Skip to main content
Dryad logo

Scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu (Philippines) based on the fragment length size of their respective alleles

Citation

Obico, Jasper John et al. (2022), Scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu (Philippines) based on the fragment length size of their respective alleles, Dryad, Dataset, https://doi.org/10.5061/dryad.xpnvx0kd2

Abstract

Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

Methods

Leaf samples from a total of 17 sampling sites in Cebu, Philippines were obtained from 25–47 individuals for each of the four forest areas. Whole genomic DNA was extracted from silica-dried leaves. Extracted DNA of one individual was sent to Macrogen (South Korea) for Next Generation Sequencing (GS-FLX Titanium). Using MSATCOMMANDER 1.0.8-beta, the DNA sequence reads were screened for microsatellite loci of two to six nucleotides and M13-tagged primers were designed for them. A total of 13 microsatellite loci was amplified. Amplified products were analyzed using the ABI 3130xL Genetic Analyzer at the University of Canterbury in New Zealand. Geneious v.6.1.8 (Biomatters, Auckland, New Zealand) was used to determine fragment lengths (bp) of the amplified loci.

Usage Notes

Files include:

1. Readme_for_T_loheri_microsat.pdf

2. T_loheri_microsat.xlsx which contains scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu based on the fragment length size of their respective alleles.

Funding

Rufford Foundation, Award: RSG Reference 20207-1

Koiata Botanical Trust

Ministry of Foreign Affairs and Trade, New Zealand, Award: ASEAN PhD Scholarship

Bill Makepeace Prize

Koiata Botanical Trust

Bill Makepeace Prize