cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v41ns1rz2
title: Management alters drought-induced mortality patterns in European beech (Fagus sylvatica L.) forests

description: The high tree mortality during the dry and hot years 2018-2019 in Europe
 affected not only even-aged and monospecific conifer stands but also
 semi-natural Fagus sylvatica L. (European beech) forests. This has
 triggered concerns on the future of European beech forests under climate
 change and raised questions as to whether forest management may increase
 tree mortality rates through creating more open canopies. We compared
 long-term mortality rates of beech between strict forest reserves and
 adjacent managed reference stands for three inventory periods at 11 sites
 in the federal state Hesse, Germany, near the centre of the European
 distribution of the species. We hypothesized that mortality would increase
 with climatic water deficits during the growing season, initial stand
 density, and decreasing dominance (canopy status) of trees. We also
 hypothesized that mortality would decrease with site moisture status and
 the intensity of tree removals. To quantify the influence of management,
 initial stand density and tree removals were used as predictor variables.
 In addition, we analyzed the influence of the climatic water balance and
 competitive status of trees on mortality. Mean annual natural mortality
 rates ranged between 0.5 % and 2.1 %. Even in the drought years beech
 mortality rates were surprisingly low. We observed no signs of striking
 canopy disintegration. The significantly higher mortality (1.6 % - 2.1 %)
 in unmanaged stands during the drought years 2018 and 2019 was largely
 confined to suppressed trees. There was no significant increase of
 mortality in managed stands during the drought years, but a shift of
 mortality towards larger canopy trees. Our study did not confirm a general
 influence of management in the form of tree removals on mortality rates.
 Yet, we showed that during drought years management changed the
 distribution of mortality within the tree community. To analyze the effect
 of management on mortality rates more comprehensively, a wider gradient in
 site moisture conditions including sites drier than in this study and
 longer post-drought periods should be employed.
description: Data of the long-term development of tree populations were
 collected on circular sample plots spread systematically over the area of
 unmanged and regularly managed beech forests. Tree individuals were
 re-identified and inter alia diameter at breast height and tree status
 (live, dead) were registered over app. 30 years in three censuses.  
   Mortality rates for beech were calculated and
 analyzed for three periods of observation. The last period spanned the
 drought yers 2018 and 2019. 
description: A README file was uploaded to explain the dataset.
DOI: 10.5061/dryad.mkkwh7126
title: Supplementary material for: Impact of ghost introgression on coalescent-based species tree inference and estimation of divergence time

description: The species studied in any evolutionary investigation generally constitute
 a small proportion of all the species currently existing or that have gone
 extinct. It is therefore likely that introgression, which is widespread
 across the tree of life, involves “ghosts,” i.e., unsampled, unknown, or
 extinct lineages. However, the impact of ghost introgression on
 estimations of species trees has rarely been studied and is poorly
 understood. Here, we use mathematical analysis and simulations to examine
 the robustness of species tree methods based on the multispecies
 coalescent model to introgression from a ghost or extant lineage. We found
 that many results originally obtained for introgression between extant
 species can easily be extended to ghost introgression, such as the
 strongly interactive effects of incomplete lineage sorting (ILS) and
 introgression on the occurrence of anomalous gene trees (AGTs). The
 relative performance of the summary species tree method (ASTRAL) and the
 full-likelihood method (*BEAST) varies under different introgression
 scenarios, with the former being more robust to gene flow between
 non-sister species whereas the latter performing better under certain
 conditions of ghost introgression. When an outgroup ghost (defined as a
 lineage that diverged before the most basal species under investigation)
 acts as the donor of the introgressed genes, the time of root divergence
 among the investigated species generally was overestimated, whereas
 ingroup introgression, as commonly perceived, can only lead to
 underestimation. In many cases of ingroup introgression that may or may
 not involve ghost lineages, the stronger the ILS, the higher the accuracy
 achieved in estimating the time of root divergence, although the topology
 of the species tree is more prone to be biased by the effect of
 introgression.
DOI: 10.5061/dryad.xksn02vhs
title: The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex

description: Speciation genomic studies have revealed that genomes of diverging
 lineages are shaped jointly by the actions of gene flow and selection.
 These evolutionary forces acting in concert with processes such as
 recombination and genome features such as gene density shape a mosaic
 landscape of divergence. We investigated the roles of recombination and
 gene density in shaping the patterns of differentiation and divergence
 between the cyclically parthenogenetic ecological sister-taxa, Daphnia
 pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale
 genome assembly using trio-binning for D. pulicaria and constructed a
 genetic map using an F2-intercross panel to understand sex-specific
 recombination rate heterogeneity. Finally, we used a ddRADseq dataset with
 broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to
 understand the patterns of genome-scale divergence and demographic
 parameters. Our study provides the first sex-specific estimates of
 recombination rates for a cyclical parthenogen, and unlike other
 eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria,
 which may be related to this somewhat unique breeding mode. Additionally,
 regions of high gene density and recombination are generally more
 divergent than regions of suppressed recombination. Outlier analysis
 indicated that divergent genomic regions are likely driven by selection on
 D. pulicaria, the derived lineage colonizing a novel lake habitat.
 Together, our study supports a scenario of selection acting on genes
 related to local adaptation shaping genome-wide patterns of
 differentiation despite high local recombination rates in this species
 complex. Finally, we discuss the limitations of our data in light of
 demographic uncertainty.
description: See Wersebe et al. 2022 in Molecular Ecology for
 details:  We constructed a reference genome de novo for
 Daphnia pulicaria using Hifi sequencing. Constructed an
 F2 linkage map using WGS of 100 F2 individuals.
 Performed population genomic analysis of D. pulicaria, D. pulex
 and its hybrids.
DOI: 10.5061/dryad.ttdz08m0z
title: Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement

description: Volition - the sense of control or agency over one’s voluntary actions -
 is widely recognized as the basis of both human subjective experience and
 natural behavior in non-human animals. To date, several human studies have
 found peaks in neural activity preceding voluntary actions, e.g. the
 readiness potential (RP), and some have shown upcoming actions could be
 decoded even before awareness. While these findings may pose a challenge
 to traditional accounts of human volition, some have proposed that random
 processes underlie and explain pre-movement neural activity. Here we seek
 to address part of this controversy by evaluating whether pre-movement
 neural activity in mice contains structure beyond that present in random
 neural activity. Implementing a self-initiated water-rewarded lever pull
 paradigm in mice while recording widefield [Ca++] neural activity we find
 that cortical activity changes in variance seconds prior to movement and
 that upcoming lever pulls or spontaneous body movements could be predicted
 between 1 second to more than 10 seconds prior to movement, similar to but
 even earlier than in human studies. We show that mice, like humans, are
 biased towards initiation of voluntary actions during specific phases of
 neural activity oscillations but that the pre-movement neural code in mice
 changes over time and is widely distributed as behavior prediction
 improved when using all vs single cortical areas. These findings support
 the presence of structured multi-second neural dynamics preceding
 voluntary action beyond that expected from random processes. Our results
 also suggest that neural mechanisms underlying self-initiated voluntary
 action could be preserved between mice and humans.
description: See Methods section biorxiv manuscript:
 https://www.biorxiv.org/content/10.1101/2021.12.17.473193v1
DOI: 10.5061/dryad.6wwpzgn18
title: Data for: Molecular and clinicopathological differences between depressed and protruded T2 colorectal cancer

