cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mpg4f4qx0
title: Data from: Barn Owls select uncultivated habitats for hunting in a winegrape growing region of California

description: Large-scale conversion of uncultivated land to agriculture threatens
 wildlife and can diminish ecosystem services provided by nature.
 Understanding how wildlife provision ecosystem services may incentivize
 wildlife conservation in agricultural landscapes. Attracting Barn Owls
 (Tyto furcata) to nest on farms for pest management has been implemented
 worldwide, but has not been evaluated in vineyard agroecosystems. Napa
 Valley, California is a renowned winegrape growing region, and
 viticulturists encourage Barn Owl occupancy to help minimize damage from
 Botta’s pocket gophers (Thomomys bottae) and voles (Microtus spp.). This
 study modeled the use of habitats in space and time by hunting Barn Owls,
 providing information about their potential to provide the critical
 ecosystem service of pest consumption. We used global positioning system
 tags to track hunting owls, and used a resource selection function to
 compare used and available habitats.  We constructed intensity of
 use and home range-movement maps using a Time Local Convex Hull (t-LoCoH)
 analysis from location data. We found that Barn Owls selected uncultivated
 habitats when hunting, some of which were relatively rare on the
 landscape. Approximately one third of Barn Owl hunting locations occurred
 in vineyards, but this use was out of proportion to the availability of
 vineyards, which comprised 50% of the area around nest boxes. 
 The owls’ use of vineyards increased with decreasing amount of selected
 uncultivated habitat in the landscape. However, as reported by a previous
 study, occupancy of nest boxes in vineyards increases with uncultivated
 habitats nearby. Future research should model landscape composition to
 determine the amount of preferred habitat necessary to support occupancy
 as well as hunting in vineyards. A true test of pest management by Barn
 Owls awaits experimentation coupled with monitoring rodent populations.
description: These data include the used (GPS tag locations) and available
 (random locations within each brds homerange) for 11 Barn Owls hunting
 nesting in wooden nest boxes winegrape vineyards of Napa Valley, CA,
 2016-2017.
DOI: 10.5061/dryad.k0p2ngf67
title: A genomics resource for genetics, physiology, and breeding of West African sorghum

description: Local landrace and breeding germplasm is a useful source of genetic
 diversity for regional and global crop improvement initiatives. Sorghum
 (Sorghum bicolor L. Moench) in West Africa has diversified across a mosaic
 of cultures and end-uses, and along steep precipitation and photoperiod
 gradients. To facilitate germplasm utilization, a West African sorghum
 association panel (WASAP) of 756 accessions from national breeding
 programs of Niger, Mali, Senegal, and Togo was assembled and
 characterized. Genotyping-by-sequencing was used to generate 159,101
 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in
 genic regions. High genetic diversity was observed within the WASAP (π =
 0.00045), only slightly less than in a global diversity panel (π =
 0.00055). Linkage disequilibrium decayed to background level (r2 &lt;
 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by
 botanical type, and by populations within botanical type, with eight
 ancestral populations identified. Most populations were distributed across
 multiple countries, suggesting several potential common gene pools across
 the national programs. Genome-wide association studies of days to
 flowering and plant height revealed eight and three significant
 quantitative trait loci (QTL), respectively, with major height QTL at
 canonical height loci Dw3 and SbHT7.1. Colocalization of two of eight
 major flowering time QTL with flowering genes previously described in US
 germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in West
 Africa sorghum is conditioned by both known and novel genes. This genomic
 resource provides a foundation for genomics-enabled breeding of
 climate-resilient varieties in West Africa.
DOI: 10.5061/dryad.5qfttdz31
title: Reintroduced wolves and hunting limit the abundance of a subordinate apex predator in a multi-use landscape

description: Top-down effects exhibited by apex predators are modulated by human
 impacts on community composition and species abundances. For these
 reasons, research supporting strong top-down effects of apex predators
 occurs almost entirely within protected areas rather than the much more
 common multi-use landscapes dominating modern ecosystems. Based on 16
 years of monitoring, we developed an integrated population model to
 disentangle the concurrent contributions of a reintroduced apex predator,
 the gray wolf, human hunting, and prey abundances on vital rates and
 abundance of a subordinate apex predator, the puma. Increasing wolf
 numbers had strong negative effects on puma fecundity, and subadult and
 adult survival. Puma survival was also influenced by density-dependence.
 Overall, our results showed that puma dynamics in our multi-use landscape
 were more strongly influenced by top-down forces exhibited by a
 reintroduced apex predator, than by human hunting or bottom-up forces
 (prey abundance) subsidized by human activities. Quantitatively, the
 average annual impact of human hunting on equilibrium puma abundance was
 approximately equivalent to the effects of 20 wolves. Based on these
 results, wolves may have limited pumas across North America historically,
 and dictated puma scarcity in systems lacking sufficient refugia to
 mitigate the effects of competition.
description: Monitoring data for individual pumas marked with VHF and GPS
 collars, delineated in 3-month time steps. Mortality codes, age at
 capture, and notes included as well. F=female, and M=male.
 UC=unknown   Code used in analyses
 are provided in a Word document
DOI: 10.5061/dryad.7h44j0zs3
title: Phylogenomic dataset used for evolutionary rate covariation analyses in Forsythe et al.

