Quantitative trait loci mapping in cichlid fishes: Aulonocara koningsi x Metriaclima mbenjii and Labidochromis caeruleus x Labeotropheus trewavasae

Since the time of Darwin, biologists have sought to understand the evolution and origins of phenotypic variation. To understand the genetic and molecular sources of morphological differences, we capitalize on the cichlid fish system. Cichlids of the East African Rift Lakes have undergone an extensive adaptive radiation, including variation in body shape, head shape, and pigmentation. These morphological differences are often intimately linked to the ecology and behavior of these animals. Here, we investigate the genetic basis of these phenotypes using quantitative trait loci (QTL) mapping using four genera of Lake Malawi cichlids and two F2 hybrid populations. The first hybrid cross is between Aulonocara koningsi, which lives in the open sandy region and feeds insects from the open sand, and Metriaclima mbenjii, an omnivore rock-dwelling fish. The second cross is between Labidochromis caeruleus, a suction-feeding insectivore that swims continuously searching for prey, and Labeotropheus ..., For the first hybrid cross, a single Metriaclima female crossed to two Aulonocara males; the inclusion of the second grandsire was inadvertent and resulted from an unexpected fertilization event in these species with external fertilization. This single F1 family was subsequently incrossed to produce a hybrid F2 population of 491 fishes. For the second cross, a single Labidochromis caeruleus female was crossed with a single Labeotropheus trewavasae male to create one F1 family, which was subsequently incrossed to produce a hybrid F2 population of 447 fishes. Hybrid fish and 10 each of the pure parental species were euthanized and 2D imaged at five months, with each image including a color standard and scale. Sex of each animal was determined based on gonad dissection and omitted if there was any ambiguity. Linear measures were collected from these images using the program ImageJ as pixels, converted to cm using measures of a scale in each picture using Excel, and processed to residu..., .CSV files can be opened in Microsoft Excel, OpenOffice, or a data analysis environment such as R (https://www.r-project.org/). .TPS files can be opened and analyzed using software available at https://sbmorphometrics.org/, specifically TPSutil, TpsDig, and TPSrelw for file management (e.g. sample removal), landmark digitization, and geometric morphometric analysis, respectively. .TPS files can be converted in TPSutil to be analyzed in R. Genotype files are formatted for upload and analysis in R/qtl. File names with \"MmAk\" indicates the Metriaclima x Aulonocara cross, while \"LcLt\" refers to Labidochromis x Labeotropheus., # Quantitative trait loci mapping in cichlid fishes: Aulonocara koningsi x Metriaclima mbenjii and Labidochromis caeruleus x Labeotropheus trewavasae [https://doi.org/10.5061/dryad.4mw6m90cz](https://doi.org/10.5061/dryad.4mw6m90cz) This data set describes data from two F2 hybrid populations of cichlid fishes, further described below. ## Description of the data and file structure All of the files included in this repository were collected to compare morphologies and perform quantitative trait loci mapping for four genera of Lake Malawi cichlid fishes and two F2 hybrid populations. The first hybrid cross is between Aulonocara koningsi, which lives in the open sandy region and feeds insects from the open sand, and Metriaclima mbenjii, an omnivore rock-dwelling fish. The second cross is between Labidochromis caeruleus, a suction-feeding insectivore that swims continuously searching for prey, and Labeotropheus trewavasae, which feeds by biting or scraping attached algae from the rocks i...,自达尔文时代以来，生物学家一直致力于解析表型变异（phenotypic variation）的演化历程与起源。为阐明形态差异的遗传与分子根源，我们以东非裂谷湖（East African Rift Lakes）中的丽鱼科鱼类研究系统为对象。东非裂谷湖的丽鱼经历了广泛的适应性辐射（adaptive radiation），其形态变异涵盖体型（body shape）、头部形态（head shape）与色素沉着（pigmentation）等多个维度，且这些形态差异往往与该类群的生态与行为习性紧密关联。本研究利用马拉维湖（Lake Malawi）四个属的丽鱼与两个F2杂交群体（F2 hybrid populations），通过数量性状位点（quantitative trait loci, QTL）定位技术解析上述表型的遗传基础。 首个杂交组合为栖息于开阔沙质区域、以开阔沙地昆虫为食的康氏绚丽鱼（Aulonocara koningsi）与杂食性岩栖鱼类姆本吉隐带丽鱼（Metriaclima mbenjii）的杂交。第二个杂交组合为持续游动搜寻猎物的吸吮食性昆虫食者蓝体唇色鲷（Labidochromis caeruleus）与特雷瓦撒唇鱼（Labeotropheus ...）的杂交。 针对首个杂交组合，我们以单只姆本吉隐带丽鱼雌性个体与两只康氏绚丽鱼雄性个体进行杂交；由于该类群为体外受精（external fertilization），第二只父本的引入系意外事件，源于一次未预期的受精事件。由此获得的单个F1家系随后进行近交，得到包含491尾个体的杂交F2群体。针对第二个杂交组合，我们以单只蓝体唇色鲷雌性个体与单只特雷瓦撒唇鱼（Labeotropheus trewavasae）雄性个体杂交得到单个F1家系，随后通过近交获得包含447尾个体的杂交F2群体。 杂交个体与各纯种亲本各10尾均在五个月龄时实施安乐死，并进行二维成像，每张图像均附带颜色校准标准与比例尺。个体性别通过性腺解剖（gonad dissection）确定，若存在性别判定歧义则剔除该样本。利用ImageJ软件从图像中以像素为单位采集线性测量数据，结合每张图片中的比例尺通过Excel转换为厘米单位，并进行残差处理（residu...）。 本数据集的.CSV文件可使用Microsoft Excel、OpenOffice或R（https://www.r-project.org/）等数据分析环境打开。.TPS文件可通过https://sbmorphometrics.org/提供的软件进行打开与分析，其中TPSutil用于文件管理（如样本移除）、TpsDig用于标志点数字化（landmark digitization）、TPSrelw用于几何形态计量分析（geometric morphometric analysis）。此外，可通过TPSutil将.TPS文件转换为适配R分析的格式。基因型文件格式适配R/qtl软件的上传与分析。文件名中带有"MmAk"的文件对应姆本吉隐带丽鱼×康氏绚丽鱼杂交组合，而"LcLt"则对应蓝体唇色鲷×特雷瓦撒唇鱼杂交组合。 # 丽鱼科鱼类的数量性状位点定位：康氏绚丽鱼×姆本吉隐带丽鱼与蓝体唇色鲷×特雷瓦撒唇鱼 [https://doi.org/10.5061/dryad.4mw6m90cz](https://doi.org/10.5061/dryad.4mw6m90cz) 本数据集包含马拉维湖丽鱼科鱼类四个属与两个F2杂交群体的相关数据，详细说明如下。 ## 数据与文件结构说明 本仓库收录的所有文件均用于比较形态学分析与数量性状位点定位研究。首个杂交组合为栖息于开阔沙质区域、以开阔沙地昆虫为食的康氏绚丽鱼与杂食性岩栖鱼类姆本吉隐带丽鱼的杂交。第二个杂交组合为持续游动搜寻猎物的吸吮食性昆虫食者蓝体唇色鲷与以刮食岩石附着藻类为食的特雷瓦撒唇鱼（原文后半部分未完成，保留省略）。