cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bvq83brh
title: Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

description: Gene flow shapes spatial genetic structure as well as the potential for
 local adaptation of populations. Among marine animals with non-migratory
 adults, the presence or absence of a pelagic larval stage is thought to be
 a key determinant in shaping gene flow and the genetic structure of
 populations. In addition, the spatial distribution of suitable habitats
 will influence the distribution of biological populations and their
 pattern of gene flow. We used whole genome sequencing to study demographic
 history and reduced representation (ddRAD) sequencing data to analyze
 spatial genetic structure in the broadnosed pipefish (Syngnathus typhle).
 Its main habitat are seagrass meadows, which along the study coast (SW
 Norway) have a patchy distribution. Combining the results from several
 analyses including scans for selection, suggests that stochastic genetic
 drift has shaped the observed population structure largely due to its
 patchy habitat distribution. The restricted gene flow is further driven by
 life history traits such as the presence of parental care combined with no
 pelagic life stages, resulting in a clear isolation-by-distance pattern
 spanning 100s of kilometers. The spatial scale of demographic connectivity
 was inferred from long-term (~30 year) census population counts that
 uncovered a sharp decline in spatial correlations in abundance with
 distance (37% decorrelation over 2 km). These findings were contrasted
 with data from two other fish species sampled along the same coastline,
 both having pelagic larval stages lasting ~20 days (corkwing wrasse,
 Symphodus melops, and black goby, Gobus niger) where the population
 structure is not that evident. For these species, we found a wider spatial
 scale of demographic connectivity (decorrelation distances of 14 and 28
 km, respectively), and weaker isolation-by-distance except at one point
 along the coast where both species revealed a strong barrier to gene flow,
 seemingly due to a lack of suitable habitat. Combined, these findings
 suggest that habitat fragmentation and absence of a pelagic larval stage
 in pipefish strongly increases geographic structuring, while the pelagic
 larvae of wrasse and goby increase genetic and demographic connectivity,
 except over extensive habitat shifts.
DOI: 10.5061/dryad.qrfj6q5hg
title: Diversification of Crassula: Phylogenetic analysis and life-form traits

description: These datasets are associated with the published paper -
 "Evidence linking life form to a major shift in diversification rate
 in Crassula" (DOI:10.1002/ajb2.1797)  Crassula L.
 (Crassulaceae) is a characteristic element of the southern African flora,
 occurring in a wide range of habitats, and it exhibits a remarkable
 diversity of life forms. However, whether any particular
 life-form trait has shaped species diversification in Crassula has
 remained unexplored. Our study aimed to investigate
 diversification patterns within Crassula and identify potential links to
 its life-form evolution. A phylogenetic tree of 140 Crassula taxa was
 reconstructed using plastid and nuclear loci, and dated based on the
 nuclear DNA information only. We reconstructed ancestral life-form
 characters to estimate the evolutionary trends of ecophysiological change,
 and subsequently estimated net diversification
 rates. The datasets presented here summarise the
 life-form classification (incl. life-history strategies and growth
 forms) of all Crassula species and the data from our phylogenetic
 analysis.
DOI: 10.5061/dryad.05qfttf45
title: Higher-order sequences of vocal mimicry performed by male Albert’s lyrebirds are socially transmitted and enhance acoustic contrast

description: Most studies of acoustic communication focus on short units of
 vocalisation such as songs, yet these units are often hierarchically
 organised into higher-order sequences, and outside human language, little
 is known about the drivers of sequence structure. Here we investigate the
 organisation, transmission, and function of vocal sequences sung by male
 Albert’s lyrebirds (Menura alberti), a species renowned for vocal
 imitations of other species. We quantified the organisation of mimetic
 units into sequences and examined the extent to which these sequences are
 repeated within and between individuals and shared among populations. We
 found that individual males organised their mimetic units into stereotyped
 sequences. Sequence structures were shared within and to a lesser extent
 among populations, implying that sequences were socially transmitted.
 Across the entire species range, mimetic units were sung with immediate
 variety and a high acoustic contrast between consecutive units, suggesting
 that sequence structure is a means to enhance receiver perceptions of
 repertoire complexity. Our results provide evidence that higher-order
 sequences of vocalisations can be socially transmitted, and that the order
 of vocal units can be functionally significant. We conclude that, to fully
 understand vocal behaviours, we must study both the individual vocal units
 and their higher-order temporal organisation.
DOI: 10.5061/dryad.7d7wm37wm
title: Hawksbill turtle ddRAD raw sequencing data

