Phylogeography and subspecies taxonomy of dunlins (Calidris alpina) in western Palearctic analysed by DNA microsatellites and amplified fragment length polymorphism markers

In a circumpolar wader, the dunlin ( Calidris alpina ), there are 11 named subspecies, but only five mitochondrial DNA (mtDNA) lineages have been found. In the present study, we investigated the genetic structure of dunlins in western Palearctic (from East Greenland to Taimyr peninsula) using DNA microsatellites and amplified fragment length polymorphism (AFLP) markers that may detect more recent differentiation than mtDNA. In this region, we consider four described subspecies; alpina , schinzii , arctica and centralis , together comprising two mtDNA lineages. We analyse seven polymorphic microsatellite loci and 91 AFLP markers in 287 and 152 unrelated individuals, respectively, originating from 17 populations. Neither microsatellites nor AFLPs reveal distinct groups that correspond to currently recognized subspecies. There is a clear pattern of isolation by distance in microsatellites. Our results do not contradict the former mtDNA results that there are two phylogenetic lineages (approximately corresponding to schinzii and centralis ) that have met and formed a cline ( alpina ). We find no difference between schinzii and arctica (East Greenland). We conclude that, given the lack of distinct groups and the gradual changes in microsatellite allele frequencies, these markers provide little genetic support for the dunlin subspecies taxonomy in the western Palearctic.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 713–726.     

Reticulate evolution: ancient introgression of the Adriatic brown trout mtDNA in softmouth trout Salmo obtusirostris (Teleostei: Salmonidae)

Two populations of softmouth trout ( Salmo obtusirostris ) from the rivers Neretva (Bosnia and Herzegovina) and Jadro (Croatia), along with two neighbouring populations of brown trout ( Salmo trutta ) were analysed with a suite of genetic markers (two mtDNA genes, two nuclear genes, and nine microsatellites) as well as morphological characters. The Jadro softmouth trout were fixed for a brown trout mtDNA haplotype of the Adriatic lineage, which is 1.7% divergent from a previously described haplotype characteristic for the Neretva softmouth trout. All other genetic markers, as well as morphological analysis, supported the clear distinction of softmouth trout from the rivers Neretva and Jadro from brown trout in neighbouring populations, and thus a mtDNA capture event is assumed. Population specific microsatellite allele profiles, as well as a high number of private alleles for both populations of softmouth trout, support the hybridization between brown trout and the Jadro softmouth trout most likely being of ancient origin, thus leading to a reticulate evolutionary pattern of mtDNA in this taxon.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 139–152.     

Markedly discordant mitochondrial DNA and allozyme phylogenies of tube-nosed fruit bats, Nyctimene, at the Australian–Oriental biogeographical interface

Australo-Papuan tube-nosed fruit bats of the genus Nyctimene reach their most westerly distribution on the island archipelagos of eastern Indonesia. A recent morphological examination indicates three species occur on Moluccan islands. Both allozyme electrophoresis and mitochondrial DNA (mtDNA) sequencing reveal there are only two species present, Nyctimene cephalotes and Nyctimene albiventer , but there is considerable disparity between the results obtained from the two genetic data sets. Allozyme data indicate N. albiventer occurs on Wokam, which sits on the Australian continental shelf and was joined to Australo-Papua during the last glacial maximum, and N. cephalotes on the other Moluccan islands, all of which are off the continental shelf. Divergence of these two species is dated at approximately 1.5 Mya. By contrast, the mtDNA gene tree shows two deep clades, one containing all specimens from Wokam and Yamdena, and the second all the specimens from the other islands. This especially marked incongruence between the two genetic data sets is ascribed to either a single introgression event of N. albiventer mtDNA into N. cephalotes on Yamdena at around 100 000 ya or lineage sorting of very old mtDNA lineages that coalesce a rather long time before the speciation event. These results highlight that caution should be exercised when relying on mtDNA as barcodes in species taxonomy. The continental-associated N. albiventer on Wokam has higher levels of allozyme heterozygosity and mtDNA nucleotide diversity than the N. cephalotes populations occurring on the more remote islands, indicating that this colonizing species has experienced bottlenecks and/or a low effective population size since speciation.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 589–602.     

