cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cm1h0p6
title: Data from: Polymorphism and multiple correlated characters: do asymmetry flatfish morphs also differ in swimming performance and metabolic rate?

description: 1. Phenotypic polymorphisms often differ in multiple correlated traits
 including morphology, behavior, and physiology, all of which can affect
 performance. How selection acts on these suites of traits can be complex
 and difficult to discern. Starry flounder (Platichthys stellatus) is a
 pleuronectid flatfish that exhibits rare polymorphism for the direction of
 eye migration and resulting whole-body asymmetry. P. stellatus asymmetry
 morphs differ subtly in several anatomical traits, foraging behavior, and
 stable isotope signatures, suggesting they may be ecologically segregated,
 yet performance and metabolic differences are unknown. 2. Here we tested
 the hypothesis that sinistral and dextral P. stellatus asymmetry morphs
 diverge in performance and routine metabolic rate (RMR) by comparing
 prolonged swimming endurance (time to exhaustion at a constant swimming
 speed), fast-start swimming velocity and acceleration, and rate of oxygen
 consumption. Based on subtle morphological differences in caudal tail
 size, we expected sinistral P. stellatus to have superior prolonged
 swimming endurance relative to dextral fish, but inferior fast-start
 performance. 4. Sinistral P. stellatus exhibited both significantly
 greater prolonged swimming performance and fast-start swimming
 performance. However, sinistral P. stellatus also exhibited greater RMR,
 suggesting that their general swimming performance could be enhanced by an
 elevated metabolic rate. 5. Divergence between P. stellatus asymmetry
 morphs in swimming performance and metabolic rates contributes to growing
 evidence of ecological segregation between them, as well as our
 understanding of possible ecological consequences of asymmetry direction
 in flatfishes. These data provide an example of the complexity of
 polymorphisms associated with multiple correlated traits in a rare case of
 asymmetry polymorphism in a marine flatfish species.
description: Fast-start swimming
 dataBergstrom_2019_starryflounder_faststart.xlsxOxygen consumption rate dataBergstrom_2019_starryflounder_metabolism.xlsxProlonged swimming endurance dataBergstrom_2019_starryflounder_prolongedswimming.xlsx
DOI: 10.5061/dryad.5g46558
title: Data from: Social experience shape behavioural individuality and within-individual stability

description: Individual repeatability characterises many behaviours. Repeatable
 behaviour may result from repeated social interactions among familiar
 group members, owing to adaptive social niche specialisation. In the
 context of aggression, in species like field crickets, social niche
 specialisation should also occur when individuals repeatedly interact with
 unfamiliar individuals. This would require the outcome of social
 interactions to have carry-over effects on fighting ability and
 aggressiveness in subsequent interactions, leading to long-term
 among-individual differentiation. To test this hypothesis, we randomly
 assigned freshly emerged adult males of the southern field cricket Gryllus
 bimaculatus to either a solitary or social treatment. In the social
 treatment, males interacted with a same-sex partner but experienced a new
 partner every three days. After three weeks of treatment, we repeatedly
 subjected treated males to dyadic interactions to measure aggression.
 During this time, we also continuously measured the three-daily rate of
 carbohydrate and protein consumption. Individual differentiation was
 considerably higher among males reared in the social versus solitary
 environment for aggressiveness but not for nutrient intake.
 Simultaneously, social experience led to lower within-individual stability
 (i.e. increased within-individual variance) in carbohydrate intake. Past
 social experiences, thus, shaped both behavioural individuality and
 stability. While previous research has emphasised behavioural
 individuality resulting from repeated interactions among familiar
 individuals, our study implies that behavioural individuality, in the
 context of aggression, may generally result from social interactions,
 whether with familiar or unfamiliar individuals. Our findings thus imply
 that social interactions may have a stronger effect on individual
 differentiation than previously appreciated.
description: datafile
DOI: 10.5061/dryad.f3v185t
title: Data from: Lake and catchment-scale determinants of aquatic vegetation across almost 1000 lakes and the contrasts between lake types

