cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hhmgqnkff
title: Antipredator tactics: a kin-selection benefit for defensive spines in coral catfish?

description: Morphological features that impair a predator’s ability to consume a prey
 item may benefit individual prey; but what of features that prolong
 prey-handling but do not enhance prey survival? For example, a Striped Eel
 Catfish (Plotosus lineatus) will be fatally envenomated if struck by its
 specialist predator, the Greater Sea Snake (Hydrophis major). Nonetheless,
 the catfish typically erects long, toxic pectoral and dorsal spines that
 increase prey-handling times for the snake by around eightfold. Because
 the catfish travel in swarms of closely-related individuals, the delay
 enforced by spines may enable the victim’s swarm-mates to disperse before
 the snake is able to search for another meal. In keeping with that
 hypothesis, defensive spines tend to be longer in catfish from regions
 where the Greater Sea Snake occurs, than from areas where the snake does
 not occur. Our data thus suggest that defensive weaponry in catfish, as in
 some eusocial insects, can evolve via kin selection as well as natural
 selection.
description: Coral catfish (Plotosus lineatus) were measured either from live
 specimens or preserved museum specimens, to quantify lengths of the
 pectoral and dorsal defensive spines relative to catfish body length and
 maximum body diameter.   Times taken
 for Greater Seasnakes (Hydrophis major) to handle and ingest coral catfish
 were measured in captivity.
DOI: 10.5061/dryad.4qrfj6q8c
title: Weather variation affects the dispersal of grasshoppers beyond their elevational ranges

description: Understanding how abiotic conditions influence dispersal patterns of
 organisms is important for understanding the degree to which species can
 track and persist in the face of changing climate. The goal of
 this study was to understand how weather conditions (temperature,
 precipitation and wind patterns) influence the dispersal
 patterns of multiple non-migratory grasshopper species from lower
 elevation grassland habitats in which they ­­complete their life-cycles to
 higher elevations that extend beyond their range limits. The study also
 explored the role of weather factors (temperature and precipitation) in
 influencing the population sizes of species found at lower
 elevations. 
description: <i>Field sites and grasshopper surveys</i> Grasshoppers were sampled from four sites along an elevational gradient within Boulder County, Colorado, USA. These sites, running along the 40th parallel, are Chautauqua Mesa (1752 m; 39.999 -105.283), A1 (2195 m; 40.015 N -105.377 W), meadow west of B1 (2591 m; 40.023 -105.430), and C1 (3048 m; 40.036 -105.547) and they reflect grassy clearings associated with the foothills, premontane, montane and sub-alpine life zones, respectively.  The grasshopper data used were collected via weekly surveys beginning in June and extending into mid-September during two time periods constituting a historic 1959-60 survey by G. Alexander, and a contemporary 2007-15 survey by C. Nufio.  Each survey consisted of systematic 1.5-person-hours of sweep-netting (divided among 1 to 3 surveyors) and 0.75 person-hours of time spent searching for adults  that may have been missed by sweep netting.   <i>Weather data</i> To explore how weather conditions influence grasshopper dispersal patterns, temperature, precipitation, and wind data from 2007-15, obtained from the National Renewable Energy Laboratory’s National Wind Technology Center’s (NWTC) M2 Tower (1855m. 39.9106 -105.2348), were correlated with the number of dispersers collected at the sites from June to mid-September. To explore the role of weather variables in influencing grasshopper populations sizes,  temperature and precipitation data from May 1 to September 7 from the United States Department of Commerce's National Oceanic and Atmospheric Administration (NOAA) weather station data (Cooperative ID 050848; 39.9919  -105.2667), were correlated with the population sizes of resident grasshoppers at the lowest site during the 1959-60 and 2007-12 surveys.  
description: See manuscript for further details.
DOI: 10.5061/dryad.2v6wwpzkj
title: Evolution in alternating environments with tunable inter-landscape correlations

