cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d11x18
title: Data from: Modifications during early plant development promote the evolution of nature’s most complex woods

description: Secondary growth is the developmental process by which woody plants grow
 radially. The most complex presentations of secondary growth are found in
 lianas (woody vines) as a result of their unique demand to maintain stems
 that can twist without breaking. The complex woody forms in lianas arise
 as non-circular stem outlines, aberrant tissue configurations, and/or
 shifts in the relative abundance of secondary tissues. Previous studies
 demonstrate that abnormal activity of the vascular cambium leads to
 variant secondary growth, however the developmental and evolutionary basis
 for this shift is still largely unknown. Here, we adopt an integrative
 approach, leveraging techniques from historically distinct
 disciplines—developmental anatomy and phylogenetic comparative methods—to
 elucidate the evolution of development of the complex woody forms in a
 large lineage of tropical lianas, Paullinia L. (Sapindaceae). We find that
 all forms of variant secondary growth trace back to the same modification
 during early stem development, which results in young plants with lobed
 stem outlines and a discontinuous distribution of vascular bundles. By
 placing development in a phylogenetic context, we further show that the
 lobed primary plant bauplan is the evolutionary precursor to all complex
 woody forms in the Sapindaceae lianas. We find evidence for three
 evolutionary mechanisms that generate phenotypic novelty: exaptation and
 co-opting of the ancestral bauplan; the quasi-independence of the
 interfascicular and fascicular cambia; and the inclusion of additional
 developmental stages to the end of the ancestral ontogeny. Our study
 demonstrates the utility of integrating developmental data within a
 phylogenetic framework to investigate the evolution of complex traits.
DOI: 10.5061/dryad.31zcrjdgc
title: Long-term monitoring of a highly invaded annual grassland community through drought, before and after an unintentional fire.

description: Questions: 1) How did seedling numbers and species composition change in
 the first year after a wildfire during drought, relative to pre-fire
 variation? 2) Has the community returned to pre-fire composition after
 five years? 3) Has the degree of dominance by exotic annual grasses
 changed? 4) Is there any evidence that drought conditions affected
 community cover, before or after fire? Location: Exotic-dominated annual
 grassland in southern California, U.S.A. Methods:  We monitored
 community cover and native annual forb densities for four years before and
 four (cover) to five (densities) years after an unintentional fire (fall
 2013) coinciding with the spring 2012-2019 California drought. We also
 measured seedling emergence both before and during the first year
 post-fire. We assessed post-fire changes in cover and density relative to
 pre-fire variation, and tested correlations between community cover and
 annual rainfall measures. Results: Seedling emergence declined strongly
 after fire for exotic grasses, but remained stable for exotic forbs.
 Seedling densities of the most common native forbs declined, but several
 previously-rare natives increased. Community cover initially shifted
 towards the exotic forbs Erodium spp., then returned to higher exotic
 grass densities. Yet the previously-dominant Bromus diandrus declined
 steeply, even as other exotic grasses and some native forbs increased. Up
 to five years after fire, relative cover and abundance of the most common
 exotic and native species still differed from pre-fire composition. Common
 species were uncorrelated with annual precipitation, but several may have
 responded to shorter growing seasons. Conclusions: Immediate post-fire
 conditions favored exotic and native forbs over grasses, as predicted. Yet
 in contrast to many previous studies, the community did not return quickly
 to pre-fire composition but showed persistent changes that favored neither
 natives nor exotics. Our results suggest post-fire recovery in this
 habitat may be contingent on abiotic conditions, with drought one
 potential explanation for changes.
description: Please see published paper and metadata file.
description: Please see published paper and metadata file.
DOI: 10.6071/m3xw9t
title: Linguistic laws in speech: the case of Catalan and Spanish

description: In this work we explore in an oral corpus of Catalan and Spanish
 (Glissando Corpus) four classical linguistic laws (Zipf's law,
 Herdan's law, Brevity law, and Menzerath-Altmann's law) in oral
 communication, both in physical units and in symbolic units measured in
 speech transcriptions, and we also reviewed two more laws recently
 reformulated: lognormality law and size-rank law. Our results reinforce
 with empirical evidence in two more languages the 'physical
 hypothesis' according to which linguistic laws could be explained by
 physical laws and the principles of information theory. In this sense,
 linguistic laws would have an oral origin and the evidences recovered in
 written texts would be a byproduct of the complexity that takes place in
 speech.
DOI: 10.5061/dryad.hhmgqnkcf
title: Genotypic variation in parasite avoidance behavior and other mechanistic, non-linear components of transmission

