cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bvq83bkb1
title: Discussions of the not-so-fit: how ableism limits diverse thought and investigative potential in evolutionary biology

description: Evolutionary biology and many of its foundational concepts are grounded in
 a history of ableism and eugenics. The field has not made a concerted
 effort to divest our concepts and investigative tools from this fraught
 history and as a result, an ableist investigative lens has persisted into
 present-day evolutionary research, limiting the scope of research and
 harming the ability to communicate and synthesize knowledge about
 evolutionary processes. This failure to divest from our eugenicist and
 ableist history has harmed progress in evolutionary biology and allowed
 principles from evolutionary biology to continue to be weaponized against
 marginalized communities in the modern-day. To rectify this problem,
 scholars in evolutionary research must come to terms with how the history
 of the field has influenced their investigations and work to establish a
 new framework for defining and investigating concepts, such as selection
 and fitness.
description: These data were generated by performing an advanced search in the
 Web of Science database on 6/1/21. The advanced search criteria included
 documents of all types, restricted the publication years to 2010-2020, and
 limited results to only the Web of Science Categories "Ecology"
 and "Evolutionary Biology.” We searched for works published on the
 four main drivers of evolution using keywords including: "Genetic
 Drift," "Genetic Mutation," "Gene Flow," and the
 topic of selection broken down into two search terms, "Natural
 Selection" and "Sexual Selection." After
 performing the search, we used the Web of Science “Analyze Results”
 feature to obtain the number of records generated for each search term in
 each of the publication years of interest. These results were downloaded
 directly from Web of Science and added to the “AmNat Paper Figure 1 Data.
 csv” file and used to generate figure 1.
description: In the data file: topic: The search term for
 each of the drivers of evolution explained above<br> pub_year: The
 year of publication under consideration <br> records: The number of
 results Web of Science reported as matching the search criteria for the
 given publication year These results were plotted in
 figure 1 using the R code in “Am Nat Figure 1 code. Rmd”
DOI: 10.5061/dryad.sqv9s4n5g
title: Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)

description: Obovaria olivaria is a species of freshwater mussel native to the
 Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages
 of North America. This mussel has experienced population declines across
 large parts of its distribution and is imperiled in many jurisdictions.
 Obovaria olivaria uses the similarly imperiled Acipenser fulvescens (Lake
 Sturgeon) as a host for its glochidia. We employed mitochondrial DNA
 sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to
 assess patterns of genetic diversity and population structure of O.
 olivaria from 19 collection locations including the St. Lawrence River
 drainage, the Great Lakes drainage, the Upper Mississippi River drainage,
 the Ohioan River drainage and the Mississippi Embayment. Heterozygosity
 was highest in Upper Mississippi and Great Lakes populations, followed by
 a reduction in diversity and relative effective population size in the St.
 Lawrence populations. Pairwise FST ranged from 0.00 to 0.20, and analyses
 of genetic structure revealed two major ancestral populations, one
 including all St. Lawrence River/Ottawa River sites and the other
 including remaining sites; however, significant admixture and isolation by
 river distance across the range were evident. The genetic diversity and
 structure of O. olivaria is consistent with the existing literature on
 Acipenser fulvescens and suggest that, although northern and southern O.
 olivaria populations are genetically distinct, genetic structure in O.
 olivaria is largely clinal rather than discrete across its range.
 Conservation and restoration efforts of O. olivaria should prioritize the
 maintenance and restoration of locations where O. olivaria remain,
 especially in northern rivers, and to ensure connectivity that will
 facilitate dispersal of Acipenser fulvescens and movement of encysted
 glochidia.
description: # *Obovaria olivaria* (Bivalvia:Unionidae) maf filtered vcf file
 This is the MAF filtered
 VCF file from Bucholz et al. 2022, "RAD-tag and mitochondrial DNA
 sequencing reveal the genetic structure of a widespread and regionally
 imperiled freshwater mussel, *Obovaria olivaria* (Bivalvia:
 Unionidae)." For full publication please see:
 [https://doi.org/10.1002/ece3.8560.
 ](https://doi.org/10.1002/ece3.8560.)). SNP data were filtered to create a
 final dataset with SNPs present in ≥75% of individuals at all sampling
 locations. We required a minimum minor allele frequency of 0.02 to reduce
 the impact of rare alleles on our analyses. ## Description of the data and
 file structure These data are RADtag generated SNPs from the Northern
 portion of the range of *Obovaria olivaria*. ## Sharing/Access information
 Links to other publicly accessible locations of the data: * Raw sequence
 reads are available on the Sequence Read Archive (SAMN20978488-
 SAMN20978580; BioProject: PRJNA757768).
DOI: 10.34740/kaggle/dsv/14648316
title: Public Opinion on Climate Change (Updated Daily)
DOI: 10.6076/d1nc78
title: Viral protein instability enhances host-range evolvability

