cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7m0cfxptt
title: Schoenoplectus salinity tolerance and regional environmental records

description: Evidence is mounting that climate-driven shifts in environmental
 conditions can elicit organismal evolution, yet there are sparingly few
 long-term records that document the tempo and progression of responses,
 particularly for plants capable of transforming ecosystems. In this study,
 we ‘resurrected’ cohorts of a foundational coastal marsh sedge
 (Schoenoplectus americanus) from a time-stratified seed bank to
 reconstruct a century-long record of heritable variation in response to
 salinity exposure. Common-garden experiments revealed that S. americanus
 exhibits heritable variation in phenotypic traits and biomass-based
 measures of salinity tolerance. We found that responses to salinity
 exposure differed among the revived cohorts, with plants from the early
 20th century exhibiting greater salinity tolerance than those from the mid
 to late 20th century. Fluctuations in salinity tolerance could reflect
 stochastic variation but a congruent record of genotypic variation points
 to the alternative possibility that the loss and gain in functionality is
 driven by selection, with comparisons to historical rainfall and
 paleosalinity records suggesting that selective pressures vary according
 to shifting estuarine conditions. Because salinity tolerance in
 S. americanus is tightly coupled to primary productivity and other vital
 ecosystem attributes, these findings indicate that organismal evolution
 merits further consideration as a factor shaping coastal marsh responses
 to climate change.
description: Please refer to Blum et al. Evolution Letters for details.
description: Please refer to ReadMe file.
DOI: 10.5061/dryad.pg4f4qrpr
title: Patterns and causes of signed linkage disequilibria in flies and plants: original data

description: Most empirical studies of linkage disequilibrium (LD) study its magnitude,
 ignoring its sign. Here, we examine patterns of signed LD in two
 population genomic datasets, one from Capsella grandiflora and one from
 Drosophila melanogaster. We consider how processes such as drift,
 admixture, Hill-Robertson interference, and epistasis may contribute to
 these patterns. We report that most types of mutations exhibit positive
 LD, particularly, if they are predicted to be less deleterious. We show
 with simulations that this pattern arises easily in a model of admixture
 or distance biased mating, and that genome-wide differences across site
 types are generally expected due to differences in the strength of
 purifying selection even in the absence of epistasis. We further explore
 how signed LD decays on a finer scale, showing that loss of function
 mutations exhibit particularly positive LD across short distances, a
 pattern consistent with intragenic antagonistic epistasis. Controlling for
 genomic distance, signed LD in C. grandiflora decays faster within genes,
 compared to between genes, likely a by-product of frequent recombination
 in gene promoters known to occur in plant genomes. Finally, we use
 information from published biological networks to explore whether there is
 evidence for negative synergistic epistasis between interacting radical
 missense mutations. In D. melanogaster networks, we find a modest but
 significant enrichment of negative LD, consistent with the possibility of
 intra-network negative synergistic epistasis.
DOI: 10.5061/dryad.gmsbcc2ng
title: Seasonal and annual dynamics of litterfall

description: Long-term data of litterfall can indicate overall forest
 functions in forest ecosystems. We collected monthly (May –
 October) and annual (1981 – 2018) litterfall including leaves, twigs,
 bark, reproductive and miscellaneous fractions in a mixed mature Pinus
 koraiensis forest on Changbai Mountain in Northeast,
 China, across 30 years. Based on these long-term litterfall data,
 we analyzed the seasonal and annual variations in different litterfall
 fractions and their relationships with climatic factors. Climate
 data were obtained from the meteorological observation field (738 m above
 sea level) of the Changbai Mountain forest ecosystems research station,
 Institute of Applied Ecology, Chinese of Academy of
 Sciences. Both the leaf and total litterfall exhibited a strong,
 similar seasonal pattern, with the highest levels between September and
 October, and the annual litterfall had an “S-shaped” increasing
 pattern from 1981 – 2018. Distinct monthly and yearly fluctuations for the
 other litterfall fractions across the 30 years were
 observed. Mean monthly evapotranspiration and temperature (minimum and
 maximum) were the best predictors for monthly litterfall. By contrast, the
 models that best predicted the annual litterfall production included mean
 annual precipitation, and mean monthly precipitation and temperature in
 May and October. This unique dataset of detailed long-term litterfall
 dynamics has potentially major significance for enhancing our
 understanding on the role of climatic factors controlling forest
 litterfall amount and seasonality in temperate mixed mature
 forests.
DOI: 10.5061/dryad.v9s4mw6w5
title: Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