description: Background Colorectal cancer (CRC) can be classified into four consensus
 molecular subtypes (CMS) according to genomic aberrations and gene
 expression profiles. CMS is expected to be useful in predicting prognosis
 and selecting chemotherapy regimens. However, there are still no reports
 on the relationship between the morphology and CMS. Methods This
 retrospective study included 55 subjects with T2 CRC undergoing surgical
 resection, of whom 30 had the depressed type and 25 the protruded type. In
 the classification of the CMS, we first defined cases with deficient
 mismatch repair as CMS1. And then, CMS2/3 and CMS4 were classified using
 an online classifier developed by Trinh et al. The staining intensity of
 CDX2, HTR2B, FRMD6, ZEB1, and KER and the percentage contents of CDX2,
 FRMD6, and KER are input into the classifier to obtain automatic output
 classifying the specimen as CMS2/3 or CMS4. Results According to the
 results yielded by the online classifier, of the 30 depressed-type cases,
 15 (50%) were classified as CMS2/3 and 15 (50%) as CMS4. Of the 25
 protruded-type cases, 3 (12%) were classified as CMS1 and 22 (88%) as
 CMS2/3. All of the T2 CRCs classified as CMS4 were depressed CRCs. More
 malignant pathological findings such as lymphatic invasion were associated
 with the depressed rather than protruded T2 CRC cases.
DOI: 10.5061/dryad.41ns1rng2
title: Finding love: fruit fly males evolving under higher sexual selection are inherently better at finding receptive females

description: Courtship is an important component of male reproductive behaviour that
 enables males to learn about the suitability of their mating partners.
 Experimental evidence suggests that Drosophila melanogaster males can
 learn to modify their courtship behaviour based on their prior experience
 with unreceptive females. This courtship learning is expected to provide a
 fitness advantage to males and could therefore evolve given suitable
 heritable variation. We investigated the role of sexual selection in the
 evolution of courtship learning ability of males, using populations of D.
 melanogaster evolving under high and low levels of sexual selection for
 over 170 generations. We exposed males from both types of population to
 unreceptive females and then tested their ability to discriminate between
 receptive and unreceptive females in a complex mating environment. After
 being exposed to unreceptive females, males from both types of population
 (1) courted females less (both receptive and unreceptive), (2) took longer
 to initiate courtship, but took less time to start mating after initiating
 courtship and (3) increased the proportion of courtship directed towards
 receptive females, indicating the ability of both types of male to learn
 from experience. We did not find any difference in the courtship learning
 ability of males from the two types of population. However, males from
 populations with higher levels of sexual selection were better able to
 recognize and court receptive females, even when they were not previously
 exposed to unreceptive females. Taken together, these results show that
 sexual selection may not result in improved learning abilities but can
 lead to the evolution of an improved innate ability of males to assess the
 receptivity of females.
DOI: 10.5061/dryad.3n5tb2rk2
title: Data from: Differential defoliation and mortality of white spruce and balsam fir by Eastern spruce budworm

description: White spruce (Picea glauca) and Balsam fir (Abies balsamea) tree mortality
 data and tree characteristics recorded in July 2019 following an Eastern
 spruce budworm outbreak detected at two sites in northern Wisconsin,
 USA in 2014. These data were collected at the individual tree
 level, and include tree status, tree diameter at breast height (cm) and
 canopy class.
description: Dataset collection: Fieldwork was conducted in July 2019. We
 assessed the characteristics of a total of 113 individual white spruce and
 balsam fir trees across the two sites to determine if they were related to
 individual-level tree mortality (KDD: n = 34 white spruce, n = 26 balsam
 fir; KPE: n = 26 white spruce, n = 27 balsam fir). For each tree, we
 recorded its species, status (alive or dead), measured its diameter at
 breast height (DBH; with a minimum DBH cutoff for inclusion being 10 cm),
 and its crown class. We adapted crown classes (DeYoung and Sutton 2016) as
 an assessment of tree height relative to other trees in the stand, based
 on access to sunlight. Dataset processing: Two trees
 were omitted from the analysed dataset because they had been cut down so
 canopy class data were not available.  (see Corona et
 al 2022 for more information)
description: Each row is an individual tree.  Column names
 and definitions (See Corona et al. 2022 for more information): 
 Site: KDD or KPE Species: WS = White spruce;
 BF = Balsam fir Dead0_Alive1_2019: This indicates
 whether in July 2019 the tree was completely defoliated (no needles;
 classified as 'dead') or had green needles (classified as
 'alive'). Note that trees had been monitored up to 2021, and no
 tree classified as 'dead' regained needles.
 DBH_cm: Diameter at breast height, measured in
 centimetres. CrownClass: We adapted crown classes from
 DeYoung and Sutton (2016) as an assessment of tree height relative to
 other trees in the stand, based on access to sunlight. Open grown (OP)
 trees either grew separated from other trees or had a crown that
 substantially surpassed (in height) the trees that surrounded it. Dominant
 (DO) were trees that were able to intercept more sunlight from the top and
 sides of the tree for most of the day than surrounding trees. Codominant
 (CO) trees were similar in height to surrounding trees and intercepted
 sunlight via the top of the crown for most of the day. Intermediate (IN)
 trees gather little sunlight through small gaps within the canopies of CO
 and DO trees in their respective populations. Overtopped (OV) were
 subcanopy trees that had little to no direct sunlight.
DOI: 10.5061/dryad.02v6wwq4z
title: Data from: Some of supporting data for attitude of respondents towards wildlife conservation

