Abstract
A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).
Highlights
BackgroundKnowing and understanding the organisms around us has always been important for mankind and describing and comparing phenotypes has a long tradition that goes beyond the emergence of academic disciplines (e.g., Pruvost et al.Handling editor: Pamela Burger.Extended author information available on the last page of the article2011)
Features associated with physiology, behaviour, ecology, or lifestyle traits are important to characterize intra- and interspecific differences and to describe biodiversity
It would be advantageous for this emerging science field to fall back to phenotype knowledge made digitally available in fully referenced data repositories. This should be a compendium of phenotype information on model and non-model species but should presented them in a discretized from, e.g., using a numeric code to label distinct phenotype categories. This is because currently available methods and approaches in comparative genomics cannot handle continuous data
Summary
Knowing and understanding the organisms around us has always been important for mankind and describing and comparing phenotypes has a long tradition that goes beyond the emergence of academic disciplines Even if model organism research would reveal all genes necessary to develop a given phenotype (e.g., the digestive system), it would still remain unknown which of these genes played the significant role in evolution and caused specific phenotypic differences between species (e.g., adaptation to particular diets) Given these limitations, novel approaches to explore genome–phenotype relationships were developed using the availability of an increasing number of fully sequenced genomes. This should be a compendium of phenotype information on model and non-model species but should presented them in a discretized from, e.g., using a numeric code to label distinct phenotype categories This is because currently available methods and approaches in comparative genomics (including Forward Genomics) cannot handle continuous data. Homology of phenotypes over the web; building the Tree of Life with phenotypes, publicly accessible containing images and matrices
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