description: Traditional epidemiological models assume that transmission increases
 proportionally to the density of parasites. However, empirical data
 frequently contradict this assumption. General yet mechanistic models can
 explain why transmission depends non-linearly on parasite density and
 thereby identify potential defensive strategies of hosts. For example,
 hosts could decrease their exposure rates at higher parasite densities
 (via behavioral avoidance) or decrease their per-parasite susceptibility
 when encountering more parasites (e.g., via stronger immune responses). To
 illustrate, we fit mechanistic transmission models to 19 genotypes of
 Daphnia dentifera hosts over gradients of the trophically-acquired
 parasite, Metschnikowia bicuspidata. Exposure rate (foraging, F)
 frequently decreased with parasite density (Z), and per-parasite
 susceptibility (U) frequently decreased with parasite encounters (FxZ).
 Consequently, infection rates (FxUxZ) often peaked at intermediate
 parasite densities. Moreover, host genotypes varied substantially in these
 responses. Exposure rates remained constant for some genotypes, but
 decreased sensitively with parasite density for others (up to 78%).
 Furthermore, genotypes with more sensitive foraging/exposure also foraged
 faster in the absence of parasites (suggesting ‘fast and sensitive’ versus
 ‘slow and steady’ strategies). These relationships suggest that high
 densities of parasites can inhibit transmission by decreasing exposure
 rates and/or per-parasite susceptibility, and identify several intriguing
 axes for the evolution of host defense.
DOI: 10.5061/dryad.vx0k6djmr
title: Environmental correlates of Leguminosae species richness in Mexico: quantifying the contributions of energy and environmental seasonality

description: Explaining species richness patterns is a central issue in
 ecology, but a general explanation remain elusive. Environmental
 conditions have been proposed to be important drivers of these patterns,
 but we still need to better understand the relative contribution of
 environmental factors. Here we aim at testing two environmental hypotheses
 for richness gradients: energy availability and environmental seasonality
 using diversity patterns of the family Leguminosae across Mexico. We
 compiled a database of 502 species and 32,962 records. After dividing
 Mexico into 100x100 km grid cells, we constructed a map of variation in
 species richness that accounts for heterogeneity in sampling effort. We
 found, the cells with the highest species richness of legumes are in the
 Neotropical region of Pacific coastal and southern Mexico, where the
 legume family dominates the tropical rain forests and seasonally dry
 tropical forests. Regression models show that energy and seasonality
 predictors can explain 25% and 49% of the variation in richness,
 respectively. Spatial autocorrelation analysis showed that richness has a
 strong spatial structure, but that most of this structure disappears when
 both energy and seasonality are used to account for richness gradient. Our
 study demonstrates multiple environmental conditions contribute
 complementarily to explain diversity gradients. Moreover, it shows that in
 some regions, environmental seasonality can be more important than energy
 availability, contradicting studies at coarser spatial scales. More basic
 taxonomic and floristic work is needed to help describe patterns of
 diversity for many groups to allow for testing the underlying mechanisms
 responsible for diversity gradients.
DOI: 10.7280/d1696j
title: Data from: Complementarity in spatial subsidies of carbon associated with resource partitioning along multiple niche axes

