Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America
Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America
复制标题
DOI：
10.1016/j.ympev.2023.107701
复制
发表时间：
2023-01-16
影响因子：
4.1
通讯作者：
Blois，Jessica L.
中科院分区：
文献类型：
--
作者：
Boria，Robert A.;Blois，Jessica L.
人为气候变化对生物多样性的影响已经在每个大陆、海洋和不同的分类群体中得到了承认。在这里，我们研究了一个世界性物种的范围动态和人口学：鹿鼠，松材线虫。我们使用ddRADseq协议生成了一个多位点SNP数据集，涵盖了该物种群体在北美西部的三个谱系中的218个个体。我们用几种方法评估了种群结构，并探索了地理距离和遗传距离之间的相关性。我们使用现场频谱方法对人口历史进行建模，并使用机器学习算法来推断当前和过去(末次冰期最大值；LGM)的环境适宜性。最后，我们对所识别的谱系的人口扩张的起源进行了探讨。全基因组的SNP数据集能够识别出三个不同的区域群体--1)P.M.Gambeli(南加州)；2)P.Keeni(太平洋西北)；3)P.M.sonoriens(横跨太平洋西北，穿过加利福尼亚州中部，穿过落基山脉进入大平原的广泛种群)。人口统计分析表明，这三个种群之间的分裂发生在过去50万年内，其中一次是最近(全新世晚期)的分裂。每一个谱系的生态位模型都预测了在其已知范围内目前条件下存在的适宜环境，以及过去北方栖息地的严重减少。鹿鼠对过去气候变化的反应是在间冰期扩大活动范围，在冰期缩小活动范围，导致种群分化强烈。但全新世间冰期较低幅度的气候变化或其他过程也导致了种群分化，鉴于人类世期间人类造成的重大人为气候变化和其他景观变化，这种分化可能至今仍在进行。通过了解导致当代生物多样性地理分布的历史过程，我们可以确定塑造生物多样性的不同因素在现在和未来的相对重要性。
The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse,Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify-three regionally distinct groups— 1)P. m. gambelii(southern California); 2)P. keeni(Pacific Northwest); 3)P. m. sonoriensis(a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.