BACKGROUND
a major goal of biogeography is to investigate the influences of geological and climatic changes on the divergence and distribution of populations, species, and higher taxa.
a reasonable expectation in biogeographic studies is that episodes of geographic isolation, and consequently, opportunities for divergence should be favored on topographically complex landscapes  <cit> .
the complex western north american landscape has a dynamic history of dramatic alterations resulting from tectonic processes as well as pleistocene glacial cycles.
these geological and climatic processes have influenced patterns of gene flow and diversification across a wide variety of taxa  <cit> .
such processes have heavily influenced the evolution of the north american fish fauna as well  <cit> .
in western north america, the evolution of freshwater fishes has resulted from long term isolation of populations  <cit> , but with intermittent dispersal occurring between hydrological basins for at least some taxa during major events such as stream captures and floods, some of which have been facilitated by climatic events  <cit> .
climatic oscillations during the pleistocene have played a significant role in the evolution of the western north american biota by forcing organisms through a series of range contractions and expansions, range shifts, or localized extinctions as glacial ice sheets expanded and retracted  <cit> .
in northwestern north america, refugia are postulated to have occurred in several areas, including beringia  <cit> , the chehalis river valley  <cit> , the lower columbia river drainage  <cit> , the upper columbia river drainage  <cit> , haida gwaii   <cit> , and the klamath-siskiyou region  <cit>  .
additionally, some taxa have retained genetic signatures of survival in northern and southern refugia along the pacific coast  <cit> .
in addition to ice sheets, glacial-age lakes associated with the ice sheets altered the landscape of western north american in ways that may have affected gene flow.
perhaps the best studied of these is lake missoula, a glacial lake that formed in western montana when the clark fork river was dammed by a lobe of the cordilleran ice sheet  <cit> .
catastrophic flooding occurred when the ice dam broke, and the rushing waters carved the channeled scablands of eastern washington  <cit> .
this process is hypothesized to have occurred approximately  <dig>  times during the pleistocene  <cit> .
while most of those flooding events were small, some were catastrophic  <cit> .
the highest magnitude missoula floods were responsible for the capture of the palouse river  by the lower snake river, and the formation of palouse falls which now stand as a barrier to dispersal for aquatic taxa  <cit> , likely affecting patterns of gene flow for many of the aquatic taxa in the area.
glacial floods were also responsible for completely filling the willamette valley in western oregon  <cit> , an event that appears to have influenced genetic structure for at least some taxa by forming a barrier between populations of terrestrial organisms  <cit> , and possibly providing more connectivity of aquatic habitats and thus more opportunities for aquatic organisms to disperse.
glacial lakes and similar flooding events were also operating in northern areas  as the ice sheets retreated at the end of the pleistocene  <cit> .
the increased precipitation and decreased evaporation associated with glacial maxima resulted in the formation of pluvial lakes in many of the valleys of the basin and range province during the pleistocene.
pluvial lake bonneville in the bonneville basin experienced lake high-stands coincident with glacial melt waters  <cit> .
the highest level reached by lake bonneville is attributed to the capture of the bear river from the upper snake river into the bonneville basin approximately  <dig>  years ago  <cit> .
the influx of water from the bear river caused lake bonneville to rise until approximately  <dig>  years ago when the lake breached a northern sill in red rocks pass idaho.
lake bonneville drained catastrophically into the upper snake river in an event known as the bonneville flood  <cit> .
this and similar pluvial lake outflows have been hypothesized to be important inter-basin transfer mechanisms for fish and other aquatic taxa  <cit> .
one western north american fish species, redside shiner richardsonius balteatus , occurs in many areas heavily influenced by pleistocene climatic oscillations, either by glaciation directly, or by glacial and pluvial lakes.
the species’ native range spans the bonneville basin and the snake-columbia river basins west of the rocky mountains, ranging from southern utah to northern british columbia, and westward to the pacific coast of oregon, washington and british columbia .
phylogenetic analyses based on mitochondrial dna  data have demonstrated that r. balteatus is a monophyletic species that exhibits phylogeographic structure  <cit> .
pronounced morphological variation occurs among natural populations  <cit> .
variation in the number of anal fin rays, along with geographic distribution are the primary considerations for dividing the species into two subspecies, r. b. balteatus and r. b. hydrophlox.
such morphological variation could be the result of genetic differences resulting from historical isolation among populations, or of phenotypic plasticity in the face of different selective pressures in different environments.
moreover, subspecies r. b. hydrophlox exhibits geographic variation in somatic growth rates, at least some of which reflects genetic differences between populations  <cit> .
richardsonius balteatus is estimated to have diverged from its sister species, lahontan redside shiner richardsonius egregius , during the pliocene  <cit> , but genetic divergence within r. balteatus occurred more recently, during the early to mid pleistocene and the species exhibits relatively shallow phylogenetic structure  <cit> .
such shallow structure is often attributed to influences of late quaternary climatic shifts on patterns of gene flow.
because many parts of the current range of r. balteatus were affected by pleistocene climatic oscillations, well-documented changes in hydrological connections are postulated to have influenced range expansion.
the southernmost portion of the range, where r. b. hydrophlox occurs, includes the bonneville basin and upper snake river plain .
hubbs and miller  <cit>  postulated that r. balteatus invaded the bonneville basin from the snake river at the time of the bonneville flood because it occurred above barrier falls in northern parts of its range.
this proposed dispersal pathway is opposite to the direction of this massive flooding event, but hubbs and miller stated that fish moved in both directions through this connection.
their scenario of a southward invasion of the bonneville basin at the time of the bonneville flood is consistent with the fossil record, which shows that the extinct taxon r. durranti was present in pliocene sediments of lake idaho  <cit> , indicating that the genus occurred in the snake river system in the pliocene.
the earliest known r. balteatus fossil in the bonneville basin is late pleistocene in age  <cit> .
however, fossil data merely place a minimum age for the occurrence of taxa in an area, so it is possible that r. balteatus entered the bonneville basin from the snake river earlier in the pleistocene, or has been in the bonneville basin for a much longer period of time.
molecular data have shown that both the bear river capture and the bonneville flood transferred some freshwater fishes  <cit> , but the biogeography of other cyprinids suggests older  connections between the upper snake river and bonneville basin existed  <cit> .
richardsonius balteatus populations in previously glaciated areas must have colonized post-glacially.
it is hypothesized that r. balteatus colonized the northernmost parts of its range  post-glacially from a refugium in the upper columbia river basin based on current distributions above barrier falls and several known geomorphic connections  <cit> .
the upper columbia river drainage  is a hypothesized refugial area for fishes, amphibians, and plants  <cit> , and could have been for r. balteatus as well.
however, the current distribution of r. balteatus includes many proposed refugia other than the upper columbia river drainage, including the chehalis river valley, the lower columbia river, and areas along the oregon coast.
it is unknown whether r. balteatus colonized the aforementioned refugial areas post-glacially, or if the species occurred in one or more of them throughout the pleistocene.
some phylogeographic evidence supports the latter scenario based on divergence times among three clades that date to the early to mid pleistocene  <cit> .
if the species did occur in pleistocene refugia other than the upper columbia river drainage during the pleistocene, then the species may have colonized northern environments from outside the upper columbia river system.
herein, we use mtdna sequence data to test two hypotheses regarding proposed range expansion events by r. balteatus: 1) we test the hypothesis that the species invaded the bonneville basin at the time of the bonneville flood  <cit>  by assessing whether a pattern consistent with such a scenario exists.
if r. balteatus did enter the bonneville basin at that time, then bonneville basin populations should exhibit signs of recent rapid expansion, and molecular dating estimates should be consistent with a late pleistocene divergence time between bonneville basin populations and those in the upper snake/columbia river drainage.
