scholarly journals Ancient divergence time estimates inEutropis rugiferasupport the existence of Pleistocene barriers on the exposed Sunda Shelf

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3762 ◽  
Author(s):  
Benjamin R. Karin ◽  
Indraneil Das ◽  
Todd R. Jackman ◽  
Aaron M. Bauer
Keyword(s):  
Sea Level ◽  
Divergence Time ◽  
Peninsular Malaysia ◽  
Middle Pleistocene ◽  
Divergence Times ◽  
Sea Level Changes ◽  
Sunda Shelf ◽  
Sea Levels ◽  
Island Populations ◽  
Divergence Time Estimates

Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf.Eutropis rugiferais a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1,BRCA2,RAG1, andMC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations ofE. rugiferaoccurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find thatE. rugiferashows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence withinE. rugiferaseparates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the PleistoceneE. rugiferastill faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes.

Sundaland's subsidence requires revisiting its biogeography

2020 ◽  
Author(s):  
Laurent Husson ◽  
Florian Boucher ◽  
Anta-Clarisse Sarr ◽  
Pierre Sepulchre ◽  
Sri Yudawati Cahyarini
Keyword(s):  
Sea Level ◽  
Divergence Time ◽  
Fold Increase ◽  
Biodiversity Hotspot ◽  
Marine Isotope Stage ◽  
Malay Peninsula ◽  
Sea Level Changes ◽  
Sunda Shelf ◽  
Late Pliocene ◽  
Sea Level Variations

<div> <div> <div> <p>It is widely accepted that sea level changes intermittently inun- dated the Sunda Shelf throughout the Pleistocene, separating Java, Sumatra and Borneo from the Malay Peninsula and from each other. On this basis, the dynamics of the biodiversity hotspot of Sundaland is consistently regarded as solely contingent on glacial sea level os- cillations, with interglacial highstands creating intermittent dispersal barriers between disjunct landmasses. However, recent findings on the geomorphology of the currently submerged Sunda shelf sug- gest that it subsided during the Pleistocene and that, over the Late Pliocene and Quaternary, is was never submerged prior to Marine Isotope Stage 11 (MIS 11, 400 ka). This would have enabled the dispersal of terrestrial organisms regardless of sea level variations until 400 ka and hampered movements thereafter, at least during interglacial periods. Existing phylogeographic data for terrestrial organisms conform to this scenario: available divergence time esti- mates reveal an 8‐ to 9‐fold increase in the rate of vicariance be- tween landmasses of Sundaland after 400 ka, corresponding to the onset of episodic flooding of the Sunda shelf. These results highlight how reconsidering the paleogeographic setting of Sundaland chal- lenges understanding the mechanisms generating Southeast Asian biodiversity.</p> </div> </div> </div>

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i884-i894
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

scholarly journals SEA LEVEL CHANGES ALONG THE COASTS OF KEA ISLAND AND PALEOGEOGRAPHICAL COASTAL RECONSTRUCTION OF ARCHAEOLOGICAL SITES

2017 ◽  
Vol 43 (1) ◽  
pp. 453 ◽  
Author(s):  
N.D Mourtzas
Keyword(s):  
Sea Level ◽  
Human Activity ◽  
Human Activities ◽  
Archaeological Sites ◽  
Classical Period ◽  
Sea Level Changes ◽  
Coastal Morphology ◽  
Sea Levels

Sea level changes during the Upper Holocene submerged the coasts of Kea in three different phases about 5.50m, 3.90m and 1.50m respectively below the contemporary sea level thus causing sea transgression along the shores of Kea, which varied from 8m to 78m depending on the coastal morphology. These changes caused the alteration of the earlier morphology at coastal archaeological sites of the Island, as the prehistoric settlement of Ayia Irini and Classical period port of Karthaia, as well as, submerged under the sea areas of coastal human activity during antiquity, as the ancient schist quarry at Spathi bay. The study of historical, geomorphological and sedimentological data indicative of previous sea levels allow the paleogeographical reconstruction of the coasts during the period of human activities in these areas.

scholarly journals Reliable confidence intervals for RelTime estimates of evolutionary divergence times

2019 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

AbstractConfidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

scholarly journals Atmospheric circulation changes and their impact on extreme sea levels around Australia

2019 ◽  
Vol 19 (5) ◽  
pp. 1067-1086 ◽  
Author(s):  
Frank Colberg ◽  
Kathleen L. McInnes ◽  
Julian O'Grady ◽  
Ron Hoeke
Keyword(s):  
Sea Level ◽  
Large Scale ◽  
Climate Models ◽  
Tide Gauge ◽  
Austral Summer ◽  
Sea Level Changes ◽  
Sea Level Variability ◽  
Sea Levels ◽  
Extreme Sea Levels ◽  
Coastal Sea

