cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sbcc2fr5g
title: Data for: Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure

description: Many coral reef fishes are fished, often resulting in detrimental genetic
 effects; however, reef fishes often show unpredictable patterns of genetic
 variation, which potentially mask the effects of fishing. Our goals were
 to characterize spatial and temporal genetic variation and determine the
 effects of fishing on an exploited reef fish, Plectropomus
 leopardus, Lacepède (the common coral trout). To determine
 population structure, we genotyped 417 Great Barrier Reef coral trout from
 four populations sampled in two years (1996 and 2004) at nine
 microsatellite loci. To test for exploitation effects, we additionally
 genotyped 869 individuals from a single cohort (ages 3-5) across eight
 different reefs, including fished and control populations. Genetic
 structure differed substantially in the two sampled years, with only one
 year exhibiting isolation by distance. Thus, genetic drift likely plays a
 role in shaping population genetic structure in this species. Although we
 found no loss of genetic diversity associated with exploitation, our
 relatedness patterns show that pulse fishing likely affects populations.
 Additionally, genetic structure in the cohort samples likely reflected
 spatial variation in recruitment contributing to genetic structure at the
 population level. Overall, we show that fishing does impact coral reef
 fishes, highlighting the importance of repeated widespread sampling to
 accurately characterize the genetic structure of reef fishes, as well as
 the power of analysing cohorts to avoid the impacts of recruitment-related
 genetic swamping. The high temporal and spatial variability in genetic
 structure, combined with possible selection effects, will make
 conservation/management of reef fish species complex.
description: <strong>Genotypes for spatial/temporal
 samples</strong>: spatial_temporal_genepop_417.txt
 <strong>Genotypes for cohort
 samples</strong>: cohort_genepop_all.txt See
 README.txt for details on population codes.
DOI: 10.15468/dl.bf9srq
title: Occurrence Download

description: A dataset containing 5511 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Ibaraki Nature Museum, Mollusk collection"
 ]
}

 The dataset includes 5511 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002724-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0gb5mkm0b
title: The importance of environmental conditions in maintaining lineage identity in Epithelantha (Cactaceae)

description:  The use of environmental variables to explain the evolution of
 lineages has gained relevance in recent studies. Additionally, it has
 allowed the recognition of species by adding more characters to
 morphological and molecular information. This study focuses on identifying
 environmental and landscape variables that have acted as barriers that
 could have influenced the evolution of Epithelantha species and its close
 genera. Our results show that soil pH, isothermality, temperature
 seasonality, and annual precipitation have a significant phylogenetic
 signal for Epithelantha. Soil type and landforms are also relevant as
 ecological barriers that maintain the identity of Epithelantha species.
 The variables associated with the soil (pH) have influenced the evolution
 of Epithelantha and probably in other genera of Cactaceae. Additionally,
 Epithelantha is frequent in the piedmont and haplic kastanozems.
 Bioclimatic variables reinforce the recognition of E. micromeris and E.
 cryptica as independent species. Therefore, ecology can be considered as a
 factor to explain the high level of endemism in Cactaceae.
description: The following regions were amplified and sequenced following the
 methods in Aquino et al. 2019 (https://doi.org/10.1600/036364419X15620113920635): petL-psbE, psbA-trnH, trnL-F and trnQ-rps16.
DOI: 10.5061/dryad.zw3r22876
title: Data from: Reticulate evolution, ancient chloroplast haplotypes, and rapid radiation of the Australian plant genus Adenanthos (Proteaceae)

description: Cytonuclear discordance, commonly detected in phylogenetic studies, is
 often attributed to hybridisation and/or incomplete lineage sorting (ILS).
 New sequencing technologies and analytical approaches can provide new
 insights into the relative importance of these processes. Hybridisation
 has previously been reported in the Australian endemic plant
 genus Adenanthos (Proteaceae). Like many Australian
 genera, Adenanthos is of relatively ancient origin, and
 provides an opportunity to examine long-term evolutionary consequences of
 gene flow between lineages. Using a hybrid capture approach, we assembled
 densely sampled low-copy nuclear and plastid DNA sequences
 for Adenanthos, inferred its evolutionary history, and used a
 Bayesian posterior predictive approach and coalescent simulations to
 assess relative contributions of hybridisation and ILS to cytonuclear
 discordance. Our analyses indicate that strong incongruence detected
 between our plastid and nuclear phylogenies is not only the result of ILS,
 but also result from extensive ancient introgression as well as recent
 chloroplast capture and introgression between
 extant Adenanthos species. The deep
 reticulation was also detected from long-persisting chloroplast haplotypes
 shared between evolutionarily distant species. These haplotypes may have
 persisted for over 12 Ma in localised populations across southwest Western
 Australia, indicating that the region is not only an important area for
 old endemic lineages and accumulation of species, but is also
 characterized by persistence of high genetic diversity. Deep introgression
 in Adenanthos coincided with the rapid radiation of the
 genus during the Miocene, a time when many Australian temperate plant
 groups radiated in response to large-scale climatic change. This study
 suggests that ancient introgression may play an important role in the
 evolution of the Australian flora more broadly.
DOI: 10.5061/dryad.jsxksn083
title: Data from: Complex evolution of novel red floral color in Petunia

