Microgeographic adaptation corresponds with elevational distributions of congeneric montane grasshoppers

Local adaptation can occur at small spatial scales relative to the dispersal capacity of species. Alpine ecosystems have sharp environmental clines that offer an opportunity to investigate the effects of fine scale shifts in species’ niche breadth on adaptive genetic processes. Here we examine two grasshopper species endemic to the Australian Alps (Kosciuscola spp.) that differ in elevational niche breadth; one broader, K. usitatus (1400-2200m), and one narrower, K. tristis (1600-2000m). We examine signatures of selection with respect to environmental and morphological variables in two mountain regions using FST outlier tests and environmental association analyses (EAA) applied to Single Nucleotide Polymorphism data (K. usitatus: 9,017 SNPs, n = 130; K. tristis: 7,363 SNPs, n = 135). Stronger genetic structure was found in the more narrowly distributed K. tristis, which showed almost twice the number of SNPs under putative selection (10.8%) compared with K. usitatus (5.3%). When examining SNPs in common across species (n = 3,058), 260 SNPs (8.5%) were outliers shared across species, and these were mostly associated with elevation, a proxy for temperature, suggesting parallel adaptive processes in response to climatic drivers. Additive polygenic scores (an estimate of the cumulative signal of selection across all candidate loci) were non-linearly and positively correlated with elevation in both species. However, a steeper correlation in K. tristis indicated a stronger signal of spatially varying selection towards higher elevations. Our study illustrates that the niche breadth of co-occurring and related species distributed along the same environmental cline is associated with differences in patterns of microgeographic adaptation.

Methods
Sampling was undertaken for two weeks in late February to early March of 2017. Three transects ranging from 1400-2200m in elevation were sampled within each of two mountain regions, Thredbo and Guthega within Kosciuszko National Park in New South Wales. DNA was extracted from the tissue of one femur per collected specimen at the Diversity Arrays Technology sequencing facility, Canberra (DArTseq). A modified double-digest RAD sequencing protocol was used to generate data at DArTseq. SNPs were further filtered using the Radiator r package.

Usage Notes
Files: K.usitatus_9017_SNPs.ped, K.usitatus_9017_SNPs.map

Genotype information of 130 individuals of Kosciuscola usitatus analysed at 9,017 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers

File: K.usitatus_3321_SNPs.str

File with 3,321 SNPs and 130 individuals, used to analyse pairwise Fst, genetic structure, isolation by distance and spatial autocorrelation analyses for Kosciuscola usitatus. The file is STRUCTURE formatted. Missing values are coded as -9

File: K.usitatus_envt_data.csv

Environmental data information used to detect signatures of selection (EAA analysis, pRDA and RDA).

pop= population information representing the area of collection for each individual

transect= transect information for each individual

location= Location

individual= unique name of individual

elevation= elevation in meter above sea level

FPC= Foliage Projective Cover (%)

precipseas = precipitation seasonality

roughness = terrain roughness

FZ = number of frost days

bd = soil bulk density

ph = soil ph     

femur length = measured in mm

sex = sex per individual, binary coded: male = 0, female = 1

Files: K.tristis_7363_SNPS.ped, K.tristis_7363_SNPS.map

Genotype information of a total of 135 individuals of Kosciuscola usitatus analysed at 7,363 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers

File: K.tristis_3566_SNPS.str

File with 3,566 SNPs and 135 individuals, used to analyse pairwise Fst, genetic structure, isolation by distance and spatial autocorrelation analyses for Kosciuscola tristis. The file is STRUCTURE formatted. Missing values are coded as -9

File: K.tristis_envt_data

Environmental data information used to detect signatures of selection (EAA analysis, pRDA and RDA).

pop= population information representing the area of collection for each individual

transect= transect information for each individual

location= Location

individual= unique name of individual

elevation= elevation in meter above sea level

FPC= Foliage Projective Cover (%)

precipseas = precipitation seasonality

roughness = terrain roughness

FZ = number of frost days

bd = soil bulk density

ph = soil ph     

femur length = measured in mm

sex = sex per individual, binary coded: male = 0, female = 1

File: Whole_data_3058_SNPs.ped, Whole_data_3058_SNPs.map

Genotype information of 266 individuals (129 K. usitatus, 137 K. tristis) analysed at 3,058 SNPs. The data was used to perform selection detection tests. The files are in PED and MAP format. MAP file= list of names of SNP markers

File: Whole_data_2143_SNPs.str

File with 2,143 SNPs and 266 individuals, used to perform genetic structure analysis for the common dataset for the two species. The file is STRUCTURE formatted. Missing values are coded as -9

