cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j723v
title: Data from: Introduction bias affects relationships between the characteristics of ornamental alien plants and their naturalization success

description: Aim: Alien plants with certain characteristics may have been introduced
 earlier and more frequently than others. Such introduction bias may cause
 spurious associations between plant characteristics and naturalization
 (the establishment of self-sustaining populations in the wild). We aimed
 to disentangle direct and indirect (i.e. mediated by introduction history)
 effects of species characteristics on the naturalization success of alien
 plants introduced for horticulture. Location: Germany (non-native range);
 rest of the world (native range). Methods: We compiled a dataset of 435
 alien plant species introduced in cultivation in Germany, including data
 on their year of introduction, the number of botanical gardens where they
 are planted, native range, biological traits and naturalization success.
 We used path analysis to estimate the direct effects of geographical
 origin and biological traits on naturalization, and their indirect effects
 mediated by year and/or frequency of introduction. Results: We found
 significant direct positive effects of native range size and winter
 hardiness on naturalization. Alien species native to other parts of Europe
 and species with a large native range were brought to the country earlier
 than other species. In addition, woody species, winter-hardy species and
 tall species were planted more frequently than others. Because the number
 of botanical gardens where a species is planted increased naturalization
 success directly, and residence time did so indirectly through a
 significant positive association with the number of botanical gardens,
 most of the species characteristics had indirect effects on
 naturalization. Main conclusions: Our approach allowed us to show that
 apparent effects of species characteristics on naturalization success can
 be at least partly indirect, due to introduction biases. This indicates
 that failure to recognize such introduction biases could impair our
 ability to explain the success of alien plant species.
description: DatasetThe file contains the dataset. A brief description of the variables is available in the ReadMe file. The data are explained in more detail in the Methods section of the paper (see Maurel et al., 2016, Global Ecology and Biogeography).Maurel_GEB_2016_dataset.csv
DOI: 10.5061/dryad.841k6
title: Data from: The evolution of signal-reward correlations in bee and hummingbird-pollinated species of Salvia

description: Within-individual variation in floral advertising and reward traits is a
 feature experienced by pollinators that visit different flowers of the
 same plant. Pollinators can use advertising traits to gather information
 about the quality and amount of rewards, leading to the evolution of
 signal–reward correlations. As long as plants differ in the reliability of
 their signals and pollinators base their foraging decisions on this
 information, natural selection should act on within-individual
 correlations between signals and rewards. Because birds and bees differ in
 their cognitive capabilities, and use different floral traits as signals,
 we tested the occurrence of adaptive divergence of the within-individual
 signal–reward correlations among Salvia species that are pollinated either
 by bees or by hummingbirds. They are expected to use different floral
 advertising traits: frontal traits in the case of bees and side traits in
 the case of hummingbirds. We confirmed this expectation as bee- and
 hummingbird-pollinated species differed in which specific traits are
 predominantly associated with nectar reward at the within-individual
 level. Our findings highlight the adaptive value of within-individual
 variation and covariation patterns, commonly disregarded as ‘environmental
 noise’, and are consistent with the hypothesis that pollinator-mediated
 selection affects the correlation pattern among floral traits.
description: advertisement and reward
 traits in Salvia flowersInclude morphological
 and nectar measurements from 3251 flowers belonging to 503 individual
 plants and 18 Salvia species.data for
 repeatabilityInclude data for ten
 randomly chosen flowers per species, in which area measurements (frontal
 area of the lower lip and area of corolla tube) were taken three
 times.
DOI: 10.5061/dryad.73n28
title: Data from: Palenque de San Basilio in Colombia: genetic data supports an oral history of a paternal ancestry in Congo