description: Natural populations are often exposed to temporally varying environments.
 Evolutionary dynamics in varying environments have been extensively
 studied, though understanding the effects of varying selection pressures
 remains challenging. Here we investigate how cycling between a pair of
 statistically related fitness landscapes affects the evolved fitness of an
 asexually reproducing population. We construct pairs of fitness landscapes
 that share global fitness features but are correlated with one another in
 a tunable way, resulting in landscape pairs with specific correlations. We
 find that switching between these landscape pairs, depending on the
 ruggedness of the landscape and the inter-landscape correlation, can
 either increase or decrease steady-state fitness relative to evolution in
 single environments. In addition, we show that switching between rugged
 landscapes often selects for increased fitness in both landscapes, even in
 situations where the landscapes themselves are anti-correlated. We
 demonstrate that positively correlated landscapes often possess a shared
 maximum in both landscapes that allows the population to step through
 sub-optimal local fitness maxima that often trap single landscape
 evolution trajectories. Finally, we demonstrate that switching between
 anti-correlated paired landscapes leads to ergodic-like dynamics where
 each genotype is populated with nonzero probability, dramatically lowering
 the steady-state fitness in comparison to single landscape evolution.
description: This data was accumulated through numerical simulations.
DOI: 10.5061/dryad.h70rxwdgw
title: Plastid genome evolution in subtribe Gentianinae (Gentianaceae)

description: We investigated plastome evolution in Subtribe Gentianinae of the
 Gentianaceae, which encompasses ca. 450 species distributed around the
 world, particularly in alpine and subalpine environments. We sequenced,
 assembled and annotated the plastomes of 41 species, representing all six
 genera in subtribe Gentianinae as well as all 14 sections of the
 species-rich genus Gentiana. Here, we upload (1) original alignments,
 Gblock alignments and tree topology file in phylogenetic analysis, and
 (2) results about a 5 kb insertion in
 Gentiana cuneibarba, including Sanger sequencing results
 which verified its two boundaries as well as the middle, and annotation
 results.
description: 1. alignments Sequences of all protein coding
 genes were extracted from each plastome in PhyloSuite (Zhang et al. 2020)
 and aligned respectively using MAFFT (Katoh et al. 2002). A protein-coding
 matrix was constructed where we excluded genes that were absent in some
 species, or that showed high-sequence variability that made alignment
 difficult. We examined the matrix and removed the most rapidly evolving
 sites using Gblocks (Talavera & Castresana, 2007) using default
 setting. 2. tree topology file
 Phylogenetic analyses were performed with IQ-TREE (Nguyen et al.
 2014) implemented in PhyloSuite (Zhang et al. 2020) using the maximum
 likelihood (ML) method with 1000 rapid bootstrap replicates. The
 substitution model was chosen using ModelFinder (Kalyaanamoorthy et al.,
 2017). 3. Sanger sequencing results
  One 5 kb insertion was detected in
 <em>Gentiana</em> <i>cuneibarba. </i>We designed
 three pairs of primers to verified its two boundaries as well as the
 middle via PCR and Sanger sequencing. 4. Alignment
 descriptions of the 5kb insertion The 5kb insertion
 in <em>Gentiana</em> <i>cuneibarba</i> is BLAST
 with default settings. The top 100 alignment descriptions are
 provided.  
description: 1 Phylogeny_64_genes_Original_alignments.fasta: Original
 alignment of 64 protein coding genes in Subtribe Gentianinae.
 2 Phylogeny_64_genes_Gblocks_alignments.fasta: Gblocks alignment
 of 64 protein coding genes in Subtribe Gentianinae. 3
 ML tree IQTREE.contree: ML tree file  in Subtribe Gentianinae
 4 G.cuneibarba insertion sequence.txt: The insertion sequence of
 the insertion
 in <em>Gentiana</em> <i>cuneibarba.</i>
 <i>5 Gcun1_F2.P91104845.ab1</i>: Sanger suquencing
 result of primer Gcun1, verifying the first boundary. 6
 Gcun2_F1.P91104847.ab1: Sanger suquencing result of primer Gcun2,
 verifying the middle of the insertion. 7
 Gcun3_F2.P91104848.ab1: Sanger suquencing result of primer Gcun3,
 verifying the end boundary. 8
 Insertion-Alignment-Descriptions.xls: The top 100 alignment descriptions
 of the insertion sequence by BLAST.
DOI: 10.5061/dryad.jh9w0vt9b
title: Midbrain dopaminergic inputs gate amygdala intercalated cell clusters by distinct and cooperative mechanisms in male mice

