cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tmpg4f52h
title: The opportunity for selection: an important but slippery concept in ecology and evolution.

description: 1. The concept of the opportunity for selection (I), measured as the
 variance in relative fitness, is over 60 years old, yet remains poorly
 understood by, or even unknown to, many ecologists and evolutionary
 biologists. This essay aims to clarify key conceptual and practical issues
 concerning use and estimation of I, which represents a theoretical upper
 limit on the rate of evolutionary adaptation. 2. The component of I caused
 by linear selection on a single trait is equal to the square of its
 standardised selection differential i. Even if no phenotypic selection
 occurs (i=0), however, realised I will typically be nonzero, owing to
 environmental or stochastic variation in fitness. 3. The opportunity for
 viability selection depends only on the mean survival rate, but selective
 mortality will typically account for only a small fraction of total
 mortality. 4. Fecundity selection is accompanied by expected
 overdispersion in reproductive success (variance &gt; mean), but
 overdispersion can also occur for reasons unrelated to phenotype, or by
 chance. The estimated opportunity for fecundity selection can also vary
 independently of i if estimated mean reproductive success is affected by
 study design, e.g. offspring are counted at different life stages or a
 variable fraction are missed. 5. For these reasons, I alone should not be
 used to make inferences about selection in progress and its drivers.
 Nevertheless, some empirical studies have documented weak to moderate
 correlations between I and phenotypic selection, so variation in I or
 related metrics across ecological contexts might provide clues that
 unmeasured traits are under variable selection. 20-Oct-2022 --
description: Data collected and collated by staff at the Netherlands Institute
 of Ecology over many years at the National Park de Hoge Veluwe.
DOI: 10.5061/dryad.63xsj3v5s
title: Data from: Endogenous tagging of multiple cellular components in the sea anemone Nematostella vectensis

description: Data from: Endogenous tagging of multiple cellular components in the sea
 anemone Nematostella vectensis The cnidarian Nematostella vectensis is a
 powerful model system to study the mechanisms underlying animal
 development. However, endogenous protein tagging is still challenging.
 Here we provide information to knock-in fluorescent protein reporters (at
 lamin, actin, mhc, cdh1, sec61b, rab11a and col4 loci) in the Nematostella
 genome using CRISPR/Cas9.
DOI: 10.5061/dryad.4tmpg4fds
title: Simulated data for: Long-term persistence of exaggerated ornaments under Fisherian runaway despite costly mate search

description: This repository contains simulated datasets relating to: Anna Waffender,
 Jonathan M. Henshaw "Long-term persistence of exaggerated ornaments
 under Fisherian runaway despite costly mate search"
   We simulate the evolution of male ornaments and female
 preferences under Fisherian runaway. We include costly mate search effort,
 reducing female fecundity.  Datasets are organized into CSV files
 named after the corresponding figure in the publication. For further
 information see the publication and the file README.md in this repository.
description: The code for the model was
 written in Julia, Version 1.6.2 (2021-07-14), and performed
 in Atom.
DOI: 10.15468/dl.5zq7hk
title: Occurrence Download

description: A dataset containing 464 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gabonius ngouniensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 464 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003338-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.905qfttpt
title: GCMS data files for: Detection of dairy products from multiple taxa in Late Neolithic pottery from Poland: an integrated biomolecular approach

