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1.  Whole-genome analyses resolve early branches in the tree of life of modern birds 
Jarvis, Erich D. | Mirarab, Siavash | Aberer, Andre J. | Li, Bo | Houde, Peter | Li, Cai | Ho, Simon Y. W. | Faircloth, Brant C. | Nabholz, Benoit | Howard, Jason T. | Suh, Alexander | Weber, Claudia C. | da Fonseca, Rute R. | Li, Jianwen | Zhang, Fang | Li, Hui | Zhou, Long | Narula, Nitish | Liu, Liang | Ganapathy, Ganesh | Boussau, Bastien | Bayzid, Md. Shamsuzzoha | Zavidovych, Volodymyr | Subramanian, Sankar | Gabaldón, Toni | Capella-Gutiérrez, Salvador | Huerta-Cepas, Jaime | Rekepalli, Bhanu | Munch, Kasper | Schierup, Mikkel | Lindow, Bent | Warren, Wesley C. | Ray, David | Green, Richard E. | Bruford, Michael W. | Zhan, Xiangjiang | Dixon, Andrew | Li, Shengbin | Li, Ning | Huang, Yinhua | Derryberry, Elizabeth P. | Bertelsen, Mads Frost | Sheldon, Frederick H. | Brumfield, Robb T. | Mello, Claudio V. | Lovell, Peter V. | Wirthlin, Morgan | Schneider, Maria Paula Cruz | Prosdocimi, Francisco | Samaniego, José Alfredo | Velazquez, Amhed Missael Vargas | Alfaro-Núñez, Alonzo | Campos, Paula F. | Petersen, Bent | Sicheritz-Ponten, Thomas | Pas, An | Bailey, Tom | Scofield, Paul | Bunce, Michael | Lambert, David M. | Zhou, Qi | Perelman, Polina | Driskell, Amy C. | Shapiro, Beth | Xiong, Zijun | Zeng, Yongli | Liu, Shiping | Li, Zhenyu | Liu, Binghang | Wu, Kui | Xiao, Jin | Yinqi, Xiong | Zheng, Qiuemei | Zhang, Yong | Yang, Huanming | Wang, Jian | Smeds, Linnea | Rheindt, Frank E. | Braun, Michael | Fjeldsa, Jon | Orlando, Ludovic | Barker, F. Keith | Jønsson, Knud Andreas | Johnson, Warren | Koepfli, Klaus-Peter | O’Brien, Stephen | Haussler, David | Ryder, Oliver A. | Rahbek, Carsten | Willerslev, Eske | Graves, Gary R. | Glenn, Travis C. | McCormack, John | Burt, Dave | Ellegren, Hans | Alström, Per | Edwards, Scott V. | Stamatakis, Alexandros | Mindell, David P. | Cracraft, Joel | Braun, Edward L. | Warnow, Tandy | Jun, Wang | Gilbert, M. Thomas P. | Zhang, Guojie
Science (New York, N.Y.)  2014;346(6215):1320-1331.
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
doi:10.1126/science.1253451
PMCID: PMC4405904  PMID: 25504713
2.  Distance-dependent patterns of molecular divergences in tuatara mitogenomes 
Scientific Reports  2015;5:8703.
Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection.
doi:10.1038/srep08703
PMCID: PMC4346810  PMID: 25731894
3.  Evidence for a recent origin of penguins 
Biology Letters  2013;9(6):20130748.
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.
doi:10.1098/rsbl.2013.0748
PMCID: PMC3871361  PMID: 24227045
penguin evolution; climate change; rate of evolution
4.  Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment 
GigaScience  2014;3:27.
Background
Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].
Results
Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.
Conclusions
Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
Electronic supplementary material
The online version of this article (doi:10.1186/2047-217X-3-27) contains supplementary material, which is available to authorized users.
doi:10.1186/2047-217X-3-27
PMCID: PMC4322438  PMID: 25671092
Penguins; Avian genomics; Evolution; Adaptation; Antarctica
5.  The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred 
Background
The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors’ remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred.
Results
We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire.
Conclusions
The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.
doi:10.1186/1471-2148-14-136
PMCID: PMC4099497  PMID: 25027719
Spotted Green Pigeon; Caloenas maculata; Dodo; Raphus cucullatus; Extinct; Museum specimen; DNA extraction; Ancient DNA; Mini-barcode; Phylogeny
6.  Identification, Classification, and Growth of Moa Chicks (Aves: Dinornithiformes) from the Genus Euryapteryx 
PLoS ONE  2014;9(6):e99929.
