cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wpzgmsbj5
title: Data from: Regulation of fatty acid composition related to ontogenetic changes and niche differentiation of a common aquatic consumer

description: Fatty acids (FAs) are key nutrients for fitness which take part in
 multiple physiological processes over the ontogeny of organisms. Yet, we
 lack evidence on how FA nutrition mediates life-history trade-offs and
 ontogenetic niche shifts in natural populations. In a field study, we
 analyzed ontogenetic changes in the FAs of Eurasian perch (Perca
 fluviatilis L.), a widespread fish that goes through ontogenetic
 niche shifts and can have high individual niche specialization. Diet
 explained most of the variation in the FA composition of perch dorsal
 muscle over early ontogeny (28%), while the total length explained 23%,
 suggesting that perch significantly regulated FA composition over early
 ontogeny. Condition explained 1% of the remaining variation. 18:3n-3 (ALA)
 and 18:4n-3 (SDA) indicated planktivory; 18:1n-7, benthivory; and 22:6n-3
 (DHA), piscivory in perch diet. Conversely, perch regulated
 long-chained polyunsaturated fatty acids (PUFAs), such as 20:5n-3 (EPA),
 20:4n-6 (ARA) and 22:6n-3 (DHA) over ontogeny, emphasizing the role of
 such FAs in early growth and sexual maturation. Adult perch increasingly
 retained 16:1n-7 and 18:1n-9 suggesting higher energy storage in older
 perch. Furthermore, differences in DHA availability in diet correlated
 with intra-cohort differences in perch growth, potentially hindering the
 overall use of benthic resources and promoting earlier shifts to piscivory
 in littoral habitats. Overall, this study indicates that in addition to
 diet, internal regulation may be more important for FA composition than
 previously thought. Differences between FA needs and FA availability may
 lead to life-history trade-offs that affect the ecology of consumers,
 including their niche.
description: Please reference the published article for more information
description: This dataset contains a series of variables over the ontogeny of
 a polymorphic perch (<em>Perca fluviatilis</em>) that live in
 pelagic and littoral habitats. The variables include: body size, growth,
 condition factor, C and N stable isotopes, diet estimations and % of
 different fatty acids in the dorsal muscle of perch. It also shows the
 isotope values of the food sources that were used as endpoints in the
 isotope mixing model. The dataset provides metadata of each
 variable.
DOI: 10.5061/dryad.5hqbzkh3d
title: Data from: Activin A forms a non-signaling complex with ACVR1 and type II Activin/BMP receptors via its finger 2 tip loop

description: Activin A functions in BMP signaling in two ways: it either engages ACVR1B
 to activate Smad2/3 signaling or binds ACVR1 to form a non-signaling
 complex (NSC).  Although the former property has been
 studied extensively, the roles of the NSC remain
 unexplored.  The genetic disorder fibrodysplasia
 ossificans progressiva (FOP) provides a unique window into ACVR1/Activin A
 signaling because in that disease Activin can either signal through
 FOP-mutant ACVR1 or form NSCs with wild type ACVR1.  To
 explore the role of the NSC, we generated ‘agonist-only’ Activin A muteins
 that activate ACVR1B but cannot form the NSC with
 ACVR1.  Using one of these muteins we demonstrate that
 failure to form the NSC in FOP results in more severe disease pathology.
 These results provide the first evidence for a biological role for the
 NSC in vivo and pave the way for further exploration of
 the NSC’s physiological role in corresponding knock-in mice.
description: We engineered different Activin A muteins to explore the role of the ACVR1•Activin A•type II receptor NSC.
DOI: 10.5061/dryad.7sqv9s4q7
title: Data from: Species loss drives ecosystem function in experiments, but in nature the importance of species loss depends on dominance