description: Data support analyses describing the potential for niche
 partitioning and complementarity in a guild of suspension-feeding rocky
 shore invertebrates. I focused on the mussels Perna canaliculus, Mytilus
 galloprovincialis, Aulacomya maoriana, and Xenostrobus pulex, all of which
 coexist along the coastline of the South Island of New Zealand. I
 quantified the mussel species’ distributions, both vertically on the shore
 and within the three-dimensional mussel bed matrix, and used carbon
 (delta13C) and nitrogen (delta15N) stable isotope ratios to compare
 species’ diets. Mussels exhibited niche partitioning along all resource
 axes, including patterns of tide-height zonation, depth in the mussel bed,
 and diet. Given the mussels’ use of different spatial and food resources,
 I evaluated the potential for complementarity with respect to mussels’
 roles as mediators of carbon inputs into rocky-shore ecosystems. In these
 systems, mussels are basal species, capturing and consuming particulate
 organic matter in the nearshore ocean and making it available for local
 consumption within the benthic community. I found that mussels accumulated
 appreciable amounts of carbon via growth and that even the most productive
 species – Perna canaliculus – only contributed about half of the
 mussel-mediated carbon that accumulated over a year.
description: This dataset includes data from surveys of mussel beds,
 destructive sampling to quantify abundances, measurements of lengths and
 masses, measurements of annual growth rates, and carbon and nitrogen
 percentages and stable isotope values. Samples are from mussel beds
 at four sites on the South Island of New Zealand: Blue Duck (42.28º S,
 173.75° E) and Box Thumb (43.58° S, 172.78° E) on the east coast and Nile
 River (41.90° S, 171.44° E) and Nine Mile (42.34° S, 171.26°E) on the west
 coast. Mussels were surveyed and sampled at each site at three tidal
 elevations: 1.0, 1.5, and 2.0 m above the lowest astronomical tide. Mussel
 species included <i>Perna canaliculus</i>, <i>Mytilus
 galloprovincialis</i>, <i>Aulacomya maoriana</i>, and
 <i>Xenostrobus pulex</i>, all of which coexist at these
 sites.
description: The dataset is described in the associated ReadMe file:
 BRACKEN_10-7280D1696J_Readme.txt. All data are in .csv files. Contact the
 author (m.bracken@uci.edu) for additional information.
DOI: 10.5061/dryad.08kprr4xt
title: Climate-driven habitat change causes evolution in Threespine Stickleback

description: Climate change can shape evolution directly by altering abiotic conditions
 or indirectly by modifying habitats, yet few studies have investigated the
 effects of climate-driven habitat change on contemporary evolution. We
 resampled populations of Threespine Stickleback (Gasterosteus aculeatus)
 along a latitudinal gradient in California bar-built estuaries to examine
 their evolution in response to changing climate and habitat. We took
 advantage of the strong association between stickleback lateral plate
 phenotypes and Ectodysplasin A (Eda) genotypes to infer changes in allele
 frequencies over time. Results show that the frequency of low-plated
 alleles has generally increased and heterozygosity has decreased over
 time. Latitudinal patterns in stickleback plate phenotypes suggest that
 evolution at Eda is a response to climate-driven habitat transformation
 rather than a direct consequence of climate. As climate change has reduced
 precipitation and increased temperature and drought, bar-built estuaries
 have transitioned from lotic (flowing-water) to lentic (still-water)
 habitats, where the low-plated allele is favored. The low-plated allele
 has achieved fixation at the driest, hottest southernmost sites, a trend
 that is progressing northward with climate change. Climate-driven habitat
 change is therefore causing a reduction in genetic variation that may
 hinder future adaptation for populations facing multiple threats.
DOI: 10.5061/dryad.fj6q573q7
title: Future of the human climate niche

description: All species have an environmental niche, and despite technological
 advances, humans are unlikely to be an exception. Here, we demonstrate
 that for millennia, human populations have resided in the same narrow part
 of the climatic envelope available on the globe, characterized by a major
 mode around ∼11 °C to 15 °C mean annual temperature (MAT). Supporting the
 fundamental nature of this temperature niche, current production of crops
 and livestock is largely limited to the same conditions, and the same
 optimum has been found for agricultural and nonagricultural economic
 output of countries through analyses of year-to-year variation. We show
 that in a business-as-usual climate change scenario, the geographical
 position of this temperature niche is projected to shift more over the
 coming 50 y than it has moved since 6000 BP. Populations will not simply
 track the shifting climate, as adaptation in situ may address some of the
 challenges, and many other factors affect decisions to migrate.
 Nevertheless, in the absence of migration, one third of the global
 population is projected to experience a MAT &gt;29 °C currently found
 in only 0.8% of the Earth’s land surface, mostly concentrated in the
 Sahara. As the potentially most affected regions are among the poorest in
 the world, where adaptive capacity is low, enhancing human development in
 those areas should be a priority alongside climate mitigation.
DOI: 10.5061/dryad.8sf7m0chc
title: Data from: Predation of potential insect pests in oil palm plantations, rubber tree plantations and fruit orchards

