Population genetic structure and demography of Magnolia kobus: variety borealis is not supported genetically

Species delimitations by morphological and by genetic markers are not always congruent. Magnolia kobus consists of two morphologically different varieties, kobus and borealis. The latter variety is characterized by larger leaves than the former. For the conservation of M. kobus genetic resources in natural forests, the relationships between morphological and genetic variation should be clarified. We investigated variations in nuclear microsatellites, chloroplast DNA (cpDNA) sequences and leaf morphological traits in 23 populations of M. kobus over the range of species. Two genetically divergent lineages, northern and southern were detected and their geographical boundary was estimated to be at 39°N. The northern lineage consisted of two genetic clusters and a single cpDNA haplotype, while the southern one had multiple genetic clusters and cpDNA haplotypes. The northern lineage showed significantly lower genetic diversity than the southern. Approximate Bayesian computation indicated that the northern and southern lineages had experienced, respectively, population expansion and long-term stable population size. The divergence time between the two lineages was estimated to be 565,000 years ago and no signature of migration between the two lineages after divergence was detected. Ecological niche modeling showed that the potential distribution area in northern Japan at the last glacial maximum was very small. It is thus considered that the two lineages have experienced different population histories over several glacial-inter-glacial cycles. Individuals of populations in the central to northern part of Honshu on the Sea of Japan side and in Hokkaido had large leaf width and area. These leaf characteristics corresponded with those of variety borealis. However, the delimitation of the northern and southern lineages detected by genetic markers (39°N) was not congruent with that detected by leaf morphologies (36°N). It is therefore suggested that variety borealis is not supported genetically and the northern and southern lineages should be considered separately when identifying conservation units based not on morphology but on genetic markers.

     

Genomic divergence in sympatry indicates strong reproductive barriers and cryptic species within Eucalyptus salubris

Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow‐up study required to verify their geographic or evolutionary limits. Here, we follow‐up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species’ range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome‐wide divergence (F _ST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species’ range. Within lineages, gene flow was high, with low differentiation (mean F _ST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non‐contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.     

Widespread co‐occurrence of divergent mitochondrial haplotype lineages in a Central American species of poison frog (Oophaga pumilio)

Aim To analyse the phylogeographic structure of the strawberry poison frog, Oophaga pumilio (Dendrobatidae), across a large part of its range using a combination of mitochondrial and nuclear markers. Location Costa Rica and Panama. Methods Sequence analyses of a mitochondrial (cytochrome b) and a nuclear (RAG‐1) gene fragment as well as analyses of seven microsatellite loci were carried out on 269 individuals of O. pumilio sampled from 24 localities and on two individuals of O. vicentei. Results Two main mitochondrial haplotype lineages, corresponding to a northern (north Costa Rica) and a southern (south Costa Rica and eastern Panama) lineage, were identified. They differed by up to 7% uncorrected distance. We observed co‐occurrence of both lineages in seven populations in Costa Rica and Panama, indicating a pattern of extensive admixture. The two main mitochondrial lineages of O. pumilio roughly corresponded to a previously described phylogeographic pattern. Microsatellites indicate admixture spanning over a wide geographic area, but significant variation between the northern and southern groups was also found with microsatellite data. While microsatellite data reconstructed a separation south of an assumed Caribbean valley barrier, mitochondrial haplotypes of the ‘southern lineage’ shifted this barrier towards the north. Main conclusions Despite admixture, all three markers showed significant variation between the northern and southern groups. Phylogeographical breaks known from other anuran species in the study region could not be verified for O. pumilio. The unexpected clustering of the population from Escudo de Veraguas and the individuals of O. vincentei with the northern O. pumilio lineage indicates the need for a fundamental and careful taxonomic revision, including an interspecific phylogeography of the entire genus.     

Population and phylogenomic decomposition via genotyping‐by‐sequencing in Australian Pelargonium

Species delimitation has seen a paradigm shift as increasing accessibility of genomic‐scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognized entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognized species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.     

