Nuclear and Mitochondrial Sequence Data Reveal and Conceal Different Demographic Histories and Population Genetic Processes in Caribbean Reef Fishes

Abstract

Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species' Caribbean ranges. Although both species shared a similar pattern of genetic subdivision, A. spinosa had 20-25 times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fish.

Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

“…Mitochondrial data suffer from greater NT composition bias and site saturation [27]. Nuclear genes generally exhibit lower levels of site saturation [36], and studies using only nuclear genes may therefore yield younger estimates compared with those incorporating mitochondrial sequences if model misspecification is a factor [37] and the calibrated node is deeper than the node of interest (as is generally the case). It has been anticipated that increased focus on nuclear data will reinvigorate avian divergence studies [8].…”

Isolation by distance and low connectivity in the peppery furrow shell Scrobicularia plana (Bivalvia)

“…Results were, however, obtained using only mitochondrial COI data. Since different genetic markers can reflect different aspects of population biology and history, only by combining data from several markers is fully understanding the complex demographic history of a species possible (Eytan & Hellberg 2010). …”

Evolution of a Neotropical marine fish lineage (Subfamily Chaenopsinae, Suborder Blennioidei) based on phylogenetic analysis of combined molecular and morphological data

“…Several aspects of their life-history, including possessing demersal eggs (Hastings, 1988a), short pelagic larval duration (Almany and Baldwin, 1996), near-shore development (Brogan, 1994), and limited adult dispersal ability, increase the possibilities of genetic differentiation of local populations. Chaenopsins have been the focus of several studies that have documented significant genetic structure among allopatric populations in the Gulf of California region (Bernardi et al, 2003;Lin et al, 2009;Lin and Galland, 2010;Riginos, 2005) and Caribbean (Eytan and Hellberg, 2010). In addition, closure of the Isthmus of Panama has clearly played an important role in shaping the current amphi-American distribution of the group (Table 1).…”