cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f7m0cfxww
title: Benthic and benthopelagic Ostracoda from a wide depth range (189-6224 m) in the Atlantic Sector of the Southern Ocean

description: This dataset contains abundance (i.e., absolute number of
 speicmens/individuals) of ostracod genera collected during three
 cruises of the German Research Vessel Polarstern in the Atlantic
 Sector of the Southern Ocean. The cruises are EASIZ II (PS
 48/ANT XV-3), ANDEEP I (PS 61/ANT XIX-3), ANDEEP
 II (PS 67/ANTXXII-3), and ANDEEP III (PS 67/ANTXXII-4). The
 samples related to the present file were all collected using an epibenthic
 sledge, described by (Brandt & Barthel, 1995; Brenke, 2005, see
 compelte references in Brandão et al., 2021, Zoological Journal of the
 Linnean Society). These ostracods are both benthic (most
 specimens collected) and bentho-pelagic (Halocyprididae, which in the case
 of the present dataset, swam just above the sea floor).
description: From the Material and Methods session of the paper, which
 analysed this dataset (Brandão et al., 2021): "The 51 samples studied
 herein (Fig. 1, Tab. 1) were collected in the Atlantic sector of the SO
 during four cruises of the projects ANDEEP (I, II and III cruises) and
 EASIZ (Ecology of the Antarctic Sea Ice Zone) (II cruise) (for details see
 Brandt <i>et al.,</i> 2007b; Arntz & Gutt, 1999). The
 ANDEEP (Antarctic benthic DEEP-sea biodiversity: colonization history and
 recent community patterns) project provided samples from the deep
 continental shelf (753 m) to the abyss (6340 m). While during the EASIZ 
 project samples were recovered from the relatively shallow continental
 shelf (189 m) to the deep slope (2076 m). The gear used in the sampling
 was an EpiBenthic Sledge (EBS), which holds two sampling boxes (opening of
 100 cm width and 33 cm height), with one sampler plankton net attached
 (0.5 mm mesh size for the epinet and supranet, and 0.3 mm for the cod
 ends) (for a detailed description of the gear, see Brandt
 <i>& </i>Barthel, 1995; Brenke, 2005). The sledge was
 hauled over the ground for 10 min at a mean velocity of 1 knot (1852 m/h)
 . Haul distances were calculated on the basis of the GPS-derived positions
 of the ship at the start of the haul to the time when the sledge left the
 ground, and varied from 807 to 6464 m. As soon as the sledge arrived on
 board, samples were immediately fixed in 96% pre-cooled ethanol and kept
 for at least 48 h at -20°C. Contrary to most published
 studies on ostracods, which are based on subrecent specimens (empty
 valves), herein the species density data includes only living specimens
 (=with soft parts). Additionally, because small-sized ostracods could pass
 through the EBS mesh (300 and 500 μm) during trawling, taxa with a
 carapace shorter than 500 μm (e.g. Xestoleberididae, some Pontocyprididae,
 <i>Pseudocythere</i>) were excluded from the statistical
 analyses. The ostracods were identified to species level (except for the
 Krithidae) based on appendage and valve morphology. The ostracods from the
 supra and epibenthic-sledges were pooled as one sample."
DOI: 10.5061/dryad.4tmpg4fb4
title: Data from: Volatile fatty acid concentration, soil pH and soil texture during anaerobic soil conditions affect germination of Athelia (Sclerotium) rolfsii sclerotia

description: Anaerobic growth chamber trials were conducted to evaluate effects of VFA
 and VFA concentration, and interactions with soil pH and soil texture, on
 A. rolfsii sclerotia germination. In the first objective, sclerotia were
 exposed to 4, 8, or 16 mmol/kg soil of acetic or n-butyric acids in sandy
 soil; soil pH was buffered to 5, 6, or 7. In the second objective,
 sclerotia in sandy or sandy loam soil were exposed to 4 or 16 mmol VFA/kg
 soil at soil pH 5 or 6. VFAs are probable important factors in A. rolfsii
 suppression due to ASD treatment in many soil environments, and activity
 is dependent on VFA concentration, soil solution pH, and soil texture.
description: See Swilling et al.
 &lt;https://dx.doi.org/10.1007/s10658-021-02392-8&gt; for data
 collection and processing methods.
description: Data entries on non-relevant/non-applicable fields are indicated
 by '.'
DOI: 10.5061/dryad.2jm63xsq4
title: Aboveground net primary productivity in regenerating seasonally dry tropical forest: contributions of rainfall, forest age, and soil

