our analyses can be run using R, mothur, and QIIME, all of
 which are open-source.
DOI: 10.5061/dryad.fxpnvx0x4
title: Data for: Climatic oscillation promoted diversification of spinous assassin bugs during Pleistocene glaciation

description: Insect speciation is among the most fascinating topics in evolutionary
 biology; however, its underlying mechanisms remain unclear. Allopatric
 speciation represents one of the major types of speciation and is believed
 to have frequently occurred during glaciation periods, when climatic
 oscillation may have caused suitable habitats to be fragmented repeatedly,
 creating geographical isolation among populations. However, supporting
 evidence for allopatric speciation of insects in East Asia during the
 Pleistocene glaciation remains lacking. We aim to investigate the effect
 of climatic oscillation during the Pleistocene glaciation on the
 diversification pattern and evolutionary history of hemipteran insects and
 to test the hypothesis of Pleistocene species stability using spinous
 assassin bugs Sclomina (Hemiptera: Reduviidae), a small genus widely
 distributed in southern China but was lately found to have cryptic species
 diversity. Here, using the whole mitochondrial genome (mitogenome) and
 nuclear ribosomal RNA genes, we investigated both interspecific and
 intraspecific diversification patterns of spinous assassin bugs.
 Approximate Bayesian computation, ecological niche modeling and
 demographic history analyses were also applied to understand the
 diversification process and driven factors. Our data suggest that the five
 species of Sclomina are highly diverged, despite three of them currently
 being cryptic. Speciation occurred during Pleistocene when suitable
 distribution areas were possibly fragmentated. Six phylogeographic groups
 in the type species S. erinacea were identified, among which two groups
 underwent expansion during early Last Glacial Period and after Last
 Glacier Maximum. Our analyses suggest that this genus may have experienced
 climate-driven habitat fragmentation and post-glacial expansion in the
 Pleistocene, promoting allopatric speciation and intraspecific
 diversification. Our results reveal underestimated species diversity in a
 small insect group and illustrate a remarkable example of allopatric
 speciation of insects in East Asia promoted by Pleistocene climatic
 oscillations. These findings provide important insights into the
 speciation processes and aid the conservation of insect species diversity.
DOI: 10.5061/dryad.3xsj3txmf
title: Selection-driven trait loss in independently evolved cavefish populations

description: Laboratory studies have demonstrated that a single phenotype can be
 produced by many different genotypes; however, in natural systems, it is
 frequently found that phenotypic convergence is due to parallel genetic
 changes. This suggests a substantial role for constraint and determinism
 in evolution and indicates that certain mutations are more likely to
 contribute to phenotypic evolution. Here we use whole-genome resequencing
 in the Mexican tetra, Astyanax mexicanus, to investigate how selection has
 shaped the repeated evolution of both trait loss and enhancement across
 independent cavefish lineages. We show that selection on standing genetic
 variation and de novo mutations both contribute substantially to repeated
 adaptation. Our findings provide empirical support for the hypothesis that
 genes with larger mutational targets are more likely to be the substrate
 of repeated evolution and indicate that features of the cave environment
 may impact the rate at which mutations occur.
description: The data is comprised of summary statisitcs and annotations for
 each gene in the assembly Astyanax_mexicanus-2.0 GCF_000372685.2. These
 data were generated using whole genome sequences from a total of 248
 <em>Astyanax mexicanus</em> individuals across 18 cave and
 eight surface populations throughout the range of <em>A. mexicanus
 </em>in northeastern and central Mexico. We conducted scans for
 selection within populations and generated population genetic statistics.
 We also used Ensembl's biomart tool to retrieve phenotype annotations
 and GO terms associated with each gene in the genome.
DOI: 10.5061/dryad.rxwdbrvdf
title: VCF of structural variant calls of Nanopore data aligned to dm6 reference genome