description: Aim: Decades of experimental research have conclusively shown a positive
 relationship between species richness and ecosystem function. However,
 authoritative reviews find no consensus on how species loss affects
 function in natural communities. We analyse experimental and observational
 data in an identical way and test whether they produce similar results.
 Location: North America and Europe (experimental communities); global
 (natural communities). Time period: Experimental communities: 1998–2013;
 natural communities: 1982–2018. Major taxa studied:  Experimental
 communities: temperate grassland plants; natural communities: temperate
 grassland plants, tropical forest trees, kelp forest producers and native
 bees. Methods: We used an approach inspired by the Price equation to
 analyse 129 datasets from experimental and natural communities worldwide.
 We tested how the effects of species loss on ecosystem function varied
 with dominance and the nonrandomness of species loss and, in turn, how
 these two factors differed between experiments and observations. Results:
 Studies carried out in experimental and natural communities reached
 different conclusions regarding the effects of species loss. First,
 species loss had greater effects on ecosystem function in experiments than
 in nature. Second, the importance of species loss was negatively
 correlated with dominance in nature because as dominance increased, lost
 species were increasingly those contributing little to ecosystem function.
 Although experimental and natural communities exhibited similar levels of
 dominance, an analogous relationship was not possible in experiments
 because the order of species loss was randomized by design. Main
 conclusions: Species loss was sometimes, but not always, the major driver
 of loss of function in nature. Variation in the importance of species loss
 was not messy and context dependent; instead, it was predicted by
 functional dominance. Although results from experimental and natural
 communities were similar in several key ways, they differed in that
 species loss was a consistent predictor of ecosystem function in
 experiments and not in nature.
description: Data was collected from sources described in the original paper
 and processed into species (rows) by sites (columns) matrices where each
 matrix cell is the species' contribution to function at that site.
 Data is in an RDS format as a list with three entires. The first entry has
 one matrix for each of the 129 datasets. The second and third entry
 describe, for each matrix, the specific ecosystem function and whether it
 was natural vs. experiment, respectively.
DOI: 10.5061/dryad.6hdr7sqxr
title: Parasite infestation influences life-history but not boldness behavior in placental live-bearing fish

description: Parasites can negatively affect the reproductive success of hosts.
 Placental species may be particularly susceptible, because
 parasite-induced stress during pregnancy could potentially influence
 embryo development. Here we examine the consequences of a trematode
 infestation (black spot disease, BSD) for fetal development and adult
 behavior in 19 natural populations of the placental live-bearing fish
 species Poeciliopsis retropinna (Poeciliidae) in Costa Rica. First, we
 observed substantial variation in parasite infestation among populations
 which correlated with a number of local environmental conditions
 (elevation, river width, depth, and flow velocity). Furthermore, we
 observed substantial variation in parasite infestation among females
 within populations associated with maternal age and size. We found that
 the infestation rate significantly influenced embryonic development, with
 more heavily parasitized females producing smaller and worse-conditioned
 offspring at birth, possibly because a costly immune response during
 pregnancy limits, either directly or indirectly, nourishment to developing
 embryos. Finally, a behavioral experiment in the field showed that the
 infestation rate did not affect an individual’s boldness. Our study
 indicates that in placental live-bearing fish parasite infestation leads
 to reduced embryo provisioning during pregnancy, resulting in a smaller
 offspring size and quality at birth potentially with negative implications
 for offspring fitness.
DOI: 10.5061/dryad.0vt4b8gwh
title: Historical analysis of seagrass loss in the United Kingdom

description: This dataset includes empirical and qualitative data from a
 multitude of sources using systematic review methods to provide
 analysis on seagrass occurrence and loss in the United Kingdom. We
 document 8,493 ha of recently mapped seagrass in the UK since
 1998. 
description: The
 purpose of the search was to extract qualitative and quantitative data on
 historic seagrass presence and trends of declines as far back as possible.
 To achieve this, we designed a search term that would capture all the
 literature on seagrass in the United Kingdom, including NOT terms to avoid
 irrelevant hits from places sharing part of their name with UK locations: 
 (Seagrass OR zostera
 OR “zostera marina” OR “z. marina” OR “z. noltii” OR “zostera noltii”) AND
 (uk OR “united kingdom” OR “great britain” OR england OR wales OR scotland
 OR “northern Ireland” OR ireland OR “scilly isles” OR “isles of scilly”
 “isle of wight” OR guernsey OR jersey OR “isle of man”) NOT (“New England”
 OR “New Jersey” OR “New South Wales”) The search term was entered into Web of Science, producing 160 papers. These were sifted by abstract based on the following criteria: 1) the paper refers to an area within the UK and; a) seagrass is the primary focus or; b) seagrass is the secondary focus but the primary focus suggests significant contribution of seagrass to the paper e.g. feeding habitats for wintering wildfowl; coastal WFD assessments; ecosystem services of coastal habitats. If there was any doubt that UK seagrass formed a significant contribution to any of the papers, it was also included for review Based on these criteria 59 papers were considered relevant for this work. The database of papers was synthesised for qualitative and quantitative data on seagrass presence, loss, and trends of changing distribution. Because these data were being used to supplement quantitative data on areal extent only, data on density and condition of seagrass meadows was not captured.
DOI: 10.5061/dryad.ghx3ffbkk
title: Artificial light at night amplifies seasonal relapse of haemosporidian parasites in a widespread songbird