description: Aim: The factors controlling macrophyte (aquatic plant) composition are
 complex, recent research showing that the well-studied filtering effects
 of lake environmental factors are constrained by hydrological and
 landscape factors. We investigated the factors determining macrophyte
 composition in lakes over water body and catchment- scales and the
 transferability of this pattern across lake types. Location: Almost 1000
 lakes distributed across Britain. Taxon: Lake macrophytes. Methods: Lakes
 were partitioned into five types based on subdivision of alkalinity and
 elevation gradients. Data from botanical surveys were used to compare
 spatial turnover and nestedness components of beta diversity between lake
 types. The relative importance of lake environment (based on local
 physicochemical data), hydrology (e.g. lake and stream density), landscape
 (e.g. fragmentation indices, land cover) and spatial autocorrelation in
 explaining macrophyte composition were derived from variance partitioning.
 Results: Species composition showed strong spatial structuring, suggestive
 of overland dispersal, enhanced by spatially-correlated abiotic factors
 such as alkalinity and elevation. Catchment-scale factors (e.g. land use,
 connectivity) promoted the establishment of different communities (more or
 less diverse, or differing in composition) but were of secondary
 importance. Turnover in composition between upland lakes was lower than in
 other lake types, reflecting a more specialist flora and increased
 potential for propagule exchange due to spatial aggregation and
 hydrological connectivity. Main conclusions: Vegetation composition in
 lakes is more spatially-structured than previously appreciated, consistent
 with the importance of dispersal limitation, but this does not apply
 evenly to all lakes, being most acute in lowland high alkalinity lakes.
 Thus, spatially-structured abiotic factors, such as alkalinity, influence
 macrophyte composition most (suggestive of niche filtering) in those lakes
 where human impacts tend to be greatest, although nestedness was also
 lowest there. By contrast, hydrological connectivity has a proportionally
 stronger structuring role in upland lakes.
description: all961The lake- and
 catchment-scale environment data used in the study for the variance
 partitioning analyses can be accessed here
DOI: 10.5061/dryad.k3583p1
title: Data from: Predator-prey role reversal may impair the recovery of declining pike populations

description: Many fish populations have experienced declines in recent decades due to
 anthropogenic disturbances, such as overfishing and habitat exploitation.
 Despite management actions many populations show a limited capacity to
 recover. This may be attributed to reversal of predatory‐prey roles, yet
 empirical evidence to that effect remains scarce. Here we combine field
 and laboratory studies to investigate the interaction between pike (Esox
 lucius), a large keystone top predatory fish, and the small‐bodied
 mesopredatory threespine stickleback (Gasterosteus aculeatus) in the
 Baltic Sea where pike populations have declined. Our data suggest that
 stickleback predation on pike larvae depletes a large proportion of the
 recruitment and influences the size distribution through size‐selective
 predation, which is corroborated by a gape‐limitation experiment and diet
 analysis of wild captured sticklebacks. The effects of stickleback
 predation are present across several populations and years, and our data
 suggests that early arrival of sticklebacks has stronger effects on
 juvenile pike survival. Finally, we use data on pike gape‐limitation and
 the size distribution of sticklebacks to illustrate the process of role
 reversal. These findings suggest that mesopredator behaviour can reduce
 recruitment of a top predator species and impair the capacity of
 populations to recover. This emphasizes predator‐prey role reversal as an
 important ecological and evolutionary driver that influences the outcome
 of restoration and management actions.
description: Gape-limitationData on relationships between total length (mm)/body depth (mm) and total length (mm)/gape size (mm) for both juvenile pike and adult sticklebacks.Spatial variation in abundancesData on the number of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data were sampled in 2014 and represent four populations of anadromous pike.Spatial variation in size distributionData on the size distribution (total length mm) of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data sampled in 2014 and represent 4 populations.Temporal variation in abundancesData on the number of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data sampled in one popualtion (pop O) across 5 years (2007-2009, 2013-2014)Temporal variation in size distributionData on the size distribution (mm total length) of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data sampled in one popualtion (pop O) across 5 years (2007-2009, 2013-2014)
DOI: 10.5061/dryad.jg30j4v
title: Data from: Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils

description: It is a plausible hypothesis that parallel adaptation events to the same
 environmental challenge should result in genetic changes of similar or
 identical effects, depending on the underlying fitness landscapes.
 However, systematic testing of this is scarce. Here we examine this
 hypothesis in two closely related plant species, Arabidopsis halleri and
 Arabidopsis arenosa, which co-occur at two calamine metalliferous (M)
 sites harbouring toxic levels of the heavy metals zinc and cadmium. We
 conduct individual genome resequencing alongside soil elemental analysis
 for 64 plants from eight populations on M and non-metalliferous (NM)
 soils, and identify genomic footprints of selection and local adaptation.
 Selective sweep and environmental association analyses indicate a modest
 degree of gene as well as functional network convergence, whereby the
 proximal molecular factors mediating this convergence mostly differ
 between site pairs and species. Notably, we observe repeated selection on
 identical single nucleotide polymorphisms in several A. halleri genes at
 two independently colonized M sites. Our data suggest that
 species-specific metal handling and other biological features could
 explain a low degree of convergence between species. The parallel
 establishment of plant populations on calamine M soils involves convergent
 evolution, which will probably be more pervasive across sites purposely
 chosen for maximal similarity in soil composition.
description: Preite_etal_2019_data.tarThis tar zipped folder contains the input and output files used for the genome scans described in the publication plus the SnpEff annotation data used.
DOI: 10.5061/dryad.3161qp0
title: Data from: Genetic population structure and demography of an apex predator, the tiger shark Galeocerdo cuvier

description: Population genetics have been increasingly applied to study large sharks
 over the last decade. Whilst large shark species are often difficult to
 study with direct methods, improved knowledge is needed for both
 population management and conservation, especially for species vulnerable
 to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier,
 is an apex predator known to play important direct and indirect roles in
 tropical and sub-tropical marine ecosystems. While the global and
 Indo-West Pacific population genetic structure of this species has
 recently been investigated, questions remain over population structure and
 demographic history within the Western Indian (WIO) and within the Western
 Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional
 population structures, the genetic diversity of 286 individuals sampled in
 seven localities was investigated using 27 microsatellite loci and three
 mitochondrial genes (CR, COI, cytb). A weak genetic differentiation was
 observed between the WIO and the WPO, suggesting high genetic
 connectivity. This result agrees with previous studies, and highlights the
 importance of the pelagic behaviour of this species to ensure gene flow.
 Using Approximate Bayesian Computation to couple information from both
 nuclear and mitochondrial markers, evidence of a recent bottleneck in the
 Holocene (2,000-3,000 years ago) was found, which is the most probable
 cause for the low genetic diversity observed. A contemporary effective
 population size as low as 111 [43,369] was estimated during the
 bottleneck. Together, these results indicate low genetic diversity that
 may reflect a vulnerable population sensitive to regional pressures.
 Conservation measures are thus needed to protect a species that is
 classified as Near Threatened.
description: Samples information and
 microsatellite genotypes_Galeocerdo cuvierTab delimited text. On
 each line is indicated: the individual ID (ID); the oceanic basin where it
 was sampled (Oceanic basin); the sampling locality (Locality); the
 sampling locality code (Locality code); the date of sampling (Date of
 sampling); the sex of the individual (Sex); the total length of the
 individual in cm (TL (cm)); the mitochondrial haplotypes of the control
 region, the COI gene and the cytb gene (Haplotype CR, Haplotype COI,
 Haplotype cytb); the genotype of the individual at the 27 microsatellite
 loci used. Missing data are indicated by NA.microsatellite
 genotypes.txt
DOI: 10.5061/dryad.k7m5vf4
title: Data from: Digging the optimum pit: antlions, spirals and spontaneous stratification

