cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.1594/pangaea.984095
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 1, no artificial wind (wind level 0), and turbulence or cooling not induced

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.1594/pangaea.984129
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 2, no artificial wind (wind level 0), cooling unit set to 23 °C (same as the starting water temperature), and pumps turned on

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.1594/pangaea.984130
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 3, strong wind applied (wind level 3), but no wind applied during the first and last 30 min of the dataset and no turbulence or cooling induced

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.1594/pangaea.984136
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 4, strong wind applied (wind level 3), but no wind applied during the first and last 30 min of the dataset, cooling unit set to 17°C and pumps turned on

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.5061/dryad.p8cz8w9nk
title: Patterns of speciation are similar across mountainous and lowland regions for a Neotropical plant radiation (Costaceae: Costus)

description: High species richness and endemism in tropical mountains are recognized as
 major contributors to the latitudinal diversity gradient. The processes
 underlying mountain speciation, however, are largely untested. The
 prevalence of steep ecogeographic gradients and the geographic isolation
 of populations by topographic features are predicted to promote speciation
 in mountains. We evaluate these processes in a species-rich Neotropical
 genus of understory herbs that range from the lowlands to montane forests
 and have higher species richness in topographically complex regions. We
 ask whether climatic niche divergence, geographic isolation, and
 pollination shifts differ between mountain-influenced and lowland
 Amazonian sister pairs inferred from a 756-gene phylogeny. Neotropical
 Costus ancestors diverged in Central America during a period of mountain
 formation in the last 3 My with later colonization of Amazonia. Although
 climatic divergence, geographic isolation, and pollination shifts are
 prevalent in general, these factors don’t differ between
 mountain-influenced and Amazonian sister pairs. Despite higher climatic
 niche and species diversity in the mountains, speciation modes in Costus
 appear similar across regions. Thus, greater species richness in tropical
 mountains may reflect differences in colonization history, diversification
 rates, or the prevalence of rapidly evolving plant life forms, rather than
 differences in speciation mode.
description: The repository is organized in three main folders comprising the
 three main set of analyses presented in the paper.
 Folders are organized sequentially according to the order they
 appear in the manuscript, with titles indicating the specific analysis
 associated with the file contents. Inside each one of
 the folders you will find the code used for every component of the
 pipeline and the main inputs and outputs.
description: Code in the repository have the following suffixes:
 
 .sh = to be executed in
 bash .r .R = to be executed in R
 .py = to be executed in python
 2 Fasta and
 tree files have additive inserts in the name to indicate their
 processing: 
 .mafft = aligned with MAFFT
 .norr = outgroups removed and tree is
 rooted in ingroup .oc = columns with less than 95%
 occupancy were removed from the alignment 
 .pr
 = tree pruned to match
 climatic data occupancy .rd = alignment/tree reduced to
 monophyletic taxa .rr = tree was re-rooted
 .spur = outliers individual sequences
 were removed with TrimAl .trim = sections for the alignment were
 trimmed with TrimAl 
 s.ts = extreme long branches and/or taxa
 with long branches flagged by TreeShrink exclude
DOI: 10.1594/pangaea.984137
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 5, alternating wind speeds (off, medium, strong) applied at 30- or 60-min intervals (wind levels 0, 2, 3) and no turbulence or cooling induced

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.1594/pangaea.984138
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 6, alternating wind speeds (off, medium, strong) applied at 30- or 60-min intervals (wind levels 0, 2, 3), cooling unit turned off, and pumps turned on

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.1594/pangaea.984139
title: Measurements of sea surface temperatures and salinity in a large seawater basin - Experiment 7, alternating wind speeds (off, low, medium) applied at 30- or 60-min intervals (wind levels 0, 1, 2), cooling unit turned off, and pumps turned on

description: We provide experimental data from a mesocosm study in a seawater basin (L: 8.5 m x W: 2.0 m x H: 0.8 m). Changes in sea surface temperature and salinity were investigated under different wind speeds, solar radiation levels, and turbulence conditions. Seven experiments were performed at the Sea sURface Facility (SURF; Institute of Chemistry and Biology of the Marine Environment; 53.5148 °N, 8.1463 °E) in late summer 2024. Each experiment generally lasted for 22h, running from 22:00 UTC to 20:00 UTC the following day. Four different wind conditions were applied: no wind (level 0), low wind (level 1), medium wind (level 2), and strong wind (level 3). The basin was equipped with a cooling unit, which was used to differentiate between two levels of turbulence: on (flow generated by pumps) and off (no flow). Water temperature control with a hysteresis of 1 °C was applied in some of the experiments. Various parameters were measured during the experiments. High-resolution temperature sensors captured temperatures at multiple depths at a specific location and distributed measurements across the basin. Conductivity, temperature, and depth (CTD) sensors recorded the temperature and conductivity at various depths, enabling the calculation of absolute salinity using the thermodynamic equation of seawater 2010 (TEOS-10). Further measurements included air temperature and humidity at multiple positions over the basin, wind speed, wave height, incoming and reflected shortwave radiation, downward and upward longwave irradiance, and evaporation. To quantify turbulence, acoustic doppler velocimeters (ADV) were positioned at two depths (13 cm and 37 cm) to measure the three-dimensional velocity components. These data were used to calculate turbulent kinetic energy (TKE) in 15-minute intervals. The dataset offers valuable insights into small-scale variations in sea surface temperature and salinity under changing heat flux conditions, focusing on latent and shortwave heat fluxes to enhance our understanding of their counteracting effects.
DOI: 10.5061/dryad.vt4b8gtq9
title: Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

