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Prosopis laevigata microsatellite and sequence alignment data

Citation

González-Rodríguez, Antonio; Contreras-Negrete, Gonzalo; Letelier, Luis; Piña-Torres, Javier (2021), Prosopis laevigata microsatellite and sequence alignment data, Dryad, Dataset, https://doi.org/10.5061/dryad.w3r2280pr

Abstract

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

Methods

We collected fresh leaves of 224 individuals from 21 populations of P. laevigata 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 Prosopis chilensis (Molina) Stuntz and Prosopis flexuosa DC. (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 MgCl2 (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 MgCl2 (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).

Usage Notes

Missing data : -9 (Microsatellite Data)

Funding

Universidad Nacional Autónoma de México, Award: Antonio González-Rodríguez (PO)