description: Dopaminergic signaling plays an important role in associative learning
 including fear and extinction learning. Dopaminergic midbrain neurons
 encode prediction error-like signals when threats differ from
 expectations. Within the amygdala, GABAergic intercalated cell (ITC)
 clusters receive one of the densest dopaminergic projections, but their
 physiological consequences are incompletely understood. ITCs are important
 for fear extinction, a function thought to be supported by activation of
 ventromedial ITC cluster that inhibits central amygdala fear output. In
 mice, we reveal two distinct novel mechanisms how mesencephalic
 dopaminergic afferents control ITCs. Firstly, they co-release GABA to
 mediate rapid, direct inhibition. Secondly, dopamine suppresses inhibitory
 interactions between distinct ITC clusters via presynaptic D1-receptors.
 Early extinction training augments both, GABA co-release onto dorso-medial
 ITCs and dopamine-mediated suppression of dorso- to ventromedial
 inhibition between ITC clusters. These findings provide novel insights
 into dopaminergic mechanisms shaping the activity balance between distinct
 ITC clusters that could support their opposing roles in fear behavior.
DOI: 10.5061/dryad.qnk98sfdz
title: Data from: Climate-driven prediction of land water storage anomalies: An outlook for water resources monitoring across the conterminous United States

description: These research data are associated with the manuscript entitled
 “Climate-driven prediction of land water storage anomalies: An outlook for
 water resources monitoring across the conterminous United States”
 (https://doi.org/10.1016/j.jhydrol.2020.125053). The study focused on the
 conterminous United States (CONUS) which extends over a region of
 contrasting climates with an uneven distribution of freshwater resources.
 Under climate change, an exacerbation of the contrast between dry and wet
 regions is expected across the CONUS and could drastically affect local
 ecosystems, agriculture practices, and communities. Hence, efforts to
 better understand long-term spatial and temporal patterns of freshwater
 resources are needed to plan and anticipate responses. Since 2002, the
 Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow-On
 (GRACE-FO) satellite observations provide estimates of large-scale land
 water storage changes with an unprecedented accuracy. However, the limited
 lifetime and observation gaps of the GRACE mission have sparked research
 interest for GRACE-like data reconstruction. This study developed a
 predictive modeling approach to quantify monthly land liquid water
 equivalence thickness anomaly (LWE) using climate variables including
 total precipitation (PRE), number of wet day (WET), air temperature (TMP),
 and potential evapotranspiration (PET). The approach builds on the
 achievements of the GRACE mission by determining LWE footprints using a
 multivariate regression on principal components model with lag signals.
 The performance evaluation of the model with a lag signals consideration
 shows 0.5 ≤ R2 ≤ 0.8 for 41.2% of the
 CONUS. However, the model’s predictive power is unevenly distributed. The
 model could be useful for predicting and monitoring freshwater resources
 anomalies for the locations with high model performances. The processed
 data used as inputs in the study are here provided including the GIS files
 of the different maps reported.
description: Methods are described in the manuscript https://doi.org/10.1016/j.jhydrol.2020.125053
description: Descriptions
 corresponding to each figure and table in the manuscript are placed in the
 Read Me.docx file that is included as part of the Dryad dataset.
DOI: 10.5061/dryad.ttdz08kwq
title: A new pipeline for removing paralogs in target enrichment data

