Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulexspecies complex

Abstract

BackgroundEvidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB.ResultsWe sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA.ConclusionsAlthough lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.

Mitochondrial Capture Misleads about Ecological Speciation in the Daphnia pulex Complex

“…The few EPC sequences included in Rab4 [23] and Ldh A and Ldh B gene trees [24], constructed primarily for the North American species, were clustered in a clade with the NAPC sequences, suggesting a different relationship than the mtDNA phylogeny (Figure 1), where EPC haplotypes are in a separate clade with Daphnia tenebrosa (TEN). In the Rab4 and Ldh phylogenies, TEN haplotypes from Canada (no Eurasian sequences were included) were a part of the same clade with the NAPC and EPC haplotypes [23,24]. Clustering analysis of microsatellite data for the same specimens used for Rab4 sequencing placed TEN genotypes in a group with EPC, but did not provide clear evidence of clustering of NAPC with any other species [23].…”

“…The interpretation of Vergilino et al [23] was that the discordance of the Rab4 gene tree with the mtDNA phylogeny was likely due to stochastic processes such as lineage sorting of Rab4 , as opposed to hybridization, which was considered a less likely explanation [23] (but see 24). However, the Ldh A and Ldh B gene trees of Crease et al [24] are both congruent with Rab4 in that the EPC and TEN sequences are clustered with NAPC sequences [24], suggesting that mtDNA is actually the outlier.…”

Gene Expression Variation in Duplicate Lactate dehydrogenase Genes: Do Ecological Species Show Distinct Responses?

“…The overall expression of Ldh B was extremely low in all three groups, in all four environmental conditions, and further analysis will be required to determine if the mRNA transcripts are actually translated into protein. It is possible that this gene is no longer expressed at a functional level, although analysis of sequences from 85 isolates from 9 different Daphnia species suggests that selection is maintaining a functional Ldh B protein-coding sequence [18].…”

“…This includes the substitution of Aspartic acid in the S allele for Glutamic acid in the F allele at amino acid position 6, and the substitution of Glutamine in S for Glutamic acid in F at position 229, which likely causes the slow/fast mobility shift. Considerably more amino acid variation was observed among LDHB proteins [18].…”

“…Hybrids of the two species, with the heterozygous SF (Slow/Fast) genotype at the Ldh A locus, can be found in disturbed, deforested ponds [17] or intermediate habitats. Detailed phylogenetic studies revealed that the main differences between the S and F alleles of the Ldh A locus are amino acid substitutions at two sites [18]. This includes the substitution of Aspartic acid in the S allele for Glutamic acid in the F allele at amino acid position 6, and the substitution of Glutamine in S for Glutamic acid in F at position 229, which likely causes the slow/fast mobility shift.…”