Background
The analysis of growth in extinct organisms is difficult. The general lack of skeletal material from a range of developmental states precludes determination of growth characteristics. For New Zealand's extinct moa we have available to us a selection of rare femora at different developmental stages that have allowed a preliminary determination of the early growth of this giant flightless bird. We use a combination of femora morphometrics, ancient DNA, and isotope analysis to provide information on the identification, classification, and growth of extinct moa from the genus Euryapteryx.
Results
Using ancient DNA, we identify a number of moa chick bones for the species Euryapteryx curtus, Dinornis novaezealandiae, and Anomalopteryx didiformis, and the first chick bone for Pachyornis geranoides. Isotope analysis shows that ∂15N levels vary between the two known size classes of Euryapteryx, with the larger size class having reduced levels of ∂15N. A growth series for femora of the two size classes of Euryapteryx shows that early femora growth characteristics for both classes are almost identical. Morphometric, isotopic, and radiographic analysis of the smallest Euryapteryx bones suggests that one of these femora is from a freshly hatched moa at a very early stage of development.
Conclusion
Using morphometric, isotopic, and ancient DNA analyses have allowed the determination of a number of characteristics of rare moa chick femora. For Euryapteryx the analyses suggest that the smaller sized class II Euryapteryx is identical in size and growth to the extant Darwin's rhea.
doi:10.1371/journal.pone.0099929
PMCID: PMC4055697  PMID: 24923666
7.  Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes) 
Background
The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.
Results
To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.
Conclusions
The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.
doi:10.1186/1471-2148-14-75
PMCID: PMC4101845  PMID: 24885927
tbx5; Moa; Gene expression; Ancient DNA; Development; Forelimb
8.  An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia 
Science (New York, N.Y.)  2011;334(6052):94-98.
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
doi:10.1126/science.1211177
PMCID: PMC3991479  PMID: 21940856
9.  Complex Species Status for Extinct Moa (Aves: Dinornithiformes) from the Genus Euryapteryx 
PLoS ONE  2014;9(3):e90212.
The exact species status of New Zealand's extinct moa remains unknown. In particular, moa belonging to the genus Euryapteryx have been difficult to classify. We use the DNA barcoding sequence on a range of Euryapteryx samples in an attempt to resolve the species status for this genus. We obtained mitochondrial control region and the barcoding region from Cytochrome Oxidase Subunit I (COI) from a number of new moa samples and use available sequences from previous moa phylogenies and eggshell data to try and clarify the species status of Euryapteryx. Using the COI barcoding region we show that species status in Euryapteryx is complex with no clear separation between various individuals. Eggshell, soil, and bone data suggests that a Euryapteryx subspecies likely exists on New Zealand's North Island and can be characterized by a single mitochondrial control region SNP. COI divergences between Euryapteryx individuals from the south of New Zealand's South Island and those from the Far North of the North Island exceed 1.6% and are likely to represent separate species. Individuals from other areas of New Zealand were unable to be clearly separated based on COI differences possibly as a result of repeated hybridisation events. Despite the accuracy of the COI barcoding region to determine species status in birds, including that for the other moa genera, for moa from the genus Euryapteryx, COI barcoding fails to provide a clear result, possibly as a consequence of repeated hybridisation events between these moa. A single control region SNP was identified however that segregates with the two general morphological variants determined for Euryapteryx; a smaller subspecies restricted to the North Island of New Zealand, and a larger subspecies, found on both New Zealand's North and South Island.
doi:10.1371/journal.pone.0090212
PMCID: PMC3940832  PMID: 24594991
10.  DNA fingerprinting in zoology: past, present, future 
In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic ‘paradigm shifts’ during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys’ identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as ‘DNA fingerprinting’, also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys’ invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys’ pioneering work.
doi:10.1186/2041-2223-5-3
PMCID: PMC3909909  PMID: 24490906
Multilocus VNTR probes; Single locus probes; Avian mating systems; Microsatellite DNA
12.  King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times 
Biology Letters  2012;8(4):586-589.
Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.
doi:10.1098/rsbl.2012.0053
PMCID: PMC3391457  PMID: 22357937
King penguin; Macquarie Island; genetic diversity; ancient DNA; conservation
13.  Highly Informative Ancient DNA ‘Snippets’ for New Zealand Moa 
PLoS ONE  2013;8(1):e50732.
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.
doi:10.1371/journal.pone.0050732
PMCID: PMC3547012  PMID: 23341875
14.  Selective Constraints Determine the Time Dependency of Molecular Rates for Human Nuclear Genomes 
Genome Biology and Evolution  2012;4(11):1127-1132.
