Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites.

ABSTRACT: We show using the most complete phylogeny of one of the most species-rich orders of vertebrates (Gobiiformes), and calibrations from the rich fossil record of teleost fishes, that the genus Typhleotris, endemic to subterranean karst habitats in southwestern Madagascar, is the sister group to Milyeringa, endemic to similar subterranean systems in northwestern Australia. Both groups are eyeless, and our phylogenetic and biogeographic results show that these obligate cave fishes now found on opposite ends of the Indian Ocean (separated by nearly 7,000 km) are each others closest relatives and owe their origins to the break up of the southern supercontinent, Gondwana, at the end of the Cretaceous period. Trans-oceanic sister-group relationships are otherwise unknown between blind, cave-adapted vertebrates and our results provide an extraordinary case of Gondwanan vicariance.

SUBMITTER: Chakrabarty P

PROVIDER: S-EPMC3429432 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The first record of a trans-oceanic sister-group relationship between obligate vertebrate troglobites.

Chakrabarty Prosanta P Davis Matthew P MP Sparks John S JS

PloS one 20120828 8

We show using the most complete phylogeny of one of the most species-rich orders of vertebrates (Gobiiformes), and calibrations from the rich fossil record of teleost fishes, that the genus Typhleotris, endemic to subterranean karst habitats in southwestern Madagascar, is the sister group to Milyeringa, endemic to similar subterranean systems in northwestern Australia. Both groups are eyeless, and our phylogenetic and biogeographic results show that these obligate cave fishes now found on opposi ...[more]

PMID: 22937155

Similar Datasets

Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate.

Project description:The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.

| S-EPMC6571479 | biostudies-literature

A first record of obligate halophilic aspergilli from the dead sea.

Project description:The isolation of obligate halophilic aspergilli from the Dead Sea and the range of salt tolerance of halophilic fungi isolated, are reported here for the first time. The mycobiota of the Dead Sea isolated in this study, was dominated by Aspergillus and Penicillium species; Cladosporium were found in lesser numbers. All three genera were obtained from the water sample; however, Aspergillus was the only genus obtained from the sediment. There was significant difference in growth of each isolate at different salt concentrations and intraspecies analysis revealed dissimilarity in response of strains to different salt concentrations in the growth medium The isolates were euryhaline, with halotolerance up to 20-25% solar salt, Aspergillus and Penicillium species showing a higher level of halotolerance, as compared to that of Cladosporium. Halophilic fungi were found in greater numbers in the sediment sample as compared to that in the water sample. Penicillium and Cladosporium species were exclusively facultative halophiles, while some species of Aspergillus were facultative halophiles. All the obligate halophiles isolated, belonged to the genus Aspergillus and were identified as A. penicillioides and A unguis, the latter being a first record of the species from the Dead Sea.

| S-EPMC3298590 | biostudies-literature

Juvenile Osprey Navigation during Trans-Oceanic Migration.

Project description:To compensate for drift, an animal migrating through air or sea must be able to navigate. Although some species of bird, fish, insect, mammal, and reptile are capable of drift compensation, our understanding of the spatial reference frame, and associated coordinate space, in which these navigational behaviors occur remains limited. Using high resolution satellite-monitored GPS track data, we show that juvenile ospreys (Pandion haliaetus) are capable of non-stop constant course movements over open ocean spanning distances in excess of 1500 km despite the perturbing effects of winds and the lack of obvious landmarks. These results are best explained by extreme navigational precision in an exogenous spatio-temporal reference frame, such as positional orientation relative to Earth's magnetic field and pacing relative to an exogenous mechanism of keeping time. Given the age (<1 year-old) of these birds and knowledge of their hatching site locations, we were able to transform Enhanced Magnetic Model coordinate locations such that the origin of the magnetic coordinate space corresponded with each bird's nest. Our analyses show that trans-oceanic juvenile osprey movements are consistent with bicoordinate positional orientation in transformed magnetic coordinate or geographic space. Through integration of movement and meteorological data, we propose a new theoretical framework, chord and clock navigation, capable of explaining the precise spatial orientation and temporal pacing performed by juvenile ospreys during their long-distance migrations over open ocean.

| S-EPMC4262435 | biostudies-literature

On the Relationship Between Oceanic Plate Speed, Tectonic Stress, and Seismic Anisotropy.

Project description:Seismic radial anisotropy (the squared ratio between the speeds of horizontally and vertically polarized shear waves, ξ=VSH2VSV2 ) is a powerful tool to probe the direction of mantle flow and accumulated strain. While previous studies have confirmed the dependence of azimuthal anisotropy on plate speed, the first order control on radial anisotropy is unclear. In this study, we develop 2D ridge flow models combined with mantle fabric calculations to report that faster plates generate higher tectonics stresses and strain rates which lower the dislocation creep viscosity and lead to deeper anisotropy than beneath slower plates. We apply the SGLOBE-rani tomographic filter, resulting in a flat depth-age trend and stronger anisotropy beneath faster plates, which correlates well with 3D global anisotropic mantle models. Our predictions and observations suggest that as plate speed increases from 2 to 8 cm/yr, radial anisotropy increases by ∼0.01-0.025 in the upper 100-200 km of the mantle between 10 and 60 Ma.

| S-EPMC9539886 | biostudies-literature

Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae).