相较于物种的扩散能力，局部适应可发生于较小的空间尺度范围内。高山生态系统拥有陡峭的环境梯度，为探究物种生态位幅度的精细尺度变化对适应性遗传过程的影响提供了理想研究契机。
本研究聚焦澳大利亚阿尔卑斯山区特有的两种科修斯科蝗属（Kosciuscola）蝗虫，二者沿海拔梯度的生态位幅度存在显著差异：其中生态位较宽的物种为Kosciuscola usitatus（简称K. usitatus，分布海拔1400-2200m），生态位较窄的为Kosciuscola tristis（简称K. tristis，分布海拔1600-2000m）。本研究基于单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据，采用FST异常值检验与环境关联分析（Environmental Association Analyses, EAA），在两个山地区域内探究了与环境及形态变量相关的选择信号：其中K. usitatus包含9017个SNP、130个样本；K. tristis包含7363个SNP、135个样本。
分布范围更窄的K. tristis展现出更强的遗传结构，其检测到的潜在受选择SNP数量约为K. usitatus的两倍：K. tristis潜在受选择SNP占比为10.8%，而K. usitatus仅为5.3%。在跨物种共有的3058个SNP中，有260个（占比8.5%）为两个物种共有的异常位点，这些位点大多与作为温度替代指标的海拔相关，表明二者在气候驱动下存在平行适应性演化过程。
加性多基因评分（即对所有候选位点上累积选择信号的估计值）在两个物种中均与海拔呈非线性正相关。但K. tristis的相关系数斜率更陡，表明其在高海拔区域受到的空间异质性选择信号更强。
本研究表明，沿同一环境梯度分布的近缘共存物种，其生态位幅度与微地理适应模式的差异密切相关。

## 研究方法
采样工作于2017年2月下旬至3月上旬开展，为期两周。在新南威尔士州科修斯科国家公园内的Thredbo与Guthega两个山地区域中，各设置3条海拔跨度为1400-2200m的样带进行采样。本研究于堪培拉的多样性阵列技术测序中心（DArTseq）对每头标本的单条后腿股骨组织进行DNA提取，采用改良的双酶切RAD测序流程在DArTseq平台生成测序数据，并通过Radiator R包对SNP进行后续过滤。

## 使用说明
### 文件：K.usitatus_9017_SNPs.ped、K.usitatus_9017_SNPs.map
该文件包含130头Kosciuscola usitatus个体在9017个SNP位点上的基因型信息，用于开展选择检测分析。文件格式为PED与MAP格式，其中MAP文件为SNP标记名称列表。

### 文件：K.usitatus_3321_SNPs.str
该文件包含130头Kosciuscola usitatus个体的3321个SNP位点数据，用于该物种的成对FST分析、遗传结构分析、距离隔离分析与空间自相关分析。文件采用STRUCTURE格式，缺失值以-9编码。

### 文件：K.usitatus_envt_data.csv
该文件包含用于选择信号检测（环境关联分析、偏冗余分析与冗余分析）的环境数据信息，各字段说明如下：
- pop：代表每个个体采样区域的种群信息
- transect：每个个体所属的样带信息
- location：采样地点
- individual：个体唯一标识符
- elevation：海拔高度（单位：米，相对于海平面）
- FPC：植被投影盖度（百分比）
- precipseas：降水季节性
- roughness：地形粗糙度
- FZ：霜冻日数
- bd：土壤容重
- ph：土壤pH值
- femur length：后腿股骨长度（单位：毫米）
- sex：个体性别，采用二元编码：雄性=0，雌性=1

### 文件：K.tristis_7363_SNPS.ped、K.tristis_7363_SNPS.map
该文件包含135头Kosciuscola tristis个体在7363个SNP位点上的基因型信息，用于开展选择检测分析。文件格式为PED与MAP格式，其中MAP文件为SNP标记名称列表。（注：原文此处存在笔误，原描述中将K. tristis误写为K. usitatus，已修正）

### 文件：K.tristis_3566_SNPS.str
该文件包含135头Kosciuscola tristis个体的3566个SNP位点数据，用于该物种的成对FST分析、遗传结构分析、距离隔离分析与空间自相关分析。文件采用STRUCTURE格式，缺失值以-9编码。

### 文件：K.tristis_envt_data
该文件包含用于选择信号检测（环境关联分析、偏冗余分析与冗余分析）的环境数据信息，各字段说明与K.usitatus_envt_data.csv一致。

### 文件：Whole_data_3058_SNPs.ped、Whole_data_3058_SNPs.map
该文件包含266个个体（129头K. usitatus、137头K. tristis）在3058个SNP位点上的基因型信息，用于开展选择检测分析。文件格式为PED与MAP格式，其中MAP文件为SNP标记名称列表。

### 文件：Whole_data_2143_SNPs.str
该文件包含266个个体的2143个SNP位点数据，用于两个物种的共有数据集的遗传结构分析。文件采用STRUCTURE格式，缺失值以-9编码。

搜集汇总

背景与挑战

背景概述

该数据集研究了澳大利亚阿尔卑斯山地区两种蚱蜢物种（Kosciuscola usitatus和K. tristis）的微地理适应过程，重点关注它们在不同海拔分布（生态位宽度差异）下的遗传选择信号。通过分析单核苷酸多态性数据，发现较窄分布的物种表现出更强的遗传结构和更多受海拔相关选择影响的位点，揭示了生态位宽度与微地理适应模式的关联。数据集包含基因型、环境变量和形态学数据，支持选择检测和遗传结构分析。