DOI: 10.5061/dryad.8cz8w9gq2
title: Genetic imprints of Brosimum alicastrum (Moraceae) in Mexico

description: PREMISE: Mechanisms generating the geographical distributions of genetic
 diversity are a central matter in evolutionary biology. The amount of
 genetic diversity and its distribution are controlled by several factors,
 including dispersal abilities, physical barriers and environmental and
 climatic changes. We investigated the patterns of genetic diversity and
 differentiation among populations of the widespread species Brosimum
 alicastrum in Mexico. METHODS: Using nuclear DNA microsatellite data, we
 determined the current state of genetic diversity and its distribution to
 determine if the genetic structure was consistent with geographical
 settings of Mexico and to infer the role of past events in the genetic
 diversity patterns. RESULTS: Our results suggested that Mexican B.
 alicastrum is well differentiated into three main lineages. Patterns of
 the genetic structure at a finer scale did not entirely correspond with
 the present-day geographic barriers to gene flow. CONCLUSIONS: We propose
 that differentiation patterns might reflect: 1) an ancient differentiation
 that occurred in Central America and South America; 2) the effects of past
 climatic changes, and 3) the action of some physical barriers to gene
 flow. This study provides insights into the possible mechanisms underlying
 the geographic genetic variation of B. alicastrum along a moisture
 gradient in tropical lowland forests.
description: We collected foliar tissue from 328 adult trees from 33
 populations of <i>Brosimum alicastrum</i> Sw. (Moraceae)
 sampled in tropical and subtropical evergreen and deciduous forests across
 its distribution in Mexico. Genomic DNA was extracted from ~100 mg of leaf
 tissue following the CTAB protocol for plants as described by Doyle and
 Doyle (1987). We amplified 15 nuclear microsatellite loci (Bro5, Bro7,
 Bro9, Bro10, Bro11, Bro12, Bro13, Bro14, Bro15, Bro16, Bro17, Bro18,
 Bro20, Bro24, and Bro28), and PCRs were performed individually in a total
 volume of 5 μL containing 3 μL of 2x QIAGEN Multiplex PCR Master Mix
 (QIAGEN, Maryland, United States), 0.5 μL of each primer (10 mM), and 1 μL
 of template DNA (20 ng/μL). Thermal cycling conditions consisted of an
 initial denaturation step of 95 °C for 15 minutes, 35 cycles of 95 °C for
 15 seconds, an annealing temperature for 30 seconds, 72 °C for 1 min and a
 final extension step at 72 °C for 10 min. Multiplex PCR products were
 combined with a GeneScan-500 LIZ Size Standard (Applied Biosystems,
 California, United States) and DNA analysis was performed on an ABI-PRISM
 3100 Avant sequencer (Applied Biosystems, California, United States).
 Fragment sizes were recorded using the Peak Scanner program 1.0 (Thermo
 Fisher Scientific, Waltham, Massachusetts, United States).
 Once the sizes of the fragments have been obtained, to infer the
 presence of null alleles, we employed two approaches: FreeNA (Chapuis and
 Estoup, 2007) and Microchecker version 2.2.3 (Van Oosterhout et al.,
 2004). For FreeNA, we used 103 replicates with 95% confidence intervals
 (CIs), while for Microchecker, we used 103 bootstrap simulations and 95%
 CIs. Scoring errors caused by large allele dropout or stuttering in the
 microsatellite data were assessed using Microchecker with the same
 parameters. Deviations from Hardy-Weinberg equilibrium (HWE) were
 evaluated for each population across all loci and locus by locus across
 all populations. We also tested for nonrandom associations between alleles
 of different loci. For both analyses, we used Genepop on web version 4.7
 (Raymond and Rousset, 1995; Rousset, 2008) with 104 dememorization steps,
 103 batches, and 104 iterations per batch. For HWE, we applied a
 Bonferroni correction with the standard procedure (Miller, 1980; Lessios,
 1992) using a critical value of 0.05. With the revised
 database we proceeded to carry out the corresponding analyzes.
description: The database includes the columns: 1) Name of
 population. (A)<br> 2) Abbreviation of the name of the population.
 (B)<br> 3) Individuals by population. (C)<br> 4) Values of the
 alleles for each individual for each locus. (D-AG)
 Missing data are indicated by zero.