Cranial morphology has been used to determine patterns of population history, but it is not "neutral" but is correlated with climate. For example, equatorial populations in Africa and Oceania have rather wide noses and narrow skulls compared to more northerly populations; this is not due to any close family relationship, but rather because of adaptation in similar environments.
This new paper tries to determine how different parts of cranial morphology reflect climate vs. population history.
The Anatomical Record Part A: Discoveries in Molecular, Cellular, and Evolutionary Biology, Volume 288A, Issue 12 , Pages 1225 - 1233
Human cranial anatomy and the differential preservation of population history and climate signatures
Katerina Harvati, Timothy D. Weaver
Cranial morphology is widely used to reconstruct evolutionary relationships, but its reliability in reflecting phylogeny and population history has been questioned. Some cranial regions, particularly the face and neurocranium, are believed to be influenced by the environment and prone to convergence. Others, such as the temporal bone, are thought to reflect more accurately phylogenetic relationships. Direct testing of these hypotheses was not possible until the advent of large genetic data sets. The few relevant studies in human populations have had intriguing but possibly conflicting results, probably partly due to methodological differences and to the small numbers of populations used. Here we use three-dimensional (3D) geometric morphometrics methods to test explicitly the ability of cranial shape, size, and relative position/orientation of cranial regions to track population history and climate. Morphological distances among 13 recent human populations were calculated from four 3D landmark data sets, respectively reflecting facial, neurocranial, and temporal bone shape; shape and relative position; overall cranial shape; and centroid sizes. These distances were compared to neutral genetic and climatic distances among the same, or closely matched, populations. Results indicate that neurocranial and temporal bone shape track neutral genetic distances, while facial shape reflects climate; centroid size shows a weak association with climatic variables; and relative position/orientation of cranial regions does not appear correlated with any of these factors. Because different cranial regions preserve population history and climate signatures differentially, caution is suggested when using cranial anatomy for phylogenetic reconstruction.