Human and chimpanzee gene expression differences replicated in mice fed different diets

Although the human diet is markedly different from the diets of closely related primate species, the influence of diet on phenotypic and genetic differences between humans and other primates is unknown. In this study, we analyzed gene expression in laboratory mice fed diets typical of humans and of chimpanzees. The effects of human diets were found to be significantly different from that of a chimpanzee diet in the mouse liver, but not in the brain. Importantly, 10% of the genes that differ in their expression between humans and chimpanzee livers differed also between the livers of mice fed the human and chimpanzee diets. Furthermore, both the promoter sequences and the amino acid sequences of these diet-related genes carry more differences between humans and chimpanzees than random genes. Our results suggest that the mouse can be used to study at least some aspects of human-specific traits.     

Dental topography and molar wear in Alouatta palliata from Costa Rica

Paleoprimatologists depend on relationships between form and function of teeth to reconstruct the diets of fossil species. Most of this work has been limited to studies of unworn teeth. A new approach, dental topographic analysis, allows the characterization and comparison of worn primate teeth. Variably worn museum specimens have been used to construct species-specific wear sequences so that measurements can be compared by wear stage among taxa with known differences in diet. This assumes that individuals in a species tend to wear their molar teeth in similar ways, a supposition that has yet to be tested. Here we evaluate this assumption with a longitudinal study of changes in tooth form over time in primates. Fourteen individual mantled howling monkeys (Alouatta palliata) were captured and then recaptured after 2, 4, and 7 years when possible at Hacienda La Pacifica in Costa Rica between 1989-1999. Dental impressions were taken each time, and molar casts were produced and analyzed using dental topographic analysis. Results showed consistent decreases in crown slope and occlusal relief. In contrast, crown angularity, a measure of surface jaggedness, remained fairly constant except with extreme wear. There were no evident differences between specimens collected in different microhabitats. These results suggest that different individual mantled howling monkeys wear their teeth down in similar ways, evidently following a species-specific wear sequence. Dental topographic analysis may therefore be used to compare morphology among similarly worn individuals from different species.     

Patterns of mandibular variation in Pan and Gorilla and implications for African ape taxonomy

Pan and Gorilla taxonomy is currently in a state of flux, with the number of existing species and subspecies of common chimpanzee and gorilla having been recently challenged. While Pan and Gorilla systematics have been evaluated on the basis of craniometric and odontometric data, only a handful of studies have evaluated multivariate craniometric variation within P. troglodytes, and none have evaluated in detail mandibular variation in either P. troglodytes or Gorilla gorilla. In this paper, we examine ontogenetic and adult mandibular variation in Pan and Gorilla. We test the hypothesis that patterns and degrees of mandibular variation in Pan and Gorilla closely correspond to those derived from previous analyses of craniometric variation. We then use these data to address some current issues surrounding Pan and Gorilla taxonomy. Specifically, we evaluate the purported distinctiveness of P.t. verus from the other two subspecies of Pan troglodytes, and the recent proposals to recognize Nigerian gorillas as a distinct subspecies, Gorilla gorilla diehli, and to acknowledge mountain and lowland gorillas as two separate species. Overall, patterns and degrees of multivariate mandibular differentiation parallel those obtained previously for the cranium and dentition. Thus, differences among the three conventionally recognized gorilla subspecies are somewhat greater than among subspecies of common chimpanzees, but differences between P. paniscus and P. troglodytes are greater than those observed between any gorilla subspecies. In this regard, the mandible does not appear to be more variable, or of less taxonomic value, than the face and other parts of the cranium. There are, however, some finer differences in the pattern and degree of morphological differentiation in Pan and Gorilla, both with respect to cranial and dental morphology, and in terms of the application and manner of size adjustment. Mandibular differentiation supports the conventional separation of bonobos from chimpanzees regardless of size adjustment, but size correction alters the relative alignment of taxa. Following size correction, intergroup distances are greatest between P.t. verus and all other groups, but there is considerable overlap amongst chimpanzee subspecies. Amongst gorillas, the greatest separation is between eastern and western gorillas, but adjustment relative to palatal vs. basicranial length results in a greater accuracy of group classification for G.g. gorilla and G.g. graueri, and more equivalent intergroup distances amongst all gorilla groups. We find no multivariate differentiation of the Nigerian gorillas based on mandibular morphology, suggesting that the primary difference between Nigerian and other western lowland gorillas lies in the nuchal region. Though intergroup distances are greatest between P.t. verus and other chimpanzee subspecies, the degree of overlap amongst all three groups does not indicate a markedly greater degree of distinction in mandibular, as opposed to other morphologies. Finally, mandibular differentiation corroborates previous craniodental studies indicating the greatest distinction amongst gorillas is between eastern and western groups. Thus, patterns and degrees of mandibular variation are in agreement with other kinds of data that have been used to diagnose eastern and western gorillas as separate species.     