Enhanced colour polymorphisms in island populations of the land snail Euhadra peliomphala

Variations in visible genetic polymorphisms are assumed to decrease in populations on small islands because of intense founder effects, genetic drift and inbreeding. However, we have found evidence of a marked enhancement of colour polymorphisms within populations on small oceanic islands that were colonized from the mainland. The source populations on the mainland of the land snail Euhadra peliomphala in four oceanic islands were estimated by phylogenetic analysis of mitochondrial DNA sequences. Diversity of shell colour was higher in the island populations than in the source populations on the mainland. In addition, the shell colour morphs differed not only among populations from different islands but also between the island populations and the source populations on the mainland. By contrast, no mtDNA variations were found in any of the island populations, even though the source populations possessed high mtDNA diversity. Thus, components of colour morphs changed in the island populations after their colonization, and colour polymorphisms are enhanced in these islands despite the loss of genetic variation. The above findings suggest that ecological mechanisms such as morphological release owing to a release from competition may overcome the tendency toward reduced genetic variation in islands to enhance the colour polymorphism.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 417–425.     

Phylogenetic relationships of Atherina hepsetus and Atherina boyeri (Pisces: Atherinidae) populations from Greece, based on mtDNA sequences

The genetic divergence and the phylogenetic relationships of six Atherina boyeri (freshwater and marine origin) and five Atherina hepsetus populations from Greece were investigated using partial sequence analysis of 12s rRNA, 16s rRNA and control region mtDNA segments. Three different well divergent groups were revealed; the first one includes A. boyeri populations living in the sea, the second includes A. boyeri populations living in the lakes and lagoons whereas the third one includes all A. hepsetus populations. Fifty-seven different haplotypes were detected among the populations studied. In all three mtDNA segments examined, sequence analysis revealed the existence of fixed haplotypic differences discriminating A. boyeri populations inhabiting the lagoon and the lakes from both the coastal A. boyeri and the A. hepsetus populations. The genetic divergence values estimated between coastal (marine) A. boyeri populations and those living in the lagoon and the lakes are of the same order of magnitude as those observed among coastal A. boyeri and A. hepsetus populations. The results obtained by different phylogenetic methods were identical. The deep sequence divergence with the fixed different haplotypes observed suggests the occurrence of a cryptic or sibling species within A. boyeri complex.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 151–161.     

Genetic variation and structure in native populations of the fire ant Solenopsis invicta: evolutionary and demographic implications

We studied population genetic variation and structure in the fire ant Solenopsis invicta using nuclear genotypic and mitochondrial DNA (mtDNA) sequence data obtained from samples collected throughout its native range. Geographic populations are strongly differentiated at both genomes, with such structure more pronounced in Brazil than in Argentina. Higher-level regional structure is evident from the occurrence of isolation-by-distance patterns among populations, the recognition of clusters of genetically similar, geographically adjacent populations by ordination analysis, and the detection of an mtDNA discontinuity between Argentina and Brazil coinciding with a previously identified landform of biogeographical relevance. Multiple lines of evidence from both genomes suggest that the ancestors of the ants we studied resembled extant northern Argentine S. invicta , and that existing Brazilian populations were established more recently by serial long-distance colonizations and/or range expansions. The most compelling evidence for this is the corresponding increase in F _K (a measure of divergence from a hypothetical ancestor) and decrease in genetic diversity with distance from the Corrientes population in northern Argentina. Relatively deep sequence divergence among several mtDNA clades, coupled with geographical partitioning of many of them, suggests prolonged occupation of South America by S. invicta in more-or-less isolated regional populations. Such populations appear, in some cases, to have come into secondary contact without regaining the capacity to freely interbreed. We conclude that nominal S. invicta in its native range comprises multiple entities that are sufficiently genetically isolated and diverged to have embarked on independent evolutionary paths.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 541–560.     