description: Identifying factors controlling forest productivity is critical to
 understanding forest-climate change feedbacks, modeling vegetation
 dynamics, and carbon finance schemes. However, little research has focused
 on productivity in regenerating tropical forest which are expanding in
 their fraction of global area have an order of magnitude larger carbon
 uptake rates relative to older forest. We examined aboveground net primary
 productivity (ANPP) and its components (wood production and litterfall)
 over ten years in forest plots that vary in successional age, soil
 characteristics, and species composition using band dendrometers and
 litterfall traps in regenerating seasonally dry tropical forests in
 northwestern Costa Rica. We show that the components of ANPP are
 differentially driven by age and annual rainfall and that local soil
 variation is important. Total ANPP was explained by a combination of age,
 annual rainfall, and soil variation. Wood production comprised 35% of ANPP
 on average across sites and years, and was explained by annual rainfall
 but not forest age. Conversely, litterfall increased with forest age and
 soil fertility yet was not affected by annual rainfall. In this region,
 edaphic variability is highly correlated with plant community composition.
 Thus, variation in ecosystem processes explained by soil may also be
 partially explained by species composition. These results suggest that
 future changes in annual rainfall can alter the secondary forest carbon
 sink, but that this effect will be buffered by the litterfall flux which
 varies little among years. In determining the long-term strength of the
 secondary forest carbon sink, both rainfall and forest age will be
 critical variables to track. We also conclude that a detailed
 understanding of local site variation in soils and plant communities may
 be required to accurately predict the impact of changing rainfall on
 forest carbon uptake. Synthesis We show that in seasonally dry tropical
 forests, annual rainfall has a positive relationship with the growth of
 aboveground woody tissues of trees and that droughts lead to significant
 reductions in aboveground productivity. These results provide evidence for
 climate change – carbon cycle feedbacks in the seasonal tropics and
 highlight the value of longitudinal data on forest regeneration.
DOI: 10.5061/dryad.vdncjsxvq
title: Data from: Thermal history of alfalfa leafcutting bees affects nesting and diapause incidence

description: Variable spring temperatures may expose developing insects to sublethal
 conditions, resulting in long-term consequences. The alfalfa leafcutting
 bee, Megachile rotundata, overwinters as a prepupa inside a brood
 cell, resuming development in spring. During these immobile stages of
 development, bees must tolerate unfavourable temperatures. In this study,
 we test how exposure to low temperature stress during development affects
 subsequent reproduction and characteristics of the F1 generation.
 Developing male and female M. rotundata were exposed to
 either constant (6°C) or fluctuating (1 h/day at 20°C) low temperature
 stress for one week, during the pupal stage to mimic a
 spring cold snap. Treated adults were marked and released into field
 cages, and reproductive output was compared to that of untreated control
 bees. Exposure to low temperatures during the pupal stage had mixed
 effects on reproduction and offspring characteristics. Females treated
 with fluctuating low temperatures were more likely to nest compared to
 control bees or those exposed to constant low temperature stress.
 Sublethal effects may have contributed to low nesting rates of bees
 exposed to constant low temperatures. Females from that group that were
 able to nest had fewer, larger offspring with high viability, suggesting a
 trade-off. Interestingly, offspring of bees exposed to fluctuating low
 temperatures were more likely to enter diapause, indicating that thermal
 history of parents, even during development, is an important factor in
 diapause determination.
DOI: 10.5061/dryad.d7wm37q26
title: Exon-based phylogenomics and the relationships of African cichlids: Tackling the challenges of reconstructing phylogenies with repeated rapid radiations