description: Nuclear and plastid (chloroplast) genomes experience different mutation
 rates, levels of selection, and transmission modes, yet key cellular
 functions depend on coordinated interactions between proteins encoded in
 both genomes. Functionally related proteins often show correlated changes
 in rates of sequence evolution across a phylogeny (evolutionary rate
 covariation or ERC), offering a means to detect previously unidentified
 suites of coevolving and cofunctional genes. We performed phylogenomic
 analyses across angiosperm diversity, scanning the nuclear genome for
 genes that exhibit ERC with plastid genes. As expected, the strongest hits
 are highly enriched for plastid-targeted proteins, providing evidence that
 cytonuclear interactions affect rates of molecular evolution at
 genome-wide scales. Many identified nuclear genes function in
 post-transcriptional regulation and the maintenance of protein homeostasis
 (proteostasis), including protein translation (in both the plastid and
 cytosol), import, quality control and turnover. We also identified nuclear
 genes that exhibit strong signatures of coevolution with the plastid
 genome but lack organellar-targeting annotations, making them candidates
 for having previously underibed roles in plastids. In sum, our genome-wide
 analyses reveal that plastid-nuclear coevolution extends beyond the
 intimate molecular interactions within chloroplast enzyme complexes and
 may be driven by frequent rewiring of the machinery responsible for
 maintenance of plastid proteostasis in angiosperms.
description: See methods from Forsythe et al. 
description: See README file for information about the files fond in each
 directory.
DOI: 10.5061/dryad.msbcc2fw9
title: Trends and Transitions in 150 years of The American Naturalist

description: The American Naturalist recently passed its sesquicentennial.
 Throughout this long history, it regularly encountered moments of
 introspection and debate over its goals, mission, identity and audience.
 Here, we chronicle the history of those debates and transitions at
 critical moments. The Naturalist began as a popular
 magazine for amateur naturalists in the late 1860’s. In the late 1870’s it
 transitioned to an increasingly academic journal for professional
 scientists, from all branches of the natural sciences. By the turn of the
 century, academic specialization led to increasing fragmentation of the
 sciences into a multitude of societies and journals, creating an identity
 crisis for the once broad-reaching American
 Naturalist. This identity crisis was resolved when the journal
 pivoted around 1910 to focus on fundamental advances in the newly-emerging
 field of genetics. In the 1960’s the journal underwent a remarkably rapid
 transition to its present focus on evolution and ecology. The profound
 shifts in the journal’s contents over this time are a reflection of the
 historical changes in science as a whole: from amateur naturalists, to
 polymath professionals, to increasingly specialized academics. This
 chronicle reveals the ways in which the American
 Naturalist has left its mark on many disciplines, many of which
 are today only loosely affiliated with the journal, if at all.
DOI: 10.15468/dl.ts9auk
title: Occurrence Download

description: A dataset containing 60411 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ictalurus punctatus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 60411 records from 105 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002490-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jq2bvq876
title: Functional traits of avian frugivores have shifted following species extinction and introduction in the Hawaiian Islands

description: The extinction and introduction of species can alter ecological processes
 owing to the loss or gain of species roles. In vertebrate-dependent seed
 dispersal, mutualisms between frugivores and fruiting plants depend, in
 part, on matching of functional traits. High species turnover of
 frugivores has occurred on the Hawaiian Islands, owing to both the loss of
 native frugivores and the introduction of a new suite of frugivores. How
 this turnover has altered the functional traits of frugivores and the
 potential impacts on seed dispersal remain unclear. We investigated how
 avian frugivore traits differed between historic and modern assemblages of
 the Hawaiian Islands. We also tested how traits shifted within foraging
 guilds (ground versus arboreal) to distinguish potential impacts on plants
 within low versus high forest strata. Compared to historic frugivores, the
 modern assemblage is smaller in gape width and body mass in both ground
 and arboreal guilds. Wing shape did not significantly change between
 assemblages. From results, we postulate that changes in the frugivore
 community have likely altered seed dispersal processes by reducing (1) the
 size of seeds consumed, (2) frugivory rates per animal, and (3) seed
 dispersal distances. Owing to seed size placing strong constraints on
 consumption, we reviewed recent studies on frugivory by modern birds in
 the Hawaiian Islands and compared the size of seeds consumed versus seeds
 available. We found that larger-seeded plants (&gt;8.1mm seed width)
 were not consumed by modern birds and were more likely to be of
 conservation risk compared to smaller-seeded plants. Consequently,
 dispersal limitation may threaten Hawaiian plant communities, with
 larger-seeded plants at greatest risk of extinction. Broadly, we show that
 extensive turnover within assemblages may lead to significant changes in
 functional traits, with potential knock-on effects for mutualistic
 interactions and communities.
DOI: 10.5061/dryad.s1rn8pk5j
title: Thermal transgenerational effects remain after two generations

