cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tmpg4f5w
title: Recent responses to climate change reveal the drivers of species extinction and survival

description: Climate change may be a major threat to biodiversity in the next 100
 years. Although there has been important work on mechanisms of decline in
 some species, it generally remains unclear which changes in climate
 actually cause extinctions, and how many species will likely be lost. Here
 we identify the specific changes in climate that are associated with the
 widespread local extinctions that have already occurred. We then use this
 information to predict the extent of future biodiversity loss and to
 identify which processes may forestall extinction. We used data from
 surveys of 538 plant and animal species over time, 44% of which have
 already had local extinctions at one or more sites. We found that
 locations with local extinctions had larger and faster changes in hottest
 yearly temperatures than those without. Surprisingly, sites with local
 extinctions had significantly smaller changes in mean annual temperatures,
 despite the widespread use of mean annual temperatures as proxies for
 overall climate change. Based on their past rates of dispersal, we
 estimate that 57–70% of these 538 species will not disperse quickly enough
 to avoid extinction. However, we show that niche shifts appear to be far
 more important for avoiding extinction than dispersal, although most
 studies focus only on dispersal. Specifically, considering both dispersal
 and niche shifts, we project that only 16–30% of these 538 species may go
 extinct by 2070. Overall, our results help identify the specific climatic
 changes that cause extinction and the processes that may help species to
 survive.
DOI: 10.5061/dryad.qv9s4mw9w
title: TRANSPARENT TESTA GLABRA1 (TTG1) regulates leaf trichome density in tea (Camellia sinensis)

description: Plant leaf trichomes not only are an essential trait for taxonomy but also
 participate in the resistance to biotic and abiotic stress. Leaf trichomes
 vary significantly among different tea varieties, ranging from leaves with
 high trichome density to relatively glabrous leaves. Leaf trichomes are a
 crucial diagnostic characteristic in tea identification and taxonomy. In
 addition, trichomes are also a valued trait in tea production; leaf
 trichomes are generally considered to be associated with improved taste.
 However, the molecular mechanisms of trichome formation and the genetic
 control of trichome density in tea plants remain unknown. In this study,
 we identified a gene named TRANSPARENT TESTA GLABRA1 (CsTTG1), which
 encodes a WD-repeat protein and is associated with trichome
 formation in tea. The results also showed that CsTTG1 is highly expressed
 in the top bud of tea, which is consistent with trichome formation in this
 tissue. CsTTG1 encodes a protein localized in both the nucleus and
 cytoplasm. In addition, the transcription level of CsTTG1 was related to
 the length and/or density of the trichomes in different tea cultivars with
 diverse leaf trichome densities. Moreover, overexpressing CsTTG1 increased
 the number of trichomes in Arabidopsis thaliana. Collectively, our results
 indicated that CsTTG1 is involved in regulating trichome formation and
 that the expression level of CsTTG1 may be related to trichome density in
 tea plants. Our results may facilitate research on tea taxonomy and the
 adaptation of tea to its habitats.
DOI: 10.5061/dryad.4j0zpc87c
title: Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

description: Natural populations are exposed to seasonal variation in environmental
 factors that simultaneously affect several demographic rates (survival,
 development, reproduction). The resulting covariation in these rates
 determines population dynamics, but accounting for its numerous biotic and
 abiotic drivers is a significant challenge. Here, we use a factor-analytic
 approach to capture partially unobserved drivers of seasonal population
 dynamics. We use 40 years of individual-based demography from
 yellow-bellied marmots (Marmota flaviventer) to fit and project population
 models that account for seasonal demographic covariation using a latent
 variable. We show that this latent variable, by producing positive
 covariation among winter demographic rates, depicts a measure of
 environmental quality. Simultaneous, negative responses of winter survival
 and reproductive-status change to declining environmental quality result
 in a higher risk of population quasi-extinction, regardless of summer
 demography where recruitment takes place. We demonstrate how complex
 environmental processes can be summarized to understand population
 persistence in seasonal environments.
DOI: 10.21223/p3/4ftdo8
title: Dataset for: Stability of resistance and yield of 15 advanced clones across environments in Peru