description: The detection of dairy processing is pivotal to our understanding of
 ancient subsistence strategies. This culinary process is linked to key
 arguments surrounding the evolution of lactase persistence in prehistory.
 Despite extensive evidence indicating the presence of dairy products in
 ceramics in the European Neolithic, questions remain about the nature and
 extent of milk (and lactose) processing and consumption. In order to
 investigate past patterns of dairy processing, here we analyse ancient
 proteins identified from Late Neolithic Funnel Beaker ceramics,
 scrutinising the principle that curd and whey proteins partition during
 the production of dairy foods from milk. Our results indicate the presence
 of casein-rich dairy products in these vessels suggesting the creation of
 curd-enriched products from raw milk. Moreover, this analysis reveals the
 use of multiple species for their dairy products in the Late Neolithic
 Funnel Beaker culture, adding to a growing body of evidence that multiple
 taxa were exploited for dairying in the Neolithic. Alongside
 palaeoproteomic analysis we also apply lipid residue analysis, with
 discrepancies in these two approaches suggesting that effects from isotope
 mixing may be underestimating the frequency of milk use in prehistoric
 pottery, highlighting the utility of a multi-stranded approach.
description: This data set is comprised of data files produced by Gas
 Chromatography-Mass Spectrometry (GC-MS) of lipids extracted using acid
 extraction method from pottery sherds from the Late Neolithic
 site Sławęcinek, Poland These data are linked to the
 published journal where methods of extraction, the context of pottery and
 the interpretation of data are fully described.  Each
 file corresponds to the sample name as recorded in the paper and contains
 a usable cdf. file alongside the acquisition method in TEXT
 format.
description: .cdf files can be converted to .d files to be read using
 masshunter or chemstation software.
DOI: 10.5061/dryad.kd51c5b9b
title: Summary statistics from a genome-wide association study of narcolepsy

description: Type 1 narcolepsy (T1N) is a neurological condition, in which the death of
 hypocretin-producing neurons in the lateral hypothalamus leads to
 excessive daytime sleepiness and symptoms of abnormal Rapid Eye Movement
 (REM) sleep. Known triggers for narcolepsy are influenza-A infection and
 associated immunization during the 2009 H1N1 influenza pandemic. Here, we
 genotyped all remaining consented narcolepsy cases worldwide and assembled
 this with the existing genotyped individuals. We used this multi-ethnic
 sample in genome wide association study (GWAS) to dissect disease
 mechanisms and interactions with environmental triggers (5,339 cases and
 20,518 controls). Overall, we found significant associations with HLA (2
 GWA significant subloci) and 11 other loci. Six of these other loci have
 been previously reported
 (TRA, TRB, CTSH, IFNAR1, ZNF365 and P2RY11) and five are new (PRF1, CD207, SIRPG, IL27 and ZFAND2A). Strikingly, in vaccination-related cases, GWA significant effects were found in HLA, TRA, and in a novel variant near SIRPB1. Furthermore, IFNAR1-associated polymorphisms regulated dendritic cell response to influenza-A infection in vitro (p-value =1.92*10-25). A partitioned heritability analysis indicated specific enrichment of functional elements active in cytotoxic and helper T cells. Furthermore, functional analysis showed the genetic variants in TRA and TRB loci act as remarkably strong chain usage QTLs for TRAJ*24 (p-value = 0.0017), TRAJ*28 (p-value = 1.36*10-10) and TRBV*4-2 (p-value = 3.71*10-117). This was further validated in TCR sequencing of 60 narcolepsy cases and 60 DQB1*06:02 positive controls, where chain usage effects were further accentuated. Together these findings show that the autoimmune component in narcolepsy is defined by antigen presentation, mediated through specific T cell receptor chains, and modulated by influenza-A as a critical trigger.
DOI: 10.5061/dryad.pg4f4qrtg
title: Masai giraffe population change over 40 years in Arusha National Park

description: A population of Masai giraffes (Giraffa camelopardalis tippelskirchi)
 occurs in Arusha National Park (ANP), which is not part of the regular
 Tanzanian national wildlife monitoring scheme. Urban development of Arusha
 city and agricultural expansion have contributed to the increasing
 isolation of ANP from other protected areas in northern Tanzania. The only
 published data on the Masai giraffe population of ANP were
 individual-based data collected in 1979 and 1980. Here, we used
 individual-based data from 2021 to 2022 to provide an update on the
 current population size, population sex and age structure, movements, and
 genetic connectivity of giraffes in ANP. We documented a 49% population
 decline and changes in the age distribution, adult sex ratio, reproductive
 rate, and movement patterns relative to the previous study. Mitochondrial
 DNA analysis revealed genetic connectivity between ANP and other
 populations east of the Gregory Rift Escarpments in northern Tanzania and
 south-eastern Kenya, evidence that the Masai giraffe once moved widely
 across the landscape.
description: # Masai giraffe population change over 40 years in Arusha National Park
 --- ## Description of the Data and file structure This file contains
 mitochondrial DNA data, short fragments of DNA sequences obtained from the
 cytochrome B gene (cytb) within the mitochondrial DNA of the Masai
 Giraffe. We only sequenced a fragment which is 1140 bp. For each Sequence
 in the FASTA format, we included the name of the sequence and the location
 where that data was collected. For Example, TNP208|Tarangire means sample
 208 from Tarangire National Park (TNP). All other abbreviations have been
 described in the open-access article (Lee et al., 2023). In this data set,
 we have included all unique haplotypes used in the analysis.  ##
 Sharing/Access Information Links to other publicly accessible locations of
 the data: We compared our data with already published data (Brown et al.,
 2007 GenBank Accession number EU088329.1-EU088342.1) and OP442601–OP442932
 Lohay et al., 2023.
DOI: 10.5061/dryad.9cnp5hqnp
title: Dataset associated with: The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo

description: mRNA localization and transport are integral in regulating
 gene expression. In Caenorhabditis elegans' embryos, the
 maternally inherited mRNA erm-1 (Ezrin/Radixin/Moesin) becomes
 concentrated in anterior blastomeres. erm-1 mRNA localizes within those
 blastomeres to the plasma membrane where the essential ERM-1 protein, a
 membrane-actin linker, is also found. We demonstrate that the localization
 of erm-1 mRNA to the plasma membrane is translation dependent and requires
 its encoded N-terminal, membrane-binding (FERM) domain. By perturbing
 translation through multiple methods, we found that erm-1 mRNA
 localization at the plasma membrane persisted only if the nascent peptide
 remained in complex with the translating mRNA. Indeed, re-coding the erm-1
 mRNA coding sequence while preserving the encoded amino acid sequence did
 not disrupt erm-1 mRNA localization, corroborating that the information
 directing mRNA localization resides within its membrane-binding protein
 domain. A single-molecule inexpensive fluorescence in situ hybridization
 screen of 17 genes encoding similar membrane-binding domains identified
 three plasma membrane-localized mRNAs in the early embryo. Ten additional
 transcripts showed potential membrane localization later in development.
 These findings point to a translation-dependent pathway for localization
 of mRNAs encoding membrane-associated proteins.
description: All images were acquired
 on a Photometrics Cool Snap HQ2 camera using a DeltaVision Elite inverted
 microscope (GE Healthcare), with an Olympus PLAN APO 60X (1.42 NA,
 PLAPON60XOSC2) objective, an Insight SSI 7-Color Solid State Light Engine,
 and SoftWorx software (Applied Precision) using 0.2 um z-stacks.
description: This dataset contains all primary microscopy data presented or
 analyzed in the publication "The ERM-1 membrane-binding domain
 directs erm-1 mRNA localization to the plasma membrane in the
 <em>C</em>. <em>elegans</em>
 embryo".
DOI: 10.5061/dryad.sf7m0cg9j
title: Data for: Decoupling of sexual signals and their underlying morphology facilitates rapid phenotypic diversification

description: How novel phenotypes evolve is challenging to imagine because traits are
 often underlain by numerous integrated phenotypic components, and changes
 to any one form can disrupt the function of the entire module. Yet novel
 phenotypes do emerge, and research on adaptive phenotypic evolution
 suggests that complex traits can diverge while either maintaining existing
 form-function relationships or through innovations that alter
 form-function relationships. How these alternate routes contribute to
 sexual signal evolution is poorly understood, despite the role of sexual
 signals in generating biodiversity. In Hawaiian populations of the Pacific
 field cricket, male song attracts both female crickets and a deadly
 acoustically orienting parasitoid fly. In response to this conflict
 between natural and sexual selection, male crickets have evolved altered
 wing morphologies multiple times, resulting in loss and dramatic
 alteration of sexual signals. More recently, we and others have observed a
 radical increase in sexual signal variation and the underlying
 morphological structures that produce song. We conducted the first
 combined analysis of form (wing morphology), function (emergent signal),
 and receiver responses to characterize novel variation, test alternative
 hypotheses about form-function relationships (Form-Function Continuity vs.
 Form-Function Decoupling) and investigate underlying mechanistic changes
 and fitness consequences of novel signals. We identified three
 sound-producing male morphs (one previously undescribed, named “rattling”)
 and found that relationships between morphology and signals have been
 rewired (Form-Function Decoupling), rapidly and repeatedly, through the
 gain, loss, and alteration of morphological structures, facilitating the
 production of signals that exist in novel phenotypic space. By integrating
 across a hierarchy of phenotypes, we uncovered divergent morphs with
 unique solutions to the challenge of attracting mates while evading fatal
 parasitism.
DOI: 10.5061/dryad.8pk0p2nrf
title: Hidden species diversity in an iconic living fossil vertebrate

