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1471-2148-9-139.Pdf BMC Evolutionary Biology BioMed Central Research article Open Access Investigations of fine-scale phylogeography in Tigriopus californicus reveal historical patterns of population divergence Christopher S Willett*1 and Jason T Ladner1,2 Address: 1Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill NC 27599-3280, USA and 2Current address: Hopkins Marine Station of Stanford University, Department of Biological Sciences, Oceanview Blvd, Pacific Grove 93950, USA Email: Christopher S Willett* - [email protected]; Jason T Ladner - [email protected] * Corresponding author Published: 23 June 2009 Received: 5 February 2009 Accepted: 23 June 2009 BMC Evolutionary Biology 2009, 9:139 doi:10.1186/1471-2148-9-139 This article is available from: http://www.biomedcentral.com/1471-2148/9/139 © 2009 Willett and Ladner; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The intertidal copepod Tigriopus californicus is a model for studying the process of genetic divergence in allopatry and for probing the nature of genetic changes that lead to reproductive isolation. Although previous studies have revealed a pattern of remarkably high levels of genetic divergence between the populations of this species at several spatial scales, it is not clear what types of historical processes are responsible. Particularly lacking are data that can yield insights into population history from the finest scales of geographic resolution. Results: Sequence variation in both cytochrome b (CYTB, mtDNA) and the rieske iron-sulfur protein (RISP, nuclear) are examined at a fine scale within four different regions for populations of T. californicus. High levels of genetic divergence are seen for both genes at the broader scale, and genetic subdivision is apparent at nearly all scales in these populations for these two genes. Patterns of polymorphism and divergence in both CYTB and RISP suggest that selection may be leading to non-neutral evolution of these genes in several cases but a pervasive pattern of neither selection nor coadaptation is seen for these markers. Conclusion: The use of sequence data at a fine-scale of resolution in this species has provided novel insights into the processes that have resulted in the accumulation of genetic divergence among populations. This divergence is likely to result from an interplay between a limited dispersal ability for this copepod and the temporal instability of copepod habitat. Both shorter-term processes such as the extinction/recolonization dynamics of copepod pools and longer-term processes such as geological uplift of coastline and sea level changes appear to have impacted the patterns of differentiation. Some patterns of sequence variation are consistent with selection acting upon the loci used in this study; however, it appears that most phylogeographic patterns are the result of history and not selection on these genes in this species. Background accumulation of reproductive isolation between popula- Genetically divergent populations of the intertidal cope- tions [1-7]. Important questions still remain to be pod Tigriopus californicus have become an important answered in this species concerning the nature of the his- model system for studying how populations diverge in torical processes that have led to the dramatic levels of allopatry and how this genetic divergence can lead to the genetic divergence between populations. Studies of varia- Page 1 of 20 (page number not for citation purposes) BMC Evolutionary Biology 2009, 9:139 http://www.biomedcentral.com/1471-2148/9/139 tion in DNA sequences can be a powerful tool for intra- high when compared with other invertebrates and arthro- specific phylogeography and can help reveal historical pods [10,17,18]. There is some evidence for positive selec- patterns of population differentiation but have not yet tion acting upon a limited number of sites in one mtDNA been applied to the finest scales of resolution in this spe- gene in T. californicus, cytochrome oxidase subunit 2, COII cies, the scale over which gene flow is likely to be occur- [11], but in general the rapid accumulation of synony- ring [2,3,5,8,9]. An examination of this type of data may mous differences between these populations weakens the help reveal the nature of the interplay between gene flow, power of these rate-based tests of selection to detect selec- geography, geological processes, and extinction that con- tion on amino acid substitutions. tribute to genetic divergence in this system. Despite the limited evidence to date for selection on Despite the apparent ephemeral nature of their habitat mtDNA in T. californicus from patterns of sequence diver- (high intertidal rock pools that individually dry up on a gence there are reasons to believe that evolution of regular basis), data from T. californicus populations show mtDNA in this species has resulted in the functional diver- convincing evidence of long-term persistence within an gence of mtDNA-encoded proteins between populations. outcrop and limited gene flow between rocky outcrops A number of experiments in T. californicus examining that results in the accumulation of substantial genetic dif- hybrid fitness and enzymatic rates have suggested that a ferentiation between these populations [2]. Over the portion of the genetic variation between populations range of this copepod species from southern Alaska to leads to divergence in intergenomic coadaptation [6]. central Baja California, Mexico, nucleotide sequences can MtDNA-encoded proteins in the electron transport system show high levels of genetic divergence between regions on are part of large, multi-subunit proteins and interact the scale of 100 km apart or less, which in mtDNA- directly with many nuclear-encoded proteins so that inti- encoded genes can exceed twenty percent [3,5,10,11]. mate co-evolution between these proteins is likely to Studies of allozyme variation [12,13] and transplant occur. Studies in T. californicus have shown that the inter- experiments [9] reveal that between rocky outcrops, actions between mtDNA-encoded and nuclear-encoded within a region, there is also little gene flow. In fact, proteins in the electron transport system have resulted in longer-term monitoring of differences in allozyme fre- divergence in genomic coadaptation and include exam- quencies between outcrops (some as close as 500 m apart) ples of the loss of functional coadaptation as measured by reveal that differences remained stable for at least 18 examining electron transport system enzyme and gene years, potentially more than 100 copepod generations [2]. activities [19-22], impaired mitochondrial function [21], However, over time local population extinctions are and lowered hybrid copepod fitness [21,23-28]. It is not likely, due to the ephemeral nature of copepod habitat clear if this coadaptation between mtDNA-encoded and [14,15] and long distance gene flow must occur occasion- nuclear-encoded proteins of the ETS has lead to consistent ally as evidenced by the recolonization of previously gla- selection acting upon mtDNA and if this selection on ciated regions [5]. Most of this previous work primarily mtDNA could alter phylogeographic patterns. utilized allozyme markers at the finest scales of geo- graphic resolution with the result that patterns of DNA In this study we will characterize nucleotide sequence var- sequence variation have not yet been studied at the geo- iation in CYTB (a mtDNA-encoded protein of complex III graphic scale necessary to yield insights into the longer- of the electron transport system) to study fine-scale phyl- term historical processes of extinction and recolonization. ogeography in T. californicus and the potential impacts of non-neutral evolution upon its diversification among The high levels of mtDNA divergence between popula- these copepod populations. In addition, variation in a tions of T. californicus reflect large numbers of differences nuclear-encoded protein of complex III of the electron in both synonymous and non-synonymous (or amino transport system, the rieske iron-sulfur protein (RISP) will acid changing) sites. For example in the cytochrome b be studied for use as a nuclear-encoded marker for phylo- gene (CYTB, 1128 bp) between two California popula- geographic inferences. A unique aspect of this study is that tions (Santa Cruz, SCN and Abalone Cove, AB) there are although there have been a number of studies in T. califor- 197 synonymous differences and 28 amino acid changes nicus examining fine-scale population structure (within [10]. These high levels of divergence are likely to reflect and between adjacent outcrops) using allozymes and both long periods of isolation between populations and broader-scale studies (involving geographically distant high mutation rates. Willett and Burton [10] showed that populations) using both allozymes and mtDNA/nuclear mtDNA is evolving at a much more rapid rate than gene sequences, there are few data available for sequence nuclear genes in this species, between 26 and 38-fold evolution and differentiation at the finer population higher at synonymous sites. Although higher rates of scale. These sequence comparisons will have the added mtDNA than nuclear DNA evolution are found in other advantage of bringing a historical
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