description: Heterozygous chromosome inversions suppress meiotic crossover (CO)
 formation within an inversion, potentially because they lead to gross
 chromosome rearrangements that produce inviable gametes. Interestingly,
 COs are also severely reduced in regions nearby but outside of inversion
 breakpoints even though COs in these regions do not result in
 rearrangements. Our mechanistic understanding of why COs are suppressed
 outside of inversion breakpoints is limited by a lack of data on the
 frequency of noncrossover gene conversions (NCOGCs) in these regions. To
 address this critical gap, we mapped the location and frequency of rare CO
 and NCOGC events that occurred outside of the dl-49 chrX inversion in D.
 melanogaster. We created full-sibling wildtype and inversion stocks and
 recovered COs and NCOGCs in the syntenic regions of both stocks, allowing
 us to directly compare rates and distributions of recombination events. We
 show that COs are completely suppressed within 500 kb of inversion
 breakpoints, are severely reduced within 2 Mb of an inversion breakpoint,
 and increase above wildtype levels 2–4 Mb from the breakpoint. We find
 that NCOGCs occur evenly throughout the chromosome and, importantly, occur
 at wild-type levels near inversion breakpoints. We propose a model in
 which COs are suppressed by inversion breakpoints in a distance-dependent
 manner through mechanisms that influence DNA double-strand break repair
 outcome but not double-strand break location or frequency. We suggest that
 subtle changes in the synaptonemal complex and chromosome pairing might
 lead to unstable interhomolog interactions during recombination that
 permits NCOGC formation but not CO formation.
description: FASTQ files were aligned to dm6 using minimap2, then SVs were
 called using Sniffles2.
DOI: 10.5061/dryad.8sf7m0ct6
title: Legacy effects of canopy gaps on liana abundance 25 years later in a seasonal tropical evergreen forest in northeastern Thailand

description: Lianas require host trees to reach and stay in the forest canopy, but as
 seedlings and juveniles, they benefit from canopy gaps created by
 treefalls. Here, we evaluated the relative importance of these two
 aspects, i.e., the availability of potential hosts vs. the legacy effect
 of past treefall gaps, on the local abundance of liana stems in a seasonal
 tropical evergreen forest in the Sakaerat Biosphere Reserve in
 northeastern Thailand. Within a 2.5-ha plot for forest dynamics
 monitoring, canopy height was measured in 1993 and 2018 at 5-m intervals
 to distinguish areas of mature (canopy height ≥ 20 m), building (10-20 m),
 and gap phases (&lt; 10 m). In 2017–2018, we surveyed all liana stems
 ≥ 1 cm in diameter at breast height within 50 subplots (10 m × 10 m each)
 and recorded their diameter and the diameter of the host tree. Of a total
 of 445 liana individuals, 242 could be identified at least to the family
 level, while the others had clear morphological traits of climbing
 mechanisms. The number of liana stems was higher in areas that had been at
 the building/gap phase than those at the mature phase in 1993. When this
 25-year-old legacy of past gap locations was considered, there was a
 positive association of local abundance between lianas and trees in areas
 at the mature phase in 2018. In conclusion, liana abundance reflected a
 long-term legacy of past treefall gaps more than 25 years earlier in this
 seasonal evergreen forest.
DOI: 10.5061/dryad.0cfxpnw6w
title: Dataset for: Plasticity and genetic effects contribute to different axes of neural divergence in a community of mimetic Heliconius butterflies

