About
Dr. Siwo de Kloet
RECENT
PUBLICATIONS:
Rolf
S. de Kloet, Siwo R. de Kloet
The evolution of the spindlin gene in birds: sequence analysis of
an intron of the spindlin W and Z gene reveals four major divisions
of the Psittaciformes.
Mol Phylogenet Evol.
2005 Sep;36(3):706-21.
ABSTRACT:The
Psittaciformes (parrots, parakeets) are among the most widely held captive
birds. Yet, their evolution and their phylogenetic relationships have
been relatively little studied. This paper describes the phylogenetic
relationships between a number of Psittaciformes as derived from the
sequences of the third intron of the Z-chromosomal and W-chromosomal
spindlin genes. The Z-chromosomal sequences of the kakapo (Strigops
habroptilus), the kea (Nestor notabilis), and the kaka (Nestor meridionalis)
from New Zealand form a cluster which is the sister group to all other
Psittaciformes. The results show further that the Z-chromosomal sequences
of the other species can be divided into two groups based on the occurrence
of a sequence element ACCCT. The group with the insert (A) is mainly
from species with an Australasian geographical distribution and includes
such species as the Lories (Lorius, etc.), the budgerigar (Melospittacus
undulatus), and the rosellas (Platycercus). It also includes the African
lovebirds (Agapornidae), which are the only representative of group
A outside Australasia. Group B, without the insert, includes the neotropical
parrots and parakeets such as the amazons (Amazona, etc.), the macaws
(Ara, etc.), and the conures (Aratinga, etc.), the Australian Cacatuini
and the African species such as the African grey parrot (Psittacus erithacus)
as well as Coracopsis vasa from Madagascar and Psittrichas fulgidus
from New Guinea. The W-chromosomal sequence data show that another division
of the Psittacidae is found in the replacement of a pyrimidine-rich
segment occurring in many non-psittacines as well as the kakapo (S.
habroptilus), the kea (N. notabilis), the kaka (N. meridionalis), and
the Cacatuini by a microsatellite consisting of a variable number of
TATTA monomers in the other Psittaciformes. The results support a Gondwanan
origin of the Psittaciformes and the suggestion that paleogeographic
events were a major force in psittacine divergence.
Edwin
de Kloet, Siwo R. de Kloet
Analysis of the Beak and Feather Disease Viral Genome Indicates the
Existence of Several Genotypes Which Have a Complex Psittacine Host
Specificity
Arch Virol. 2004 Dec;149(12):2393-412. Epub 2004
Jul 15.
ABSTRACT: A study was made of the phylogenetic
relationships between fifteen complete nucleotide sequences as well
as 43 nucleotide sequences of the putative coat protein gene of different
strains of Beak and Feather Disease virus obtained from 39 individuals
of 16 psittacine species. The species included among others, cockatoos
(Cacatuini), African grey parrots (Psittacus erithacus) and peach-faced
lovebirds (Agapornis roseicollis), which were infected at different
geographical locations, within and outside Australia, the native origin
of the virus. The derived amino acid sequences of the putative coat
protein were highly diverse, with differences between some strains amounting
to 50 of the 250 amino acids. Phylogenetic analysis demonstrated that
the putative coat gene sequences form six clusters which show a varying
degree of psittacine species specificity. Most, but not all strains
infecting African grey parrots formed a single cluster as did the strains
infecting the cockatoos. Strains infecting the lovebirds clustered with
those infecting such Australasian species as Eclectus roratus, Psittacula
kramerii and Psephotus haematogaster. Although individual birds included
in this study were, where studied, often infected by closely related
strains, infection by highly diverged trains was also detected. The
possible relationship between BFD viral strains and clinical disease
signs is discussed.
Rolf
S. de Kloet, Siwo R. de Kloet
Independent cessation of recombination of sex chromosomes at the spindlin
locus in neognathous birds and tinamous, a palaeognathous avian family.
Genetica 199: 333-342,
2003.