description: African cichlids (subfamily: Pseudocrenilabrinae) are among the most
 diverse vertebrates, and their propensity for repeated rapid radiation has
 made them a celebrated model system in evolutionary research. Nonetheless,
 despite numerous studies, phylogenetic uncertainty persists, and riverine
 lineages remain comparatively underrepresented in higher-level
 phylogenetic studies. Heterogeneous gene histories resulting from
 incomplete lineage sorting (ILS) and hybridization are likely sources of
 uncertainty, especially during episodes of rapid speciation. We
 investigate relationships of Pseudocrenilabrinae and its close relatives
 while accounting for multiple sources of genetic discordance using species
 tree and hybrid network analyses with hundreds of single-copy exons. We
 improve sequence recovery for distant relatives, thereby extending the
 taxonomic reach of our probes, with a hybrid reference guided/de novo
 assembly approach. Our analyses provide robust hypotheses for most
 higher-level relationships and reveal widespread gene heterogeneity,
 including in riverine taxa. ILS and past hybridization are identified as
 sources of genetic discordance in different lineages. Sampling of various
 Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for
 convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to
 other potentially useful protein-coding markers across the order. A
 reliable phylogeny with representatives from diverse environments will
 support ongoing taxonomic and comparative evolutionary research in the
 cichlid model system.
description: The dataset associated with this article consists of alignments
 for 588 single-copy exons for 178 taxa, most of which are African cichlids
 from the subfamily Pseudocrenilabrinae: 165 cichlids (Pseudocrenilabrinae: 150,
 Cichlinae: 3, Etroplinae: 5, Ptychochrominae: 7); 13 non-cichlid
 Blenniiformes). Raw reads were obtained through targeted exon
 capture with probes designed based on an <em>Oreochromis
 niloticus</em> genome. Target sequences were assembled using a
 combination of Bowtie2 guided, hybrid guided/de novo and
 reduced-sensitivity approaches. Target sequences were aligned in
 MUSCLE.
DOI: 10.5061/dryad.cz8w9gj48
title: The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution

description: Patterns of genomic architecture across insects remain largely
 undocumented or decoupled from a broader phylogenetic context. For
 instance, it is unknown whether translocation rates differ between insect
 orders. We address broad scale patterns of genome architecture across
 Insecta by examining synteny in a phylogenetic framework from open-source
 insect genomes. To accomplish this, we add a chromosome level genome to a
 crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus
 sulphureomaculatus genome is the first chromosome scale genome for the
 hyperdiverse Phytophaga lineage and currently the largest insect genome
 assembled to this scale. The genome is significantly larger than those of
 other weevils, and this increase in size is caused by repetitive elements.
 Our results also indicate that, among beetles, there are instances of
 long-lasting (&gt;200 Ma) localization of genes to a particular
 chromosome with few translocation events. While some chromosomes have a
 paucity of translocations, intra-chromosomal synteny was almost absent,
 with gene order thoroughly shuffled along a chromosome. This large amount
 of reshuffling within chromosomes with few inter-chromosomal events
 contrasts with patterns seen in mammals in which the chromosomes tend to
 exchange larger blocks of material more readily. To place our findings in
 an evolutionary context, we compared syntenic patterns across Insecta in a
 phylogenetic framework. For the first time, we find that synteny decays at
 an exponential rate relative to phylogenetic distance. Additionally, there
 are significant differences in decay rates between insect orders, this
 pattern was not driven by Lepidoptera alone which has a substantially
 different rate.
description: sequence and Hi-C files, same as found
 on https://www.dnazoo.org/assemblies/Pachyrhynchus_sulphureomaculatus but journal does not accept dropbox as a data repository
DOI: 10.15468/dl.zhnbgk
title: Occurrence Download

description: A dataset containing 831 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dipterocarpaceae"
 ]
}