Abstract. Projections of sea level rise (SLR) will lead to increasing coastal impacts during extreme sea level events globally; however, there is significant uncertainty around short-term coastal sea level variability and the attendant frequency and severity of extreme sea level events. In this study, we investigate drivers of coastal sea level variability (including extremes) around Australia by means of historical conditions as well as future changes under a high greenhouse gas emissions scenario (RCP 8.5). To do this, a multi-decade hindcast simulation is validated against tide gauge data. The role of tide–surge interaction is assessed and found to have negligible effects on storm surge characteristic heights over most of the coastline. For future projections, 20-year-long simulations are carried out over the time periods 1981–1999 and 2081–2099 using atmospheric forcing from four CMIP5 climate models. Changes in extreme sea levels are apparent, but there are large inter-model differences. On the southern mainland coast all models simulated a southward movement of the subtropical ridge which led to a small reduction in sea level extremes in the hydrodynamic simulations. Sea level changes over the Gulf of Carpentaria in the north are largest and positive during austral summer in two out of the four models. In these models, changes to the northwest monsoon appear to be the cause of the sea level response. These simulations highlight a sensitivity of this semi-enclosed gulf to changes in large-scale dynamics in this region and indicate that further assessment of the potential changes to the northwest monsoon in a larger multi-model ensemble should be investigated, together with the northwest monsoon's effect on extreme sea levels.

scholarly journals Relative sea-level changes in crete: reassessment of radiocarbon dates from Sphakia and west Crete

2002 ◽  
Vol 97 ◽  
pp. 171-200 ◽  
Author(s):  
Simon Price ◽  
Tom Higham ◽  
Lucia Nixon ◽  
Jennifer Moody
Keyword(s):  
Sea Level ◽  
Late Antiquity ◽  
Isotopic Fractionation ◽  
Sea Level Changes ◽  
Relative Sea Level ◽  
Radiocarbon Dates ◽  
Sea Levels ◽  
Catastrophic Earthquake ◽  
Radiocarbon Data ◽  
Calendar Dates

This article is concerned with the recognition and dating of Holocene relative sea-level changes along the coast of west Crete (an island located in the active Hellenic subduction arc of the southern Aegean) and in particular in Sphakia. Radiocarbon data for changes in sea levels collected and analysed previously must (a) be recorrected to take into account isotopic fractionation, and (b) recalibrated by using the new marine reservoir value. These new radiocarbon dates are analysed using Bayesian statistics. The resulting calendar dates for changes in sea level are younger than previously assumed. In particular the Great Uplift in western Crete in late antiquity must be dated to the fifth or sixth century AD, not to AD 365. Moreover, recent work on tectonics suggests that the Great Uplift need not have been accompanied by a catastrophic earthquake. Finally, we consider the consequences of the Great Uplift for some coastal sites in Sphakia.

Venice lagoon salt marsh vulnerability and halophytic vegetation vertical migration in response to sea level rise

2020 ◽  
Author(s):  
Zhicheng Yang ◽  
Sonia Silvestri ◽  
Marco Marani ◽  
Andrea D’Alpaos
Keyword(s):  
Salt Marsh ◽  
Sea Level Rise ◽  
Sea Level ◽  
Salt Marshes ◽  
Current Knowledge ◽  
Venice Lagoon ◽  
Sea Level Changes ◽  
Human Pressure ◽  
Sea Levels ◽  
Vegetation Species

<p>Salt marshes are biogeomorphic systems that provide important ecosystem services such as carbon sequestration and prevention of coastal erosion. These ecosystems are, however, threatened by increasing sea levels and human pressure. Improving current knowledge of salt-marsh response to changes in the environmental forcing is a key step to understand and predict salt-marsh evolution, especially under accelerated sea level rise scenarios and increasing human pressure. Towards this goal, we have analyzed field observations of marsh topographic changes and halophytic vegetation distribution with elevation collected over 20 years (between 2000 and 2019) in a representative marsh in the Venice lagoon (Italy).</p><p>Our results suggest that: 1) on average, marsh elevation with respect to local mean sea level decreased , (i.e. the surface accretion rate was lower than the rate of sea level rise); 2) elevational frequency distributions are characteristic for different halophytic vegetation species, highlighting different ecological realized niches that change in time; 3) although the preferential elevations at which different species have changed in time, the sequence of vegetation species with increasing soil elevation was preserved and simply shifted upward; 4) we observed different vegetation migration rates for the different species, suggesting that the migration process is species-specific. In particular, vegetation species colonizing marsh edges (Juncus and Inula) migrated faster facing to changes in sea levels than Limonium and Spartina , while Sarcocornia was characterized by delayed migration in response to sea level changes. These results bear significant implications for long-term biogeomorphic evolution of tidal environments.</p>

The sedimentary record of climatic variation in the southern North Sea

1988 ◽  
Vol 318 (1191) ◽  
pp. 523-537 ◽  
Keyword(s):  
Sea Level ◽  
North Sea ◽  
Climatic Changes ◽  
Sea Level Changes ◽  
Offshore Area ◽  
Sea Levels ◽  
Indirect Response ◽  
Southern North Sea ◽  
Sedimentary Sequences ◽  
Glaciofluvial Deposits

The sedimentary sequence on the shelf of the southern North Sea records Quaternary climatic changes in two ways. They are indicated directly by moraine and glaciofluvial deposits from the Elsterian, Saalian and Weichselian glacial periods when the British and the Scandinavian ice sheets covered parts of the area. An indirect response to the climate is indicated by sea-level changes. Phases of cooling are characterized by regressions and low sea-level stands; phases of warming are indicated by marine transgressions and high sea levels during the Holsteinian, Eemian and Holocene periods. The seismic characteristics of the different lithological units, the sedimentary sequences and their fossil content are described for the offshore area and the adjacent coastal zone. This provides a record of the interaction of sedimentary processes and the palaeogeographic development as a response to climatic changes.

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