Speciation on the Rocks: Integrated Systematics of the Heteronotia spelea Species Complex (Gekkota; Reptilia) from Western and Central Australia

The isolated uplands of the Australian arid zone are known to provide mesic refuges in an otherwise xeric landscape, and divergent lineages of largely arid zone taxa have persisted in these regions following the onset of Miocene aridification. Geckos of the genus Heteronotia are one such group, and have been the subject of many genetic studies, including H. spelea, a strongly banded form that occurs in the uplands of the Pilbara and Central Ranges regions of the Australian arid zone. Here we assess the systematics of these geckos based on detailed examination of morphological and genetic variation. The H. spelea species complex is a monophyletic lineage to the exclusion of the H. binoei and H. planiceps species complexes. Within the H. spelea complex, our previous studies based on mtDNA and nine nDNA loci found populations from the Central Ranges to be genetically divergent from Pilbara populations. Here we supplement our published molecular data with additional data gathered from central Australian samples. In the spirit of integrative species delimitation, we combine multi-locus, coalescent-based lineage delimitation with extensive morphological analyses to test species boundaries, and we describe the central populations as a new species, H. fasciolatus sp. nov. In addition, within the Pilbara there is strong genetic evidence for three lineages corresponding to northeastern (type), southern, and a large-bodied melanic population isolated in the northwest. Due to its genetic distinctiveness and extreme morphological divergence from all other Heteronotia, we describe the melanic form as a new species, H. atra sp. nov. The northeastern and southern Pilbara populations are morphologically indistinguishable with the exception of a morpho-type in the southeast that has a banding pattern resembling H. planiceps from the northern monsoonal tropics. Pending more extensive analyses, we therefore treat Pilbara H. spelea as a single species with phylogenetic structure and morphological heterogeneity.     

Molecular and morphological diversity in species of Kronichthys (Teleostei,Loricariidae) from Atlantic coastal rivers of Brazil

The Neotropical catfish genus Kronichthys contains three species distributed along coastal rivers of southern and southeastern Brazil. Although phylogenetic hypotheses are available, the molecular and morphological diversity and species boundaries within the genus remain unexplored. In this study, the authors generated mitochondrial data for 90 specimens combined with morphometric and meristic data to investigate species diversity, species boundaries and putative morphological signatures in Kronichthys. Phylogenetic and species delimitation results clearly show the presence of four genetic lineages, three within Kronichthys heylandi along the coast from Rio de Janeiro to southern São Paulo and a single lineage encompassing both the nominal species Kronichthys lacerta and Kronichthys subteres from the Ribeira de Iguape basin to Santa Catarina in southern Brazil. Nonetheless, morphological data show overlapped ranges in morphometrics and a definition of only two morphotypes, with clear phenotypic differences in the teeth number: K. heylandi differs from K. subteres + K. lacerta by the higher number of premaxillary teeth (30–52 vs. 19–28) and higher number of dentary teeth (28–54 vs. 17–28). Headwater captures and connections of paleodrainages because of sea-level fluctuations represent the two major biogeographic processes promoting species diversification and lineage dispersal of Kronichthys in the Atlantic coastal range of Brazil.     

CHLOROPLAST-DNA VARIATION IN TELLIMA GRANDIFLORA (SAXIFRAGACEAE)

Tellima grandiflora, a herbaceous, diploid (2n = 14) perennial, is distributed from the peninsula and panhandle of Alaska to central California. Restriction site variation of chloroplast DNA was surveyed in 51 populations representing the geographic range of T. grandiflora using 20 endonucleases. Two well-differentiated clades of populations differing by 19 restriction site mutations and several length mutations are geographically structured. A northern group comprises populations from Alaska to central Oregon; populations from central Oregon to San Francisco, California, form a southern group. The southern lineage of the monotypic Tellima appears to have obtained its chloroplast genome via ancient hybridization with a species of Mitella. Although northern and southern lineages have well-differentiated chloroplast genomes, populations of T. grandiflora show a high degree of genetic similarity of nuclear-encoded allozymes; furthermore, no apparent morphological differences characterize the lineages. Significantly, several populations of T. grandiflora that possess the typical southern chloroplast genome also occur disjunctly on Prince of Wales Island, Alaska, and the Olympic Peninsula, Washington. Because both areas are proposed glacial refugia, we suggest that past glaciation may have created discontinuities in the geographic distribution of T. grandiflora. Following glaciation, migration of once-isolated populations possessing different chloroplast genomes resulted in the formation of a continuous geographic distribution with a major organellar discontinuity. Additional support for this hypothesis is provided by the presence of well-differentiated northern and southern chloroplast DNA lineages in Tolmiea menziesii, a species having a geographic distribution and life history traits similar to those of Tellima.     