description: Viruses are highly evolvable, but what traits endow this property? The
 high mutation rates of viruses certainly play a role, but factors that act
 above the genetic code, like protein thermostability, are also expected to
 contribute. We studied how the thermostability of a model virus,
 bacteriophage l, affects its ability to evolve to use a new receptor, a
 key evolutionary transition that can cause host-range evolution. Using
 directed evolution and synthetic biology techniques we generated a library
 of host-recognition protein variants with altered stabilities and then
 tested their capacity to evolve to use a new receptor. Variants fell
 within three stability classes: stable, unstable, and catastrophically
 unstable. The most evolvable were the two unstable variants, whereas seven
 of eight stable variants were significantly less evolvable, and the two
 catastrophically unstable variants could not grow. The slowly evolving
 stable variants were delayed because they required an additional
 destabilizing mutation. These results are particularly noteworthy because
 they contradict a widely supported contention that thermostabilizing
 mutations enhance evolvability of proteins by increasing mutational
 robustness. Our work suggests that the relationship between
 thermostability and evolvability is more complex than previously thought,
 provides evidence for a new molecular model of host-range expansion
 evolution, and identifies instability as a potential predictor of viral
 host-range evolution.
description: Please see assoicated publication for details.
DOI: 10.25338/b8bk9v
title: Sacramento bike share surveys

description: This tabular dataset describes the travel behavior and
 travel mode related attitudes of residents
 and bike-share users in the greater Sacramento region. The data
 includes the socio-demographics, travel and mode related attitudes, and
 mode use pattern of both users and non-users of the bike-share service.
 The data was collected from both stratified random mail-to-web and
 intercept flier-to-web recruitment methods during time periods
 from 2016 to 2019. This includes surveys before bike share existing in the
 Sacramento region, and during the Jump operated dockless e-bike fleet
 prior to the start of the COVID-19 pandemic.
description: A before-and-after survey was designed to measure the effect of
 the bike-share service on levels of bicycling, transit use, and
 vehicle-miles of travel as well as attitudes towards bicycling. Data
 gathered for this project are from several waves of household and
 bike-share user surveys. Before the introduction of the bike-share, in the
 spring of 2016, a household survey was conducted in the Sacramento region.
 Then after the introduction of bike-share, in the spring of 2019, another
 household survey was conducted in the Sacramento region. The method of
 survey sample recruitment was repeat cross-sectional address-based
 stratified random sampling.  After the introduction of bike-share, in the
 fall of 2018, a bike-share user survey was conducted. In the spring of
 2019, another bike-share user survey was conducted. In the bike-share user
 survey, sample recruitment was done by intercepting the bike-share users
 with fliers. Additionally, a bike-share user panel survey was conducted
 (re-recruitment of prior participants). In each of the surveys,
 respondents were asked about their access to and use of different
 transportation modes, attitudes towards bicycling and other aspects of
 transportation, experience with bike-share services in other regions, and
 socio-demographic characteristics including income and race/ethnicity. All
 surveys were done through an online web survey system
 (Qualtrics).
description: A description for each variable is provided in an associated
 metadata file. Missing values are present in many variables when survey
 participants chose not to answer a question (indicated by NA or
 blanks).
DOI: 10.5061/dryad.fn2z34tw7
title: Dataset for: An optimisation approach for designing wildlife corridors with ecological and spatial considerations

