| Summary: | The North American ecological species
Daphnia
pulicaria
and
Daphnia
pulex
are thought to have diverged from a common ancestor by adaptation to sympatric but ecologically distinct lake and pond habitats respectively. Based on mtDNA relationships, European
D
. pulicaria
is considered a different species only distantly related to its North American counterpart, but both species share a lactate dehydrogenase (Ldh) allele F supposedly involved in lake adaptation in North America, and the same allele is also carried by the related Holarctic
Daphnia
tenebrosa
. The correct inference of the species’ ancestral relationships is therefore critical for understanding the origin of their adaptive divergence. Our species tree inferred from unlinked nuclear loci for
D
. pulicaria
and
D
. pulex
resolved the European and North American
D
. pulicaria
as sister clades, and we argue that the discordant mtDNA gene tree is best explained by capture of
D
. pulex
mtDNA by
D
. pulicaria
in North America. The Ldh gene tree shows that F-class alleles in
D
. pulicaria
and
D
. tenebrosa
are due to common descent (as opposed to introgression), with
D
. tenebrosa
alleles paraphyletic with respect to
D
. pulicaria
alleles. That
D
. tenebrosa
still segregates the ancestral and derived amino acids at the two sites distinguishing the pond and lake alleles suggests that
D
. pulicaria
inherited the derived states from the
D
. tenebrosa
ancestry. Our results suggest that some adaptations restricting the gene flow between
D
. pulicaria
and
D
. pulex
might have evolved in response to selection in ancestral environments rather than in the species’ current sympatric habitats. The Arctic (
D
. tenebrosa
) populations are likely to provide important clues about these issues.
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