Examining the phylogeny of the Australasian Lymnaeidae (Heterobranchia: Pulmonata: Gastropoda) using mitochondrial, nuclear and morphological markers

We examined the species groups relationships of the freshwater snail genus Austropeplea using mitochondrial, nuclear and morphological markers in addition to traditional methods of shell shape analysis. Based primarily on the results of a combined molecular and morphological analysis, samples of the nominal species A. tomentosa form distinct lineages. The New Zealand populations of A. tomentosa are a very distinct lineage from any of the Australian populations attributed to A. tomentosa. Furthermore, within the Australian group, three lineages, south Australia, Tasmania and eastern Australia, appear to have undergone recent and/or rapid speciation events. Samples assigned to A. lessoni were resolved as two distinct lineages, representing the eastern and northern Australian populations. Kutikina hispida was resolved within the Australian A. tomentosa clade. Molecular results for A. viridis suggests that it is also composed of at least two distinct lineages that could be treated as species. Incongruence observed between the single mitochondrial, nuclear and morphological topologies highlight the importance of using a number of different datasets in the delimitation of species-group taxa.     

The impact of Quaternary climate oscillations on divergence times and historical population sizes in Thylamys opossums from the Andes

Climate oscillations during the Quaternary altered the distributions of terrestrial animals at a global scale. In mountainous regions, temperature fluctuations may have led to shifts in range size and population size as species tracked their shifting habitats upslope or downslope. This creates the potential for both allopatric speciation and population size fluctuations, as species are either constrained to smaller patches of habitat at higher elevations or able to expand into broader areas at higher latitudes. We considered the impact of climate oscillations on three pairs of marsupial species from the Andes (Thylamys opossums) by inferring divergence times and demographic changes. We compare four different divergence dating approaches, using anywhere from one to 26 loci. Each pair comprises a northern (tropical) lineage and a southern (subtropical to temperate) lineage. We predicted that divergences would have occurred during the last interglacial (LIG) period approximately 125 000 years ago and that population sizes for northern and southern lineages would either contract or expand, respectively. Our results suggest that all three north–south pairs diverged in the late Pleistocene during or slightly after the LIG. The three northern lineages showed no signs of population expansion, whereas two southern lineages exhibited dramatic, recent expansions. We attribute the difference in responses between tropical and subtropical lineages to the availability of ‘montane‐like’ habitats at lower elevations in regions at higher latitudes. We conclude that climate oscillations of the late Quaternary had a powerful impact on the evolutionary history of some of these species, both promoting speciation and leading to significant population size shifts.     

Northern glacial refugia for the pygmy shrew Sorex minutus in Europe revealed by phylogeographic analyses and species distribution modelling

The southern European peninsulas (Iberian, Italian and Balkan) are traditionally recognized as glacial refugia from where many species colonized central and northern Europe after the Last Glacial Maximum (LGM). However, evidence that some species had more northerly refugia is accumulating from phylogeographic, palaeontological and palynological studies, and more recently from species distribution modelling (SDM), but further studies are needed to test the idea of northern refugia in Europe. Here, we take a rarely implemented multidisciplinary approach to assess if the pygmy shrew Sorex minutus, a widespread Eurasian mammal species, had northern refugia during the LGM, and if these influenced its postglacial geographic distribution. First, we evaluated the phylogeographic and population expansion patterns using mtDNA sequence data from 123 pygmy shrews. Then, we used SDM to predict present and past (LGM) potential distributions using two different training data sets, two different algorithms (Maxent and GARP) and climate reconstructions for the LGM with two different general circulation models. An LGM distribution in the southern peninsulas was predicted by the SDM approaches, in line with the occurrence of lineages of S. minutus in these areas. The phylogeographic analyses also indicated a widespread and strictly northern‐central European lineage, not derived from southern peninsulas, and with a postglacial population expansion signature. This was consistent with the SDM predictions of suitable LGM conditions for S. minutus occurring across central and eastern Europe, from unglaciated parts of the British Isles to much of the eastern European Plain. Hence, S. minutus likely persisted in parts of central and eastern Europe during the LGM, from where it colonized other northern areas during the late‐glacial and postglacial periods. Our results provide new insights into the glacial and postglacial colonization history of the European mammal fauna, notably supporting glacial refugia further north than traditionally recognized.     

Paraphyly of Cinclodes fuscus (Aves: Passeriformes: Furnariidae): Implications for taxonomy and biogeography