description: The fragmentation of wildlife habitats caused by anthropogenic activities
 has reduced biodiversity and impaired key ecosystem functions. Wildlife
 corridors play an important role in linking detached habitats. The optimal
 design of such corridors considering spatial, ecological, and economic
 factors is addressed in this paper. We present a novel graph-theoretic
 optimisation approach and a mixed-integer linear programming model to
 determine an optimal wildlife corridor connecting two given habitat
 patches. The model maximises the total quality of the corridor and
 satisfies pre-specified corridor width and length requirements under a
 resource constraint. Compared to the corridor design models presented in
 the literature, our model is conceptually simpler, and it is
 computationally convenient. We applied the model to a real data set for
 Eldorado National Forest in California, USA, involving 1,363 irregular
 land parcels. The model can be extended to design multiple corridors that
 connect two or more existing habitat patches.
description: This dataset contains
 a GAMS code used to test the model's computational efficiency, and
 another GAMS code and the data used in the empirical application for
 Eldorado National Forest in California, USA.  We prepared the empirical
 application data using ArcGIS. Specifically, we transformed the 1,363
 polygons of the Eldorado National Forest into 4,214 polylines using the
 Polygon-To-Line function in ArcToolbox and identified all pairs of
 adjacent land parcels and their common edges using the attribute table of
 the resulting polyline file. We identified 2,858 junction points for those
 polylines using the Planarize-Lines function in Advanced Editing, and we
 found all pairs of edges within a distance under 300 meters using the
 Generate-Near-Table function included in Analysis Tools in ArcToolbox. We
 created a personal geodatabase in ArcGIS to place these data and used the
 program <i>mdb2gms.exe</i> included in GAMS to convert them to
 a GAMS readable format (.inc). We used Gurobi 9.0.2 integrated
 with GAMS 32.1.0 as the solver for the mixed-integer linear programming
 model presented in the paper.
DOI: 10.5061/dryad.dr7sqvb0x
title: Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways

description: It is well established that dominant plants shape belowground communities,
 which in turn influence ecosystem functioning. Similarly, herbivores
 affect belowground communities through physical disturbance and
 redistribution of organic inputs, but also through their interactions with
 the plants themselves. However, we know little about how grazing moderates
 effects of dominant plants on belowground organisms. We established a
 three-year removal experiment in a grazed and an ungrazed alpine meadow on
 the Qinghai-Tibet plateau to explore how grazing mediates the effects of
 the dominant shrub, Dosiphora fruticosa, on nematode communities. We
 applied structural equation modelling to assess how grazing moderates the
 effects of D. fruticosa on nematode communities both directly and
 indirectly via changes in soil physicochemical properties, root biomass
 and microbial communities. We found that 1) grazing changed the direction
 of the direct effect of shrub on nematode communities as indicated by the
 shift from a negative to a positive path coefficient; 2) shrub affected
 nematode richness mainly through microbial richness. Accordingly, nematode
 community composition was more closely related to microbial community
 composition in the ungrazed alpine meadow, while edaphic properties were
 stronger predictors of nematode community composition responses to shrubs
 in the grazed meadow; and 3) grazing suppressed the indirect effects of
 shrub on nematode communities via microbial communities. Our study shows
 that grazing plays an important role in regulating dominant plant’s
 effects on belowground community composition and interactions in alpine
 meadows.
DOI: 10.5061/dryad.wstqjq2p0
title: Gene drives for vertebrate pest control: realistic spatial modelling of eradication probabilities and times for island mouse populations