description: The objective of this study was determinate the phenotypic stability for resistance to late blight of 15 late blight resistant B3 clones during 4 seasons in two locations in Peru. The experiments were performed under a randomized complete block designs (RCBD) with 4 replications of 40 hill-plots. All the plants were exposed to natural infection in the field and disease spread was enhanced by spreader rows planted systematically throughout the field and also by favorable weather conditions.
DOI: 10.5061/dryad.79cnp5hrn
title: Variation in host home range size decreases rabies vaccination effectiveness by increasing the spatial spread of rabies virus

description: 1. Animal movement influences the spatial spread of directly-transmitted
 wildlife disease through host-host contact structure. Wildlife disease
 hosts vary in home range-associated foraging and social behaviors, which
 may increase the spread and intensity of disease outbreaks. The
 consequences of variation in host home range movement and space use on
 wildlife disease dynamics are poorly understood, but could help to predict
 disease spread and determine more effective disease management strategies.
 2. We developed a spatially-explicit individual-based model to examine the
 effect of spatiotemporal variation in host home range size on the spatial
 spread rate, persistence, and incidence of rabies virus (RABV) in raccoons
 (Procyon lotor). We tested the hypothesis that variation in home range
 size increases RABV spread and decreases vaccination effectiveness in host
 populations following pathogen invasion into a vaccination zone. 3. We
 simulated raccoon demography and RABV dynamics across a range of
 magnitudes and variances in weekly home range size for raccoons. We
 examined how variable home range size influenced the relative
 effectiveness of three components of oral rabies vaccination (ORV)
 programs targeting raccoons—timing and frequency of bait delivery, width
 of the ORV zone, and proportion of hosts immunized. 4. Variability in
 weekly home range size increased RABV spread rates by 1.2 - 5.2-fold
 compared to simulations that assumed a fixed home range size. More
 variable host home range sizes decreased relative vaccination
 effectiveness by 71% compared to less variable host home range sizes under
 conventional vaccination conditions. We found that vaccination timing was
 more influential for vaccination effectiveness than vaccination frequency
 or vaccination zone width. 5. Our results suggest that variation in
 wildlife home range movement behavior increases the spatial spread and
 incidence of RABV. Our vaccination results underscore the importance of
 prioritizing individual-level space use and movement data collection to
 understand wildlife disease dynamics and plan their effective control and
 elimination. 
description: This dataset contains model code for the spatially-explicit,
 individual-based model of raccoon demography, rabies dynamics, and oral
 rabies vaccination strategies presented in this paper.
description: Files for rabies vaccination IBM model, in Matlab (M files) and
 csv format. See README for more information.
DOI: 10.5061/dryad.tdz08kpw6
title: phyloregion: R package for biogeographic regionalization and spatial conservation

description: Biogeographical regionalization is the classification of regions in terms
 of their biotas and is key to understanding biodiversity patterns across
 the world. Previously, it was only possible to perform analysis of
 biogeographic regionalization on small datasets, often using tools that
 are difficult to replicate. Here, we present phyloregion, a package for
 the analysis of biogeographic regionalization and spatial conservation in
 the R computing environment, tailored for mega phylogenies and
 macroecological datasets of ever-increasing size and complexity. Compared
 to available packages, phyloregion is three to four orders of magnitude
 faster and memory efficient for cluster analysis, determining optimal
 number of clusters, evolutionary distinctiveness of regions, as well as
 analysis of more standard conservation measures of phylogenetic diversity,
 phylogenetic endemism, and evolutionary distinctiveness and global
 endangerment. A case study for zoogeographic regionalization of 9574
 species of squamate reptiles (amphisbaenians, lizards, and snakes) across
 the globe, reveals their evolutionary affinities using visualization tools
 that allow rapid identification of patterns and underlying processes with
 user-friendly colours–for example–indicating the levels of differentiation
 of the taxa in different regions. Ultimately, phyloregion would facilitate
 rapid biogeographic analyses that accommodates the ongoing mass-production
 of species occurrence records and phylogenetic datasets at any scale and
 for any taxonomic group into completely reproducible R workflows.
DOI: 10.5061/dryad.kprr4xh1b
title: Maternal investment, ecological lifestyle, and brain evolution in sharks and rays

