Preferred orientation of calcite in the ratite and tinamou eggshells

Using X-ray diffractometry, the development of preferred orientation was studied in one species from each of the extant ratite families, from two moas and two tinamous and, as a preliminary comparison, from representative species from 16 of the other carinate orders. A preferred orientation begins to develop immediately after the start of shell deposition, and in all shells studied was one in which the (001) planes tend to lie parallel to the shell surface. The degree of (001) texture that develops in the ratite and tinamou shells is greater than that developed in the other carinate orders. Development in the ostrich, kiwi and tinamou is uninterrupted so that there is a very high degree of (001) preferred orientation at the exteriors of the shells. In the Emu, cassowary, rhea and the two moa species, a very high degree of (001) texture reverses gradually within the central layer of the shell, and in some species this is accompanied by the development of a very weak (104) preferred orientation. The weak (001) textures observed in the shells of the 20 species from the carinate orders other than the Tinamiformes develop slowly and without interruption through the shell; in four species a weak (104) texture develops simultaneously to that of the (001), forming a double texture similar to that already reported in the majority of shells of the domestic fowl.     

The expression of alpha D-chains in the hemoglobin of adult ostrich (Struthio camelus) and American rhea (Rhea americana). The different evolution of adult bird alpha A-, alpha D- and beta-chains

The hemoglobin of adult American rhea (Rhea americana) and ostrich (Struthio camelus) contains two components identified to be HbA (alpha 2A beta 2) and HbD (alpha 2D beta 2). The amino-acid sequence of alpha D-chains from HbD of adult American rhea and ostrich has been determined. The sequence was studied by Edman degradation of tryptic peptides and chemical cleavage products in a liquid phase sequencer. By homologous comparison with pheasant HbD (Phasianus colchicus colchicus), the alpha D-chains of American rhea differ by 28 amino-acid exchanges, the alpha D-chains of ostrich by 23 residues. These differences are higher than those observed for alpha A- as well as for beta-chains of HbA from the same species. The ratio of amino-acid exchanges for beta:alpha A:alpha D for American rhea and ostrich is found to be 1:5.5:6.5. At present the reason for the differences in evolution rates for the beta-, alpha A- and alpha D-chains of bird hemoglobins is still unclear.     

Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis

The ratites have stimulated much debate as to how such large flightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of flight. Hypotheses regarding the relationships among taxa differ for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of five extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary and two tinamous from different genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and non-homogeneous maximum likelihood, the ratites are found to be monophlyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor-descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages fit the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.     

Chromosome studies in four species of Ratitae (Aves)

Chromosomes were studied in female specimens of the ostrich, Struthio camelus L., cassowary, Casuarius casuarius (L.), emu, Dromiceius novaehollandiae (Lath.) and rhea, Rhea americana L. by means of blood and feather pulp culture techniques. Male karyotypes were also studied in the emu and rhea. The diploid chromosome number was most likely 80 in the ostrich and rhea and 82 in the emu, while the exact number could not be determined in the cassowary. Karyotypes of the 4 species were strikingly similar and apparently interchangeable with one another with slight modifications of the centromeric position in one or two pairs of macrochromosomes. No heteromorphic macrochromosomal pair was found either in female specimens or in male ones of the ratite species so far examined, except for a female rhea. This specimen was found to possess an acrocentric chromosome which was evidently a member of nos. 4–6, but considerably smaller than any other chromosome of the group. ³H-thymidine autoradiography provided no more information than the straightforward morphological analysis with regard to the differentiation of the sex-chromosomes.Contributions from the Chromosome Research Unit, Hokkaido University. Dedicated to Emeritus Professor Sajiro Makino on the occasion of his retirement, in honor of his 40 years' service with the University. Supported by a grant from the Scientific Research Fund of the Ministry of Education (No. 584099).     

Is a large-scale DNA-based inventory of ancient life possible?

A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.     