ABSTRACT: Tinamous (Aves, Palaeognathae,
Tinamiformes) are primitive birds, generally considered to be the sister
group to the ratites. Tinamous possess a W sex-chromosome, intermediate
in heterochromatization between the largely euchromatic W chromosome
of the ratites and the highly condensed W chromosome of the neognathous
birds. Of the four genes which are known to have diverged copies on
the neognathous avian W and Z chromosome (ATP5A1, CHD1, PKC and SPIN)
only the spindlin gene has W- and Z-chromosomal forms in the tinamiformes.
This paper describes experiments which show that the sequences of these
forms are more similar to each other and to the homologous undifferentiated
spindlin gene sequences in the ratite genome than to the W or Z forms
of the spindlin gene in other, neognathous species. This suggests that
cessation of recombination at the spindlin locus of the ancestral W
and Z chromosomes of the tinamiformes and the neagnathous avian species
were independent events.
de Kloet, SR (2002)
Molecular sex identification of tinamous with PCR using primers derived
from the spindlin gene.
Molecular Ecology Notes 2:465 - 466.
ABSTRACT: This paper describes results
which show that the spindlin gene has different forms on the tinamid
W and Z chromosome, providing a sensitive and accurate procedure for
a molecular, PCR-based, procedure for sex-identification of tinamous.
de
Kloet, SR. (2001c)
A repetitive DNA sequence on the W chromosome of owls (Strigiformes)
with sequence similarity to the chicken W chromosomal repeat.
The Auk, submitted
de
Kloet, SR (2001b).
Development of a CAPS (Cleaved Amplified Polymorphics Sequence) assay
for sex identification of the emu (Dromaius novaehollandiae).
Molecular Ecology Letters 1: 273 - 275 .
ABSTRACT: Polymerase chain rection (PCR)
based procedures that have been used to identify the sex of most birds
cannot be used in ratites. This paper described the identification of
a female (W-chromosomal) specific randomly amplified polymorphic (RAPD)
1.3 kb DNA fragment (ESEXW) in the emu (Dromaius novaehollandiae). Southern
blot experiments and sequence analysis revealed that a related (96%
similarity) sequence exists of the emu Z-chromosome (ESEXZ). The sequences
of ESEXW and ESEXZ have been used for the development of a two-primer
CAPS (cleaved amplified polymorphic sequence) assay for reliable sex
identification of the emu.
de Kloet, SR.
(2001a)
Loss of the gene of the alpha subunit of ATP synthase (ATP5A1) from
the W chromosome of the African grey parrot (Psittacus erithacus).
Journal of Molecular Evolution 53: 135 - 143.
ABSTRACT: This study describes the results
of an analysis using Southern blotting, the polymerase chain reaction,
and sequencing which shows that the African grey parrot (Psittacus erithacus)
lacks the W-chromosomal gene for the alpha subunit of mitochondrial
ATP synthase (ATP5A1W). Additional evidence shows that in other psittacines
a fragment of the ATP5A1W gene contains five times as many nonsynonymous
nucleotide replacements as the homologous fragment of the Z gene. Therefore,
whereas in these other psittacines the corresponding ATP5A1Z protein
fragment is highly conserved and varies by only a few, moderately conservative
amino acid substitutions, the homologous ATP5A1W fragments contain a
considerable number of, sometimes highly nonconservative, amino acid
replacements. In one of these species, the ringneck parakeet (Psittacula
krameri), the ATP5A1W gene is present in an inactive form because of
the presence of a nonsense codon. Other changes, possibly leading to
an inactive ATP5A1W gene product, involve the substitution of arginine
residues by cysteine in the ATP5A1W protein of the mitred conure (Aratinga
mitrata) and the blue and gold macaw (Ara ararauna). The data suggest
also that although the divergence of the psittacine ATP5A1W and ATP5A1Z
genes preceded the origin of the psittacidae, this divergence occurred
independently of a similar process in the myna (Gracula religiosa),
the outgroup used in this study.