description: Invasive alien species continue to threaten global biodiversity.
 CRISPR-based gene drives, which can theoretically spread through
 populations despite imparting a fitness cost, could be used to suppress or
 eradicate pest populations. We develop an individual-based, spatially
 explicit, stochastic model to simulate the ability of CRISPR-based homing
 and X-chromosome shredding drives to eradicate populations of invasive
 mice (Mus muculus) from islands. Using the model, we explore the
 interactive effect of the efficiency of the drive constructs and the
 spatial ecology of the target population on the outcome of a gene-drive
 release. We also consider the impact of polyandrous mating and sperm
 competition, which could compromise the efficacy of some gene-drive
 strategies. Our results show that both drive strategies could be used to
 eradicate large populations of mice. Whereas parameters related to drive
 efficiency and demography strongly influence drive performance, we find
 that sperm competition following polyandrous mating is unlikely to impact
 the outcome of an eradication effort substantially. Assumptions regarding
 the spatial ecology of mice influenced the probability of and time
 required for eradication, with short-range dispersal capabilities and
 limited mate-search areas producing `chase' dynamics across the
 island characterised by cycles of local extinction and recolonization by
 mice. We also show that highly efficient drives are not always optimal,
 when dispersal capabilities are low, rapid local population supression
 around the introduction sites can cause loss of the gene drive before it
 can spread to the entire island. We conclude that, although the design of
 efficient gene drives is undoubtedly critical, accurate data on the
 spatial ecology of target species is critical for predicting the result of
 a gene-drive release.
DOI: 10.5061/dryad.n2z34tmzb
title: Pest defenses under weak selection exert a limited influence on the evolution of height growth and drought avoidance in marginal pine populations

description: Whilst droughts, intensified by climate change, have been affecting
 forests worldwide, pest epidemics are a major source of uncertainty for
 assessing drought impacts on forest trees. Thus far, little information
 has documented the adaptability and evolvability of traits related to
 drought and pests simultaneously. We conducted common-garden experiments
 to investigate how several phenotypic traits (i.e., height growth, drought
 avoidance based on water-use efficiency inferred from δ13C, and pest
 resistance based on defense traits) interact in five mature lodgepole pine
 populations established in four progeny trials in western Canada. The
 relevance of interpopulation variation in climate sensitivity highlighted
 that seed-source warm populations had greater adaptive capability than
 cold populations. In test sites, warming generated taller trees with
 higher δ13C and increased the evolutionary potential of height growth and
 δ13C across populations. We found, however, no pronounced gradient in
 defenses and their evolutionary potential along populations or test sites.
 Response to selection was weak in defenses across test sites, but high for
 height growth, particularly at warm test sites. Response to selection of
 δ13C varied depending on its selective strength relative to height growth.
 We conclude that warming could promote the adaptability and evolvability
 of growth response and drought avoidance with limited evolutionary
 influence from pest (biotic) pressures.
DOI: 10.5061/dryad.8pk0p2npp
title: Shearwaters sometimes take long homing detours when denied natural outward journey information

description: The cognitive processes (learning and processing of information)
 underpinning long-distance navigation of birds are poorly understood.
 Here, we utilised the homing motivation of the Manx shearwater to
 investigate navigational decision making in a wild bird by displacing them
 294km to the far side of a large island (the Island of Ireland). Since
 shearwaters are reluctant to fly over land, the island blocked the direct
 route home, forcing a navigational decision. Further still, on the far
 side of the obstacle, we chose a release site where use of local knowledge
 could facilitate a 20% improvement in route efficiency if shearwaters were
 able to anticipate and avoid a large inlet giving the appearance of open
 water in the home direction. We found that no shearwater took the most
 efficient initial route home, but instead oriented in the home direction
 (even once the obstacle became visible). Upon reaching the obstacle, four
 shearwaters subsequently circumnavigated the land mass via the long route,
 travelling a further 900km as a result. Hence, despite readily orienting
 homewards immediately after displacement, shearwaters seem unaware of the
 scale of the obstacle formed by a large land mass despite this being a
 prominent feature of their regular foraging environment.
description: These are the raw GPS files detailing the time, latitude and
 longitude of fixes taken evey ~5 mins. The data are cut to include only
 GPS fixes taken between releasee of the birds and their arrival at the
 colony at Copeland Bird Observatory, Northern Ireland.
description: See readme file
DOI: 10.5061/dryad.tb2rbp02d
title: Dissorophoid temnospondyl Parioxys from the Permian of Texas