Characterization of the cDNA encoding bullfrog, Rana catesbeiana, osteocalcin and two forms of the protein isolated from bone

A full-length cDNA clone encoding osteocalcin from the bullfrog, Rana catesbeiana (bone Gla-protein, BGP) has been isolated, and the complete coding sequence for the 100-amino-acid pre-pro-osteocalcin protein was determined. The amino acid sequence of Rana catesbeiana osteocalcin, especially the mature 49-amino acid sequence, is closer to the mammalian than to the fish, Sparus osteocalcin. Rana mature osteocalcin has a similarity of 67% with human or 59% with rat osteocalcin, and only 42% with fish mature osteocalcin. The 51-amino-acid pre-pro-peptide contains the expected hydrophobic leader sequence and the dibasic Arg-Arg sequence preceding the NH2-terminal Ser of the mature 49-amino-acid Rana osteocalcin. The pro-peptide sequence also contains the expected motif of polar and hydrophobic residues, which targets vitamin K-dependent gamma-carboxylation of three specific Glu residues at positions 17, 21, and 24 in the mature protein. At the native protein expression levels, extraction from Rana cortical bone in the presence of protease inhibitor cocktail resulted in the isolation of two distinct forms of osteocalcin, P-1 and P-2, with a 3:2 distribution. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and amino acid sequence analysis of the N-terminal domain, we confirmed that P-1 is the intact 49-residue osteocalcin with N-terminal SNLRNAVFG., and that P-2 lacks four amino acids from the N-terminus, (NAVFG.). These results demonstrate the existence of a form of osteocalcin lacking four N-terminal amino acids in Rana bone, and that mature Rana osteocalcins remained highly conserved in their molecular evolution, especially with respect to the conservation of the C-terminal domain (residues 14-49).     

A DNA test to sex ratite birds

DNA-based sex tests now exist for many avian species. However, none of these tests are widely applicable to ratites. We present DNA sequence data for a locus that is W chromosome-linked in the kiwi, ostrich, cassowary, rhea, and emu. At the amino acid level, this sequence has significant homology to X-linked genes in platyfish and Caenorhabditis elegans. Polymerase chain reaction (PCR) primers designed to this locus allow the assignment of sex in all species of living ratites.     

High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland moa (Megalapteryx didinus)

Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand's largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 (14)C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.     

Biochemical and structural comparative study between bird and mammal pancreatic colipases

Three colipases were purified from pancreas of two birds (ostrich and turkey) and one mammal (dromedary). After acidic and/or heat treatment and precipitation by sulfate ammonium and then ethanol, cofactors were purified by Sephadex G-50 gel filtration followed by ion-exchange chromatography first on Mono S and then on Mono Q. One molecular form was obtained from each species with a molecular mass of approximately 10 kDa. Cofactors were not glycosylated. The N-terminal sequences of the three purified cofactors showed high sequence homology. A 90 amino acid sequence of the ostrich cofactor was established based on peptide sequences from four different digests of the denaturated protein using trypsin, chymotrypsin, thermolysin, or staphylococcal protease. This sequence exhibited a high degree of homology with chicken and mammal cofactors. Bile salt-inhibited pancreatic lipases from five species were activated to variable extents by colipases from bird and mammal origins. The bird pancreatic lipase-colipase system appears to be functionally similar to homologous lipolytic systems from higher mammals. Our comparative study showed that mammal colipase presents a lower activation level toward bird lipases than the bird counterpart. Three-dimensional modeling of ostrich colipase suggested a structural explanation of this fact.     

Palaeogenomics

In many ways, palaeogenomics began when the first ancient DNA sequence was reported. This first sequence was derived from a stuffed museum specimen of the quagga, an extinct mammal related to the zebra. Unspecified and unselected DNA was extracted from the quagga specimen, cloned into a bacterial library, and then sequenced. It took another 17 years and the development of PCR before two independent groups successfully sequenced the complete mitochondrial genomes from several extinct moa species. Only 4 years later, using the original approach of cloning nonspecific ancient DNA extract and shotgun sequencing, the first ancient nuclear DNA sequences were determined, this time from the extinct cave bear. Since these early successes, palaeogenomics has rapidly expanded, because of both technological development and increasing interest in ancient DNA research. New methods, developed since the cave bear sequence was reported, have produced nuclear DNA on a megabase scale from two extinct species, the mammoth and the Neanderthal, our closest relative. For both species, low-coverage genome-sequencing projects have been proposed. It is likely that these will be successful, given the rapid technical development in sequencing techniques. This review carefully examines both the promise and the current limitations of palaeogenomic analyses for both mitochondrial and nuclear DNA.     