description: The volvocine algae, which include the single-celled
 species Chlamydomonas reinhardtii and the colonial
 species Volvox carteri, serve as a model in which to study the
 evolution of multicellularity and cellular differentiation. Studies
 reconstructing the history of this group have by and large relied on
 datasets of one to a few genes for phylogenetic inference and ancestral
 character state reconstruction. As a result, volvocine phylogenies lack
 concordance depending on the number and/or type of genes (i.e.,
 chloroplast vs nuclear) chosen for phylogenetic inference. While multiple
 studies suggest that multicellularity evolved only once in the volvocine
 algae, that each of its three colonial families is monophyletic, and that
 there have been at least three independent origins of cellular
 differentiation in the group, other studies call into question one or more
 of these conclusions. An accurate assessment of the evolutionary history
 of the volvocine algae requires inference of a more robust
 phylogeny. We performed RNA sequencing (RNA-seq) on 55 strains
 representing 47 volvocine algal species and obtained similar data from
 curated databases on 13 additional strains. We then compiled a dataset
 consisting of transcripts for 40 single-copy, protein-coding, nuclear
 genes, and subjected the predicted amino acid sequences of these genes to
 maximum likelihood, Bayesian inference, and coalescent-based analyses.
 These analyses show that multicellularity independently evolved at least
 twice in the volvocine algae and that the colonial family Goniaceae is not
 monophyletic. Our data further indicate that cellular differentiation
 arose independently at least four, and possibly as many as six times,
 within the volvocine algae. Altogether, our results demonstrate
 that multicellularity and cellular differentiation are evolutionarily
 labile in the volvocine algae, affirming the importance of this group as a
 model system for the study of major transitions in the history of life.
DOI: 10.5061/dryad.7d7wm37vd
title: AMS dates and Neolithic cereal measurements from the Kashmir Prehistory Project

description: The Kashmir Valley is understood to be an important centre of early
 agriculture in the Western Himalayas. Direct dates of prehistoric cereal
 remains indicate the valley as a likely route of transmission of
 agricultural systems between South, Central and East Asia. The movement of
 these crops into novel mountain environments may have exerted
 environmental stresses influencing the morphology of cereal crops. This
 dataset presents AMS dates and measurements of carbonised cereal remains
 from prehistoric sites recorded during the first phase of the Kashmir
 Prehistory Project. These data may be of particular utility to regional
 meta-analyses of change in cereal size in relation to cultural or
 environmental factors.
description: Sediment layers processed using bucket flotation in field.
 Buoyant carbonised materials were collected by passing through 3mm and
 0.3mm meshes. Identifications were made under
 dissecting stereoscopes at University of Kashmir, Srinagar and Birbal
 Sahni Institute of Palaoescience, Lucknow. Length, width and thickness of
 domesticated cereal types were measured in mm.
DOI: 10.5061/dryad.tx95x69xx
title: Data for: Characterizing individual tree-level snags using airborne lidar-derived forest canopy gaps within closed-canopy conifer forests