In contrast to molecular rates for neutral mitochondrial sequences, rates for constrained sites (including nonsynonymous sites, D-loop, and RNA) in the mitochondrial genome are known to vary with the time frame used for their estimation. Here, we examined this issue for the nuclear genomes using single-nucleotide polymorphisms (SNPs) from six complete human genomes of individuals belonging to different populations. We observed a strong time-dependent distribution of nonsynonymous SNPs (nSNPs) in highly constrained genes. Typically, the proportion of young nSNPs specific to a single population was found to be up to three times higher than that of the ancient nSNPs shared between diverse human populations. In contrast, this trend disappeared, and a uniform distribution of young and old nSNPs was observed in genes under relaxed selective constraints. This suggests that because mutations in constrained genes are highly deleterious, they are removed over time, resulting in a relative overabundance of young nSNPs. In contrast, mutations in genes under relaxed constraints are nearly neutral, which leads to similar proportions of young and old SNPs. These results could be useful to researchers aiming to select appropriate genes or genomic regions for estimating evolutionary rates and species or population divergence times.
doi:10.1093/gbe/evs092
PMCID: PMC3514959  PMID: 23059453
rates of evolution; natural selection; time dependency; deleterious polymorphisms; population genetic theory
15.  Ancient DNA Analyses Reveal Contrasting Phylogeographic Patterns amongst Kiwi (Apteryx spp.) and a Recently Extinct Lineage of Spotted Kiwi 
PLoS ONE  2012;7(8):e42384.
The little spotted kiwi (Apteryx owenii) is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis), with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii) formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species) survived on the South Island mainland until more recently than previously thought.
doi:10.1371/journal.pone.0042384
PMCID: PMC3410920  PMID: 22876319
16.  Time Dependency of Molecular Evolutionary Rates? Yes and No 
Genome Biology and Evolution  2011;3:1324-1328.
Some previous studies have suggested that rates of evolution inferred using molecular sequences vary substantially depending on the time frame over which they are measured, whereas a number of other studies have argued against this proposition. We examined this issue by separating positions of primate mitochondrial genomes that are under different levels of selection constraints. Our results revealed an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop, and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated. Although the evolutionary rate at nonsynonymous sites obtained using the European (H1 haplogroup) mitogenomes is 9–15 times higher than that estimated using the human–chimpanzee pair, in contrast, the rates at synonymous sites are similar between these comparisons. We also show that the ratio of divergence at nonsynonymous to synonymous sites estimated using intra- and interspecific comparisons vary up to nine times, which corroborates our results independent of calibration times.
doi:10.1093/gbe/evr108
PMCID: PMC3236606  PMID: 22016336
rates of evolution; natural selection; neutral evolution; time dependency; divergence times; population coalescent times
17.  Ancient DNA Suggests Dwarf and ‘Giant’ Emu Are Conspecific 
PLoS ONE  2011;6(4):e18728.
Background
The King Island Emu (Dromaius ater) of Australia is one of several extinct emu taxa whose taxonomic relationship to the modern Emu (D. novaehollandiae) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu.
Methodology and Results
We investigated the evolutionary relationships between the King Island and modern Emu by the recovery of both nuclear and mitochondrial DNA sequences from sub-fossil remains. The complete mitochondrial control (1,094 bp) and cytochrome c oxidase subunit I (COI) region (1,544 bp), as well as a region of the melanocortin 1 receptor gene (57 bp) were sequenced using a multiplex PCR approach. The results show that haplotypes for King Island Emu fall within the diversity of modern Emu.
Conclusions
These data show the close relationship of these emu when compared to other congeneric bird species and indicate that the King Island and modern Emu share a recent common ancestor. King Island emu possibly underwent insular dwarfism as a result of phenotypic plasticity. The close relationship between the King Island and the modern Emu suggests it is most appropriate that the former should be considered a subspecies of the latter. Although both taxa show a close genetic relationship they differ drastically in size. This study also suggests that rates of morphological and neutral molecular evolution are decoupled.
doi:10.1371/journal.pone.0018728
PMCID: PMC3073985  PMID: 21494561
18.  Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi 
Background
Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold.
Results
Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes.
Conclusions
The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.
doi:10.1186/1471-2148-10-387
PMCID: PMC3009673  PMID: 21156082
19.  The Molecular Ecology of the Extinct New Zealand Huia 
PLoS ONE  2009;4(11):e8019.
