Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf Following the Last Glacial Maximum

The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting similar to 18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates

Expansion Dating: Calibrating Molecular Clocks in Marine Species from Expansions onto the Sunda Shelf following the Last Glacial Maximum

The rate of change in DNA is an important parameter for understanding molecular evolution, and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 million years, and are typically 0.5% - 2% per lineage per million years. Recently, calibrations made with ancient DNA from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. Ancient DNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ~18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3% - 6.6% per lineage per million years), lending additional support to the hypothesis of calibration time-dependency for molecular rates

Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential

The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (F(ST) = 0.07; P < 0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00227-010-1577-3) contains supplementary material, which is available to authorized users

Data Paper. Data Paper

<h2>File List</h2><div> <p><a href="MARSPEC_HighResFiles/bathymetry_30s.7z">bathymetry_30s.7z</a> (MD5: dd855211bbcdee7d6862414da23d6da2)</p> <p><a href="biogeo01_07_30s.7z">biogeo01_07_30s.7z</a> (MD5: 396525db0abd9de2ede3d8fdeb15e8ee)</p> <p><a href="biogeo08_17_30s.7z">biogeo08_17_30s.7z</a> (MD5: 96c2417eed84e85f9896536b934c53e1)</p> <p><a href="Monthly_Variables_30s.7z">Monthly_Variables_30s.7z</a> (MD5: 89016a8d17e8d8a1dddef0a121a83f5d)</p> <blockquote> <p>Additional high resolution raster files:</p> </blockquote> <p><a href="MARSPEC_HighResFiles/Sea_Ice_30s.7z">Sea_Ice_30s.7z</a> (MD5: 547d355294c530f63b9b0a73dedd2f3a)</p> <blockquote> <p>Low resolution MARSPEC data files:</p> </blockquote> <p><a href="MARSPEC_LowResFiles/MARSPEC_2o5m.7z">MARSPEC_2o5m.7z</a> (MD5: 923c97d185adb0c72f158a84e2981391)</p> <p><a href="MARSPEC_LowResFiles/MARSPEC_5m.7z">MARSPEC_5m.7z</a> (MD5: 95f7c3739c4f2889c2eff18afeffa489)</p> <p><a href="MARSPEC_LowResFiles/MARSPEC_10m.7z">MARSPEC_10m.7z</a> (MD5: d91f3127f46f7004d116f14328bf4b71)</p> </div><h2>Description</h2><div> <p>Ecological niche models are widely used in terrestrial studies to address critical ecological and evolutionary questions related to past and future climate change, local adaptation and speciation, the discovery of rare endemics, and biological invasions. However the application of niche models to similar questions in marine ecosystems has lagged behind, in part due to the lack of a centralized high-resolution spatial data set representing both benthic and pelagic marine environments. Here we describe the creation of MARSPEC, a high-resolution GIS database of ocean climate layers intended for marine ecological niche modeling and other applications in marine spatial ecology. MARSPEC combines information related to topographic complexity of the seafloor with bioclimatic measures of sea surface temperature and salinity for the world ocean. We derived seven geophysical variables from a high-resolution raster grid representing depth of the seafloor (bathymetry) to characterize six facets of topographic complexity (east-west and north-south components of aspect, slope, concavity of the seafloor, and plan and profile curvature) and distance from shore. We further derived 10 bioclimatic variables describing the annual mean, range, variance and extreme values for temperature and salinity from long-term monthly climatological means obtained from remotely sensed and in situ oceanographic observations. All variables were clipped to a common land mask, interpolated to a nominal 1-km (30 arc-second) grid, and converted to an ESRI raster grid file format compatible with popular GIS programs. MARSPEC is a 10-fold improvement in spatial resolution over the next-best data set (Bio-ORACLE) and is the only high-resolution global marine data set to combine variables from the benthic and pelagic environments into a single database. Additionally, we provide the monthly climatological layers used to derive the bioclimatic variables, allowing users to calculate equivalent MARSPEC variables from anomaly data for past and future climate scenarios. A detailed description of GIS processing steps required to calculate the MARSPEC variables can be found in the metadata. </p> <p> <i>Key words: climate change; ecological niche modeling; GIS; marine spatial ecology; ocean climate; salinity; sea surface temperature; species distribution modeling.</i> </p> </div

Regional differentiation and post-glacial expansion of the Atlantic silverside, Menidia menidia, an annual fish with high dispersal potential.

The coastal marine environment of the Northwest Atlantic contains strong environmental gradients that create distinct marine biogeographic provinces by limiting dispersal, recruitment, and survival. This region has also been subjected to numerous Pleistocene glacial cycles, resulting in repeated extirpations and recolonizations in northern populations of marine organisms. In this study, we examined patterns of genetic structure and historical demography in the Atlantic silverside, Menidia menidia, an annual marine fish with high dispersal potential but with well-documented patterns of clinal phenotypic adaptation along the environmental gradients of the Northwest Atlantic. Contrary to previous studies indicating genetic homogeneity that should preclude regional adaptation, results demonstrate subtle but significant (FST&nbsp;=&nbsp;0.07; P&nbsp;&lt;&nbsp;0.0001) genetic structure among three phylogeographic regions that partially correspond with biogeographic provinces, suggesting regional limits to gene flow. Tests for non-equilibrium population dynamics and latitudinal patterns in genetic diversity indicate northward population expansion from a single southern refugium following the last glacial maximum, suggesting that phylogeographic and phenotypic patterns have relatively recent origins. The recovery of phylogeographic structure and the partial correspondence of these regions to recognized biogeographic provinces suggest that the environmental gradients that shape biogeographic patterns in the Northwest Atlantic may also limit gene flow in M. menidia, creating phylogeographic structure and contributing to the creation of latitudinal phenotypic clines in this species