cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3860586
title: Supplementary Material S4 from Evolution of bacterial recombinase A (<i>recA</i>) in eukaryotes explained by addition of genomic data of key microbial lineages

description: Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, eubacteria, archaea and eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic <i>recA</i> genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the <i>recA</i> genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by <i>Dictyostelium</i>. We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial <i>recA</i> homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.
DOI: 10.7910/dvn/v1rjpf/awpczc
title: snk20170407_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860586.v1
title: Supplementary Material S4 from Evolution of bacterial recombinase A (<i>recA</i>) in eukaryotes explained by addition of genomic data of key microbial lineages

description: Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, eubacteria, archaea and eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic <i>recA</i> genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria–eukaryote) and/or secondary (eukaryote–eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the <i>recA</i> genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by <i>Dictyostelium</i>. We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial <i>recA</i> homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.
DOI: 10.7910/dvn/v1rjpf/2qahg3
title: snk20170105_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gqr0is
title: snk20170829_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860577
title: Supplementary Table 6 from Strong influence of palaeoclimate on the structure of modern African mammal communities

description: Ecological research often assumes that species are adapted to their current climatic environments. However, climate fluctuations over geologic time scales have influenced species dispersal and extinction, which in turn may affect community structure. Modern community structure is likely to be the product of both palaeoclimate and modern climate, with the relative degrees of influence of past and present climates unknown. Here, we assessed the influence of climate at different time periods on the phylogenetic and functional trait structure of 203 African mammal communities. We found that the climate of the mid-Holocene (approx. 6,000 years ago) and Last Glacial Maximum (approx. 22 000 years ago) were frequently better predictors of community structure than modern climate for mammals overall, carnivorans and ungulates. Primate communities were more strongly influenced by modern climate than palaeoclimate. Overall, community structure of African mammals appears to be related to the ecological flexibility of the groups considered here and the regions of continental Africa that they occupy. Our results indicate that the future redistribution, expansion and contraction of particular biomes due to human activity, such as climate and land-use change, will differentially affect mammal groups that vary in their sensitivity to environmental change.
DOI: 10.7910/dvn/v1rjpf/hqjaj9
title: snk20171011_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860574
title: Supplementary Data 2. Raw experimental foot pressure data for all African elephants from Foot pressure distributions during walking in African elephants (<i>Loxodonta africana</i>)

description: Elephants, the largest living land mammals, have evolved a specialized foot morphology to help reduce locomotor pressures while supporting their large body mass. Peak pressures that could cause tissue damage are mitigated passively by the anatomy of elephants' feet, yet this mechanism does not seem to work well for some captive animals. This study tests how foot pressures vary among African and Asian elephants from habitats where natural substrates predominate but where foot care protocols differ. Variations in pressure patterns might be related to differences in husbandry, including but not limited to trimming and the substrates that elephants typically stand and move on. Both species' samples exhibited the highest concentration of peak pressures on the lateral digits of their feet (which tend to develop more disease in elephants) and lower pressures around the heel. The trajectories of the foot's centre of pressure were also similar, confirming that when walking at similar speeds, both species load their feet laterally at impact and then shift their weight medially throughout the step until toe-off. Overall, we found evidence of variations in foot pressure patterns that might be attributable to husbandry and other causes, deserving further examination using broader, more comparable samples.
DOI: 10.6084/m9.figshare.3860577.v1
title: Supplementary Table 6 from Strong influence of palaeoclimate on the structure of modern African mammal communities

description: Ecological research often assumes that species are adapted to their current climatic environments. However, climate fluctuations over geologic time scales have influenced species dispersal and extinction, which in turn may affect community structure. Modern community structure is likely to be the product of both palaeoclimate and modern climate, with the relative degrees of influence of past and present climates unknown. Here, we assessed the influence of climate at different time periods on the phylogenetic and functional trait structure of 203 African mammal communities. We found that the climate of the mid-Holocene (approx. 6,000 years ago) and Last Glacial Maximum (approx. 22 000 years ago) were frequently better predictors of community structure than modern climate for mammals overall, carnivorans and ungulates. Primate communities were more strongly influenced by modern climate than palaeoclimate. Overall, community structure of African mammals appears to be related to the ecological flexibility of the groups considered here and the regions of continental Africa that they occupy. Our results indicate that the future redistribution, expansion and contraction of particular biomes due to human activity, such as climate and land-use change, will differentially affect mammal groups that vary in their sensitivity to environmental change.
DOI: 10.7910/dvn/v1rjpf/qsgnaj
title: snk20170902_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/idnew2
title: snk20170412_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860562
title: Model results for 'all mammals' from Strong influence of palaeoclimate on the structure of modern African mammal communities

description: Linear model results and sum of AICc weights for 'all mammals' communities
DOI: 10.6084/m9.figshare.3860562.v1
title: Model results for 'all mammals' from Strong influence of palaeoclimate on the structure of modern African mammal communities

description: Linear model results and sum of AICc weights for 'all mammals' communities
DOI: 10.7910/dvn/v1rjpf/otpqui
title: snk20171121_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/qxtrvy
title: snk20171226_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/ugrzsx
title: snk20171110_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860553
title: Community and climate data from Strong influence of palaeoclimate on the structure of modern African mammal communities

description: Community species lists and climate data for African mammal communities
DOI: 10.7910/dvn/v1rjpf/nuz0og
title: snk20170315_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860553.v1
title: Community and climate data from Strong influence of palaeoclimate on the structure of modern African mammal communities