Cladistic analyses of behavioural variation in wild Pan troglodytes: exploring the chimpanzee culture hypothesis

Long-term field studies have revealed considerable behavioural differences among groups of wild Pan troglodytes. Here, we report three sets of cladistic analyses that were designed to shed light on issues relating to this interpopulation variation that are of particular relevance to palaeoanthropology.In the first set of analyses, we focused on the proximate cause of the variation. Some researchers have argued that it is cultural, while others have suggested that it is the result of genetic differences. Because the eastern and western subspecies of P. troglodytes are well differentiated genetically while groups within the subspecies are not, we reasoned that if the genetic hypothesis is correct, the phylogenetic signal should be stronger when data from the eastern and western subspecies are analysed together compared to when data from only the eastern subspecies are analysed. Using randomisation procedures, we found that the phylogenetic signal was substantially stronger with in a single subspecies rather than with two. The results of the first sets of analyses, therefore, were inconsistent with the predictions of the genetic hypothesis.The other two sets of analyses built on the results of the first and assumed that the intergroup behavioural variation is cultural in nature. Recent work has shown that, contrary to what anthropologists and archaeologists have long believed, vertical intergroup transmission is often more important than horizontal intergroup transmission in human cultural evolution. In the second set of analyses, we sought to determine how important vertical transmission has been in the evolution of chimpanzee cultural diversity. The first analysis we carried out indicated that the intergroup similarities and differences in behaviour are consistent with the divergence of the western and eastern subspecies, which is what would be expected if vertical intergroup transmission has been the dominant process. In the second analysis, we found that the chimpanzee cultural data are not only comparable to a series of modern human cultural data sets in terms of how tree-like they are, but are also comparable to a series of genetic, anatomical, and behavioural data sets that can be assumed to have been produced by a branching process. Again, this is what would be expected if vertical inter-group transmission has been the dominant process in chimpanzee cultural evolution.Human culture has long been considered to be adaptive, but recent studies have suggested that this needs to be demonstrated rather than assumed. With this in mind, in the third set of analyses we investigated whether chimpanzee culture is adaptive. We found the hypothesis that chimpanzee culture is adaptive was supported by an analysis of data from the Eastern African subspecies, but not by an analysis of data from the eastern and western subspecies.The results of our analyses have implications for the number of subspecies in Pan troglodytes, the relationship between hominin taxa and Palaeolithic industries, and the evolution of hominin cognition and behaviour.     

Stereophotogrammetric analysis of occlusal morphology of extant hominoid molars: phenetics and function

Because teeth are commonly preserved in the fossil record, dental remains have often been employed in estimating evolutionary relationships among fossil hominoids. This is appropriate, however, only to the extent that dental morphology is phylogenetically informative. I have used phenetic analytic techniques to assess whether hominoid molars are likely to be useful for phylogenetic inference. Thirty-four occlusal landmarks for first and second molars were chosen; seven on each maxillary and ten on each mandibular tooth. Three-dimensional locations of these points were determined from stereophotographs of dental arcades of more than 260 specimens from six taxa (gorilla, chimpanzee, human, orangutan, siamang, and gibbon). Analytic emphasis was on canonical variates analyses of landmark coordinates for mandibular and maxillary second molars, adjusted for intergroup size differences. There is little correspondence between the systematic implications of hominoid molar morphometrics and reliable estimates of evolutionary propinquity based on interhominoid biomolecular similarities. The former seem to have been determined largely by dietary constraints. Although this suggests the possibility of using the protocol employed here to infer diets of fossil hominoids, molar crown measurements seem unlikely to serve well as phylogenetic indicators in the Hominoidea.     