description: Transitions to a new floral color tend to be genetically simple, almost
 always involving a few loss-of-function mutations of major phenotypic
 effect. Here we report on the complex evolution of a novel red floral
 color in the hummingbird-pollinated Petunia exserta (Solanaceae) from a
 colorless ancestor. The presence of a red color is remarkable because P.
 exserta retains a nonfunctional copy of the floral anthocyanin activating
 MYB transcription factor AN2, and additionally the genus cannot synthesize
 monohydroxylated red anthocyanins. We show that moderate up-regulation and
 a shift in tissue specificity of an AN2 paralog, DEEP PURPLE (DPL)
 restores anthocyanin biosynthesis in P. exserta, a case of regulatory
 neofunctionalization. An essential shift in anthocyanin hydroxylation
 occurred through re-balancing the expression of three hydroxylating genes.
 Furthermore, the down-regulation of an acyltransferase promotes reddish
 hues in typically purple delphinidin pigments by preventing acyl group
 decoration of anthocyanins. Finally, additional mutations of relatively
 small effect are also involved. This study demonstrates that commonly
 observed phenotypic transitions, such as in floral color, can involve many
 more loci than predicted. Repeated evolution of red flowers has occurred
 in the Solanaceae and in the same biosynthetic pathway, yet the precise
 mechanism is less predictable and complex.
description: Supplemental Dataset 1. Fasta alignment of MYB Subgroup 6 and PH4
 clade (<em>P. exserta, P. axillaris, P.
 secreta</em>) Supplemental Dataset 2. Newick tree
 file for MYB Subgroup 6 and PH4 clade (<em>P. exserta, P. axillaris,
 P. secreta</em>) Supplemental Dataset 3. Fasta
 alignment of entire MYB tree (<em>P. exserta, P.
 axillaris</em>) Supplemental Dataset 4. Newick
 tree file for entire MYB tree (<em>P. exserta, P.
 axillaris</em>) Supplemental Dataset
 5. Normalized read counts for flavonoid and phenylpropanoid gene
 expression across <i>Petunia </i>species.
 Additionally: Supplemental
 protein alignments for <em>Petunia</em>
 <em>DPL</em> and <em>PH4</em> transcription
 factors Supplemental protein alignments for
 <em>Petunia</em> flavonoid pathway biosynthetic
 genes Supplemental nucleotide alignments of
 <em>AN4</em> and <em>AN4</em>-like genes detected
 in the draft <em>P. exserta </em>genome
 Supplemental R/qtl datafile for RILs Genome
 annotation file for <em>P. secreta </em>genome
 assembly
DOI: 10.5061/dryad.qz612jmdk
title: Data for: Lava crickets (Caconemobius spp.) on Hawai´i Island: first colonizers or persisters in extreme habitats?

description: 1. Primary succession after a volcanic eruption is a major ecological
 process, but relatively little is known about insects that colonize barren
 lava before plants become established. 2. On Hawai´i Island, the endemic
 cricket, Caconemobius fori Gurney & Rentz, 1978, is known as the
 first multicellular life form to colonize lava after an eruption from
 Kīlauea Volcano. In the Kona region, a congener, Caconemobius anahulu
 Otte,1994 inhabits unvegetated lava flows from Hualālai Volcano, but
 little has been documented about its distribution. 3. Our aim was to
 characterize the presence/absence of Caconemobius spp. across lava flows
 that are largely unvegetated, but differ in age since eruption and
 connectivity to older flows. We used baited live traps to survey 9
 month–50 year-old Kīlauea lava flows for C. fori, and ~220 year-old
 Hualālai lava flows for C. anahulu. 4. We found no evidence that C. fori
 has colonized the Kīlauea flows from the 2018 eruption. However, we did
 discover that C. fori was persistent and widespread on Kīlauea lava up to
 50 years old within Hawai´i Volcanos National Park. We also captured C.
 anahulu across much of the Hualālai lava flows we surveyed in Kona. 5. We
 demonstrated that C. fori do not always arrive on new lava within months
 after an eruption, in contrast to previous reports, and that both C. fori
 and C. anahulu can remain on lava longer than previously appreciated.
 Vegetation successional state may be more important than true age for the
 persistence of these endemic crickets.
description: Detailed methods can be found in Heinen-Kay et al. (2021)
 Ecological Entomology. In short, we sampled for two species of endemic
 <em>Caconemobius</em> crickets on mostly barren lava on Hawaii
 Island. We used live traps baited with shrimp paste. Sampling sites were
 distributed among three regions:  <i>C. anahulu</i> was
 present in Kona, <i>C. fori</i> was present in HVNP, and
 <i>C. fori</i> was expected to be present in Puna. 
  