description: The Palenque, a black community in rural Colombia, have an oral history of
 fugitive African slaves founding a free village near Cartagena in the
 seventeenth century. Recently, linguists have identified some 200 words in
 regular use that originate in a Kikongo language, with Yombe, mainly
 spoken in the Congo region, being the most likely source. The
 non-recombining portion of the Y chromosome (NRY) and mitochondrial DNA
 were analysed to establish whether there was greater similarity between
 present-day members of the Palenque and Yombe than between the Palenque
 and 42 other African groups (for all individuals, n = 2799) from which
 forced slaves might have been taken. NRY data are consistent with the
 linguistic evidence that Yombe is the most likely group from which the
 original male settlers of Palenque came. Mitochondrial DNA data suggested
 substantial maternal sub-Saharan African ancestry and a strong founder
 effect but did not associate Palenque with any particular African group.
 In addition, based on cultural data including inhabitants' claims of
 linguistic differences, it has been hypothesized that the two districts of
 the village (Abajo and Arriba) have different origins, with Arriba founded
 by men originating in Congo and Abajo by those born in Colombia. Although
 significant genetic structuring distinguished the two from each other, no
 supporting evidence for this hypothesis was found.
description: Supplementary-Tables_S1_S14
DOI: 10.5061/dryad.bv7tv
title: Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

description: The genetic mechanisms underlying regressive evolution—the degeneration or
 loss of a derived trait—are largely unknown, particularly for complex
 structures such as eyes in cave organisms. In several eyeless animals, the
 visual photoreceptor rhodopsin appeared to retain functional amino-acid
 sequences. Hypotheses to explain apparent maintenance of function include
 weak selection for retention of light-sensing abilities and its
 pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we
 show that there has been repeated loss of functional constraint of
 rhodopsin in amblyopsid cavefishes, as at least three cave lineages have
 independently accumulated unique loss-of-function mutations over the last
 10.3 My. While several cave lineages still possess functional rhodopsin,
 they exhibit increased rates of nonsynonymous mutations that have greater
 effect on the structure and function of rhodopsin compared to those in
 surface lineages. These results indicate that functionality of rhodopsin
 has been repeatedly lost in amblyopsid cavefishes. The presence of a
 functional copy of rhodopsin in some cave lineages is likely explained by
 stochastic accumulation of mutations following recent subterranean
 colonization.
description: Amblyopsidae-ND2Amblyopsidae-PLAGAmblyopsidae-PTRAmblyopsidae-RAG1Amblyopsidae-SH3Amblyopsidae-TBRAmblyopsidae-MYHAmblyopsidae-S7Amblyopsidae-RHO
DOI: 10.5061/dryad.tn6vn
title: Data from: Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

description: With the increasing democratization of high-throughout sequencing (HTS)
 technologies, along with the concomitant increase in sequence yield per
 dollar, many researchers are exploring HTS for microbial community
 ecology. Many elements of experimental design can drastically affect the
 final observed community structure, notably the choice of primers for
 amplification prior to sequencing. Some targeted microbes can fail to
 amplify due to primer-targeted sequence divergence and be omitted from
 obtained sequences, leading to differences among primer pairs in the
 sequenced organisms even when targeting the same community. This potential
 source of taxonomic bias in HTS makes it prudent to investigate how primer
 choice will affect the sequenced community prior to investing in a costly
 community-wide sequencing effort. Here we use Fluidigm’s micro-fluidic
 Access Arrays (IFC) followed by Illumina® MiSeq Nano sequencing on a
 culture-derived local mock community to demonstrate how this approach
 allows for a low-cost combinatorial investigation of primer pairs and
 experimental samples (up to 48 primer pairs and 48 samples) to determine
 the most effective primers that maximize obtained communities whilst
 minimizing taxonomic biases.
description: LR0Rre.LSU401.Mock.fastaFasta file containing repetitiveness sequences of OTUs described using the primer pair LR0R(Rehner)-nuLSU401.LR0R.LR3.Mock.fastaFasta file containing repetitiveness sequences of OTUs described using the primer pair LR0R-LR3.ITS1F.ITS2.Mock.fastaFasta file containing repetitiveness sequences of OTUs described using the primer pair ITS1F-ITS2.fITS7.ITS4.Mock.fastaFasta file containing repetitiveness sequences of OTUs described using the primer pair fITS7-ITS4.ITS3KYO2.ITS4KYO3.Mock.fastaFasta file containing repetitiveness sequences of OTUs described using the primer pair ITS3KYO2-ITS4KYO3.Mock.Community.fasta.RepFasta File containing Sanger sequences fungal isolates used as a the Mock Community. Sequences are the rRNA region from the forward primer ITS1F and the reverse primer LR3. Label for each sequences includes river in which each culture was isolated on Coiba Island, Panama.mothur.commands.annotatedA list of mothur commands used for these analyses along with annotations regarding what these commands are doing.
DOI: 10.5061/dryad.8447
title: Data from: Eating local: influences of habitat on the diet of little brown bats (Myotis lucifugus)