The Andes are a hotspot of global avian diversity, but studies on the historical diversification of Andean birds remain relatively scarce. Evolutionary studies on avian lineages with Andean–Patagonian distributions have focused on reconstructing species-level phylogenies, whereas no detailed phylogeographic studies on widespread species have been conducted. Here, we describe phylogeographic patterns in the Bar-winged Cinclodes (Cinclodes fuscus), a widespread and common species of ovenbird (Furnariidae) that breeds from Tierra del Fuego to the northern Andes. Traditionally, C. fuscus has been considered a single species composed of nine subspecies, but its long and narrow range suggests the possibility of considerable genetic variation among populations. Sequences of two mitochondrial genes revealed three discrete and geographically coherent groups of C. fuscus, occupying the southern, central, and northern Andes. Surprisingly, phylogenetic analyses indicated that these groups were more closely related to other species of Cinclodes than to each other. Relationships of the southern and northern C. fuscus clades to other species of Cinclodes were straightforward; in combination with available information on plumage, behavioral, and vocal variation, this suggests that each should be recognized as a distinct biological species. The central Andean group was paraphyletic with respect to C. oustaleti, and relationships among these taxa and C. olrogi were poorly resolved. We suggest that the central Andean C. fuscus should also be considered a different species, pending new information to clarify species limits in this group. These new phylogenetic data, along with recently developed methods, allowed us to review the biogeography of the genus, confirming southern South America and the central Andes as important areas for the diversification of these birds.     

Multilocus and morphological analysis of south-eastern Iberian Wall lizards (Squamata,Podarcis)

The phylogenetic relationships among the wall lizards of the Podarcis hispanicus complex that inhabit the south-east (SE) of the Iberian Peninsula and other lineages of the complex remain unclear. In this study, four mitochondrial and two nuclear markers were used to study genetic relationships within this complex. The phylogenetic analyses based on mtDNA gene trees constructed with ML and BI, and a species tree using *BEAST support three divergent clades in this region: the Valencia, Galera and Albacete/Murcia lineages. These three lineages were also corroborated in species delimitation analyses based on mtDNA using bPTP, mPTP, GMYC, ABGD and BAPS. Bayesian inference species delimitation method (BPP) based on both nuclear data and a combined data set (mtDNA + nuclear) showed high posterior probabilities for these three SE lineages (≥0.94) and another Bayesian analysis (STACEY) based on combined data set recovered the same three groups in this region. Divergence time dating of the species tree provided an estimated divergence of the Galera lineage from the other SE group (Podarcis vaucheri, (Albacete/Murcia, Valencia)) at 12.48 Ma. During this period, the Betic–Rifian arc was isolated, which could have caused the isolation of the Galera form distributed to the south of the Betic Corridor. Although lizards from the Albacete/Murcia and Galera lineage are morphologically similar, they clearly represent distinct genetic lineages. The noteworthy separation of the Galera lineage enables us to conclude that this lineage must be considered as a new full species.     

Delimiting species in the genus Otospermophilus (Rodentia: Sciuridae), using genetics,ecology, and morphology

We apply an integrative taxonomy approach to delimit species of ground squirrels in the genus Otospermophilus because the diverse evolutionary histories of organisms shape the existence of taxonomic characters. Previous studies of mitochondrial DNA from this group recovered three divergent lineages within Otospermophilus beecheyi separated into northern, central, and southern geographical populations, with Otospermophilus atricapillus nested within the southern lineage of O. beecheyi. To further evaluate species boundaries within this complex, we collected additional genetic data (one mitochondrial locus, 11 microsatellite markers, and 11 nuclear loci), environmental data (eight bioclimatic variables), and morphological data (23 skull measurements). We used the maximum number of possible taxa (O. atricapillus, Northern O. beecheyi, Central O. beecheyi, and Southern O. beecheyi) as our operational taxonomic units (OTUs) and examined patterns of divergence between these OTUs. Phenotypic measures (both environmental and morphological) showed little differentiation among OTUs. By contrast, all genetic datasets supported the evolutionary independence of Northern O. beecheyi, although they were less consistent in their support for other OTUs as distinct species. Based on these data, we support the conclusions from a previous study that synonymized O. atricapillus with O. beecheyi, and we elevate the northern lineage of O. beecheyi to a separate species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1136–1151.     

Species delimitation with abc and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the liolaemus darwinii complex (squamata: liolaemidae)

Species delimitation is a major research focus in evolutionary biology because accurate species boundaries are a prerequisite for the study of speciation. New species delimitation methods (SDMs) can accommodate nonmonophyletic species and gene tree discordance as a result of incomplete lineage sorting via the coalescent model, but do not explicitly accommodate gene flow after divergence. Approximate Bayesian computation (ABC) can incorporate gene flow and estimate other relevant parameters of the speciation process while testing alternative species delimitation hypotheses. We evaluated the accuracy of BPP, SpeDeSTEM, and ABC for delimiting species using simulated data and applied these methods to empirical data from lizards of the Liolaemus darwinii complex. Overall, BPP was the most accurate, ABC showed an intermediate accuracy, and SpeDeSTEM was the least accurate under most simulated conditions. All three SDMs showed lower accuracy when speciation occurred despite gene flow, as found in previous studies, but ABC was the method with the smallest decrease in accuracy. All three SDMs consistently supported the distinctness of southern and northern lineages within L. darwinii. These SDMs based on genetic data should be complemented with novel SDMs based on morphological and ecological data to achieve truly integrative and statistically robust approaches to species discovery.     

