cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7280/d1mt2x
title: Data from: Progeny contribution scores in offense double-matings of different genotypes for the Sdic region

description: In many species, both morphological and molecular traits related to sex
 and reproduction evolve faster in males than in females. Ultimately, rapid
 male evolution relies on the acquisition of genetic variation associated
 with differential reproductive success. Many newly evolved genes are
 associated with novel functions that might enhance male fitness. However,
 functional evidence of the adaptive role of recently originated genes in
 males is still lacking. The Sperm dynein intermediate
 chain multigene family, which encodes a Sperm dynein intermediate
 chain presumably involved in sperm motility, originated from complex
 genetic rearrangements in the lineage that leads to Drosophila
 melanogaster within the last 5.4 million years since its split
 from Drosophila simulans. We deleted all the members of this
 multigene family resident on the X chromosome of D.
 melanogaster by chromosome engineering and found that, although
 the deletion does not result in a reduction of progeny number, it impairs
 the competence of the sperm in the presence of sperm from wild-type males.
 Therefore, the Sperm dynein intermediate chain multigene
 family contributes to the differential reproductive success among males
 and illustrates precisely how quickly a new gene function can be
 incorporated into the genetic network of a species.
description: Offense double-mating experiments for duplication-bearing males
 were performed as reported (Yeh, et al. 2013), and concomitantly with those for other male genotypes whose results were already published (Clifton et al. 2020).  Briefly, sperm competitive ability for any given male genotype was calculated with the P2 metric, which measures the relative contribution of the second male to mate to the total progeny of doubly-mated females.  The angular transformation was applied to the P2 values (Sokal and Rohlf 1994).
DOI: 10.5061/dryad.xgxd254d0
title: Extensive cytonuclear discordance in a crested newt from the Balkan Peninsula glacial refugium

description: Integrating multilocus data and species distribution modelling into
 phylogeography allows mtDNA-based scenarios to be fine-tuned. We address
 the question of whether extensive mtDNA substructuring in the crested newt
 Triturus macedonicus from the Balkan Peninsula is matched in the nuclear
 genome. We determine the intraspecific population structure based on 52
 nuclear DNA markers and project a species distribution model on climate
 layers for the Last Glacial Maximum. We show that T. macedonicus
 accumulated nuclear DNA population structure in an area predicted to have
 been climatically stable during the Pleistocene, with four nuclear DNA
 groups in the western part of T. macedonicus’ range. The distribution of
 these nuclear DNA groups shows little agreement with that of mtDNA
 structuring, which shows three highly distinct species-specific clades and
 a fourth one introgressed from another crested newt species. This
 cytonuclear discordance conveys that historical biogeographical scenarios
 based on mtDNA exclusively should be interpreted with caution. Our
 findings further highlight the important role the Balkan Peninsula has
 played in the evolution and preservation of Europe’s biodiversity.
DOI: 10.25338/b80g7z
title: Global human influence maps reveal clear opportunities in conserving Earth’s remaining intact terrestrial ecosystems

description: Leading up to the 2020 Convention on Biological Diversity there is
 momentum around setting bold conservation targets. Yet it remains unclear
 how much of Earth’s land area remains without significant human influence
 and where this land is located. We compare four recent global maps of
 human influences across Earth’s land, Anthromes, Global Human
 Modification, Human Footprint, and Low Impact Areas, to answer these
 questions. Despite using various methodologies and data, these different
 spatial assessments independently estimate similar percentages of the
 Earth’s terrestrial surface as having very low (20-34%) and low (48-56%)
 human influence. Three out of four spatial assessments agree on 46% of the
 non-permanent ice- or snow-covered land as having low human influence.
 However, much of the very low and low influence portions of the planet are
 comprised of cold (e.g., boreal forests, montane grasslands and tundra) or
 arid (e.g., deserts) landscapes. Only four biomes (boreal forests,
 deserts, temperate coniferous forests and tundra) have a majority of
 datasets agreeing that at least half of their area has very low human
 influence. More concerning, &lt;1% of temperate grasslands, tropical
 coniferous forests and tropical dry forests have very low human influence
 across most datasets, and tropical grasslands, mangroves and montane
 grasslands also have &lt;1% land identified as very low influence
 across all datasets. These findings suggest that about half of Earth’s
 terrestrial surface has relatively low human influence and offers
 opportunities for proactive conservation actions to retain the last intact
 ecosystems on the planet. However, though the relative abundance of
 ecosystem areas with low human influence varies widely by biome,
 conserving these last intact areas should be a high priority before they
 are completely lost.
description: See Methods in
 publication.
DOI: 10.5061/dryad.hmgqnk9d0
title: Data from: Machine learning based detection of adaptive divergence of the stream mayfly Ephemera strigata populations

