Replication Data for: Ice age refugium shows potential of geohistorical data to guide modern conservation efforts

This repository contains the code and data required to replicate Figures 3, 4, S1, and S2, and Movies S1-S3 for the manuscript entitled "Ice age refugium shows potential of geohistorical data to guide modern conservation efforts." Also contains the code required to perform the Monte Carlo simulation used to calculate the probability of a refugium explaining the regional decline and recovery in spruce incidence. Manuscript summary: Many biologists regard refugia as locations that shelter a population during an environmental crisis, thus facilitating post-crisis ecological recovery. However, identifying refugia based on short-term contraction and survivorship alone is problematic as this approach fails to account for whether the species survives and recovers in the long-term. Protecting refugia that are unstable in the long-term could lead to wasted conservation efforts and the species’ extinction. Here, we present a novel method for identifying geohistorical refugia that emphasizes a population’s long-term success and post-crisis recovery. To test this method’s utility, we present a case-study using pollen data for three ecologically distinct plant taxa from lake cores over the past 20 kyr in northern Alaska, USA. Using Monte Carlo methods, we found a statistically significant decrease in spruce incidence across the study region between 13.0 – 10.0 ka. During this interval, spruce persisted at relatively high abundance in one locality that may have provided the cool, humid conditions necessary for spruce survival during an interval of warmer, drier regional climate. This locality acted as the center for post-crisis re-expansion after the warm, dry conditions passed, indicating that this location was likely a refugium. If successful geohistorical refugia can be identified, subsequent analyses should aim to identify which environmental conditions allowed the population to survive within the refugium and re-expand after the crisis, thus providing critical information for policymakers when identifying locations for successful, long-term protected areas in the face of the ongoing biodiversity crisis.

本仓库包含复现题为《冰期避难所（refugium）展示地史数据指导现代保护工作的潜力》的手稿中图3、4、S1、S2及补充影片S1-S3所需的代码与数据，还包含执行蒙特卡洛模拟（Monte Carlo simulation）所需的代码——该模拟用于计算避难所解释云杉发生率区域衰退与恢复概率的核心逻辑。手稿摘要：众多生物学家将避难所视为环境危机期间庇护种群的区域，进而推动危机后的生态恢复。然而，仅凭借短期种群收缩与存活情况识别避难所存在局限，因其未考虑物种能否实现长期存续与恢复。保护长期不稳定的避难所可能导致保护资源浪费及物种灭绝。本文提出一种识别地史避难所的创新方法，该方法聚焦种群的长期成功存续与危机后恢复能力。为验证此方法的实用性，我们以美国阿拉斯加北部过去20千年（kyr）湖芯中三种生态特征差异显著的植物类群花粉数据为案例展开研究。通过蒙特卡洛模拟，我们发现13.0–10.0千年（ka）期间研究区域的云杉发生率呈现统计显著下降。在此阶段，云杉在某一区域维持相对较高丰度，该区域或为云杉在区域气候暖干化时期提供了生存必需的凉爽湿润条件。暖干期结束后，该区域成为危机后种群重新扩张的中心，表明其可能为一处避难所。若能成功识别有效的地史避难所，后续分析应致力于明确哪些环境条件支撑种群在避难所内生存并于危机后扩张，从而为政策制定者在当前生物多样性危机下识别长期有效的保护区提供关键依据。