description: Native cattle breeds can carry specific signatures of selection reflecting
 their adaptation to the local environmental conditions and response to the
 breeding strategy used. In this study, we comprehensively analysed
 high-density single nucleotide polymorphism (SNP) genotypes to
 characterise the population structure and detect the selection signatures
 in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have
 been little influenced by introgression with transboundary breeds.
 Fifty-six samples of pedigree-recorded purebred animals, originating from
 different breeding farms and representing different sire lines, of the two
 studied breeds were genotyped using a genome-wide bovine genotyping array
 (Bovine HD BeadChip). Three statistical analyses—calculation of fixation
 index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK
 analysis, and estimation of the runs of homozygosity (ROH) islands shared
 in more than 50% of animals—were combined for detecting the selection
 signatures in the genome of the studied cattle breeds. We confirmed nine
 and six known regions under putative selection in the genomes of Yaroslavl
 and Kholmogor cattle, respectively; the flanking positions of most of
 these regions were elucidated. Only two of the selected regions (localised
 on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in
 Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three
 novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp,
 BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor
 breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18
 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We
 expanded the list of candidate genes associated with the selected genomic
 regions and performed their functional annotation. We discussed the
 possible involvement of the identified candidate genes in artificial
 selection in connection with the origin and development of the breeds. Our
 findings on the Yaroslavl and Kholmogor breeds obtained using high-density
 SNP genotyping and three different statistical methods allowed the
 detection of novel putative genomic regions and candidate genes that might
 be under selection. These results might be useful for the sustainable
 development and conservation of these two oldest Russian native cattle
 breeds.
description: The Illumina Bovine HD BeadChip (Illumina, San Diego, CA, USA)
 was used for genotyping. Valid genotypes for each SNP were determined by
 setting the cut-off of 0.5 for the GenCall (GC) and GenTrain (GT) scores.
 PLINK 1.9 software was used to perform SNP quality control.
DOI: 10.5061/dryad.4b8gthtb4
title: The Long Lives of Primates and the 'Invariant Rate of Ageing' Hypothesis

description: Is it possible to slow the rate of ageing, or do biological constraints
 limit its plasticity? We test the ‘invariant rate of ageing’ hypothesis,
 which posits that the rate of ageing is relatively fixed within species,
 with a collection of 39 human and nonhuman primate datasets across seven
 genera. We first recapitulate, in nonhuman primates, the highly regular
 relationship between life expectancy and lifespan equality seen in humans.
 We next demonstrate that variation in the rate of ageing within genera is
 orders of magnitude smaller than variation in pre-adult and
 age-independent mortality. Finally, we demonstrate that changes in the
 rate of ageing, but not other mortality parameters, produce striking,
 species-atypical changes in mortality patterns. Our results support the
 invariant rate of ageing hypothesis, implying biological constraints on
 how much the human rate of ageing can be slowed.
description: We assembled a dataset on age-specific mortality rates in
 multiple populations of several different primate genera. Our combined
 dataset includes data from both wild and captive primate populations. The
 data from wild populations consist of individual-based birth and death
 data on males and females from 17 continuous long-term studies of wild
 primate populations representing 6 genera distributed across the order
 Primates, and include Old World monkeys (2 genera), New World monkeys (1
 genus), great apes (2 genera, both African), and an indriid (1 genus,
 endemic to Madagascar). We also included data from 13 species in zoos
 using the Species360’s Zoological Information Management System (ZIMS),
 and from nine human datasets from populations that had not benefited from
 modern advances in public health, medicine and standards of living, which
 allowed us to carry out the most salient comparisons with nonhuman
 primates. We compared age-specific changes in the risk of death across
 multiple populations of each genus, and calculated Siler mortality
 parameters for each population. 
description: We recommend that the user begins with the 'Metadata'
 tab in the excel sheet for a description of the data file.