Sunday, February 23, 2014

Genetic Convergence among Echolocating Taxa

Parker et al. report in Nature that the genomes of several echolocating species show remarkable convergence at the amino acid level, especially in hearing-related genes. Echolocating bats do not form a monophyletic clade, indicating that echolocation has evolved more than once in the bat order. Parker et al. sequenced and assembled the genomes of four bats, including echolocating and non-echolocating species, and aligned these sequences to the mammalian genomes available on Ensembl, including those of other bats and the bottlenose dolphin, an echolocating cetacean. They estimated a likelihood value for each amino acid position's fit to the accepted species tree. Sites with poor fit where the amino acid residue present was concordant among echolocating species were considered evidence of convergence. Seven known hearing-related genes ranked high among loci containing the greatest numbers of convergent amino acids among echolocating bats and between bats and dolphins. Interestingly, so did several genes related to vision, likely reflecting adaptation to low light levels in both bats and dolphins.

Saturday, February 22, 2014

Researchers find Eurasian ancestry in eastern and southern African populations

In the most recent issue of PNAS Pickrell et al. examine the history of hunter-gatherer and pastoralist populations of southern and eastern Africa using patterns of admixture linkage disequilibrium. These populations are among the most culturally, linguistically and genetically diverse human populations. The authors found that all of these populations have some ancestry related to Europeans and Middle Easterners and infer that the presence of west Eurasian ancestry in southern Africa occurred 900-1800 y ago. They propose that a large migration of people from west Eurasia into Ethiopia occurred around 3000 y ago, which resulted in the dispersal of west Eurasian ancestry throughout eastern Africa. They then suggest that a migration of an admixed population from eastern Africa to southern Africa took place 1500 y ago, contributing to the genetic diversity seen in southern and eastern Africa today.

New discovery in Drosophila color vision

In the December 2013 issue of Current Biology Schnaitmann et al. discovered that Drosophila color vision functions differently than originally thought.  Drosophila have 8 long-wavelength-sensitive receptors, called R1-8, that play a role in vision. Previous studies equated Drosophila color vision to that of humans; where R1-6 functioned in achromatic vision similar to human rods, and R1-8 functioned in chromatic vision similar to human cones. The authors found, however, that R1-6 also contribute to color vision. This implies that fly color vision is more efficient than previously thought. The authors also suggest that flies have a conserved insect color vision system, and this new discovery will inform the understanding of vision in bees and other insects.

Sunday, February 16, 2014

Authors create a 'genetic atlas' of human admixture history

An article in the most recent issue of Science produced what they called an ‘atlas' of worldwide human admixture history. They used genetic data and identified over 100 admixture events that occurred over the past 4000 years. The authors identified admixture events by looking at alleles at multiple successive SNPs in order to identify the shared portions of DNA between individuals in different populations to determine ancestry. They found the genetic impact of several historical events including the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism. The authors also identified admixture events that did not correspond with any recorded historical events.

Thursday, February 13, 2014

Coming Soon: Richard III Complete Genome

University of Leicester Professor Turi King is to lead a project sequencing the full genome of King Richard III, the Guardian reports. The DNA was extracted from bones discovered in a Leicester parking lot (you can read about this incredible find, the forensic evidence for Richard's gruesome end, and the skeleton's severe scoliosis here). The genome sequencing is apparently driven by such questions as "Did he have straight or curly hair?," "Was the scoliosis genetic?" and "What was his susceptibility for diabetes?"

Wednesday, February 12, 2014

Clovis: The Latest Ancient Genome

This week's Nature features a report on the sequencing of the genome of a ~11,000-year-old human child buried at the Clovis site of Anzick in Montana. Comparison of the genome to those of representatives of contemporary human groups demonstrates that the child is most closely related to Native American groups currently located in Central and South America than those of Canada and the Arctic, suggesting that the split between northerly and southernly indigenous American populations predates Clovis. Further analysis supports a model in which the Clovis child belonged to a population directly ancestral to modern-day Central and South American indigenous group. These findings also strongly support the hypotheses that the Clovis people arrived in the Americans via an Asian migration, not a European migration.

Sunday, February 9, 2014

Evolutionary genetics of twinning in callitrichine primates

In a January 2014 issue of PNAS Harris et al. analyze the common marmoset genome to explore the genetic basis of the species’ unique reproductive adaptations, including multiple gestations (i.e. dichorionic twins and trichorionic triplets). The authors identified callitrichine-specific nonsynonymous substitutions that they found to be associated with the inhibition of growth factors and bone morphogenetic proteins. They postulated that positive selection affected New World monkey growth patterns, with callitrichine miniaturization coevolving with reproductive adaptations that bear benefit when gestating multiples. Polymorphisms in GDF9 and BMP15 were candidate genes for twinning in callitrichines based on studies in other species, and two other candidates were identified, BMP4 and WFIKKN1. These analyses contribute a set of candidate loci to be further characterized in human populations with a higher heritability for twinning.

Molecular adaptations in the Chinese alligator

In the September 2013 issue of Cell Research Wan et al. report the genome sequence of a single Chinese alligator. They identify several positively-selected molecular adaptations in protein-coding genes that are associated with traits for predation in aquatic habitats. Alligators are top predators, and they are able to ambush prey from underwater, remain submerged for long periods, and can sense small prey. The authors focused on genes that regulated these functions and found unique molecular signatures, including a diving adaptation that allows alligators to tolerate hypoxia and regulate metabolic demands for long periods of submersion. They found gene expansion in olfactory, synaptic, auditory, and immune function genes, as well. This study provides a new perspective into hypoxia resistance by elucidating the genetic signature of aerobic diving, which is a form of voluntarily tolerant hypoxia.

Independent Mutations within the Agouti Gene Underlie Different Aspects of Pigmentation Phenotype

Linnen et al. found that the light pigmentation phenotype of light habitat-dwelling deer mice was actually composed of several distinct independently-varying traits (including dorsal lightening, ventral lightening, the placement of the dorsal-ventral boundary, and the coloration of the tail), suggesting an independent genetic basis for each trait. This was confirmed by subsequent sequencing and mapping of the Agouti gene: several SNPs in equilibrium within Agouti contributed to different traits. Implications of this study include a.) that what appears to be a large-effect QTL may actually be a cluster of QTL of small- to moderate-effect; and, b.) that similar seeming phenotypic traits controlled by the same gene may not actually the product of pleiotropy.