description: Urban habitats can shape interactions between hosts and parasites by
 altering within-host processes such as resistance. Artificial light at
 night is common in urban environments, and chronic exposure can impair
 host immunity in ways that may increase infection. However, studies of
 causal links between this stressor, immunity, and infection dynamics are
 rare, particularly in migratory animals. Here, we experimentally tested
 how artificial light at night affects cellular immunity and intensity of
 infection with haemosporidian parasites across the annual cycle of migrant
 and resident subspecies of the dark-eyed junco (Junco hyemalis). We
 exposed an experimental group to light at night and compared them to
 control birds under nighttime darkness. Both groups were monitored as they
 passed through short days simulating early spring to longer days
 simulating the breeding season, followed by fall migration. Using
 generalized additive models, we show that artificial light at night
 increased inflammation, and leukocyte counts were greatest in early spring
 and fall. At the beginning of the experiment, few birds had active
 infections based on microscopy, but nested PCR revealed that many birds
 had chronic infections. Artificial light at night increased parasitemia
 across the annual cycle, with pronounced peaks in spring and fall that
 were largely absent in control birds. Because all birds were kept in
 indoor aviaries to prevent vector exposure, these pulses in parasite
 intensity indicate relapse of chronic infection during costly life history
 stages (i.e., reproduction, migration). Although the immunological and
 parasitological time series were in phase for control birds,
 cross-correlation analyses revealed that artificial light at night
 desynchronized leukocyte profiles and haemosporidian intensity, which
 could suggest immune dysregulation. Our study shows how a common
 anthropogenic influence can shape within-host processes to affect
 infection dynamics.
DOI: 10.7280/d1zt21
title: Fibrin fiber fluctuation

description: Understanding force propagation through the fibrous extracellular matrix
 can elucidate how cells interact mechanically with their surrounding
 tissue. Presumably, due to elastic nonlinearities of the constituent
 filaments and their random connection topology, force propagation in fiber
 networks is quite complex, and the basic problem of force propagation in
 structurally heterogeneous networks remains unsolved. We report on a new
 technique to detect displacements through such networks in response to a
 localized force, using a fibrin hydrogel as an example. By studying the
 displacements of fibers surrounding a two-micron bead that is driven
 sinusoidally by optical tweezers, we develop maps of displacements in the
 network. Fiber movement is measured by fluorescence intensity fluctuations
 recorded by a laser scanning confocal microscope. We find that the Fourier
 magnitude of these intensity fluctuations at the drive frequency
 identifies fibers that are mechanically coupled to the driven bead. By
 examining the phase relation between the drive and the displacements, we
 show that the fiber displacements are, indeed, due to elastic couplings
 within the network. Both the Fourier magnitude and phase depend on the
 direction of the drive force, such that displacements typically propagate
 farther, but not exclusively, along the drive direction. This technique
 may be used to characterize the local mechanical response in 3-D tissue
 cultures, and to address fundamental questions about force propagation
 within fiber networks. 
description: Images were taken using Olympus Fluoview 1200 system with 60x oil
 1.45 NA objective. Files in OIF.zip are not
 processed. Images in MATLAB.zip were generated using
 ImageJ 'substack' command. Updated MATLAB code can be found at
 this Github repository.  
description: Readme can be found in MATLAB.zip for instructions on how to use
 the matlab code. For additional details regarding the
 OIF image files, please contact Elliot Botvinick.
DOI: 10.5061/dryad.gf1vhhmm2
title: Impacts of selective logging on the oxidative status of tropical understory birds

description: 1. Selective logging is the dominant form of human disturbance in tropical
 forests, driving changes in the abundance of vertebrate and invertebrate
 populations relative to undisturbed old-growth forests. 2. A key
 unresolved question is understanding which physiological mechanisms
 underlie different responses of species and functional groups to selective
 logging. Regulation of oxidative status is thought to be one major
 physiological mechanism underlying the capability of species to cope with
 environmental changes. 3. Using a correlational cross-sectional approach,
 we compared a number of oxidative status markers among 15 understory bird
 species in unlogged and selectively logged forest in Borneo in relation to
 their feeding guild. We then tested how variation of markers between
 forest types was associated with that in population abundance. 4. Birds
 living in logged forests had a higher activity of the antioxidant enzyme
 superoxide dismutase and a different regulation of the glutathione cycle
 compared to conspecific birds in unlogged forest. However, neither
 oxidative damage nor oxidized glutathione differed between forest types.
 We also found that omnivores and insectivores differed significantly in
 all markers related to the key cellular antioxidant glutathione
 irrespective of forest type. Species with higher levels of certain
 antioxidant markers in a given type of forest were less abundant in that
 forest type compared to the other. 5. Our results suggest that there was
 no long-term effect of logging (last logging rotation occurred ~15 years
 prior to the study) on the oxidative status of understory bird species.
 However, it is unclear if this was owing to plasticity or evolutionary
 change. Our correlative results also point to a potential negative
 association between some antioxidants and population abundance
 irrespective of forest type.
DOI: 10.5061/dryad.q2bvq83gj
title: Data from: Modeling the effect of environmental temperatures, microhabitat, and behavioral thermoregulation on predicted activity patterns in a desert lizard across its thermally diverse distribution