2) we test the hypothesis that r. balteatus colonized british columbia post-glacially from a single refugium in the upper columbia river drainage  <cit> .
if r. balteatus expanded northward into british columbia from a single refugium, then genetic diversity in northernmost populations would be expected to be low, and should resemble that of the ancestral population.
if r. balteatus expanded from multiple refugia, then haplotypes observed in previously glaciated areas should resemble those of each of the refugia from which r. balteatus dispersed.
furthermore, if r. balteatus expanded from multiple refugia, then greater genetic diversity would be expected in some populations representing suture zones where genetic admixture may have occurred.
lastly, we discuss an overview of the phylogeography of the species.
to test these hypotheses, we generated a phylogeny using maximum likelihood and bayesian inference to assess the evolutionary relationships among redside shiner populations.
we also generated a haplotype network to visualize the finer-scale phylogeographic structure.
we estimated divergence times and evaluated changing population sizes through time to determine if divergence times and population expansions were consistent with late pleistocene events.
methods
sampling
we compiled a dataset comprising  <dig> individuals from thirty-four populations throughout the native range of r. balteatus, along with  <dig> r. egregius individuals from five populations that were used as the outgroup .
we used previously published dna sequences from  <dig> of those populations  <cit> , and generated dna sequence data for  <dig> individuals from  <dig> additional populations.
we sampled individuals from those six populations using a backpack electroshocker, a beach seine, or baited minnow traps.
once we sampled fish, we euthanized them by administering a lethal overdose of tricaine methanesulfonate , then immediately placed whole specimens into 95% ethanol to preserve tissues for genetic analyses.
we placed the ethanol preserved samples on ice and transported them to the university of nevada, las vegas  where we assigned monte l. bean life science museum  catalogue numbers and las vegas tissue  numbers to them before taking tissues for genetic analysis.
all specimens were deposited in the mlbm fish collection as vouchers at the completion of this study, and all specimens also have a sample of muscle tissue stored in the lvt collection at unlv.
the unlv animal care and use committee approved the protocols for the whole project, including the sampling and sacrificing of these minnows for the purpose of this research, as well as all subsequent handling of tissues/dna samples .
we performed all collections under the appropriate state and provincial permits .
location information for the thirty-five populations of r. balteatus included in this study, along with the number of individuals from each population  that we included in our analyses.
population abbreviations are given in parentheses after the name of the sampling locality.
accession numbers are given for the las vegas tissue collection  where muscle tissues are stored, the monte l bean museum  where whole specimens are stored, and genbank where control region and cyt b sequences have been deposited.
*denote populations for which sequences were newly generated for this study.
dna extraction and polymerase chain reaction
we extracted whole genomic dna from muscle tissues using the manufacturer’s recommended protocol for the qiagen dneasy tissue kit.
we verified successful extractions qualitatively by viewing the dna product under ultra-violet radiation following gel electrophoresis in a  <dig> % agarose gel.
we chose to amplify the control region  and the cytochrome b protein coding gene  of the mitochondrial genome because they are rapidly evolving markers in fishes  <cit> , but neither of them exhibits saturation in closely related cyprinid species  <cit> , and therefore they should be useful in detecting phylogeographic structure caused by pleistocene events.
moreover, gene sequences for many populations were already available  <cit> .
we amplified both markers via the polymerase chain reaction  using the oligonucleotide primers ha-a and la-a for cyt b <cit> , and l-pro and mrt- <dig> for cr  <cit> .
we mixed reaction cocktails for pcr using approximately  <dig>  ng dna template,  <dig>  pmoles of each oligonucleotide primer,  <dig>  μl of molecular grade water, and  <dig>  μl of promega gotaq hot start green master mix for a total reaction volume of  <dig>  μl.
we used the following thermal profile for pcr: an initial denature of  <dig> °c for four minutes, followed by thirty-five cycles of  <dig> °c for  <dig> seconds, annealing at  <dig> °c for  <dig> seconds, and extension at  <dig> °c for  <dig> seconds, a final extension at  <dig> °c for  <dig> minutes, and a rapid cool down to  <dig> °c.
we verified successful pcr qualitatively by viewing bands of appropriate size following electrophoresis on  <dig> % agarose gels.
we purified pcr products using the manufacturer’s recommended protocol for the qiagen qiaquick pcr purification kit.
dna sequencing and alignment
we used the same primers for sanger sequencing as we used for amplifying both markers, and sequenced light and heavy strands for each.
we performed cycle sequencing reactions using big dye chemistry.
reaction cocktails contained  <dig>  μl of purified pcr product,  <dig>  μl of molecular grade water,  <dig>  μl of  <dig> x tris buffer,  <dig>  μl of  <dig> mm mgcl <dig>   <dig>  μl of  <dig>  μm oligonucleotide primer, and  <dig>  μl of dye terminator reaction mix for an overall reaction volume of  <dig>  μl.
the thermal profile consisted of twenty-five cycles of  <dig> °c for  <dig> seconds,  <dig> °c for  <dig> sec, and  <dig> °c for  <dig> minutes followed by a  <dig> ° hold.
in some cases it was necessary to use internal sequencing primers to complete the sequence, so for cyt b we used either sq7hrs  <cit>  or sq3l  <cit> , and for cr we used 12rrs and cr7h  <cit> .
we removed excess dye terminators from cycle sequencing products using g- <dig> fine sephadex™ in centri-sep™ spin columns, and performed all sequencing on an abi  <dig> automated sequencer.
we aligned sequences using the automatic assembly function in sequencher v.  <dig>   then inspected the aligned sequences by eye and made corrections manually.
we used amino acid sequence and a r. balteatus cyt b sequence  as references for aligning and editing cyt b sequences.
there were no gaps in the final cyt b alignment, but there were in the final cr alignment.
individuals carried between three and five insertion/deletion sequences  in their non-coding cr sequences, but these were straightforward to align.
because both cr and cyt b are in the mitochondrial genome, and are thus inherited as a unit, we concatenated the sequences prior to performing phylogenetic analyses.
phylogenetic analyses
to get a broad assessment of redside shiner phylogeography, we generated phylogenies using maximum likelihood  and bayesian inference.
we selected the appropriate model of sequence evolution to be used in the phylogenetic analyses using jmodeltest  <cit> , and we reconstructed the ml phylogeny using treefinder   <cit> .
we performed  <dig> bootstrap replicates to estimate nodal support for ml analysis.
in bayesian analysis, we employed a markov chain monte carlo approach with one cold chain and three heated chains using the program mrbayes v. <dig> .
<dig>  <cit> .
we ran the bayesian analysis for  <dig> , <dig> generations, sampling every  <dig> generations.
we verified that the analysis reached stationarity and evaluated mixing among chains using tracer v. <dig> .