Lineage diversification on an evolving landscape: phylogeography of the California newt, Taricha torosa (Caudata: Salamandridae)

We used mitochondrial cytochrome  b sequences (up to 778 bp) and starch gel electrophoresis (45 loci) to examine the phylogeographical history of 39 populations of the California newt, Taricha torosa . Phylogenetic and population genetic methods were integrated to infer history at deep and shallow time depths. Using a molecular clock, the subspecies T. t. torosa and T. t. sierrae were estimated to have diverged 7–13 Mya. Within T. t. torosa, genetically differentiated groups were identified along coastal California, in southern California, and in the southern Sierra Nevada. The coastal group exhibited isolation by distance, but a lack of genetic variation north of present-day Monterey was indicative of a recent range expansion. In southern California, a disjunct population in central San Diego County was genetically diverged from coastal populations to the north (Nei's genetic distance of 0.113). However, mtDNA and protein data were geographically discordant regarding the boundary between the coastal and southern Californian groups, and a biogeographical scenario was developed to account for this discordance. The southern Sierran clade of T. t. torosa was weakly diverged from coastal populations for mtDNA sequence variation, yet was strongly differentiated for allozyme variation (Nei's genetic distance of 0.17–0.20). Populations of T. t. sierrae exhibited substantial population structure, and showed a steeper pattern of isolation by distance than did coastal populations of T. t. torosa . These results are interpreted in consideration of the known geomorphological history of California.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 213–239.     

Do taxonomic divisions reflect genetic differentiation? A comparison of morphological and genetic data in Coenonympha tullia (Müller), Satyrinae

Historically, morphological variation has been used to classify many species (and subspecies) of Lepidoptera. However, some of this variation may be unsuitable for inferring the recent evolutionary history of populations. Genetic data provide an alternative. We examine the morphological and genetic variation within and between British subspecies of Coenonympha tullia (Müller 1764) to test the hypothesis that neutral genetic variation corresponds to morphological variation. We find that most morphological and genetic variation occurs within populations and that those populations designated as subspecies based on morphological characters are not necessarily most closely related for mitochondrial DNA or nuclear DNA (amplified fragment length polymorphisms and allozymes). Thus, the notion that wing spot variation reflects population isolation and therefore genetic differentiation does not hold. The present study highlights the need for genetic data where taxonomy may be based on environmentally plastic or locally adapted characters because such characters will not reflect the true population genetic history.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 314–327.     

Occurrence of tetraploid and octoploid cytotypes in Senecio jacobaea ssp. jacobaea (Asteraceae) in Pannonia and the Carpathians

Four different cytotypes have been reported for Senecio jacobaea L. ssp. jacobaea throughout Europe, with the most common occurrence of tetraploids (2 n  = 40). Here we present a survey of previously published chromosome number data on this subspecies and its geographical distribution, and focus on populations from Pannonia and the Carpathians. Two ploidy levels have been determined in the study area, using chromosome counting and flow cytometry: tetraploid (2 n  = 40) and octoploid (2 n  = 80). Fifty-one populations originating from Slovakia, Austria, the Czech Republic, Hungary, Ukraine and Romania have been analysed. Multivariate morphometric analyses have been performed on 39 populations to study morphological differentiation between these two cytotypes. Despite slight morphological tendencies expressed on the level of populations, tetraploid and octoploids cannot be reliably distinguished morphologically and they are not taxonomically classified formally here.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 153 , 231–242.     

Mitochondrial DNA phylogeny and morphological diversity in the genus Mastus (Beck, 1837): a study in a recent (Holocene) island group (Koufonisi, south-east Crete)

Three endemic Cretan land snail species of the genus Mastus (Beck, 1837) from the island group of Koufonisi (south-east Crete) and the eastern part of Crete, were studied by multivariate analysis of shell morphology and analysis of mtDNA sequences. The phylogeny of the populations studied and the processes effecting the genetic and morphological diversity of the species were investigated. Extremely high mtDNA sequence divergence was observed both within and between populations. The Cretan populations could not be distinguished morphologically, while the populations of the islets were more distinct. We argue that the active geological past of the area (including sea level changes) and the long-term presence of humans has produced a mixing up of Mastus populations leading to the accumulation of high divergence of mtDNA sequences on a small spatial scale. The limited morphological diversity and the distinct shell 'identity' of the islets' populations can be attributed to the selective pressures of the island group.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78, 383–399.     

