The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes.

The origin of tetrapods is a major outstanding issue in vertebrate phylogeny. Each of the three possible principal hypotheses (coelacanth, lungfish, or neither being the sister group of tetrapods) has found support in different sets of data. In an attempt to resolve the controversy, sequences of 44 nuclear genes encoding amino acid residues at 10,404 positions were obtained and analyzed. However, this large set of sequences did not support conclusively one of the three hypotheses. Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy.

Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes.

Extant vertebrates are divided into three major groups: hagfishes (Hyperotreti, myxinoids), lampreys (Hyperoartia, petromyzontids), and jawed vertebrates (Gnathostomata). The phylogenetic relationships among the groups and within the jawed vertebrates are controversial, for both morphological and molecular studies have rendered themselves to conflicting interpretations. Here, we use the sequences of 35 nuclear protein-encoding genes to provide definitive evidence for the monophyly of the Agnatha (jawless vertebrates, a group encompassing the hagfishes and lampreys). Our analyses also give a strong support for the separation of Chondrichthyes (cartilaginous fishes) before the divergence of Osteichthyes (bony fishes) from the other gnathostomes.

Sequencing of amphioxus PSMB5/8 gene and phylogenetic position of agnathan sequences.

Reanalyses of vertebrate PSMB5 and PSMB8 genes were conducted with a newly obtained amphioxus sequence. The phylogenetic analysis indicated that the amphioxus sequence is an outgroup of both vertebrate PSMB5 and PSMB8 genes. The agnathan sequences were previously thought to be closer to PSMB5 than PSMB8 sequences. However, in this study the phylogenetic trees supported the clustering of agnathan sequences with PSMB8 rather than with PSMB5 sequences. In the alignment there are many sites in which the agnathan sequences are more similar to PSMB5 than PSMB8 sequences. Parsimony analysis showed that the amino acid pattern at these sites could be explained by one substitution on the ancestral branch leading to the jawed vertebrate PSMB8 cluster. The number of substitutions required at these sites was the same for different tree topologies with respect to the position of agnathans. The phylogenetic analyses of PSMB6/PSMB9 and PSMB7/PSMB10 genes indicated that all the interferon-gamma-inducible forms have evolved two to three times faster than the housekeeping forms in the jawed vertebrate lineage. Hence although the agnathan sequences cluster with the PSMB8 sequences, they have a slower rate of evolution similar to that of the housekeeping forms, and may be functioning as housekeeping forms.

Persistence of Mhc heterozygosity in homozygous clonal killifish, Rivulus marmoratus: implications for the origin of hermaphroditism.

The mangrove killifish Rivulus marmoratus, a neotropical fish in the order Cyprinodontiformes, is the only known obligatorily selfing, synchronous hermaphroditic vertebrate. To shed light on its population structure and the origin of hermaphroditism, major histocompatibility complex (Mhc) class I genes of the killifish from seven different localities in Florida, Belize, and the Bahamas were cloned and sequenced. Thirteen loci and their alleles were identified and classified into eight groups. The loci apparently arose approximately 20 million years ago (MYA) by gene duplications from a single common progenitor in the ancestors of R. marmoratus and its closest relatives. Distinct loci were found to be restricted to different populations and different individuals in the same population. Up to 44% of the fish were heterozygotes at Mhc loci, as compared to near homozygosity at non-Mhc loci. Large genetic distances between some of the Mhc alleles revealed the presence of ancestral allelic lineages. Computer simulation designed to explain these findings indicated that selfing is incomplete in R. marmoratus populations, that Mhc allelic lineages must have diverged before the onset of selfing, and that the hermaphroditism arose in a population containing multiple ancestral Mhc lineages. A model is proposed in which hermaphroditism arose stage-wise by mutations, each of which spread through the entire population and was fixed independently in the emerging clones.

Linkage Relationships and Haplotype Variation of the Major Histocompatibility Complex Class I A Genes in the Cichlid Fish Oreochromis niloticus.

The haplochromine cichlid species flocks of the East African Great Lakes are one of the best examples of adaptive radiation. Analysis of genetic variation among these species provides valuable information on species relationships and timing of speciation events. Although the haplochromine cichlids generally display little genetic variation, the major histocompatibility complex (Mhc) genes have been found to be highly variable. A study of the linkage relationships of the Mhc class I A genes in the cichlid fish Oreochromis niloticus was therefore undertaken. Class I loci were identified, and their segregation in seven mothers and their haploid embryos was determined. In total, 56 class I A sequences were found among the seven families. A strong concordance of segregation was observed in five haplotypes among the embryos, indicating a close linkage of all loci. The number of loci per haplotype varied from 11 to 17, while the total number of distinct loci found among all families was 22. These findings show that all class I A loci are linked in a single genetic cluster in O. niloticus.