How to use Mammalian Traits for Comparative Genomics (MaTrics). Design Principles for a Project Trait Matrix in Morph∙D∙Base

Abstract

This manual has been developed in the framework of the project ‘Identifying genomic loci underlying mammalian phenotypic variability using Forward Genomics’ which was funded by the Leibniz Gemeinschaft (SAW-2016-SGN-2). The project brought together an interdisciplinary scientific network covering the fields of morphology (Work Modules M1/M2, ‘Phenotyping’), bioinformatics (Work Module M3, ‘Documentation’), and genetics (Work Modules M4, ‘Forward Genomics’; M5, ‘Evolution Phylogenetics’; and M6/M7, ‘Experimental validation’). In this comprehensive project selected phenotypic –primarily skeletal and soft tissue– traits of mammals are documented in an online database called Morph∙D∙Base (MDB; https://www.morphdbase.de/), and regrouped in a project trait matrix called MaTrics (Mammalian Traits for Comparative Genomics). The mammalian taxa included in this MaTrics file are constrained to the species whose genome has been completely sequenced. They cover all 21 extant placental orders listed by Wilson & Reeder (2005). The goal of the project was to identify candidate gene loci which underlie natural mammalian phenotypic variability using the Forward Genomics approach. For example, one part of the study focused on the effects of convergent gene losses on their expressed characters among different mammalian taxa (e.g., Hecker et al. 2019).