description: We employ molecular methods to profile the diet of the little brown bat,
 Myotis lucifugus, and describe spatial and temporal changes in diet over
 their maternity season. We identified 61 prey species of insects and 5
 species of arachnid. The largest proportion of prey (∼32%) were identified
 as species of the mass-emerging Ephemeroptera (mayfly) genus Caenis. Bats
 roosting in agricultural settings had lower dietary richness than those
 occupying a roost located on a forest fragment in a conservation area. We
 detected temporal fluctuations in diet over the maternity season. Dipteran
 (fly) species dominated the diet early in the season, replaced later by
 species of mayfly. Because our methodology provides species-level
 identification of prey, we were able to isolate environmental indicator
 species in the diet and draw conclusions about the location and type of
 their foraging habitat and the health of these aquatic systems. The
 species detected suggested that the bats use variable habitats; members of
 one agricultural roost foraged on insects originating in rivers or streams
 while those in another agricultural roost and the forest roost fed on
 insects from pond or lake environments. All source water for prey was of
 fair to good quality, though no species detected are intolerant of
 pollution thus the habitat cannot be classified as pristine. Our study
 outlines a model system to investigate the abiotic and biotic interactions
 between habitat factors through this simple food chain to the top
 predator.
description: Clare
 dataSequences generated from
 guano collected from the bat Myotis lucifugus. Please contact the
 corresponding author for details regarding the appropriate use of these
 data.
DOI: 10.6084/m9.figshare.29539088
title: Parramatta Historical Spatial Data Infrastructure v1

description: This supporting material contains a description of the methodologies used to create the core data contained in the lightweight historical spatial data infrastructure (HSDI) described in the manuscript, ‘Mapping people, labour, and the movement of things in the first decades (1788-1825) of colonial Parramatta, Australia’.The dataset includes the following tables:<b>‘grants_leases’</b> – land grants and leases mostly up to around 1820 with sporadic later coverage. This has an associated geometry in GDA2020/MGA zone 56 projection (EPSG:7856).<b>‘people’</b> – people associated with Parramatta. For this pilot dataset release, this is limited to people who have associated grants or leases. This has no associated geometry.<b>‘grants_leases_parramatta_ids’ </b>– a table documenting the connections between people and grants and leases. This allows reciprocal, many-to-many relationships between the ‘people’ and ‘grants_leases’ tables. One person may have held several grants. One grant may have been held by several people. This has no associated geometry.<b>‘districts’</b> – a digitised version of the regional districts (Figure 1) as shown on an 1813 map:A correct map of the British settlement in N.S.W., divided into the different districts and townships (1813), The National Archives [UK]/Australian Joint Copying Project, CO 700/New South Wales 21/AJCP Reel no. 6937, Item 21. Available at http://nla.gov.au/nla.obj-1845276701 (accessed 4 June 2025).Corresponding metadata tables are included to describe the fields in each table.The <b>districts </b>table is a stand-alone collection of geospatial features. The <b>grants_leases </b>and <b>people </b>tables are joined by the <b>grants_leases_parramatta_ids </b>table.<br>
DOI: 10.6084/m9.figshare.29539088.v1
title: Parramatta Historical Spatial Data Infrastructure v1