<dig>  <cit> .
to get appropriate levels of mixing between chains we lowered the temperature setting to t =  <dig> .
we discarded the first  <dig> , <dig> generations  as burn-in, and obtained posterior probabilities using a majority rule consensus of the remaining topologies.
to better visualize intraspecific genetic variation within r. balteatus, we created a haplotype network using the software program tcs v. <dig>   <cit> , using the default connection limit of 95% and treating gaps as a fifth character state.
in some cases it was necessary to break loops among haplotypes that were not very divergent , which we did using three criteria that are based on coalescent theory and are outlined by kauwe et al.
<cit> .
these three criteria are as follows: 1) geography – haplotypes are more likely to be closely related to those from individuals with close geographic proximity than to those from individuals that were sampled from locations that are further away.
2) topology – haplotypes are more likely to be closely related to those branching from basal nodes in a phylogeny than they are to be closely related to haplotypes that occur in the tips of a phylogenetic tree.
3) frequency – haplotypes are more likely to be closely related to haplotypes that are shared than they are to be closely related to those that are carried by just one individual.
molecular dating estimation
molecular dating estimates allowed us to estimate whether divergence times between clades of redside shiner were consistent with the late pleistocene time-frame of the phylogeographic hypotheses we sought to test.
we performed molecular dating analyses using an uncorrelated lognormal relaxed clock in beast v.  <dig> .
<dig>  <cit>  to estimate divergence times for clades within r. balteatus.
we used the gtr + i + g model of sequence evolution  and the coalescent constant model to set the prior on the tree.
for the mutation rate prior distribution, we used a lognormal distribution with a mean rate of  <dig> % sequence divergence per million years as estimated for richardsonius, and specified a range of  <dig> % to  <dig> % sequence divergence per million years to cover the range of mutation rates for cyt b for closely related genera  <cit>  as well as reported mutation rates for cr in other cyprinids  <cit> .
we ran the mcmc chain for  <dig> , <dig> generations, sampling every  <dig> generations, and discarded the first  <dig> , <dig> generations as burn-in.
we verified that the program reached stationarity and that there was proper mixing of chains by viewing the results in tracer v. <dig> .
<dig>  <cit> .
trees were annotated using treeannotator v. <dig> .
<dig>   <cit> .
historical demography
if redside shiner dispersed into the bonneville basin at the time of the bonneville flood, and into british columbia from a single refugium as glaciers retreated, then redside shiner populations in these areas are predicted to exhibit signs of recent rapid expansion.
we tested for recent rapid expansion in each of the three major redside shiner clades .
to do so, we used beast v. <dig> .
<dig>  <cit>  to generate bayesian skyline plots that use coalescent modeling to infer population size over time  <cit> .
we used a coalescent constant size tree prior, and employed a strict clock  using a uniform prior distribution with a mutation rate prior of  <dig> % sequence divergence per million years  <cit> , but allowing for a range of  <dig> % to  <dig> % sequence divergence per million years.
we used the hky substitution model of sequence evolution for each individual clade .
the model differed from that used in the phylogenetic analyses because model selection was run on each clade individually, and no outgroup taxa were included.
we ran the analysis for  <dig> million generations, logging every  <dig> generations, and discarded the first  <dig> million generations  as burn-in.
each of the three lineages was analyzed separately, but the parameters were the same for all three analyses.
we performed the same mcmc diagnostics as described in our divergence time analysis.
RESULTS
dna sequencing and alignment
dna sequencing yielded  <dig> bp of cyt b and  <dig> bp of cr from  <dig> r. balteatus individuals from  <dig> populations, and  <dig> r. egregius individuals from five populations  <cit> , for a total of  <dig> individuals.
of those  <dig> characters,  <dig> were invariable,  <dig> were variable, and  <dig> of the variable characters were parsimony informative.
ninety-seven unique mtdna haplotypes were found among all sampled populations of r. balteatus.
all dna sequences are available in genbank .
phylogenetic analyses
the jmodeltest results selected the gtr + i + g model of sequence evolution as the best fit for the concatenated mtdna data set under the akaike information criterion and the bayesian information criterion.
phylogenies produced by ml and bayesian analyses were similar, so only the ml phylogeny is shown, but ml bootstrap values and bayesian posterior probabilities are mapped onto the nodes .
for clarity, the major clades are presented in three different figures .
pacific northwest populations do not form a well-supported monophyletic clade although ml analysis did offer very weak support  for combining these lineages into a monophyletic group .
the pacific northwestern clade was not supported in mrbayes analysis .
collapsing that node leads to a series of monophyletic lineages that stem from a basal polytomy for the species.
hereafter, we refer to these collective lineages as the pacific northwestern clade as a matter of convenience.
two well supported clades are nested within r. balteatus : one clade corresponds to individuals sampled from the bonneville basin and upper snake river drainage , and is hereafter referred to as the bonneville/upper snake clade.
the other, comprising individuals from inland populations along the columbia plateau and british columbia , is hereafter referred to as the northern inland clade.
a sister relationship between the northern inland clade and the bonneville/upper snake clade was supported by bayesian analysis, but not by ml analysis .
collapsing that node would lead to a basal polytomy with pacific northwestern lineages, the northern inland clade, and the bonneville/upper snake clade all stemming out of it.
one individual sampled from the bonneville system  carried a haplotype that is one base different from the most widespread haplotype found in the northern inland clade .
five other populations  contained individuals carrying divergent haplotypes from the pacific northwestern clade and the northern inland clade .
a haplotype network shows intraspecific genetic variation within and among clades .
bonneville basin/upper snake river haplotypes are separated from pacific northwestern haplotypes by  <dig> steps, and southern bonneville haplotypes are separated from northern bonneville/upper snake river haplotypes by  <dig> steps.
northern bonneville/upper snake river haplotypes exhibit a star-burst pattern.
haplotypes from the northern inland clade are separated from haplotypes in the pacific northwestern clade by  <dig> steps.
a number of northern inland clade haplotypes differ by one or two base pairs from the most widespread shared haplotype, and also exhibit a star-burst pattern, whereas other haplotypes within this clade  are as divergent from the northern inland haplotype as they are from the pacific northwestern haplotypes.
some of the haplotypes from the pacific northwestern lineages  are  <dig> bp divergent from the other pacific northwestern haplotypes as well.
molecular dating estimation
molecular dating estimates show that divergence between r. balteatus and r. egregius occurred approximately  <dig>  ma , well within the 95% credible intervals for other divergence time estimates between the species  <cit> .
divergence within r. balteatus began approximately  <dig>  ma .
diversification within the bonneville/upper snake, pacific northwestern, and northern inland clades began almost simultaneously, with divergence time estimates of  <dig>  ma,  <dig>  ma, and  <dig>  ma, respectively .
historical demography
bayesian skyline plots indicate that each of the three major clades experienced demographic expansions during the pleistocene .
the bonneville/upper snake clade began expanding approximately  <dig>  years before present, the pacific northwestern lineages were expanding prior to  <dig>  years ago, and the most pronounced signature of expansion occurred in the northern inland clade, which began expanding approximately  <dig>  years ago.
