Historical demography, selection, and coalescence of mitochondrial and nuclear genes in Prochilodus species of northern South America

  • Moyer G
  • Winemiller K
  • McPhee M
 et al. 
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Abstract

Fishes of the genus Prochilodus are ecologically and commercially
important, ubiquitous constituents of large river biota in South
America. Recent ecologic and demographic studies indicate that these
fishes exist in large, stable populations with adult census numbers
exceeding one million individuals. Abundance data present a stark
contrast to very low levels of genetic diversity (theta) and small
effective population sizes (Ne) observed in a mitochondrial (mt)
DNA dataset obtained for two species, Prochilodus mariae, and its
putative sister taxon, Prochilodus rubrotaeniatus. Both species occupy
major river drainages (Orinoco, Essequibo, and Negro) of northeastern
South America. Disparity between expectations based on current abundance
and life history information and observed genetic data in these lineages
could result from historical demographic bottlenecks, or alternatively,
natural selection (i.e., a mtDNA selective sweep). To ascertain underlying
processes that affect mtDNA diversity in these species we compared
theta and Ne estimates obtained from two, unlinked nuclear loci (calmodulin
intron-4 and elongation factor-1alpha intron-6) using an approach
based on coalescent theory. Genetic diversity and Ne estimated from
mtDNA and nuclear sequences were uniformly low in P. rubrotaeniatus
from the Rio Negro, suggesting that this population has encountered
a historical bottleneck. For all P. mariae populations, theta and
Ne based on nuclear sequences were comparable to expectations based
on current adult census numbers and were significantly greater than
mtDNA estimates, suggesting that a selective mtDNA sweep has occurred
in this species. Comparative genetic analysis indicates that a suite
of evolutionary processes involving historical demography and natural
selection have influenced patterns of genetic variation and speciation
in this important Neotropical fish group.

Author-supplied keywords

  • Calmodulin
  • Effective population size
  • Elongation factor-1
  • Intron
  • LAMARC
  • Purifying selection

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