description: Changes in ecological preference, often driven by spatial and temporal
 variation in resource distribution, can expose populations to environments
 with divergent information content. This can lead to adaptive changes in
 the degree to which individuals invest in sensory systems and downstream
 processes, to optimize behavioural performance in different contexts. At
 the same time, environmental conditions can produce plastic responses in
 nervous system development and maturation, providing an alternative route
 to integrating neural and ecological variation. Here, we explore how these
 two processes play out across a community
 of Heliconius butterflies. Heliconius communities exhibit multiple Mullerian mimicry rings, associated with habitat partitioning across environmental gradients. These environmental differences have previously been linked to heritable divergence in brain morphology in parapatric species pairs. They also exhibit a unique dietary adaptation, known as pollen feeding, that relies heavily on learning foraging routes, or trap-lines, between resources, which implies an important environmental influence on behavioural development. By comparing brain morphology across 133 wild-caught and insectary reared individuals from seven Heliconius species, we find strong evidence for interspecific variation in patterns of neural investment. These largely fall into two distinct patterns of variation; first, we find consistent patterns of divergence in the size of visual brain components across both wild and insectary reared individuals, suggesting genetically encoded divergence in the visual pathway. Second, we find interspecific differences in mushroom body size, a central component of learning and memory systems, but only among wild caught individuals. The lack of this effect in common-garden individuals suggests an extensive role for developmental plasticity in interspecific variation in the wild. Finally, we illustrate the impact of relatively small-scale spatial effects on mushroom body plasticity by performing experiments altering the cage size and structure experienced by individual H. hecale. Our data provide a comprehensive survey of community level variation in brain structure, and demonstrate that genetic effects and developmental plasticity contribute to different axes of interspecific neural variation.
DOI: 10.5061/dryad.4xgxd25f2
title: Data from: Prediction of three years of annual rain attenuation statistics at Ka-band in French Guiana using the Numerical Weather Prediction model WRF

description: This study highlights the interest in using an Atmospheric Numerical
 Simulator (ANS) relying on a high-resolution weather forecast model
 coupled with an ElectroMagnetic Module (EMM) to compute Ka-band rain
 attenuation statistics in an equatorial region. An optimization of the
 parametrisation of the Weather Research and Forecasting meteorological
 model (WRF) is carried out using measurements collected from a propagation
 experiment carried out by CNES and ONERA near Kourou in French Guiana.
 Both simulated and experimental annual Complementary Cumulative
 Distribution Functions (CCDF) of rain attenuation are presented in this
 dataset. More specifically, this dataset includes the statistical
 distribution from both the WRF-EMM model and from the propagation
 experiment for the years 2017, 2018, 2020 and the whole three-year period.
description: These statistical distributions have been processed with
 numerical time series from both the WRF-EMM model and from the
 experiment.
DOI: 10.5061/dryad.pg4f4qrvh
title: Data from: Natural singing interactions in Parus major

description: Eavesdropping on interactions between conspecific animals provides a
 low-cost method for assessing other individuals. Asymmetries in
 territorial counter-singing interactions in songbirds provide a rich
 source of information for eavesdroppers about differences between the
 singers. Yet, little is known about the relationship between interactive
 singing in a natural, low-arousal context among territorial neighbours and
 individual traits of males. We used a microphone array to monitor natural
 counter-singing interactions in great tits (Parus major) during nest
 building, at the onset of the breeding season. We quantified song
 overlapping and song matching for 30 pairs (dyads) of interacting males,
 singing at their nest, respectively. We then compared these behaviours to
 five traits for 28 males: body condition, plumage ornamentation, offspring
 provisioning behaviour, offspring weight, and breeding site quality. We
 found no relationship between a male song overlapping or matching
 behaviour and any of the measured traits. Therefore, our results do not
 support the idea that short-term asymmetries in low-arousal long-range
 singing interactions among neighbours reflect differences in these
 fitness-related traits. Instead, our findings suggest that such singing
 asymmetries have less signal value in the absence of an immediate conflict
 but instead reflect short-term motivational differences, as shown in
 previous investigations.
description: Data were colleced from a field population of great tits. Singing
 data are from natural singing interactions between two males, each singing
 from near their own nestbox, i.e. during a low arousal situation at a
 distance at which no visual cues were available. The other phenotypic and
 fitness data were collected from the birds in the field as described in
 the manuscript.
description: Statistical analyses were conducted in R.
DOI: 10.5061/dryad.sqv9s4n7s
title: Data from: Reciprocal transplants reveal asymmetric local adaptation of Himalayan Rhododendron approaching elevational range limit

