cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs325
title: Data from: Stay at home aphids: comparative spatial and seasonal metapopulation structure and dynamics of two specialist tansy aphid species studied using microsatellite markers

description: Two tansy-feeding aphids – Macrosiphoniella tanacetaria (MA) and
 Metopeurum fuscoviride (ME) – were studied at a small spatial scale in and
 around Jena (&lt; 80 km2) using polymorphic microsatellite markers.
 Both species were found in ~ 60% of sites formerly known to harbour the
 aphids, although generally when they did occur, they occurred singly (MA ~
 50%; ME ~60%) and rarely together on the same plant at the same time
 (~10%) and then usually only in the early part of the growing season. This
 difference may be due to quasi-apparent competition effects elicited to
 ants farming ME aphids, and preferentially actively eliminating or
 disturbing MA aphids. In terms of population genetics, both aphids showed
 extreme genetic heterogeneity within a metapopulation structure, ME more
 than MA, i.e. higher FST values, ~ 0.4 vs. 0.15, respectively, and limited
 levels of interpopulation gene flow. Subpopulations often deviated from
 Hardy-Weinberg equilibrium and showed linkage disequilibria, as expected
 in animals with extended parthenogenetic reproduction, and had positive
 FIS values for most large samples, suggesting inbreeding, and possibly
 philopatry, certainly in ME. Hierarchical analysis (allele range and
 number per locus, analysis of molecular variance and FST) strongly
 suggested that the plant rather than site governs the level of genetic
 variation. Bayesian clustering analysis revealed that both species had
 heterogeneous historical genetic patterning, with K (number of subgroups)
 ranging from 3-7. Evidence is also provided from isolation by distance
 (IBD) and private allele analyses, that in MA, the presence of winged
 autumn males, absent in ME where males are wingless, influences
 comparative population genetic structuring, such that ME subpopulations
 are comparatively more inbred and genetically differentiated than MA
 subpopulations. Lastly, additional spatial arrangement (ALLELES-IN-SPACE)
 analysis showed that in both species, certain subpopulations were
 genetically isolated from the remainder, probably due to geographical
 barriers, including intervening buildings and woods. As such, the biology
 of these tansy aphids living in semi-natural habitats is very different
 from many pest aphid species examined within agro-ecosystems and infesting
 ephemeral crops, since the former seem much more reluctant to fly and
 hence show contrastingly much higher levels of interpopulation divergence,
 even at small spatial scales as here investigated. Indeed, the number of
 genotypic clusters found for tansy aphids found using Bayesian approaches
 is similar to that for the major pest the peach-potato aphid, Myzus
 persicae, globally.
description: Tansy aphid data - Hugh
 D. Loxdale,FLS, 2007Tansy aphid collecting
 sites, Jena - May 2007 (09.12.08)
DOI: 10.5061/dryad.pb2sq
title: Data from: Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria

description: Symbiotic associations can allow an organism to acquire novel traits by
 accessing the genetic repertoire of its partner. In the Dictyostelium
 discoideum farming symbiosis, certain amoebas (termed “farmers”) stably
 associate with bacterial partners. Farmers can suffer a reproductive cost
 but also gain beneficial capabilities, such as carriage of bacterial food
 (proto-farming) and defense against competitors. Farming status previously
 has been attributed to amoeba genotype, but the role of bacterial partners
 in its induction has not been examined. Here, we explore the role of
 bacterial associates in the initiation, maintenance, and phenotypic
 effects of the farming symbiosis. We demonstrate that two clades of
 farmer-associated Burkholderia isolates colonize D. discoideum nonfarmers
 and infectiously endow them with farmer-like characteristics, indicating
 that Burkholderia symbionts are a major driver of the farming phenomenon.
 Under food-rich conditions, Burkholderia-colonized amoebas produce fewer
 spores than uncolonized counterparts, with the severity of this reduction
 being dependent on the Burkholderia colonizer. However, the induction of
 food carriage by Burkholderia colonization may be considered a
 conditionally adaptive trait because it can confer an advantage to the
 amoeba host when grown in food-limiting conditions. We observed
 Burkholderia inside and outside colonized D. discoideum spores after
 fruiting body formation; this observation, together with the ability of
 Burkholderia to colonize new amoebas, suggests a mixed mode of symbiont
 transmission. These results change our understanding of the D. discoideum
 farming symbiosis by establishing that the bacterial partner,
 Burkholderia, is an important causative agent of the farming phenomenon.
description: Fig2a Spot
 testFig2c Serial
 transferFig3a Spore counts Kp
 abundantFig3b Spore counts Kp
 scarceFig4a Spot test tet
 treatmentFig4b Serial transfer
 tet cured farmersFig4d Spore counts
 farmer v tet treatedS1a Spot
 testS1b Spot test serial
 transferS3 Spore count original
 host v nonfarmer dosage
DOI: 10.5061/dryad.vh1qk
title: Data from: Genomic signatures of divergent selection and speciation patterns in a 'natural experiment', the young parallel radiations of Nicaraguan crater lake cichlid fishes

