Congruence, consensus, and the comparative phylogeography of codistributed species in California

Comparative phylogeography has emerged as a means of understanding the spatial patterns of genetic divergence of codistributed species. However, researchers are often frustrated because of the lack of appropriate statistical tests to assess concordancy of multiple phylogeographic trees. We develop a method for testing congruence across multiple species and synthesizing the data into a regional supertree. Nine phylogeographic data sets of species with different life histories and ecologies were statistically compared using maximum agreement subtrees (MAST) and showed a high degree of concordancy. A supertree combining the different phylogeographic trees was then computed using matrix representation with parsimony, and the groups defined by this supertree were tested against climatic data to investigate a potential mechanism driving divergence. Our data suggest that species and genetic lineages in California are shaped by climatic regimes. The supertree method in combination with MAST represents a new approach to test congruence hypotheses and detect common geographic signals in comparative phylogeography.     

Application of non-coding DNA regions in intraspecific analyses

In this review we discuss the use of non-coding DNA at the intraspecific level in plants. Both nuclear and organelle non-coding regions are widely used in interspecific phylogenetic approaches. However, they are also valuable in analyses on the intraspecific level. Besides taxonomy, that is, defining subspecies or varieties, large fields for the application of non-coding DNA are population genetic and phylogeographic studies. Population genetics tries to explain the genetic patterns within species mostly by the amount of extant gene flow among populations, while phylogeography explicitly tries to reconstruct historic events. Depending on the study different molecular markers can be used, varying between very fast evolving microsatellites or some more slowly changing regions like intergenic spacers and introns. Here, we focus mainly on the use of non-coding regions in phylogeographic analyses. Mostly used in this context are regions of the genomes of the chloroplasts and mitochondria. In phylogeography, the correct estimation of allele or haplotype relationships is particularly important. As tree-based methods are mostly insufficient to depict relationships within species, network approaches are better suitable to infer gene or locus genealogies. Problematic for phylogeographic studies are alleles shared among multiple species, which could result from either hybridization or incomplete lineage sorting. Especially the latter can severely influence the interpretation of the phylogeographic patterns. Therefore, it seems necessary for us to also include close relatives of the species under study in phylogeographic analyses. Not only the sample design but also the analysis methods are currently changing, as some new methods such as statistical phylogeography were emerging recently and widely used methods like nested clade analysis might not be reliable in every case. During the last few years, a multitude of studies were published, which mainly analyzed phylogeographic patterns in European and North American plants. Phylogeographic studies in other regions of the earth are still comparably rare, although questions like the influence of the ice age on the vegetation in the tropics or southern hemisphere are still open and phylogeography provides an excellent remedy to answer them.     

鸟类分子系统地理学研究进展

分子系统地理学是当代生物地理学的重要分支,是以分子生物学方法重建种内和种上水平的系统发育关系,阐释进化历史,并通过分析近缘生物类群的系统发育关系与其空间和时间分布格局间的相关性构建生物区系历史的研究,是分子生物学与生物地理学结合的产物。中性进化学说和溯祖理论分析的建立,以及线粒体DNA和微卫星标记等分子遗传标记的应用,为分子系统地理学研究的开展提供了理论和实践基础。近年来,分子系统地理方法在鸟类学研究中的应用揭示了许多不同于传统认知的发现,为准确而深入的了解鸟类分子系统地理格局的差异和不同类群的起源中心提供了新颖的证据。目前的研究多从隔离分化说和扩散说的角度对鸟类分子系统地理格局的成因进行分析,而迁徙行为不同对鸟类系统地理格局的影响为成因的解释提供了新的角度。结合区域特点的比较分子系统地理研究,在更广泛的地域和更多类群中开展研究是我国鸟类分子系统地理研究的方向。此外,展望了第二代测序技术对分子生态生物地理研究具有的潜在促进作用。     

Lizards as model organisms for linking phylogeographic and speciation studies

Lizards have been model organisms for ecological and evolutionary studies from individual to community levels at multiple spatial and temporal scales. Here we highlight lizards as models for phylogeographic studies, review the published population genetics/phylogeography literature to summarize general patterns and trends and describe some studies that have contributed to conceptual advances. Our review includes 426 references and 452 case studies: this literature reflects a general trend of exponential growth associated with the theoretical and empirical expansions of the discipline. We describe recent lizard studies that have contributed to advances in understanding of several aspects of phylogeography, emphasize some linkages between phylogeography and speciation and suggest ways to expand phylogeographic studies to test alternative pattern‐based modes of speciation. Allopatric speciation patterns can be tested by phylogeographic approaches if these are designed to discriminate among four alternatives based on the role of selection in driving divergence between populations, including: (i) passive divergence by genetic drift; (ii) adaptive divergence by natural selection (niche conservatism or ecological speciation); and (iii) socially‐mediated speciation. Here we propose an expanded approach to compare patterns of variation in phylogeographic data sets that, when coupled with morphological and environmental data, can be used to to discriminate among these alternative speciation patterns. [Correction made after online publication (28/07/2010): (minor deletion in the last line of the abstract)].     

