DOI: 10.5061/dryad.7998
title: Data from: Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes

description: 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. While 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
 fishes.
description: STRUCTURE Data File for
 western Caribbean A. spinosa populationsThis is the project file
 for the STRUCTURE analyses covering the western Caribbean A. spinosa
 populations. The .spj file containing the run parameters are contained in
 a separate file.spinosa.structure.west.dataSTRUCTURE Data File for eastern Caribbean A. spinosa populationsThis is the project file for the STRUCTURE analyses covering the eastern Caribbean A. spinosa populations. The .spj file containing the run parameters are contained in a separate file.spinosa.structure.east.dataSTRUCTURE Data File for all A. spinosa populationsThis is the project file for the STRUCTURE analyses covering all A. spinosa populations. The .spj file containing the run parameters are contained in a separate file.spinosa.structure.dataSTRUCTURE .spj file for all A. spinosa populationsspinosa.spjSTRUCTURE .spj file for eastern Caribbean A. spinosa populationsSpinosaEast.spjSTRUCTURE .spj file for western Caribbean A. spinosa populationsSpinosaWest.spjSTRUCTURE Data File for all A. aspera populationsThis is the project file for the STRUCTURE analyses covering all A. aspera populations. The .spj file containing the run parameters are contained in a separate file.aspSTRUCTUREinput.txtSTRUCTURE Data File for eastern Caribbean A. aspera populationsThis is the project file for the STRUCTURE analyses covering the eastern Caribbean A. aspera populations. The .spj file containing the run parameters are contained in a separate file.aspSTRUCTUREinput.east.txtSTRUCTURE Data File for western Caribbean A. aspera populationsThis is the project file for the STRUCTURE analyses covering the western Caribbean A. aspera populations. The .spj file containing the run parameters are contained in a separate file.aspSTRUCTUREinput.west.txtSTRUCTURE .spj file for eastern Caribbean A. aspera populationsAsperaEast.spjSTRUCTURE .spj file for western Caribbean A. aspera populationsAsperaWest.spjSTRUCTURE .spj file for all A. aspera populationsasperaAll.spj