Enzyme gene expression in house sparrow populations

Phenotypic plasticity is a major mechanism whereby organisms adjust their traits within generations to complement environmental conditions.  In the context of range expansions, plasticity is thought to be especially important, as plastic changes in traits can lead to rapid adaptation.  For these reasons, there has been growing interest in the roles of molecular epigenetic processes in the context of range expansions.  One epigenetic process in particular, DNA methylation, enables organisms to adjust gene expression contingent on the environment, which probably explains why it has played a role in some invasions.  Nevertheless, we still know very little about how methylation is regulated in wildlife, especially the expression of the enzymes responsible for altering methyl marks on the genome.  The most important forms of these enzymes in vertebrates are DNA methyltransferase 1, which largely maintains existing methyl marks, DNA methyltransferase 3, which creates ..., Bird capture, husbandry, and tissue collection:
We captured adult house sparrows using mist nets from sunrise until ~1100 at each location (Table 1). Upon capture, we measured wing chord (to the nearest 1 mm), tarsus length (to the nearest 1 mm), and body mass (to the nearest 0.1 g). We also collected approximately 50 µl of blood from the brachial vein of each bird, which was stored in 300 µl of DNA/RNA Shield (Zymo R1100-50). Immediately after, each bird was injected subcutaneously with 100 µl of 1 mg ml⁻¹ LPS (from E. coli 055; Fisher L4005) in sterile saline over the breast muscle. Birds were housed individually in wire songbird cages (approx. 35.6 x 40.6 x 44.5 cm) with food and water provided ad libitum, while maintaining visual and vocal contact. Forty-eight hours post-injection, between 0700 and 1000, birds were euthanized via isoflurane overdose followed by rapid decapitation. We collected liver, spleen, and gut samples in 500 µl of DNA/RNA Shield, and all samples were stored at..., , # Enzyme gene expression in house sparrow populations

[https://doi.org/10.5061/dryad.n8pk0p369](https://doi.org/10.5061/dryad.n8pk0p369)

## Description of the data and file structure

### Files and variables

#### File: DNMTdataforDryad.xlsx

For R code used on these data, see R_Code__enzyme_gene_expression_in_house_sparrow_populations.txt

**Description:** 

##### Variables

* Band = individual identifier for a bird
* Country = location of capture
* pop.type = category of introduction history (native or non-native)
* latitude = location on globe in degrees and minutes
* genetic group = ancestry based on assignments implicated by Ravinet et al., 2018
* altitudem = in meters
* urbanization = percent of habitat experiencing urbanization within 10km of location where a bird was caught
* tempP = Colwell's index for temperature predictability
* prep = Colwell's index for precipitation predictability
* Gex = gene expression
* LogGex = log10-transformed gene expression
* bodymass0 = body mas...,

表型可塑性（Phenotypic Plasticity）是生物在世代内调整自身性状以适配环境条件的核心机制。在物种分布范围扩张的背景下，表型可塑性被认为尤为关键，因为性状的塑性变化可推动快速适应。基于上述原因，学界对分子表观遗传过程在物种分布范围扩张中的作用愈发关注。其中尤为关键的一类表观遗传过程是DNA甲基化（DNA Methylation），它可使生物根据环境条件调控基因表达，这或许可以解释其为何在部分生物入侵事件中发挥了作用。尽管如此，我们对野生生物体内甲基化的调控机制仍知之甚少，尤其是负责修饰基因组甲基化标记的酶的表达情况。脊椎动物中此类酶的主要形式为DNA甲基转移酶1（DNA Methyltransferase 1），其主要功能是维持现存的甲基化标记；以及DNA甲基转移酶3（DNA Methyltransferase 3），负责建立……，鸟类捕获、饲养与样本采集：
我们于各采样点（见表1）从日出至当日约11:00，使用雾网捕捉成年家麻雀。捕获后，我们测量其翼弦（精确至1mm）、跗跖长度（精确至1mm）与体质量（精确至0.1g）。同时从每只鸟的臂静脉采集约50µl血液，储存在300µl的DNA/RNA Shield（Zymo R1100-50）中。采血后立即对每只鸟于胸肌部位皮下注射100µl浓度为1mg·ml⁻¹的脂多糖（LPS，来自大肠杆菌055株；Fisher L4005），溶剂为无菌生理盐水。将每只鸟单独饲养于金属鸣禽笼（规格约35.6×40.6×44.5cm）中，自由采食饮水，并保持视觉与听觉交流。注射后48小时，于07:00至10:00之间，通过异氟烷过量麻醉后快速断头处死鸟类。采集肝脏、脾脏与肠道样本，置于500µl的DNA/RNA Shield中，所有样本储存于……

# 家麻雀种群的酶基因表达
[https://doi.org/10.5061/dryad.n8pk0p369](https://doi.org/10.5061/dryad.n8pk0p369)

## 数据与文件结构说明
### 文件与变量
#### 文件：DNMTdataforDryad.xlsx
用于处理该数据的R代码请参见R_Code__enzyme_gene_expression_in_house_sparrow_populations.txt

**说明：**
##### 变量说明
* Band：鸟类个体识别编号
* Country：捕获地点所属国家
* pop.type：引入历史类别（本地种群或非本地种群）
* latitude：采样点的经纬度坐标（度分格式）
* genetic group：基于Ravinet等人2018年研究的祖先血统分组
* altitudem：海拔高度，单位为米
* urbanization：采样点周边10km范围内城市化生境占比
* tempP：温度可预测性的科尔韦尔（Colwell）指数
* prep：降水可预测性的科尔韦尔（Colwell）指数
* Gex：基因表达量
* LogGex：经过log10转换的基因表达量
* bodymass0：初始体质量……