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We investigated the geographic variation of eight Ethiopian populations of the rodent Lophuromys flavopunctatus and compared them to the Bale endemic species L. melanonyx. We used multivariate morphometrics and analysed independently skull and external body linear measurements, in an attempt to relate morphological variability to geography (latitude, longitude, altitude). There is a high morphological diversity in these Ethiopian populations, which form three distinct recognizable groups, with the Bale population being the most distinct. The results of analyses on the two character sets corroborate each other and indicate that the kind of variation is not ‘ecological’ but rather there is a phylogenetic cause, and relations at higher taxonomic level are suggested. There is a homogeneous group with five populations within which there is a recognizable pattern of clinal variation related to altitude, with a decrease in body size and a change in skull shape.