New tools suggest local variation in tool use by a montane community of the rare Nigeria–Cameroon chimpanzee, <Emphasis Type="Italic">Pan troglodytes ellioti</Emphasis>, in Nigeria

Regional variations in tool use among chimpanzee subspecies and between populations within the same subspecies can often be explained by ecological constraints, although cultural variation also occurs. In this study we provide data on tool use by a small, recently isolated population of the endangered Nigeria–Cameroon chimpanzee Pan troglodytes ellioti, thus demonstrating regional variation in tool use in this rarely studied subspecies. We found that the Ngel Nyaki chimpanzee community has its own unique tool kit consisting of five different tool types. We describe a tool type that has rarely been observed (ant-digging stick) and a tool type that has never been recorded for this chimpanzee subspecies or in West Central Africa (food pound/grate stone). Our results suggest that there is fine- scale variation in tool use among geographically close communities of P. t. ellioti, and that these variations likely reflect both ecological constraints and cultural variation.     

Permanent tooth mineralization in bonobos (Pan paniscus) and chimpanzees (P. troglodytes)

The timing of tooth mineralization in bonobos (Pan paniscus) is virtually uncharacterized. Analysis of these developmental features in bonobos and the possible differences with its sister species, the chimpanzee (P. troglodytes), is important to properly quantify the normal ranges of dental growth variation in closely related primate species. Understanding this variation among bonobo, chimpanzee and modern human dental development is necessary to better contextualize the life histories of extinct hominins. This study tests whether bonobos and chimpanzees are distinguished from each other by covariance among the relative timing and sequences of tooth crown initiation, mineralization, root extension, and completion. Using multivariate statistical analyses, we compared the relative timing of permanent tooth crypt formation, crown mineralization, and root extension between 34 P. paniscus and 80 P. troglodytes mandibles radiographed in lateral and occlusal views. Covariance among our 12 assigned dental scores failed to statistically distinguish between bonobos and chimpanzees. Rather than clustering by species, individuals clustered by age group (infant, younger or older juvenile, and adult). Dental scores covaried similarly between the incisors, as well as between both premolars. Conversely, covariance among dental scores distinguished the canine and each of the three molars not only from each other, but also from the rest of the anterior teeth. Our study showed no significant differences in the relative timing of permanent tooth crown and root formation between bonobos and chimpanzees. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.     

Another look at shape variation in the distal femur of Australopithecus afarensis: implications for taxonomic and functional diversity at Hadar

Previous studies have recognized two patterns of distal femoral morphology among the specimens from Hadar (Ethiopia) assigned to Australopithecus afarensis. Size and shape differences between the well-preserved large (AL 333-4) and small (AL 129-1a) distal femora have been used to invoke both taxonomic and functional differences within the A. afarensis hypodigm. Nevertheless, prior studies have not analyzed these specimens in a multivariate context, nor have they compared the pattern of shape differences between the fossils to patterns of sexual dimorphism among extant taxa (i.e., the manner in which males and females differ). This study reexamines morphometric differences between the above specimens in light of observed levels of variation and patterns of sexual dimorphism among extant hominoids. Eight extant reference populations were sampled to provide a standard by which to consider size and shape differences between the fossils. Samples include three populations of modern humans, two subspecies of Pan troglodytes, three subspecies of Gorilla gorilla, Pan paniscus, and Pongo pygmaeus. Using size ratios and scale-free "shape" data (both derived from 2-D coordinate landmarks), size and shape differences between the fossils were evaluated against variation within each reference population using an exact randomization procedure. Growth Difference Matrix Analysis (GDMA) was used to test whether the pattern of morphological differences between the fossils differs significantly from patterns of sexual dimorphism observed among the ten extant groups. Overall morphometric affinities of the fossils to extant taxa were explored using canonical variates analysis (CVA).Results of the randomization tests indicate that the size difference between the Hadar femora can be easily accommodated within most hominoid taxa at the subspecific level (though not within single-sex samples). In addition, the magnitude of shape differences between the fossils can be commonly sampled even within most single-sex samples of a single hominoid subspecies. The pattern of morphological differences between the fossils does not differ statistically from any average pattern of femoral shape dimorphism observed among living hominoids. Moreover, contrary to prior claims, and despite a size disparity between the fossils greater than is typically observed within some chimpanzee and human populations, the two Hadar fossils appear to be much more similar to one another in overall shape than either specimen is to any extant hominoid group.     

