Code from: Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species

Mountains are renowned for their bountiful biodiversity. Explanations on
the origin of such abundant life are usually regarded to their orogenic
history. However, ancient mountain systems with geological stability also
exhibit astounding levels of number of species and endemism, as
illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South
America. Thus, cycles of climatic changes over the last couple of million
years are usually assumed to play impotant role in the origin of
mountainous biota. These climatic oscillations potentially isolated and
reconnected adjacent populations, a phenomenon known as flickering
connectivity, accelerating speciation events due to range fragmentation,
dispersion, secondary contact, and hybridization. To evaluate the role of
the climatic fluctuations on the diversification of the BQM biota, we
estimated the ancient demography of distinct endemic species of animals
and plants using hierarchical approximate Bayesian computation analysis
and Ecological Niche Modeling. Additionally, we evaluated if climatic
oscillations have driven a genetic spatial congruence in the genetic
structure of co-distributed species from the Espinhaço Range, one of the
main BQM areas. Our results show that the majority of plant lineages
underwent a synchronous expansion over the Last Glacial Maximum (LGM, ca.
21 thousand years ago), although we could not obtain a clear demographic
pattern for the the animal lineages.We also obtained a signal of congruent
phylogeographic break between lineages endemic to the Espinhaço Range,
suggesting how ancient climatic oscillations might have driven the
evolutionary history of the Espinhaço’s biota.

山地以其丰富的生物多样性而闻名于世。这类丰富生命的起源传统上被归因于其造山历史（orogenic history）。然而，地质稳定的古老山地系统同样展现出惊人的物种丰富度与特有性（endemism）水平，以南美洲东部的巴西石英岩山地（Brazilian Quartzitic Mountains, BQM）为例。因此，过去数百万年间的气候变化周期通常被认为是山地生物区系起源的关键驱动因素。这些气候振荡（climatic oscillations）可能会隔离并重新连接相邻种群，这一现象被称为闪烁连通性（flickering connectivity），可通过分布区破碎化（range fragmentation）、扩散（dispersion）、二次接触（secondary contact）与杂交（hybridization）过程加速物种形成事件（speciation events）。
为评估气候波动（climatic fluctuations）对巴西石英岩山地生物区系多样化的作用，本研究采用分层近似贝叶斯计算分析与生态位建模（Ecological Niche Modeling, ENM）方法，估算了不同动植物特有物种的古代种群动态历史。此外，本研究还探讨了气候振荡是否推动了巴西石英岩山地核心区域之一——埃斯皮尼亚苏山脉（Espinhaço Range）的同分布物种（co-distributed species）种群遗传结构呈现遗传空间一致性（genetic spatial congruence）。
研究结果显示，绝大多数植物支系（plant lineages）在末次冰盛期（Last Glacial Maximum, LGM，约2.1万年前）发生了同步种群扩张，但我们未能在动物支系中观测到清晰的种群动态模式（demographic pattern）。
本研究还在埃斯皮尼亚苏山脉特有支系间检测到了一致的系统地理断裂（phylogeographic break）信号，表明古代气候振荡可能塑造了埃斯皮尼亚苏山地生物区系的演化历史。