cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cc202
title: Data from: Climate-driven build-up of temporal isolation within a recently formed avian hybrid zone

description: Divergence in the onset of reproduction can act as an important source of
 reproductive isolation (i.e. allochronic isolation) between co-occurring
 young species, but evidence for the evolutionary processes leading to such
 divergence is often indirect. While advancing spring seasons strongly
 affect the onset of reproduction in many taxa, it remains largely
 unexplored whether contemporary spring advancement directly affects
 allochronic isolation between young species. We examined how increasing
 spring temperatures affected onset of reproduction and thereby
 hybridization between pied and collared flycatchers (Ficedula spp.) across
 habitat types in a young secondary contact zone. We found that both
 species have advanced their timing of breeding in 14 years. However,
 selection on pied flycatchers to breed earlier was weaker, resulting in a
 slower response to advancing springs compared to collared flycatchers and
 thereby build-up of allochronic isolation between the species. We argue
 that a pre-adaptation to a broader niche use (diet) of pied flycatchers
 explains the slower response to raising spring temperature, but that
 reduced risk to hybridize may contribute to further divergence in the
 onset of breeding in the future. Our results show that minor differences
 in the response to environmental change of co-occurring closely related
 species can quickly cause allochronic isolation.
description: Sirkiä et al. data for
 depositionSirkiä et al data for
 deposition.xlsx
DOI: 10.5281/zenodo.17875099
title: Southern Ocean Phytoplankton Functional Types and Size-Class Diversity Matchup Data

description: This dataset contains both CSV and NetCDF (NC) files:



CSV files include eight pigment variables from the SeaBASS database and the Hayward et al., (2024) dataset for the period 1998–2024. These data are limited to surface observations (0–20 m) in the Southern Ocean, within the latitude range from south to 40°S and longitude range 180°W–180°E.

NetCDF (NC) files contain gridded monthly phytoplankton size classes (PSCs) and phytoplankton functional types (PFTs) for the period 1998–2024, covering the austral spring–summer season from September to February. These data are derived using an empirical approach applied to the CSV dataset, combined with Ocean Colour Climate Change Initiative (OC-CCI) satellite products.


NC file DescriptionThis dataset provides gridded estimates of the PFTs/PSCs expressed as both percentage contribution and concentration (mg m⁻³), derived from satellite ocean-colour observations spanning 1998–2024. The product is designed to support analyses of long-term phytoplankton community structure, size-class variability, and ecosystem change.

PFT/PSC estimates are generated using a fourth-degree polynomial diagnostic approach applied to log₁₀-transformed chlorophyll. The resulting fractional contribution is constrained to the 0–100% range and subsequently converted to concentration by scaling it by the total chlorophyll. This approach is consistent with abundance-based phytoplankton size-class reconstruction methods commonly used in satellite biogeochemical studies.

The dataset is provided in NC format, following CF-conventions where applicable, and includes spatial and temporal coordinates suitable for regional, basin-scale, and climatological analyses.

Spatial Coverage





Latitude: 1176 grid points (degrees north)




Longitude: 8640 grid points (degrees east)




Global ocean coverage at high spatial resolution



Temporal Coverage





Time dimension: 162 monthly time steps




Reference time: days since 1998-01-01 00:00:00




Calendar: proleptic Gregorian




Aggregated for the September–February seasonal window over 1998–2024



Variables

1. Latitude





Units: degrees_north




Description: Latitude coordinate




Axis: Y



2. Longitude





Units: degrees_east




Description: Longitude coordinate




Axis: X



3. Time





Units: days since 1998-01-01 00:00:00




Description: Time coordinate




Axis: T



4. PFT/PSC_pct





Units: %




Description: Percentage contribution of PFT/PSC to total chlorophyll




Method: Derived from a 4th-degree polynomial applied to log₁₀(CHL), clipped to [0, 100]