description: Divergent selection is the main driving force in sympatric ecological
 speciation and may also play a strong role in divergence between
 allopatric populations. Characterizing the genome-wide impact of divergent
 selection constitutes often a first step in the process of unraveling the
 genetic bases underlying adaptation and ecological speciation. The Midas
 cichlid fish (Amphilophus citrinellus) species complex in Nicaragua is a
 powerful system for studying evolutionary processes. Independent
 colonizations of isolated young crater lakes by Midas cichlid populations
 from the older and great lakes of Nicaragua resulted in the repeated
 evolution of adaptive radiations by intralacustrine sympatric speciation.
 In this study we performed genome scans on two repeated radiations of
 crater lake species and their great lake source populations (1030
 polymorphic AFLPs, n ≈ 30 individuals per species). We detected regions
 under divergent selection (0.3 % in the crater lake Xiloá flock and 1.7 %
 in the older crater lake Apoyo radiation) that might be responsible for
 the sympatric diversification. We find no evidence that the same genomic
 regions have been involved across crater lake flocks. The data provide
 evidence, however, for some genetic parallelism (seven out of 51 crater
 lake to great lake outlier loci are shared; 13.7%) associated with the
 allopatric divergence of both crater lake flocks. Furthermore, our results
 suggest that the number of outlier loci involved in sympatric and
 allopatric divergence increases with time. A phylogeny based on our data
 clearly supports the monophyly of both crater lake species flocks and
 provides evidence for a parallel branching order with a primary divergence
 along the limnetic-benthic axis in both radiations.
description: Binary AFLP data
 matrixData generated by
 genotyping of 13 different AFLP primer combinations. Matrix holds data, as
 used for analyses, after data refinement procedures. Rows represent
 different specimens. 1st column indicates species, 2nd column an
 individual ID. Following columns hold dominant binary data for 1030
 polymorphic loci. Letters in loci names correspond to the three selective
 nucleotides of selective primers on the EcoRI and MseI site and numbers to
 the size of respective fragments. "?" indicates missing
 data.Dryad_entry_AFLP_binary_matrix.txt
DOI: 10.5061/dryad.p6r7d
title: Data from: Plant quantity affects development and survival of a gregarious insect herbivore and its endoparasitoid wasp

description: Virtually all studies of plant-herbivore-natural enemy interactions focus
 on plant quality as the major constraint on development and survival.
 However, for many gregarious feeding insect herbivores that feed on small
 or ephemeral plants, the quantity of resources is much more limiting, yet
 this area has received virtually no attention. Here, in both lab and
 semi-field experiments using tents containing variably sized clusters of
 food plants, we studied the effects of periodic food deprivation in a
 tri-trophic system where quantitative constraints are profoundly important
 on insect performance. The large cabbage white Pieris brassicae, is a
 specialist herbivore of relatively small wild brassicaceous plants that
 grow in variable densities, with black mustard (Brassica nigra) being one
 of the most important. Larvae of P. brassicae are in turn attacked by a
 specialist endoparasitoid wasp, Cotesia glomerata. Increasing the length
 of food deprivation of newly molted final instar caterpillars
 significantly decreased herbivore and parasitoid survival and biomass, but
 shortened their development time. Moreover, the ability of caterpillars to
 recover when provided with food again was correlated with the length of
 the food deprivation period. In outdoor tents with natural vegetation, we
 created conditions similar to those faced by P. brassicae in nature by
 manipulating plant density. Low densities of B. nigra lead to potential
 starvation of P. brassicae broods and their parasitoids, replicating
 nutritional conditions of the lab experiments. The ability of both
 unparasitized and parasitized caterpillars to find corner plants was
 similar but decreased with central plant density. Survival of both the
 herbivore and parasitoid increased with plant density and was higher for
 unparasitized than for parasitized caterpillars. Our results, in
 comparison with previous studies, reveal that quantitative constraints are
 far more important that qualitative constraints on the performance of
 gregarious insect herbivores and their gregarious parasitoids in nature.
description: Data for
 archiveData for the paper of
 plant quantity represents a greater constraint than quality for a
 gregarious insect herbivore and its endoparasitoid waspArchive.xlsx
DOI: 10.5061/dryad.kn8b72m5
title: Data from: Camerate and disparid crinoids from the late Kinderhookian Meadville Shale, Cuyahoga Formation of Ohio

