Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

Summary

Research Aims - The extent of Madagascar’s grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C4 fire-adapted grass, Loudetia simplex, as a proxy for estimating grassland change through time. We carefully examined the utility of target-enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target-enrichment data and how assumptions about ploidy could affect analyses.

Methods - We developed a novel bioinformatic pipeline based to estimate ploidy and genotypes from target-enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data.

Key Result - All Malagasy Loudetia simplex individuals sampled in this study formed a clade and possibly indicated an ancestral high-altitude distribution. Demographic models suggested grassland expansions occurred prior to the Last Interglacial Period and supported extensive grasslands prior to human colonization. Though there are limitations to target-enrichment data for population genetic studies, we find that analyses of population structure are reliable.

Key Point - Genetic variation in Loudetia simplex supports widespread grasslands in Madagascar prior to the more recent periods of notable paleoclimatic change. However, the methods explored here could not differentiate between paleoclimatic change near the Last Glacial Maximum and anthropogenic effects. Target-enrichment data can be a valuable tool for analyses of population structure in the absence a reference genome.

Societal Impact Statement

Recognizing Loudetia dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component to Madagascar’s biodiversity. Urgently required are biodiversity inventories and risk assessments for unique grassland flora and fauna under present day environmental conditions to recognize and quantify modern human impacts within ecosystems historically regarded as wastelands. Substantial financial and logistic barriers exist to implementing conservation studies using contemporary genomic tools that we seek to ameliorate by developing computational resources to leverage a cost-effective data generation strategy that requires no prior genetic knowledge of the target species.
Methods
Methods are described in detail in Tiley et al. (2023).

Tiley GP, Crowl AA, Almary TOM, Luke WRQ, Solofondranohatra CL, Besnard G, Lehmann CER, Yoder AD, Vorontsova MS. 2023. Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar. bioRxiv. https://doi.org/10.1101/2023.04.07.536094

## 研究概要

### 研究目标
人类殖民前马达加斯加草原的覆盖范围尚未明确。本研究以广泛占优势的C4耐火草本植物**Loudetia simplex**为研究对象，通过其种群遗传分析作为替代指标，重建历史时期草原的动态变化。同时，本研究细致评估了目标富集数据（target-enrichment data）在种群遗传学研究中的应用价值，以期为保护遗传学提供实践建议；此外还探索了利用目标富集数据估算个体倍性水平（ploidy level）的可行性，以及倍性假设对后续分析的影响。

### 研究方法
我们开发了一套新型生物信息学流程，用于从目标富集数据中估算倍性与基因型。除构建物种树（species tree）与分析种群结构（population structure）外，我们还计算了标准种群遗传汇总统计量；并通过扩展贝叶斯天际线图（Extended Bayesian skyline plots）对实证数据与模拟数据的种群规模动态进行了估算。

### 主要结果
本研究采样的所有马达加斯加**Loudetia simplex**个体均构成一个演化支（clade），这暗示该物种可能具有祖先高海拔分布特征。种群动态模型显示，草原扩张事件发生在末次间冰期（Last Interglacial Period）之前，同时证实了人类殖民前马达加斯加已存在大面积草原。尽管目标富集数据在种群遗传学研究中存在一定局限，但我们的分析表明，种群结构相关研究结果具有可靠性。

### 核心结论
**Loudetia simplex**的遗传变异数据支持：在近期显著古气候变化发生之前，马达加斯加就已广泛分布草原。不过本研究探索的方法无法区分末次盛冰期（Last Glacial Maximum）前后的古气候变化与人为活动影响。在缺乏参考基因组（reference genome）的情况下，目标富集数据可作为种群结构分析的有效工具。

## 社会影响声明
确认**Loudetia simplex**主导的草原在人类殖民前广泛分布，这一结果凸显了开放生态系统过去是、现在仍是马达加斯加生物多样性的重要组成部分。当前，在现代环境条件下，针对独特草原动植物区系开展生物多样性调查与风险评估迫在眉睫，以识别并量化现代人类活动对历史上被视为荒地的生态系统的影响。利用当代基因组学工具开展保护研究存在显著的资金与后勤障碍，我们通过开发计算资源，构建了无需预先掌握目标物种遗传背景的低成本高效数据生成策略，以期改善这一现状。

## 研究方法
详细研究方法见Tiley等人（2023）的研究。

Tiley GP、Crowl AA、Almary TOM、Luke WRQ、Solofondranohatra CL、Besnard G、Lehmann CER、Yoder AD、Vorontsova MS. 2023. **Loudetia simplex**的遗传变异证实马达加斯加曾存在古草原. bioRxiv. https://doi.org/10.1101/2023.04.07.536094