Immunochemical detection and characterisation of osteocalcin from moa bone

Osteocalcin (the 6,000 dalton Mr gamma-carboxyglutamate-containing protein of bone) has been detected in acid extracts of bones of the extinct class of New Zealand ratite birds, the moas, using a radioimmunoassay for sheep osteocalcin. The immunoreactive osteocalcin of the extracts of two of these bones (the fibulae from two specimens of Pachyornis elephantopus found in South Island swamps) has been fractionated by gel filtration chromatography and reversed-phase high performance liquid chromatography, and behaves in a manner characteristic of osteocalcin from modern bones. Carbon-14 dating of bones and gizzard contents found in association with these specimens indicates approximate ages of 3,600 and 7,400 years respectively.     

A Megafauna’s Microfauna: Gastrointestinal Parasites of New Zealand’s Extinct Moa (Aves: Dinornithiformes)

We perform the first multidisciplinary study of parasites from an extinct megafaunal clade using coprolites from the New Zealand moa (Aves: Dinornithiformes). Ancient DNA and microscopic analyses of 84 coprolites deposited by four moa species (South Island giant moa, Dinornis robustus; little bush moa, Anomalopteryx didiformis; heavy-footed moa, Pachyornis elephantopus; and upland moa, Megalapteryx didinus) reveal an array of gastrointestinal parasites including coccidians (Cryptosporidium and members of the suborder Eimeriorina), nematodes (Heterakoidea, Trichostrongylidae, Trichinellidae) and a trematode (Echinostomida). Parasite eggs were most prevalent and diverse in coprolites from lowland sites, where multiple sympatric moa species occurred and host density was therefore probably higher. Morphological and phylogenetic evidence supports a possible vicariant Gondwanan origin for some of the moa parasites. The discovery of apparently host-specific parasite taxa suggests paleoparasitological studies of megafauna coprolites may provide useful case-studies of coextinction.     

Moa diet fits the bill: virtual reconstruction incorporating mummified remains and prediction of biomechanical performance in avian giants

The moa (Dinornithiformes) are large to gigantic extinct terrestrial birds of New Zealand. Knowledge about niche partitioning, feeding mode and preference among moa species is limited, hampering palaeoecological reconstruction and evaluation of the impacts of their extinction on remnant native biota, or the viability of exotic species as proposed ecological ‘surrogates''. Here we apply three-dimensional finite-element analysis to compare the biomechanical performance of skulls from five of the six moa genera, and two extant ratites, to predict the range of moa feeding behaviours relative to each other and to living relatives. Mechanical performance during biting was compared using simulations of the birds clipping twigs based on muscle reconstruction of mummified moa remains. Other simulated food acquisition strategies included lateral shaking, pullback and dorsoventral movement of the skull. We found evidence for limited overlap in biomechanical performance between the extant emu (Dromaius novaehollandiae) and extinct upland moa (Megalapteryx didinus) based on similarities in mandibular stress distribution in two loading cases, but overall our findings suggest that moa species exploited their habitats in different ways, relative to both each other and extant ratites. The broad range of feeding strategies used by moa, as inferred from interspecific differences in biomechanical performance of the skull, provides insight into mechanisms that facilitated high diversities of these avian herbivores in prehistoric New Zealand.     

Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters

It is commonly acknowledged that the basal divergence among extant birds is between Palaeognathae and Neognathae. However, recent analyses of mitochondrial sequences have challenged that notion. In order to investigate this fundamental phylogenetic question, the complete mitochondrial DNA (mtDNA) molecule of the rook Corvus frugilegus (Passeriformes) was sequenced and included in phylogenetic analyses with the previously reported complete mtDNAs of the chicken Gallus gallus (Galliformes) and two ratite species, the ostrich Struthio camelus and the rhea Rhea americana (Struthioniformes). The analyses reconstructed a split between Passeriformes and a branch including Galliformes and Struthioniformes. Thus, the result is inconsistent with the traditional understanding of a basal avian divergence between Palaeognathae and Neognathae. The findings suggest that the morphological characteristics of the ratites are secondarily acquired, probably through neoteny and that the ratites are descendants of flying, neognathous ancestors.     