description: Crinoids were first reported from the Cuyahoga Formation in northeastern
 Ohio by James Hall in 1863. However, these crinoids have essentially not
 been re-examined in detail since the late 18th century. With the restudy
 of classical and more recent collections, ten (nine camerate and one
 disparid) species-level taxa are recognized from the late Kinderhookian
 Cuyahoga Formation, including the camerates Amphoracrinus viminalis (Hall,
 1863); Aorocrinus helice Hall, 1863; Aorocrinus meyeri n. sp.;
 Aryballocrinus martini n. sp.; Cusacrinus daphne (Hall, 1863);
 Platycrinites s.l. contritus (Hall, 1863); Platycrinites s.l. graphicus
 (Hall, 1863); Platycrinites s.l. lodensis (Hall and Whitfield, 1875); and
 Platycrinites s.l. burki n. sp. In addition, Halysiocrinus sp. is the
 first disparid reported from this fauna. Platycrinites s.l. bedfordensis
 (Hall and Whitfield, 1875) is designated a nomen dubium. Growth is
 evaluated for Aorocrinus helice and Cusacrinus daphne, which had
 contrasting development. The Aorocrinus helice calyx was largely not
 allometric but the growth of the primaxil plate was, suggesting the arms
 may have grown allometrically. In contrast, much of the calyx of
 Cusacrinus daphne displayed allometric growth.
description: SUPPLEMENTARY DATABASE
 F0R Ausich & RoerserOntogey
 figures
DOI: 10.5061/dryad.15fn7
title: Data from: Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

description: Environmentally induced phenotypic plasticity is thought to play an
 important role in the adaption of plant populations to heterogeneous
 habitat conditions, and yet the importance of epigenetic variation as a
 mechanism of adaptive plasticity in natural plant populations still merits
 further research. In this study, we investigated populations of Vitex
 negundo var. heterophylla (Chinese chastetree) from adjacent habitat types
 at seven sampling sites. Using several functional traits, we detected a
 significant differentiation between habitat types. With amplified fragment
 length polymorphisms (AFLP) and methylation-sensitive AFLP (MSAP), we
 found relatively high levels of genetic and epigenetic diversity but very
 low genetic and epigenetic differences between habitats within sites.
 Bayesian clustering showed a remarkable habitat-related differentiation
 and more genetic loci associated with the habitat type than epigenetic,
 suggesting that the adaptation to the habitat is genetically based.
 However, we did not find any significant correlation between genetic or
 epigenetic variation and habitat using simple and partial Mantel tests.
 Moreover, we found no correlation between genetic and ecologically
 relevant phenotypic variation and a significant correlation between
 epigenetic and phenotypic variation. Although we did not find any direct
 relationship between epigenetic variation and habitat environment, our
 findings suggest that epigenetic variation may complement genetic
 variation as a source of functional phenotypic diversity associated with
 adaptation to the heterogeneous habitat in natural plant populations.
description: Raw data of phenotypic,
 genetic and epigenetic variationRaw data of phenotypic,
 genetic (AFLP) and epigenetic (MSAP) variationAPPENDIX_RawData.xlsx
DOI: 10.5061/dryad.4tv0s
title: Data from: The assembly of ant-farmed gardens: mutualism specialization following host broadening