description: Most animal traps are constructed from self-secreted silk, so antlions are
 rare among trap builders because they use only materials found in the
 environment. We show how antlions exploit the properties of the substrate
 to produce very effective structures in the minimum amount of time. Our
 modelling demonstrates how antlions (1) exploit self-stratification in
 granular media differentially to expose deleterious large grains at the
 bottom of the construction trench where they can be ejected preferentially
 and (2) minimize completion time by spiral rather than central digging.
 Both phenomena are confirmed by our experiments. Spiral digging saves time
 because it enables the antlion to eject material initially from the
 periphery of the pit where it is less likely to topple back into the
 centre. As a result, antlions can produce their pits — lined almost
 exclusively with small slippery grains to maximize powerful avalanches and
 hence prey capture — much more quickly than if they simply dig at the
 pit’s centre. Our demonstration, for the first time, of an animal
 utilizing self-stratification in granular media exemplifies the
 sophistication of extended phenotypes even if they are only formed from
 material found in the animal’s environment.
description: Model
 codeAntlionStratificationCode190206.py
DOI: 10.5061/dryad.5sv75bd
title: Data from: Biotic and abiotic drivers of species loss rate in isolated lakes

description: 1. Today, anthropogenic impacts are causing a serious crisis for global
 biodiversity, with rates of extinction increasing at an unprecedented
 rate. Extinctions typically occur after a certain delay and understanding
 the mechanisms causing delays is a key challenge for both fundamental and
 applied perspectives. 2. Here, we make use of natural experiments, the
 isolation of lakes by land up-lift in Northern Scandinavia, to examine how
 yearly extinction rates are affected by time since isolation and a range
 of abiotic and biotic factors. 3. In this aim, we adapted a model of
 delayed species loss within isolated communities to test the effects of
 time since isolation, area, pH, depth and presence/absence of piscivores
 on extinction rates. 4. As expected, we found that small and/or young
 lakes experience a higher annual rate of extinctions per species than
 larger and/or older ones. Compared to previous studies that were conducted
 for either young (few thousand years ago) or very old (&gt;10 000
 years ago) isolates, we demonstrated over a large and continuous temporal
 scales (50-5000 yr), similar relationship between extinction rates and
 age. We also show that extinction rates are modified by local
 environmental factors such as a strong negative effect of increasing pH.
 5. Our results urge for the need to consider the time since critical
 environmental changes occurred when studying extinction rates. In a wider
 perspective our study demonstrates the need to consider extinction debts
 when modeling future effects of climate change, land-use changes, or
 biological invasions on biodiversity.
description: Data of isolated
 lakesData of Isolated lakes
 including, lake ID, name of the lake, presence/absence of species
 including presence of piscivores (noted pisc in the table), species
 richness (excluding piscivores), altitude, depth, pH, distance to sea,
 area, and catchment.DataArticle.xlsx
DOI: 10.5061/dryad.47p0h64
title: Data from: The effects of male social environment on sperm phenotype and genome integrity

description: Sperm function and quality are primary determinants of male reproductive
 performance and hence fitness. The presence of rival males has been shown
 to affect ejaculate and sperm traits in a wide range of taxa. However,
 male physiological conditions may not only affect sperm phenotypic traits
 but also their genetic and epigenetic signatures, affecting the fitness of
 the resulting offspring. We investigated the effects of male-male
 competition on sperm quality using TUNEL assays and geometric
 morphometrics in the zebrafish, Danio rerio. We found that the sperm
 produced by males exposed to high male-male competition had smaller heads
 but larger midpiece and flagellum than sperm produced by males under low
 competition. Head and flagella also appeared less sensitive to the osmotic
 stress induced by activation with water. In addition, more sperm showed
 signals of DNA damage in ejaculates of males under high competition. These
 findings suggest that the presence of a rival male may have positive
 effects on phenotypic traits but negative effects on DNA integrity.
 Overall, males facing the presence of rival males may produce faster
 swimming and more competitive sperm but this may come at a cost for the
 next generation.
description: Raw data_sperm
 phenotypes and genotypesExcel file containing
 all data used for the analyses presented in the
 manuscript.2019-silva-jeb-si.xlsx
DOI: 10.5061/dryad.8m3t2p2
title: Data from: Black abalone (Haliotis cracherodii) population structure shifts through deep time: Management implications for southern California's northern Channel Islands

