Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial sampling heterogeneity limits the detectability of deep time latitudinal biodiversity gradients.

ABSTRACT: The latitudinal biodiversity gradient (LBG), in which species richness decreases from tropical to polar regions, is a pervasive pattern of the modern biosphere. Although the distribution of fossil occurrences suggests this pattern has varied through deep time, the recognition of palaeobiogeographic patterns is hampered by geological and anthropogenic biases. In particular, spatial sampling heterogeneity has the capacity to impact upon the reconstruction of deep time LBGs. Here we use a simulation framework to test the detectability of three different types of LBG (flat, unimodal and bimodal) over the last 300 Myr. We show that heterogeneity in spatial sampling significantly impacts upon the detectability of genuine LBGs, with known biodiversity patterns regularly obscured after applying the spatial sampling window of fossil collections. Sampling-standardization aids the reconstruction of relative biodiversity gradients, but cannot account for artefactual absences introduced by geological and anthropogenic biases. Therefore, we argue that some previous studies might have failed to recover the 'true' LBG type owing to incomplete and heterogeneous sampling, particularly between 200 and 20 Ma. Furthermore, these issues also have the potential to bias global estimates of past biodiversity, as well as inhibit the recognition of extinction and radiation events.

SUBMITTER: Jones LA

PROVIDER: S-EPMC7934898 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Population divergence in plant species reflects latitudinal biodiversity gradients.

Project description:The trend for increasing biodiversity from the poles to the tropics is one of the best-known patterns in nature. This latitudinal biodiversity gradient has primarily been documented so far with extant species as the measure of biodiversity. Here, we evaluate the global pattern in biodiversity across latitudes based on the magnitude of genetic population divergence within plant species, using a robust spatial design to compare published allozyme datasets. Like the pattern of plant species richness across latitudes, we expected the divergence among populations of current plant species would have a similar pattern and direction. We found that lower latitudinal populations showed greater genetic differentiation within species after controlling for geographical distance. Our analyses are consistent with previous population-level studies in animals, suggesting a high possibility of tropical peaks in speciation rates associated with observed levels of species richness.

| S-EPMC2610133 | biostudies-literature

Sampling plant diversity and rarity at landscape scales: importance of sampling time in species detectability.

Project description:Documenting and estimating species richness at regional or landscape scales has been a major emphasis for conservation efforts, as well as for the development and testing of evolutionary and ecological theory. Rarely, however, are sampling efforts assessed on how they affect detection and estimates of species richness and rarity. In this study, vascular plant richness was sampled in 356 quarter hectare time-unlimited survey plots in the boreal region of northeast Alberta. These surveys consisted of 15,856 observations of 499 vascular plant species (97 considered to be regionally rare) collected by 12 observers over a 2 year period. Average survey time for each quarter-hectare plot was 82 minutes, ranging from 20 to 194 minutes, with a positive relationship between total survey time and total plant richness. When survey time was limited to a 20-minute search, as in other Alberta biodiversity methods, 61 species were missed. Extending the survey time to 60 minutes, reduced the number of missed species to 20, while a 90-minute cut-off time resulted in the loss of 8 species. When surveys were separated by habitat type, 60 minutes of search effort sampled nearly 90% of total observed richness for all habitats. Relative to rare species, time-unlimited surveys had ? 65% higher rare plant detections post-20 minutes than during the first 20 minutes of the survey. Although exhaustive sampling was attempted, observer bias was noted among observers when a subsample of plots was re-surveyed by different observers. Our findings suggest that sampling time, combined with sample size and observer effects, should be considered in landscape-scale plant biodiversity surveys.

| S-EPMC3989307 | biostudies-literature

Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons

Project description:Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability. Here, we considered a well-defined, canonical neuronal population â hippocampal CA1 pyramidal cells â and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits. Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population

2016-01-05 | E-GEOD-67403 | biostudies-arrayexpress

Molecular evolution and the latitudinal biodiversity gradient.

Project description:Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

| S-EPMC3656639 | biostudies-other

Contrarian clade confirms the ubiquity of spatial origination patterns in the production of latitudinal diversity gradients.

Project description:The latitudinal diversity gradient (LDG), wherein the number of species and higher taxa peaks in the tropics and decreases toward the poles, is the best-documented large-scale diversity pattern on Earth, but hypotheses explaining the standard LDG must also account for rare "contrarian" taxa that show diversity maxima outside of the tropics. For marine bivalves, one of the few groups that provide spatially explicit temporal data on a global scale, we show that a major contrarian group, the Anomalodesmata, unexpectedly exhibits the same large-scale dynamics as related clades having normal LDGs in two key respects. First, maxima in standing genus diversity and genus origination rates coincide spatially. Second, the strength of a clade's present-day LDG is significantly related to the proportion of its living genera that originated in the tropics during the late Cenozoic, with the contrarian gradient strength at both species and genus level predicted quantitatively by the values for the other clades. Geologic age distributions indicate that the anomalous LDG results from origination that is damped in the tropics rather than heightened in the temperate zones. The pervasive role of spatial origination patterns in shaping LDGs, regardless of the position of their diversity maxima, corroborates hypotheses based on clades showing standard gradients and underscores the insights that contrarian groups can provide into general principles of diversity dynamics.

| S-EPMC2084308 | biostudies-literature

Seafloor heterogeneity influences the biodiversity-ecosystem functioning relationships in the deep sea.