discussion
genetic diversification within r. balteatus occurred well within the pleistocene, however most of it does not appear to have been associated with the lgm.
our results are inconsistent with a late pleistocene colonization of the bonneville basin during the bonneville flood.
rather, molecular dating estimates show that divergence between northern and southern bonneville clades was likely much earlier, approximately  <dig>  years ago, and that the northern and southern bonneville clades began diversifying  <dig>  and  <dig>  years before present, respectively .
despite the uncertainty surrounding molecular dating using mtdna, the 95% credible intervals surrounding these divergence time estimates did not include the late pleistocene when the bonneville flood occurred.
it is plausible that r. balteatus entered the bonneville basin during an earlier flooding event that connected the snake river to the bonneville basin  <cit> .
the earliest margin of the 95% credible interval of this divergence time estimate overlaps with the presence of a large lake that formed in the bonneville basin approximately  <dig>  years ago  <cit> , although it remains unclear whether the catastrophic flooding event proposed by ore  <cit>  occurred at that time.
the star-burst pattern of northern bonneville and upper snake river haplotypes on the haplotype network  is suggestive that some northward dispersal from the bonneville basin into the snake river at the time of the bonneville flood may have occurred.
the development and use of more fine scale genetic markers would be useful in addressing this hypothesis.
post-glacial colonization of most british columbia sampling locations appears to have been from a single refugium in the upper columbia river drainage, with the lone exception being the alouette lake population east of vancouver, bc.
individuals from alouette lake, which is in a pacific coastal drainage basin, were affiliated with lineages in the pacific northwestern clade .
the inland british columbia populations all carried northern inland clade haplotypes , and the northern inland clade exhibited a pronounced signature of recent rapid demographic expansion .
the star-burst pattern of many closely related haplotypes  is consistent with this scenario.
the low genetic diversity in these populations in previously glaciated areas is consistent with the prediction that genetic diversity should be low after having undergone recent rapid expansion.
hence, the phylogeographic scenario proposed by mcphail and lindsey  <cit> , wherein r. balteatus colonized british columbia from a refugium in the upper columbia drainage via a series of connections between glacial lakes, is plausible.
the clearwater and salmon rivers of northern idaho have been identified as pleistocene refugia  <cit> , and could have sheltered r. b. balteatus as well.
secondary contact between northern inland clade and pacific northwestern lineages appears to have occurred in five populations in the columbia river drainage .
we postulate that this secondary contact is relatively recent because there is no apparent admixture of mtdna haplotypes in the populations that we sampled in british columbia, suggesting that post-glacial colonization occurred prior to the two clades coming back into contact with one another.
moreover, several populations that are isolated by physical barriers to gene flow do not appear to have mixed mtdna haplotypes.
for example, coastal drainages  have not been connected to the main drainage of the columbia basin since the end of the pleistocene  <cit> , so gene flow has not been possible in recent times.
other populations  occur above barrier falls, or above seemingly impassable rapids, such as hurry back creek .
such barriers seem to have prevented migrants from reaching these populations.
non-admixed populations above these barriers suggest that expansion of the clades did not occur until after the formation of these barriers.
palouse falls , which formed during one of the more severe events associated with the missoula floods, has a population above it containing only individuals affiliated with the pacific northwestern lineages.
another population in the willamette valley in oregon  also contained haplotypes from the pacific northwestern lineages, so it is probable that pacific northwestern lineages were widespread during the pleistocene.
if the missoula floods themselves were responsible for transferring individuals from the northern inland clade into habitats occupied by the pacific northwestern lineages, it does not appear to have done so during the most severe events such as the one that filled the willamette valley, otherwise the callapooia river population above the falls would be expected to show genetic admixture as well, yet it does not.
it warrants mentioning that our sample sizes for each population are small , and may not have been sufficient to detect rare haplotypes in some areas.
additional sampling may reveal that non-admixed populations above barriers also experienced secondary contact that we did not detect with our limited sampling.
additional sampling may also reveal areas in the fraser river drainage where the northern inland clade and pacific northwestern lineages have come into secondary contact.
individuals from a lower fraser river population  have pacific northwestern haplotypes, whereas individuals from upper fraser river populations  carry northern inland haplotypes.
this sampling bias is unlikely to change our conclusion that the inland british columbia populations dispersed from a refugium in the upper columbia river drainage because all individuals from those populations had haplotypes associated with the northern inland clade.
if r. b. balteatus did survive the pleistocene in multiple refugia, as our data suggest, the locations appear to be in the lower columbia river system and/or along the pacific coast, and somewhere in the upper columbia river drainage, as noted above.
this scenario fits the biogeography of several other taxa.
the lower columbia river itself has been identified as a refugial area for various taxa  <cit> , as have areas along the pacific coast, including the chehalis river valley in washington state  <cit> .
unique haplotypes  occur in the satsop river within the chehalis river valley , but others  were more closely affiliated with other populations along the pacific coast.
the existence of the two divergent haplotypes in the satsop river, as well as the three that are associated with other pacific northwestern lineages suggests that the chehalis river valley may have been invaded by r. b. balteatus individuals from other areas, representing a unique instance where rather than expansion out of a pleistocene refugium, the refugium may have been invaded instead.
the pacific northwestern lineages were likely widespread during the pleistocene given that they showed the earliest signs of population expansion , and that they range from the pacific coastal drainages to as far inland as the north fork palouse river in eastern washington .
similarly, the northern inland clade appears to have been widespread with populations ranging from the lower snake river in southern idaho to the upper columbia drainage , although it appears that only the upper columbia populations contributed to the post-glacial colonization of inland british columbia.
the timing of the northern inland clade’s expansion corresponds to the wisconsin glacial period  and into the holocene, which is consistent with the idea of post-glacial expansion into inland british columbia as the glaciers retreated.
population expansion of the bonneville/upper snake clade appears to be associated with the illinoian glacial period , or perhaps the sangamonian interglacial , which is not consistent with a late-pleistocene invasion at the time of the bonneville flood.
expansion of the pacific northwestern lineages appears to be associated pre-illinoisan glacial cycles , as does the timing of the initial diversification within the species.
a single fish  carrying a haplotype that nested well within the northern inland clade was sampled in a northern bonneville basin stream at the utah/idaho border.
it may have been a “bait-bucket” transfer because no recent hydrological connections between that location  and the middle snake river are known and the required overland dispersal event from the nearest columbia river location with its closely related haplotype  is over three hundred km.
such “bait-bucket” transfer incidents appear to be limited in our dataset, but are well known between the bonneville basin and colorado river drainage of utah  <cit> .
nevertheless, the biogeography of richardsonius reflects historical distributions and drainage connections rather than recent anthropogenic introductions through most of its range, as is presumed to be the case for the majority of western north american freshwater fishes  <cit> .