Scale factor: 0.01




Fill value: −32767



5. PFT/PSC_conc





Units: mg m⁻³




Description: PFT/PSC concentration




Calculation: (PFT/PSC_pct / 100) × total chlorophyll




Scale factor: 0.001




Fill value: −32767
DOI: 10.5061/dryad.5jd7j
title: Data from: A novel method for estimating the strength of positive mating preference by similarity in the wild

description: Mating preference can be a driver of sexual selection and assortative
 mating and is, therefore, a key element in evolutionary dynamics. Positive
 mating preference by similarity is the tendency for the choosy individual
 to select a mate which possesses a similar variant of a trait. Such
 preference can be modelled using Gaussian-like mathematical functions that
 describe the strength of preference, but such functions cannot be applied
 to empirical data collected from the field. As a result, traditionally,
 mating preference is indirectly estimated by the degree of assortative
 mating (using Pearson's correlation coefficient, r) in wild captured
 mating pairs. Unfortunately, r and similar coefficients are often biased
 due to the fact that different variants of a given trait are nonrandomly
 distributed in the wild, and pooling of mating pairs from such
 heterogeneous samples may lead to “false–positive” results, termed “the
 scale-of-choice effect” (SCE). Here we provide two new estimators of
 mating preference (Crough and Cscaled) derived from Gaussian-like
 functions which can be applied to empirical data. Computer simulations
 demonstrated that r coefficient showed robust estimations properties of
 mating preference but it was severely affected by SCE, Crough showed
 reasonable estimation properties and it was little affected by SCE, while
 Cscaled showed the best properties at infinite sample sizes and it was not
 affected by SCE but failed at biological sample sizes. We recommend using
 Crough combined with the r coefficient to infer mating preference in
 future empirical studies.
description: Choice software ver
 1This
 present a Windows executable software that allows to estimate in a series
 of mating pair samples two mating preference estimators (r coefficient and
 Crough). The ZIP fie includes the executable, the software intructions (in
 pdf) and one file data example (sample.txt).Choice ver
 1.zip
DOI: 10.5061/dryad.47574
title: Data from: Male killing Spiroplasma protects Drosophila melanogaster against two parasitoid wasps

description: Maternally transmitted associations between endosymbiotic bacteria and
 insects are diverse and widespread in nature. Owing to imperfect vertical
 transmission, many heritable microbes have evolved compensational
 mechanisms to enhance their persistence in host lineages, such as
 manipulating host reproduction and conferring fitness benefits to host.
 Symbiont-mediated defense against natural enemies of hosts is increasingly
 recognized as an important mechanism by which endosymbionts enhance host
 fitness. Members of the genus Spiroplasma associated with distantly
 related Drosophila hosts are known to engage in either reproductive
 parasitism (i.e., male killing) or defense against natural enemies (the
 parasitic wasp Leptopilina heterotoma and a nematode). A male-killing
 strain of Spiroplasma (strain Melanogaster Sex Ratio Organism (MSRO))
 co-occurs with Wolbachia (strain wMel) in certain wild populations of the
 model organism Drosophila melanogaster. We examined the effects of
 Spiroplasma MSRO and Wolbachia wMel on Drosophila survival against
 parasitism by two common wasps, Leptopilina heterotoma and Leptopilina
 boulardi, that differ in their host ranges and host evasion strategies.
 The results indicate that Spiroplasma MSRO prevents successful development
 of both wasps, and confers a small, albeit significant, increase in
 larva-to-adult survival of flies subjected to wasp attacks. We modeled the
 conditions under which defense can contribute to Spiroplasma persistence.
 Wolbachia also confers a weak, but significant, survival advantage to
 flies attacked by L. heterotoma. The host protective effects exhibited by
 Spiroplasma and Wolbachia are additive and may provide the conditions for
 such cotransmitted symbionts to become mutualists. Occurrence of
 Spiroplasma-mediated protection against distinct parasitoids in divergent
 Drosophila hosts suggests a general protection mechanism.
description: Fly
 SurvivalFly and Wasp survival
 from the experiment setting.MsroSurvival1017.xlsOvipositionDifferential oviposition.WaspGrowthSexRatio
DOI: 10.5061/dryad.g180s
title: Data from: Bayesian long branch attraction bias and corrections