Impacts of introduced deer and extinct moa on New Zealand ecosystems

There has been considerable ongoing debate about the extent to which the impacts of introduced deer on native vegetation have replaced those of moa, and since the 1980s there have been major changes in thinking about the impacts of deer and ratites on ecosystems. Although it has long been known that deer caused a predictable sequence of changes in forest understorey composition, recent work has shown that the foliage of species preferred by deer contains lower concentrations of fibre ? and decomposes faster ? than avoided species. Analyses of long-term permanent plot data suggest that some preferred species are failing to regenerate in forest types where deer are present. As well as likely altering the long-term biogeochemistry of forest ecosystems, deer have a strong negative effect on the abundance of litter-dwelling macrofauna (most likely through trampling). Estimating the impacts of extinct taxa on an ecosystem has much uncertainty, but recent experiments have shown that extant ratites and deer may have more similar feeding preferences than previously believed. It is likely that moa were important seed dispersers, but this has not been studied for deer in New Zealand. Although collectively the various taxa of deer in New Zealand use all of the habitats utilised by moa, and there is partial overlap in the diets of deer and moa, deer can attain densities and biomasses 100- fold greater than reasonably surmised for moa. We believe that the impacts of introduced deer on ecosystems are markedly different from those of moa. One way to compare the impacts of moa and deer is to use pollen to reconstruct the vegetation at a forested site in recent millennia and evaluate vegetation dynamics during the moa period, following the extinction of moa but prior to the arrival of deer (i.e. the moa gap), and following the arrival of deer. We illustrate the potential of this approach with a soil core from Chester Burn, Murchison Mountains in Fiordland. Five other areas that deserve further research are also identified.     

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.     

The primary structure of a novel goose-type lysozyme from rhea egg white

G-type lysozyme is a hydrolytic enzyme sharing a similar tertiary structure with plant chitinase. To discover the relation of function and structure, we analyzed the primary structure of new G-type lysozyme. The complete 185 amino acid residues of lysozyme from rhea egg white were sequenced using the peptides hydrolyzed by trypsin, V8 protease, and cyanogen bromide. Rhea lysozyme had sequence similarity to ostrich, cassowary, goose, and black swan, with 93%, 90%, 83%, and 82%, respectively. The six substituted positions were newly found at positions 3 (Asn), 9 (Ser), 43 (Arg), 114 (Ile), 127 (Met), and 129 (Arg) when compared with ostrich, cassowary, goose, and black swan lysozymes. The amino acid substitutions of rhea lysozyme at subsite B were the same as ostrich and cassowary lysozymes (Ser122 and Met123). This study was also constructed in a phylogenetic tree of G-type lysozyme that can be classified into at least three groups of this enzyme, namely, group 1; rhea, ostrich, and cassowary, group 2; goose, black swan, and chicken, and group 3; Japanese flounder. The amino acid sequences in assembled three alpha-helices found in this enzyme group (Thammasirirak, S., Torikata, T., Takami, K., Murata, K., and Araki, T., Biosci. Biotechnol. Biochem., 66, 147-156 (2002)) were also highly conserved, so that they were considered to be important for the formation of the hydrophobic core structure of the catalytic site and for maintaining a similar three-dimensional structure in this enzyme group.     