description: 1. Airborne lidar is often used to calculate forest metrics about trees
 but it may also provide a wealth of information about the space between
 trees. Forest canopy gaps are defined by the absence of vegetative
 structure and serve important roles for wildlife, such as facilitating
 animal movement. Forest canopy gaps also occur around snags, keystone
 structures that provide important substrates to wildlife species for
 breeding, roosting, and foraging. 2. We wanted to test a method for
 quantifying canopy gaps around individual snags and live trees, with the
 working hypothesis that snags would have more gaps surrounding them
 overall than live trees. We evaluated canopy gaps around individual snags
 (n=270) and live trees (n=2186) and evaluated correlations between canopy
 structure and snag occurrence in dense conifer stands of the Idaho
 Panhandle National Forest, USA. We paired airborne lidar with ground
 reference data collected at fixed-radius plots (n=53) to evaluate local
 gap structure. The R package ForestGapR was used to quantify canopy gaps
 throughout the canopy to determine where the differences were greatest. A
 canopy space profile was created for each tree by mapping gaps (a)
 vertically every 2 m in height (2–50 m above ground), and (b) horizontally
 across small (16 m2), medium (36 m2), and large (64 m2) footprint sizes.
 3. Our results suggest this method is robust for quantifying canopy gaps
 around individual trees. The canopy space profiles were distinctly
 different for snags and live trees, with more canopy gaps within the area
 surrounding snags relative to live trees. The greatest differences
 occurred at mid-canopy heights (~20 m above ground) and at the smallest
 footprint size (16 m2). 4. These results show potential to improve
 understanding of gap dynamics in closed-canopy conifer forests, and we
 suggest snag modeling could be improved by incorporating lidar-derived
 canopy gap analyses alongside existing methodologies.
DOI: 10.5061/dryad.j6q573ndv
title: Environmental drivers of annual population fluctuations in a trans-Saharan insect migrant

description: Many latitudinal insect migrants, including agricultural pests, disease
 vectors and beneficial species, show huge fluctuations in the year-to-year
 abundance of spring immigrants reaching temperate zones. It is widely
 believed that this variation is driven by climatic conditions in the
 winter-breeding regions, but evidence is lacking. We identified the
 environmental drivers of the annual population dynamics of a cosmopolitan
 migrant butterfly (the painted lady Vanessa cardui), using a combination
 of long-term monitoring, climate and atmospheric data within the western
 part of its Afro-Palearctic migratory range. Our population models show
 that a combination of high winter NDVI (normalised difference vegetation
 index) in the Savannah/Sahel of sub-Saharan Africa, high spring NDVI in
 the Maghreb of North Africa, and frequent favourably-directed tailwinds
 during migration periods, are the three most important drivers of the size
 of the immigration to Western Europe, while our atmospheric trajectory
 simulations demonstrate regular opportunities for windborne trans-Saharan
 movements. The effects of sub-Saharan vegetative productivity and wind
 conditions confirm that painted lady populations either side of the Sahara
 are linked by regular mass migrations, making this the longest annual
 insect migration circuit so far known. Our results provide the first
 quantification of the environmental drivers of large annual population
 fluctuations of an insect migrant, and hold much promise for predicting
 invasions of migrant insect pests, disease vectors and beneficial species.
description: The dataset was derived from a 22 year's data (1994-2015) of
 the Butterfly Monitoring Scheme [BMS] records from the Mediterranean
 (northeastern Spain) and NW Europe (the United Kingdom and the
 Netherlands).  BMS data follow a standardized data collection (see more
 detail in: E. Pollard, T. J. Yates, Monitoring Butterflies for Ecology and
 Conservation (Chapman & Hall, 1993)). In this dataset, the
 population density of the painted lady butterfly were calculated for each
 record.  
description: The dataset contains six columns: transect_id, Year, Month, Day,
 Region and Population density.  Information on how the measurements were
 done can be found in the associated manuscript referenced
 above.
DOI: 10.5061/dryad.dv41ns1zc
title: Springtail coloration at a finer scale: mechanisms behind vibrant Collembolan metallic colours