description: Previous work on the star-tree paradox has shown that Bayesian methods
 suffer from a long branch attraction bias. That work is extended to
 settings involving more taxa and partially resolved trees. The long branch
 attraction bias is confirmed to arise more broadly and an additional
 source of bias is found. A by-product of the analysis is methods that
 correct for biases toward particular topologies. The corrections can be
 easily calculated using existing Bayesian software. Posterior support for
 a set of two or more trees can thus be supplemented with corrected
 versions to cross-check or replace results. Simulations show the
 corrections to be highly effective.
description: Supplementary Material
 for Bayesian Long-Branch Attraction Bias and Correctionsbayes-LBA-bias-correction-supplementary.pdfSoftware Documentationpbf.pdfSource Code for SoftwareThis file contains source code for software to correct Bayesian posterior probabilities of topologies. This is Version 1.0, used for the Systematic Biology publication "Bayesian Long Branch Attraction Bias and Corrections". To access the most recent version of the software, please see pbfv1.0.tar.gz
DOI: 10.5061/dryad.fg25kk0
title: Data from: Role of temperature and coinfection in mediating pathogen life-history traits

description: Understanding processes maintaining variation in pathogen life-history
 traits is a key challenge in disease biology, and of importance for
 predicting when and where risks of disease emergence are highest.
 Pathogens are expected to encounter tremendous levels of variation in
 their environment – both abiotic and biotic – and this variation may
 promote maintenance of variation in pathogen populations through space and
 time. Here, we measure life-history traits of an obligate fungal pathogen
 at both asexual and sexual stages under both single infection and
 coinfection along a temperature gradient. We find that temperature had a
 significant effect on all measured life-history traits while coinfection
 only had a significant effect on the number of sexual resting structures
 produced. The effect of temperature on life-history traits was both direct
 as well as mediated through a genotype-by-temperature interaction. We
 conclude that pathogen life-history traits vary in their sensitivity to
 abiotic and biotic variation in the environment.
description: Powdery mildew
 coinfections at different temperaturesPowdery mildew
 (Podosphaera plantaginis) inoculations on leaves of Plantago lanceolata on
 petri dishes at different temperatures with and without coinfection.
 Timing of sporulation of asexual spores and germination of sexual spores.
 Viability of sexual spores. File contains also the
 metadata.Temperature_coinfection_Vaumourin_Laine_2018.xlsx
DOI: 10.5061/dryad.59b85
title: Data from: Bryophyte abundance, diversity and composition after retention harvest in boreal mixedwood forest

description: 1. Variable-retention harvest is widely recognised as an alternative to
 more intensive methods such as clear-cutting. However, present information
 is inadequate to judge impact of variable-retention on biodiversity of
 indigenous forest organisms intolerant of canopy removal, such as
 forest-inhabiting bryophytes. 2. We examined how bryophyte species cover,
 richness, diversity and composition change with time in response to a
 broad range of dispersed retention harvest treatments (2% (clear-cut),
 10%, 20%, 50%, 75% retention of original basal area) contrasted with uncut
 controls (100% retention)) in broadleaf deciduous, mixedwood and
 conifer-dominated boreal forests in NW Alberta, Canada. Bryophytes were
 studied in 432 permanent sample plots within 72 compartments before
 harvest and at three, six and eleven years after harvest. 3. Clear-cut and
 lower (10% and 20%) retention levels resulted in lower cover and richness
 of bryophytes than in unharvested control compartments in mixed and
 conifer-dominated forests, but less so in deciduous-dominated forests,
 which generally supported low cover and richness. Species composition in
 each forest type varied along the gradient of harvesting intensity;
 clear-cuts and lower levels of retention supported similar composition, as
 did control plots and those representing higher retention levels. Over
 time the retention harvest treatments became more similar to uncut
 controls. 4. Synthesis and applications. Increased retention moderated the
 negative impacts of harvesting on bryophyte assemblages across all forest
 types, and our results suggest that even 10% retention will facilitate
 faster post-harvest recovery of bryophytes.02-Aug-2017
description: Bryophyte abundance,
 diversity and composition after retention harvest in boreal mixedwood
 forestData were acquired
 through long-term field observations as part of the Ecosystem Management
 Emulating Natural Disturbance (EMEND) project (http://emendproject.org).
 Data are provided in the sheets designated as “Compt-CoverType,”
 “Compt-Treatments” and “Bry-data,” and column headings are defined in the
 “Description” sheet of the excel workbook.Bartels et al. 2017-for Dryad
 Depository.xlsx
DOI: 10.5061/dryad.2g9p0
title: Data from: Time-series analysis reveals genetic responses to intensive management of razorback sucker (Xyrauchen texanus)