description: Pleistocene environmental changes are generally assumed to have
 dramatically affected species’ demography via changes in habitat
 availability, but this is challenging to investigate due to our limited
 knowledge of how Pleistocene ecosystems changed through time. Here, we
 tracked changes in shallow marine habitat availability resulting from
 Pleistocene sea level fluctuations throughout the last glacial cycle (120
 – 14 thousand years ago; kya) and assessed correlations with past changes
 in genetic diversity inferred from genome-wide SNPs, obtained via ddRAD
 sequencing, in Caribbean hawksbill turtles, which feed in coral reefs
 commonly found in shallow tropical waters. We found sea level regression
 resulted in an average 75% reduction in shallow marine habitat
 availability during the last glacial cycle. Changes in shallow marine
 habitat availability correlated strongly with past changes in hawksbill
 turtle genetic diversity, which gradually declined to ~1/4th of
 present-day levels during the Last Glacial Maximum (LGM; 26 – 19 kya).
 Shallow marine habitat availability and genetic diversity rapidly
 increased after the LGM, signifying a population expansion in response to
 warming environmental conditions. Our results suggest a positive
 correlation between Pleistocene environmental changes, habitat
 availability and species’ demography, and that demographic changes in
 hawksbill turtles were potentially driven by feeding habitat availability.
 However, we also identified challenges associated with disentangling the
 potential environmental drivers of past demographic changes, which
 highlight the need for integrative approaches. Our conclusions underline
 the role of habitat availability on species’ demography and biodiversity,
 and that the consequences of ongoing habitat loss should not be
 underestimated.
description: The dataset consists of two gzipped FASTQ files that raw Illumina
 sequencing data (ddRADs) obtained from 55 hawksbill turtles
 (<em>Eretmochelys imbricata</em>).
description: Please see the published manuscript and accompanying
 supplementary material for a detailed description of the methods and steps
 required to analyze the raw data.
DOI: 10.5061/dryad.cvdncjt5h
title: Species specific plant-mediated effects between herbivores converge at high damage intensity

description: Plants are often exposed to multiple herbivores and densities of these
 attackers (or corresponding damage intensities) generally fluctuate
 greatly in the field. Plant-mediated interactions vary among herbivore
 species and with changing feeding intensity, but little is known about how
 herbivore identity and density interact to determine plant responses and
 herbivore fitness. Here, we investigated this question using Triadica
 sebifera (tallow) and its two major specialist insect herbivores, Bikasha
 collaris (flea beetle) and Heterapoderopsis bicallosicollis (weevil). By
 manipulating densities of leaf-feeding adults of these two insects, we
 tested how variations in the intensity of leaf damage caused by flea
 beetle or weevil adults affected the performance of root-feeding flea
 beetle larvae and evaluated the potential of changed traits of tallow root
 as predictions of flea beetle larval performance. We found that weevil
 adults consistently decreased the survival of flea beetle larvae with
 increasing leaf damage intensities. In contrast, conspecific flea beetle
 adults increased their larval survival at low damage then decreased larval
 survival at high damage, resulting in a unimodal pattern. Chemical
 analyses showed that increasing leaf damage from weevil adults linearly
 decreased root carbohydrates and increased root tannin, whereas flea
 beetle adults had opposite effects as weevil adults at low damage and
 similar effects as them at high damage. Furthermore, across all feeding
 treatments, flea beetle larval survival was positively correlated with
 concentrations of carbohydrates and negatively correlated with
 concentration of tannin, suggesting that root primary and secondary
 metabolism might underlie observed effects on flea beetle larvae. Our
 study demonstrates that herbivore identity and density interact to
 determine systemic plant responses and plant-mediated effects on
 herbivores. In particular, effects are species specific at low densities,
 but converge at high densities. These findings emphasize the importance of
 considering herbivore identity and density simultaneously when identifying
 factors driving plant-mediated interactions between herbivores, advancing
 our understanding of the structure and composition of herbivore
 communities and terrestrial food-webs.
DOI: 10.5061/dryad.zcrjdfndg
title: Ecological network complexity scales with area