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human–chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1–1.5, 1.1–0.76 and 0.25–0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.     

A study of microwear on chimpanzee molars: Implications for dental microwear analysis

Recent investigations of dental microwear have shown that such analyses may ultimately provide valuable information about the diets of fossil species. However, no background information about intraspecific variability of microwear patterns has been available until now. This study presents the results of an SEM survey of microwear patterns found on occlusal enamel of chimpanzee molars. Methods of pattern analysis are described. Selected sites on the occlusal surface included shearing, grinding, and puncture-crushing surfaces formed by both phases of the power stroke of mastication. The microwear patterns found in this sample of chimpanzees showed a high degree of regularity. However, certain parameters such as relative pit-to-striation frequencies, feature density, striation length, and pit diameter were significantly affected by facet type and molar position. Sex and age of individuals also influenced some microwear parameters, but due to the small sample size these findings are considered to be preliminary. These results show that microwear within a single species may vary because of factors that are due more to biomechanics than to diet. The study also supplies some metrical estimates of “normal” pattern variability due to functional and morphological influences. These estimates should provide a useful baseline for assessing the significance of microwear pattern differences that may be found between species of differing diets.     

An ontogenetic approach to facial variation in three Native American populations

Various explanations have been formulated regarding high levels of craniofacial variation among Native American populations but the contribution of developmental processes to the establishment of these patterns of variation remains unknown. In this study, we compare facial morphology in ontogenetic series of three Native South American populations, one hunter-gatherer group and two farmer groups, in order to test the null hypothesis that indicates that the pattern of facial differentiation between populations does not change during ontogeny. If diet-related factors contribute to outline facial morphology, it is likely to find greater differences between hunter-gatherer and both farmer groups than between two groups of farmers and this differentiation is expected to increase with age, especially in those structures that are influenced by the mechanical load of mastication. According to our results, hunter-gatherers clearly differ from the two groups of farmers. Non-heritable factors linked to diet, such as nutritional content of food, may increase differentiation across ontogeny in some cases. However, as hunter-gatherers were clearly separated from farmer populations during entire postnatal ontogeny, an important proportion of size variation may not necessarily reflect eco-sensitive changes. Consequently, the hypothesis cannot be completely rejected.     

The Neanderthal taxonomic position: models of intra- and inter-specific craniofacial variation

The Neanderthal taxonomic position is a matter of wide disagreement among paleoanthropologists. Some workers consider this fossil human group to represent a different species, Homo neanderthalensis, while others see it as a subspecies of Homo sapiens. This study developed two models of morphological variation to be applied to a comparison between Neanderthals and modern humans: modern human populations provided a measure of intra-specific variation, while the species and subspecies of Pan provided measures of both intra- and inter-specific morphological differences. Although such an approach has been advocated strongly, it has not been systematically undertaken until recently. The techniques of geometric morphometrics were used to collect data in the form of three-dimensional coordinates of craniofacial landmarks. The data were processed using generalized procrustes analysis, and analyzed by an array of multivariate statistical methods, including principal components analysis, canonical variates analysis and Mahalanobis D(2). The morphological distances between Neanderthals and modern humans, and between Neanderthals and Late Paleolithic/early anatomically modern specimens, are consistently greater than the distances among recent human populations, and greater than the distances between the two chimpanzee species. Furthermore, no strong morphological similarities were found between Neanderthals and Late Paleolithic Europeans. This study does not find evidence for Neanderthal contribution to the evolution of modern Europeans. Results are consistent with the recognition of Neanderthals as a distinct species.     

