cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zs7h44j4m
title: Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania

description: Increasing human population growth, exurban development, and associated
 habitat fragmentation is accelerating the isolation of many natural areas
 and wildlife populations across the planet. In Tanzania, rapid and ongoing
 habitat conversion to agriculture has severed many of the country’s former
 wildlife corridors between protected areas. To identify
 historically-linked protected areas, we investigated the genetic structure
 and gene flow of African savanna elephants in Tanzania using
 microsatellite and mitochondrial DNA markers in 688 individuals. Our
 results indicate distinct population genetic structure within and between
 ecosystems across Tanzania, and reveal important priority areas for
 connectivity conservation. Elephants sampled from the Tarangire-Manyara
 ecosystem appear marginally, yet significantly isolated from elephants
 sampled from the greater Serengeti ecosystem (mean FST = 0.03), where two
 distinct subpopulations were identified.Unexpectedly, elephants in the
 Lake Manyara region appear to be more closely related to those across the
 East African Rift wall in the Ngorongoro Conservation Area than they are
 to the neighboring Tarangire subpopulations. We concluded that the Rift
 wall has had a negligible influence on genetic differentiation up to this
 point, but differentiation may accelerate in the future because of ongoing
 loss of corridors in the area. Interestingly, relatively high genetic
 similarity was found between elephants in Tarangire and Ruaha although
 they are separated by &gt;400 km. In southern Tanzania, there was
 little evidence of female-mediated gene flow between Ruaha and Selous,
 probably due to the presence of the Udzungwa Mountains between them.
 Despite observing evidence of significant isolation, the populations of
 elephants we examined generally exhibited robust levels of allelic
 richness (mean AR = 9.96), heterozygosity (mean µHE = 0.73), and effective
 population sizes (mean Ne = 148). Our results may inform efforts to
 restore wildlife corridors between protected areas in Tanzania in order to
 facilitate gene flow for long-term survival of elephants and other
 species.
description: Fecal samples were collected from wild elephants in Tanzania from
 four ecosystems; Serengeti, Tarangire, Ruaha and Selous. DNA was extracted
 from 800 samples but only 711 samples were successfully PCR amplified at
 all 10 loci. We used capillary electrophoresis for fragement analysis and
 scored alleles automatically and then verified manually using genemapper
 V.5
description: Individuals with missing data at some loci, we indicated 0.
DOI: 10.5061/dryad.f4qrfj6rz
title: Reproductive systems and low outbreeding barriers between Jacaranda cuspidifolia and J. mimosifolia (Jacarandeae, Bignoniaceae)

description: The genus Jacaranda shows notable karyotype stability and a prevailing
 self-sterile breeding system with evidence of late-acting
 self-incompatibility in several species. However, some studies have
 indicated self-compatibility in J. mimosifolia, a species cultivated
 worldwide in tropical and subtropical areas. Jacaranda
 cuspidifolia is a close related species with natural distribution
 broadly overlapping to that of J. mimosifolia, and manual heterospecific
 pollination studies have indicated that these species are interfertile,
 but there is no report on the breeding system of the former. In this
 study, we used hand-pollination experiments, pistil longevity,
 epi-fluorescence and histological analysis of post-pollination events to
 determine the breeding system of J. cuspidifolia. We also employed intra
 and interspecific crosses and seed germination tests to reevaluate the
 breeding system in J. mimosifolia and the inter-fertility between
 the two species. Some fruits were initiated from self-pollinated pistils
 in J. mimosifolia, but none of them reached maturity. On the other hand,
 complete absence of fruit development by self-pollination was verified in
 J. cuspidifolia, while in situ pollen tube growth and
 histological analysis of post-pollination events in selfed pistils
 revealed the characteristic ovule penetration, fertilization and endosperm
 initiation, as observed in other bignoniaceous species with late-acting
 self-incompatibility. Low outbreeding barriers seem to operate between
 these species because reciprocal interspecific crosses and hybrid seed
 germination tests indicated they are bilaterally interfertile. However,
 fruit/seed production and seed germinability were significantly lower when
 pistils of J. cuspidifolia were pollinated with pollen of J.
 mimosifolia, compared with crosses in the opposite direction, which
 indicates a partial unilateral incompatibility. This result is discussed
 in the contest of the possible occurrence of self-compatibility of J.
 mimosifolia. The low level of incongruity operating between the two
 species also points to their recent evolutionary divergence.
DOI: 10.60707/0hwh-5d68
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.60707/3vgt-m667
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5061/dryad.mcvdncjwc
title: Pressure Correction in the Calibration of Heat Dissipation Sensors