description: Adaptive divergence is a key mechanism shaping the genetic variation of
 natural populations. A central question linking ecology with evolutionary
 biology is how spatial environmental heterogeneity can lead to adaptive
 divergence among local populations within a species. In this study, using
 a genome scan approach to detect candidate loci under selection, we
 examined adaptive divergence of the stream mayfly Ephemera strigata in the
 Natori River Basin in north eastern Japan. We applied a new machine
 learning method (i.e. Random Forest) besides traditional distance-based
 redundancy analysis (dbRDA) to examine relationships between environmental
 factors and adaptive divergence at non-neutral loci. Spatial
 autocorrelation analysis based on neutral loci was employed to examine the
 dispersal ability of this species. We conclude the following: 1) E.
 strigata show altitudinal adaptive divergence among the populations in the
 Natori River Basin; 2) random forest showed higher resolution for
 detecting adaptive divergence than traditional statistical analysis; 3)
 separating all markers into neutral and non-neutral loci could provide
 full insight into parameters such as genetic diversity, local adaptation,
 and dispersal ability.
DOI: 10.5061/dryad.zw3r2285q
title: Data from: Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological “hotspot”

description: Andøya on the NW coast of Norway is a key site for understanding the Last
 Glacial Maximum (LGM) in northern Europe. Controversy has arisen
 concerning the local conditions, especially about the timing and extent of
 local glacial cover, maximum July temperatures and whether pine and/or
 spruce could have grown there. We reviewed all existing data and add newly
 analysed ancient sedimentary DNA, pollen, macrofossils, geochemistry and
 stable isotopes from three lake sediment cores from Øvre Æråsvatnet. A
 total of 23 new dates and age-depth modelling suggests the lake has been
 ice-free since GI2 (&lt;22.8 k cal. BP) and possibly GS3 (&lt;27.4
 k cal. BP). Pinus and Picea sedimentary ancient DNA (sedaDNA) was found in
 all three cores but at such low frequencies that it could not be
 distinguished from background contamination. LGM samples have an
 exceptionally high organic matter content, with isotopic values indicating
 that carbon and nitrogen derives from a marine source. Along with finds of
 bones of the little auk (Alle alle), this indicates that the lake received
 guano from an adjacent bird colony. DNA, pollen and macrofossil
 assemblages were dominated by Poaceae, Brassicaceae and Papaver, but
 scattered occurrence of species currently restricted to the Low Arctic
 Tundra Zone (July temperature of 8-9°C) such as Apiaceae (DNA, 8-9°C), and
 Alchemilla alpina (macrofossil, 8-9°C) were also recorded. The review
 showed 94 recorded vascular plant taxa, of which 38% have a northern limit
 in Shrub Tundra or more southern vegetation zones. This unusual assemblage
 likely stems from a combination of proximity to ice-free water in summer,
 geographical isolation linked with stochastic long- distance dispersal
 events, and the presence of bird-fertilized habitats. The environmental
 reconstruction based on all records from the area does not preclude local
 growth of tree species, as the local climate combined with high nutrient
 input may have led to periodically suitable environmental ‘hotspot’
 conditions.
description: DNA metabarcoding of ancient lake sediments collected from
 Andøya, Norway. The chloroplast <em>trn</em>L (UAA) intron, or
 p6-loop, was amplified for the sediment extracts.
description: This dataset includes two raw Illumina NextSeq 500 libraries
 (paired-end sequenced) and the associated OBITools PCR-tag lookup tables
 required for demultiplexing.
DOI: 10.5061/dryad.05qfttf0d
title: Soil carbon, nitrogen, and phosphorus cycling microbial populations and their resistance to global change depend on C:N:P stoichiometry