description: This supporting material contains a description of the methodologies used to create the core data contained in the lightweight historical spatial data infrastructure (HSDI) described in the manuscript, ‘Mapping people, labour, and the movement of things in the first decades (1788-1825) of colonial Parramatta, Australia’.The dataset includes the following tables:<b>‘grants_leases’</b> – land grants and leases mostly up to around 1820 with sporadic later coverage. This has an associated geometry in GDA2020/MGA zone 56 projection (EPSG:7856).<b>‘people’</b> – people associated with Parramatta. For this pilot dataset release, this is limited to people who have associated grants or leases. This has no associated geometry.<b>‘grants_leases_parramatta_ids’ </b>– a table documenting the connections between people and grants and leases. This allows reciprocal, many-to-many relationships between the ‘people’ and ‘grants_leases’ tables. One person may have held several grants. One grant may have been held by several people. This has no associated geometry.<b>‘districts’</b> – a digitised version of the regional districts (Figure 1) as shown on an 1813 map:A correct map of the British settlement in N.S.W., divided into the different districts and townships (1813), The National Archives [UK]/Australian Joint Copying Project, CO 700/New South Wales 21/AJCP Reel no. 6937, Item 21. Available at http://nla.gov.au/nla.obj-1845276701 (accessed 4 June 2025).Corresponding metadata tables are included to describe the fields in each table.The <b>districts </b>table is a stand-alone collection of geospatial features. The <b>grants_leases </b>and <b>people </b>tables are joined by the <b>grants_leases_parramatta_ids </b>table.<br>
DOI: 10.5061/dryad.qk643
title: Data from: Therian mammals experience an ecomorphological radiation during the Late Cretaceous and selective extinction at the K-Pg boundary

description: It is often postulated that mammalian diversity was suppressed during the
 Mesozoic Era and increased rapidly after the Cretaceous–Palaeogene (K–Pg)
 extinction event. We test this hypothesis by examining macroevolutionary
 patterns in early therian mammals, the group that gave rise to modern
 placentals and marsupials. We assess morphological disparity and dietary
 trends using morphometric analyses of lower molars, and we evaluate
 generic level taxonomic diversity patterns using techniques that account
 for sampling biases. In contrast with the suppression hypothesis, our
 results suggest that an ecomorphological diversification of therians began
 10–20 Myr prior to the K–Pg extinction event, led by disparate
 metatherians and Eurasian faunas. This diversification is concurrent with
 ecomorphological radiations of multituberculate mammals and flowering
 plants, suggesting that mammals as a whole benefitted from the ecological
 rise of angiosperms. In further contrast with the suppression hypothesis,
 therian disparity decreased immediately after the K–Pg boundary, probably
 due to selective extinction against ecological specialists and
 metatherians. However, taxonomic diversity trends appear to have been
 decoupled from disparity patterns, remaining low in the Cretaceous and
 substantially increasing immediately after the K–Pg extinction event. The
 conflicting diversity and disparity patterns suggest that earliest
 Palaeocene extinction survivors, especially eutherian dietary generalists,
 underwent rapid taxonomic diversification without considerable
 morphological diversification.
description: Fossil occurrence
 datasetFossil occurrences of
 tribosphenidan mammals from the Cretaceous through Selandian. This dataset
 is modified from an occurrence list downloaded from the Paleobiology
 Database (www.paleobiodb.org) on November 19, 2015.Grossnickle&Newham2016_FossilOccurrenceDataset.xlsxMolar landmark and outline coordinatesThese are the original point coordinates (in tps format) used in a geometric morphometric analysis of lower molar shape. For each genus, the first seven coordinates are cusp landmarks, the next 20 coordinates outline the talonid, and the final 20 coordinates outline the trigonid. (Note that the outline coordinates are not equally-spaced semilandmarks.) See Grossnickle & Newham (2016) for information concerning how these coordinates were analyzed.molar_LM_coords_GrossnickleNewham2016.xlsx
DOI: 10.5061/dryad.j8m6718
title: Data from: Pleistocene range expansions promote divergence with gene flow between migratory and sedentary populations of Calothorax hummingbirds