description: Heat dissipation sensors (HDSs) infer soil matric potential based on the
 measured rate of temperature rise from a heat source. The process for
 calibrating these sensors may use a pressure plate apparatus (PPA) to
 remove water to a certain calibration point that is controlled by
 pressure. Conventionally, the pressure within the PPA is released before
 the temperature change calibration points are measured (DT0). This
 conventional HDS calibration approach can take several weeks. We propose
 that the equilibrated temperature change at pressure (DTp) can be
 corrected empirically to the value at zero pressure. Based on measurements
 of 14 HDSs between 0.02 and 0.1 MPa, DTp was on average 6.2% larger than
 DT0. After pressure correction, using an empirical equation, the
 difference between the corrected DTp and DT0 was only 0.28%. These results
 demonstrate that this empirical approach provides sufficient accuracy to
 achieve HDS calibration without performing a PPA pressure release.
DOI: 10.5061/dryad.4mw6m906h
title: Phylogeography and population genetics of pine butterflies: sky islands increase genetic divergence

description: The sky islands of southeastern Arizona (AZ) mark a major transition zone
 between tropical and temperate biota and are considered a neglected
 biodiversity hotspot. Dispersal ability and host plant specificity are
 thought to impact the history and diversity of insect populations across
 the sky islands. We aimed to investigate the population structure and
 phylogeography of two pine-feeding pierid butterflies, the pine white
 (Neophasia menapia) and the Mexican pine white (N. terlooii), restricted
 to these "islands" at this transition zone. Given their
 dependence on pines as the larval hosts, we hypothesized that habitat
 connectivity affects population structure and is at least in part
 responsible for their allopatry. We sampled DNA from freshly collected
 butterflies from 17 sites in the sky islands and adjacent high-elevation
 habitats and sequenced these samples using ddRADSeq. Up to 15,399 SNPs
 were discovered and analyzed in population genetic and phylogenetic
 contexts with Stacks and pyRAD pipelines. Low genetic differentiation in
 N. menapia suggests that it is panmictic. Conversely, there is strong
 evidence for population structure within N. terlooii. Each sky island
 likely contains a population of N. terlooii, and clustering is
 hierarchical, with populations on proximal mountains being more related to
 each other. The N. menapia habitat, which is largely contiguous,
 facilitates panmixia, while the N. terlooii habitat, restricted to the
 higher elevations on each sky island, creates distinct population
 structure. Phylogenetic results corroborate those from population genetic
 analyses. The historical climate-driven fluxes in forest habitat
 connectivity have implications for understanding the biodiversity of
 fragmented habitats.
description: DNA was extracted from freshly-caught butterfly
 specimens A ddRADSeq library was prepared using the
 MseI and EcoRI restriction enzymes Library was
 sequenced using the Illumina platform Reads were
 demultiplexed, quality-filtered, and trimmed for downstream
 analyses SNPs were called using Stacks and
 pyRAD Structure and IQTree were used for population
 genetic and phylogeneitc analyses, respectively
description: The code_with_annotations.docx file provides the code used in all
 downstream processing and analyses. There are annotations in the code to
 explain each step.
DOI: 10.60707/kg62-4q53
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5281/zenodo.18332051
title: GATSBI: Improving context-aware protein embeddings through biologically motivated data splits

