cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w0vt4b8ps
title: Deep-time reticulation and ancient mitochondrial genome capture during the radiation of Jamaican Anolis lizards (Squamata; Iguanidae)

description: Gene flow and reticulation are increasingly recognized as important
 processes in the diversification of many taxonomic groups. With the
 increasing ease of collecting genomic data and the development of
 multispecies coalescent network approaches, such reticulations can be
 accounted for when inferring phylogeny and diversification. Caribbean
 Anolis lizards are a classic example of an adaptive radiation in which
 species have independently radiated on the islands of the Greater Antilles
 into the same ecomorph classes. Within the Jamaican radiation at least one
 species, A. opalinus, has been documented to be polyphyletic in its
 mitochondrial DNA, which could be the result of an ancient reticulation
 event or incomplete lineage sorting. Here we generate mtDNA and
 genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree,
 and multispecies coalescent network methods to infer the diversification
 of this group. Our mtDNA gene-tree recovers the same relationships
 previously inferred for this group, which is strikingly different from the
 species-tree inferred from our GBS data. Posterior predictive simulations
 suggest that our genomic data violate commonly adopted assumptions of the
 multispecies coalescent model, so we use network approaches to infer
 phylogenetic relationships. The inferred network topology contains a
 reticulation event but does not explain the mtDNA polyphyly observed in
 this group, however coalescent simulations suggest that the observed mtDNA
 topology is likely the result of past introgression. How common a
 signature of gene flow and reticulation is across the radiation of Anolis
 is unknown; however, the reticulation events that we demonstrate here may
 have allowed for adaptive evolution, as has been suggested in other, more
 recent adaptive radiations.
description: Rad-seq and Sanger sequencing
DOI: 10.5061/dryad.cjsxksn4v
title: Sensitivity analysis of the maximum entropy production method to model evaporation in boreal and temperate forests

description: The maximum entropy production (MEP) approach has been little used to
 simulate evaporation in forests and its sensitivity to input variables has
 yet to be systematically evaluated. This study addresses these
 shortcomings. First, we show that the MEP model performed well in
 simulating evaporation during the snow-free period at six sites in
 temperate and boreal forests (0.68 ≤ NSE ≤ 0.82). Second, we computed a
 sensitivity coefficient S  representing the proportion of change
 in the input variable transferred to the latent heat flux (λE). Net
 radiation (Rn) was the most influential variable (S » 1) at all sites,
 indicating that an increase in Rn translates into an equivalent increase
 in λE. The MEP model avoided the issue of oversensitivity to air
 temperature (S &lt; 0.5 at peak evaporation) and captured limitations
 to transpiration associated with the atmospheric evaporative demand.
 Overall, the MEP model offers a promising tool for climate change studies.
description: We selected six sites hosting eddy-covariance flux towers from
 the AmeriFlux and Fluxnet networks. At each site, we modeled evaporation
 using the maximum entropy production method (Wang and Bras, 2011) for the
 snow-free period. We performed a sensitivity analysis using the method of
 Beven (1979) to assess the sensitivity of the MEP model to variations to
 input variables.
description: FOLDER ORGANIZATION |- Figure 1 --&gt;
 ETpred<br> | |- Data<br> | |- Code<br> | |-
 Results<br> | |- Plot |- Figure 2 --&gt;
 Sensitivity analysis<br> | |- Data<br> | |- Code<br> |
 |- Results<br> | |- Plot |- Figure 3 --&gt;
 VPD vs ET/Rn<br> | |- Code<br> | |- Plot |-
 Table 2 --&gt; performance ETpred<br> | |- Code<br> | |-
 Results |- Table S2 --&gt; impact of fixing
 ns=1<br> | |- Code<br> | |- Data<br> | |-
 Results |- Table S3 --&gt; impact of energy budget
 closure correction<br> | |- Code<br> | |- Data<br> | |-
 Results
DOI: 10.5061/dryad.2jm63xsn9
title: Data from: Biogeography of ITS variation in the Helenium autumnale (Asteraceae) species complex