description: The mechanisms and evolution of metallic structural colours are of both
 fundamental and applied interest, yet most work in arthropods has focused
 on derived butterflies and beetles with distinct hues. In particular,
 basal hexapods - groups with many scaled, metallic representatives – are
 currently poorly studied and controversial, with some recent studies
 suggesting either that thin- film (lamina thickness) or diffraction
 grating elements (longitudinal ridges, crossribs) produce these colors in
 early Lepidoptera and one springtail (Collembola) species. Especially the
 Collembolan basal scale design, consisting of a singlelamina and
 longitudinal ridges with smooth valleys lacking crossribs, makes them an
 interesting group to explore the mechanisms of metallic colouration. Using
 microspectroscopy, Raman spectroscopy, electron microscopy and FDTD
 optical modelling we investigated scale colour in seven springtail species
 that show clear metallic colouration. Reflectance spectra are largely
 uniform and exhibit a broadband metallic/golden colouration with peaks in
 the violet/blue region. Our simulations confirm the role of the
 longitudinal ridges, working in conjunction with thin-film effects to
 produce a broadband metallic colouration. Broadband colouration occurs
 through spatial colour mixing which likely results from nanoscale
 variation in scale thickness and ridge height and distance. These results
 provide crucial insights into the colour production mechanisms in a basal
 scale design and highlight the need for further investigation of scaled,
 basal arthropods.
description: SEM and TEM pictures were collected using a FEG-SEM (FEI Quanta
 200F, Netherlands) and a JEOL JEM 1010 (Jeol, Ltd, Tokyo, Japan)
 transmission electron microscope. Reflectance spectra
 of scales and scales on body result from measurements on a CRAIC AX10
 UV–Visible micro-spectrophotometer (CRAIC Technologies, Inc.,
 USA). Simulation spectra were obtained from
 Finite-Difference Time-Domain - (FDTD) modelling using a commercial
 Maxwell equation solver (Lumerical Solutions, Inc).
DOI: 10.5061/dryad.mpg4f4r0b
title: Rhinocerotidae from the early Miocene of the Negev (Israel) and implications for the dispersal of early Neogene rhinoceroses

description: A revision of the rhinocerotid material from the Negev (Israel), dating
 back to the early Miocene (MN3 in the European Mammal Biochronology),
 highlights the presence of Brachypotherium and a taxon close to
 Gaindatherium in the Levantine Corridor. A juvenile mandible, investigated
 using CT scanning, displays morphologically distinct characters consistent
 with B. cf. B. snowi rather than with other Eurasian representatives of
 this genus. Some postcranial remains from the Negev, such as a humerus,
 display features that distinguish it among Miocene taxa. We attribute
 these postcrania to cf. Gaindatherium sp., a taxon never recorded outside
 the Siwaliks until now. This taxon dispersed into the Levantine region
 during the late early Miocene following a pattern similar to other South
 Asian taxa. Brachypotherium cf. B. snowi probably occurred in the
 Levantine region and then in North Africa during the early Miocene, as its
 remains are known from slightly younger localities such as Moghara (Egypt)
 and Jebel Zelten (Libya). The occurrence cf. Gaindatherium sp. represents
 a previously unrecorded range expansion out of Southeast Asia. These new
 records demonstrate the paleogeographic importance of the Levantine region
 showcasing the complex role of the Levantine corridor in intercontinental
 dispersals between Asia and Europe as well as Eurasia and Africa.
DOI: 10.5061/dryad.bk3j9kdc7
title: Experimentally broadcast ocean surf and river noise alters birdsong structure

description: Anthropogenic noise and its effects on acoustic communication have
 received considerable attention in recent decades. Yet, the natural
 acoustic environment’s influence on communication and its role in shaping
 acoustic signals remains unclear. Using landscape-level playbacks of ocean
 surf and river noise in coastal and riparian habitat, respectively, we
 investigated how water-generated noise influences spectral and temporal
 song characteristics in six songbird species. We recorded individuals
 defending territories across 37 sites, with each site representing one of
 four acoustic environments: naturally quiet ‘controls’, naturally noisy
 ‘positive controls’ adjacent to the ocean or a whitewater river, ‘phantom’
 playback sites with continuous broadcast of low-frequency water noise, and
 ‘shifted’ playback sites with continuous broadcast of high-frequency water
 noise. We predicted that song structure would generally correlate with
 background sound amplitude and that signal features would differ across
 site types based on the spectral profile of the acoustic environment. No
 two species altered songs in precisely the same way. However, song
 structure of all six species varied with amplitude and/or frequency of
 background noise, providing strong evidence that natural soundscapes
 influence vocal behavior.
description: Data were collected and processed as described in the methods
 of "Experimentally Broadcast Ocean Surf and River Noise Alters
 Birdsong Structure."
description: Each data file is accompanied by a ReadMe file that provides
 variable code definitions.
DOI: 10.5061/dryad.5mkkwh763
title: The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)

