Showing papers by "David M. Lambert published in 2013"

Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau

Abstract: The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and 'tit-to-jay' change for coping with the life in an extreme environment.

Ancient DNA: Towards a million-year-old genome

Abstract: The sequencing of a complete horse genome from a bone dating to around 700,000 years ago sheds light on equine evolution and dramatically extends the known limit of DNA survival. See Letter p.74 A low-coverage draft genome sequence has been obtained from a horse bone recovered from a permafrost site in the Yukon Territory, Canada, dated to around 560,000–780,000 years before present. This is by far the earliest genome sequence so far determined. The data were compared to draft genome sequences for a Late Pleistocene horse, those of five contemporary domestic horse breeds, a Przewalski's horse and a donkey. Comparative genomics suggest that the Equus lineage that gave rise to all contemporary horses, zebras and donkeys originated about 4.0–4.5 million years ago — much earlier than previously suspected. The data support the contention that Przewalski's horses — an endangered subspecies native to the Mongolian steppes — represent the last surviving wild horse population.

Measurement of $J/\psi$ production in $pp$ collisions at $\sqrt{s}=2.76$ TeV

Abstract: The production of J/psi mesons is studied with the LHCb detector using data from pp collisions at root s = 2.76 TeV corresponding to an integrated luminosity of 71 nb(-1). The differential cross-section for inclusive J/psi production is measured as a function of its transverse momentum p(T). The cross-section in the fiducial region 0 < p(T) < 12 GeV/c and rapidity 2.0 < y < 4.5 is measured to be 5.6 +/- 0.1 (stat) +/- 0.4 (syst) mu b, with the assumption of unpolarised J/psi production. The fraction of J/psi production from b-hadron decays is measured to be (7.1 +/- 0.6 (stat) +/- 0.7 (syst))%.

Evidence for a recent origin of penguins

Abstract: Penguins are a remarkable group of birds, with the 18 extant species living in diverse climatic zones from the tropics to Antarctica. The timing of the origin of these extant penguins remains controversial. Previous studies based on DNA sequences and fossil records have suggested widely differing times for the origin of the group. This has given rise to widely differing biogeographic narratives about their evolution. To resolve this problem, we sequenced five introns from 11 species representing all genera of living penguins. Using these data and other available DNA sequences, together with the ages of multiple penguin fossils to calibrate the molecular clock, we estimated the age of the most recent common ancestor of extant penguins to be 20.4 Myr (17.0–23.8 Myr). This time is half of the previous estimates based on molecular sequence data. Our results suggest that most of the major groups of extant penguins diverged 11–16 Ma. This overlaps with the sharp decline in Antarctic temperatures that began approximately 12 Ma, suggesting a possible relationship between climate change and penguin evolution.

Gene flow maintains genetic diversity and colonization potential in recently range‐expanded populations of an Oriental bird, the Light‐vented Bulbul (Pycnonotus sinensis, Aves: Pycnonotidae)

Abstract: Aim Two alternative genetic patterns are typical in recently established populations. One is reduced genetic diversity but significant population structuring compared with original populations. The other is the persistence of genetic polymorphisms and the lack of differentiation in frontier populations. This study aims to test for these patterns by examining population genetics of the Light-vented Bulbul (Pycnonotus sinensis), an Oriental bird that has been undergoing rapid range expansion. Location Eastern China. Methods Molecular analyses were conducted on mitochondrial DNA and microsatellite datasets from 256 individuals. Intraspecific phylogeny was reconstructed by Bayesian inference and network analysis. Analysis of molecular variance (AMOVA) and Bayesian clustering were applied to determine population structure. Genetic diversity was tested to determine whether there were significant differences between frontier and source populations. Population expansions were tested in mtDNA and microsatellites. Gene flow and recent migrants were estimated by Bayesian methods. Results Both high- and low-nucleotide diversities were recorded in frontier populations, and differences in genetic diversity between frontier and source populations were not statistically significant. Population differentiation was recorded in some source but not in frontier populations. Population size expansion was detected both in frontier and in source populations, and for the whole dataset, commencing before the Last Glacial Maximum. Main conclusions Genetic diversity can be maintained in expanding populations of the Light-vented Bulbul, and genetic differentiation can be avoided, where substantial genetic exchanges are occurring. This study also discusses the potential effects of evolutionary properties such as historical population growth on recently recorded range expansion.

Using ancient DNA to enhance museum collections: a case study of rare kiwi (Apteryx spp.) specimens

Abstract: Six museum kiwi (Apteryx spp.) specimens of unknown or uncertain provenance were assigned to species using ancient DNA methods in conjunction with a reference database of modern and ancient kiwi DNA sequences. Four of the five species of kiwi exhibit a substantial overlap in bone morphology but can be identified with DNA sequences. The origin of one specimen, an articulated kiwi skeleton, was determined to be Stewart Island, a region that is currently poorly represented in museum collections. This study demonstrates that DNA analyses can add value to museum collections by determining species and provenance of specimens.

Highly Informative Ancient DNA ‘Snippets’ for New Zealand Moa

Abstract: Background Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand’s moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species. Methodology/Principal Findings By targeting such ‘snippets’, we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments. Conclusions/Significance Short highly variable mitochondrial ‘snippets’ allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.

Non-Darwinian Evolution

Abstract: The term ‘non-Darwinian evolution’ was brought to prominence in the now-famous paper by Jack Lester King and Thomas H. Jukes published in Science in 1969. The title was deliberately provocative and it is clear that the authors had chosen their title with the intention of stimulating the evolutionary establishment. It worked! The title was even later described by some as ‘blasphemous’. King and Jukes’ colleague Motoo Kimura actually asked them to change the title to emphasize molecular evolution instead of evolution in general, but they declined. However, Jukes himself later felt that a better title would have been ‘nonadaptive evolution’. More generally, the King and Jukes’ paper was a challenge to the molecular panselectionism advocated by authors such as George Gaylord Simpson and Emil Smith. After the early 1970s, the term became, essentially, a synonym for the ‘neutral theory of molecular evolution’. However, literally, the term is defined by what it is not since its meaning depends on our understanding of the nature of ‘Darwinian evolution’ itself. In addition, taking a broader and more literal interpretation of ‘non-Darwinian evolution’ suggests that a broad range of phenomena can be grouped legitimately under this term.