description: Across vertebrates increased maternal investment (via increased pre- and
 postnatal provisioning) is associated with larger relative brain size, yet
 it remains unclear how brain organization is shaped by life history and
 ecology. Here, we tested whether maternal investment and ecological
 lifestyle are related to variation in brain size and organization across
 100 chondrichthyans. We hypothesized that brain size and organization
 would vary with level of maternal investment and habitat depth and
 complexity. We found that chondrichthyan brain organization varies along
 four main axes, according to: (1) absolute brain size, (2) relative
 diencephalon and mesencephalon size, (3) relative telencephalon and
 medulla size, and (4) relative cerebellum size. Increased maternal
 investment is associated with larger relative brain size, while ecological
 lifestyle is informative for variation between relative telencephalon and
 medulla size, and relative cerebellum size after accounting for the
 independent effects of reproductive mode. Deep-water chondrichthyans
 generally provide low levels of yolk-only (lecithotrophic) maternal
 investment and have relatively small brains, predominantly comprised of
 medulla (a major portion of the hindbrain). Whereas, matrotrophic
 chondrichthyans – which provide maternal provisioning beyond the initial
 yolk-sac – found in coastal, reef, or shallow oceanic habitats have large
 relative brain sizes, predominantly comprised of telencephalon (a major
 portion of the forebrain). We demonstrated, for the first time, that both
 ecological lifestyle and maternal investment are independently associated
 with brain organization in a lineage with diverse life history strategies
 and reproductive modes.
description: Data on brain size, body size, brain region size, reproductive
 mode, and ecological lifestyle for 100 species of sharks, skates, rays,
 and chimaeras.
DOI: 10.5061/dryad.s1rn8pk44
title: A new Changhsingian (Lopingian) brachiopod fauna of the shallow-water clastic-shelf facies from Fujian Province, southeastern China

description: Although much attention has been paid to Changhsingian brachiopods in
 South China, there are only two Chinese studies, published in 1979 and
 1990, on Changhsingian brachiopods from the southeastern part of South
 China. Based on systematically collected fossil material, this paper
 describes and quantitatively analyses a Changhsingian brachiopod fauna
 from the Luokeng Formation at the Hongtian section, Fujian Province,
 southeastern China, for the first time. Among the brachiopods (30 species
 in 18 genera) described and illustrated,Cathaysia
 yongdingensis Liao and an endemic genus of South China
 (Qinglongia) are reported in English for the first time. Two new
 species,Neochonetes(Sommeriella)longaand Neochonetes(Sommeriella)transversa,are also proposed. The Hongtian fauna is mainly composed of Cathaysia (29.4%),Neochonetes (19.3%), Linoproductus(13.5%), Orthothetina(11.7%), and is correlated with the brachiopod fauna from the lower part of the Luokeng Formation in Fujian Province.
DOI: 10.5061/dryad.6t1g1jwvk
title: Potential benefits of incorporating arable wildflowers into living mulches for sustainable agriculture