description: In human-modified landscapes, important ecological functions such as
 predation are negatively affected by anthropogenic activities, including
 the use of pesticides and habitat degradation. Predation of insect pests
 is an indicator of healthy ecosystem functioning, which provides important
 ecosystem services, especially for agricultural systems. In this study, we
 compare predation attempts from arthropods, mammals, and birds on
 artificial caterpillars in the understory, between three tropical
 agricultural land-use types: oil palm plantations, rubber tree
 plantations, and fruit orchards. We collected a range of local and
 landscape-scale data including: undergrowth vegetation structure;
 elevation; proximity to forest; and canopy cover in order to understand
 how environmental variables can affect predation. In all three land-use
 types, our results showed that arthropods and mammals were important
 predators of artificial caterpillars and there was little predation by
 birds. We did not find any effect of the environmental variables on
 predation. There was an interactive effect between land-use type and
 predator type. Predation by mammals was considerably higher in fruit
 orchards and rubber tree than in oil palm plantations, likely due to their
 ability to support higher abundances of insectivorous mammals. In order to
 maintain or enhance natural pest-control in these common tropical
 agricultural land-use types, management practices that benefit
 insectivorous animals should be introduced, such as the reduction of
 pesticides, improvement of understory vegetation and local and landscape
 heterogeneity.
DOI: 10.5061/dryad.0p2ngf1vx
title: Multiple sequence alignment for the native Norwegian vascular plant phylogeny

description: Methods: We produced a multi-locus Maximum Likelihood
 (ML) phylogeny using a combination of newly produced DNA
 sequences from herbarium specimens and sequences available from public
 repositories. We combined the phylogeny with species
 occurrence data to estimate phylogenetic diversity and phylogenetic
 endemism across Norway, using a spatial randomization to judge statistical
 significance. We used multiple-model inference to identify environmental
 variables that contributed the most to the patterns of phylogenetic
 diversity. Finally, we estimated phylogenetic turnover and used this to
 identify Norwegian plant assemblages in terms
 of composition and evolutionary history. Results: Our
 ML phylogeny contained 87% of all currently
 described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway. Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.
description: Multiple sequence alignment (FASTA format) of DNA sequences used
 for reconstructing the Norway flora phylogenetic tree. The three genetic
 markers ITS, matK and rbcL were used to create the multiple sequence
 alignment.
DOI: 10.5061/dryad.1vhhmgqp3
title: Quantifying the structure and dynamics of fish shoals under predation threat in three-dimensions

description: Detailed quantifications of how predators and their grouping prey interact
 in three dimensions (3D) remain rare. Here we record the structure and
 dynamics of fish shoals (Pseudomugil signifer) in 3D both with and without
 live predators (Philypnodon grandiceps) under controlled laboratory
 conditions. Shoals adopted two distinct types of shoal structure;
 ‘sphere-like’ geometries at depth, and flat ‘carpet-like’ structures at
 the water’s surface, with shoals becoming more compact in both horizontal
 and vertical planes in the presence of a predator. The predators actively
 stalked and at- tacked the prey, with attacks being initiated when the
 shoals were not in their usual configurations. These attacks caused the
 shoals to break apart, but shoal reformation was rapid, and involved
 individuals adjusting their positions in both horizontal and vertical
 dimensions. Our analyses revealed that targeted prey were more isolated
 from other conspecifics, and were closer in terms of distance and
 direction to the predator compared to non-targeted prey. Moreover, which
 prey were targeted could largely be identified based on individuals’
 positions from a single plane. This highlights that previously proposed 2D
 theoretical models and their assumptions appear valid when considering how
 predators target groups in 3D. Our work provides experimental, and not
 just anecdotal, sup- port for classic theoretical predictions, and also
 lends new insights into predatory-prey interactions in three-dimensional
 environments.
DOI: 10.5061/dryad.kkwh70s1n
title: Phylogeny of the Norwegian flora

description: Abstract: Aim: In this study, we explored spatial patterns of phylogenetic
 diversity and endemism in the flora of Norway and tested hypothesized
 post-glacial environmental drivers of phylogenetic diversity, including
 temperature, precipitation, edaphic factors, and time since glacial
 retreat. Location: Norway. Taxon: Vascular plants
 (Trachaeophyta). Methods: We produced a multi-locus Maximum Likelihood
 (ML) phylogeny using a combination of newly produced DNA
 sequences from herbarium specimens and sequences available from public
 repositories. We combined the phylogeny with species
 occurrence data to estimate phylogenetic diversity and phylogenetic
 endemism across Norway, using a spatial randomization to judge statistical
 significance. We used multiple-model inference to identify environmental
 variables that contributed the most to the patterns of phylogenetic
 diversity. Finally, we estimated phylogenetic turnover and used this to
 identify Norwegian plant assemblages in terms
 of composition and evolutionary history. Results: Our
 ML phylogeny contained 87% of all currently
 described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway. Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.
description: The Norway native flora phylogeny (Newick format) relating 1238
 study species.