description: The study was conducted between September 2018 and March 2019 to
 investigate the nature and extent of human-wildlife conflict (HWC) in the
 surrounding area of Alage College, the Central Rift Valley of Ethiopia and
 to assess the perception of the local people to wildlife. For data
 collection, a total of 140 household heads were selected randomly for
 interviews from nine villages using structured and semi-structured
 questionnaires. Moreover, focus group discussion, key informant
 interviews, and personal observation were carried out to obtain additional
 information. Descriptive statistics, Chi-square test (2 tailed), one-way
 ANOVA, Pearson correlation coefficient, and Likert scale statements were
 used to analyze the data. Based on, 66 (47.1%) of the respondents,
 households heads, the local people of the area experienced livestock
 predation leading to HWC. Whereas, (40.7%, n=57) of the respondents
 perceived both crop damage and livestock predation as a cause of conflict.
 A total of 932.43 Total Livestock Unit (TLU) of livestock and 218 dogs’
 losses were reported by households due to predators over the last five
 years. Thus, the largest numbers of livestock (89.9%) and dogs (100%)
 attacks was happened due to spotted hyenas. Nearly half of the respondents
 (49.3%, n = 69) ranked warthogs as the primary crop raiders, while the
 majority of respondents (82.1%, n = 115) reported maize as a severely
 damaged cereal crop. More than half, (57.1%, n=80) of respondents used
 different methods simultaneously to minimize damage caused by wild
 animals. About half, (48.6%, n=68) of respondents had negative attitude
 towards wildlife conservation. The level of education and amount of money
 imposed as a penalty for illegal grazing were affecting the local
 community's attitudes to wildlife conservation. Using effective
 methods reduce damage and loss to crop including, improved livestock
 husbandry, and creating better awareness to the local community could make
 the locals actor of conservation.
description: The data has been collected by using quesstionnaire interviews,
 focus group disscutions, key informant interviews and personal
 observations and data were analyzed using SPSS software and
 Excel.
description: Data will be used as supporting information of the a manuscript
 in progress of publication at Ecology and Evolution.
DOI: 10.15468/dl.nypkkw
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cupressus dupreziana atlantica"
 ]
}