Dietary adaptations in the teeth of murine rodents (Muridae): a test of biomechanical predictions

Functional dental theory predicts that tooth shape responds evolutionarily to the mechanical properties of food. Most studies of mammalian teeth have focused on qualitative measures of dental anatomy and have not formally tested how the functional components of teeth adapt in response to diet. Here we generated a series of predictions for tooth morphology based on biomechanical models of food processing. We used murine rodents (Old World rats and mice) to test these predictions for the relationship between diet and morphology and to identify a suite of functional dental characteristics that best predict diets. One hundred and five dental characteristics were extracted from images of the upper and lower tooth rows and incisors for 98 species. After accounting for phylogenetic relationships, we showed that species evolving plant‐dominated diets evolved deeper incisors, longer third molars, longer molar crests, blunter posteriorly angled cusps, and more expanded laterally oriented occlusal cusps than species adapting to animal‐dominated diets. Measures of incisor depth, crest length, cusp angle and sharpness, occlusal cusp orientation, and the lengths of third molars proved the best predictors of dietary adaptation. Accounting for evolutionary history in a phylogenetic discriminant function analysis notably improved the classification accuracy. Molar morphology is strongly correlated with diet and we suggest that these dental traits can be used to infer diet with good accuracy for both extinct and extant murine species.     

Patterns of microsatellite polymorphism in the range-restricted bonobo (Pan paniscus): considerations for interspecific comparison with chimpanzees (P. troglodytes)

The endangered great ape, Pan paniscus (bonobo) has the smallest range of the African apes. Virtually nothing is known about the genetic diversity or genetic structure of this species, while substantial amounts of polymorphism have been reported for the bonobo’s widespread congener, the chimpanzee (P. troglodytes). Given its restricted range, what is the extent of genetic variation in the bonobo relative to the chimpanzee, and is the bonobo genetically depauperate? To investigate patterns of genetic polymorphism, bonobos of wild origin were genotyped for 28 microsatellite loci. The mean number of alleles per locus (5.2) and the mean observed heterozygosity (0.52) in bonobos were similar to variation observed in a wild chimpanzee community (P. t. schweinfurthii). The rarer bonobo is not genetically depauperate and may have genetic diversity comparable to the eastern chimpanzee subspecies. Bonobos have approximately 55% of the allelic diversity and 66% of the observed heterozygosity exhibited by all three chimpanzee subspecies sampled across equatorial Africa. Resampling techniques were used to quantify the effects of sample size differences and number and choice of loci between bonobos and chimpanzees. The examination of these variables underscores their importance in accurately interpreting interspecific comparisons of diversity estimates.     

Interdemic variation in the foraging ecology of the African cyprinid, Barbus neumayeri

In the African cyprinid, Barbus neumayeri, populations from hypoxic waters have larger gills than populations from well-oxygenated streams. Differences in trophic morphology and feeding performance between these populations suggest a reduction in feeding efficiency in large-gilled fish that may reflect spatial constraints of the gills. However, this variation may also reflect interdemic variation in diets. In this study, we describe patterns of variation in diet, gut morphology, and prey availability for populations of B. neumayeri from swamp (low-oxygen) and stream (high-oxygen) sites in Kibale National Park, Uganda. Our results indicate that B. neumayeri are omnivorous, feeding primarily on benthic prey items; however, diets differed among swamp and stream sites for certain prey types. The observed dietary differences do not provide direct support for predictions based on variation in trophic musculature; hard-bodied prey were more common in low-oxygen sites. Prey availability also differed among sites; in particular, insect abundance and richness was generally lower in the swamp sites. Gut length was longer in one of the four populations, but did not conform to expectations based on diet differences. Condition and growth rates did not differ between populations from hypoxic and well-oxygenated sites, despite observed differences in prey availability and diet, suggesting that B. neumayeri may be distributed in a way that equalizes fitness among populations in different habitats.     