A refined model of body mass and population density in flightless birds reconciles extreme bimodal population estimates for extinct moa

Flightless birds were once the largest and heaviest terrestrial fauna on many archipelagos around the world. Robust approaches for estimating their population parameters are essential for understanding prehistoric insular ecosystems and extinction processes. Body mass and population density are negatively related for extant flightless bird species, providing a method for quantifying densities and population sizes of extinct flightless species. Here we assemble an updated global data set of body mass and population densities for extant flightless birds and estimate the relationship between these variables. We use generalised least squares models that account for phylogenetic relatedness and incorporate the effects of limiting factors (e.g. habitat suitability) on population density. We demonstrate the applicability of this allometric relationship to extinct species by estimating densities for each of the nine species of moa (Dinornithiformes) and generating a combined spatially explicit map of total moa density across New Zealand. To compare our density estimates with those previously published, we summed individual species' abundances to generate a mean national density of 2.02–9.66 birds km⁻² for low- and high-density scenarios, respectively. Our results reconcile the extreme bimodality of previous estimates (< 2 birds km⁻² and > 10 birds km⁻²) and are comparable to contemporary densities of large herbivorous wild mammals introduced into New Zealand about 150 yr ago. The revised moa density has little effect on the harvest rates required to bring about extinction within 150–200 yr, indicating that rapid extinction was an inevitable response to human hunting, irrespective of the initial population of moa.     

A new marker based on the avian spindlin gene that is able to sex most birds,including species problematic to sex with CHD markers

We have developed a new marker (Z43B) that can be successfully used to identify the sex of most birds (69%), including species difficult or impossible to sex with other markers. We utilized the zebra finch Taeniopygia guttata EST microsatellite sequence (CK309496) which displays sequence homology to the 5′ untranslated region (UTR) of the avian spindlin gene. This gene is known to be present on the Z and W chromosomes. To maximize cross‐species utility, the primer set was designed from a consensus sequence created from homologs of CK309496 that were isolated from multiple distantly related species. Both the forward and reverse primer sequences were 100% identical to 14 avian species, including the Z chromosome of eight species and the chicken Gallus gallus W chromosome, as well as the saltwater crocodile Crocodylus porosus. The Z43B primer set was assessed by genotyping individuals of known sex belonging to 61 non‐ratite species and a single ratite. The Z and W amplicons differed in size making it possible to distinguish between males (ZZ) and females (ZW) for the majority (69%) of non‐ratite species tested, comprising 10 orders of birds. We predict that this marker will be useful for obtaining sex‐typing data for ca 6,869 species of birds (69% of non‐ratites but not galliforms). A wide range of species could be sex‐typed including passerines, shorebirds, eagles, falcons, bee‐eaters, cranes, shags, parrots, penguins, ducks, and a ratite species, the brown kiwi, Apteryx australis. Those species sexed include species impossible or problematic to sex‐type with other markers (magpie, albatross, petrel, eagle, falcon, crane, and penguin species). Zoo Biol. 35:533–545, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.     

The isolation and partial characterization of precursor forms of ostrich carboxypeptidase

Ostrich carboxypeptidases A and B were recently purified and characterized. The aim of this study was to isolate and purify, and partially characterize in terms of molecular weight, pI, amino acid composition and N-terminal sequencing, the precursor forms of carboxypeptidases from the ostrich pancreas. Inhibition studies with soybean trypsin inhibitor and activation studies with three proteases (bovine trypsin, bovine chymotrypsin and porcine elastase) were performed on crude ostrich acetone powder and the carboxypeptidase A and B activities were determined. SDS-PAGE was carried out after every incubation to monitor the rate and degree of conversion of a M(r) 66K component to procarboxypeptidase and carboxypeptidase A and B. The precursor forms were purified by Toyopearl Super Q and Pharmacia Mono Q chromatography. All three proteases converted the M(r) 66K component to procarboxypeptidases and carboxypeptidases over a set time interval, with carboxypeptidase A and B activities being detected in the acetone powder. Chymotrypsin was the preferred protease since it exhibited a more controlled activation of the procarboxypeptidases. The amino acid composition of procarboxypeptidase A revealed 525 residues. The N-terminal sequence of procarboxypeptidase A showed considerable homology when compared with several other mammalian sequences. M(r) and pI values of 52K and 5.23 were obtained for procarboxypeptidase A, respectively. This study indicated that ostrich procarboxypeptidase A is closely related to other mammalian procarboxypeptidase A molecules in terms of physicochemical properties.