DISSERTATION RESEARCH: Surviving habitat loss: Physiological and evolutionary basis underlying tolerance to deforestation

热带森林砍伐重塑了生物群落，使一些物种受益，同时将其他物种推向局部灭绝。这项研究将通过关注两种密切相关的中美洲青蛙物种的遗传学来研究对森林砍伐的耐受性的生态和进化基础。沿着气候变化和疾病，栖息地的丧失正将许多两栖动物物种推向灭绝。了解热适应的生物化学基础是一个重要的研究领域，因为人类正在加热当地，区域和全球气候的多方面方式。这项研究将通过深入了解一些物种能够对抗这一全球趋势的原因来为保护结果提供信息。该项目还将涉及对一名研究生和本科生的培训，其中包括来自科学界代表性不足的群体的个人。研究人员将研究两种在森林和森林砍伐地区生活的倾向不同的Craugastor。他们之前的研究将耐热性确定为解释一个物种是否能在温暖的森林砍伐地区生存的主要因素。他们将这两个物种置于森林或牧场般的温度条件下，然后使用基于Illumina的RNA测序来测试组成型表达的种间差异和上调热胁迫耐受基因的能力（例如，热休克蛋白）对应于生境亲和力。因此，他们可以开始评估基因调控如何促进在森林砍伐的栖息地生存。虽然差异表达可以促进存活，但结构差异（即，在蛋白质编码序列中）也可能发挥作用。他们将比较物种之间的序列数据，通过采用传统的分子进化测试进行正向选择（即，dN/dS），以及开发一种新的基于结构的方法，该方法研究了DNA水平的变化如何改变蛋白质在温暖温度下的稳定性。利用蛋白质同源性建模和RNA序列数据，他们将测试这一假设，即在毁林耐受物种的蛋白质表现出增加的热稳定性。由于常规的阳性选择测试方法容易出现假阴性，因此使用基于结构的假设测试框架将大大增加热适应的检测。这项研究将把人类活动引起的生态变化放在宏观进化的背景下，并提供一个具体的结构假设，以检测在一个日益温暖，人类主导的生物圈热适应。

Tropical deforestation reshapes biological communities, benefitting some species, while pushing others towards local extinction. This research will examine the ecological and evolutionary underpinnings of tolerance to deforestation by focusing on the genetics of two closely related Central American frog species. Along with climate change and disease, habitat loss is pushing numerous amphibian species towards extinction. Understanding the biochemical basis for thermal adaptation is a crucial area of research given the multifaceted ways that humans are heating local, regional, and global climates. This research will inform conservation outcomes by providing insight into the reasons that some species are capable of bucking this global trend. The project also will involve the training of a graduate student and undergraduates, including individuals from groups that are underrepresented in the sciences.The researchers will study two species in the genus Craugastor that differ in their tendency to live in forested and deforested areas. Their previous research identified thermal tolerance as the primary factor explaining whether a species can survive in warmer, deforested areas. They will subject both species to forest- or pasture-like temperature regimes, and then uses Illumina-based RNA sequencing to test whether interspecific differences in constitutive expression and capacity to upregulate thermal stress tolerance genes (e.g., heat shock proteins) correspond to habitat affinity. They can thus begin to assess how gene regulation facilitates survival in deforested habitats. While differential expression may facilitate survival, structural differences (i.e., in protein coding sequence) also likely play a role. They will compare sequence data between species to scan for signatures of adaptation by employing both conventional molecular evolutionary tests for positive selection (i.e., dN/dS), as well as developing a novel structure-based approach that examines how changes at the DNA level are expected to alter protein stability at warm temperatures. Using protein homology modeling and RNA sequence data, they will test the hypothesis that proteins in the deforestation-tolerant species exhibit increased thermal stability. Because conventional methods of testing for positive selection are prone to false negatives, the use of a structure based, hypothesis-testing framework will substantially increase the detection of thermal adaptation. This study will place ecological changes caused by human activity in a macroevolutionary context, and provide a specific structural hypothesis to detect thermal adaption in an increasingly warm, human-dominated biosphere.