description: GATSBI, a framework for learning protein embeddings using Graph Attention Networks (GATs) and biologically informed data splits. The learned embeddings are evaluated across multiple downstream biological tasks, including interaction prediction, function prediction, and pathway-level inference.
DOI: 10.5061/dryad.c2fqz6145
title: Body size, light intensity and nutrient supply determine plankton stoichiometry in mixotrophic plankton food webs

description: Trophic strategy determines stoichiometry of plankton. In general,
 heterotrophic zooplankton have lower and more stable C:N and C:P ratios
 than photoautotrophic phytoplankton whereas mixotrophic protists, which
 consume prey and photosynthesize, have stoichiometry between zooplankton
 and phytoplankton. As trophic strategies change with cell size, body size
 may be a key trait influencing eukaryotic plankton stoichiometry. However,
 the relationship between body size and stoichiometry remains unclear.
 Here, we measured plankton size-fractionated C:N ratios under different
 intensities of light and nutrient supply in subtropical freshwater and
 marine systems. We found a unimodal body size-C:N ratio pattern with a
 maximum C:N ratio at ~50 μm diameter in marine and freshwater systems.
 Moreover, the variation in C:N ratios is mainly explained by body size,
 followed by light intensity and nutrient concentration. To investigate the
 mechanisms behind this unimodal pattern, we constructed a size-based
 plankton food web model in which the trophic strategy and C:N ratio is an
 emergent result. Our model simulations reproduce the unimodal pattern with
 C:N ratio of photoautotrophs ≤ 50 μm increasing with body size due to
 increase of photosynthetic carbon, whereas C:N ratios of organisms
 &gt; 50 μm decreases with size due to decreasing photoautotrophic but
 increasing heterotrophic uptake. Based on our field observations and
 simulation, we extend the classic “light-nutrient” theory that determines
 plankton C:N ratio to include body size and trophic strategy dependency.
 We conclude that body size and size-dependent uptake of resources (light,
 nutrients and prey) determine plankton stoichiometry at various light and
 nutrient supplies.
description: The datasets of freshwater and marine size-fractionated
 plankton C:N ratio were collected by Norpac net of 50 and 200 um in
 Feitsui Reservoir and East China Sea. The plankton collected were
 seperated to several size classes (see Appendix A of the manuscript) and
 the C and N contents were measured by elemental analyzer (EA1108, Fisons,
 Italy, and FLASH 2000, Thermo SCIENTIFIC, USA). The molar C:N ratios were
 calculated according to the C and N contents of the plankton.
 For model simulation, the original m-files can be found here.
 Parametere_AN.m includes the parameters that were kept constant in
 each simulation. ControlParam_AN.m includes parameters that could be
 changed in the simulation, such as the nutrient supply and light
 intensity. MixotrophWeb_AN.m is the main model ODEs.
description: Missing data in Table S1 and S2 are labeled NA.
DOI: 10.5281/zenodo.18332050
title: GATSBI: Improving context-aware protein embeddings through biologically motivated data splits

description: GATSBI, a framework for learning protein embeddings using Graph Attention Networks (GATs) and biologically informed data splits. The learned embeddings are evaluated across multiple downstream biological tasks, including interaction prediction, function prediction, and pathway-level inference.
DOI: 10.60707/ay3f-bz81
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5061/dryad.fttdz08nj
title: Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).

