Landscape genetics of the endangered Atacama Desert shrub Balsamocarpon brevifolium in the context of habitat fragmentation

Abstract

Abstract Balsamocarpon brevifolium C los (Fabaceae), an endangered endemic shrub of the Chilean Atacama Desert, nowadays occurs in fragmented populations, which are exploit since at least 200 years. Understanding its genetic diversity, population structure and distribution patterns are essential for conservation planning and sustainable management. Based on Low-coverage shotgun sequencing (2 × 250 bp) of genomic DNA on the Illumina MiSeq platform we developed microsatellite (SSR) markers. In the nuclear genome we identified 6042 loci with potentially useful microsatellite motifs (83.1% di- and 13.1% tri-nucleotide repeats). Only 2% out of the initially tested 135 tri-nucleotide loci provided reliable amplicons. Back mapping of sequence reads to our initial assembly revealed that the high rate of unsuccessful amplifications was caused by erroneously assembled contigs and/or heterozygosity of the loci at the primer binding sites, highlighting the need of additional control steps such as back mapping especially when dealing with low genomic coverage sequencing. Fifteen markers were finally used to characterize the genetic diversity and variation in 18 populations across the species' natural distribution area. We found in total 183 alleles and inferred moderate genetic diversity from values of HO = 0.611 (STD = 0.018) and HE = 0.557 (STD = 0.015). Genetic variation was higher within populations (91%) than among them (9%). A low but significant correlation between geographical and genetic distances was detected among populations (Mantel test, R2 = 0.16; P = 0.01). Even though distribution barriers might exist due to fragmentation, we found moderate gene flow (Nm = 3.58), which might be explained be seed dispersal by native parrots. S tructure analysis suggests the existence of three genetic clusters, which are not completely distinct from each other. However, we found that habitat discontinuities in the case of B. brevifolium did not yet noticeably impact gene flow and genetic population structure. Taking into account the genetic structure and Ecological Niche prediction under future climate scenarios, in situ conservation efforts for B. brevifolium should focus on populations in the coastal mountains.