CONCLUSIONS
diversification among redside shiner clades occurred during the pleistocene, but the early divergences do not appear to be associated with the lgm.
it is unlikely that the species entered the bonneville basin at the time of the bonneville flood as postulated by hubbs and miller  <cit> .
all but one of the british columbia populations are related to upper columbia river populations with the exception of alouette lake east of vancouver, which is more closely related to coastal populations of redside shiner.
hence, the biogeographic scenario outlined by mcphail and lindsey  <cit>  is plausible.
these conclusions are based on mtdna data, and analyses using additional unlinked markers would greatly enhance our understanding of this system.
availability of supporting data
the data set supporting the results of this article is available in the dryad digital repository   <cit> .
competing interests
the authors declare that they have no financial or non-financial competing interests.
authors’ contributions
ddh, dks, and brr designed the study.
ddh obtained field samples and generated dna sequence data.
ddh and bts performed the data analyses.
all authors contributed to the writing of the manuscript.
all authors read and approved the final manuscript.

 a major goal of biogeography is to investigate the influences of geological and climatic changes on the divergence and distribution of populations, species, and higher taxa. a reasonable expectation in biogeographic studies is that episodes of geographic isolation, and consequently, opportunities for divergence should be favored on topographically complex landscapes. the complex western north american landscape has a dynamic history of dramatic alterations resulting from tectonic processes as well as pleistocene glacial cycles. these geological and climatic processes have influenced patterns of gene flow and diversification across a wide variety of taxa. such processes have heavily influenced the evolution of the north american fish fauna as well. in western north america, the evolution of freshwater fishes has resulted from long term isolation of populations, but with intermittent dispersal occurring between hydrological basins for at least some taxa during major events such as stream captures and floods, some of which have been facilitated by climatic events. climatic oscillations during the pleistocene have played a significant role in the evolution of the western north american biota by forcing organisms through a series of range contractions and expansions, range shifts, or localized extinctions as glacial ice sheets expanded and retracted. in northwestern north america, refugia are postulated to have occurred in several areas, including beringia, the chehalis river valley, the lower columbia river drainage, the upper columbia river drainage, haida gwaii, and the klamath-siskiyou region. additionally, some taxa have retained genetic signatures of survival in northern and southern refugia along the pacific coast. in addition to ice sheets, glacial-age lakes associated with the ice sheets altered the landscape of western north american in ways that may have affected gene flow. perhaps the best studied of these is lake missoula, a glacial lake that formed in western montana when the clark fork river was dammed by a lobe of the cordilleran ice sheet. catastrophic flooding occurred when the ice dam broke, and the rushing waters carved the channeled scablands of eastern washington. this process is hypothesized to have occurred approximately times during the pleistocene. while most of those flooding events were small, some were catastrophic. the highest magnitude missoula floods were responsible for the capture of the palouse river by the lower snake river, and the formation of palouse falls which now stand as a barrier to dispersal for aquatic taxa, likely affecting patterns of gene flow for many of the aquatic taxa in the area. glacial floods were also responsible for completely filling the willamette valley in western oregon, an event that appears to have influenced genetic structure for at least some taxa by forming a barrier between populations of terrestrial organisms, and possibly providing more connectivity of aquatic habitats and thus more opportunities for aquatic organisms to disperse. glacial lakes and similar flooding events were also operating in northern areas as the ice sheets retreated at the end of the pleistocene. the increased precipitation and decreased evaporation associated with glacial maxima resulted in the formation of pluvial lakes in many of the valleys of the basin and range province during the pleistocene. pluvial lake bonneville in the bonneville basin experienced lake high-stands coincident with glacial melt waters. the highest level reached by lake bonneville is attributed to the capture of the bear river from the upper snake river into the bonneville basin approximately years ago. the influx of water from the bear river caused lake bonneville to rise until approximately years ago when the lake breached a northern sill in red rocks pass idaho. lake bonneville drained catastrophically into the upper snake river in an event known as the bonneville flood. this and similar pluvial lake outflows have been hypothesized to be important inter-basin transfer mechanisms for fish and other aquatic taxa. one western north american fish species, redside shiner richardsonius balteatus, occurs in many areas heavily influenced by pleistocene climatic oscillations, either by glaciation directly, or by glacial and pluvial lakes. the species’ native range spans the bonneville basin and the snake-columbia river basins west of the rocky mountains, ranging from southern utah to northern british columbia, and westward to the pacific coast of oregon, washington and british columbia. phylogenetic analyses based on mitochondrial dna data have demonstrated that r. balteatus is a monophyletic species that exhibits phylogeographic structure. pronounced morphological variation occurs among natural populations. variation in the number of anal fin rays, along with geographic distribution are the primary considerations for dividing the species into two subspecies, r. b. balteatus and r. b. hydrophlox. such morphological variation could be the result of genetic differences resulting from historical isolation among populations, or of phenotypic plasticity in the face of different selective pressures in different environments. moreover, subspecies r. b. hydrophlox exhibits geographic variation in somatic growth rates, at least some of which reflects genetic differences between populations. richardsonius balteatus is estimated to have diverged from its sister species, lahontan redside shiner richardsonius egregius, during the pliocene, but genetic divergence within r. balteatus occurred more recently, during the early to mid pleistocene and the species exhibits relatively shallow phylogenetic structure. such shallow structure is often attributed to influences of late quaternary climatic shifts on patterns of gene flow. because many parts of the current range of r. balteatus were affected by pleistocene climatic oscillations, well-documented changes in hydrological connections are postulated to have influenced range expansion. the southernmost portion of the range, where r. b. hydrophlox occurs, includes the bonneville basin and upper snake river plain. hubbs and miller postulated that r. balteatus invaded the bonneville basin from the snake river at the time of the bonneville flood because it occurred above barrier falls in northern parts of its range. this proposed dispersal pathway is opposite to the direction of this massive flooding event, but hubbs and miller stated that fish moved in both directions through this connection. their scenario of a southward invasion of the bonneville basin at the time of the bonneville flood is consistent with the fossil record, which shows that the extinct taxon r. durranti was present in pliocene sediments of lake idaho, indicating that the genus occurred in the snake river system in the pliocene. the earliest known r. balteatus fossil in the bonneville basin is late pleistocene in age. however, fossil data merely place a minimum age for the occurrence of taxa in an area, so it is possible that r. balteatus entered the bonneville basin from the snake river earlier in the pleistocene, or has been in the bonneville basin for a much longer period of time. molecular data have shown that both the bear river capture and the bonneville flood transferred some freshwater fishes, but the biogeography of other cyprinids suggests older connections between the upper snake river and bonneville basin existed. richardsonius balteatus populations in previously glaciated areas must have colonized post-glacially. it is hypothesized that r. balteatus colonized the northernmost parts of its range post-glacially from a refugium in the upper columbia river basin based on current distributions above barrier falls and several known geomorphic connections. the upper columbia river drainage is a hypothesized refugial area for fishes, amphibians, and plants, and could have been for r. balteatus as well. however, the current distribution of r. balteatus includes many proposed refugia other than the upper columbia river drainage, including the chehalis river valley, the lower columbia river, and areas along the oregon coast. it is unknown whether r. balteatus colonized the aforementioned refugial areas post-glacially, or if the species occurred in one or more of them throughout the pleistocene. some phylogeographic evidence supports the latter scenario based on divergence times among three clades that date to the early to mid pleistocene. if the species did occur in pleistocene refugia other than the upper columbia river drainage during the pleistocene, then the species may have colonized northern environments from outside the upper columbia river system. herein, we use mtdna sequence data to test two hypotheses regarding proposed range expansion events by r. balteatus: 1) we test the hypothesis that the species invaded the bonneville basin at the time of the bonneville flood by assessing whether a pattern consistent with such a scenario exists. if r. balteatus did enter the bonneville basin at that time, then bonneville basin populations should exhibit signs of recent rapid expansion, and molecular dating estimates should be consistent with a late pleistocene divergence time between bonneville basin populations and those in the upper snake/columbia river drainage. 