description: Community species lists and climate data for African mammal communities
DOI: 10.7910/dvn/v1rjpf/xqtynw
title: snk20170610_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kccke8
title: snk20170917_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xuxaix
title: snk20171101_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/xjhfwm
title: snk20170325_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860532
title: Treefile 2. Maximum-Likelihood Phylogeny (nexus format) estimated from complete mitochondrial dataset. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

description: Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene.
DOI: 10.6084/m9.figshare.3860532.v1
title: Treefile 2. Maximum-Likelihood Phylogeny (nexus format) estimated from complete mitochondrial dataset. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

description: Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene.
DOI: 10.7910/dvn/v1rjpf/lvw67r
title: snk20170925_03.txt.gz

description: :unav
DOI: 10.23721/1519321
title: Infusion pump Control via OpenICE FROA App - Normal and Non-Normal State Data (2020-06-24 to 2020-06-24)
DOI: 10.7910/dvn/v1rjpf/jletkb
title: snk20171230_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/eqhleu
title: snk20170903_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860520
title: Treefile 1. Chronogram (nexus format) estimated using nuclear data alignment, with two partitions, Yule prior and uncorrelated lognormal model implemented in BEAST v. 1.8. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

description: Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene.
DOI: 10.6084/m9.figshare.3860523
title: Data file from Coping with a changing environment: the effects of early life stress

description: Ongoing rapid domestication of Atlantic salmon implies that individuals are subjected to evolutionarily novel stressors encountered under conditions of artificial rearing, requiring new levels and directions of flexibility in physiological and behavioural coping mechanisms. Phenotypic plasticity to environmental changes is particularly evident at early life stages. We investigated the performance of salmon, previously subjected to an unpredictable chronic stress (UCS) treatment at an early age (10 month old parr), over several months and life stages. The UCS fish showed an overall higher specific growth rates compared with unstressed controls after smoltification, a particularly challenging life stage, and after seawater transfer. Furthermore, subjecting fish to acute stress at the end of the experiment, we found that UCS groups had an overall lower hypothalamic catecholaminergic and brain stem serotonergic response to stress compared with control groups. In addition, serotonergic activity was negatively correlated with final growth rates, which implies that serotonin responsive individuals have growth disadvantages. Altogether, our results may imply that a subdued monoaminergic response in stressful farming environments may be beneficial, because in such situations individuals may be able to reallocate energy from stress responses into other life processes, such as growth.
DOI: 10.7910/dvn/v1rjpf/3jafrp
title: snk20170314_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860523.v1
title: Data file from Coping with a changing environment: the effects of early life stress

description: Ongoing rapid domestication of Atlantic salmon implies that individuals are subjected to evolutionarily novel stressors encountered under conditions of artificial rearing, requiring new levels and directions of flexibility in physiological and behavioural coping mechanisms. Phenotypic plasticity to environmental changes is particularly evident at early life stages. We investigated the performance of salmon, previously subjected to an unpredictable chronic stress (UCS) treatment at an early age (10 month old parr), over several months and life stages. The UCS fish showed an overall higher specific growth rates compared with unstressed controls after smoltification, a particularly challenging life stage, and after seawater transfer. Furthermore, subjecting fish to acute stress at the end of the experiment, we found that UCS groups had an overall lower hypothalamic catecholaminergic and brain stem serotonergic response to stress compared with control groups. In addition, serotonergic activity was negatively correlated with final growth rates, which implies that serotonin responsive individuals have growth disadvantages. Altogether, our results may imply that a subdued monoaminergic response in stressful farming environments may be beneficial, because in such situations individuals may be able to reallocate energy from stress responses into other life processes, such as growth.
DOI: 10.7910/dvn/v1rjpf/iwdvs9
title: snk20170920_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860520.v2
title: Treefile 1. Chronogram (nexus format) estimated using nuclear data alignment, with two partitions, Yule prior and uncorrelated lognormal model implemented in BEAST v. 1.8. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

description: Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene.
DOI: 10.6084/m9.figshare.3860520.v1
title: Treefile 1. Chronogram (nexus format) estimated using nuclear data alignment, with two partitions, Yule prior and uncorrelated lognormal model implemented in BEAST v. 1.8. from Young relicts and old relicts: a novel palaeoendemic vertebrate from The Australian Central Uplands

description: Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the Mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here, we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus <i>Oedura</i> from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected <i>Oedura cincta</i> has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the Early Pliocene. A new taxon (described herein) diverged from all extant <i>Oedura</i> much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including <i>Oedura cincta</i>), geneflow with other parts of Australia probably occurred until at least the very Late Miocene or Pliocene. There are however a small number of palaeoendemic taxa—often ecologically specialized forms—that show evidence of having persisted since earlier intensification of aridity in the Late Miocene.
DOI: 10.7910/dvn/v1rjpf/vileji
title: snk20170321_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gfot3i
title: snk20171008_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7pvkia
title: snk20170717_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jlibud
title: snk20171025_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/huxcah
title: snk20171027_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/n2gf52
title: snk20170330_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/wtzme7
title: snk20171013_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860475
title: R code from Estimating shifts in diversification rates based on higher-level phylogenies

description: .ZIP file with R code to perform our simulation study
DOI: 10.7910/dvn/v1rjpf/hlpra3
title: snk20170309_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3860475.v1
title: R code from Estimating shifts in diversification rates based on higher-level phylogenies

description: .ZIP file with R code to perform our simulation study
DOI: 10.7910/dvn/v1rjpf/xftcaq
title: snk20170316_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/elgb0i
title: snk20170926_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/0uskoe
title: snk20170213_03.txt.gz

description: :unav