 The dataset includes 282 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003035-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hdr7sqvk8
title: Polygenic risk score in Africa populations: progress and challenges

description: Polygenic Risk Score (PRS) analysis is a method that predicts the genetic
 risk of an individual towards targeted traits. Even when there are no
 significant markers, it gives evidence of a genetic effect beyond the
 results of Genome-Wide Association Studies (GWAS). Moreover, it selects
 SNPs that contribute to the disease with low effect size making it more
 precise at individual level risk prediction. PRS analysis addresses the
 shortfall of GWAS by taking into account the SNPs/alleles with low effect
 size but play an indispensable role to the observed phenotypic/trait
 variance. PRS analysis has application which investigate the
 genetic basis of several traits which includes rare diseases. However, the
 accuracy of PRS analysis depends on the genomic data of the underlying
 population. For instance, several studies show that obtaining higher
 prediction power of PRS analysis is challenging for non-Europeans. In this
 manuscript, we reviewed the conventional PRS methods and their application
 to Sub-Saharan African communities. We concluded that lack of sufficient
 GWAS data and tools is the limiting factor of applying PRS analysis to
 Sub-Saharan populations. We recommend developing Africa-specific PRS
 methods and tools for estimating, and analyzing Africa population data for
 clinical evaluation of PRSs of interest and predicting rare diseases.
DOI: 10.5061/dryad.crjdfn35v
title: Turgor loss point predicts survival responses to experimental and natural drought in tropical tree seedlings

description: Identifying key traits that can serve as proxies for species drought
 resistance is crucial for predicting and mitigating effects of climate
 change in diverse plant communities. Turgor loss point (πtlp) is a
 recently emerged trait that has been linked to species distributions
 across gradients of water availability. However, a direct relationship
 between πtlp and species ability to survive drought has yet to be
 established for woody species. Using a manipulative field experiment to
 quantify species drought resistance (i.e. their survival response to
 drought), combined with measurements of πtlp for 16 tree species, we show
 a negative relationship between πtlp and seedling drought resistance.
 Using long-term forest plot data, we also show that πtlp predicts seedling
 survival responses to a severe El Niño-related drought, although
 additional factors are clearly also important. Our study demonstrates that
 species with lower πtlp exhibit higher survival under both experimental
 and natural drought. These results provide a missing cornerstone in the
 assessment of the traits underlying drought resistance in woody species
 and strengthen πtlp as a proxy for evaluating which species will lose or
 win under projections of exacerbating drought regimes.
DOI: 10.5061/dryad.p2ngf1vs8
title: Telomeres and anthropogenic disturbances in wildlife: a systematic review and meta-analysis

description: Human-driven environmental changes are affecting wildlife across the
 globe. These challenges do not influence species or populations to the
 same extent and therefore, a comprehensive evaluation of organismal health
 is needed to determine their ultimate impact. Evidence suggests that
 telomeres (the terminal chromosomal regions) are sensitive to
 environmental conditions and have been posited as a surrogate for animal
 health and fitness. Evaluation of their use in an applied ecological
 context is still scarce. Here, using information from molecular and
 occupational biomedical studies, we aim to deliver ecologists and
 evolutionary biologists an accessible synthesis of the links between human
 disturbances and telomere length. In addition, we perform a systematic
 review and meta-analysis on studies measuring telomere length in
 wild/wild-derived animals facing anthropogenic disturbances. Despite the
 relatively small number of studies to date, our meta-analysis revealed a
 significant small negative association between disturbances and telomere
 length (-0.092 [-0.153, -0.030]; n= 28; k=159). Yet, our systematic review
 suggests that the use of telomeres as a biomarker to understand the
 anthropogenic impact on wildlife is limited. We propose some research
 avenues that will help to broadly evaluate their
 suitability: i) further causal studies on the link
 between human disturbances and
 telomeres; ii) investigating the organismal
 implications, in terms of fitness and performance, of a given telomere
 length in anthropogenically-disturbed
 scenarios; iii) better understanding of the underlying
 mechanisms of telomere dynamics. Future studies in these facets will help
 to ultimately determine their role as markers of health and fitness in
 wildlife facing anthropogenic disturbances.
description: Sytematic review and meta-analysis. See sections:
 "<i>4.1 | Literature Search, Data extraction and Effect Size
 calculation</i>" and "<i>4.2 | Meta-analytic
 technique and Publication Bias</i>" for details on the data
 collection and analyses.
description: See README.