description: Trap histories for <i>Caconemobius</i> on the Big
 Island of Hawai’i, 2019.  Data accompanies Heinen-Kay et al. (2021)
 Ecological Entomology, which details the sampling design.  Each line
 represents a single trap that was open for 1 to 5 nights, beginning on the
 date given.  “1” represents a trap-night on which a Caconemobius was
 captured, “0” a trap-night on which one was not.  Sampling sites were
 distributed among three regions:  <i>C. anahulu</i> was
 present in Kona, <i>C. fori</i> was present in HVNP, and
 <i>C. fori</i> was expected to be present in Puna.
DOI: 10.15468/dl.c7rxba
title: Occurrence Download

description: A dataset containing 4384 records in GBIF matching the query:
SELECT
 '449' 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;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= 77.9229717807129
 AND decimalLongitude &lt;= 88.12157328514692
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 4384 records were derived from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002713-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.31zcrjdjv
title: The Camouflage Machine: Optimising protective colouration using deep learning with genetic algorithms

description: Evolutionary biologists frequently wish to measure the fitness of
 alternative phenotypes using behavioural experiments. However, many
 phenotypes are complex. For example colouration: camouflage aims to make
 detection harder, while conspicuous signals (e.g. for warning or mate
 attraction) require the opposite. Identifying the hardest and easiest to
 find patterns is essential for understanding the evolutionary forces that
 shape protective colouration, but the parameter space of potential
 patterns (coloured visual textures) is vast, limiting previous empirical
 studies to a narrow range of phenotypes. Here we demonstrate how deep
 learning combined with genetic algorithms can be used to augment
 behavioural experiments, identifying both the best camouflage and the most
 conspicuous signal(s) from an arbitrarily vast array of patterns. To show
 the generality of our approach, we do so for both trichromatic (e.g.
 human) and dichromat (e.g. typical mammalian) visual systems, in two
 different habitats. The patterns identified were validated using human
 participants; those identified as the best for camouflage were
 significantly harder to find than a tried-and-tested military design,
 while those identified as most conspicuous were significantly easier than
 other patterns. More generally, our method, dubbed the ‘Camouflage
 Machine’, will be a useful tool for identifying the optimal phenotype in
 high dimensional state-spaces.
DOI: 10.5061/dryad.t4b8gtj13
title: Insecticide resistance governed by gut symbiosis in a rice pest, Cletus punctiger, under laboratory conditions

description: Resistance to toxins in insects is generally thought of as their own
 genetic trait, but recent studies have revealed that gut microorganisms
 could mediate resistance by detoxifying phytotoxins and man-made
 insecticides. By laboratory experiments, we here discovered a striking
 example of gut symbiont-mediated insecticide resistance in a serious rice
 pest, Cletus punctiger. The rice bug horizontally acquired
 fenitrothion-degrading Burkholderia through oral infection and housed it
 in midgut crypts. Fenitrothion-degradation test revealed that the
 gut-colonizing Burkholderia retains a high degrading activity of the
 organophosphate compound in the insect gut. This gut symbiosis remarkably
 increased resistance against fenitrothion treatment in the host rice bug.
 Considering that many stinkbug pests are associated with soil-derived
 Burkholderia, our finding strongly supports that a number of stinkbug
 species could instantly resistant against insecticide only by acquiring
 insecticide-degrading gut bacteria.
DOI: 10.5061/dryad.2ngf1vhmq
title: Sick of attention: The effect of a stress-related disease on juvenile green sea turtle behaviour in the face of intense and prolonged tourism