description: Transgenerational plasticity (TGP) is increasingly recognized as a
 mechanism by which organisms can respond to environments that change
 across generations. Although recent empirical and theoretical studies have
 explored conditions under which TGP is predicted to evolve, it is still
 unclear whether the effects of the parental environment will remain beyond
 the offspring generation. Using a small cyprinodontid fish, we explored
 multi-generational thermal TGP to address two related questions. First
 (experiment 1), does the strength of TGP decline or accumulate across
 multiple generations? Second (experiment 2), how does the experience of a
 temperature novel to both parents and offspring affect the strength of
 TGP? In the first experiment, we found a significant interaction between
 F1 and F2 temperatures and juvenile growth, but no effect of egg diameter.
 The strength of TGP between F0 and F1 generations was similar in both
 experiments but declined in subsequent generations. Further, experience of
 a novel temperature accelerated the decline. This pattern, although
 similar to that found in other species, is certainly not universally
 observed, suggesting that theoretical and empirical effort is needed to
 understand the multi-generational dynamics of TGP.
description: See methods in paper.
DOI: 10.5061/dryad.dv41ns1vz
title: Data from: Thermal physiology responds to interannual temperature shifts in a montane horned lizard, Phrynosoma orbiculare

description: As climate change marches on, rapidly rising temperatures shatter records
 every year, presenting ever‐growing physiological challenges to organisms
 worldwide. Ectotherms rely on behavioral and physiological plasticity to
 contend with environmental fluctuations. Nonetheless, our understanding of
 thermal plasticity has been largely limited to laboratory settings. Here,
 we test whether aspects of thermal physiology respond to interannual
 shifts in thermal environment in a natural population
 of Phrynosoma orbiculare, a montane horned lizard, from Hidalgo,
 Mexico. At our field site, 2019 was markedly warmer than the year that
 preceded it. We detected population‐level increases in three key thermal
 physiological traits: preferred temperature, the critical thermal minimum,
 and the critical thermal maximum. Thus, thermal phenotypes appear to shift
 in tandem in response to environmental fluctuations. A subset of
 individuals were resampled across years, allowing insight into plastic
 shifts within an organism's lifetime. We detected parallel increases
 in these lizards for the preferred temperature and the critical thermal
 minimum, but not for the critical thermal maximum. Our results support a
 growing body of literature indicating that preferred conditions and cold
 tolerance can be highly labile over the course of an organism's
 lifetime, whereas hardening over shorter time periods is more common for
 heat tolerance. Given that heat tolerance increased at the
 population‐level, but not in resampled individuals, it is possible that
 rapid evolution occurred due to temperature increases. In short,
 physiological shifts can be observed in natural populations over
 relatively short timespans, and these shifts might reflect a combination
 of evolutionary and acclimatory responses.
description: This data package contains raw data files associated with
 "Thermal physiology responds to interannual temperature shifts in a
 montane horned lizard, <i>Phrynosoma
 orbiculare" </i> by Domínguez‐Guerrero and colleagues. These
 data comprise phentoypic traits data and meterological data.
DOI: 10.5061/dryad.x3ffbg7gq
title: How female × male and male × male interactions influence competitive fertilization in Drosophila melanogaster