Comparative phylogeography of Nearctic and Palearctic fishes

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.     

Phylogeographic Triangulation: Using Predator-Prey-Parasite Interactions to Infer Population History from Partial Genetic Information

Phylogeographic studies, which infer population history and dispersal movements from intra-specific spatial genetic variation, require expensive and time-consuming analyses that are not always feasible, especially in the case of rare or endangered species. On the other hand, comparative phylogeography of species involved in close biotic interactions may show congruent patterns depending on the specificity of the relationship. Consequently, the phylogeography of a parasite that needs two hosts to complete its life cycle should reflect population history traits of both hosts. Population movements evidenced by the parasite’s phylogeography that are not reflected in the phylogeography of one of these hosts may thus be attributed to the other host. Using the wild rabbit (Oryctolagus cuniculus) and a parasitic tapeworm (Taenia pisiformis) as an example, we propose comparing the phylogeography of easily available organisms such as game species and their specific heteroxenous parasites to infer population movements of definitive host/predator species, independently of performing genetic analyses on the latter. This may be an interesting approach for indirectly studying the history of species whose phylogeography is difficult to analyse directly.     

Methods in comparative phylogeography, and their application to studying evolution in the north american aridlands

Historical biogeography and comparative phylogeography havemuch in common. Both seek to discover common historical patternsin the elements of biotas, although typically at different tiersof evolutionary history. Comparative phylogeography is basedon phylogeographic analyses of multiple taxa, usually widespreadspecies. By comparing the phylogeographic structures of numerouswidespread sympatric species, one can infer whether the currentfauna has been historically stable, as evidenced by the relativefrequency of geographically congruent reciprocally monophyleticgroups. Alternatively, if species distributions are ephemeralover evolutionary time, a mixture of phylogeographic structuresis expected. Coalescence analyses contribute information abouthistory irrespective of whether haplotype phylogenies are structuredor not. In the aridlands of North America, several isolatingevents are evident in the phylogeographic patterns of birds,mammals and herps. A mid-peninsular seaway in Baja California,dated at ca. one million years before present, had a pervasiveeffect, with 13 of 16 assayed species showing a concordant split.Hence, this community appears to have been a stable assemblageof species over the past one million years. In contrast, theavifauna of the Sonoran-Chihuahuan deserts consists of two specieswith a concordant split and three other species that are undifferentiatedacross both deserts. Hence, the species in this area have haddifferent histories. The Baja biota appears to resemble itsancestral configuration to a greater degree than the Sonoran-Chihuahuanone. A deeper evolutionary event separated taxa in Baja Californiafrom the eastern deserts, showing that the aridlands fauna wasaffected by events at different times resulting in overlaintiers of history.     

Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionize phylogeography.     

Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species

The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.     

Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas

Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a diversity of patterns and processes rivalling the complexities of LCA landscapes themselves. Even so, phylogeography is providing novel insights into regional diversification (e.g. cryptic lineage divergences), and general evolutionary patterns are emerging. Congruent multi‐taxon phylogeographic breaks are found across the Nicaraguan depression, Chorotega volcanic front, western and central Panama, and the Darién isthmus, indicating that a potentially shared history of responses to regional‐scale (e.g. geological) processes has shaped the genetic diversity of LCA communities. By contrast, other species show unique demographic histories in response to overriding historical events, including no phylogeographic structure at all. These low‐structure or incongruent patterns provide some evidence for a role of local, ecological factors (e.g. long‐distance dispersal and gene flow in plants and bats) in shaping LCA communities. Temporally, comparative phylogeographical structuring reflects Pliocene–Pleistocene dispersal and vicariance events consistent with the timeline of emergence of the LCA isthmus and its major physiographic features, e.g. cordilleras. We emphasise the need to improve biogeographic inferences in LCA through in‐depth comparative phylogeography projects capitalising on the latest statistical phylogeographical methods. While meeting the challenges of reconstructing the biogeographical history of this complex region, phylogeographers should also take up the critical service to society of applying their work to the conservation of its fascinating biodiversity.     

