Nicholas I. Mundy

Insights into hominid evolution from the gorilla genome sequence.

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

A window on the genetics of evolution: MC1R and plumage colouration in birds

Melanins are a ubiquitous component of plumage colouration in birds and serve a wide variety of functions. Although the genetic control of melanism has been studied in chickens and other domestic species, little was known about the molecular genetics of melanin distribution in wild birds until recently. Studies have now revealed that a single locus, the melanocortin-1 receptor (MC1R) locus, is responsible for melanic polymorphisms in at least three unrelated species: the bananaquit, the snow goose and the arctic skua. Results show that melanism was a derived trait and allow other evolutionary inferences about the history of melanism to be made. The role of MC1R in plumage patterning is surprisingly diverse among different species. The conserved molecular basis for the evolution of melanism in birds and several other vertebrates is probably related to low pleiotropic effects at the MC1R.

Evolution and selection of trichromatic vision in primates

Trichromatic colour vision is of considerable importance to primates but is absent in other eutherian mammals. Primate colour vision is traditionally believed to have evolved for finding food in the forest. Recent work has tested the ecological importance of trichromacy to primates, both by measuring the spectral and chemical properties of food eaten in the wild, and by testing the relative foraging abilities of dichromatic and trichromatic primates. Molecular studies have revealed the genetic mechanisms of the evolution of trichromacy, and are providing new insight into visual pigment gene expression and colour vision defects. By drawing together work from these different fields, we can gain a better understanding of how natural selection has shaped the evolution of trichromatic colour vision in primates and also about mechanisms of gene duplication, heterozygote advantage and balancing selection.

The molecular basis of an avian plumage polymorphism in the wild: A melanocortin-1-receptor point mutation is perfectly associated with the melanic plumage morph of the bananaquit, Coereba flaveola

BACKGROUND Evolution depends on natural selection acting on phenotypic variation, but the genes responsible for phenotypic variation in natural populations of vertebrates are rarely known. The molecular genetic basis for plumage color variation has not been described in any wild bird. Bananaquits (Coereba flaveola) are small passerine birds that occur as two main plumage variants, a widespread yellow morph with dark back and yellow breast and a virtually all black melanic morph. A candidate gene for this color difference is the melanocortin-1 receptor (MC1R), a key regulator of melanin synthesis in feather melanocytes. RESULTS We sequenced the MC1R gene from four Caribbean populations of the bananaquit; two populations of the yellow morph and two populations containing both the yellow morph and the melanic morph. A point mutation resulting in the replacement of glutamate with lysine was present in at least one allele of the MC1R gene in all melanic birds and was absent in all yellow morph birds. This substitution probably causes the color variation, as the same substitution is responsible for melanism in domestic chickens and mice. The evolutionary relationships among the MC1R haplotypes show that the melanic alleles on Grenada and St. Vincent had a single origin. The low prevalence of nonsynonymous substitutions among yellow haplotypes suggests that they have been under stabilizing selection, whereas strong selective constraint on melanic haplotypes is absent. CONCLUSIONS We conclude that a mutation in the MC1R is responsible for the plumage polymorphism in a wild bird population and that the melanic MC1R alleles in Grenada and St. Vincent bananaquit populations have a single evolutionary origin from a yellow allele.

Demonstration of a foraging advantage for trichromatic marmosets (Callithrix geoffroyi) dependent on food colour

It has been suggested that the major advantage of trichromatic over dichromatic colour vision in primates is enhanced detection of red/yellow food items such as fruit against the dappled foliage of the forest. This hypothesis was tested by comparing the foraging ability of dichromatic and trichromatic Geoffroys marmosets (Callithrix geoffroyi) for orange– and green–coloured cereal balls (Kix®) in a naturalized captive setting. Trichromatic marmosets found a significantly greater number of orange, but not green, Kix® than dichromatic marmosets when the food items were scattered on the floor of the cage (at a potential detection distance of up to 6 m from the animals). Under these conditions, trichromats but not dichromats found significantly more orange than green Kix®, an effect that was also evident when separately examining the data from the end of the trials, when the least conspicuous Kix® were left. In contrast, no significant differences among trichromats and dichromats were seen when the Kix® were placed in trays among green wood shavings (detection distance < 0.5 m). These results support an advantage for trichromats in detecting orange–coloured food items against foliage, and also suggest that this advantage may be less important at shorter distances. If such a foraging advantage for trichromats is present in the wild it might be sufficient to maintain the colour vision polymorphism seen in the majority of New World monkeys.

The effect of colour vision status on the detection and selection of fruits by tamarins (Saguinus spp.)

SUMMARY The evolution of trichromatic colour vision by the majority of anthropoid primates has been linked to the efficient detection and selection of food, particularly ripe fruits among leaves in dappled light. Modelling of visual signals has shown that trichromats should be more efficient than dichromats at distinguishing both fruits from leaves and ripe from unripe fruits. This prediction is tested in a controlled captive setting using stimuli recreated from those actually encountered by wild tamarins (Saguinus spp.). Dietary data and reflectance spectra of Abuta fluminum fruits eaten by wild saddleback (Saguinus fuscicollis) and moustached (Saguinus mystax) tamarins and their associated leaves were collected in Peru. A. fluminum leaves, and fruits in three stages of ripeness, were reproduced and presented to captive saddleback and red-bellied tamarins (Saguinus labiatus). Trichromats were quicker to learn the task and were more efficient at selecting ripe fruits than were dichromats. This is the first time that a trichromatic foraging advantage has been demonstrated for monkeys using naturalistic stimuli with the same chromatic properties as those encountered by wild animals.

