Evolution 57 9 2003 pp 2101 2118 LINEAR HABITATS AND THE NESTED CLADE ANALYSIS AN EMPIRICAL EVALUATION OF GEOGRAPHIC VERSUS RIVER DISTANCES USING AN OZARK CRAYFISH DECAPODA CAMBARIDAE JAMES W FETZNER JR 1 2 1 Department AND KEITH A CRANDALL1 3 of Integrative Biology Brigham Young University 675 Widtsoe Building Provo Utah 84602 L Bean Life Science Museum Brigham Young University Provo Utah 84602 E mail keithpcrandall byu edu 3 Monte Abstract The nested clade analysis can be extremely useful in testing for an association between genetic variation and geography and in explaining these observed patterns in terms of historical or contemporary population processes The strength of this method lies in its ability to test a variety of processes simultaneously under a rigorous statistical framework Indeed many recent studies have used the nested analysis in a wide range of terrestrial and aquatic taxa However it has been suggested that riverine riparian or coastal species may be better examined using river or coastal distances rather than the standard geographic great circle distances among populations It is thought that the standard geographic distances may not adequately describe the actual distances involved between populations of species inhabiting these one dimensional riverine habitats Therefore we analyzed population data from an Ozark crayfish Orconectes luteus to examine the effects on the results of a nested clade analysis using river distances In most cases the haplotypes detected in this crayfish were unique to a particular drainage or a group of neighboring drainages indicating very little movement of individuals among drainages Five major population groups were detected corresponding to many of the major river drainages sampled in this study The two types of distance analyses obtain similar results for higher level older clades but differ in many of the inferences made for lower level younger clades However we suggest that the comparison of both types of analyses for riverine species may enhance the process of elucidating historical and contemporary population processes especially in cases where the transfer of individuals among different drainages are involved Key words Cambaridae crayfish genetic variation linear habitats nested clade analysis phylogeography Received August 23 2002 The basic goal of population genetic studies is to describe how genetic variation is distributed within and among populations However additional information from gene genealogies has added a temporal perspective to phylogeographic analyses which allows such studies to examine the geographic distribution of genetic variation in a historical framework This combination of spatial and temporal information has enlightened many of our views of underlying population processes Many phylogeographic methods fall short however because the detection of an association between haplotype distributions and geography does not necessarily lead to an explanation of this observed pattern Templeton et al 1995 One method developed to specifically address this problem is the nested clade analysis NCA of Templeton et al 1987 and later extended by Templeton et al 1995 and Templeton 1998 2001 The NCA is a powerful method for examining the geographic associations of haplotypes under a rigorous statistical framework The method also goes further than other phylogeographic methods by explaining these associations in terms of contributions from either historical e g fragmentation colonization or range expansion or present day e g restricted gene flow processes that have played a role in defining the currently observed patterns of population structure Templeton et al 1995 Templeton 1998 Several other methods are also currently available that use temporal information contained in haplotype data These in2 Present address Section of Invertebrate Zoology Carnegie Museum of Natural History 4400 Forbes Avenue Pittsburgh Pennsylvania 15213 E mail fetznerj carnegiemuseums org Accepted March 17 2003 clude the analysis of molecular variance AMOVA of Excoffier et al 1992 and the variance in ordered alleles method NST of Dumolin Lapegue et al 1997 However the NCA allows for the analysis of more complex population processes than the NST method and provides a more objective assessment of geographic partitioning of haplotypes and clades than does the AMOVA method Cruzan and Templeton 2000 Emerson et al 2001 but see also Knowles and Maddison 2002 In addition a few alternative methods have been used to infer population histories and include the mismatch pair distribution method of Rogers and Harpending 1992 and the skyline plot method of Pybus et al 2000 However both of these methods are limited in that they only deal with a single historical event or deal strictly with range expansions or contractions While the NCA has been used in numerous analyses e g Turner et al 2000 Bernatchez 2001 Carbone and Kohn 2001 Sivasundar et al 2001a most such studies use geographic coordinates latitude and longitude to calculate the great circle distance between sampling sites or populations For many riverine riparian or coastal species however these geographic distances may not adequately represent the actual distances separating such populations Fig 1 In such cases user defined distances hereafter referred to as river distances calculated by following river courses or coastlines may better reflect the actual distances that must be traversed if individuals were to migrate between populations Linear river distances are often much larger than the geographic distances calculated among populations see Fig 2 Appendix 1 However no empirical studies have been con 2101 q 2003 The Society for the Study of Evolution All rights reserved 2102 J W FETZNER JR AND K A CRANDALL FIG 1 An illustration of the difference in estimating distances among populations of a riverine or riparian species using either geographic or river distances A Demonstration of the different distances calculated among three hypothetical populations n from the same river drainage B An illustration of the difference in distances calculated using the different methods For geographic distances the distance between populations 1 and 2 is the smallest whereas for the river distances populations 1 and 2 have the largest distance C How these distances are calculated among the populations ducted to compare the effects these two different distances may have on results obtained from an NCA or whether the added
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