description: As plant species expand their upper limit of distribution under current
 warming, some retain both traditional climate space and biotic environment
 while others encounter novel conditions.  The latter is
 the case for Rhododendron campanulatum,a woody shrub that grows
 both above and below treeline at our study site in the Eastern Himalaya
 where a very conspicuous, stable treeline was defined by a nearly
 contiguous canopy of tall Abies spectabilis trees, many
 of them over a century old.  Prior work showed that
 treeline had remained static in this region while R.
 campanulatum expanded its elevational range limit. We tested
 local adaptation of R. campanulatum by performing reciprocal
 transplants between the species’ current elevational range limit
 (4023masl) and just above treeline (3876 masl). Contrary to
 expectation, the coldest temperatures of late winter and early-mid spring
 were experienced by plants at the lower elevation: R.
 campanulatum at species’ limit (upper site) were covered by snow
 for a longer period (40 more days) and escaped the coldest temperatures
 suffered by conspecifics at treeline (lower site). The harsher spring
 conditions at treeline likely explains why leaves were smaller at
 treeline (15.3 cm2) than at species-limit (21.3
 cm2). Contrary to results from equivalent studies in other regions,
 survival was reduced more by downslope than by upslope movement, again
 potentially due to extreme cold temperatures observed at treeline in
 spring.  Upslope transplantation had no effect on
 mortality, but mortality of species-limit saplings transplanted downslope
 was three times higher than that of residents at both
 sites.  A general expectation is that locals should
 survive better than foreign transplants, but survival of locals and
 immigrants at our species-limit site was identical. However, those
 species-limit saplings that survive the transplant to treeline grew faster
 than both locals at treeline and the transplants at species-limit.
 Overall, we found asymmetric adaptation: compared to treeline saplings,
 those at species-limit (147 m above treeline) were more tolerant of
 extremes in the growing season but less tolerant of extremes in winter and
 early-mid spring, displaying local adaptation in a more complex manner
 than simply home advantage, and complicating predictions about impacts of
 future regional climate change.
description: The dataset was collected by making various measurements of
 plants and sites in the field in Nepal Himalaya. Please see the README
 document of this repository and the accompanying publishied article:
 Mainali K, S Adhikari, S Shrestha, C Parmesan, MC Singer, J White. 2023.
 Reciprocal transplants reveal asymmetric local adaptation of Himalayan
 Rhododendron approaching elevational range limit. Ecosphere
 [accepted]. 
description: Any program can be used that reads excel and csv files. However,
 we have also provided R code to process and analyze the data, and plot the
 output.
DOI: 10.5061/dryad.8gtht76tg
title: Data for: Ant nests increase litter decomposition to mitigate the negative effect of warming in an alpine grassland ecosystem

description: Warming can decrease feeding activity of soil organisms and affect
 biogeochemical cycles in alpine ecosystems. Ants (Formica manchu) are
 active on their nest surface, and prefer a hot and dry environment.
 Therefore, warming may provide a favorable environment for their activity.
 We hypothesized that ants might benefit from warming and increase the
 robustness of ecosystem functions to warming. To test this hypothesis, we
 examined the effects of ant nests (ant nest absence vs. ant nest presence)
 and warming (ambient temperature, + 1.3°C and + 2.3°C) on litter
 decomposition, soil properties and the plant community in an alpine
 grassland ecosystem. Decomposition stations with two mesh sizes were used
 to differentiate effects of microorganisms (0.05mm) and macroinvertebrate
 (1cm) to litter decomposition. Ant nests increased litter decomposition
 with and without macroinvertebrates accessing the decomposition station
 when compared to plots without ant nests. Only the litter decomposition in
 ant nests with macroinvertebrates accessing the decomposition station was
 not negatively affected by warming. Plots with ant nests had greater soil
 organic carbon, nutrient contents and plant growth than plots without ant
 nests, regardless of warming. Consequently, ant nests can mitigate the
 negative effects of warming on litter decomposition and improve ecosystem
 functions under warming.