Phylogenetic analyses of mtDNA sequences reveal three cryptic lineages in the widespread neotropical frog Leptodactylus fuscus (Schneider, 1799) (Anura, Leptodactylidae)

Leptodactylus fuscus is a neotropical frog ranging from Panamá to Argentina, to the east of the Andes mountains, and also inhabiting Margarita, Trinidad, and the Tobago islands. We performed phylogenetic analyses of 12S rRNA, 16S rRNA, tRNA-Leu, and ND1 mitochondrial (mt) DNA sequences from specimens collected across the geographic distribution of L. fuscus to examine two alternative hypotheses: (i) L. fuscus is a single, widely distributed species, or (ii) L. fuscus is a species complex. We tested statistically for geographic association and partitioning of genetic variation among mtDNA clades. The mtDNA data supported the hypothesis of several cryptic species within L. fuscus. Unlinked mtDNA and nuclear markers supported independently the distinctness of a 'northern' phylogenetic unit. In addition, the mtDNA data divided the southern populations into two clades that showed no sister relationship to each other, consistent with high differentiation and lack of gene flow among southern populations as suggested by allozyme data. Concordance between mtDNA and allozyme patterns suggests that cryptic speciation has occurred in L. fuscus without morphological or call differentiation. This study illustrates a case in which lineage splitting during the speciation process took place without divergence in reproductive isolation mechanisms (e.g. advertisement call in frogs), contrary to expectations predicted using a biological species framework.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 325–341. No claim to original US government works.     

Sympatric occurrence of diverged mtDNA lineages of Pityogenes chalcographus (Coleoptera, Scolytinae) in Europe

Differentiation among the European populations of the six-toothed spruce bark beetle Pityogenes chalcographus was observed for the first time in the 1970s as mating males from Northern Europe with females from Central Europe led to a significant decline in fecundity. Morphological examination revealed that P. chalcographus can be separated into two European races. Here, we investigated the genetic background of this separation by analysing 39 populations ( n  = 695), sequencing almost the complete cytochrome oxidase I gene (1543 bp) and applying single-strand conformation polymorphism. Phylogenetic analysis of 58 haplotypes yielded three major clades with a maximum sequence divergence of 2.33%, indicating that the demographic events took place in the late Pleistocene. These results support the hypothesis of allopatric divergence of the mtDNA lineages, which postglacially came into sympatric existence in Europe. However, as a result of partial crossing incompatibility the diverged lineages retained their genetic identity during postglacial times.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 331–340.     

Genetic and morphological variability of the endangered Syngonanthus mucugensis Giul. (Eriocaulaceae) from the Chapada Diamantina, Brazil: implications for conservation and taxonomy

Allozymic and morphometric studies were carried out on ten populations of Syngonanthus mucugensis (Eriocaulaceae), a species from north-eastern Brazil threatened by extinction. Genetic and morphological variability was low or moderately low in all populations, being lower in populations from Rio de Contas/Catolés ( P _L = 14.3–21.4, A  = 1.1–1.2, H _e = 0.026–0.059, D2M = 26.893–33.157) than in those from Mucugê ( P _L = 28.6–35.7, A  = 1.3–1.5, H _e = 0.078–0.164, D2M = 28.999–45.077). A high coefficient of endogamy ( F _is = 0.257) was found, which can be explained by the reproductive characteristics and distribution of the species. The values for genetic and morphological structuring ( F _st = 0.512 and A _MRPP = 0.175, respectively) were high as a result of the differentiation between populations from the two areas. The mean genetic identity between populations from the two areas (0.812) was much lower than between populations from the same area (Mucugê, 0.980; Rio de Contas/Catolés, 0.997). These results indicate that we are dealing with two distinct taxa and, as a result of the nature of the morphological differences found, a new subspecies is described for the populations of the region of Rio de Contas and Catolés, Syngonanthus mucugensis ssp. riocontensis . Such conclusions raise important implications for the conservation of Syngonanthus mucugensis , and will be used in the drawing up of management plans for its conservation.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 401–416.     

