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.

研究概述
## 研究目标
人类殖民前马达加斯加草原的分布范围至今尚未明确。本研究以广泛占据优势的C4火适应性草本（C4 fire-adapted grass）单花卢德草（Loudetia simplex）作为代用指标，以此估算草原随时间的变化情况。我们严谨评估了靶向富集数据（target-enrichment data）在群体遗传学研究中的应用价值，以期为保护遗传学提供建议；同时探索了从靶向富集数据中估算个体倍性水平的潜力，以及倍性假设可能对分析结果产生的影响。
## 研究方法
我们开发了一套全新的生物信息学流程（bioinformatic pipeline），用于从靶向富集数据中估算倍性与基因型。除构建物种树与分析群体结构外，我们还估算了标准群体遗传汇总统计量。扩展贝叶斯天际线图（Extended Bayesian skyline plots）被用于估算经验数据与模拟数据的种群大小随时间的变化情况。
## 主要研究结果
本研究中所有采样的马达加斯加单花卢德草（Loudetia simplex）个体均形成一个单系群，这可能暗示其祖先类群具有高海拔分布特征。种群人口统计学模型表明，草原扩张事件发生在末次间冰期（Last Interglacial Period）之前，同时支持了人类殖民前马达加斯加已存在大面积草原的结论。尽管靶向富集数据在群体遗传学研究中存在一定局限性，但我们的分析证实，群体结构分析的结果具备可靠性。
## 核心论点
单花卢德草（Loudetia simplex）的遗传变异支持了：在近期显著古气候变化发生之前，马达加斯加境内已广泛分布草原。不过，本研究探索的方法无法区分末次盛冰期（Last Glacial Maximum）附近的古气候变化与人类活动的影响。在缺乏参考基因组（reference genome）的情况下，靶向富集数据可作为开展群体结构分析的有效工具。
## 社会影响声明
确认单花卢德草占优的草原在人类殖民前已广泛分布，这表明开放生态系统过去是、且至今仍是马达加斯加生物多样性的重要组成部分。当前亟需针对独特的草原动植物类群开展生物多样性普查与风险评估，以识别并量化现代人类活动对这片曾被视为荒地的生态系统造成的影响。利用当代基因组工具开展保护研究存在显著的资金与后勤壁垒，本研究通过开发计算资源，以无需目标物种预先具备遗传背景信息的低成本数据生成策略，旨在缓解这一困境。