2) we test the hypothesis that r. balteatus colonized british columbia post-glacially from a single refugium in the upper columbia river drainage. if r. balteatus expanded northward into british columbia from a single refugium, then genetic diversity in northernmost populations would be expected to be low, and should resemble that of the ancestral population. if r. balteatus expanded from multiple refugia, then haplotypes observed in previously glaciated areas should resemble those of each of the refugia from which r. balteatus dispersed. furthermore, if r. balteatus expanded from multiple refugia, then greater genetic diversity would be expected in some populations representing suture zones where genetic admixture may have occurred. lastly, we discuss an overview of the phylogeography of the species. to test these hypotheses, we generated a phylogeny using maximum likelihood and bayesian inference to assess the evolutionary relationships among redside shiner populations. we also generated a haplotype network to visualize the finer-scale phylogeographic structure. we estimated divergence times and evaluated changing population sizes through time to determine if divergence times and population expansions were consistent with late pleistocene events. methods sampling we compiled a dataset comprising individuals from thirty-four populations throughout the native range of r. balteatus, along with r. egregius individuals from five populations that were used as the outgroup. we used previously published dna sequences from of those populations, and generated dna sequence data for individuals from additional populations. we sampled individuals from those six populations using a backpack electroshocker, a beach seine, or baited minnow traps. once we sampled fish, we euthanized them by administering a lethal overdose of tricaine methanesulfonate, then immediately placed whole specimens into 95% ethanol to preserve tissues for genetic analyses. we placed the ethanol preserved samples on ice and transported them to the university of nevada, las vegas where we assigned monte l. bean life science museum catalogue numbers and las vegas tissue numbers to them before taking tissues for genetic analysis. all specimens were deposited in the mlbm fish collection as vouchers at the completion of this study, and all specimens also have a sample of muscle tissue stored in the lvt collection at unlv. the unlv animal care and use committee approved the protocols for the whole project, including the sampling and sacrificing of these minnows for the purpose of this research, as well as all subsequent handling of tissues/dna samples. we performed all collections under the appropriate state and provincial permits. location information for the thirty-five populations of r. balteatus included in this study, along with the number of individuals from each population that we included in our analyses. population abbreviations are given in parentheses after the name of the sampling locality. accession numbers are given for the las vegas tissue collection where muscle tissues are stored, the monte l bean museum where whole specimens are stored, and genbank where control region and cyt b sequences have been deposited. *denote populations for which sequences were newly generated for this study. dna extraction and polymerase chain reaction we extracted whole genomic dna from muscle tissues using the manufacturer’s recommended protocol for the qiagen dneasy tissue kit. we verified successful extractions qualitatively by viewing the dna product under ultra-violet radiation following gel electrophoresis in a % agarose gel. we chose to amplify the control region and the cytochrome b protein coding gene of the mitochondrial genome because they are rapidly evolving markers in fishes, but neither of them exhibits saturation in closely related cyprinid species, and therefore they should be useful in detecting phylogeographic structure caused by pleistocene events. moreover, gene sequences for many populations were already available. we amplified both markers via the polymerase chain reaction using the oligonucleotide primers ha-a and la-a for cyt b, and l-pro and mrt- for cr. we mixed reaction cocktails for pcr using approximately ng dna template, pmoles of each oligonucleotide primer, μl of molecular grade water, and μl of promega gotaq hot start green master mix for a total reaction volume of μl. we used the following thermal profile for pcr: an initial denature of °c for four minutes, followed by thirty-five cycles of °c for seconds, annealing at °c for seconds, and extension at °c for seconds, a final extension at °c for minutes, and a rapid cool down to °c. we verified successful pcr qualitatively by viewing bands of appropriate size following electrophoresis on % agarose gels. we purified pcr products using the manufacturer’s recommended protocol for the qiagen qiaquick pcr purification kit. dna sequencing and alignment we used the same primers for sanger sequencing as we used for amplifying both markers, and sequenced light and heavy strands for each. we performed cycle sequencing reactions using big dye chemistry. reaction cocktails contained μl of purified pcr product, μl of molecular grade water, μl of x tris buffer, μl of mm mgcl μl of μm oligonucleotide primer, and μl of dye terminator reaction mix for an overall reaction volume of μl. the thermal profile consisted of twenty-five cycles of °c for seconds, °c for sec, and °c for minutes followed by a ° hold. in some cases it was necessary to use internal sequencing primers to complete the sequence, so for cyt b we used either sq7hrs or sq3l, and for cr we used 12rrs and cr7h. we removed excess dye terminators from cycle sequencing products using g- fine sephadex™ in centri-sep™ spin columns, and performed all sequencing on an abi automated sequencer. we aligned sequences using the automatic assembly function in sequencher v. then inspected the aligned sequences by eye and made corrections manually. we used amino acid sequence and a r. balteatus cyt b sequence as references for aligning and editing cyt b sequences. there were no gaps in the final cyt b alignment, but there were in the final cr alignment. individuals carried between three and five insertion/deletion sequences in their non-coding cr sequences, but these were straightforward to align. because both cr and cyt b are in the mitochondrial genome, and are thus inherited as a unit, we concatenated the sequences prior to performing phylogenetic analyses. phylogenetic analyses to get a broad assessment of redside shiner phylogeography, we generated phylogenies using maximum likelihood and bayesian inference. we selected the appropriate model of sequence evolution to be used in the phylogenetic analyses using jmodeltest, and we reconstructed the ml phylogeny using treefinder. we performed bootstrap replicates to estimate nodal support for ml analysis. in bayesian analysis, we employed a markov chain monte carlo approach with one cold chain and three heated chains using the program mrbayes v... we ran the bayesian analysis for, generations, sampling every generations. we verified that the analysis reached stationarity and evaluated mixing among chains using tracer v... to get appropriate levels of mixing between chains we lowered the temperature setting to t = . we discarded the first, generations as burn-in, and obtained posterior probabilities using a majority rule consensus of the remaining topologies. to better visualize intraspecific genetic variation within r. balteatus, we created a haplotype network using the software program tcs v., using the default connection limit of 95% and treating gaps as a fifth character state. in some cases it was necessary to break loops among haplotypes that were not very divergent, which we did using three criteria that are based on coalescent theory and are outlined by kauwe et al.. these three criteria are as follows: 1) geography – haplotypes are more likely to be closely related to those from individuals with close geographic proximity than to those from individuals that were sampled from locations that are further away. 2) topology – haplotypes are more likely to be closely related to those branching from basal nodes in a phylogeny than they are to be closely related to haplotypes that occur in the tips of a phylogenetic tree. 3) frequency – haplotypes are more likely to be closely related to haplotypes that are shared than they are to be closely related to those that are carried by just one individual. molecular dating estimation molecular dating estimates allowed us to estimate whether divergence times between clades of redside shiner were consistent with the late pleistocene time-frame of the phylogeographic hypotheses we sought to test. we performed molecular dating analyses using an uncorrelated lognormal relaxed clock in beast v.. to estimate