Harmonized microsatellite dataset for circumpolar populations of reindeer and caribou (Rangifer tarandus)
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This repository contains a harmonized microsatellite genotype dataset for circumpolar populations of reindeer and caribou (Rangifer tarandus). The dataset was compiled from previously published population genetic studies conducted in Alaska, Canada, and Russia and subsequently standardized to enable joint analysis across regions. Because the original datasets were generated in different laboratories and genotyped using different electrophoretic platforms, systematic allele-size offsets among datasets were corrected using a reference-based mode-shift normalization procedure. The Russian dataset was selected as the reference alignment because it required the smallest overall adjustment and produced the most conservative correction of allele-size distributions. The resulting harmonized dataset was used for all downstream population genetic analyses presented in the associated manuscript. The final aligned dataset includes 1,544 individuals from 42 populations distributed across three major geographic regions of the circumpolar range of Rangifer tarandus. Genotypes are provided for nine microsatellite loci, each represented by two allele columns corresponding to diploid genotypes.The loci included in the dataset are: RT1, RT6, RT7, RT9, RT24, OHEQ, FCB193, BMS745, BMS1788. Allele sizes are reported as fragment lengths in base pairs after normalization of dataset-specific allele-size shifts. Data sources The harmonized dataset integrates microsatellite data from several previously published studies: 1) Colson K.E., Mager K.H., Hundertmark K.J. Reindeer Introgression and the Population Genetics of Caribou in Southwestern Alaska. Journal of Heredity. 2014;105(5):585–596. DOI: 10.1093/jhered/esu030. 2) Serrouya R., Paetkau D., McLellan B.N., Boutin S., Campbell M., Jenkins D.A. Population size and major valleys explain microsatellite variation better than taxonomic units for caribou in western Canada. Mol Ecol. 2012 Jun;21(11):2588-601. doi: 10.1111/j.1365-294X.2012.05570.x. Epub 2012Apr 16. PMID: 22502637. 3) Weckworth B.V., Musiani M., McDevitt A.D., Hebblewhite M., Mariani S. Reconstruction of caribou evolutionary history in Western North America and its implications for conservation. Mol Ecol. 2012 Jul;21(14):3610-24. doi: 10.1111/j.1365-294X.2012.05621.x. Epub 2012 May 22. PMID: 22612518. 4) Svishcheva, G.; Babayan, O.; Sipko, T.; Kashtanov, S.; Kholodova, M.; Stolpovsky, Y. Genetic Differentiation Between Coexisting Wild and Domestic Reindeer (Rangifer Tarandus L. 1758) in Northern Eurasia. GenResJ 2022, 3, 1-14.
本数据集仓库收录了一套针对环极地分布的驯鹿与北美驯鹿（*Rangifer tarandus*）的标准化微卫星（microsatellite）基因型数据集。该数据集整合了此前在阿拉斯加、加拿大与俄罗斯开展的已发表种群遗传学（population genetics）研究数据，并经过标准化处理以支持跨区域联合分析。 由于原始数据集由不同实验室生成，且使用了不同的电泳（electrophoresis）平台进行基因分型（genotyping），因此本研究采用基于参考的峰移（mode-shift）标准化流程，对各数据集间存在的系统性等位基因（allele）长度偏移进行了校正。鉴于俄罗斯数据集所需的整体调整幅度最小，且对等位基因长度分布的校正最为保守，因此将其选为参考对齐数据集。最终得到的标准化数据集被用于相关论文中呈现的全部后续种群遗传学分析。 最终对齐后的数据集涵盖了环极地驯鹿（*Rangifer tarandus*）分布范围内3个主要地理区域的42个种群，共计1544个个体。 数据集包含9个微卫星位点的基因型信息，每个位点对应两列等位基因以表示二倍体（diploid）基因型。本数据集包含的位点为：RT1、RT6、RT7、RT9、RT24、OHEQ、FCB193、BMS745、BMS1788。在校正数据集特有的等位基因长度偏移后，等位基因长度以标准化后的片段碱基对（base pair）长度形式报告。 数据来源 本标准化数据集整合了多项已发表研究的微卫星数据： 1) Colson K.E.、Mager K.H.、Hundertmark K.J. 阿拉斯加西南部驯鹿基因渐渗与北美驯鹿种群遗传学. 《遗传杂志》(Journal of Heredity), 2014;105(5):585–596. DOI: 10.1093/jhered/esu030. 2) Serrouya R.、Paetkau D.、McLellan B.N.、Boutin S.、Campbell M.、Jenkins D.A. 加拿大西部北美驯鹿的种群规模与主要山谷比分类单元更能解释微卫星变异. 《分子生态学》(Mol Ecol), 2012年6月;21(11):2588-2601. DOI: 10.1111/j.1365-294X.2012.05570.x. 2012年4月16日在线优先出版. PMID: 22502637. 3) Weckworth B.V.、Musiani M.、McDevitt A.D.、Hebblewhite M.、Mariani S. 北美西部北美驯鹿进化历史重建及其保护意义. 《分子生态学》(Mol Ecol), 2012年7月;21(14):3610-3624. DOI: 10.1111/j.1365-294X.2012.05621.x. 2012年5月22日在线优先出版. PMID: 22612518. 4) Svishcheva G.、Babayan O.、Sipko T.、Kashtanov S.、Kholodova M.、Stolpovsky Y. 欧亚北部野生与家养驯鹿（*Rangifer tarandus* L. 1758）共存种群间的遗传分化. *GenResJ*, 2022, 3: 1-14.