Fluvial range expansion, allopatry, and parallel evolution in a Danubian snail lineage (Neritidae: Theodoxus)

The snails Theodoxus danubialis and Theodoxus prevostianus form a single clade native to freshwaters of south-eastern Europe whose inter- and intraspecific relationships remain unresolved. The present study utilized a phylogeographical approach to clarify the relationship of these species as well as to reconstruct the evolutionary and demographic history of populations in the western portion of their range. Phylogenetic, population genetic, and nested clade analyses reveal a clade that has distributed itself upriver from a lower Danube River source population and become genetically distinct primarily through range expansion and localized allopatric divergence. Notably, this geographical pattern is replicated phylogenetically in the form of two cytochrome c oxidase subunit I (CO I) lineages that are present simultaneously in individual snails. Haplotypes from polymorphic individuals form two distinct clades, both of which show phylogenetic and nucleotide substitution patterns consistent with a mitochondrial origin, and whose common ancestor must have occurred in a lower Danube source population. Separated allopatrically from their Danubian relatives, populations of T. danubialis in northern Italy have also undergone substantial range expansion, much more recently than Danube watershed lineages. In addition to repeated patterns of range expansion, parallelism is found in T. prevostianus , which is shown to be a nonmonophyletic taxon of remarkable morphological and ecological similarity.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 603–617.     

Sister species within the Triops cancriformis lineage (Crustacea, Notostraca)

We investigated the phylogenetic relationships among the three presently recognized subspecies of the tadpole shrimp, Triops cancriformis , using mitochondrial 16S and 12S rDNA sequences. Our results indicate that the taxon is divided into two distinct lineages. One lineage is formed of T. c. cancriformis populations and samples from northern Spain that had been classified as T. c. simplex in the most recent literature. The second lineage comprises all populations of T. c. mauritanicus and northern African populations of T. c. simplex . These two main lineages separated 2.3 to 8.9 million years ago, based on the range of inferred molecular clocks recognized for crustacean mtDNA sequence divergence. Percentages of divergence are in the range reported for recognized species in other notostracan lineages and we therefore propose to recognize them as two species, Triops cancriformis and Triops mauritanicus . The latter would comprise two subspecies in northern Africa, one consisting of the Moroccan populations of the former T. c. mauritanicus , the other comprising the African populations of the former T. c. simplex . It also includes three as-yet unnamed lineages. A comparison of morphological characters with the molecular data revealed that the former T. c. simplex cannot be reliably separated from T. c. cancriformis , using morphological characters that have hitherto been used to distinguish among subspecies of T. cancriformis . Our investigation is the first to demonstrate the presence of T. c. cancriformis in Africa (Tunisia). The genetic haplotypes of these populations are identical with haplotypes also occurring in Central and Western Europe, as well as in Sicily. Therefore, we hypothesize that the African populations of T. c. cancriformis represent a result of repeated long-distance dispersal across the Mediterranean Sea.     

Divergent and reticulate processes in evolution of Ethiopian Lophuromys flavopunctatus species complex: evidence from mitochondrial and nuclear DNA differentiation patterns

Molecular study of mitochondrial and nuclear genes and cytogenetic analysis were performed to examine possible patterns of speciation in the diverse Lophuromys flavopunctatus species complex of Ethiopia. Phylogenetic analysis of mtDNA data resulted in an unresolved bush of ten deeply diverged haplotype groups corresponding to potential species either well supported by various types of character or 'cryptic'. The cytogenetic analysis showed representatives of five of these mtDNA lineages to share an identical karyotype (2 n  = 70, NFa = 84), that has not been found previously in Ethiopia. One of them, L.  cf.  sikapusi , being a member of the L. flavopunctatus species complex, demonstrates remarkable morphological similarity to representatives of another species complex, L. sikapusi s.l ., which might be considered as a result of convergent evolution in analogous environments. Analysis of RAPD data suggests that at least two mtDNA types might have been subject to interspecific transfer due to hybridization. In the case of two sympatric haplotypes of L. brunneus we may assume that the contemporary pattern of variation between them can be explained by relatively recent hybridization with another distinct species, L. flavopunctatus . The formation of two groups belonging to distinct mitochondrial lineages within northern populations could be associated with more complex processes including ancient hybridization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 301–316.     