description: Anthropogenic activities are increasingly linked to emerging diseases that
 cause mortality across many taxa. Human interference through ecotourism,
 in particular, can increase the stress levels of wild populations and
 promote the spread of disease. In Akumal Bay, Mexico, green sea turtles
 (Chelonia mydas) are increasingly infected with fibropapillomatosis (FP),
 an infectious disease associated with stress-induced immunosuppression
 linked to high human density, which is particularly high in this area
 because of intense and prolonged ecotourism. To examine if FP might be
 associated with behavioural indicators of stress and varying levels of
 tourist pressure, we observed the behaviour of turtles and the number of
 tourists through 20-minute focal sampling periods from May to August 2017.
 We related disease presence and tourist pressure to several aspects of
 turtle behaviour, specifically feeding, resting, vertical movements (i.e.,
 surfacing and diving), and evasive responses. Turtles that had FP engaged
 in fewer feeding periods, vertical movements, and evasive responses.
 Additionally, with increasing tourist pressure, all turtles spent less
 time engaging in vertical movements and had more evasive responses. Our
 results suggest that the presence of FP affects green sea turtle behavior,
 potentially increasing their exposure to tourists. Sick and healthy
 turtles appear to react differently to tourists, suggesting that FP
 weakens behavioural responses to tourist pressure. Future management
 strategies should consider regulating tourist pressure on turtles to
 reduce the incidence and progression of FP.
description: This upload contains the input data describing the duration of
 green sea turtle behaviours within a sample ("activity budget
 clean"), the number of times these behaviours were initiated
 ("Activity Budget Counts (V2)"), as well as the count of evasive
 responses demonstrated by turtles with and without Fibropapillomatosis
 ("clean data for analysis ev (V3)"). The associated R code will
 be uploaded following any necessary revisions during the review
 process.
DOI: 10.5061/dryad.z612jm6b7
title: Lineage-level distribution models lead to more realistic climate change predictions for a threatened crayfish

description: Aim: As climate change presents a major threat to biodiversity in the next
 decades, it is critical to assess its impact on species habitat
 suitability to inform biodiversity conservation. Species distribution
 models (SDMs) are a widely used tool to assess climate change impacts on
 species’ geographical distributions. As the term suggests, the
 species-level is the most commonly used taxonomic unit in SDMs. However,
 recently it has been demonstrated that SDMs considering taxonomic
 resolution below (or above) the species-level can make more reliable
 predictions of biodiversity change when different populations exhibit
 local adaptation. Here, we tested this idea using the Japanese crayfish
 (Cambaroides japonicus), a threatened species encompassing two
 geographically structured and phylogenetically distinct genetic lineages.
 Location: Northern Japan. Methods: We first estimated niche
 differentiation between the two lineages of C. japonicus using
 n-dimensional hypervolumes, then made climate change predictions of
 habitat suitability using SDMs constructed at two phylogenetic levels:
 species and intraspecific lineage. Results: Our results showed only
 intermediate niche overlap, demonstrating measurable niche differences
 between the two lineages. The species-level SDM made future predictions
 that predicted much broader and severe impacts of climate change. However,
 the lineage-level SDMs led to reduced climate change impacts overall, and
 also suggested that the eastern lineage may be more resilient to climate
 change than the western one. Main conclusions: The two lineages of C.
 japonicus occupy different niche spaces. Compared with lineage-level
 models, species-level models can overestimate climate change impacts.
 These results not only have important implications for designing future
 conservation strategies for this threatened species, but also highlight
 the need for incorporating genetic information into SDMs to obtain
 realistic predictions of biodiversity change.
description: We developed Maxent models for Japanese
 crayfish <i>Cambaroides japonicus</i>. During model
 development, we tuned Maxent with different combinations of feature
 classes and regularization multipliers using the R package
 <i>ENMeval </i>1.9.0.
description: Users should use their own species distribution data and
 environmental layers when running this R scripts. For more details, please
 refer to the R package
 <i>ENMeval</i><em>.</em>
DOI: 10.5061/dryad.wpzgmsbkw
title: Data from: Competition sensing changes antibiotic production in Streptomyces

description: One of the most important ways that bacteria compete for resources and
 space is by producing antibiotics that inhibit competitors. Because
 antibiotic production is costly, the biosynthetic gene clusters
 coordinating their synthesis are under strict regulatory control and often
 require “elicitors” to induce expression, including cues from competing
 strains. Although these cues are common, they are not produced by all
 competitors, and so the phenotypes causing induction remain unknown. By
 studying interactions between 24 antibiotic-producing strains of
 streptomycetes, we show that strains commonly inhibit each other’s growth
 and that this occurs more frequently if strains are closely related. Next,
 we show that antibiotic production is more likely to be induced by cues
 from strains that are closely related or that share secondary metabolite
 biosynthetic gene clusters (BGCs). Unexpectedly, antibiotic production is
 less likely to be induced by competitors that inhibit the growth of a
 focal strain, indicating that cell damage is not a general cue for
 induction. In addition to induction, antibiotic production often decreases
 in the presence of a competitor, although this response was not associated
 with genetic relatedness or overlap in BGCs. Finally, we show that
 resource limitation increases the chance that antibiotic production
 declines during competition.  Our results reveal the importance
 of social cues and resource availability in the dynamics of interference
 competition in streptomycetes.