The extinct Huia (Heteralocha acutirostris) of New Zealand represents the most extreme example of beak dimorphism known in birds. We used a combination of nuclear genotyping methods, molecular sexing, and morphometric analyses of museum specimens collected in the late 19th and early 20th centuries to quantify the sexual dimorphism and population structure of this extraordinary species. We report that the classical description of Huia as having distinctive sex-linked morphologies is not universally correct. Four Huia, sexed as females had short beaks and, on this basis, were indistinguishable from males. Hence, we suggest it is likely that Huia males and females were indistinguishable as juveniles and that the well-known beak dimorphism is the result of differential beak growth rates in males and females. Furthermore, we tested the prediction that the social organisation and limited powers of flight of Huia resulted in high levels of population genetic structure. Using a suite of microsatellite DNA loci, we report high levels of genetic diversity in Huia, and we detected no significant population genetic structure. In addition, using mitochondrial hypervariable region sequences, and likely mutation rates and generation times, we estimated that the census population size of Huia was moderately high. We conclude that the social organization and limited powers of flight did not result in a highly structured population.
doi:10.1371/journal.pone.0008019
PMCID: PMC2777306  PMID: 19946368
20.  Ancient DNA Resolves Identity and Phylogeny of New Zealand's Extinct and Living Quail (Coturnix sp.) 
PLoS ONE  2009;4(7):e6400.
Background
The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands.
Methodology/Principal Findings
Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure.
Conclusion/Significance
Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology.
doi:10.1371/journal.pone.0006400
PMCID: PMC2712072  PMID: 19636374
21.  Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic 
PLoS Genetics  2008;4(10):e1000209.
Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (μ) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.
Author Summary
Molecular evolutionary theory suggests that for neutral DNA sequences, rates of mutation and evolution should be equal. However, there has been considerable variation in empirical estimates of rates of molecular change in vertebrate animals, even for the same regions of the mitochondrial genome. A difficulty is that evolutionary rates estimated from ancient DNA and short-term mutation rates are not available for the same species. We present data on the rate of mutation of the mitochondrial hypervariable region in Adélie penguins from the Antarctic. All recorded mutations were heteroplasmic in mothers, and almost invariably, both genetic variants were passed to their offspring. We compared this rate of mutation to the rate of evolution estimated using serially preserved ancient remains. We show that these two estimates were not statistically different from each other.
doi:10.1371/journal.pgen.1000209
PMCID: PMC2546446  PMID: 18833304
22.  Pulse Oximetry: Evaluation of Accuracy during Outpatient General Anesthesia for Oral Surgery 
Anesthesia Progress  1988;35(2):53-60.
Pulse oximetry has been shown to be accurate under steady state conditions. In this study, the accuracy of four pulse oximeters are evaluated and compared during outpatient general anesthesia for third molar extractions. The oximeters evaluated are the Nellcor N-100, the Ohmeda 3700, the Novametrix model 500, and the Bird 4400 portable pulse oximeter.
Ultralight general anesthesia for oral surgery presents a unique challenge for respiratory monitoring in that patients are often not intubated and commonly experience periods of hyper- and hypoventilation. Airway obstruction, apnea, and laryngospasm may occur easily and patients often vocalize and move during surgery. Because hypoxemia is the primary cause of morbidity and mortality during anesthesia, an accurate, continuous, and noninvasive monitor of oxygenation is critical to risk management.
Twenty ASA class I and II patients underwent outpatient general anesthesia for third molar removal using nitrous oxide-oxygen, midazolam, fentanyl, and methohexital. Arterial blood samples were obtained at five-minute intervals during anesthesia, as well as any time a desaturation of >5% occurred, for measurement of arterial SaO2 with an IL282 CO-Oximeter. These values were compared with simultaneously recorded saturations observed for each pulse oximeter. A total of 122 arterial samples were obtained over a range of PaO2 from 52-323 mm Hg and observed saturations of 70-100%.
The Bird 4400 portable pulse oximeter proved to be the most accurate and reliably predicted arterial saturation under these conditions (y = 1.03x - 2.8, r = 0.85). The Novametrix model 500 pulse oximeter also demonstrated a high degree of accuracy by linear regression analysis, but displayed the lowest correlation coefficient (spread of data points) overall (y = 0.97x + 2.8, r = 0.80.) The Nellcor N-100 pulse oximeter also proved to be highly accurate. (y = 1.05x - 4.1, r = 0.84.) In contrast, regression analysis of the observed saturations obtained with the Ohmeda 3700 pulse oximeter revealed that this unit significantly underestimated arterial saturation (y = 1.20x - 19.6, r = 0.83.)
This study demonstrates that despite the rigorous conditions imposed by outpatient general anesthesia for oral surgery, three of the pulse oximeters tested were linearly accurate in predicting arterial oxyhemoglobin saturation over the range of 70-100%. The Ohmeda 3700 was found to significantly underestimate arterial saturation.
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PMCID: PMC2148593  PMID: 3166346

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