Geographic variation in the long-nosed snake, Rhinocheilus lecontei (Colubridae): beyond the subspecies debate

Scalation, colour pattern, linear and geometric morphometrics were used to quantify geographical differentiation in the long-nosed snake, Rhinocheilus lecontei, and to test the hypothesis that all four subspecies are morphologically distinct. Also investigated were potential associations between morphological (scalation, colour pattern, linear measurements) and environmental variables (climate, vegetation, soil). Sexual dimorphism was weakest for geometric and strongest for linear morphometric variables. Morphological variables differed widely in their ability to differentiate subspecies. Linear morphometric variables achieved the most statistically significant pairwise Mahalanobis distances between subspecies, while geometric morphometrics largely failed to differentiate them. Colour pattern showed the strongest and linear morphometrics the weakest correlation with environment. Several characters varied continuously along latitudinal or longitudinal gradients, such that, in some cases, the clines for closely related traits were discordant. No one subspecies was consistently divergent in all analyses, leading to the conclusion that the three mainland subspecies are not sufficiently distinct to warrant separate subspecies status. The island subspecies, though not always statistically distinct, is geographically separate from other populations and differs in characters related to size. Given the small number of specimens available, a decision regarding its taxonomic status (i.e. elevation to species level) is best deferred until additional specimens can be examined and data on molecular variation can be analysed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 65–85.     

Genetic differentiation and gene flow of two sparidae subspecies, Diplodus sargus sargus and Diplodus sargus cadenati in Atlantic and south-west Mediterranean populations

A total of nine enzymes coded by 14 loci were assayed for each of six populations (from the north-eastern Atlantic and the Mediterranean) of two sea bream subspecies ( Diplodus sargus sargus and Diplodus sargus cadenati ). Diagnostic alleles were observed for each subspecies, although there were several common alleles. Estimates of variance in allele frequencies among samples ( F _ST) revealed significant differences ( P  < 0.05) among both subspecies. Genetic divergence was found between Atlantic and Mediterranean samples: values for genetic distances were higher than 0.163. Furthermore, D. sargus cadenati populations displayed a higher mean weight and length than D. sargus sargus populations and significant differences in growth were found among subspecies and populations. These results are discussed in terms of levels of gene flow and its respective relationships with water circulation in the Strait of Gibraltar and geological events.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 705–717.     

High variability of genetic pattern in giant clam (Tridacna maxima) populations within French Polynesia

Nine populations of giant clams, Tridacna maxima, from six islands of French Polynesia were screened for allozyme variation at ten polymorphic loci. The genetic structure of populations of T. maxima were studied at different spatial scales: within an island, between islands of the same archipelago and between archipelagos. Significant genetic differences were observed only between populations from different archipelagos, and genetic differentiation was correlated with geographical separation. However, these results were only supported by a single locus, PEP * and all other loci were homogeneous between studied populations. According to Lewontin & Krakauer's model, the genetic structure can be explained by selection. The selective factors most likely depend on the respective habitat of each archipelago. We also studied genotype–phenotype correlation using the colour of the clam mantle, and did not find any relationship between the mantle colour and the genetic structure of the individuals.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 221–231.     

Morphological and genetic analysis of fish of a Carassius complex (Cyprinidae) in Lake Kasumigaura with reference to the taxonomic status of two all-female triploid morphs

The classification of the Carassius complex (Cyprinidae) including all-female triploids, called ginbuna in Japanese, is so confused that three sympatric morphs of crucian carp in Lake Kasumigaura are categorized into two different subspecies within a species. We examined them in order to explain the coexistence of more than one subspecies and determine the founder of the triploid lineages in the crucian carp fauna in the lake. Principal component analysis proved that the three sympatric morphs had a morphometric basis distinguishable from each other. Ploidy was determined by flow cytometry which showed triploids in two morphs and diploids in the other morph. Stepwise discriminant analysis using only meristic characteristics could separate the diploids from the triploids. Phylogenetic analysis using mitochondrial DNA inferred two lineages in which one was composed of a triploid morph and the other was a diploid–triploid mixture. Disagreement between the taxonomic status and the phylogenetic status is explicable by assuming that the triploids in the Carassius complex had independent origins leading to the different subspecies. C. auratus langsdorfii appears to show genetic complexities that traditional taxonomic classification can not unravel.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 351–357.