description: How males and females contribute to joint reproductive success has been a
 long-standing question in sexual selection. Under postcopulatory sexual
 selection (PSS), paternity success is predicted to derive from complex
 interactions among females engaging in cryptic female choice and males
 engaging in sperm competition. Such interactions have been identified as
 potential sources of genetic variation in sexually selected traits but are
 also expected to inhibit trait diversification. To date, studies of
 interactions between females and competing males have focused almost
 exclusively on genotypes and not phenotypic variation in sexually selected
 traits. Here, we characterize within- and between-sex interactions in
 Drosophila melanogaster using isogenic lines with heritable variation in
 both male and female traits known to influence competitive fertilization.
 We confirmed, and expanded on, previously reported genotypic interactions
 within and between the sexes, and showed that several reproductive events,
 including sperm transfer, female sperm ejection and sperm storage, were
 explained by two- and three-way interactions among sex-specific
 phenotypes. We also documented complex interactions between the lengths of
 competing males’ sperm and the female seminal receptacle, which are known
 to have experienced rapid female-male co-diversification. Our results
 highlight the non-independence of sperm competition and cryptic female
 choice and demonstrate that complex interactions between the sexes do not
 limit the ability of multivariate systems to respond to directional sexual
 selection.
description: Data were collected experimentally by staging competitive matings
 between males and females. Flies were observed, measured, dissected and
 processed as described in the Methods section of the article.
description: The dataset contains missing data because not all variables could
 be measured for each individual because, for example, not all females
 ejected a sperm mass (or it could not be found), or the precise start or
 end time of copulation or female sperm ejection were missed. If the
 ejected mass was missing, the number of first-male sperm residing in the
 female reproductive tract at remating, or the number of sperm transferred
 by the second male, were also missing by extention. However, the numbers
 of sperm stored by the female after sperm ejection would have been
 affected. Very few further specimens had missing data due to accidents
 during dissection (e.g. losing a spermatheca or bursting the female
 reproductive tract, preventing assignment of leaked sperm to specific
 storage organs). Rather than including only those females with complete
 data, we included all females that mated twice, but excluded those records
 with missing data for any given analysis.
DOI: 10.5061/dryad.g79cnp5nh
title: Habitat features and colony characteristics influencing ant personality and its fitness consequences

description: Several factors can influence individual and group behavioral variation
 that can have important fitness consequences. In this study, we tested how
 two habitat types (semi-natural meadows and meadows invaded by Solidago
 plants) and factors like colony and worker size and nest density influence
 behavioral (activity, meanderness, exploration, aggression, nest
 displacement) variation on different levels of the social organization of
 Myrmica rubra ants and how these might affect the colony productivity. We
 assumed that the factors within the two habitat types exert different
 selective pressure on individual and colony behavioral variation that
 affects colony productivity. Our results showed
 individual-/colony-specific expression of both mean and residual
 behavioral variation of the studied behavioral traits. Although habitat
 type did not have any direct effect, habitat-dependent factors, like
 colony size and nest density influenced the individual mean and residual
 variation of several traits. We also found personality at the individual
 level and at the colony level. Exploration positively influenced the
 total- and worker production in both habitats. Worker aggression
 influenced all the productivity parameters in semi-natural meadows,
 whereas activity had a positive effect on the worker and total production
 in invaded meadows. Our results suggest that habitat type, through its
 environmental characteristics, can affect different behavioral traits both
 at the individual and colony level and those with a high influence on
 colony productivity will form the personality of individuals. Our results
 highlight the need for complex studies on the behavioral variation of
 social insects to fully understand the effects shaping their behavior and
 productivity parameters.
DOI: 10.5061/dryad.tqjq2bvwx
title: The effect of intra-articular injection of secretome of umbilical cord mesenchymal stem cells in articular cartilage repair in sheep model

description: Introduction: Articular cartilage is an avascular, aneural, and
 alymphatic tissue that has limited capacity to regenerate. Numerous
 techniques have been employed to repair or regenerate; however, the
 success rate varies. In fact, most of them result in the formation of
 fibrocartilage, not hyaline cartilage. The future of treating cartilage
 defects lies in providing biologic solutions through cartilage
 regeneration. Mesenchymal stem cells (MSCs) represent a promising therapy
 for cartilage regeneration. These cells secrete factors that enhance
 cartilage repair. In this study, the effects of intra-articular injection
 of human umbilical cord MSC (hUC-MSC) secretome on cartilage damage was
 studied in a sheep model. Methods: Standardized rectangular (5x5 mm)
 full-thickness chondral defects were created in the lateral femoral
 condyle of 15 adult sheep and debrided down to the subchondral bone plate.
 Three treatment groups were tested: 4 microfracture perforations using
 1.0mm diameter awls (group 1), intra-articular injection of hUC-MSC
 secretome (group 2), and combination of microfracture and intra-articular
 injection of hUC-MSC secretome (group 3). Osteochondral repair was
 assessed at 6 months in vivo using established macroscopic and
 histological analyses. Results: Macroscopically, application of combined
 therapy shows significant improvement of cartilage repair compared to
 microfracture alone (p=0.004). Microscopically, the application of
 combined therapy shows significant improvement of cartilage repair
 compared to secretome injection alone (p=0.031) Conclusion: Microfracture
 combined with injection of hUCB-MSCs secretome could be an effective
 alternative for repairing articular cartilage defects in vivo.
description: Standardized rectangular (5x5 mm) full-thickness chondral defects
 were created in the lateral femoral condyle of 15 adult sheep and debrided
 down to the subchondral bone plate. Three treatment groups were tested: 4
 microfracture perforations using 1.0mm diameter awls (group 1),
 intra-articular injection of hUC-MSC secretome (group 2), and combination
 of microfracture and intra-articular injection of hUC-MSC secretome (group
 3). Osteochondral repair was assessed at 6 months in vivo using
 established macroscopic and histological analyses.