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      Phylogeographic Structure in Benthic Marine Invertebrates of the Southeast Pacific Coast of Chile with Differing Dispersal Potential

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          Abstract

          The role of dispersal potential on phylogeographic structure, evidenced by the degree of genetic structure and the presence of coincident genetic and biogeographic breaks, was evaluated in a macrogeographic comparative approach along the north-central coast of Chile, across the biogeographic transition zone at 30°S. Using 2,217 partial sequences of the mitochondrial Cytochrome Oxidase I gene of eight benthic invertebrate species along ca. 2,600 km of coast, we contrasted dispersal potential with genetic structure and determined the concordance between genetic divergence between biogeographic regions and the biogeographic transition zone at 30°S. Genetic diversity and differentiation highly differed between species with high and low dispersal potential. Dispersal potential, sometimes together with biogeographic region, was the factor that best explained the genetic structure of the eight species. The three low dispersal species, and one species assigned to the high dispersal category, had a phylogeographic discontinuity coincident with the biogeographic transition zone at 30°S. Furthermore, coalescent analyses based on the isolation-with-migration model validate that the split between biogeographic regions north and south of 30°S has a historic origin. The signatures of the historic break in high dispersers is parsimoniously explained by the homogenizing effects of gene flow that have erased the genetic signatures, if ever existed, in high dispersers. Of the four species with structure across the break, only two had significant albeit very low levels of asymmetric migration across the transition zone. Historic processes have led to the current biogeographic and phylogeographic structure of marine species with limited dispersal along the north-central coast of Chile, with a strong lasting impact in their genetic structure.

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          Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.

          Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
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            Ecological roulette: the global transport of nonindigenous marine organisms.

            Ocean-going ships carry, as ballast, seawater that is taken on in port and released at subsequent ports of call. Plankton samples from Japanese ballast water released in Oregon contained 367 taxa. Most taxa with a planktonic phase in their life cycle were found in ballast water, as were all major marine habitat and trophic groups. Transport of entire coastal planktonic assemblages across oceanic barriers to similar habitats renders bays, estuaries, and inland waters among the most threatened ecosystems in the world. Presence of taxonomically difficult or inconspicuous taxa in these samples suggests that ballast water invasions are already pervasive.
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              Time-dependent rates of molecular evolution.

              For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events. © 2011 Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                19 February 2014
                : 9
                : 2
                : e88613
                Affiliations
                [1 ]Laboratorio de Diversidad Molecular, Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte & Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
                [2 ]Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
                [3 ]Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
                [4 ]Centro de Conservación Marina, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
                Technical University of Denmark, Denmark
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: PH EP SF. Performed the experiments: NIS NCM FEG A Martínez A Meynard MCP-G. Analyzed the data: NIS NCM FEG A Martínez A Meynard MCP-G. Contributed reagents/materials/analysis tools: PH EP SF. Wrote the paper: PH SF NIS.

                Article
                PONE-D-12-04040
                10.1371/journal.pone.0088613
                3929388
                24586356
                b68b7326-4a44-403f-a41f-c82a55b67621
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 6 February 2012
                : 15 January 2014
                Page count
                Pages: 15
                Funding
                This research was mainly funded by the Chilean National Fund of Science and Technology FONDECYT (grant Fondecyt 1090670 to PH and SF). Partial funding was provided by Iniciativa Científica Mileno (ICM P05-002 and PFB-23 to A. Martínez and EP; ICM P10-033F to A. Meynard and SF) and INCAR (grant FONDAP 15110027 to PH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Computational biology
                Population genetics
                Gene flow
                Ecology
                Ecological environments
                Marine environments
                Biogeography
                Marine ecology
                Evolutionary biology
                Evolutionary systematics
                Phylogenetics
                Evolutionary genetics
                Marine biology
                Marine monitoring

                Uncategorized
                Uncategorized

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