description: Understanding the evolutionary history of crops, including identifying
 wild relatives, helps to provide insight for conservation and crop
 breeding efforts. Cultivated Brassica oleracea has intrigued researchers
 for centuries due to its wide diversity in forms, which include cabbage,
 broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the
 evolutionary history of this species remains understudied. With such
 different vegetables produced from a single species, B. oleracea is a
 model organism for understanding the power of artificial selection.
 Persistent challenges in the study of B. oleracea include conflicting
 hypotheses regarding domestication and the identity of the closest living
 wild relative. Using newly generated RNA-seq data for a diversity panel of
 224 accessions, which represents 14 different B. oleracea crop types and
 nine potential wild progenitor species, we integrate phylogenetic and
 population genetic techniques with ecological niche modeling,
 archaeological, and literary evidence to examine relationships among
 cultivars and wild relatives to clarify the origin of this horticulturally
 important species. Our analyses point to the Aegean endemic B. cretica as
 the closest living relative of cultivated B. oleracea, supporting an
 origin of cultivation in the Eastern Mediterranean region. Additionally,
 we identify several feral lineages, suggesting that cultivated plants of
 this species can revert to a wild-like state with relative ease. By
 expanding our understanding of the evolutionary history in B. oleracea,
 these results contribute to a growing body of knowledge on crop
 domestication that will facilitate continued breeding efforts including
 adaptation to changing environmental conditions.
description: Colors in transcript abudances and the module number they relate
 to in the manuscript: 
 1 grey 2 turquoise 3 blue 4 brown 5 yellow 6 green 7 red 8 black 9 pink 10 magenta 11 purple 12 greenyellow 13 tan 14 salmon 15 cyan 16 midnightblue 17 lightcyan 18 grey60 19 lightgreen 20 lightyellow 21 royalblue 22 darkred 23 darkgreen 24 darkturquoise 25 darkgrey 26 orange 27 darkorange 28 white 29 skyblue 30 saddlebrown 31 steelblue 32 paleturquoise 33 violet 34 darkolivegreen 35 darkmagenta 36 sienna3 37 yellowgreen 38 skyblue3 39 plum1 40 orangered4 41 mediumpurple3 42 ivory 43 lightcyan1 44 lightsteelblue1 45 floralwhite 46 darkorange2 47 brown4 48 bisque4
DOI: 10.5061/dryad.1c59zw3vq
title: Repeated genetic and adaptive phenotypic divergence across tidal elevation in a foundation plant species

description: Microgeographic genetic divergence can create fine-scale trait variation.
 When such divergence occurs within foundation species, then it might
 impact community structure and ecosystem function, and cause
 other cascading ecological effects. We tested for parallel
 microgeographic trait and genetic divergence in 
 Spartina  alterniflora , a foundation species that dominates salt
 marshes of the US Atlantic and Gulf coasts.  Spartina 
 is characterized by tall-form (1-2m) plants at lower tidal elevations and
 short-form (&lt;0.5m) plants at higher tidal elevations, yet whether
 this trait variation reflects plastic and/or genetically differentiated
 responses to these environmental conditions remains unclear. In the
 greenhouse, seedlings raised from tall-form plants grew taller than those
 from short-form plants, indicating a heritable difference in height. When
 we reciprocally transplanted seedlings back into the field for a growing
 season, composite fitness (survivorship and seed production) and key plant
 traits (plant height and biomass allocation) differed interactively across
 origin and transplant zones in a manner indicative of local adaptation.
 Further, a survey of single nucleotide polymorphisms revealed repeated,
 independent genetic differentiation between tall- and short-form 
 Spartina  at 5 of 6 tested marshes across the native range. The
 observed parallel, microgeographic genetic differentiation in 
 Spartina  likely underpins marsh health and functioning,
 and provides an underappreciated mechanism that might increase
 capacity of marshes to adapt to rising sea levels.
description: Data was collected from a common garden experiment, reciprocial
 transplant experiment and genetic survey of natural marshes to test for
 parallel microgeographic trait and genetic divergence
 in <em>Spartina alterniflora</em>