description: Abstract—We used ITS sequences as species barcodes to evaluate 127 samples
 of 12 Helenium species from the eastern and central USA, focusing on a
 species complex of H. autumnale (76 sequences from 11 US states and two
 Canadian provinces), the federally “threatened” H. virginicum, now
 recommended for delisiting (30 sequences from three US states), and H.
 flexuosum (11 sequences from four US states).  ITS sequences
 confirmed most species identifications and supported the presence of the
 first population of the “threatened” endemic Missouri-Virginia disjunct,
 Helenium virginicum, in Indiana.   Because the Indiana plants
 grow in a restored wetland, have a cpDNA haplotype previously known only
 from Missouri, with a morphology similar to Missouri variants, and a
 herbarium search for additional populations in Indiana found none, it is
 unclear whether the Indiana population is natural or planted.
  The presence of a putative sister-lineage to H. virginicum
 thought to exist on the Bruce Peninsula, Ontario, Canada, was not
 supported after sequencing 36 plants with the sister morphology that grew
 there along 18 km of beach fens and finding they had H. autumnale
 sequences.   Fine-scale biogeographic patterns of intraspecific
 sequence variation were found mostly in H. autumnale, with centers of
 different base site polymorphisms found in northern North America and the
 Missouri Ozarks.  As in a previous study, we found DNA evidence
 of hybridization between Helenium species in Missouri.  We offer
 hypotheses to explain the biogeography of North American Helenium,
 focusing on the three species that compose the H. autumnale species
 complex and suggesting that H. autumnale may be a compilospecies showing
 incomplete lineage sorting.   We encourage exploration of more
 Helenium species and their conspecific populations in search of fine-scale
 ITS base site polymorphisms to reveal emerging lineages and resolve the
 origins and evolutionary implications of these biogeographic patterns.
DOI: 10.5061/dryad.xsj3tx9dc
title: Data from: Archaeological Central American maize genomes suggest ancient gene flow from South America

description: Maize (Zea mays ssp. mays) domestication began in
 southwestern Mexico ~9,000 calendar years before present (cal. BP) and
 humans dispersed this important grain to South America by at least 7000
 cal. BP as a partial domesticate. South America served as a secondary
 improvement center where the domestication syndrome became fixed and new
 lineages emerged in parallel with similar processes in Mesoamerica. Later,
 Indigenous cultivators carried a second major wave of maize southward from
 Mesoamerica, but it has been unclear until now whether the deeply
 divergent maize lineages underwent any subsequent gene flow between these
 regions. Here we report ancient maize genomes (2,300-1,900 cal. BP) from
 El Gigante rock-shelter, Honduras, that are closely related to ancient and
 modern maize from South America. Our findings suggest that the second wave
 of maize brought into South America hybridized with long-established
 landraces from the first wave, and that some of the resulting newly
 admixed lineages were then reintroduced to Central America. Direct
 radiocarbon dates and cob morphological data from the rock-shelter suggest
 that more productive maize varieties developed between 4,300 and 2,500
 cal. BP. We hypothesize that the influx of maize from South America into
 Central America may have been an important source of genetic diversity as
 maize was becoming a staple grain in Central and Mesoamerica.
description: Methods for genomic data collection, processing, and analysis are
 described in detail in Kistler et al, 2020<i> Proc Nat Acad Sci
 USA</i>. "
DOI: 10.15468/dl.mgubgm
title: Occurrence Download

description: A dataset containing 696 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coursetia glandulosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 696 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002676-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cjsxksn4w
title: Livestock grazing is associated with seasonal reduction in pollinator biodiversity and functional dispersion but cheatgrass invasion is not: variation in bee assemblages in a multi-use shortgrass prairie

