Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi

<p>Abstract</p> <p>Background</p> <p>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 (<it>Apteryx australis mantelli</it>) 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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p

The Molecular Ecology of the Extinct New Zealand Huia

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

Investigating the global dispersal of chickens in prehistory using ancient mitochondrial dna signatures

Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testingExcavations in Fais by MI were made possible by a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science. DB gratefully acknowledges support from the Marsden Fund, and the Allan Wilson Centre for Molecular Ecology and Evolution. During the course of this research AS was supported by a Postgraduate Scholarship from the University of Auckland and a Fellowship from the Allan Wilson Centre for Molecular Ecology and Evolutio

An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution

Studies of the evolution of development characterize the way in which gene regulatory dynamics during ontogeny constructs and channels phenotypic variation. These studies have identified a number of evolutionary regularities: (1) phenotypes occupy only a small subspace of possible phenotypes, (2) the influence of mutation is not uniform and is often canalized, and (3) a great deal of morphological variation evolved early in the history of multicellular life. An important implication of these studies is that diversity is largely the outcome of the evolution of gene regulation rather than the emergence of new, structural genes. Using a simple model that considers a generic property of developmental maps—the interaction between multiple genetic elements and the nonlinearity of gene interaction in shaping phenotypic traits—we are able to recover many of these empirical regularities. We show that visible phenotypes represent only a small fraction of possibilities. Epistasis ensures that phenotypes are highly clustered in morphospace and that the most frequent phenotypes are the most similar. We perform phylogenetic analyses on an evolving, developmental model and find that species become more alike through time, whereas higher-level grades have a tendency to diverge. Ancestral phenotypes, produced by early developmental programs with a low level of gene interaction, are found to span a significantly greater volume of the total phenotypic space than derived taxa. We suggest that early and late evolution have a different character that we classify into micro- and macroevolutionary configurations. These findings complement the view of development as a key component in the production of endless forms and highlight the crucial role of development in constraining biotic diversity and evolutionary trajectories

Ancient DNA Suggests Dwarf and ‘Giant’ Emu Are Conspecific

) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu. 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.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

By Any Other Name: Heterologous Replacement of the Escherichia coli RNase P Protein Subunit Has In Vivo Fitness Consequences

Bacterial RNase P is an essential ribonucleoprotein composed of a catalytic RNA component (encoded by the rnpB gene) and an associated protein moiety (encoded by rnpA). We construct a system that allows for the deletion of the essential endogenous rnpA copy and for its simultaneous replacement by a heterologous version of the gene. Using growth rate as a proxy, we explore the effects on fitness of heterologous replacement by increasingly divergent versions of the RNase P protein. All of the heterologs tested complement the loss of the endogenous rnpA gene, suggesting that all existing bacterial versions of the rnpA sequence retain the elements required for functional interaction with the RNase P RNA. All replacements, however, exact a cost on organismal fitness, and particularly on the rate of growth acceleration, defined as the time required to reach maximal growth rate. Our data suggest that the similarity of the heterolog to the endogenous version — whether defined at the sequence, structure or codon usage level — does not predict the fitness costs of the replacement. The common assumption that sequence similarity predicts functional similarity requires experimental confirmation and may prove to be an oversimplification

Complex Species Status for Extinct Moa (Aves: Dinornithiformes) from the Genus <i>Euryapteryx</i>

<div><p>The exact species status of New Zealand's extinct moa remains unknown. In particular, moa belonging to the genus <i>Euryapteryx</i> have been difficult to classify. We use the DNA barcoding sequence on a range of <i>Euryapteryx</i> samples in an attempt to resolve the species status for this genus. We obtained mitochondrial control region and the barcoding region from <i>Cytochrome Oxidase Subunit I</i> (<i>COI</i>) 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 <i>Euryapteryx</i>. Using the <i>COI</i> barcoding region we show that species status in <i>Euryapteryx</i> is complex with no clear separation between various individuals. Eggshell, soil, and bone data suggests that a <i>Euryapteryx</i> subspecies likely exists on New Zealand's North Island and can be characterized by a single mitochondrial control region SNP. <i>COI</i> divergences between <i>Euryapteryx</i> 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 <i>COI</i> differences possibly as a result of repeated hybridisation events. Despite the accuracy of the <i>COI</i> barcoding region to determine species status in birds, including that for the other moa genera, for moa from the genus <i>Euryapteryx</i>, <i>COI</i> 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 <i>Euryapteryx</i>; 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.</p></div

COI sequence differences, biogeography, and eggshell thicknesses of <i>Euryapteryx</i>.

<p><b>A</b>. Phylogenetic analysis and grouping of <i>Euryapteryx</i> samples at various levels of COI sequence divergence. A phylogenetic tree was constructed in MEGA 5.05 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Tamura1" target="_blank">[18]</a> using Maximum Likelihood and Tamura-Nei parameters (log likelihood −1581.8; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Tamura2" target="_blank">[20]</a>). Bootstrap values were calculated from 500 replications. Sequence differences were calculated using K2 parameters. Individual <i>Euryapteryx</i> samples are numbered (for museum voucher numbers see supplementary information) and coloured according to location (see B). Samples are grouped according to percent COI divergence (<0.8%, <1.25%, and <1.6%). See supplementary information for divergence tables. Approximate sizes for two genetic variants (557C/T) of <i>Euryapteryx</i> (see text) are shown against that of an adult chicken. <b>B</b>. Biogeography of <i>Euryapteryx</i> populations according to (left) mitochondrial control region sequences from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a> or (right) COI sequences. Samples that form clades are joined by colour. The main COI groups were determined using a <1.25% divergence limit. This limit most closely approximated the clades formed using control region sequences. The complex interactions between individual members of each COI clade (see A) are not shown. Figure numbers refer to moa samples; 1 - AIM B6595ii <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 2 - WO 527 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 3 - AIM B6580 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 4 - AIM B6228 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 5 - MNZ S40891 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 6 - MNZ S465 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 7 - CM Av21330 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 8 - CM Av29440a <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 9 - CM Av8378 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 10 - MNZ S39965 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 11 - CM Av9188 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 12 - AM 6237 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 13 - OU Anthro FB271 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 14 - OM Av4735 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 15 - OM Av5191 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Bunce1" target="_blank">[4]</a>, 16 - AIM B9243, 17 - OM Av9821 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>, 18 - CM Av38561 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Baker1" target="_blank">[3]</a>. <b>C</b>. Eggshell thicknesses of <i>Euryapteryx</i>. Eggshell thicknesses from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Huynen2" target="_blank">[10]</a> (mm) are grouped according to association with class I (blue) or class II (orange) control region sequences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Huynen2" target="_blank">[10]</a>. These sequences cover a highly variable ∼30 bp fragment that is capable of distinguishing ‘thin’ <i>Euryapteryx</i> eggshells from ‘thick’. *The association of a class II sequence with this 1.11 mm eggshell may be in doubt as the sequence was obtained from the outer layer of the eggshell <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090212#pone.0090212-Huynen2" target="_blank">[10]</a>.</p