description: Larger geographical areas contain more species–an observation raised to a
 law in ecology. Less explored is whether biodiversity changes are
 accompanied by a modification of interaction networks. We use data from 32
 spatial interaction networks from different ecosystems to analyse how
 network structure changes with area. We find that basic community
 structure descriptors (number of species, links, and links per species)
 increase with area following a power-law. Yet, the
 distribution of links per species varies little with area, indicating that
 the fundamental organization of interactions within networks is conserved.
 Our null model analyses suggest that the spatial scaling of network
 structure is determined by factors beyond species richness and the number
 of links. We demonstrate that biodiversity–area relationships can be
 extended from species counts to higher levels of network complexity.
 Therefore, the consequences of anthropogenic habitat destruction may
 extend from species loss to wider simplification of natural communities.
DOI: 10.5061/dryad.m37pvmd3h
title: Effect of heat shock and competition on the antioxidant system of round goby

description: Monitoring oxidative stress biomarkers has become a powerful and common
 tool to estimate organismal condition and response to endogenous and
 environmental factors. In the present study, we used round goby (Neogobius
 melanostomus) from non-native European populations, as a model species to
 test sex differences in oxidative stress biomarkers. Considering sex
 differences in reproductive investment, we hypothesized that males would
 display lower resistance to abiotic stress. Fish were exposed to a heat
 shock (temperature elevated by 10°C) for 1h, 6h, and 12h and catalase
 activity (CAT), reduced glutathione (GSH), total antioxidant capacity
 (TAC) and lipid peroxidation (LPO) were measured in liver and muscle
 tissues. Liver of males was significantly more responsive compared to
 liver of females in all tested parameters. GSH was found to be
 the most responsive to heat stress exposure in both sexes. The results
 supported our hypothesis that male reproductive investment
 (territoriality, courtship, and brood care) and likelihood of only a
 single spawning period in their lifetime influenced on higher sensitivity
 of their antioxidant defence. On the other hand, for
 females antioxidant defence is considered more important to survive the
 environmental changes and successfully reproduce in the next season. Our
 experiments exposed fish to acute thermal stress. Further research should
 determine the effects of exposure to chronic thermal stress to corroborate
 our understanding on sex differences in antioxidant defence in the round
 goby.
DOI: 10.5061/dryad.pvmcvdnn7
title: Persistence of seed dispersal in agroecosystems: effects of landscape modification and intensive soil management practices in avian frugivores, frugivory and seed deposition in olive croplands