description: Target enrichment (such as Hyb-Seq) is a well-established high throughput
 sequencing method that has been increasingly used for phylogenomic
 studies. Unfortunately, current widely used pipelines for analysis of
 target enrichment data do not have a vigorous procedure to remove paralogs
 in target enrichment data. In this study, we develop a pipeline we call
 Putative Paralogs Detection (PPD) to better address putative paralogs from
 enrichment data. The new pipeline is an add-on to the existing HybPiper
 pipeline, and the entire pipeline applies criteria in both sequence
 similarity and heterozygous sites at each locus in the identification of
 paralogs. Users may adjust the thresholds of sequence identity and
 heterozygous sites to identify and remove paralogs according to the level
 of phylogenetic divergence of their group of interest. The new pipeline
 also removes highly polymorphic sites attributed to errors in sequence
 assembly and gappy regions in the alignment. We demonstrated the value of
 the new pipeline using empirical data generated from Hyb-Seq and the
 Angiosperm 353 kit for two woody genera Castanea (Fagaceae, Fagales) and
 Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of datasets showed
 that the PPD identified many more putative paralogs than the popular
 method HybPiper. Comparisons of tree topologies and divergence times
 showed evident differences between data from HybPiper and data from our
 new PPD pipeline. We further evaluated the accuracy and error rates of PPD
 by BLAST mapping of putative paralogous and orthologous sequences to a
 reference genome sequence of Castanea mollissima. Compared to HybPiper
 alone, PPD identified substantially more paralogous gene sequences that
 mapped to multiple regions of the reference genome (31 genes for PPD
 compared with 4 genes for HybPiper alone). In conjunction with HybPiper,
 paralogous genes identified by both pipelines can be removed resulting in
 the construction of more robust orthologous gene datasets for phylogenomic
 and divergence time analyses. Our study demonstrates the value of Hyb-Seq
 with data derived from the Angiosperm 353 probe set for elucidating
 species relationships within a genus, and argues for the importance of
 additional steps to filter paralogous genes and poorly aligned regions
 (e.g., as occur through assembly errors), such as our new PPD pipeline
 described in this study.
DOI: 10.5061/dryad.qz612jmd3
title: Numerical response of predators to large variations of grassland vole abundance and long-term community change

description: Voles can reach high densities with multi-annual population fluctuations
 of large amplitude, and they are at the base of predator communities in
 Northern Eurasia and Northern America. This status places them at the
 heart of management conflicts wherein crop protection and health concerns
 are often raised against conservation issues. Here, a 20-year survey
 describes the effects of large variations in grassland vole populations on
 the densities and the daily theoretical food intakes (TFI) of vole
 predators based on roadside counts. Our results show how the predator
 community responded to prey variations of large amplitude and how it
 reorganized with the increase in a dominant predator, here the red fox,
 which likely negatively impacted hare, European wildcat and domestic cat
 populations. This population increase did not lead to an increase in the
 average number of predators present in the study area, suggesting
 compensations among resident species due to intra-guild predation or
 competition. Large variations in vole predator number could be clearly
 attributed to the temporary increase in the populations of mobile birds of
 prey in response to grassland vole outbreaks. Our study provides empirical
 support for more timely and better-focused actions in wildlife management
 and vole population control, and it supports an evidence-based and
 constructive dialogue about management targets and options between all
 stakeholders of such socio-ecosystems. The data set includes: S1 kml file.
 Location of the study area (can be dropped in a Google Earth window or
 read from a GIS) S2 Excel file. Road-side counts (sheet 1) and list of
 species observed (sheet 2) S3 Excel file. Small mammal data S4 Excel file.
 Data for computing theoretical daily food intakes
description: All details are given in the article cited above.
description: S2, S3 and S4 files have self-sufficient comments corresponding
 to methods described in the article cited above.
DOI: 10.5061/dryad.ffbg79csr
title: Determinants of offspring sex in kangaroos: a test of multiple hypotheses