description: Maintaining the stability of ecosystem functions to global
 change calls for a better understanding the regulatory factors of
 functionally specialized microbial-groups and their
 population-response to disturbance. Here, we
 explored this issue by collecting soils from 54
 managed ecosystems in China and building a predictive model of
 microcosm experiments. Soil carbon:nitrogen:phosphorus (C:N:P)
 stoichiometry (35%~49%) imparted a greater individual
 effects on the abundances of microbial-groups associated with
 main carbon C, N, and P biogeochemical processes in
 comparison with geographical
 conditions (7%~10%). Soil total C and N
 contents were significantly positively correlated with the
 abundances of diazotrophs (nifH), nitrifiers (bacterial
 amoA), nitrate reducers (narG) and
 denitrifiers (nirS/K and nosZ genes). Soil
 C:N ratio not only exhibited a negative relationship
 with the abundances of P
 activators (phoD, phoC and
 pqqC genes), but also with
 cellulolytic decomposers (fungcbhIR and
 GH74 genes). Nitrogen cycling genes, including bacterial
 amoA, nirS, narG and
 norB, exhibited higher genetic resistance to N
 deposition compared with the drying-wetting cycles and
 warming. Soil total C, N and P contents, and their
 ratios had a strong direct effect on the genetic
 resistance of microbial-groups. Soil C:P ratio was selected by
 random forest analyses as the main predictor of N cycling genetic
 resistance to N deposition. Soil total C and N contents, and their ratios
 were the main predictors of the P cycling genetic resistance to
 three global change drivers. Overall, our
 work highlights the importance of soil stoichiometric balance for
 maintaining the ability of microbially-driven ecosystem functions to
 withstand global change.
DOI: 10.5061/dryad.nvx0k6dp9
title: Antibiotic resistance in Gram-negative Bacteria Causing Blood stream infections

description: Background: The pathogenic spectrum of blood stream infections (BSIs)
 varies across regions. Monitoring the pathogenic profile and antimicrobial
 resistance is a prerequisite for effective therapy and infection control.
 The study analyzed the pathogenic spectrum of blood cultures with special
 focus on the resistance pattern of A.baumannii, E.coli and K. pneumoniae
 from a referral hospital of Saudi Arabia.
description: Culture and sensitivity reports
DOI: 10.15468/dl.zv5535
title: Occurrence Download

description: A dataset containing 8657656 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Butterfly distribution records for the UK from Butterfly Conservation, up to 2019",
 "TaxonKey is Nymphalidae",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 8657656 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002322-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cz8w9gj0t
title: Comparison of environmental inference approaches for ecometric analyses: Using hypsodonty to estimate precipitation

description: Ecometrics is the study of community-level functional trait-environment
 relationships. We use ecometric analyses to estimate paleoenvironment and
 to investigate community-level functional changes through time. We
 evaluate four methods that have been used or have the potential to be used
 in ecometric analyses for estimating paleoenvironment to determine whether
 there have been systematic differences in paleoenvironmental estimation
 due to choice of the estimation method. Specifically, we evaluated linear
 regression, polynomial regression, nearest neighbor, and maximum
 likelihood methods to explore the predictive ability of the relationship
 for a well-known ecometric dataset of mammalian herbivore hypsodonty
 metrics (molar tooth crown to root height ratio) and annual precipitation.
 Each method was applied to 43 Pleistocene fossil sites and compared to
 annual precipitation from global climate models. Sites were categorized as
 glacial or interglacial, and paleoprecipitation estimates were compared to
 the appropriate model. Estimation methods produce results that are highly
 correlated with log precipitation and estimates from the other methods (p
 &lt; 0.001). Differences between estimated precipitation and observed
 precipitation are not significantly different across the four methods, but
 maximum likelihood produces the most accurate estimates of precipitation.
 When applied to paleontological sites, paleoprecipitation estimates align
 more closely with glacial global climate models than with interglacial
 models regardless of the age of the site. Each method has constraints that
 are important to consider when designing ecometric analyses to avoid
 misinterpretations when ecometric relationships are applied to the
 paleontological record. We show interglacial fauna estimates of
 paleoprecipitation more closely match glacial global climate models. This
 is likely because of the anthropogenic effects on community reassembly in
 the Holocene.
DOI: 10.5061/dryad.0p2ngf1x6
title: Vocal recognition suggests premating isolation between lineages of a lekking hummingbird