description: For over 10,000 years, black abalone (Haliotis cracherodii) were an
 important resource in southern California, first for coastal Native
 Americans, then beginning in the nineteenth century, as one of the
 state's first commercial shellfisheries. By 1993, after years of
 heavy fishing, rising sea surface temperatures (SST), and the spread of
 withering syndrome (WS), black abalone populations declined dramatically,
 resulting in the closure of the Alta California fishery. After nearly 25
 years of management and recovery efforts, black abalone are showing signs
 of ecological rebound along some Channel Island shorelines. These include
 the presence of juvenile abalone and increasing densities, largely from
 data collected by Channel Islands National Park (CINP) monitoring efforts
 that began in 1985. In an effort to apply deeper historical perspectives
 to modern fisheries management and restoration, we analyzed black abalone
 size data from San Miguel Island at prehistoric and historical
 archeological sites spanning the last 10,000 years and compared these
 populations to those described by CINP biologists between 1985 and 2013.
 We found a statistically significant relationship between SST and black
 abalone size distributions during the ancient record, along with dramatic
 shifts in population size structure toward larger individuals between the
 nineteenth century and modern periods. A pattern of larger mean black
 abalone sizes was identified during warm SSTs, when compared against
 intervals of cooler SSTs. Synthesis and applications. Our study provides a
 deep historical perspective of abalone population size distributions,
 patterns within these distributions through time, and parallels to modern
 abalone populations. Our results may help managers determine whether the
 current (and future) size and age structure of intertidal black abalone
 populations around the northern Channel Islands are “natural” and healthy,
 measured against the 10,000 year history of black abalone fishing in
 southern California.
description: Black abalone size data
 through time on the Channel IslandsFile contains size data
 of black abalone from island archaeological sites and modern survey
 dataHaas et
 al. 2018 Master Data.xls
DOI: 10.5061/dryad.1hg2n56
title: Data from: Does perspective matter? A case study comparing Eulerian and Lagrangian estimates of common murre (Uria aalge) distributions

description: Studies estimating species’ distributions require information about animal
 locations in space and time. Location data can be collected using surveys
 within a predetermined frame of reference (i.e., Eulerian sampling) or
 from animal-borne tracking devices (i.e., Lagrangian sampling).
 Integration of observations obtained from Eulerian and Lagrangian
 perspectives can provide insights into animal movement and habitat use.
 However, contemporaneous data from both perspectives are rarely available,
 making examination of biases of each sampling approach difficult to
 quantify. We compared distributions of a mobile seabird observed
 concurrently from ship, aerial, and satellite tag surveys during May,
 June, and July 2012 in the northern California Current. We calculated
 utilization distributions to quantify and compare variability in common
 murre (Uria aalge) space use and examine how sampling perspective and
 platform influence observed patterns. Spatial distributions of murres were
 similar in May, regardless of sampling perspective. Greatest density
 distributions occurred in coastal waters off southern Washington and
 northern Oregon, near large murre colonies and the mouth of the Columbia
 River. Density distributions of murres estimated from ship and aerial
 surveys in June and July were similar to those observed in May, whereas
 distributions of satellite-tagged murres in June and July indicated
 northward movement into British Columbia, Canada, resulting in different
 patterns observed from Eulerian and Lagrangian perspectives. These results
 suggest that the population of murres observed in the northern California
 Current during spring and summer includes relatively stationary
 individuals attending breeding colonies and non-stationary, vagile adults
 and subadults. Given the expected growth of telemetry studies and advances
 in survey technology (e.g., unmanned aerial systems), these results
 highlight the importance of considering methodological approaches, spatial
 extent, and synopticity of distribution data sets prior to integrating
 data from different sampling perspectives.
description: Phillips_etal_EcoEvol_SurveyDataFinalShip, aerial, and telemetry survey data