Genetic consequences of human driven habitat fragmentation on endangered Atacama Desert shrub Balsamocarpon brevifolium Clos.

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Title:Main Title: Genetic consequences of human driven habitat fragmentation on endangered Atacama Desert shrub Balsamocarpon brevifolium Clos.
Description:Abstract: Balsamocarpon brevifolium CLOS (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. STRUCTURE 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.
Identifier:10.1016/j.gloplacha.2019.103059 (DOI)
Citation Advice:Stoll A, Harpke D, Schütte C, Jimenez L, Letelier L, Blattner F, Quandt D. Genetic consequences of human driven habitat fragmentation on endangered Atacama Desert shrub Balsamocarpon brevifolium Clos. Global and Planetary Change 184: 103059
Responsible Party
Creators:Alexandra Stoll (Author), Doerte Harpke (Author), Claudia Schütte (Author), Lissette Jimenez (Author), Luis Letelier (Author), Frank R Blattner (Author), Dietmar Quandt (Author)
Funding References:Deutsche Forschungsgemeinschaft (DFG): CRC 1211: Earth - Evolution at the Dry Limit
Fondo Nacional de Desarrollo Científico y Tecnológico: 1131089: Regular grant
Publication Year:2021
CRC1211 Topic:Biology
Related Subproject:B1
Subjects:Keywords: Biodiversity, Biogeography, Ecology of Plants, Population Genetics
Geogr. Information Topic:Biota
File Details
Data Type:Text - Article
File Size:2.4 MB
Date:Available: 25.10.2019
Mime Type:application/pdf
Data Format:PDF
Download Permission:Only Project Members
General Access and Use Conditions:According to the CRC1211DB data policy agreement.
Access Limitations:According to the CRC1211DB data policy agreement.
Specific Information - Publication
Publication Status:Published
Review Status:Peer reviewed
Publication Type:Article
Article Type:Journal
Source:Global and Planetary Change
Source Website:
Number of Pages:10 (1 - 10)
Metadata Details
Metadata Creator:Dietmar Quandt
Metadata Created:27.01.2021
Metadata Last Updated:27.01.2021
Funding Phase:1
Metadata Language:English
Metadata Version:V50
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