description: We investigate the influence of postglacial population expansion on
 genetic structure of reproductively isolated populations that come into
 secondary contact and produce hybrid zones. We test migratory behaviour to
 explain geographic patterns of genetic diversity and phylogeographic
 structure in migratory and sedentary populations of hummingbirds in the
 Chihuahuan Desert. We assessed genetic structure, demographic expansion
 and introgression in Calothorax hummingbirds using mitochondrial DNA
 (mtDNA) and nuclear microsatellites (nSSRs), and ecological niche
 modelling (ENM) to predict where migratory and sedentary populations
 resided during Pleistocene climate events. Bayesian analysis yielded three
 clusters. However, only two clusters match mtDNA haplogroups, one parental
 in the south (pulcher) and a cluster with two admixed taxa (sedentary and
 migratory lucifer) that cannot be attributed to any pure parental
 population. Demographic expansion, gene flow and admixture in the lucifer
 range, postglacial northern expansion predicted by ENM, and approximate
 Bayesian computation strongly supported a scenario of divergence with gene
 flow: a Pleistocene basal split separating pulcher and the other two
 clades are derived from a second split (migratory and sedentary lucifer).
 Population genetic admixture was higher in localities with lower inferred
 habitat suitability stability. The genetic differentiation of Calothorax
 may be explained by the combined effects of (1) gene flow and recent
 postglacial northern expansion from southern sedentary populations, (2)
 increased genetic admixture with lower stability of habitat suitability,
 and (3) the evolution of long-distance seasonal migration during
 glacial/interglacial cycles, suggesting a role for diversification through
 the divergence of migratory subpopulations that become sedentary.
description: ND2_File.nexNEXUS data files contain alignments of Calothorax hummingbirds (Trochilidae) ND2 and ATPase 6 and ATPase 8 mtDNA sequences.ATPase_File.nex2. ATPase_File: Calothorax lucifer and Calothorax pulcher ATP synthase subunit 6 gene (ATPase 6) and ATP synthase subunit 8 gene (ATPase 8) mitochondrial sequences.Licona-Vera et al_microsatellites_info.xlsMicrosatellite sizing for 72 hummingbirds samples genotyped at eight autosomal microsatellite loci previously designed for Selasphorus platycercus (HumB1, HumB2, HumB3, HumB9, HumB10, HumB11, HumB12 and HumB15; Oyler-McCance et al., 2011).Licona-Vera et al_morphology_infoSeven body measurements from each of 122 hummingbirds (males and females) used in morphological analyses.Licona-Vera et al_MAXENT_inputfileThe MAXENT input file used in the analysis of the climatic preferences of Calothorax hummingbirds (Trochilidae).
DOI: 10.5061/dryad.2784g
title: Data from: Trait-associated loss of frugivores in fragmented forest does not affect seed removal rates

description: Seed dispersal by frugivorous animals forms the basis for regeneration of
 numerous plant species. Habitat fragmentation has been found to be one
 major factor perturbing frugivore communities and dependent plant species.
 Yet, community-wide consequences of fragmentation for both frugivore and
 plant communities are still hardly understood. Here, we studied the
 effects of habitat fragmentation on the seed removal by frugivorous birds
 and mammals from nine fleshy-fruited plant species in Białowieża Forest
 (Eastern Poland). This last relict of old-growth lowland forest in Europe
 poses an exceptional reference site for studying the impact of habitat
 fragmentation on seed dispersal processes in temperate forest ecosystems.
 In particular, (i) we tested for associations between forest fragmentation
 and response traits of frugivores, that is forest specialization and body
 mass; (ii) we studied the relationship between frugivore response and
 effect traits, that is centrality (number of consumed plant species) and
 interaction type (mutualistic vs. antagonistic); and (iii) we assessed the
 feedback of fragmentation-induced changes on plant–frugivore interactions
 and seed removal rates. We found that fragmentation led to shifts in the
 frugivore community, associated with the response traits forest
 specialization and body mass, with fewer forest specialists and
 large-bodied frugivores in fragmented than in continuous forests. However,
 forest generalists and small-bodied frugivores were more central in the
 plant–frugivore associations than forest specialists and large-bodied
 frugivores. Therefore, the loss of vulnerable species did not result in
 reduced seed removal rates in fragmented compared with continuous forest.
 Synthesis. These results indicate that seed removal may be relatively
 robust in spite of shifts in the frugivore community in forest fragments.
 The correlation between response and effect traits of frugivores
 highlights the importance of forest generalists and small-bodied
 frugivores for maintaining dispersal processes in fragmented forests in
 temperate regions. Yet, future studies should aim at quantifying the
 consequences of seed disperser loss on other aspects of dispersal, such as
 long-distance dispersal, spatial patterns of seed deposition, seed
 germination and plant regeneration.
description: data_package_FarwigEtAl2016_JournalOfEcologyThis data package contains data from the publication: Farwig, Nina; Schabo, Dana & Albrecht, Jörg (2016) Trait-associated loss of frugivores in fragmented forest does not affect seed removal rates. Journal of Ecology. Details about the content of the package can be found in the README.txt file and in the data_description.txt file in the zip folder.FarwigEtAl2016JEcol.zip