description: Species with genetically differentiated allopatric populations commonly
 differ in phenotypic traits due to drift and/or selection, which can be
 important drivers of reproductive isolation. Wedge-tailed sabrewing
 (Campylopterus curvipennis) is a species complex composed of three
 genetically and acoustically differentiated allopatric lineages which
 correspond to currently recognized subspecies in Mexico: C. c. curvipennis
 (Sierra Madre Oriental), C. c. pampa (Yucatán Peninsula), and C. c.
 excellens (Los Tuxtlas). Although excellens is taxonomically recognized as
 a distinct species, there is genetic evidence that lineages excellens and
 curvipennis have diverged from each other later than pampa. In this study,
 we experimentally tested C. c. curvipennis song recognition as a major
 factor in premating reproductive isolation for lineage recognition. To
 this end, we conducted a song playback experiment to test whether
 territorial males of one C. c. curvipennis lek discriminate among
 potential competitors based on male songs from the three lineages. Males
 of curvipennis responded more aggressively to songs of their own lineage
 and excellens, than to songs of the most divergent lineage pampa, as
 evidenced by significant differences in a variety of intensity and latency
 response variables. This indicate that the pampa male song does not
 represent a competitive threat as curvipennis and excellens songs, in
 which divergence and song recognition represent premating reproductive
 isolation between these isolated lineages. However, the acoustic limits
 between curvipennis and excellens might be attenuated by gene flow in case
 of secondary contact between them, despite the strong and relatively rapid
 divergence of their sexually selected song traits.
DOI: 10.5061/dryad.pg4f4qrkc
title: Selection for increased cranial capacity in small mammals during a century of urbanization

description: Urbanization is a selective force that is known to drive changes in the
 population dynamics of wildlife. How animals adapt to changing
 environmental conditions is crucial to their survival in these
 environments. Brain size, or cranial capacity, is a known proxy of
 behavioral flexibility, and can be used to assess how well a species has
 adapted to a particular environment. We examined cranial capacity
 changes in a time series of small mammal skulls collected from urban and
 rural populations in south western Pennsylvania. Urban skulls were
 collected from Allegheny county—an area that experienced rapid
 urbanization over the past century, and rural skulls from Powdermill
 Nature Reserve (Carnegie Museum), which has remained relatively unchanged
 forest over the same period. Our results show that Peromyscus
 leucopous (white-footed mouse) and Microtus
 pennsylvanicus (meadow vole) from urban populations had
 significantly greater cranial capacity than their
 rural counterparts, but the opposite was true
 for Eptesicus fuscus (big brown bat). We found
 no difference in relative cranial capacity across time in any of the small
 mammal species. Our results suggest that a larger cranial capacity is
 selected for in an urban environment and reinforces the hypothesis that
 behavioral flexibility is important for animals to adapt to novel
 environments.
DOI: 10.5061/dryad.s7h44j145
title: Tree mycorrhizal type mediates the strength of negative density dependence in temperate forests