description: Ancient, species-poor lineages persistently occur across the Tree of Life.
 These unique lineages are likely to contain unrecognized species diversity
 masked by the low rates of morphological evolution that characterize
 living fossils. Halecomorphi is a lineage of ray-finned fishes that
 diverged from its closest relatives over 200 million years ago and is
 represented by only one living species in eastern North America, the
 Bowfin Amia calva Linnaeus. We use double digest restriction-site
 associated DNA (ddRAD) sequencing and morphology to illuminate recent
 speciation in bowfins. Our results support the delimitation of a second
 living species of Amia with the timing of diversification dating to the
 Plio-Pleistocene. This delimitation expands the species diversity of an
 ancient lineage that is integral to studies of vertebrate genomics and
 development, yet is facing growing conservation threats driven by the
 caviar fishery.
DOI: 10.7280/d13h59
title: Data for: Economic and biophysical limits to seaweed farming for climate change mitigation

description: Net-zero greenhouse gas emissions targets are driving interest in
 opportunities for biomass-based negative emissions and bioenergy,
 including from marine sources such as seaweed. Yet the biophysical and
 economic limits to farming seaweed at scales relevant to the global carbon
 budget have not been assessed in detail. We use coupled seaweed growth and
 technoeconomic models to estimate the costs of global seaweed production
 and related climate benefits, systematically testing the relative
 importance of model parameters. Under our most optimistic assumptions,
 sinking farmed seaweed to the deep sea to sequester a gigaton of CO2 per
 year costs as little as $480/tCO2 on average, while using farmed seaweed
 for products that avoid a gigaton of CO2-equivalent greenhouse gas (GHG)
 emissions annually could return a profit of $50/tCO2-eq. However, these
 costs depend on low farming costs, high seaweed yields, and assumptions
 that almost all carbon in seaweed is removed from the atmosphere (i.e.,
 competition between phytoplankton and seaweed is negligible) and that
 seaweed products can displace products with substantial embodied non-CO2
 GHG emissions. Moreover, the gigaton-scale climate benefits we model would
 require farming very large areas (&gt;90,000 km2)—a &gt;30-fold
 increase in the area currently farmed. Our results therefore suggest that
 seaweed-based climate benefits may be feasible, but targeted research and
 demonstrations are needed to further reduce economic and biophysical
 uncertainties.
DOI: 10.5061/dryad.1vhhmgqx0
title: Ocean acidification and predation risk, in isolation and in combination, show strong effects on marine mussels

description: Carbon dioxide-induced ocean acidification are producing a range of new
 selection pressures on marine calcifying organisms that show phenotypic
 plasticity in their shell morphology in response to predators. Although
 there are numerous studies on the effects of ocean acidification and
 predation risk on marine bivalves in isolation, the understanding
 concerning their combined effects is still lacking. To bridge this gap, we
 conducted a long-term mesocosm experiment using mussel populations with
 different history of predator exposure: crab-experienced and crab-naïve.
 Mussels were exposed to either lower pH or crab cue and the combination of
 both these treatments for four months. We demonstrate that both
 crab-experienced and crab-naïve mussels have heavier, thicker, rounder
 and, thus, stronger shells in response to crab cues, whereas low pH
 significantly decreased shell mass, thickness and strength. Mussels with
 previous experience to crabs showed greater plasticity in response to crab
 cues than crab-naïve mussels. However, this differential response was
 eliminated by ocean acidification. Exposure to low pH and crab cue
 resulted in antagonistic interactions for all traits, except for shell
 length where the combined effect was additive. However, there was no
 difference among populations in the interaction type for any of the
 traits. Our study may provide implications for the management of mussel
 populations under climate change.
DOI: 10.5061/dryad.xwdbrv1h8
title: Data for: Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.)