Revisiting Amazonian phylogeography: insights into diversification hypotheses and novel perspectives

The Amazon Basin harbors one of the richest biotas on Earth, such that a number of diversification hypotheses have been formulated to explain patterns of Amazonian biodiversity and biogeography. For nearly two decades, phylogeographic approaches have been applied to better understand the underlying causes of genetic differentiation and geographic structure among Amazonian organisms. Although this research program has made progress in elucidating several aspects of species diversification in the region, recent methodological and theoretical developments in the discipline of phylogeography will provide new perspectives through more robust hypothesis testing. Herein, we outline central aspects of Amazonian geology and landscape evolution as well as climate and vegetation dynamics through the Neogene and Quaternary to contextualize the historical settings considered by major hypotheses of diversification. We address each of these hypotheses by reviewing key phylogeographic papers and by expanding their respective predictions. We also propose future directions for devising and testing hypotheses. Specifically, combining the exploratory power of phylogeography with the statistical rigor of coalescent methods will greatly expand analytical inferences on the evolutionary history of Amazonian biota. Incorporation of non-genetic data from Earth science disciplines into the phylogeographic approach is key to a better understanding of the influence of climatic and geophysical events on patterns of Amazonian biodiversity and biogeography. In addition, achieving such an integrative enterprise must involve overcoming issues such as limited geographic and taxonomic sampling. These future challenges likely will be accomplished by a combination of extensive collaborative research and incentives for conducting basic inventories.     

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life‐history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait‐based phylogeography.     

Statistical phylogeography

While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field of statistical phylogeography aims to infer the history and processes underlying that structure, and to provide objective, rather than ad hoc explanations. Methods for parameter estimation are now commonly used to make inferences about demographic past. Although these approaches are well developed statistically, they typically pay little attention to geographical history. In contrast, methods that seek to reconstruct phylogeographic history are able to consider many alternative geographical scenarios, but are primarily nonstatistical, making inferences about particular biological processes without explicit reference to stochastically derived expectations. We advocate the merging of these two traditions so that statistical phylogeographic methods can provide an accurate representation of the past, consider a diverse array of processes, and yet yield a statistical estimate of that history. We discuss various conceptual issues associated with statistical phylogeographic inferences, considering especially the stochasticity of population genetic processes and assessing the confidence of phylogeographic conclusions. To this end, we present some empirical examples that utilize a statistical phylogeographic approach, and then by contrasting results from a coalescent-based approach to those from Templeton's nested cladistic analysis (NCA), we illustrate the importance of assessing error. Because NCA does not assess error in its inferences about historical processes or contemporary gene flow, we performed a small-scale study using simulated data to examine how our conclusions might be affected by such unconsidered errors. NCA did not identify the processes used to simulate the data, confusing among deterministic processes and the stochastic sorting of gene lineages. There is as yet insufficient justification of NCA's ability to accurately infer or distinguish among alternative processes. We close with a discussion of some unresolved problems of current statistical phylogeographic methods to propose areas in need of future development.     

Comparative phylogeography, genetic differentiation and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis

Multipartite symbioses are complex symbiotic relationships involving multiple interacting partners. These types of partnerships provide excellent opportunities in which to apply a comparative approach to identify common historical patterns of population differentiation and species-specific life history traits. Using three symbiotic blue-stain fungal species (Ophiostomatacea) associated with outbreaking populations of the mountain pine beetle (Dendroctonus ponderosae Hopkins) in western Canada, we applied phylogenetic, population genetic and demographic approaches to clarify phylogeographic patterns among the three fungal species. Broadly, the three species showed significant population differentiation, forming northern and southern populations, despite dramatic differences in haplotype diversity. Finer structuring and population demographic patterns were less consistent, showing some interspecific incongruence. By contrasting these species simultaneously, we were able to identify differences in recombination rate and ecological traits that can explain the observed patterns of incongruence among the fungal species. By applying a comparative approach to partners of a multipartite symbiosis, we were able to distinguish congruent population structuring and species-specific differences that help us to understand the complexity and evolution of this symbiotic system.     

History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae)

The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea-crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long-term processes rather than simply reflecting current conditions.     

Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

Phylogeographic inference can determine the timing of population divergence, historical demographic processes, patterns of migration, and when extended to multiple species, the history of communities. Single‐locus analyses can mislead interpretations of the evolutionary history of taxa and comparative analyses. It is therefore important to revisit previous single‐locus phylogeographic studies, particularly those that have been used to propose general patterns for regional biotas and the processes responsible for generating inferred patterns. Here, we employ a multilocus statistical approach to re‐examine the phylogeography of Lampropeltis zonata. Using nonparametic and Bayesian species delimitation, we determined that there are two well‐supported species within L. zonata. Ecological niche modelling supports the delimitation of these taxa, suggesting that the two species inhabit distinct climatic environments. Gene flow between the two taxa is low and appears to occur unidirectionally. Further, our data suggest that gene flow was mediated by females, a rare pattern in snakes. In contrast to previous analyses, we determined that the divergence between the two lineages occurred in the late Pliocene (c. 2.07 Ma). Spatially and temporally, the divergence of these lineages is associated with the inundation of central California by the Monterey Bay. The effective population sizes of the two species appear to have been unaffected by Pleistocene glaciation. Our increased sampling of loci for L. zonata, combined with previously published multilocus analyses of other sympatric species, suggests that previous conclusions reached by comparative phylogeographic studies conducted within the California Floristic Province should be reassessed.     

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome‐wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans‐Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter‐riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.     

Integrating coalescent and ecological niche modeling in comparative phylogeography

Understanding the factors that contribute to the formation of population genetic structure is a central goal of phylogeographic research, but achieving this goal can be complicated by the stochastic variance inherent to genetic processes. Statistical approaches to testing phylogeographic hypotheses accommodate this stochasticity by evaluating competing models of putative historical population structure, often by simulating null distributions of the expected variance. The effectiveness of these tests depends on the biological realism of the models. Information from the fossil record can aid in reconstructing the historical distributions of some taxa. However, for the majority of taxa, which lack sufficient fossils, paleodistributional modeling can provide valuable spatial-geographic data concerning ancestral distributions. Paleodistributional models are generated by projecting ecological niche models, which predict the current distribution of each species, onto a model of past climatic conditions. Here, we generate paleodistributional models describing the suitable habitat during the last glacial maximum for lineages from the mesic forests of the Pacific Northwest of North America, and use these models to generate alternative phylogeographic hypotheses. Coalescent simulations are then used to test these hypotheses to improve our understanding of the historical events that promoted the formation of population genetic structure in this ecosystem. Results from Pacific Northwest mesic forest organisms demonstrate the utility of these combined approaches. Paleodistribution models and population genetic structure are congruent across three amphibian lineages, suggesting that they have responded in a concerted manner to environmental change. Two other species, a willow and a water vole, despite being currently codistributed and having similar population genetic structure, were predicted by the paleodistributional model to have had markedly different distributions during the last glacial maximum. This suggests that congruent phylogeographic patterns can arise from incongruent ancestral distributions. Paleodistributional models introduce a much-needed spatial-geographic perspective to statistical phylogeography. In conjunction with coalescent models of population genetic structure, they have the potential to improve our understanding of the factors that promote population divergence and ultimately produce regional patterns of biodiversity.     

INTRASPECIFIC PHYLOGEOGRAPHY ACROSS THE POINT CONCEPTION BIOGEOGRAPHIC BOUNDARY

Recent studies of intraspecific phylogeography have suggested that the geographic location of genetic discontinuities, or phylogeographic breaks, may frequently coincide with biogeographic boundaries. The concordance is hypothesized to reflect similarity in the processes governing species boundaries and intraspecific lineage boundaries. This concordance has not, however, been widely tested. In the case of the Point Conception biogeographic boundary between the Oregonian and Californian marine biotas, only the supralittoral copepod Tigriopus californicus has been found to have a coincident phylogeographic break. Here I show that the apparent relationship between this break and Point Conception was, in fact, an artifact of insufficient geographic sampling. Mitochondrial DNA analyses of T. californicus populations between Morro Bay and San Diego reveal at least five equally deep phylogeographic breaks in the region (where only one biogeographic boundary is recognized). Limited nuclear DNA sequence data and allozyme data also support the occurrence of multiple genetic discontinuities along this geographic range. Lack of one-to-one correspondence between intraspecific phylogeography and biogeographic boundaries indicates that the processes affecting the genetic differentiation of populations of T. californicus differ from those responsible for determining species distributional limits at the Point Conception biogeographic boundary. A review of genetic data from other species also fails to provide evidence for concordance of biogeography and intraspecific phylogeography across Point Conception. I suggest that the concordance of phylogeography with biogeography will only be pronounced where the biogeographic boundary separates biotas that are phylogenetically related. The numerous cases of interspecific hybrid zones in the region of Cape Canaveral, for example, indicate that many sister-species pairs occur across this biogeographic boundary. Such hybrid zones are not common at Point Conception, and there appears to be no cases of intraspecific phylogeographic breaks associated with this well-recognized biogeographic boundary.