Genetics of mitochondrial glutamate-oxaloacetate transaminase (GOT-2) in Tigriopus californicus

Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus

Background

Gene conversion of duplicated genes can slow the divergence of paralogous copies over time but can also result in other interesting evolutionary patterns. Islands of genetic divergence that persist in the face of gene conversion can point to gene regions undergoing selection for new functions. Novel combinations of genetic variation that differ greatly from the original sequence can result from the transfer of genetic variation between paralogous genes by rare gene conversion events. Genetically divergent populations of the copepod Tigriopus californicus provide an excellent model to look at the patterns of divergence among paralogs across multiple independent evolutionary lineages.

Results

In this study the evolution of a set of paralogous genes encoding putative aspartate transaminase proteins (called GOT1 here) are examined in populations of the copepod T. californicus. One pair of duplicated genes, GOT1p1 and GOT1p2, has regions of high divergence between the copies in the face of apparent on-going gene conversion. The GOT1p2 gene also has unique haplotypes in two populations that appear to have resulted from a transfer of genetic variation via inter-paralog gene conversion. A second pair of duplicated genes GOT1Sr and GOT1Sd also shows evidence of gene conversion, but this gene conversion does not appear to have maintained each as a functional copy in all populations.

Conclusions

The patterns of conservation and sequence divergence across this set of paralogous genes among populations of T. californicus suggest that some interesting evolutionary patterns are occurring at these loci. The results for the GOT1p1/GOT1p2 paralogs illustrate how gene conversion can factor in the creation of a mosaic pattern of regions of high divergence and low divergence. When coupled with rare gene conversion events of divergent regions, this pattern can result in the formation of novel proteins differing substantially from either original protein. The evolutionary patterns across these paralogs show how gene conversion can both constrain and facilitate diversification of genetic sequences.

Complex deleterious interactions associated with malic enzyme may contribute to reproductive isolation in the copepod Tigriopus californicus

Dobzhansky-Muller incompatibilities can result from the interactions of more than a single pair of interacting genes and there are several different models of how such complex interactions can be structured. Previous empirical work has identified complex conspecific epistasis as a form of complex interaction that has contributed to postzygotic reproductive isolation between taxa, but other forms of complexity are also possible. Here, I probe the genetic basis of reproductive isolation in crosses of the intertidal copepod Tigriopus californicus by looking at the impact of markers in genes encoding metabolic enzymes in F₂ hybrids. The region of the genome associated with the locus ME2 is shown to have strong, repeatable impacts on the fitness of hybrids in crosses and epistatic interactions with another chromosomal region marked by the GOT2 locus in one set of crosses. In a cross between one of these populations and a third population, these two regions do not appear to interact despite the continuation of a large effect of the ME2 region itself in both crosses. The combined results suggest that the ME2 chromosomal region is involved in incompatibilities with several unique partners. If these deleterious interactions all stem from the same factor in this region, that would suggest a different form of complexity from complex conspecific epistasis, namely, multiple independent deleterious interactions stemming from the same factor. Confirmation of this idea will require more fine-scale mapping of the interactions of the ME2 region of the genome.

The intertidal harpacticoid copepod Tigriopus japonicus (Crustacea: Copepoda) beta-actin gene: cloning, sequence and intraspecies variation

The Tigriopus japonicus beta-actin genes were amplified from genomic DNA by polymerase chain reaction (PCR) and cloned into pCRII vector. Several clones of the T. japonicus beta-actin gene spanned 1662-1676 bp with gains or losses of some bases in intron 3 or 4 but they consisted generally of 5 exons and 4 introns with very high homology, implying polymorphism of this gene. The exon and intron boundaries were matched with the GT/AG rule. The T. japonicus beta-actin gene showed high homology to the fish (Rivulus marmoratus) and human genes, 99.2 and 98.4%, respectively at the amino acid sequence level. The phylogenetic implications inferred from the T. japoncius beta-actin gene are discussed.

Viability of cytochrome c genotypes depends on cytoplasmic backgrounds in Tigriopus californicus

Because of their extensive functional interaction, mitochondrial DNA (mtDNA) and nuclear genes may evolve to form coadapted complexes within reproductively isolated populations. As a consequence of coadaptation, the fitness of particular nuclear alleles may depend on mtDNA genotype. Among populations of the copepod Tigriopus californicus, there are high levels of amino acid substitutions in both the mtDNA genes encoding subunits of cytochrome c oxidase (COX) and the nuclear gene encoding cytochrome c (CYC), the substrate for COX. Because of the functional interaction between enzyme and substrate proteins, we hypothesized that the fitness of CYC genotypes would depend on mtDNA genotype. To test this hypothesis, segregation ratios for CYC and a second nuclear marker (histone H1) unrelated to mitochondrial function were scored in F2 progeny of several reciprocal interpopulation crosses. Genotypic ratios at the CYC locus (but not the H1 locus) differed between reciprocal crosses and differed from expected Mendelian ratios, suggesting that CYC genotypic fitnesses were strongly influenced by cytoplasmic (including mtDNA) background. However, in most cases the nature of the deviations from Mendelian ratios and differences between reciprocal crosses are not consistent with simple coevolution between CYC and mtDNA background. In a cross in which both newly hatched larvae and adults were sampled, only the adult sample showed deviations from Mendelian ratios, indicating that genotypic viabilities differed. In two of six crosses, large genotypic ratio differences for CYC were observed between the sexes. These results suggest that significant variation in nuclear-mtDNA coadaptation may exist between T. californicus populations and that the relative viability of specific cytonuclear allelic combinations is somehow affected by sex.

Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus

The genetic structure of natural populations is frequently inferred from geographic distributions of alleles at multiple gene loci. Surveys of allozyme polymorphisms in the tidepool copepod Tigriopus californicus have revealed sharp genetic differentiation of populations, indicating that gene flow among populations is highly restricted. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial gene genealogies. DNA sequences of the mtDNA-encoded cytochrome-c oxidase subunit I gene from 21 isofemale lines derived from seven populations reveal a phylogeographic break between populations north and south of Point Conception, California, with sequence divergence across the break exceeding 18%, the highest level of mtDNA divergence yet reported among conspecific populations. Divergence between populations based on 22 sequences of the nuclear histone H1 gene is geographically concordant with the mitochondrial sequences. In contrast with previously studied nuclear genes in other sexually reproducing metazoans, the H1 gene genealogy from T. californicus shows no evidence of recombination. The apparent absence of intragenic recombinants probably results from the persistent lack of gene flow among geographically separated populations, a conclusion strongly supported by allozyme data and the mitochondrial gene genealogy. Despite strong population differentiation at allozyme loci, the phylogeographic break identified by the DNA sequences was not evident in the allozyme data.