description: 1. Recent plant-soil feedback experiments suggest that arbuscular
 mycorrhizal (AM) tree species experience stronger conspecific negative
 density dependence (CNDD) than ectomycorrhizal (EM) tree species. Yet how
 these findings inform our understanding of natural systems is limited
 because the roles of local soil conditions, light environments and tree
 species abundances in influencing CNDD for AM and EM species are not
 clear. 2. Here we examined seedling and sapling survival in two temperate
 old-growth forests (broadleaved pine and spruce-fir forests) in Northeast
 China, to evaluate the effects of both conspecific and heterospecific
 neighbour density, as well as the soil and light environments, on the
 survival of AM and EM-dependent trees at early life stages. 3. While light
 availability increased the survival of EM seedlings, soil organic
 resources increased EM sapling survival in the spruce-fir plot. AM
 seedlings suffered stronger CNDD than did EM seedlings in both plots. In
 the spruce-fir plot, soil factors and light availability mediated species
 CNDD but their effects differed for AM and EM species, and also between
 seedlings and saplings. For seedlings in both plots, we found that AM
 species exhibited a positive relationship between species abundance and
 CNDD strength, whereas this relationship was negative for EM species. 4.
 Synthesis. Our results provide one of the few tests of how fungal
 symbioses determine species responses to intra- and interspecific
 interactions and the direct effects of local environmental conditions on
 seedling and sapling survival. We show that mycorrhizal type mediates the
 strength of CNDD and its relationship with species abundance. These
 results suggest that tree mycorrhizal association can determine the
 strength of CNDD effects on both rare and common species, and these CNDD
 differences are likely to influence the community composition of temperate
 forests.
DOI: 10.5061/dryad.jq2bvq86h
title: Data from: Disentangling the steps of the infection process responsible for juvenile disease susceptibility

description: 1. Juveniles of diverse host taxa, including vertebrates, invertebrates
 and plants, are more susceptible to parasitic infections than adults, a
 phenomenon still poorly understood. 2. To shed light on the mechanisms
 underlying this host age effect, we investigated its expression during
 different steps of the infection process of a bacterial parasite of the
 planktonic crustacean Daphnia. To do so, we infected juvenile and adult
 Daphnia magna with the bacterium Pasteuria ramosa and monitored parasite
 development in experiments specific to different steps of the infection
 process. 3. We did not find an effect of host age on parasite attachment,
 but found a strong increase in the penetration time of the parasite into
 hosts with increasing age. Host age at exposure also affected within-host
 parasite development, which was delayed in old adult D. magna in
 comparison to young adults and juveniles. Furthermore, parasite clearance
 was observed only in old adults, suggesting that old hosts have a better
 immune response than young adults and juveniles. 4. Our results reveal a
 step-specific effect of host age on disease progression, giving support
 for different hypotheses explaining high juvenile disease susceptibility.
 While these mechanisms are likely to work independently from each other,
 earlier steps of the infection process influence later steps, and thus may
 respond more readily to selection than later steps. 5. Our results also
 highlight that clearance can occur both during early parasite
 establishment and surprisingly at progressed infection phases, an
 undocumented phenomenon in invertebrates, where late infections are often
 considered chronic, lasting until host death.
DOI: 10.5061/dryad.fn2z34tr0
title: Data from: The ecological and genomic basis of explosive adaptive radiation

description: Rates of speciation vary tremendously among evolutionary lineages, with
 our understanding of what fuels the rapid succession of speciation events
 within young adaptive radiations remaining particularly incomplete. The
 cichlid fish family provides the most notable example of such variation
 among extant metazoans. It includes many slowly speciating lineages as
 well as the several exceptionally large and rapid adaptive radiations. By
 reconstructing a large phylogeny of all described cichlid species, we show
 that explosive speciation is solely concentrated in several large yet
 young lake species flocks. Across the family, speciation rate increases
 are associated with absence of top predators, and speciation rate
 decreases are associated with arid climate, but these factors are not
 nearly sufficient to explain explosive speciation in lake radiations, in
 particular the Lake Victoria adaptive radiation. Across lake radiations we
 observe a positive relationship between speciation rate and enrichment
 with large indel polymorphisms. Assembly of one hundred Victorian cichlid
 genomes comprising all extant ecological guilds and taxonomic genera
 reveals this radiation contains exceptional ‘genomic potential’ - hundreds
 of ancient haplotypes bearing indel polymorphisms, many of which are
 strongly associated with specific ecologies and are shared with
 ecologically similar species from other older lake radiations elsewhere in
 Africa. Network analysis reveals fundamentally non-treelike evolution
 through recombining old haplotypes, with origins of ecological guilds
 concentrated early in the Victoria radiation. Our results suggest that the
 combination of ecological opportunity, sexual selection and exceptional
 genomic potential is the key to understanding explosive adaptive
 radiation.