DOI: 10.5061/dryad.w3r2280pr
title: Prosopis laevigata microsatellite and sequence alignment data

description: Patterns of genetic and phylogeographic structure and recent population
 history of plant species in the Mexican arid zones has been scarcely
 investigated. Prosopis laevigata is the most widely spread species of
 mesquite in Mexico, with extensive populations in the arid and semi-arid
 zones of the central and northern plateaus and scattered presence in
 southern Mexico. We evaluated the genetic and phylogeographic structure of
 this species to infer its recent demographic history. We genotyped six
 nuclear microsatellite loci and sequenced the psbA3´-trnH chloroplast DNA
 (cpDNA) region in individuals from 21 populations covering the whole
 distribution of the species. Nuclear genetic diversity was moderately high
 (HE=0.527) and genetic differentiation was moderate (FST=0.16). A positive
 correlation between genetic diversity and latitude was observed. The cpDNA
 analyses indicated a lack of phylogeographic structure in P. laevigata
 (GST=0.090, NST=0.101; P=0.497). Historical demography statistics
 indicated a population expansion supported by a skyline plot analysis, the
 star-like shape of the haplotype network, and the unimodal shape of the
 mismatch distribution. Ecological niche modeling suggested a contracted
 distribution into west-central Mexico during the Last Interglacial (~140
 Ka), followed by an expansion in both northwards and southwards directions
 in the Last Glacial Maximum (~22 Ka), which continued in the mid-Holocene
 (~6 Ka) and the present. Results are congruent with a recent population
 growth and colonization of newly opened arid zones by P. laevigata
 populations. This pattern is consistent with the high capacity of
 colonization of nutrient-poor areas, high germination rates and resistance
 to drought reported for Prosopis species
description: We collected fresh leaves
 of 224 individuals from 21 populations of <i>P. laevigata</i>
 covering the whole distribution of the speciesGenomic DNA was extracted
 using a modified CTAB protocol (Otero-Arnaiz et al. 2005). We amplified
 six polymorphic microsatellite loci (Mo05, Mo07, Mo08, Mo09, Mo13 and
 Mo016) originally designed <i>Prosopis chilensis </i>(Molina)
 Stuntz and <i>Prosopis flexuosa </i>DC<i>.
 </i>(Mottura et al. 2005).The PCR reactions were carried out using
 Platinum Master Mix (Thermo Fisher Scientific). A final volume of 10 µL
 was used, including 5 µL of Platinum Master Mix, 0.5 µL of each primer (10
 mM), 2.8 µL of distilled water, 0.2 µL of MgCl<sub>2</sub> (2
 mM) and 1 µL of DNA (20 ng/µL). The amplification program was carried out
 as follows: five min at 94°C as initial step, followed by 35 cycles with a
 denaturalization step at 94°C for 90 s, annealing at 49°C (Mo09), and 59°C
 (Mo05, Mo07, Mo08, Mo13 and Mo016) for 90 s, extension at 72°C for 90 s
 and a final step at 72° for 10 min. The forward primer of each pair was
 fluorescently labeled. The PCR products were mixed with formamide and Gen
 Scan Liz-600 as size standard (Applied Biosystems). The samples were
 denaturalized at 95°C for two minutes and then analyzed using an ABI-PRISM
 3100-Avant (Applied Biosystems) sequencer. The fragments obtained were
 sized and scored using the PeakScanner software (Applied
 Biosystems). For the
 phylogeographic analysis, we initially tested seven universal chloroplast
 DNA (cpDNA) microsatellite loci (Weising and Gardner 1999), and the cpDNA
 intergenic region trnS-trnT, without finding any variation in these
 markers. Finally, we tested the psbA3’-trnH region (Shaw et al. 2007),
 which showed polymorphism. The amplification of this region was carried
 out in reactions with a final volume of 25 µL, including 12.5 µL of Master
 Mix (Promega, Woods Hollow Road Madison, WI, USA), 0.8 µL of forward and
 reverse primer (10 µM), 6 µL of distilled water, 1.5 µL of Bovine Serum
 Albumin (BSA), 1 µL of MgCl<sub>2</sub> (2 mM) and 2.4 µL of
 DNA (20 ng/µL). The amplification protocol was carried out as follows:
 five min at 94°C as initial step, followed by 35 cycles with a
 denaturalization step at 94°C for 90 s, an annealing step at 72°C for 90
 s, an extension step at 72°C for 90 s, and a final step at 72°C for 10
 min. The PCR products were purified using the Qiaquick kit (QIAGEN,
 Valencia, CA, USA), following the manufacturer’s instructions. Between
 three and nine individuals per population were analyzed The purified
 products were sent to MACROGEN USA for sequencing. The sequences reported
 in the present study are available from the GenBank database (accession numbers
 MK618446-MK618463).
description: Missing data : -9 (Microsatellite Data)