ABSTRACT
Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.
Subject(s)
Birds/genetics , DNA, Mitochondrial/genetics , Evolution, Molecular , Models, Biological , Phylogeny , Animals , Australia , Base Sequence , Bayes Theorem , Classification/methods , Models, Genetic , Molecular Sequence Data , New Zealand , Sequence Analysis, DNAABSTRACT
We describe the types of polymerase chain reaction (PCR) markers that we have isolated using amplified fragment length polymorphisms (AFLP) in closely related taxa from diverse plant genera. With these markers, both inter- and intraspecific differences have been identified. The characterization of the nucleotide sequences and fragment length polymorphisms of such AFLP-derived PCR markers is promising for investigating the ecology and evolution of closely related plant taxa.
Subject(s)
Genetic Markers , Plants/genetics , Ecosystem , Evolution, Molecular , Polymerase Chain Reaction , Polymorphism, GeneticABSTRACT
The pregnancy-specific beta 1-glycoproteins (PSG) form a large family of closely related proteins. Using newly developed methods of sequence analysis, in combination with protein modeling, we provide a framework for investigating the evolution and biological function of genes like the PSG. Evolutionary trees, based on C-terminal sequence, group PSG genes in a manner consistent with their genomic organization. Trees constructed using the N-terminal domain sequences are unreliable as an indicator of phylogeny because of non-neutral processes of sequence change. During duplication of the PSG genes, evolutionary pressures have resulted in a gradient of constrained change across each gene. The N-terminal domains show a nonrandom pattern of amino acid substitutions clustered in the immunoglobulin complementarity-determining region (CDR)-like regions, which appear to be important in the function of the protein.
Subject(s)
Evolution, Molecular , Multigene Family , Pregnancy-Specific beta 1-Glycoproteins/genetics , Carcinoembryonic Antigen/genetics , Female , Genetic Variation , Humans , Models, Molecular , Molecular Sequence Data , Molecular Structure , Phylogeny , Pregnancy , Pregnancy-Specific beta 1-Glycoproteins/chemistryABSTRACT
A sequence related to the C-terminal coding regions of a subgroup 1 pregnancy-specific beta 1-glycoprotein (PSG) has been characterised upstream of the PSG11 gene. The sequence can encode the Cc, Ca, and Cb, domains but there appear to be no other PSG gene exons within at least 10 kb. Based on the organisation of other PGS genes, the position of this sequence is novel.
Subject(s)
Pregnancy-Specific beta 1-Glycoproteins/genetics , Amino Acid Sequence , Base Sequence , Female , Humans , Molecular Sequence Data , Pregnancy , Protein Conformation , Restriction Mapping , Sequence Analysis, DNAABSTRACT
The pregnancy-specific beta 1-glycoproteins (PSG) form the major group of proteins synthesized in the human placenta. There are over 30 proteins in the family, encoded by 11 genes located on chromosomes 19q13.1-13.3. The genes can be divided into three subgroups based on the C-terminal exons expressed. The subgroup 1 genes have been well characterized. In this study the organization and sequence of a complete, functional, subgroup 3 gene is described. It contains the C-terminal exons, Cw, Cr, and Cs, which are expected from the transcripts characterized. Down-stream from these exons are sequences homologous to the C-termini of the subgroup 1 type genes. This demonstrates that the subgroup 1, 2, and 3 genes are related via insertions/deletions. Comparison of the C-terminal sequences of the three subgroups of genes shows that the subgroup 2 and 3 genes are more closely related than, and are distinct from, the subgroup 1 genes.
Subject(s)
Genes , Pregnancy-Specific beta 1-Glycoproteins/genetics , Amino Acid Sequence , Base Sequence , Exons , Molecular Sequence Data , Multigene Family , Sequence Alignment , Sequence Deletion , Sequence Homology, Nucleic AcidABSTRACT
Four cDNA clones representing the human pregnancy-specific beta 1-glycoprotein-11 (PSG-11) gene have been characterised. All encoded a splice variant of the PSG-11 gene designated PSG-11s, which can encode a secreted protein of 426 amino acids, containing six potential N-linked glycosylation sites, with a domain structure L-N-AI-AII-BII-C. Minor differences between the four clones sequenced included a restriction site polymorphic for ApaI that may differentiate between alleles of the PSG-11 gene.