Evolution of an avian pigmentation gene correlates with a measure of sexual selection

The extravagant plumage traits of male birds are a favourite example of sexual selection. However, to date the units that selection is acting upon, the genes themselves have been a ‘black box’. Here, we report evidence of change driven by sexual selection at a pigmentation gene locus in the galliform birds. Across species, we find a correlation between the rate of amino acid change (dN/dS) at this locus (MC1R) and the degree of sexual dichromatism, which we use as a measure of the strength of sexual selection. There is no evidence for a similar pattern in any of five other loci (four candidate and one control locus). This is consistent with previous work on colour polymorphisms and suggests that MC1R may be a key target for selection acting on plumage colour. The pattern of selection at MC1R seems to be consistent with the continuous or cyclical evolution of traits and preferences that is the outcome of several Fisherian and good-genes models of sexual selection. In contrast, we found no support for models of sexual selection that predict an increase in purifying selection as a result of purging of deleterious mutations or for models that predict an increased rate of mutation in association with stronger sexual selection.

Trans-specific evolution of opsin alleles and the maintenance of trichromatic colour vision in Callitrichine primates

Many New World (NW) primates possess a remarkable polymorphism in an X‐linked locus, which encodes for the visual pigments (opsins) used for colour vision. Females that are heterozygous for opsin alleles of different spectral sensitivity at this locus have trichromatic colour vision, whereas homozygous females and males are dichromatic, with poor colour discrimination in the red–green range. Here we describe an extensive survey of allelic variation in both exons and introns at this locus within and among species of the Callitrichines (marmosets and tamarins). All five genera of Callitrichines have the X‐linked polymorphism, and only the three functional allelic classes described previously (with maximum wavelength sensitivities at about 543 nm, 556 nm and 563 nm) were found among the 16 species and 233 or more X‐chromosomes sampled. In spite of the homogenizing effects of gene conversion, phylogenetic analyses provide direct evidence for trans‐specific evolution of alleles over time periods of at least 5–6 million years, and up to 14 million years (estimated from independent phylogenies). These conclusions are supported by the distribution of insertions and deletions in introns. The maintenance of polymorphism over these time periods requires an adaptive explanation, which must involve a heterozygote advantage for trichromats. The lack of detection of alleles that are recombinant for spectral sensitivity suggests that such alleles are suboptimal. The two main hypotheses for the selective advantage of trichromacy in primates are frugivory for ripe fruits and folivory for young leaves. The latter can be discounted in Callitrichines, as they are not folivorous.

Avian haematozoan parasites and their associations with mosquitoes across Southwest Pacific Islands

The degree to which haematozoan parasites can exploit a range of vectors and hosts has both ecological and evolutionary implications for their transmission and biogeography. Here we explore the extent to which closely related mosquito species share the same or closely related haematozoan parasites, and examine the overlap in parasite lineages with those isolated from avian hosts, Zosterops species, sampled across the same study sites. Mosquito samples were collected and analysed (14 species, n = 804) from four islands in Vanuatu and the main island of New Caledonia. Using polymerase chain reaction, 15.5% (14/90) of pooled mosquito (thoracic) samples showed positive amplifications. Subsequent phylogenetic analysis of the cytochrome b gene identified four genetically distinct Plasmodium and two Haemoproteus lineages from these samples, five of which were identical to parasite lineages (n = 21) retrieved from the avian hosts. We found that three Plasmodium lineages differing by a maximum of 0.9% sequence divergence were recovered from different species and genera of mosquitoes and two Haemoproteus lineages differing by 4.6% sequence divergence were carried by 10 distantly related (11–21% divergent) mosquito species. These data suggest a lack of both cospeciation and invertebrate host conservatism. Without experimental demonstration of the transmission cycle, it is not possible to establish whether these mosquitoes are the biological vectors of isolated parasite lineages, reflecting a limitation of a purely polymerase chain reaction‐based approach. Nonetheless, our results raise the possibility of a new transmission pathway and highlight extensive invertebrate host shifts in an insular mosquito–parasite system.

Adaptive Evolution of Four Microcephaly Genes and the Evolution of Brain Size in Anthropoid Primates

The anatomical basis and adaptive function of the expansion in primate brain size have long been studied; however, we are only beginning to understand the genetic basis of these evolutionary changes. Genes linked to human primary microcephaly have received much attention as they have accelerated evolutionary rates along lineages leading to humans. However, these studies focus narrowly on apes, and the link between microcephaly gene evolution and brain evolution is disputed. We analyzed the molecular evolution of four genes associated with microcephaly (ASPM, CDK5RAP2, CENPJ, MCPH1) across 21 species representing all major clades of anthropoid primates. Contrary to prevailing assumptions, positive selection was not limited to or intensified along the lineage leading to humans. In fact we show that all four loci were subject to positive selection across the anthropoid primate phylogeny. We developed clearly defined hypotheses to explicitly test if selection on these loci was associated with the evolution of brain size. We found positive relationships between both CDK5RAP2 and ASPM and neonatal brain mass and somewhat weaker relationships between these genes and adult brain size. In contrast, there is no evidence linking CENPJ and MCPH1 to brain size evolution. The stronger association of ASPM and CDK5RAP2 evolution with neonatal brain size than with adult brain size is consistent with these loci having a direct effect on prenatal neuronal proliferation. These results suggest that primate brain size may have at least a partially conserved genetic basis. Our results contradict a previous study that linked adaptive evolution of ASPM to changes in relative cortex size; however, our analysis indicates that this conclusion is not robust. Our finding that the coding regions of two widely expressed loci has experienced pervasive positive selection in relation to a complex, quantitative developmental phenotype provides a notable counterexample to the commonly asserted hypothesis that cis-regulatory regions play a dominant role in phenotypic evolution.