description: Background: As agriculture has intensified, many once-common
 wildflowers have declined in arable landscapes, which has widespread
 implications for associated ecosystem services. The incorporation of
 sustainable practices, for example, growing living mulches (in-field,
 non-crop plant ground cover, maintained during the target crop growing
 season), can boost arable biodiversity, but few wildflower species have
 been utilised in this context.  Aims: Our aim was to
 determine the suitability of arable wildflower species, once considered
 weeds, for use as living mulches. Methods: We first screened a
 number of arable wildflower species for germination when growing with a
 common cereal, barley (Hordeum vulgare). We then grew two (Centaurea
 cyanus and Scandix pecten-veneris) in pots in a
 glasshouse with and without barley, and grew barley alone to test the
 impact of the wildflowers on barley growth and biomass.
 Results: Neither of the wildflowers significantly negatively
 impacted barley biomass. Barley initially facilitated germination
 in S. pecten-veneris, but ultimately suppressed the above-ground
 biomass of both wildflowers. However, both wildflower species were able to
 coexist alongside barley. Conclusions: Our experiment provides
 evidence that wildflowers that were considered weeds in traditional
 agriculture have the potential to be grown alongside barley and could be
 incorporated as part of a living mulch.
description: Sixteen wildflower species were sown in monoculture or alongside
 barley in a sandy loam substrate. Germination was monitored daily for 30
 days.Two wildflower species were chosen for a further experiment
 (Centaurea cyanus and Scandix pecten-veneris). Seedds of these and barley
 Hordeum vulgare were planted into pots either in monoculture or in
 additive mixtures. Plants were grown and then one third of the pots
 harvested at 42, 92 and 162 days after planting. Above and below ground
 biomass were harvested and estimated at the first two time points. Above
 ground biomass was harvested and estimated at the third time point and
 fruiting material separated from the shoots. Data were anlysed to
 determine whether local environment (monoculture or mixture) influenced
 germination or biomass accummulation throughout the growing
 season.
DOI: 10.5061/dryad.4b8gtht89
title: Testing for deterministic succession in metazoan parasite communities of marine fish

description: Parasite communities are similar to free-living communities; decay of
 similarity over geographic distance, theory of island biogeography,
 species-area relationships and nestedness have been documented in both
 communities. Ecological succession has been studied in free-living
 communities but has rarely been examined in parasite communities. We use
 seriation with replication to test the hypothesis that succession of
 parasite community structure is deterministic, thus developing throughout
 consecutive changes along the fish ontogeny, via a seriated pattern.
 12,306 marine fishes (95 species) were studied. In 40 species, a seriated
 pattern was detected; 25 had a tendency toward a seriated pattern, and for
 31 species, succession was at random. Age-classes for each host species
 explained deterministic successional patterns for whole parasite
 communities and ectoparasites. Richness and number of age-classes
 explained this pattern for endoparasites. Seriated successional community
 pattern was evident for parasite communities of long-lived marine fish,
 indicating that parasite communities follow sequential changes over time,
 like many free-living communities.
description: A sample of 12,306 marine teleost fish belonging to 95 species
 from the Atlantic and Pacific oceans were obtained from local fishermen
 from Brazil (Rio de Janeiro), the Gulf of Mexico (Yucatan Peninsula: three
 localities) and Portugal (Madeira Islands) (samples of two populations of
 <i>Scomber colias</i>  Gmelin, 1789 were analyzed, one from
 Portugal; Madeira Islands and another from Rio de Janeiro). Samples from
 the Pacific Ocean were from Chile (five localities) and Peru (two
 localities). Metazoan parasites were collected according traditional
 techniques in parasitology. Deterministic sucession was
 evaluated using seriation with replication to test the hypothesis that
 succession of parasite community structure is deterministic, thus
 developing throughout consecutive changes along the fish ontogeny, via a
 seriated pattern using seriation with replication test of the RELATE
 analysis implemented in PRIMER 6
DOI: 10.5061/dryad.cfxpnvx2m
title: Higher rates of liana regeneration after canopy fall drives species abundance patterns in central Amazonia