description: Aim: To investigate cryptic diversity and diversification timing in the
 putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi,
 and to ask how geography (rivers, isolation by distance, IBD), ecological
 drivers (isolation by environment, IBE) and historical factors (climatic
 refugia) explain intraspecific genetic variation. Location: Central
 Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi.
 Methods: We sequenced two mitochondrial and two nuclear markers in 157
 individuals. Phylogeographic structure and the occurrence of independent
 evolving lineages where explored through phylogenetic and coalescent
 analyses. A species tree and divergence dates of lineages were inferred
 with BEAST, employing multiple DNA substitution rates. The potential
 genetic impacts of geographic distance among localities, the environment,
 and the position of localities in relation to main rivers were tested by
 Redundancy Analysis (RDA). Results: We detected 11 independently evolving
 and largely divergent intraspecific lineages. Lineage distribution
 patterns are complex and do not match any conspicuous barrier to gene
 flow, except for the Amazon River. Most lineages appear to have originated
 in the lower Miocene and Pliocene, in disagreement with the Pleistocene
 refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert
 establishing and maintaining genetic structure. However, when controlling
 for other explanatory variables, IBD explains significantly more variation
 than rivers, IBE, or historical factors. Main conclusions: Our results
 strongly suggest that L. osvaldoi is a species complex. Future taxonomic
 work should use an integrative approach to explore whether morphological
 variation is present and congruent with the genetic data. While the use of
 a sensitive dating analysis allowed us to better describe the
 diversification history of L. osvaldoi, the lack of a spatial model of
 Neogene river dynamics prevents the test of specific, more informative
 river barrier hypotheses. The data suggest that non-linear correlation
 analyses (e.g. RDA) should be preferred to detect factors that affect
 phylogeographic patterns in the Amazon, instead of linear multiple
 regressions (e.g. Mantel tests). Given the high level of cryptic diversity
 detected within this and other Amazonian species, we caution against
 hypothesis tests based solely on the distribution of nominal taxa, which
 can provide a rather incomplete view of the processes behind Amazonian
 diversity.
DOI: 10.5061/dryad.612jm63zv
title: Mother’s curse and indirect genetic effects: do males matter to mitochondrial genome evolution?

description: Maternal inheritance of mitochondrial DNA (mtDNA) was originally thought
 to prevent any response to selection on male phenotypic variation
 attributable to mtDNA, resulting in a male-biased mtDNA mutation load
 (‘mother’s curse’). However, the theory underpinning this claim implicitly
 assumes that a male’s mtDNA has no effect on the fitness of females he
 comes into contact with. If such ‘mitochondrially-encoded indirect
 genetics effects’ (mtIGEs) do in fact exist, and there is relatedness
 between the mitochondrial genomes of interacting males and females, male
 mtDNA-encoded traits can undergo adaptation after all. We tested this
 possibility using strains of Drosophila melanogaster that differ in their
 mtDNA. Our experiments indicate that female fitness is influenced by the
 mtDNA carried by males that the females encounter, which could plausibly
 allow the mitochondrial genome to evolve via kin selection. We argue that
 mtIGEs are probably common, and that this might ameliorate or exacerbate
 mother’s curse.
description: This data was collected during laboratory experiments using
 Drosophila melanogaster. It has been used in the study titled
 "Mother’s curse and indirect genetic effects: do males matter to
 mitochondrial genome evolution?", to be published in the Journal of
 Evolutionary Biology.
DOI: 10.60707/g63t-vq68
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5061/dryad.1rn8pk0pd
title: Data from: Sacred groves and serpent-gods moderate human-snake relations

description: 1. Serpent-god worship is an ancient tradition still practiced in many
 sacred groves across the Western Ghats of India. Although sacred groves
 there hold ecological conservation value, few studies have focused on
 arguably the most iconic taxon in the region, snakes. 2. We thus
 investigated the impact of sacred groves and snake deity worshipping on
 attitudes towards snakes by conducting surveys with people who had entered
 such forests prior. 3. We found that next to none of the participants who
 had encountered snakes inside sacred groves in the past harmed them under
 such circumstances. However, nearly a quarter of all participants do harm
 snakes if encountered outside sacred groves. 4. We also found that a
 larger proportion of participants who do not harm snakes outside sacred
 groves worship snake deities, relative to those that do harm them. 5. Our
 work thus highlights the influence of sacred groves and snake deity
 worshipping on pacifistic human-snake relations in Southwestern India.
description: The variables
 "acre.size", "mean1kmbuffertreecover"
 and "impervioussurfacearea1kmpercent" were obtained from ArcGIS,
 while the rest were collected via surveys.
description: This dataset includes all of the data used in the analyses for
 the study. The variables
 "acre.size", "mean1kmbuffertreecover"
 and "impervioussurfacearea1kmpercent" depict, respectively, the
 size in acres, percentage of tree cover averaged over the area extending 1
 km beyond the centrum, and percentage of impervious surface area averaged
 over the area extending 1 km beyond the centrum of each sacred grove site
 associated with the given participant.
DOI: 10.60707/fjhn-7976
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5061/dryad.x69p8czdb
title: Beak morphology predicts apparent survival of crossbills: due to selective survival or selective dispersal?