description: Time-series analysis is used widely in ecology to study complex phenomena,
 and may have considerable potential to clarify relationships of genetic
 and demographic processes in natural and exploited populations. We
 explored the utility of this approach to evaluate population responses to
 management in razorback sucker, a long-lived and fecund, but declining
 freshwater fish species. A core population in Lake Mohave (Arizona-Nevada,
 USA) has experienced no natural recruitment for decades, and is maintained
 by harvesting naturally produced larvae from the lake, rearing them in
 protective custody, and repatriating them at sizes less vulnerable to
 predation. Analyses of mtDNA and 15 microsatellites characterized for
 sequential larval cohorts collected over a 15-year time series revealed no
 changes in geographic structuring, but indicated significant increase in
 mtDNA diversity for the entire population over time. Likewise, ratios of
 annual effective breeders to annual census size (Nb/Na) increased
 significantly despite seven-fold reduction of Na. These results indicated
 that conservation actions diminished near-term extinction risk due to
 genetic factors, and should now focus on increasing numbers of fish in
 Lake Mohave to ameliorate longer-term risks. More generally, time series
 analysis permitted robust testing of trends in genetic diversity, despite
 low precision of some metrics.
description: mtDNA haplotype
 sequencesDNA sequences of each of
 the haplotypes identified in this study. This file, in conjunction with
 the haplotypes, can be used to estimate population genetic
 parameters.razorback sucker haplotype
 sequences.csvIndividual mtDNA
 haplotypesFor each individual, the
 first column provides field id number (including location and date),
 second column provides lab id (sorted by year), and the third column
 identifies the haplotype.mtDNA data 1 oct
 13.csvIndividual
 microsatellite genotypesThe first line provides
 the header, sample ID and locus name. Each locus is named twice, once for
 each allele. The following lines provides the genotypes for each
 individual.microsat data 1 oct
 13.csv
DOI: 10.5061/dryad.0520f
title: Data from: Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis

description: The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird
 with a disjunct Holarctic range. Taxonomic divisions within the Northern
 Fulmar have historically been muddled by geographical variation notably
 including highly polymorphic plumage. Recent molecular analyses (i.e., DNA
 barcoding) have suggested that genetic divergence between Atlantic and
 Pacific populations could be on par with those typically observed between
 species. We employ a multigene phylogenetic analysis to better explore the
 level of genetic divergence between these populations and to test an old
 hypothesis on the origin of the modern distribution of color morphs across
 their range. Additionally, we test whether mutations in the melanocortin-1
 receptor gene (MC1R) are associated with dark plumage in the Northern
 Fulmar. We confirmed that mitochondrial lineages in the Atlantic and
 Pacific populations are highly divergent, but nuclear markers revealed
 incomplete lineage sorting. Genetic divergence between these populations
 is consistent with that observed between many species of Procellariiformes
 and we recommend elevating these two forms to separate species. We also
 find that MC1R variation is not associated with color morph but rather is
 better explained by geographical divergence.
description: Fulmarini_PhasedNuclearHaplotypesMultiple sequence alignment of melanocortin-1 receptor (MC1R) and myoglobin intron II (MYOII) DNA sequences from Fulmarus glacialis and closely allied species. Sequences were phased either: i) in silico using the program PHASE version 2.1, or ii) via cloning using the TOPO TA Cloning kit (Invitrogen). The file is in NEXUS format.
DOI: 10.5061/dryad.gk1s2
title: Data from: A small-bodied species of Brontotheriidae from the middle Eocene Nut Beds of the Clarno Formation, John Day Basin, Oregon