Diversification across major biogeographic breaks in the African Shining/Square‐tailed Drongos complex (Passeriformes: Dicruridae)

Surprisingly, little is known about the extent of genetic structure within widely distributed and polytypic African species that are not restricted to a particular habitat type. The few studies that have been conducted suggested that speciation among African vertebrates may be intrinsically tied to habitat and the dynamic nature of biome boundaries. In the present study, we assessed the geographic structure of genetic variation across two sister‐species of drongos, the Square‐tailed Drongo (Dicrurus ludwigii) and the Shining Drongo (D. atripennis), that are distributed across multiple sub‐Saharan biogeographic regions and habitat types. Our results indicate that D. ludwigii consists of two strongly divergent lineages, corresponding to an eastern–southern lineage and a central‐western lineage. Furthermore, the central‐western lineage may be more closely related to D. atripennis, a species restricted to the Guineo‐Congolian forest block, and it should therefore be ranked as a separate species from the eastern–southern lineage. Genetic structure is also recovered within the three primary lineages of the D. atripennis–D. ludwigii complex, suggesting that the true species diversity still remains underestimated. Additional sampling and data are required to resolve the taxonomic status of several further populations. Overall, our results suggest the occurrence of complex diversification patterns across habitat types and biogeographic regions in sub‐Saharan Africa birds.     

The origin of unique diversity in deglaciated areas: traces of Pleistocene processes in north‐European endemics from the Galium pusillum polyploid complex (Rubiaceae)

The role of glacial oscillations in shaping plant diversity has been only rarely addressed in endemics of formerly glaciated areas. The Galium pusillum group represents a rare example of an ecologically diverse and ploidy‐variable species complex that exhibits substantial diversity in deglaciated northern Europe. Using AFLP and plastid and nuclear DNA sequences of 67 populations from northern, central, and western Europe with known ecological preferences, we elucidate the evolutionary history of lineages restricted to deglaciated areas and identify the eco‐geographic partitioning of their genetic variation. We reveal three distinct endemic northern lineages: (i) diploids from southern Sweden + the British Isles, (ii) tetraploids from southern Scandinavia and the British Isles that show signs of ancient hybridization between the first lineage and populations from unglaciated central Europe, and (iii) tetraploids from Iceland + central Norway. Available evidence supports a stepwise differentiation of these three lineages that started at least before the last glacial maximum by processes of genome duplication, interlineage hybridization and/or allopatric evolution in distinct periglacial refugia. We reject the hypothesis of more recent postglacial speciation. Ecological characteristics of the populations under study only partly reflect genetic variation and suggest broad niches of postglacial colonizers. Despite their largely allopatric modern distributions, the north‐European lineages of the G. pusillum group do not show signs of rapid postglacial divergence, in contrast to most other northern endemics. Our study suggests that plants inhabiting deglaciated areas outside the Arctic may exhibit very different evolutionary histories compared with their more thoroughly investigated high‐arctic counterparts.     

IDENTIFICATION OF CRYPTIC SPECIES IN THE LESSONIA NIGRESCENS COMPLEX (PHAEOPHYCEAE,LAMINARIALES)1

The kelp Lessonia nigrescens Bory is the most ecologically and economically important seaweed in rocky intertidal and shallow subtidal habitats along the temperate Pacific South American coasts. Recent molecular studies suggest the existence of two lineages, one (northern lineage) from 17° S to 30° S and a second (central lineage) from 29° S to 41° S. To identify and name these lineages we performed morphological, nomenclatural and field studies. Four external and three internal anatomical traits permitted a morphological separation of the two lineages. The internal structure of both lineages was different from the isolectotype of Lessonia nigrescens. It is therefore concluded that the name Lessonia nigrescens should not be used for the Chilean material. Chordaria spicata Suhr appears as the oldest available name for the central lineage, while Lessonia berteroana Montagne is the oldest name for the northern lineage. In both cases, the type material consisted of small‐sized, apical branches of larger plants. The new combination Lessonia spicata (Suhr) Santelices is proposed for the central lineage and we reinstate Lessonia berteroana for the northern lineage. Laminaria scissa Suhr is reduced to synonym of L. spicata. Representative specimens of Lessonia nigrescens were not found during new visits to its type locality in Cape Horn and along Chile. Future studies should verify the status of this species.     

Geographic structuring of chloroplast DNA genotypes inTiarella trifoliata (Saxifragaceae)

Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of intraspecific phylogeography to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.