description: Farming impacts on animal-mediated seed dispersal through mechanisms
 operating at least at two spatial scales: first, at the landscape scale,
 through habitat loss and land conversion to agriculture/livestock grazing,
 and second, by local intensification (farm scale) of the agricultural
 practices. Nonetheless, these two scales of farming impact on the seed
 dispersal function have been rarely integrated. In particular, studies
 evaluating the effect of agriculture in the seed dispersal function of
 frugivorous birds in Mediterranean ecosystems are lacking. We evaluate the
 role of the landscape transformation, from fruit-rich woodland habitats to
 olive grove landscapes, together with the local intensive practices of
 soil management on the persistence of the seed dispersal function for
 Mediterranean fleshy-fruited plants in olive landscapes of south Spain. We
 used bird censuses, mist-nets and seed traps to characterize avian
 frugivore assemblages, frugivory, and seed deposition in seminatural
 woodland habitat (SNWH) patches and olive fields of 40 olives farms of 20
 localities distributed across the whole range of olive cultivation in
 Andalusia (southern Spain). We found that despite of a still remarkable
 dispersal function in olive grove landscapes, avian frugivore abundance
 and diversity, frugivory, and seed arrival decreased in olive fields
 compared to SNWH patches. Likewise, SNWH cover loss and/or olive growing
 expansion decreased avian frugivory and seed arrival. Interestingly,
 habitat effects in the olive farms often depended on the landscape
 context. In particular, less diverse fruit-eating bird assemblages pooled
 in SNWH patches as olive grove cover increased or SNWH decreased in the
 landscape, while remained relatively invariant in the olive fields.
 Finally, compared to conventional intensive agriculture, low-intensity
 management increased frugivory and seed deposition. We conclude that olive
 fields are less permeable to frugivores than expected by its
 agroforest-like nature, and that presence of SNWH patches is crucial for
 the maintenance of frugivory and seed dispersal in agricultural
 landscapes. Results evidence that woodland habitat loss by olive expansion
 and the intensive practices seriously threaten the dispersal service in
 olive-dominated landscapes. Maintenance, restoration and promotion of
 woodland patches should be prioritized for the conservation of the seed
 dispersal service and for enhancing the functional connectivity in
 human-shaped olive landscapes.
DOI: 10.5061/dryad.0zpc866zj
title: Effects of COVID-19 lockdown restrictions on parents’ attitudes towards green space and time spent outside by children in Cambridgeshire and North London, United Kingdom

description: 1. In the United Kingdom, children are spending less time outdoors and are
 more disconnected from nature than previous generations. However,
 interaction with nature at a young age can benefit wellbeing and long-term
 support for conservation. Green space accessibility in the UK varies
 between rural and urban areas and is lower for children than for adults.
 It is possible that COVID-19 lockdown restrictions may have influenced
 these differences. 2. In this study, we assessed parents’ attitudes
 towards green space, as well as whether the COVID-19 lockdown restrictions
 had affected their attitudes or the amount of time spent outside by their
 children, via an online survey for parents of primary school-aged children
 in Cambridgeshire and North London, UK (n = 171). We assessed whether
 responses were affected by local environment (rural, suburban or urban),
 school type (state-funded or fee-paying) or garden access (with or without
 private garden access). 3. Parents’ attitudes towards green space were
 significantly different between local environments: 76.9% of rural parents
 reported being happy with the amount of green space to which their
 children had access, in contrast with only 40.5% of urban parents. 4.
 COVID-19 lockdown restrictions also affected parents’ attitudes to the
 importance of green space, and this differed between local environments:
 75.7% of urban parents said their views had changed during lockdown, in
 contrast with 35.9% of rural parents. The change in amount of time spent
 outside by children during lockdown was also significantly different
 between local environments: most urban children spent more time inside
 during lockdown, whilst most rural children spent more time outside. 5.
 Neither parents’ attitudes towards green space nor the amount of time
 spent outside by their children varied with school type or garden access.
 6. Our results suggest that lockdown restrictions exacerbated pre-existing
 differences in access to nature between urban and rural children in our
 sampled population. We suggest that the current increased public and
 political awareness of the value of green space should be capitalised on
 to increase provision and access to green space and to reduce inequalities
 in accessibility and awareness of nature between children from different
 backgrounds.
DOI: 10.5061/dryad.2v6wwpzpt
title: Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