divergence times for clades within r. balteatus. we used the gtr + i + g model of sequence evolution and the coalescent constant model to set the prior on the tree. for the mutation rate prior distribution, we used a lognormal distribution with a mean rate of % sequence divergence per million years as estimated for richardsonius, and specified a range of % to % sequence divergence per million years to cover the range of mutation rates for cyt b for closely related genera as well as reported mutation rates for cr in other cyprinids. we ran the mcmc chain for, generations, sampling every generations, and discarded the first, generations as burn-in. we verified that the program reached stationarity and that there was proper mixing of chains by viewing the results in tracer v... trees were annotated using treeannotator v... historical demography if redside shiner dispersed into the bonneville basin at the time of the bonneville flood, and into british columbia from a single refugium as glaciers retreated, then redside shiner populations in these areas are predicted to exhibit signs of recent rapid expansion. we tested for recent rapid expansion in each of the three major redside shiner clades. to do so, we used beast v.. to generate bayesian skyline plots that use coalescent modeling to infer population size over time. we used a coalescent constant size tree prior, and employed a strict clock using a uniform prior distribution with a mutation rate prior of % sequence divergence per million years, but allowing for a range of % to % sequence divergence per million years. we used the hky substitution model of sequence evolution for each individual clade. the model differed from that used in the phylogenetic analyses because model selection was run on each clade individually, and no outgroup taxa were included. we ran the analysis for million generations, logging every generations, and discarded the first million generations as burn-in. each of the three lineages was analyzed separately, but the parameters were the same for all three analyses. we performed the same mcmc diagnostics as described in our divergence time analysis.  dna sequencing and alignment dna sequencing yielded bp of cyt b and bp of cr from r. balteatus individuals from populations, and r. egregius individuals from five populations, for a total of individuals. of those characters, were invariable, were variable, and of the variable characters were parsimony informative. ninety-seven unique mtdna haplotypes were found among all sampled populations of r. balteatus. all dna sequences are available in genbank. phylogenetic analyses the jmodeltest results selected the gtr + i + g model of sequence evolution as the best fit for the concatenated mtdna data set under the akaike information criterion and the bayesian information criterion. phylogenies produced by ml and bayesian analyses were similar, so only the ml phylogeny is shown, but ml bootstrap values and bayesian posterior probabilities are mapped onto the nodes. for clarity, the major clades are presented in three different figures. pacific northwest populations do not form a well-supported monophyletic clade although ml analysis did offer very weak support for combining these lineages into a monophyletic group. the pacific northwestern clade was not supported in mrbayes analysis. collapsing that node leads to a series of monophyletic lineages that stem from a basal polytomy for the species. hereafter, we refer to these collective lineages as the pacific northwestern clade as a matter of convenience. two well supported clades are nested within r. balteatus: one clade corresponds to individuals sampled from the bonneville basin and upper snake river drainage, and is hereafter referred to as the bonneville/upper snake clade. the other, comprising individuals from inland populations along the columbia plateau and british columbia, is hereafter referred to as the northern inland clade. a sister relationship between the northern inland clade and the bonneville/upper snake clade was supported by bayesian analysis, but not by ml analysis. collapsing that node would lead to a basal polytomy with pacific northwestern lineages, the northern inland clade, and the bonneville/upper snake clade all stemming out of it. one individual sampled from the bonneville system carried a haplotype that is one base different from the most widespread haplotype found in the northern inland clade. five other populations contained individuals carrying divergent haplotypes from the pacific northwestern clade and the northern inland clade. a haplotype network shows intraspecific genetic variation within and among clades. bonneville basin/upper snake river haplotypes are separated from pacific northwestern haplotypes by steps, and southern bonneville haplotypes are separated from northern bonneville/upper snake river haplotypes by steps. northern bonneville/upper snake river haplotypes exhibit a star-burst pattern. haplotypes from the northern inland clade are separated from haplotypes in the pacific northwestern clade by steps. a number of northern inland clade haplotypes differ by one or two base pairs from the most widespread shared haplotype, and also exhibit a star-burst pattern, whereas other haplotypes within this clade are as divergent from the northern inland haplotype as they are from the pacific northwestern haplotypes. some of the haplotypes from the pacific northwestern lineages are bp divergent from the other pacific northwestern haplotypes as well. molecular dating estimation molecular dating estimates show that divergence between r. balteatus and r. egregius occurred approximately ma, well within the 95% credible intervals for other divergence time estimates between the species. divergence within r. balteatus began approximately ma. diversification within the bonneville/upper snake, pacific northwestern, and northern inland clades began almost simultaneously, with divergence time estimates of ma, ma, and ma, respectively. historical demography bayesian skyline plots indicate that each of the three major clades experienced demographic expansions during the pleistocene. the bonneville/upper snake clade began expanding approximately years before present, the pacific northwestern lineages were expanding prior to years ago, and the most pronounced signature of expansion occurred in the northern inland clade, which began expanding approximately years ago. discussion genetic diversification within r. balteatus occurred well within the pleistocene, however most of it does not appear to have been associated with the lgm. our results are inconsistent with a late pleistocene colonization of the bonneville basin during the bonneville flood. rather, molecular dating estimates show that divergence between northern and southern bonneville clades was likely much earlier, approximately years ago, and that the northern and southern bonneville clades began diversifying and years before present, respectively. despite the uncertainty surrounding molecular dating using mtdna, the 95% credible intervals surrounding these divergence time estimates did not include the late pleistocene when the bonneville flood occurred. it is plausible that r. balteatus entered the bonneville basin during an earlier flooding event that connected the snake river to the bonneville basin. the earliest margin of the 95% credible interval of this divergence time estimate overlaps with the presence of a large lake that formed in the bonneville basin approximately years ago, although it remains unclear whether the catastrophic flooding event proposed by ore occurred at that time. the star-burst pattern of northern bonneville and upper snake river haplotypes on the haplotype network is suggestive that some northward dispersal from the bonneville basin into the snake river at the time of the bonneville flood may have occurred. the development and use of more fine scale genetic markers would be useful in addressing this hypothesis. post-glacial colonization of most british columbia sampling locations appears to have been from a single refugium in the upper columbia river drainage, with the lone exception being the alouette lake population east of vancouver, bc. individuals from alouette lake, which is in a pacific coastal drainage basin, were affiliated with lineages in the pacific northwestern clade. the inland british columbia populations all carried northern inland clade haplotypes, and the northern inland clade exhibited a pronounced signature of recent rapid demographic expansion. the star-burst pattern of many closely related haplotypes is consistent with this scenario. the low genetic diversity in these populations in previously glaciated areas is consistent with the prediction that genetic diversity should be low after having undergone recent rapid expansion. hence, the phylogeographic scenario proposed by mcphail and lindsey, wherein r. balteatus colonized british columbia from a refugium in the upper columbia drainage via a series of connections between glacial lakes, is plausible. the clearwater and salmon rivers of northern idaho have been identified as pleistocene refugia, and could have sheltered r. b. balteatus as well. secondary contact between northern inland clade and pacific northwestern lineages appears to have occurred in five populations in the columbia river drainage. we postulate that this secondary contact is relatively recent because there is no apparent admixture of mtdna haplotypes in the populations that we sampled in british columbia, suggesting that post-glacial colonization occurred prior to the two clades coming back into contact with one another. moreover, several populations that are isolated by physical barriers