The taxonomic status of the bonobo chimpanzee

A review of past work on the taxonomic status of the bonobo chimpanzee is presented. It is suggested that differences in size and morphology of the common and the bonobo chimpanzees have been exaggerated or poorly understood. It is concluded that not enough data from the field on both bonobo and rainforest-living common chimpanzees exist to classify the bonobo. However, using Simpson's ('61) evolutionary species definition and the preliminary ecological data available, a subspecies designation for the bonobo chimpanzee is supported. Resolution of this taxonomic question through extensive field studies of both the bonobo and rainforest-dwelling common chimpanzees may greatly aid our interpretation of the hominoid fossil record.     

Dental caries prevalence as evidence for agriculture and subsistence variation during the Yayoi period in prehistoric Japan: biocultural interpretations of an economy in transition

The Yayoi period represents the earliest point of agricultural dependence in Japan, dating from approximately 2500 BP to AD 300. Yayoi period people consumed wet-rice as a primary subsistence base. This article uses dental caries prevalence to interpret the biocultural implications of agriculture among these people by testing the following hypotheses: 1) Yayoi period agriculturalists had greater frequencies of carious teeth than Jomon period foragers, 2) regional variation in carious tooth frequencies will be observed among Yayoi period agriculturalists, while 3) variation in carious tooth frequencies will be observed between male and female agriculturalists. Statistically significant differences in carious teeth were observed between the agriculturalists from Southern Honshu and all other samples. These differences suggest greater reliance on cariogenic plants among farmers from Southern Honshu and are consistent with an agricultural economy. The people of the Yayoi period from Tanegashima Island and Northern Kyushu did not have significantly different carious tooth frequencies compared to Jomon period foragers. This suggests that rice alone was not a more cariogenic dietary substance than those consumed by Jomon period foragers but a cariogenic food nonetheless. Dietary heterogeneity between the prehistoric people of the Yayoi period from Southern Honshu and those from Northern Kyushu and Tanegashima Island is also inferred from these differences. Significantly greater frequencies of carious teeth among older aged Yayoi period females compared with males suggest dietary differences between the sexes.     

Comparison of three subspecies of Trichinella spiralis by scanning electron microscopy

The surface morphology of three subspecies of Trichinella spiralis was examined by SEM in an attempt to find characteristics useful for distinguishing the subspecies. The subspecies studied were T. spiralis spiralis, which had been maintained in swine and laboratory animals for about 50 yr; T. spiralis nativa collected from Ursus maritimus at 58 degrees N latitude and 95 degrees W longitude in 1976; and, T. spiralis pseudospiralis, which was derived from the original isolation of this subspecies from Procyon lotor at 43 degrees N latitude and 47 degrees 30'E longitude in 1972. All three subspecies were passed in CFW mice and adult worms were collected from the small intestine at 4, 5, 6, 7, 8, and 11 days PI. Characteristics examined included labial and cephalic papillae, cuticular ridges and folds, hypodermal gland cell pores, pseudobursal lobes, genital papillae, cloacal aperture, copulatory bell and vulval morphology. Previous reports of subspecies differences within Trichinella spiralis in the number and distribution of hypodermal gland cell pores, position of genital papillae, shape of the cloacal aperture and shape of pseudobursal lobes were not confirmed and are believed to have been in error resulting from artifacts of fixation and a lack of knowledge of variations within the subspecies caused by low numbers of samples. Differences in surface morphology were not found among the three subspecies. The available names of the recognized biological populations of Trichinella were used at the subspecies level rather than species level because this more clearly represents the state of our knowledge of the nematodes. The question of whether the epidemiology of trichinosis is complicated by the presence of more than one species has not been answered, and it is important that our nomenclature reflect this.     

Adaptive evolution and effective population size in wild house mice

Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology. Here, we estimate α in three closely related lineages of house mice that have a similar ecology but differ widely in N(e): Mus musculus musculus (N(e) ～ 25,000-120,000), M. m. domesticus (N(e) ～ 58,000-200,000), and M. m. castaneus (N(e) ～ 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N(e), with α estimated to be approximately 40%. In contrast, estimates of α for M. m. domesticus (α = 13%) and for M. m. musculus (α = 12 %) were much smaller. Interestingly, the higher estimate of α for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N(e) contribute to differences among species in the efficacy of selection.