description: Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in
 return for nest space and food rewards. They occur in the Neotropics and
 Australasia, but not in Africa, and their evolutionary assembly remains
 unclear. We here use phylogenetic frameworks for important AG lineages in
 Australasia, namely the ant genus Philidris and domatium-bearing ferns
 (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and
 Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza,
 Myrmephytum and Squamellaria). Our analyses revealed that in these clades,
 diaspore dispersal by ants evolved at least 13 times, five times in the
 Late Miocene and Pliocene in Australasia and seven times during the
 Pliocene in Southeast Asia, after Philidris ants had arrived there, with
 subsequent dispersal between these two areas. A uniquely specialized AG
 system evolved in Fiji at the onset of the Quaternary. The farming in the
 same AG of epiphytes that do not offer nest spaces suggests that a
 broadening of the ants' plant host spectrum drove the evolution of
 additional domatium-bearing AG-epiphytes by selecting on pre-adapted
 morphological traits. Consistent with this, we found a statistical
 correlation between the evolution of diaspore dispersal by ants and
 domatia in all three lineages. Our study highlights how host broadening by
 a symbiont has led to new farming mutualisms.
description: Philidris
 matrixPhilidris (ants) matrix
 consisting of four nuclear markers (EF alpha F1, EF alpha F2, CAD and LR)
 and the mitochondrial marker COI.Philidris_matrix_EF-F1_EF-F2_CAD_LR_COI_dryad.nexLecanopteris matrixLecanopteris (ferns) matrix consisting of two pasted markers (rbcL and trnL)Lecanopteris_rbcL_trnL_dryad.nexHydnophytinae matrixHydnophytinae matrix consisting of two nuclear markers (ITS and ETS) and four plastid markers (trnL intron, trnL-trnF, ndhF, psbA-trnH)Hydnophytinae_ITS_ETS_trnL_intron_trnL_trnF_spacer_ndhF_psbA_trnH_spacer_dryad.nex
DOI: 10.5061/dryad.45672js4
title: Data from: Global gradients in vertebrate diversity predicted by historical area-productivity dynamics and contemporary environment

description: Broad-scale geographic gradients in species richness have now been
 extensively documented, but their historical underpinning is still not
 well understood. While the importance of productivity, temperature, and a
 scale-dependence of the determinants of diversity is broadly acknowledged,
 we here argue that limitation to a single analysis scale and data
 pseudoreplication have impeded an integrated evolutionary and ecological
 understanding of diversity gradients. We develop and apply a hierarchical
 analysis framework for global diversity gradients that incorporates an
 explicit accounting of past environmental variation and provides an
 appropriate measurement of richness. Due to environmental niche
 conservatism organisms generally reside in climatically defined
 bioregions, or “evolutionary arenas”, characterized by in situ speciation
 and extinction. These bioregions differ in age and their total
 productivity and have varied over time in area and energy available for
 diversification. We show that, consistently across the four major
 terrestrial vertebrate groups, current-day species richness of the world’s
 main 32 bioregions is best explained by a model that integrates area and
 productivity over geological time together with temperature. Adding
 finer-scale variation in energy availability as an ecological predictor of
 within-bioregional patterns of richness explains much of the remaining
 global variation in richness at the 110km grain. These results highlight
 the separate evolutionary and ecological effects of energy availability
 and provide a first conceptual and empirical integration of the key
 drivers of broad-scale richness gradients. Avoiding the pseudo-replication
 that impedes the evolutionary interpretation of non-hierarchical
 macroecological analyses, our findings integrate evolutionary and
 ecological mechanisms at their most relevant scales and offer a new
 synthesis regarding global diversity gradients.
description: JetzFine110kmSRRichness data (Total, Resident, Endemic; for Birds, Mammals and Amphibians) for the 9,253 110x110km grid cells analyzed. For details see Materials & Methods - Finer-scale analyses
DOI: 10.5061/dryad.34g43
title: Data from: Lifetime inbreeding depression, purging, and mating system evolution in a simultaneous hermaphrodite tapeworm