Project description:Theoretical ecology predicts that heterogeneous habitats allow more species to co-exist in a given area. In the deep sea, biodiversity is positively linked with ecosystem functioning, suggesting that deep-seabed heterogeneity could influence ecosystem functions and the relationships between biodiversity and ecosystem functioning (BEF). To shed light on the BEF relationships in a heterogeneous deep seabed, we investigated variations in meiofaunal biodiversity, biomass and ecosystem efficiency within and among different seabed morphologies (e.g., furrows, erosional troughs, sediment waves and other depositional structures, landslide scars and deposits) in a narrow geo-morphologically articulated sector of the Adriatic Sea. We show that distinct seafloor morphologies are characterized by highly diverse nematode assemblages, whereas areas sharing similar seabed morphologies host similar nematode assemblages. BEF relationships are consistently positive across the entire region, but different seabed morphologies are characterised by different slope coefficients of the relationship. Our results suggest that seafloor heterogeneity, allowing diversified assemblages across different habitats, increases diversity and influence ecosystem processes at the regional scale, and BEF relationships at smaller spatial scales. We conclude that high-resolution seabed mapping and a detailed analysis of the species distribution at the habitat scale are crucial for improving management of goods and services delivered by deep-sea ecosystems.

| S-EPMC4876447 | biostudies-other

Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons

Project description:Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability. Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits.

2016-01-05 | GSE67403 | GEO

Latitudinal diversity gradients in Mesozoic non-marine turtles.

Project description:The latitudinal biodiversity gradient (LBG)-the pattern of increasing taxonomic richness with decreasing latitude-is prevalent in the structure of the modern biota. However, some freshwater taxa show peak richness at mid-latitudes; for example, extant Testudines (turtles, terrapins and tortoises) exhibit their greatest diversity at 25° N, a pattern sometimes attributed to recent bursts of climatically mediated species diversification. Here, we test whether this pattern also characterizes the Mesozoic distribution of turtles, to determine whether it was established during either their initial diversification or as a more modern phenomenon. Using global occurrence data for non-marine testudinate genera, we find that subsampled richness peaks at palaeolatitudes of 15-30° N in the Jurassic, 30-45° N through the Cretaceous to the Campanian, and from 30° to 60° N in the Maastrichtian. The absence of a significant diversity peak in southern latitudes is consistent with results from climatic models and turtle niche modelling that demonstrate a dearth of suitable turtle habitat in Gondwana during the Jurassic and Late Cretaceous. Our analyses confirm that the modern testudinate LBG has a deep-time origin and further demonstrate that LBGs are not always expressed as a smooth, equator-to-pole distribution.

| S-EPMC5180147 | biostudies-literature

Deep-time paleogenomics and the limits of DNA survival.

Project description:Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.

| S-EPMC10586222 | biostudies-literature

Latitudinal gradients in degradation of marine dissolved organic carbon.

Project description:Heterotrophic microbial communities cycle nearly half of net primary productivity in the ocean, and play a particularly important role in transformations of dissolved organic carbon (DOC). The specific means by which these communities mediate the transformations of organic carbon are largely unknown, since the vast majority of marine bacteria have not been isolated in culture, and most measurements of DOC degradation rates have focused on uptake and metabolism of either bulk DOC or of simple model compounds (e.g. specific amino acids or sugars). Genomic investigations provide information about the potential capabilities of organisms and communities but not the extent to which such potential is expressed. We tested directly the capabilities of heterotrophic microbial communities in surface ocean waters at 32 stations spanning latitudes from 76°S to 79°N to hydrolyze a range of high molecular weight organic substrates and thereby initiate organic matter degradation. These data demonstrate the existence of a latitudinal gradient in the range of complex substrates available to heterotrophic microbial communities, paralleling the global gradient in bacterial species richness. As changing climate increasingly affects the marine environment, changes in the spectrum of substrates accessible by microbial communities may lead to shifts in the location and rate at which marine DOC is respired. Since the inventory of DOC in the ocean is comparable in magnitude to the atmospheric CO(2) reservoir, such a change could profoundly affect the global carbon cycle.

| S-EPMC3247214 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data