 The dataset includes 831 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002914-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.866t1g1rb
title: Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)

description: Human assisted movement has allowed the Asian longhorned beetle (ALB,
 Anoplophora glabripennis (Motschulsky)) to spread beyond its native range
 and become a globally regulated invasive pest. Within its native range of
 China and the Korean peninsula, human-mediated dispersal has also caused
 cryptic translocation of insects, resulting in population structure
 complexity. Previous studies used genetic methods to detangle this
 complexity but were unable to clearly delimit native populations which is
 needed to develop downstream biosurveillance tools. We used genome-wide
 markers to define historical population structure in native ALB
 populations and contemporary movement between regions. We used
 genotyping-by-sequencing to generate 6,102 single nucleotide polymorphisms
 (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total,
 we genotyped 712 individuals from ALB’s native distribution. We observed
 six distinct population clusters among native ALB populations, with a
 clear delineation between northern and southern groups. Most of the
 individuals from South Korea were distinct from populations in China. Our
 results also indicate historical divergence among populations and suggest
 limited large-scale admixture, but we did identify a restricted number of
 cases of contemporary movement between regions. We identified SNPs under
 selection and describe a clinal allele frequency pattern in a missense
 variant associated with glycerol kinase, an important enzyme in the
 utilization of an insect cryoprotectant. We further demonstrate that small
 numbers of SNPs can assign individuals to geographic regions with high
 probability, paving the way for novel ALB biosurveillance tools.
description: The dataset was obtained
 from samples of Anoplophora Glabripennis across its native range in China and South
 Korea. DNA was extracted using the DNeasy 96 Blood
 &Tissue Kit (Qiagen) following the manufacturer's
 instructions. GBS libraries were prepared and sequenced at the Institut de
 Biologie Intégrative et des Systèmes (IBIS; Université Laval, Quebec City,
 Canada) with the Ion Proton sequencer. The Fast-GBS pipeline v1.0 was adopted to process raw sequencing
 reads. Basic
 filters were applied to retain only biallelic SNPs, remove indels and
 variants with a FILTER flag other than PASS, and remove loci with more
 than 50% missing data. Samples with &gt; 60% missing data were
 removed. Finally, only loci with read depth &gt; 5, minor allele
 frequency (MAF) &gt; 0.05, minor allele count (MAC) &gt; 3, and
 missing data per site &lt; 10%.
DOI: 10.5061/dryad.7sqv9s4sm
title: Local canopy disturbance as an explanation for long-term increases in liana abundance

description: Canopy disturbance explains liana abundance and distribution within
 tropical forests and thus may also explain the widespread pattern of
 increasing liana abundance; however, this hypothesis remains untested. We
 used a 10-year study (2007 – 2017) of 117,100 rooted lianas in an
 old-growth Panamanian forest to test whether local canopy disturbance
 explains increasing liana abundance. We found that liana density increased
 29.2% and basal area 12.5%. The vast majority of these increases were
 associated with clonal stem proliferation following canopy disturbance,
 particularly in liana-dense, low-canopy gaps, which had far greater liana
 increases than did undisturbed forest. Lianas may be ecological niche
 constructors; arresting tree regeneration in gaps and thus creating a
 high-light environment that favors sustained liana proliferation. Our
 findings demonstrate that liana abundance is increasing rapidly and their
 ability to proliferate via copious clonal stem production in canopy gaps
 explains much of their increase in this and possibly other tropical
 forests.
description: Details of data collection and analyses can be found in the
 Materials and Methods section of the associated manuscript.
DOI: 10.5061/dryad.f7m0cfxwx
title: Data from 'Convergent patterns of body size variation in distinct parasite taxa with convergent life cycles'

