Systematics and the Origin of Species On Ernst Mayr's 100th Anniversary (2005) / Chapter Skim
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10 On the Origin of Lake Malawi Cichlid Species: A Population Genetic Analysis of Divergence--YONG-JIN WON, ARJUN SIVASUNDAR, YONG WANG, AND JODY HEY
10 On the Origin of Lake Malawi Cichlid Species: A Population Genetic Analysis of Divergence--YONG-JIN WON, ARJUN SIVASUNDAR, YONG WANG, AND JODY HEY
Pages 182-200
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From page 182... ...
These exceptionally recent dates suggest that Malawi cichlids as a group experience a very active and dynamic diversification process. Current effective pop ulation size estimates range form 2,000 to near 40,000, and to >120,000 for estimates of ancestral population sizes.
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In addition, we include dated outgroup sequences that allow us to estimate the actual times and effective population sizes associated with speciation events.
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The basic demographic parameters are constant effective population sizes (N1, N2, and NA) , gene flow rates per gene copy per generation (m1 and m2)
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This version of the IM model has six demographic parameters (Nielsen and Wakeley, 2001) , each scaled by the overall neutral mutation rate (Fig.
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From page 186... ...
In the case of the six-locus HapSTR data sets, the autocorrelation of parameter values over the course of individual runs of the computer program proved to be quite high, indicating that it would be difficult to achieve large samples of effectively independent observations. To improve mixing of the Markov chain and shorten the time needed for simulation, runs were done by using multiple Markov chains under the Metropolis coupling protocol (Geyer, 1991; Hey and Nielsen, 2004; Won and Hey, 2005)
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From page 187... ...
. The procedure for converting parameter estimates, for the case when outgroup data are available for only a subset of the loci that are in the IM analysis, requires two values: a quantity, X, which is the geometric mean of the mutation rate scalar estimates that are generated by the IM analysis, for just those loci for which mutation rate estimates are available based on the outgroup; and a quantity, U, which is the geometric mean of the mutation rate per year, for those same loci based on the outgroup divergence and known time of common ancestry.
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188 of (1996) cies STRs)
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. To check whether levels of polymorphism are consistent with a neutral model, we compared the estimated mutation rate scalars for the sequence portions of the six loci with the amount of divergence observed between Tropheops and Eretmodus, the outgroup.
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The time scale as been converted to years, based on mutation rate scalar estimates and outgroup divergence, as described in Methods.
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From page 191... ...
10.5) , with an estimated divergence time of 17,700 years and estimated effective population sizes several fold larger (21,300 for T
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192 / Yong-Jin Won et al.
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From page 193... ...
Another possible cause for the lack of phylogenetic resolution in genetic data, in addition to recent speciation, is that genetic variation is shared because of gene exchange. Disentangling the relative contributions of variation shared since ancestry and shared via gene flow is necessary for estimating the time since speciation and for assessing speciation models.
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From page 194... ...
(OP) population that loci species migration Parameter Population gracilior gracilior gracilior gracilior gracilior tropheops The T
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tropheops. Probability density estimates are shown for effective population sizes (Upper)
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are the result of gene exchange between ancestral populations. This kind of gene exchange cannot be estimated by the method, although it will elevate the amount of variation in ancestral populations and lead to inflated effective population size estimates.
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From page 197... ...
Necessarily, the divergence process has been viewed through the lens of the IM model, and it is not yet clear how the picture would change if we were able to consider more than two populations simultaneously or could better assess the impact of assuming the stepwise mutation model for the STR portions of loci. The consistently very large estimates for ancestral population sizes do suggest that our samples contain variation that arose not just in single ancestral populations but in a wider array of partly intermingled populations.
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From page 198... ...
(2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D
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(2002b) Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas.
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(1997b) Unusually fine-scale genetic structuring found in rapidly speci ating Malawi cichlid fishes.
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