description: Aim Temperature plays an important role in determining distributions of
 ectothermic species, yet many ectotherms have wide distributions across
 diverse environmental conditions. Our goal was to model regional
 differences in annual and seasonal activity patterns among populations of
 Phrynosoma platyrhinos across its climatically diverse distribution. We
 hypothesize that microhabitat availability and behavioral thermoregulation
 will not mitigate large-scale climatic differences across the species’
 distribution, resulting in alteration of activity patterns of populations.
 Location Western deserts of North America. Taxon Desert Horned Lizard
 (Phrynosoma platyrhinos) Methods We used biophysical models to 1) model
 microhabitat conditions at 31 localities across the species’ range, 2)
 model body temperature profiles of a theoretical lizard using microhabitat
 conditions, physiological and thermal parameters, and the ability of
 lizards to thermoregulate behaviorally, and 3) predict year-round activity
 patterns of P. platyrhinos across its range, quantified as the percentage
 of time permissible for basking or foraging. Results The models identified
 that different populations of P. platyrhinos experience differences in
 predicted activity patterns, both daily and seasonally, with up to 67%
 more time suitable for foraging in the southern than northern deserts.
  Southern populations have more potential for year-round
 activity, but predicted activity is reduced during hot summer months. The
 northern populations have less time for activity overall because of low
 temperatures in the spring and fall. However, summer predicted activity is
 greater than in the southern regions. Main conclusions We detected
 pronounced regional differences in the times available to P. platyrhinos
 for activity. We conclude that behavior and microclimate conditions are
 not able to fully mitigate the effects of large-scale thermal variation,
 and that lizards compensate for climatic variation by shifting their daily
 and seasonal predicted activity patterns. These differences can be tied to
 inter-population variation in life history traits.
description: Model output are for all sites
description: Description of column headers from model output used in the
 analyses.
DOI: 10.5061/dryad.0k6djh9x9
title: Data from: Repeated evidence that the accelerated evolution of sperm is associated with their fertilization function

description: Spermatozoa are the most morphologically diverse cell type, leading to
 the widespread assumption that they evolve
 rapidly. However, there is no direct evidence that sperm evolve
 faster than other male traits. Such a test requires comparing male traits
 that operate in the same selective environment, ideally produced from the
 same tissue, yet vary in function. Here we examine rates of
 phenotypic evolution in sperm morphology using two insect groups
 where males produce fertile and non-fertile sperm types
 (Drosophila species from the obscura group and
 Lepidoptera), where these constraints are solved. Moreover,
 in Drosophila we test the relationship between rates of
 sperm evolution and the link with the putative selective
 pressures of fertilization function and postcopulatory sexual selection
 exerted by female reproductive organs.We find repeated evolutionary
 patterns across these insect groups – lengths of fertile sperm evolve
 faster than non-fertile sperm. In Drosophila,
 fertile sperm length evolved faster than body size, but at the same rate
 as female reproductive organ length. We also compare rates of evolution of
 different sperm components, showing that head length evolves faster in
 fertile sperm while flagellum length evolves faster in non-fertile sperm.
 Our study provides direct evidence that sperm length evolves more rapidly
 in fertile sperm, likely because of their functional role in securing male
 fertility and in response to selection imposed by female reproductive
 organs.
description: Data was collected from literature sources and used in
 phylogenetic analyses. 
description: Phylogenies are provided in nexus file format (.nex). Datasets
 include a legend describing what each column name refers to.
DOI: 10.5061/dryad.5hqbzkh3g
title: On the evolutionary epidemiology of SARS-CoV-2

description: There is no doubt that the novel coronavirus SARS-CoV-2 that causes
 COVID-19 is mutating and thus has the potential to adapt during the
 current pandemic. Whether this evolution will lead to changes in the
 transmission, the duration, or the severity of the disease is not clear.
 This has led to considerable scientific and media debate, from raising
 alarms about evolutionary change to dismissing it. Here we review what
 little is currently known about the evolution of SARS-CoV-2 and extend
 existing evolutionary theory to consider how this disease might evolve
 during the COVID-19 pandemic. While there is currently no definitive
 evidence that SARS-CoV-2 is undergoing further adaptation, continued,
 evidence-based, analysis of evolutionary change is important so that
 public health measures can be adjusted in response to substantive changes
 in the infectivity or severity of COVID-19.
description: The dataset is a supplementary <em>Mathematica</em>
 package that derives the analytical results and simulates the dynamics, as
 illustrated in Figures 3-4. Additional supplementary figures explore the
 robustness of the results to alternative parameter choices.
description: The source notebook was written in
 <em>Mathematica</em> 8 (Wolfram Research Inc.) and is provided
 in .nb (<em>Mathematica</em>) and PDF formats.