to gene flow do not appear to have mixed mtdna haplotypes. for example, coastal drainages have not been connected to the main drainage of the columbia basin since the end of the pleistocene, so gene flow has not been possible in recent times. other populations occur above barrier falls, or above seemingly impassable rapids, such as hurry back creek. such barriers seem to have prevented migrants from reaching these populations. non-admixed populations above these barriers suggest that expansion of the clades did not occur until after the formation of these barriers. palouse falls, which formed during one of the more severe events associated with the missoula floods, has a population above it containing only individuals affiliated with the pacific northwestern lineages. another population in the willamette valley in oregon also contained haplotypes from the pacific northwestern lineages, so it is probable that pacific northwestern lineages were widespread during the pleistocene. if the missoula floods themselves were responsible for transferring individuals from the northern inland clade into habitats occupied by the pacific northwestern lineages, it does not appear to have done so during the most severe events such as the one that filled the willamette valley, otherwise the callapooia river population above the falls would be expected to show genetic admixture as well, yet it does not. it warrants mentioning that our sample sizes for each population are small, and may not have been sufficient to detect rare haplotypes in some areas. additional sampling may reveal that non-admixed populations above barriers also experienced secondary contact that we did not detect with our limited sampling. additional sampling may also reveal areas in the fraser river drainage where the northern inland clade and pacific northwestern lineages have come into secondary contact. individuals from a lower fraser river population have pacific northwestern haplotypes, whereas individuals from upper fraser river populations carry northern inland haplotypes. this sampling bias is unlikely to change our conclusion that the inland british columbia populations dispersed from a refugium in the upper columbia river drainage because all individuals from those populations had haplotypes associated with the northern inland clade. if r. b. balteatus did survive the pleistocene in multiple refugia, as our data suggest, the locations appear to be in the lower columbia river system and/or along the pacific coast, and somewhere in the upper columbia river drainage, as noted above. this scenario fits the biogeography of several other taxa. the lower columbia river itself has been identified as a refugial area for various taxa, as have areas along the pacific coast, including the chehalis river valley in washington state. unique haplotypes occur in the satsop river within the chehalis river valley, but others were more closely affiliated with other populations along the pacific coast. the existence of the two divergent haplotypes in the satsop river, as well as the three that are associated with other pacific northwestern lineages suggests that the chehalis river valley may have been invaded by r. b. balteatus individuals from other areas, representing a unique instance where rather than expansion out of a pleistocene refugium, the refugium may have been invaded instead. the pacific northwestern lineages were likely widespread during the pleistocene given that they showed the earliest signs of population expansion, and that they range from the pacific coastal drainages to as far inland as the north fork palouse river in eastern washington. similarly, the northern inland clade appears to have been widespread with populations ranging from the lower snake river in southern idaho to the upper columbia drainage, although it appears that only the upper columbia populations contributed to the post-glacial colonization of inland british columbia. the timing of the northern inland clade’s expansion corresponds to the wisconsin glacial period and into the holocene, which is consistent with the idea of post-glacial expansion into inland british columbia as the glaciers retreated. population expansion of the bonneville/upper snake clade appears to be associated with the illinoian glacial period, or perhaps the sangamonian interglacial, which is not consistent with a late-pleistocene invasion at the time of the bonneville flood. expansion of the pacific northwestern lineages appears to be associated pre-illinoisan glacial cycles, as does the timing of the initial diversification within the species. a single fish carrying a haplotype that nested well within the northern inland clade was sampled in a northern bonneville basin stream at the utah/idaho border. it may have been a “bait-bucket” transfer because no recent hydrological connections between that location and the middle snake river are known and the required overland dispersal event from the nearest columbia river location with its closely related haplotype is over three hundred km. such “bait-bucket” transfer incidents appear to be limited in our dataset, but are well known between the bonneville basin and colorado river drainage of utah. nevertheless, the biogeography of richardsonius reflects historical distributions and drainage connections rather than recent anthropogenic introductions through most of its range, as is presumed to be the case for the majority of western north american freshwater fishes.  diversification among redside shiner clades occurred during the pleistocene, but the early divergences do not appear to be associated with the lgm. it is unlikely that the species entered the bonneville basin at the time of the bonneville flood as postulated by hubbs and miller. all but one of the british columbia populations are related to upper columbia river populations with the exception of alouette lake east of vancouver, which is more closely related to coastal populations of redside shiner. hence, the biogeographic scenario outlined by mcphail and lindsey is plausible. these conclusions are based on mtdna data, and analyses using additional unlinked markers would greatly enhance our understanding of this system. availability of supporting data the data set supporting the results of this article is available in the dryad digital repository. competing interests the authors declare that they have no financial or non-financial competing interests. authors’ contributions ddh, dks, and brr designed the study. ddh obtained field samples and generated dna sequence data. ddh and bts performed the data analyses. all authors contributed to the writing of the manuscript. all authors read and approved the final manuscript. 
across both longer and shorter timeframes, the western north american landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the last glacial maximum that have impacted the evolution of the north american biota. here we use mitochondrial dna sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) redside shiner entered the bonneville basin at the time of the bonneville flood, and 2) redside shiner colonized british columbia post-glacially from a single refugium in the upper columbia river drainage. all but one british columbia population of redside shiner are associated with the upper columbia river drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland british columbia redside shiner populations are affiliated with a refugium in the upper columbia river drainage. divergence times between redside shiner populations in the bonneville basin and the upper snake/columbia river drainage precedes the bonneville flood, thus it is unlikely that redside shiner invaded the bonneville basin during this flooding event. redside shiner is a cyprinid species that is widely distributed throughout western north america. genetic diversification in redside shiner began in the mid to late pleistocene, but was not associated with lgm. different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas. phylogeographyredside shinerpluvial lakesglacial cyclesclimate changepost-glacial colonization the species’ native range includes several well-documented pleistocene refugia.
 biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. across both longer and shorter timeframes, the western north american landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the last glacial maximum that have impacted the evolution of the north american biota. redside shiner is a cyprinid species that is widely distributed throughout western north america. the species’ native range includes several well-documented pleistocene refugia. here we use mitochondrial dna sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) redside shiner entered the bonneville basin at the time of the bonneville flood, and 2) redside shiner colonized british columbia post-glacially from a single refugium in the upper columbia river drainage.  genetic diversification in redside shiner began in the mid to late pleistocene, but was not associated with lgm. different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas.  divergence times between redside shiner populations in the bonneville basin and the upper snake/columbia river drainage precedes the bonneville flood, thus it is unlikely that redside shiner invaded the bonneville basin during this flooding event. all but one british columbia population of redside shiner are associated with the upper columbia river drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland british columbia redside shiner populations are affiliated with a refugium in the upper columbia river drainage. phylogeographyredside shinerpluvial lakesglacial cyclesclimate changepost-glacial colonization 