description: Premise of the study: Evolutionary studies require solid phylogenetic
 frameworks, but increased volumes of phylogenomic data have revealed
 incongruent topologies among gene trees in many organisms both between and
 within genomes. Some of these incongruences indicate polytomies that may
 remain impossible to resolve. Here we investigate the degree of gene-tree
 discordance in Solanum, one of the largest flowering plant genera that
 includes the cultivated potato, tomato, and eggplant, as well as 24 minor
 crop plants. Methods: A densely sampled species-level phylogeny of Solanum
 is built using unpublished and publicly available Sanger sequences
 comprising 60% of all accepted species (742 spp.) and nine regions (ITS,
 waxy, and seven plastid markers). The robustness of this topology is
 tested by examining a full plastome dataset with 140 species and a nuclear
 target-capture dataset with 39 species of Solanum (Angiosperms353 probe
 set). Key results: While the taxonomic framework of Solanum remained
 stable, gene tree conflicts and discordance between phylogenetic trees
 generated from the target-capture and plastome datasets were observed. The
 latter correspond to regions with short internodal branches, and network
 analysis and polytomy tests suggest the backbone is composed of three
 polytomies found at different evolutionary depths. The strongest area of
 discordance, near the crown node of Solanum, could potentially represent a
 hard polytomy. Conclusions: We argue that incomplete lineage sorting due
 to rapid diversification is the most likely cause for these polytomies,
 and that embracing the uncertainty that underlies them is crucial to
 understand the evolution of large and rapidly radiating lineages.
description: <b>Appendix S17. </b>Newick treefile, with all 10
 species trees (TreeBase). <strong>Appendix
 S18.</strong> Alignment file of concatenated Sanger supermatrix,
 with partition between genes (746 taxa).
 <strong>Appendix S19.</strong> Alignment file of
 plastome exons, introns and intergenic regions used in phylogenetic
 analyses, 152 taxa. <strong>Appendix
 S20.</strong> Alignment file of A353 Target Capture 338 loci,
 filtering threshold of minimum 4 taxa per loci.
 <strong>Appendix S21. </strong>Target Capture A353
 alignments of 303 loci, filtering threshold of minimum 20 taxa per
 loci.
DOI: 10.5061/dryad.tx95x69zw
title: Genomic and environmental influences on resilience in a cold‐water fish near the edge of its range

description: Small, isolated populations present a challenge for conservation. The
 dueling effects of selection and drift in a limited pool of genetic
 diversity make the responses of small populations to environmental
 perturbations erratic and difficult to predict. This is particularly true
 at the edge of a species range, where populations often persist at the
 limits of their environmental tolerances. Populations of
 cisco, Coregonus artedi, in inland lakes have experienced
 numerous extirpations along the southern edge of their range in recent
 decades, which are thought to result from environmental degradation and
 loss of cold, well-oxygenated habitat as lakes warm. Yet, cisco
 extirpations do not show a clear latitudinal pattern, suggesting that
 local environmental factors and potentially local adaptation may influence
 resilience. Here, we used genomic tools to investigate the nature of this
 pattern of resilience. We used restriction site-associated DNA capture
 (Rapture) sequencing to survey genomic diversity and differentiation in
 southern inland lake cisco populations and compared the frequency of
 deleterious mutations that potentially influence fitness across lakes. We
 also examined haplotype diversity in a region of the major
 histocompatibility complex involved in stress and immune system response.
 We correlated these metrics to spatial and environmental factors including
 latitude, lake size, and measures of oxythermal habitat and found
 significant relationships between genetic metrics and broad and local
 factors. High levels of genetic differentiation among populations were
 punctuated by a phylogeographic break and residual patterns of
 isolation-by-distance. Although the prevalence of deleterious mutations
 and inbreeding coefficients was significantly correlated with latitude,
 neutral and non-neutral genetic diversity were most strongly correlated
 with lake surface area. Notably, differences among lakes in the
 availability of estimated oxythermal habitat left no clear population
 genomic signature. Our results shed light on the complex dynamics
 influencing these isolated populations and provide valuable information
 for their conservation.