description: Livestock grazing and non-native plant species affect rangeland habitats
 globally. These factors may have important effects on ecosystem services
 including pollination, yet, interactions between pollinators, grazing, and
 invasive plants are poorly understood. To address this, we tested the
 hypothesis that cattle grazing and site colonization by cheatgrass (Bromus
 tectorum) impact bee foraging and nesting habitats, and the biodiversity
 of wild bee communities, in a shortgrass prairie system. Bee nesting
 habitats (litter and wood cover) were marginally improved in non-grazed
 sites with low cheatgrass cover, though foraging habitat (floral cover and
 richness, bare soil) did not differ among cattle-grazed sites or
 non-grazed sites with low or high cheatgrass cover. However, floral cover
 was a good predictor of bee abundance and functional dispersion. Mean bee
 abundance, richness, diversity and functional diversity were significantly
 lower in cattle-grazed habitats than in non-grazed habitats. Differences
 in bee diversity among habitats were pronounced early in the growing
 season (May) but by late-season (August) these differences eroded as
 Melissodes spp. and Bombus spp. became more abundant at study sites.
 Fourth-corner analysis revealed that sites with high floral cover tended
 to support large, social, polylectic bees; sites with high grass cover
 tended to support oligolectic solitary bees. Both cattle-grazed sites and
 sites with high cheatgrass cover were associated with lower abundances of
 above-ground nesting bees but higher abundance of below-ground nesters
 than non-grazed sites with low cheatgrass cover.  We conclude
 that high cheatgrass cover is not associated with reduced bee biodiversity
 or abundance, but cattle grazing was negatively associated with bee
 abundances and altered species composition.  Although floral
 cover is an important predictor of bee assemblages, this was not impacted
 by cattle grazing and our study suggests that cattle likely impact bee
 communities through effects other than those mediated by forbs, including
 soil disturbance or nest destruction. Efforts aimed at pollinator
 conservation in prairie habitats should focus on managing cattle impacts
 early in the growing season to benefit sensitive bee species.
description: Bee abundance data were collected using blue vane traps.
DOI: 10.5061/dryad.02v6wwq23
title: Relaxed predation selection on rare morphs of Ensatina salamanders (Caudata: Plethodontidae) promotes a polymorphic population in a novel dune sand habitat

description: The Ensatina ring species represents a classic example of locally adapted
 lineages. The Monterey Ensatina (Ensatina eschscholtzii eschscholtzii) is
 a cryptic subspecies with brown coloration, however, a recently discovered
 polymorphic population within a wind-blown sand region also contains
 leucistic (pink) and xanthistic (orange) morphs. Leucism/xanthism
 frequency was mapped across the subspecies’ range revealing that these
 morphs are generally rare or absent except within regions containing
 light-colored substrate. Attack rates were estimated using clay models of
 the three morphs, deployed only at the crepuscular period and during the
 night, on both light and dark substrates at a site within the dune sand
 region. Model selection found that the interaction between morph and
 substrate color best predicted attack rates. Typical morphs had equal
 attack rates on both substrates while xanthistic and leucistic morphs
 incurred significantly fewer attacks on light versus dark substrate, and
 there was no significant difference in attack rates among morphs on light
 substrates. These results support the idea that xanthistic and leucistic
 morphs are poorly adapted for dark substrates compared to typical morphs,
 but they are more or less equally adapted for light substrates. We suggest
 that this microgeographic island of relaxed selection on light-colored
 morphs helps explain the existence of this polymorphic population.
description: Appendix S1 - Morph frequencies were estimated visually by
 examining georeferenced photographs depisted on iNaturalist
 (iNaturalist.org). Details can be found in the methods section of the
 published paper. Appendix S2 - Raw data from the clay
 model predation study. Details can be found in the methods section of the
 published paper. R Code - Used to generate heat maps
 from the georeferenced morph data.  Details can be found in the methods
 section of the published paper.
DOI: 10.5061/dryad.d2547d822
title: A morphometric hypothesis of taxon diversity in the freshwater snail genus Gyrotoma

