A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes.

Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level genome assemblies of 11 other bird and one turtle species. We found ratites exhibited the lowest numbers of intra- and inter-chromosomal changes among birds since their divergence with turtles. The small-sized and gene-rich emu microchromosomes have frequent inter-chromosomal contacts that are associated with housekeeping genes, which appears to be driven by clustering their centromeres in the nuclear interior, away from the macrochromosomes in the nuclear periphery. Unlike nonratite birds, only less than one-third of the emu W Chromosome regions have lost homologous recombination and diverged between the sexes. The emu W is demarcated into a highly heterochromatic region (WS0) and another recently evolved region (WS1) with only moderate sequence divergence with the Z Chromosome. WS1 has expanded its inactive chromatin compartment, increased chromatin contacts within the region, and decreased contacts with the nearby regions, possibly influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.

Ticks in wild animals at a resort and the first documentation of Amblyomma sculptum infesting Emu (Dromaius novaehollandiae) / Carrapatos em animais selvagens em um resort e o primeiro registro de Amblyomma sculptum infestando Emu (Dromaius novaehollandiae)

Abstract The study aimed to identify species of ticks present in the environment and among captive animals, in Mangaratiba, Rio de Janeiro, Brazil. Ticks were isolated from captive animals by manual examination and free-living ticks in the environment were captured using the flannel drag technique. A total of 91 ticks were obtained (51 adults, 25 nymphs and 15 larvae). The specimens were identified morphologically as Amblyomma sp., Amblyomma dubitatum, Amblyomma ovale and Amblyomma sculptum , and were distributed among five species of native mammals and an exotic bird. This study also reports the first case of infestation of the Australian emu (Dromaius novaehollandiae) by A. sculptum.

Resumo O estudo teve como objetivo identificar espécies de carrapatos presentes no ambiente e entre animais de cativeiro em Mangaratiba, Rio de Janeiro, Brasil. Os carrapatos foram removidos manualmente de animais de cativeiro e no ambiente usando a técnica de arrasto em flanela. Um total de 91 carrapatos foram capturados (51 adultos, 25 ninfas e 15 larvas). Os espécimes foram identificados morfologicamente como Amblyomma sp., Amblyomma dubitatum, Amblyomma ovale e Amblyomma sculptum, e foram distribuídos entre cinco espécies de mamíferos nativos e uma ave exótica. Este estudo também relata o primeiro caso de infestação do emu australiano (Dromaius novaehollandiae) por A. sculptum .

Ticks in wild animals at a resort and the first documentation of Amblyomma sculptum infesting Emu (Dromaius novaehollandiae).

The study aimed to identify species of ticks present in the environment and among captive animals, in Mangaratiba, Rio de Janeiro, Brazil. Ticks were isolated from captive animals by manual examination and free-living ticks in the environment were captured using the flannel drag technique. A total of 91 ticks were obtained (51 adults, 25 nymphs and 15 larvae). The specimens were identified morphologically as Amblyomma sp., Amblyomma dubitatum, Amblyomma ovale and Amblyomma sculptum , and were distributed among five species of native mammals and an exotic bird. This study also reports the first case of infestation of the Australian emu (Dromaius novaehollandiae) by A. sculptum.

Biochemical and functional characterization of transiently expressed in neural precursor (TENP) protein in emu egg white.

A protein transiently expressed in the neural precursors of developing tissues (TENP) was found to be present in emu (Dromaius novaehollandiae) egg white as one of the major proteins. Nucleotide analysis of its encoding cDNA revealed a sequence of 452 amino acids including a 19 amino acid peptide signal. Phylogenetic analysis determined that emu TENP was clustered within the bactericidal/permeability-increasing protein (BPI) superfamily together with other avian TENPs. RT-PCR analysis revealed that the emu TENP gene was highly expressed in the magnum of the oviduct, indicating that TENP is a major egg white component. Emu TENP was purified by anion exchange chromatography and ammonium sulfate fractionation. Unlike BPI, emu TENP exhibited antibacterial activity against Gram-positive bacteria, including Micrococcus luteus and Bacillus subtilis, but not against Gram-negative bacteria such as Escherichia coli and Salmonella Typhimurium. The results suggest that emu TENP is a potent novel antibacterial protein with a spectrum distinct from that of BPI.

Ancient DNA suggests dwarf and 'giant' emu are conspecific.

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.

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.