Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics

Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, calling into question the continued utility of microsatellites in population and landscape genetics. Yet highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated analyses previously done using microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open..., , , # Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics

[https://doi.org/10.5061/dryad.n5tb2rbwk](https://doi.org/10.5061/dryad.n5tb2rbwk)

## Description of the data and file structure

The same 185 black-capped vireo samples are represented in both the microsatellite (micro) and SNP genotype datasets below.

* BCVI\_Micro\_Genotypes.csv: genepop file format
* BCVI\_SNP\_Genotypes\_90GenotypeRate.vcf
* BCVI\_SNP\_Genotypes.vcf

Landscape data includes

* a) At-site predictor variables: elevation, Euclidean distance, water, development, forest, scrub, open, agriculture, riparian, the proportion of scrub habitat, and brown-headed cowbird (BHCO) management
* b) Between-site variables: elevation, Euclidean distance, water, development, forest, scrub, open, agri-culture, and riparian

BCVI\_Micro\_LandscapeGeneticData.csv

BCVI\_SNP\_LandscapeGeneticData.csv

Code files included:

* BCVI\_ANOVA.R
* LG\_HybridApproach.R
* LG\_Univar...

微卫星（microsatellite）与单核苷酸多态性（single-nucleotide polymorphisms, SNPs）的对比研究发现，在种群遗传分析中，单核苷酸多态性（SNPs）的表现优于微卫星，这使得微卫星在种群遗传学与景观遗传学中的持续应用价值受到质疑。然而，高度多态性分子标记（highly polymorphic markers）在遗传变异水平降低的物种中仍具备应用价值。本研究针对黑顶莺雀（black-capped vireo）的源-汇种群系统，采用通过双酶切RAD测序（ddRAD sequencing）获得的SNPs，重复了此前基于微卫星开展的分析。结果显示，SNPs在遗传多样性、种群分化以及迁移者检测方面具备更高的分辨率，但由于杂合度不足，无法重建亲子亲缘关系。两种分子标记得到的生物学推论一致：即基因流呈不对称性，从源种群位点流向剩余的汇种群位点。通过景观遗传学分析，我们发现两种分子标记得到了不同的结果，但与顶级环境特征（河岸带（riparian）、开阔生境（open）……）的关联……
# 物尽其用：微卫星仍是保护遗传学中兼具经济性与信息性的技术手段
https://doi.org/10.5061/dryad.n5tb2rbwk

## 数据与文件结构说明
下述微卫星（microsatellite，简称micro）与单核苷酸多态性（SNP）基因型数据集均包含同一批185份黑顶莺雀样本。
* BCVI_微卫星基因型数据.csv：采用genepop文件格式
* BCVI_SNP_基因型分型率90%.vcf
* BCVI_SNP_基因型数据.vcf

景观数据包含：
a) 样点内源预测变量：海拔、欧氏距离、水体、开发程度、森林、灌丛、开阔生境、农业用地、河岸带、灌丛生境占比以及棕头牛鹂（brown-headed cowbird, BHCO）管控措施
b) 样点间变量：海拔、欧氏距离、水体、开发程度、森林、灌丛、开阔生境、农业用地以及河岸带

* BCVI_微卫星景观遗传数据.csv
* BCVI_SNP_景观遗传数据.csv

包含的代码文件：
* BCVI_方差分析.R
* LG_混合方法分析.R
* LG_单变量分析...