description: Alabama has long been recognized as an aquatic biodiversity hotspot, and
 the Coosa River, in particular, was home to over 80 endemic freshwater
 snail species. Due to human activity, over 40% of the snails have been
 extirpated including the pleurocerid genus Gyrotoma. Gyrotoma species
 varied in terms of shell shape and sculpture and were restricted to
 certain reaches of the Coosa River. Diversity estimates based on shell
 morphology have ranged from 44 nominal taxa to the modernly recognized six
 Gyrotoma species. However, basing pleurocerid species boundaries on
 qualitative morphological features poses many taxonomic and systematic
 issues. In an effort to better estimate species diversity, geometric
 morphometrics and Gaussian mixture models were used to assign individual
 Gyrotoma shells to one of three clusters. Individuals in each cluster had
 significantly different shapes along with different combinations of
 quantifiable shell traits. No specific distributional patterns were
 observed between clusters. Though separable statistically, each cluster
 cannot be assigned to its own taxonomic unit.
description: <i>Gyrotoma</i> shells
 were borrowed from the Carnegie Museum of Natural History and digitally
 photographed in apertural view. All 612 shells used were at least 1 cm in
 length, possessed a sutural fissure, and had both the penultimate and the
 body whorl intact. For lots containing more than 50 shells that met the
 above criteria, a subset of 50 shells was randomly selected. Three curves
 on each shell were digitized using tpsDig2; each curve was resampled into
 a set of evenly-spaced landmarks for a total of 80 landmarks per specimen.
 The positions of the first and last landmarks on each curve were fixed,
 and the landmarks between them were allowed to “slide” in order to
 minimize bending energy. Shape variables were obtained from the landmark
 data using a generalized Procrustes analysis in the R package geomorph
 3.1.2 (Adams et al. 2019). Curve and outline analyses,
 however, may fail to accurately capture snail shell morphology, especially
 when fine-scale features are present. Therefore, five additional shell
 features were coded as present or absent in the analyzed individuals:
 horizontal striations on the body whorl; a posterior callus on the
 columella; a prominent ridge or row of nodules in the middle of the body
 whorl; posterior extensions of the whorls that form at the sutures; and a
 pattern of whorl constriction thought to be diagnostic in <i>G.
 pagoda</i>.
description: The TPS file contains the unaligned scaled landmark positions for
 all specimens. The data need to be processed to convert the three curves
 using the sliders file into Procrustes-aligned shape variables.
DOI: 10.5061/dryad.0k6djh9zb
title: Ecogeographical patterns of body size differ among North American paper wasp species

description: Species with widespread distributions frequently show clines in body size
 across broad geographic areas. These clines may be the result of
 “ecogeographical rules” that describe spatial patterns of phenotypic
 diferences driven by environmental variation. Intraspeciic variation in
 body size, and the mechanisms causing this variation, have been poorly
 described in social wasps. This study examined ecogeographical patterns of
 body size for 12 native species and one non-native species of North
 American paper wasps (genus: Polistes) using body size
 measurements from &gt; 14,000 pinned museum specimens. Intraspeciic
 body size was correlated with latitude, elevation, and broadscale climate
 variation. However, the direction of this relationship was idiosyncratic
 across species, with Bergmann’s clines and converse Bergmann’s clines
 equally represented. There was no evidence of a phylogenetic signal in the
 direction of the cline between body size and the environment. Within
 species, the worker caste and the reproductive caste showed the same
 direction of response between body size and latitude, although for most
 species the reproductive caste was larger than the worker caste.
 Intraspeciic variation in body size appears to be driven by diferences in
 the response among species to similar environmental variables but the
 mechanisms causing this variation remain unknown.
description: Whole boxes of pinned specimens of Polistes paper wasps from
 the collections at the American Museum of Natural History, the Cornell
 University Insect Collection, the Illinois Natural History Survey, the
 Smithsonian National Museum of Natural History, the Royal Ontario Museum,
 the University of Guelph Insect Collection, the University of Michigan
 Museum of Natural History, and the C.A. Triplehorn Insect Collection were
 photographed using a standarized set up. Boxes were placed inside of a
 light tent and photographed with a Canon 6D camera with an EF 24-105mm
 f/4L IS USM lens. The date and location of each specimen was transcribed
 from specimen labels. Latitude and longitude was determined using
 GEOlocate (http://www.geo-locate.org) and google maps (maps.google.com).
 Altitude and bioclim variables were obtained for each location. The head
 width, thorax width, and winglength of each specimen were measured in
 imageJ. The dataset includes original photographs of pinned specimens,
 measurements of size, and environmental variables. 
description: Please see READ ME document.
DOI: 10.5061/dryad.sbcc2fr58
title: Comparison of atmospheric refractivity estimation methods and their influence on radar wave propagation predictions

