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 residual af..., .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...