description: When species hybridize, one F1 hybrid cross type often predominates. Such
 asymmetry can arise from differences in a variety of reproductive
 barriers, but the relative roles and concordance of pre-mating,
 post-mating prezygotic barriers, and post-zygotic barriers in producing
 these biases in natural animal populations have not been widely
 investigated. Here, we study a population of predominantly F1 hybrids
 between two killifish species (Fundulus heteroclitus and Fundulus
 diaphanus) in which &gt;95% of F1 hybrids have F. diaphanus mothers
 and F. heteroclitus fathers (D♀×H♂). To determine why F. heteroclitus x F.
 diaphanus F1 hybrids (H♀×D♂) are so rare, we tested for asymmetry in
 pre-mating reproductive barriers (female preference, male aggression) at a
 common salinity (10 ppt) and post-mating, pre-zygotic (fertilization
 success) and post-zygotic (embryonic development time and hatching
 success) reproductive barriers at a range of ecologically relevant
 salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females
 preferred conspecific males, while F. diaphanus females did not, matching
 the observed cross bias in the wild. Naturally rare H♀×D♂ crosses also had
 lower fertilization success than all other cross types, and a lower
 hatching success than the prevalent D♀×H♂ crosses at the salinity found in
 the hybrid zone centre (10 ppt). Furthermore, the naturally predominant
 D♀×H♂ crosses had a higher hatching success than F. diaphanus crosses at
 10ppt, which may affect their relative abundance. The present study
 suggests that a combination of incomplete mating, post-mating pre-zygotic
 and post-zygotic reproductive isolating mechanisms act in concert to
 produce hybrid asymmetry in this system.
description: All analyses conduced in R.
DOI: 10.5061/dryad.3r2280gks
title: Tradeoff between pre and postcopulatory traits depends on locomotor activity in male Tribolium castaneum beetles

description: Locomotor performance is an indicator of dynamic exercise; thus, it is a
 central trait in many animal behaviors. Although higher locomotor
 endurance may increase male reproductive success (e.g., in mate searching
 and male–male contests), investment in other male reproductive traits
 (e.g., male attractiveness and sperm competition) may be decreased through
 energy consumption due to higher activity levels. Here, I investigated
 male attractiveness, mating success, and paternity success using males of
 the red flour beetle Tribolium castaneum selected for higher (H) and lower
 (L) locomotor endurance. Although there was no difference in male
 attractiveness between the selection regimes, H males had significantly
 higher mating success than L males. Conversely, L males had significantly
 higher paternity success than H males. Therefore, there was a tradeoff
 between mating success and paternity success among the selection regimes,
 suggesting that locomotor endurance affects male reproduction in T.
 castaneum, and individual variation of locomotor endurance may be
 maintained within a population.
DOI: 10.5061/dryad.q2bvq83pc
title: No phylogenomic support for a Cenozoic origin of the “living fossil” Isoetes

description: Premise: The isoetalean lineage has a rich fossil record that extends to
 the Devonian, but the age of the living clade is unclear. Recent results
 indicate that it is young, from the Cenozoic, whereas earlier work based
 on less data from a denser taxon sample yielded Mesozoic median ages.
 Methods: We investigated node ages in Isoetes using two genomic datasets
 (plastome and nuclear ribosomal cistron) analyzed using three different
 clock models implemented in MrBayes (ILN, WN and TK02 models) and a
 conservative approach to calibration. Key results: While topological
 results are consistently resolved in Isoetes, estimated crown group ages
 range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on
 datatype and clock model. The oldest estimates were retrieved using the
 autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained
 under one specific condition (plastome data analyzed with the uncorrelated
 ILN clock model). That same plastome dataset also yielded the oldest
 (mid-Permian) age estimate when analyzed with the autocorrelated TK02
 clock model. Adding the highly divergent recently established sister
 species Isoetes wormaldii to the dataset approximately doubled the average
 median node depth to the Isoetes crown group. Conclusions: There is no
 consistent support for a Cenozoic origin of the living clade Isoetes. We
 obtained seemingly well-founded, yet strongly deviating results, depending
 on datatype and clock model. The single most important future improvement
 is probably to add calibration points, which requires an improved
 understanding of the isoetalean fossil record or alternative bases for
 calibration.