description: Aim: Interspecific variation among metazoans often follows a latitudinal
 pattern, with species at higher latitudes being larger-bodied than related
 species from lower latitudes (Bergmann’s rule). For parasitic species,
 body sizes within any higher taxon often correlate with the body sizes of
 their hosts (Harrison’s rule). Whether temperature-driven latitudinal
 effects or host-driven resource constraints act independently or
 additively to shape interspecific variation in parasite body sizes remains
 unknown. We use a comparative approach to test the effects of latitude and
 host body size on parasite body sizes in two taxa of parasitic worms
 showing convergent life cycles. Location: Global. Time period:
 Contemporary. Major taxa studied: Hairworms (Nematomorpha) and mermithids
 (Nematoda) parasitic in arthropods. Methods: With 223 records for
 mermithids and 258 for nematomorphs worldwide, we used linear mixed
 effects models to test the effects of latitude and host body size on
 parasite length, intraspecific length variation, parasite egg diameter,
 and variation in egg diameter. Further, we modelled parasite length with
 local mean annual temperature as predictor instead of latitude, as a
 direct test of underlying mechanisms. All models took into account host
 and parasite taxonomic structure within the datasets. Results: For both
 taxa, host body size was clearly the main determinant of parasite body
 length, with neither latitude nor local temperature (annual mean or range)
 having an effect. No predictor affected intraspecific length variation,
 whereas egg diameter was positively associated with parasite length and
 variation in egg diameter was negatively associated with latitude. Main
 conclusions: Our results support a strong role for host traits in shaping
 the evolution of parasite body sizes (Harrison’s rule), but no role for
 latitude (Bergmann’s rule), even though these parasites infect ectothermic
 hosts. At a mechanistic level, the evolutionary driving force of external
 temperature on parasite physiology seems to be eclipsed by the
 availability of resources from the host.
description: Data compiled from primary literature sources. See article for
 details.
description: See README file
DOI: 10.5061/dryad.59zw3r27x
title: An evolutionary framework of Acanthaceae based on transcriptomes and genome skims

description: Acanthaceae is a family of tropical flowering plants with approximately
 4000 species. Despite remarkable variation in morphological traits,
 research on patterns of character evolution has been limited by uncertain
 relationships among some of the major lineages. We sampled from these
 major lineages to estimate a phylogenomic framework using a combination of
 newly sequenced shotgun genome skims plus new and publicly available
 transcriptomes. We used OrthoFinder2 to infer a species tree with strong
 branch support. Except for the placement of Crabbea, our results
 corroborate the most recent chloroplast and nrITS sequence-based topology.
 Of 587 single copy loci, 10 were recovered for all 16 species; a RAxML
 tree estimated from these 10 loci resulted in the same topology as other
 datasets assembled in this study, with the exception of relationships
 among three sampled species of Barleria; however, branch support was lower
 compared to the tree reconstructed using more data. ABBA-BABA tests were
 conducted to investigate patterns of introgression involving Crabbea; few
 nucleotides supported alternative topologies. SplitsTree networks of the
 587 loci and 6,136 trees revealed conflict among the branches leading to
 Andrographideae, Whitfieldieae, and Neuracanthus. A principal components
 analysis in treespace found no distinct clusters of trees. Our results
 strongly corroborate the previously published chloroplast and nr-ITS-based
 phylogeny of Acanthaceae with increased resolution among Barlerieae,
 Andrographideae, Whitfieldieae, and Neuracanthus. We propose that the tree
 presented here is the best estimate to date of Acanthaceae phylogeny. This
 advance in our knowledge of relationships will allow us to investigate
 character evolution and other phenomena within this diverse group of
 plants.
description: # An evolutionary framework of Acanthaceae based on transcriptomes and
 genome skims
 [https://doi.org/10.5061/dryad.59zw3r27x](https://doi.org/10.5061/dryad.59zw3r27x) ## Description of the data and file structure * SpeciesTreAlignment_AminoAcids.fa is an output of OrthoFinder that contains an alignment of 587 nuclear loci. * RAxML_bootstrap.result is an output of RAxML that is the ML estimate of the 587 nuclear loci alignment “SpeciesTreAlignment_AminoAcids.fa” * SpeciesTree_rootedMSA_Oct29.tre is an output of OrthoFinder that estimates a phylogeny based on 587 nuclear loci. * Gene_Trees is an output of OrthoFinder that is the set of 19,573 trees for all loci. * SCGenes_10.phy is an alignment of the 10 single-copy loci recovered by OrthoFinder. * RAxML_bipartitionsBranchLabels.results.newick is an output file of RAxML that is the ML estimate for the 10 single copy loci alignment. ## Sharing/Access information NA