Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

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)

Morphological and radiographic studies on the skull of the straw-coloured fruit bat Eidolon helvum (Chiroptera: Pteropodidae)

Although 20 % of the extant mammalians are chiropterans, there are only a few studies about their skull morphology. The aim of this work is to broaden the knowledge in this field by investigating Eidolon helvum skulls and describing their anatomical characters with a particular focus on general shape, sutures, foramina and processes. We study the external surface of the bones and make a detailed description of 6 rostral bones (nasal, premaxilla, maxilla, palatine, lacrimal, jugal), 9 cranial bones (frontal, parietal, interparietal, pterygoid, sphenoid complex, squamosal, petrosal, ectotympanic, occipital complex) and the mandible. We also make a radiographic analysis by taking X-ray images in lateral and dorsoventral direction. Comparisons with other bats like Pteropus lylei and Desmodus rotundus show interspecific variations. So this work helps building a solid basis for further phylogenetic, functional or systematic studies

Morphological and radiographic studies on the skull of the straw-coloured fruit bat Eidolon helvum (Chiroptera: Pteropodidae)

Although 20 % of the extant mammalians are chiropterans, there are only a few studies about their skull morphology. The aim of this work is to broaden the knowledge in this field by investigating Eidolon helvum skulls and describing their anatomical characters with a particular focus on general shape, sutures, foramina and processes. We study the external surface of the bones and make a detailed description of 6 rostral bones (nasal, premaxilla, maxilla, palatine, lacrimal, jugal), 9 cranial bones (frontal, parietal, interparietal, pterygoid, sphenoid complex, squamosal, petrosal, ectotympanic, occipital complex) and the mandible. We also make a radiographic analysis by taking X-ray images in lateral and dorsoventral direction. Comparisons with other bats like Pteropus lylei and Desmodus rotundus show interspecific variations. So this work helps building a solid basis for further phylogenetic, functional or systematic studies

Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

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)