Historical Ecology of the California Sea Mussel and Purple Sea Urchin Inferred from Multiple Gene Genealogies

从多基因谱系推断加州贻贝和紫海胆的历史生态学。众所周知，更新世的气候波动对海洋分类群的起源、灭绝和地理分布有着深远的影响。然而，海平面、海面温度、洋流模式和上升流机制的这些剧烈变化对海洋物种进化遗传学的影响尚不清楚。化石记录缺乏合理估计历史丰度的分辨率，也无法提供重要参数的估计，如物种进化的有效种群大小（Ne）。聚结理论的最新进展提供了令人兴奋的新机会来估计进化Ne，推断人口增长历史，并通过检查从多个独立位点获得的基因谱系结构来明确测试各种人口情景（包括人口瓶颈）。本研究将通过在跨越两个物种的地理范围（下加利福尼亚州到阿拉斯加东南部）的样本中重建多个核和线粒体基因区域的等位基因谱系，研究两个丰富而广泛的东北太平洋海洋分类群（加利福尼亚贻贝Mytilus California和紫色海胆strongylocentrus purpuratus）的历史生态学。从多个独立基因座获得的大谱系（每个基因座150个等位基因）将提供无与伦比的能力来推断两种物种进化的有效种群规模，并允许明确测试其他人口统计学假设。在最近的更新世，贻贝和海胆种群范围破碎和瓶颈事件的可能性将通过以下方式进行评估：(i)应用基于聚结的最大可能性方法，该方法测试多个独立谱系中多样性减少事件的时间和严重程度的一致性；（ii）模拟种群分裂和瓶颈事件，这些事件与过去50万年中已知的冰川极大期一致。通过推断基因流动的方向性，比较突变的年龄和南北种群的生长历史（它们有贯穿更新世的化石记录），也将对向北扩展的遗传特征进行测试。这些结果有望为更新世时期如何影响东北太平洋地区海洋分类群的进化史提供基本的新见解。拟议研究的更广泛影响：了解更新世的环境历史如何影响当今的海洋群落是一个基本但在很大程度上尚未解决的问题。本研究项目将通过推断东北太平洋地区两种重要生态海洋物种的历史丰度和种群遗传历史，大大促进我们对这一领域的认识。谱系学方法提供了一个令人兴奋的新框架，将古海洋学和古气候研究与现存海洋物种的生态和进化研究联系起来。当扩展到其他潮间带和潮下物种时，这些基于凝聚的方法将为海洋群落的稳定性和单个分类群对历史气候变化的敏感性提供新的见解。该项目还将延续加州大学圣地亚哥分校让本科生参与研究的强大传统，帮助培养少数民族和研究生，并资助一个博士后职位。

Pogson: Historical ecology of the California sea mussel and purple sea urchin inferred from multiple gene genealogies. Climatic fluctuations throughout the Pleistocene are known to have had profound effects on the origins, extinctions, and geographical distributions of marine taxa. However, the effects of these dramatic changes in sea level, sea surface temperature, current patterns, and upwelling regimes on the evolutionary genetics of marine species remains unclear. The fossil record lacks the resolution to reasonably estimate historical abundance and is incapable of providing estimates of important parameters such as a species evolutionary effective population size (Ne). Recent advances in coalescent theory provide exciting new opportunities to estimate evolutionary Ne, to infer population growth histories, and to explicitly test various demographic scenarios (including population bottlenecks) through the examination of the structures of gene genealogies obtained from multiple independent loci. This study will investigate the historical ecologies of two abundant and widespread NE Pacific marine taxa (the California sea mussel, Mytilus californianus, and the purple sea urchin, Strongylocentrotus purpuratus) through the reconstruction of allelic genealogies at multiple nuclear and mitochondrial gene regions in samples that span the geographic ranges of both species (Baja California to SE Alaska). The large genealogies (150 alleles per locus) obtained from the multiple independent loci will provide an unparalleled ability to infer both species evolutionary effective population sizes and allow explicit tests of alternative demographic hypotheses. The possibility of range fragmentation and bottleneck events on mussel and sea urchin populations over the recent Pleistocene will be assessed by (i) applying a coalescent-based maximum-likelihood method that tests for the concordance of the timing and severity of diversity reducing events across multiple independent genealogies, and (ii) performing coalescent simulations that will impose population fragmentation and bottleneck events coincident with known glacial maxima over the past 500,000 years. The genetic signature of northward range expansion will also be tested by inferring the directionality of gene flow and by comparing the ages of mutations and the growth histories of northern and southern populations (that have a fossil record persisting throughout the Pleistocene). The results are expected to provide fundamental new insights into how the Pleistocene period has influenced the evolutionary histories of marine taxa in the NE Pacific region. Broader impacts of the proposed research: Understanding how the environmental history of the Pleistocene has affected present-day marine communities is a fundamental yet largely unresolved question. This research project will significantly advance our understanding in this area by inferring the historical abundances and population genetic histories of two ecologically important marine species of the NE Pacific region. The genealogical approach offers an exciting new framework to link paleoceanographic and paleoclimatic research with ecological and evolutionary studies on extant marine species. When extended to other intertidal and subtidal species, these coalescent-based methods will provide new insights into the stability of marine communities and the susceptibility of individual taxa to historical climate change. This project will also continue the strong tradition at UCSC of involving undergraduate students in research, aid in the training of minority and graduate students, and fund one postdoctoral position.