description: Classical theory on mating system evolution suggests that simultaneous
 hermaphrodites should either outcross if they have high inbreeding
 depression (ID) or self-fertilize if they have low ID. However, a mixture
 of selfing and outcrossing persists in many species. Previous studies with
 the tapeworm Schistocephalus solidus have found worms to self-fertilize
 some of their eggs despite ID. The probability for selfing to spread
 depends on the relative fitness of selfers, as well as the genetic basis
 for ID and whether it can be effectively purged. We bred S. solidus
 through two consecutive generations of selfing and recorded several
 fitness-correlates over the whole life cycle. After one round of selfing,
 ID was pronounced, particularly in early-life traits, and the
 conservatively estimated lifetime fitness of selfed progeny was only 9%
 that of the outcrossed controls. After a second generation of selfing, ID
 remained high but was significantly reduced in several traits, which is
 consistent with the purging of deleterious recessive alleles (the
 estimated load of lethal equivalents dropped by 48%). Severe ID, even if
 it can be rapidly purged, likely prevents transitions towards pure selfing
 in this parasite, though we also cannot exclude the possibility that
 low-level selfing has undetected benefits.
description: Main
 dataPurging_full_dryad.csvClutch-level hatching ratesPurging_HR_dryad.csv
DOI: 10.5061/dryad.ps228b9
title: Data from: Comparative phylogeography biogeography of forest-dependent mammals reveals paleo-forest corridors throughout Sundaland

description: The evolutionary history of the colugo, a gliding arboreal mammal
 distributed throughout Sundaland, was influenced by the location of and
 connections between forest habitats. By comparing colugo phylogenetic
 patterns, species ecology, sample distributions, and times of divergence
 to those of other Sundaic taxa with different life history traits and
 dispersal capabilities, we inferred the probable distribution of
 paleo-forest corridors. We identified a consistent pattern of early
 diversification between east and west Bornean lineages in colugos, lesser
 mouse deer, and Sunda pangolins. This phylogenetic pattern has not been
 commonly described in mammals, and we found no evidence for this pattern
 in the greater mouse deer. Colugos on West Borneo diverged from colugos in
 Peninsular Malaysia and Sumatra in the late Pliocene, however most other
 mammalian populations distributed across these same geographic regions
 diverged from a common ancestor more recently in the Pleistocene. Low
 genetic divergence between colugos on large landmasses and their
 neighboring satellite islands indicated that past forest distributions
 were recently much larger than present refugial distributions. Our
 analysis of colugo evolutionary history reveals dynamic forested
 connections throughout Sundaland, and reconstructs Borneo as the most
 likely ancestral area of origin for Sunda colugos.
description: TKA_TNA_BWACNSSeqs.wTKA143491_AndReplaceTNA104416_06_01_14.align.TrimNameTragulus whole mtDNA genome alignmentsTragulus_Cytb_Align_Del143491.AmbfixTragulus Cytb mtDNA alignmentManisAllBowtie2_05_31_14.w356430.alignManis whole mtDNA genome alignmentManisAllBowtie2_TrimTo317198_05_31_14.alignManis mtDNA genome alignment. All sequences trimmed to only sites included in individual 317198.ManisCOI_AllSeqs_Align_NoZhang_TrimManis COI mtDNA sequence alignmentRAxML_bipartitions.TKA_TNA_BWACNSSeqs.wTKA143491_AndReplaceTNA104416_06_01_14.align.TrimNameRAxML bipartition tree file after 1000 bootstraps from Tragulus whole mtDNA genome sequence alignmentRAxML_bipartitions.Tragulus_Cytb_Align_Del143491.Ambfix.N1000RAxML bipartition tree file after 1000 bootstraps from Tragulus Cytb mtDNA sequence alignmentRAxML_bipartitions.ManisAllBowtie2_05_31_14.w356430.align.TrimNamesRAxML bipartition tree file after 1000 bootstraps from Manis whole mtDNA genome sequence alignmentRAxML_bipartitions.ManisAllBowtie2_TrimTo317198_05_31_14.alignRAxML bipartition tree file after 1000 bootstraps from Tragulus mtDNA genome sequence alignment trimmed to sites only present in individual 317198RAxML_bipartitionsBranchLabels.ManisCOI_AllSeqs_Align_NoZhang_Trim.N1000RAxML bipartition tree file after 1000 bootstraps from Manis COI mtDNA sequence alignmentRAxML_bipartitions.Concat.Nuclear.NoINDEL.P2.d3.pc5.FixG03.v1.40.N1000RAxML bipartition tree file after 1000 bootstraps from Galeopterus whole mtDNA genome sequence alignment. Alignment data for this tree was previously submitted to Dryad (doi:10.5061/dryad.6q738).