description: Environmental predictions in the marine atmospheric surface layer (MASL)
 are imperative to optimize X-band radar system performance in marine
 environments.  Evaporation ducts (ED) lead to anomalous
 propagation where characterization of EDs in the MASL occurs primarily
 through two methods: in-situ measurements and numerical modeling. This
 study investigates differences in co-located and synchronous refractivity
 estimations from the CASPER-East campaign. Propagation predictions are
 generated for refractive profiles from in-situ measurements, Monin-Obukov
 boundary layer similarity theory, and numerical weather prediction
 forecasts. Variations in evaporation duct height (EDH) are found to be a
 primary driver of differences in propagation between the estimated
 refractivity profiles, where location of the EDH relative to the
 transmitter changes the sensitivity of propagation predictions to EDH
 estimates. Differences in propagation are large when EDH estimates span
 the transmitter height and the lowest EDH across the methods is small,
 regardless of how much variation there is in EDH estimates. When the
 lowest EDH is small and EDH estimates span the transmitter height there
 are differences in physical regimes causing large propagation
 discrepancies – e.g., leakage into versus trapping within the duct.
 Variation in EDH between the methods is greatest in stable environments.
 M-deficit and curvature of the refractive profiles also influence
 propagation specifically in scenarios when EDH spans the transmitter. When
 all EDHs are below the transmitter, EDH variance is the primary
 contributor to propagation variance, but M-deficit and profile curvature
 variance play a secondary role. M-deficits and curvature between the
 methods agree most often during periods of atmospheric stability.
DOI: 10.5061/dryad.1zcrjdfqx
title: Brief exposure to warm temperatures reduces intron retention in Kdm6b in a species with temperature-dependent sex determination

description: Animals with temperature-dependent sex determination (TSD) respond to
 thermal cues during early embryonic development to trigger gonadal
 differentiation. TSD has primarily been studied using constant temperature
 incubations, where embryos are exposed to constant male- or
 female-producing temperatures and these studies have identified genes that
 display sex-specific expression in response to incubation temperature.
 Kdm6b, a histone demethylase, has received specific attention as it is
 among the initial genes to respond to incubation temperature and is
 necessary for testis development. Interestingly, Kdm6b retains an intron
 when eggs are incubated at a constant male-producing temperature, but the
 role of thermal variability in this developmental process is relatively
 understudied. Species with TSD regularly experience thermal cues that
 fluctuate between male- and female-producing temperatures throughout
 development but it is unclear how Kdm6b responds to such variable
 temperatures. In this study, we investigate temperature sensitive splicing
 in Kdm6b by exposing embryos to male- and female-promoting thermal
 conditions. We show a rapid decrease in levels of the intron retaining
 transcript of Kdm6b upon exposure to female-producing conditions. These
 results demonstrate that, under ecologically relevant conditions,
 temperature sensitive splicing can differentially regulate genes critical
 to TSD.
DOI: 10.5061/dryad.k3j9kd55t
title: Central processing of leg proprioception in Drosophila: Physiology and behavior data

description: Proprioception, the sense of self-movement and position, is mediated by
 mechanosensory neurons that detect diverse features of body kinematics.
 Although proprioceptive feedback is crucial for accurate motor control,
 little is known about how downstream circuits transform limb sensory
 information to guide motor output. Here, we investigate neural circuits in
 Drosophila that process proprioceptive information from the fly leg. We
 identify three cell-types from distinct developmental lineages that are
 positioned to receive input from proprioceptor subtypes encoding tibia
 position, movement, and vibration. 13Bα neurons encode femur-tibia joint
 angle and mediate postural changes in tibia position. 9Aα neurons also
 drive changes in leg posture, but encode a combination of directional
 movement, high-frequency vibration, and joint angle. Activating 10Bα
 neurons, which encode tibia vibration at specific joint angles, elicits
 pausing in walking flies. Altogether, our results reveal that central
 circuits integrate information across proprioceptor subtypes to construct
 complex sensorimotor representations that mediate diverse behaviors,
 including reflexive control of limb posture and detection of leg
 vibration.
description: See manuscript (https://doi.org/10.7554/eLife.60299) for details.