description: In tropical rainforest, most vascular plants have some capacity to
 resprout, and lianas are often effective resprouters after canopy
 fall. However, the diversity of resprouting responses of liana
 species and the consequence for plant persistence is poorly
 understood. We hypothesized that variation in regeneration among
 liana species causes differences in liana species abundance in tropical
 rainforest through differential resprouting capacity, such that liana
 species with higher densities produce more resprouts after canopy falls.
 We applied a manipulative field experiment investigating the effect of
 different levels of disturbance on the production of resprouts and
 adventitious roots in ten liana species of the tribe Bignonieae
 (Bignoniaceae) with contrasting abundances in central Amazonia.
  We selected 15 individuals of each species and assigned the
 lianas to three distinct conditions: (i) total canopy fall with lianas
 severely damaged and detached from trees; (ii) partial fall of lianas,
 without visible damage; and (iii) intact lianas (control). We
 tested whether liana species regeneration patterns were related to species
 density. Liana species density was calculated using previous research on
 liana species distribution in 30 1-ha plots systematically distributed in
 a 6 x 6 km2 grid at the Ducke Reserve. The number of aerial
 resprouts produced by lianas under the total canopy fall treatment was
 twice that of plants under lower levels of disturbance, while the
 production of adventitious roots did not differ among treatments. Liana
 species showed different intensities of resprouting, and species with
 higher average densities on the forest landscape had more resprouts after
 the total canopy fall treatment. Synthesis:  Our results
 shed new light on the factors that influence liana species abundance,
 highlighting the role of resprouting after canopy fall and its variation
 among liana species. Resprouting mitigates the negative effects of canopy
 damage, suggesting that the impact of increased tree fall disturbances
 over time, which has been attributed to Amazonian forests in the
 literature, may increase already abundant liana species with effective
 resprouting capacity. We identify liana species that are more resilient to
 disturbance and may alter forest dynamics during climatic change.
description: The dataset was collected in the field of the Ducke Reserve
 (Manaus, Brazil). More details are available in the
 associated paper in the Journal of Ecology.
description: See README file
DOI: 10.5061/dryad.0k6djh9wn
title: Plasticity in male mating behavior modulates female life-history in fruit flies

description: In many species, intense male-male competition for the opportunity to sire
 offspring has led to the evolution of selfish reproductive traits that are
 harmful to the females they mate with. In the fruit fly, Drosophila
 melanogaster, males modulate their reproductive behavior based on the
 perceived intensity of competition in their pre-mating environment.
 Specifically, males housed with other males subsequently transfer a larger
 ejaculate during a longer mating compared to males housed alone. While the
 potential fitness benefits to males from such plasticity are clear, its
 effects on females are mostly unknown. Hence we tested the long-term
 consequences to females from mating with males with distinct social
 experiences. First, we verified that competitive experience influences
 male mating behaviour and found that males housed with rivals subsequently
 have shorter mating latencies and longer mating durations. Then, we
 exposed females every other day for 20 days to males that were either
 housed alone or with rivals and subsequently measured their fitness. We
 found that females mated to males housed with rivals produce more
 offspring early in life but fewer offspring later in life and have shorter
 lifespans but similar intrinsic population growth rates. These results
 indicate that plasticity in male mating behavior can influence female
 life-histories by altering females’ relative allocation to early vs late
 investment in reproduction and survival.
DOI: 10.5061/dryad.rfj6q576s
title: Effects of different functional structure parameters of plant communities on slope runoff in different periods of the year in semiarid grasslands

description: Research on sustainable use of water resources is needed to ensure food
 security, limit erosion, and prevent land degradation. Owing to the
 importance of water conservation to ecosystems, further research on the
 water conservation functions of different ecosystems is needed. Given the
 influence on water conservation functions, it is critical to identify
 environmental factors mediating slope runoff. In this study, the focal
 study area was the Yangjuangou catchment (36°42' N, 109°31' E)
 of the Loess Plateau in Shaanxi Province, China. Using a trait-based
 approach, a quantitative analysis was conducted to research effects of the
 functional structure parameters of plant communities on runoff of grass
 slopes for different periods of the year under differing rainfall
 intensity conditions. Results show that in mid-June, which represents the
 start of the growing season, effects of root traits on slope runoff
 decrease with increasing rainfall intensity. Slope runoff was found to be
 mainly affected by various plant functional traits in late July and
 aboveground parts of plants in early September. Given that few studies
 have focused on runoff processes using a trait-based approach at the
 community scale, this research can serve as a new reference for
 investigating the relationship between slope runoff and vegetation.
DOI: 10.5281/zenodo.18394523
title: aplocheilus_panchax_decontaminated_FSCR.fasta.gz
DOI: 10.5281/zenodo.18394524
title: aplocheilus_panchax_decontaminated_FSCR.fasta.gz