description: Dozens of morphologically differentiated populations, subspecies and
 species of crossbills (genus Loxia) exist. It has been suggested that this
 divergence is due to variation in the conifer cones that each population
 specialises upon, requiring a specific beak size to efficiently separate
 the cone scales. If so, apparent survival should depend on beak size. To
 test this hypothesis, we undertook multievent capture-recapture modelling
 for 6,844 individuals monitored during 27 years in a Pyrenean Common
 crossbill (L. curvirostra) population in a forest of mountain pine (Pinus
 uncinata). Apparent survival was indeed related to beak width, resulting
 in stabilizing selection around an optimum that was close to the observed
 mean beak width, indicating that local crossbill beak morphology is
 adapted to the conifer they feed upon. Both natural selection (selective
 mortality) and selective emigration of maladapted individuals may explain
 our findings. As is often the case in capture-recapture analyses but
 rarely recognised, we could not formally decompose apparent survival into
 selective mortality versus selective permanent emigration. Nonetheless,
 there are several indications that selective permanent emigration should
 not be fully excluded. First, natural selection by itself would have to be
 unusually strong compared to other empirical estimates to create the
 observed pattern of apparent survival. Second, the observed mean beak
 width was a bit lower than the estimated optimum beak width. This can be
 explained by immigration of crossbills with smaller beaks originating from
 southern populations, which may subsequently have left the study area
 permanently in response to low food intake. This is in line with a
 detected transient effect in the data, yet apparently little influx from
 crossbills from northern Europe. When permanent emigration is
 phenotypically selective this will have ecological and evolutionary
 consequences, so this possibility deserves more attention in general.
DOI: 10.60707/yy26-2428
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE
DOI: 10.5061/dryad.jdfn2z36z
title: A phenotypic screening platform utilising human spermatozoa identifies compounds with contraceptive activity

description: There is an urgent need to develop new methods for male contraception,
 however a major barrier to drug discovery has been the lack of validated
 targets and the absence of an effective high-throughput phenotypic
 screening system. To address this deficit, we developed a fully-automated
 robotic screening platform that provided quantitative evaluation of
 compound activity against two key attributes of human sperm function:
 motility and acrosome reaction.  In order to accelerate
 contraceptive development, we screened the comprehensive collection of
 12,000 molecules that make up the ReFRAME repurposing library, comprising
 nearly all the small molecules that have been approved or have undergone
 clinical development, or have significant preclinical profiling. We
 identified several compounds that potently inhibit motility representing
 either novel drug candidates or routes to target identification. This
 platform will now allow for major drug discovery programmes that address
 the critical gap in the contraceptive portfolio as well as uncover novel
 human sperm biology.
description: This data contains raw, processed and averaged data of a
 high-throughput screen looking at downregulating the motility of human
 sperm. Raw data contains coordinates of sperm
 tracks Processed data contains calculated sperm
 motility parameters (recorded 2 positions per well)
 Averaged data contains averaged data of both
 well positions
description: The source code to look and process this file, will be provided
 with the final paper.
DOI: 10.60707/hr3q-p009
title: NANO SCALE THERMAL CONDUCTIVITY CONTRAST MEASUREMENTS OF BENNU SAMPLE OREX-800055-9 USING AN ATOMIC FORCE MICROSCOPE