Project description:The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.

| S-EPMC7613184 | biostudies-literature

Influence of anthropogenic aerosol deposition on the relationship between oceanic productivity and warming.

Project description:Satellite data and models suggest that oceanic productivity is reduced in response to less nutrient supply under warming. In contrast, anthropogenic aerosols provide nutrients and exert a fertilizing effect, but its contribution to evolution of oceanic productivity is unknown. We simulate the response of oceanic biogeochemistry to anthropogenic aerosols deposition under varying climate from 1850 to 2010. We find a positive response of observed chlorophyll to deposition of anthropogenic aerosols. Our results suggest that anthropogenic aerosols reduce the sensitivity of oceanic productivity to warming from -15.2 ± 1.8 to -13.3 ± 1.6 Pg C yr-1 °C-1 in global stratified oceans during 1948-2007. The reducing percentage over the North Atlantic, North Pacific, and Indian Oceans reaches 40, 24, and 25%, respectively. We hypothesize that inevitable reduction of aerosol emissions in response to higher air quality standards in the future might accelerate the decline of oceanic productivity per unit warming.

| S-EPMC5102162 | biostudies-literature

Genetic affinities between trans-oceanic populations of non-buoyant macroalgae in the high latitudes of the Southern Hemisphere.

Project description:Marine biologists and biogeographers have long been puzzled by apparently non-dispersive coastal taxa that nonetheless have extensive transoceanic distributions. We here carried out a broad-scale phylogeographic study to test whether two widespread Southern Hemisphere species of non-buoyant littoral macroalgae are capable of long-distance dispersal. Samples were collected from along the coasts of southern Chile, New Zealand and several subAntarctic islands, with the focus on high latitude populations in the path of the Antarctic Circumpolar Current or West Wind Drift. We targeted two widespread littoral macroalgal species: the brown alga Adenocystisutricularis (Ectocarpales, Heterokontophyta) and the red alga Bostrychiaintricata (Ceramiales, Rhodophyta). Phylogenetic analyses were performed using partial mitochondrial (COI), chloroplast (rbcL) and ribosomal nuclear (LSU / 28S) DNA sequence data. Numerous deeply-divergent clades were resolved across all markers in each of the target species, but close phylogenetic relationships - even shared haplotypes - were observed among some populations separated by large oceanic distances. Despite not being particularly buoyant, both Adenocystisutricularis and Bostrychiaintricata thus show genetic signatures of recent dispersal across vast oceanic distances, presumably by attachment to floating substrata such as wood or buoyant macroalgae.

| S-EPMC3718832 | biostudies-literature

[Relationship Between ABO Blood Group and Pregnancy Complications].

Project description:ABO blood group system is the most commonly used blood group classification system in clinic practice. The relevant antigens, A, B and H determinants, are complex carbohydrate molecules that are expressed in red blood cells and other cell lines and tissues. These antigens are determined by the ABO locus located on chromosome 9 (9q34.1-q34.2). ABO blood group is associated with the development of many human diseases, e.g., cardiovascular diseases, infectious diseases, and tumors. The relationship between the ABO blood group of pregnant women and various pregnancy complications, including preeclampsia (PE) and the related diseases, pregnancy associated venous thromboembolism (PA-VTE), gestational diabetes mellitus (GDM), and postpartum hemorrhage (PPH), have become the focus of obstetricians' recent research interest. Herein, we reviewed the relationship between ABO blood group and these pregnancy complications, and found that most of the reported findings supported the following views: 1) Blood type O is a protective factor for PE, while blood type AB increases the risk of PE; 2) blood types other than O are more prone to PA-VTE than blood type O; 3) blood type O or blood type AB may be related to the pathogenesis of GDM; 4) women of blood type O are at higher risks for PPH than those of other blood types. More in-depth epidemiological and genetic studies are needed to confirm these findings in the future. These findings can provide new ideas for researching into the pathogenesis of obstetric diseases and form the theoretical basis for obstetricians to prevent and treat related diseases.

| S-EPMC10408793 | biostudies-literature

Cis-regulatory basis of sister cell type divergence in the vertebrate retina.

Project description:Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify the key cis-regulatory features that distinguish them. By comparing open chromatin maps and transcriptomic profiles, we found that while photoreceptor and bipolar cells have divergent transcriptomes, they share remarkably similar cis-regulatory grammars, marked by enrichment of K50 homeodomain binding sites. However, cell class-specific enhancers are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. We show that converting K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific cis-regulatory elements was a critical step in the evolutionary divergence of the bipolar transcriptome from that of photoreceptors.

| S-EPMC6802965 | biostudies-literature

Ancient divergence in the trans-oceanic deep-sea shark Centroscymnus crepidater.

Project description:Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements.

| S-EPMC3493524 | 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