Short Communication: A new primer set in CHD1 gene for bird sex identification

Vera F, Wajjwalku W, Yuda P, Daryono BS. 2021. Short Communication: A new primer set in CHD1 gene for bird sex identification. Biodiversitas 22: 4977-4982. Determine sex is difficult for many bird species that are sexually monomorphic or only dimorphic in the adult stage. Many molecular markers have been developed for DNA sexing, which were mostly based on identifying Z and W chromosomes of avians. The sex determination of birds was mostly applied universal primer set such as P2/P8 or 2550F/2718R. However, those universal primers that were designed sometimes could not good result consistency in non-ratite birds or ratite birds. Therefore, we improved a specific primer design with deletion site in W chromosome to amplify the female-specific segments on Chromodomain-helicase DNA binding protein-1 (CHD1) gene from alignment sequences CHD1-Z and CHD1-W of Macrocephalon maleo S. Müller, 1846. This study aims to design a new pair of primer targeting a section of the CHD1 gene that can be amplified in non-ratite birds, the name of a new primer is In-Sex F/In-Sex R. A new primer set amplified DNA fragments in around 650 or 550 base pairs of CHD1-Z and also, 350 base pairs of CHD1-W. The result has successfully amplified the sex of multiple species on orders Galliformes, Passeriformes, Accipitriformes, and Strigiformes. This analysis can be helpful to the effort of in-situ or ex-situ management and conservation programs e.g the mating system in birds. And also, the analysis can be helpful for sexing data in the case of captive birds before releasing in natural habitat or reintroduction programs.

Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes

The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.

Structure of struthiocalcin-1, an intramineral protein fromStruthio cameluseggshell, in two crystal forms

Biomineralization is the process by which living organisms produce minerals. One remarkable example is the formation of eggshells in birds. Struthiocalcins present in the ostrich (Struthio camellus) eggshell matrix act as biosensors of calcite growth during eggshell formation. Here, the crystal structure of struthiocalcin-1 (SCA-1) is reported in two different crystal forms. The structure is a compact single domain with an α/β fold characteristic of the C-type lectin family. In contrast to the related avian ovocleidin OC17, the electrostatic potential on the molecular surface is dominated by an acidic patch. Scanning electron microscopy combined with Raman spectroscopy indicates that these intramineral proteins (SCA-1 and SCA-2) induce calcium carbonate precipitation, leading to the formation of a stable form of calcite in the mature eggshell. Finally, the implications of these two intramineral proteins SCA-1 and SCA-2 in the nucleation of calcite during the formation of eggshells in ratite birds are discussed.

Panbiogeography, its critics, and the case of the ratite birds

Panbiogeographic analysis is now used by many authors, but it has been criticised in recent reviews, with some critics even suggesting that studies using the method should not be accepted for publication. The critics have argued that panbiogeography is creationist, that it rejects dispersal, that its analyses are disingenuous, and that it deliberately ignores or misrepresents key evidence. These claims are examined here, and are all shown to be without foundation. The distributions of the molecular clades of ratites have not been mapped before, and they are considered here in some more detail as a case study illustrating panbiogeographic methodology.