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Genetic Patterns of Myrceugenia correifolia, a Rare Species of Fog-Dependent Forests of Mediterranean Chile: Is It a Climatic Relict?

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      Abstract

      Rare species frequently occur in areas with microclimatic conditions that are atypical for their regions, but that were more common in the past, and that probably have operated as climatic refugia for a long time. Myrceugenia correifolia is a rare arboreal species that grows in deep canyons and hilltops of the Coast Range of north-central Chile between 30° and 35°S. In the northern edge of its distribution M. correifolia grows in small patches of fog-dependent forest surrounding by xeric vegetation. These forest formations are thought to be remnants of an ancient and continuous rainforest that according to some authors became fragmented during aridization of the Neogene (Neogene relict) and to others during warm-dry cycles of the Pleistocene (glacial relicts). Here we asked whether the northernmost populations of M. correifolia are Neogene relicts, glacial relicts, or the result of a recent northward colonization. To answer this question we examined genetic diversity and population divergence of M. correifolia using microsatellite markers, tested various competing population history scenarios with an approximate Bayesian computation (ABC) method, and complemented these data with ecological niche modeling (ENM). We detected three genetic clusters with a distinctive latitudinal pattern (north, center, and south) and high levels of differentiation (FST = 0.36). Demographic inference supported an admixture event 31 kya between two populations that diverged from an ancient population 139 kya. The admixture time coincides with the beginning of a period of wet conditions in north-central Chile that extended from 33 to 19 kya and was preceded by dry and cold conditions. These results suggest that increased precipitation during glacial periods triggered northward expansion of the range of M. correifolia, with subsequent admixture between populations that remained separated during interglacial periods. Accordingly, ENM models showed that suitable habitats for M. correifolia in north-central Chile were larger and less fragmented during the Last Glacial Maximum than at present, suggesting that northernmost populations of this species are glacial relicts.

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      Inference of population structure using multilocus genotype data.

      We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci-e.g. , seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/ approximately pritch/home. html.
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        Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

        The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the software STRUCTURE allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated 'log probability of data' does not provide a correct estimation of the number of clusters, K. However, using an ad hoc statistic DeltaK based on the rate of change in the log probability of data between successive K values, we found that STRUCTURE accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.
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          Very high resolution interpolated climate surfaces for global land areas

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            Author and article information

            Affiliations
            1Departamento de Ecología, Pontificia Universidad Católica de Chile Santiago, Chile
            2Institute of Ecology and Biodiversity Santiago, Chile
            3Departamento de Ciencias Ecológicas, Universidad de Chile Santiago, Chile
            Author notes

            Edited by: Federico Luebert, University of Bonn, Germany

            Reviewed by: Cristian Torres, University of the Bío Bío, Chile; José Murillo, National University of Colombia at Bogotá, Colombia

            *Correspondence: Fernanda Pérez, mperezt@ 123456bio.puc.cl

            This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science

            Contributors
            Journal
            Front Plant Sci
            Front Plant Sci
            Front. Plant Sci.
            Frontiers in Plant Science
            Frontiers Media S.A.
            1664-462X
            06 July 2017
            2017
            : 8
            5498513
            10.3389/fpls.2017.01097
            Copyright © 2017 Pérez, Hinojosa, Peralta, Montenegro, Irarrázabal and Cossio.

            This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

            Counts
            Figures: 5, Tables: 1, Equations: 0, References: 64, Pages: 9, Words: 0
            Funding
            Funded by: Fondo Nacional de Desarrollo Científico y Tecnológico 10.13039/501100002850
            Award ID: 1141049
            Categories
            Plant Science
            Original Research

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