description: We diagnose a new species of Brontotheriidae from a middle Eocene
 locality, the Clarno Nut Beds, from the Clarno Formation, John Day Basin,
 Central Oregon. Though renowned for its richness in fossil flora, fossil
 vertebrates are rare in the Clarno Nut Beds and this new species is the
 most abundantly represented mammal. Radiometric dating constrains the age
 of the Nut Beds fauna to about 43.76 Ma within the Uintan North American
 Land Mammal Age. This new taxon, represented by numerous cranial,
 mandibular, and dental specimens, is comparatively small for a brontothere
 and notable for its cranio-caudally shorted nasal incision, a trait shared
 with three larger-bodied middle Eocene species, Metatelmatherium ultimum,
 Wickia brevirhinus, and Sthenodectes incisivum. Phylogenetic analysis
 suggests the sister taxon of the Nut Beds brontothere could be one of two
 species—Wickia brevirhinus from the Sand Wash Basin of Colorado and
 Washakie Formation of Wyoming, or Metatelmatherium ultimum, a
 pan-Beringian species known from the Uintan Formation of Utah (and other
 Uintan age deposits) and the “Irdin Manha” Formation of Inner Mongolia,
 China. Phylogenetic results also indicate that the Nut Beds brontothere is
 a dwarf taxon. Though brontotheres are renowned for having evolved very
 large body sizes, this new brontothere is one of several discovered in
 recent decades that suggest evolutionary reductions in body size may have
 been relatively common in Brontotheriidae.
description: Xylotitan cenosus size
 dataMeasurements of fossil
 elements of Xylotitan cenosusSupplemental Data
 1.xlsxBrontotheriidae
 phylogenetic dataPhylogenetic character
 matrix for BrontotheriidaeSupplemental data
 2.xlsxBrontotheriidae
 charactersCharacter states and
 descriptions for Brontotheriidae phylogenetic dataSupplemental data
 3.doc
DOI: 10.5061/dryad.j21v2
title: Data from: Demographic consequences of greater clonal than sexual reproduction in Dicentra canadensis

description: Clonality is a widespread life history trait in flowering plants that may
 be essential for population persistence, especially in environments where
 sexual reproduction is unpredictable. Frequent clonal reproduction,
 however, could hinder sexual reproduction by spatially aggregating ramets
 that compete with seedlings and reduce inter-genet pollination.
 Nevertheless, the role of clonality in relation to variable sexual
 reproduction in population dynamics is often overlooked. We combined
 population matrix models and pollination experiments to compare the
 demographic contributions of clonal and sexual reproduction in three
 Dicentra canadensis populations, one in a well-forested landscape and two
 in isolated forest remnants. We constructed stage-based transition
 matrices from 3 years of census data to evaluate annual population growth
 rates, λ. We used loop analysis to evaluate the relative contribution of
 different reproductive pathways to λ. Despite strong temporal and spatial
 variation in seed set, populations generally showed stable growth rates.
 Although we detected some pollen limitation of seed set, manipulative
 pollination treatments did not affect population growth rates. Clonal
 reproduction contributed significantly more than sexual reproduction to
 population growth in the forest remnants. Only at the well-forested site
 did sexual reproduction contribute as much as clonal reproduction to
 population growth. Flowering plants were more likely to transition to a
 smaller size class with reduced reproductive potential in the following
 year than similarly sized nonflowering plants, suggesting energy
 trade-offs between sexual and clonal reproduction at the individual level.
 Seed production had negligible effects on growth and tuber production of
 individual plants. Our results demonstrate that clonal reproduction is
 vital for population persistence in a system where sexual reproduction is
 unpredictable. The bias toward clonality may be driven by low fitness
 returns for resource investment in sexual reproduction at the individual
 level. However, chronic failure in sexual reproduction may exacerbate the
 imbalance between sexual and clonal reproduction and eventually lead to
 irreversible loss of sex in the population.
description: Seed and tuber
 production of Dicentra canadensisDemographic census data
 collected for three Dicentra canadensis populations in Ohio during 2008 -
 2011. Data were recorded in late spring, at the end of the species'
 growing season each year. This data file includes: life stages of
 individual plants at census time, number of seeds and clonal propagules
 (secondary tubers) produced per plant, and mass of primary tubers, as a
 measure of size of individual plants. Data for manipulative pollination
 experiments (supplemental pollination and pollinator exclusion) are also
 included.Tuber and seed
 data.xlsx
DOI: 10.5281/zenodo.18381727
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Joseph Dalton Hooker, http://www.wikidata.org/entity/Q157501. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q157501