description: Parioxys ferricolus is a long-neglected taxon of dissorophid
 temnospondyls from the early Permian (Cisuralian) of Texas. Reexamination
 of the original material and preparation of a previously undescribed
 specimen sheds some light on ontogeny and reveals numerous eucacopine
 features. P. ferricolus is characterized by (1) a
 preorbital region 1.5 times as long as the posterior skull table in
 juveniles and twice as long in adults, (2) parietal only two-thirds the
 length of the frontal, and (3) interpterygoid vacuities shorter than half
 the skull length, (4) choanae posteriorly extended, and (5) vomer with
 enlarged, V-shaped medial depression. P. ferricolus is
 found nested with Kamacops acervalis, with which it shares
 synapomorphies in the palate, within the dissorophid clade Eucacopinae.
description: Character-taxon matrix and description of morphological
 characters.
description: Data set was analyzed with TNT.
DOI: 10.5061/dryad.3j9kd51kn
title: Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance

description: Plant crop genome assemblies facilitate the characterization of
 genetically diverse cultivated and wild germplasm.  The
 cultivated tomato (Solanum lycopersicum) has been improved through the
 introgression of genetic material from related wild species, including
 genetic resistance to pandemic strains of Tobacco Mosaic virus (TMV) and
 tomato mosaic virus (ToMV) originating from Solanum peruvianum. The exact
 size and the structure of the introgression from Solanum peruvianum
 containing the TMV/ToMV resistance gene (Tm-2^2 gene) has remained
 unknown, although it was known to include at least half of the physical
 length of chromosome 9. We selected a commercial cultivated tomato
 cultivar called Funtelle, which contains the Tm-2^2 resistance
 introgression in a hemizygous state, and generated Oxford Nanopore
 sequencing reads. Using Flye, a genome assembly tool, we assembled the
 reads. The assembled DNA sequences (contigs) from the Flye assembly are
 made available here. Subsequently, as described in detail in the
 associated manuscript, we made use of the assembled contigs for
 comprehensive haplotyping of the chromosome 9 introgression region in this
 commercial hybrid. The raw Oxford Nanopore sequencing reads of the
 Funtelle variety are available via the European Nucleotide Archive under
 project number PRJEB44956.
description: S. lycopersicum cv. Funtelle F1 (Date tomato) was produced by
 Syngenta. Young unexpanded leaves were collected from
 5-week-old plants and snap frozen in liquid nitrogen before interim
 storage at -80 degrees. DNA from the S. lycopersicum
 cv. ‘Funtelle’ was extracted using the Machery Nagel Nucleobond HMW DNA
 Kit. High molecular weight DNA was size selected using
 the Circulomics Short-Read Eliminator XL Kit (Circulomics Cat# SKU
 SS-100-111-01) and used as input for a library preparation with the Oxford
 Nanopore LSK-110 ligation sequencing Kit.  Four
 libraries from the same sample were loaded onto three PromethION PRO-002
 Flowcells and one MinION Flowcell (all R9.4.1 pores) and
 sequenced.  ONT Sequencing was performed on an Oxford
 Nanopore P24 PromethION and a MinION MK1B at the Forschungszentrum Jülich
 using MinKNOW version 21.02.7 without live basecalling. 
 Basecalling of the Oxford Nanopore read data was done using guppy
 basecaller version 5.0.11 using the R9.4.1 PromethION super-high-accuracy
 model (dna_r9.4.1_450bps_sup_prom) and the R9.4.1 MinION
 super-high-accuracy model (dna_r9.4.1_450bps_sup). Flye
 v2.8.2 (Kolmogorov et al., 2019) was used to assemble the ONT reads with
 the option --nano-raw for unpolished Nanopore reads.