description: When the fitness costs and benefits of sons and daughters differ,
 offspring sex ratio manipulation could be an important reproductive
 tactic. We explored the effects of environment and maternal caring ability
 on offspring sex to test four adaptive sex ratio modification hypotheses:
 the Extrinsic Modification (EMH), Carrying Capacity (CCH), Trivers-Willard
 (TWH) and Cost-of-Reproduction (CRH) hypotheses. The EMH and CCH propose
 that environmental conditions shape offspring sex ratios, directly or in
 interaction with maternal condition. The TWH and CRH predict a positive
 relationship between maternal condition and production of the costlier
 sex. The TWH predicts that mothers with superior caring ability should
 produce more of the sex that can provide the greatest fitness returns from
 additional maternal allocation, and the CRH proposes that females with
 limited caring ability should reduce fitness costs by producing the
 cheaper sex. Repeated measures on 83 known-age eastern grey kangaroos,
 polygynous marsupials with strong sexual dimorphism, revealed that
 offspring sex ratio was independent of per capita forage, supporting
 neither the EMH nor CCH, but was dependent on maternal mass, consistent
 with the TWH and CCH. Our results, however, cannot clearly identify the
 ultimate cause of the relationship between maternal mass and greater
 production of sons. One of the three assumptions of the TWH could not be
 verified, and mothers of sons suffered only marginal additional fitness
 costs. Sex ratios in higher vertebrates are likely not solely explained by
 factors dependent on maternal control.
description: Description of the methods used to collect the data and get the
 data ready can be found in the associated paper. Individual IDs have been
 replaced by randomised numbers. Description of the
 variables can be found in the enclosed R script.
DOI: 10.5061/dryad.76hdr7sv4
title: Limb work and joint work minimisation reveal an energetic benefit to the elbows-back, knees-forward limb design in parasagittal quadrupeds. Supplementary material including data, simulation code and simulation results

description: Quadrupedal animal locomotion is energetically costly. We explore two
 forms of mechanical work that may be relevant in imposing these
 physiological demands. Limb work, due to the forces and velocities between
 the stance foot and the centre of mass, could theoretically be zero given
 vertical limb forces and horizontal centre of mass path. To prevent
 pitching, skewed vertical force profiles would then be required, with
 forelimb forces high in late stance and hindlimb forces high in early
 stance. By contrast, joint work – the positive mechanical work performed
 by the limb joints – would be reduced with forces directed through the hip
 or shoulder joints. Measured quadruped kinetics show features consistent
 with compromised reduction of both forms of work, suggesting some degree
 of, but not perfect, inter-joint energy transfer. The elbows-back,
 knees-forward design reduces the joint work demand of a low limb-work,
 skewed, vertical force profile. This geometry allows periods of high force
 to be supported when the distal segment is near vertical, imposing low
 moments about the elbow or knee, while the shoulder or hip avoids high
 joint power despite high moments because the proximal segment barely
 rotates – translation over this period is due to rotation of the distal
 segment.
description: The data are derived from previous force measurements as
 cited. The simulations are as described in
 ESM_Main
description: ESM_Main describes the folder. The folder is compressed (.zip) in
 order to maintain the folder structure to ease running of the labview
 simulation code.
DOI: 10.5061/dryad.dr7sqv9wx
title: Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation

description: Phenotypic integration is an important metric that describes the degree of
 covariation among traits in a population, and is hypothesized to arise due
 to selection for shared functional processes. Our ability to identify the
 genetic and/or developmental underpinnings of integration is marred by
 temporally overlapping cell-, tissue-, and structure-level processes that
 serve to continually ‘overwrite’ the structure of covariation among traits
 through ontogeny. Here we examine whether traits that are integrated at
 the phenotypic level, also exhibit a shared genetic basis (e.g.,
 pleiotropy). We micro-CT scanned two hard tissue traits, and two soft
 tissue traits (mandible, pectoral girdle, atrium, and ventricle
 respectively) from an F5 hybrid population of Lake Malawi cichlids, and
 used geometric morphometrics to extract 3D shape information from each
 trait. Given the large degree of asymmetric variation that may reflect
 developmental instability, we separated symmetric- from
 asymmetric-components of shape variation. We then performed quantitative
 trait loci (QTL) analysis to determine the degree of genetic overlap
 between shapes. While we found ubiquitous associations among traits at the
 phenotypic level, except for a handful of notable exceptions, our QTL
 analysis revealed few overlapping genetic regions. Taken together, this
 indicates developmental interactions can play a large role in determining
 the degree of phenotypic integration among traits, and likely obfuscate
 the genotype to phenotype map, limiting our ability to gain a
 comprehensive picture of the genetic contributors responsible for
 phenotypic divergence.
description: Files with the .tps extension contain landmark coordinate data
 and can be viewed in any text editor (e.g., TextEdit, Notepad, NotePad++,
 BBEdit, etc.). All analyses conducted with the .tps files were performed
 using the R environment for statistical computing. Files with the .R
 extension are scripts that can be run natively within R, and demonstrate
 exactly how we obtained the results presented in our manuscript.