A phylogenetic approach to species delimitation in freshwater Gastrotricha from Sweden

Gastrotricha is a cosmopolitan group of aquatic invertebrates. To date, approximately 765 species have been described. This study is the first to deal with species delimitation and cryptic species of freshwater Gastrotricha. Three commonly encountered species, Heterolepidoderma ocellatum, Lepidochaetus zelinkai, and Lepidodermella squamata, are investigated for cryptic speciation. Most of the material is based on Swedish specimens but closely related species from other parts of the world are also included. Taxonomic revisions are supported by phylogenies based on 18S rRNA, 28S rRNA, and COI mtDNA of freshwater Chaetonotidae from several genera and inferred from Bayesian and maximum likelihood approaches. Heterolepidoderma ocellatum f. sphagnophilum is raised to species level, under the name H. acidophilum n. sp. Moreover, genetic data based on COI indicate large variation between two morphologically very similar groups of Lepidodermella squamata. The extent of cryptic speciation in L. zelinkai appears low. Based on the phylogenetic hypothesis presented in this article, the new species, Lepidodermella intermedia n. sp., from northern Sweden is also described. The phylogenetic hypothesis generated shows that Chaetonotidae is a non-monophyletic group.     

Multilocus species delimitation in Mesoamerican Scaptotrigona stingless bees (Apidae: Meliponini) supports the existence of cryptic species

Accelerating taxonomic knowledge and making accurate species identifications are critically important given the current biodiversity crisis, particularly in biodiversity hotspots such as Mesoamerica. Objective species delimitation that reduces investigator‐driven bias is fundamental to the establishment of appropriate conservation strategies, above all in managed species. Previous morphological and molecular studies on three managed stingless bee species of the genus Scaptotrigona distributed in Mexico (S. mexicana, S. pectoralis and S. hellwegeri) suggested that both S. mexicana and S. hellwegeri are cryptic species complexes. Herein we tested species delimitation by analysing sequence information of five markers (two mitochondrial: cox1 and 16S, and three nuclear: ITS1, EF1‐α, ArgK) within a Bayesian coalescent framework to test the putative species. We obtained two different hypotheses using a Generalized Mixed Yule Coalescent (GMYC) model: four (cox1) and six (16S) species. After the species validation step with the Bayesian species‐delimitation analysis (BPP), we suggest that only S. mexicana is a complex of two species with different distribution (along the Pacific and the Atlantic coasts, respectively). We highly recommend avoiding colony exchange between geographical regions in order to conserve the genetic integrity of both taxa.     

Molecular phylogeny and DNA barcoding confirm cryptic species in the African freshwater oyster Etheria elliptica Lamarck, 1807 (Bivalvia: Etheriidae)

Recent molecular approaches to taxonomy have led to a steady increase in the identification of cryptic species. Within the Etheriidae, the species Etheria elliptica (freshwater oyster) is widespread and common and exists in most of the major African drainages. Within the African freshwater ecosystems, there are major threats to biodiversity and cryptic species complicate conservation strategies; unknown species exist and no conservation status has been assigned. Our objective here was to determine if E. elliptica from several locations in the Congo drainage are correctly classified as representing a single species. We analysed the genetic diversity at two mitochondrial loci (COI and 16S) and two nuclear loci (H3 and 28S), and estimated evolutionary relationships using phylogenetic and DNA barcoding techniques. Bayesian inference yielded three cryptic species of Etheria, and mismatch analysis revealed discrete differences between the cryptic species. We identified three cryptic species within these collections, and evidence indicates that the third species may resolve further with more sampling. In conclusion, the taxonomic history of E. elliptica makes finding cryptic species unsurprising. However, molecular studies such as this may finally help to resolve the number of species within this genus.     

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade

The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here, we present an in‐depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well‐supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near‐complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species C. erinus, showing an east‐west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target‐enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene‐tree discordance within such datasets.     

Integrative analyses of Nervilia (Orchidaceae) section Linervia reveal further undescribed cryptic diversity in Thailand

The delimitation of cryptic species is necessary to accurately classify and appropriately conserve biodiversity. Integrative analyses can be incisive in detecting and circumscribing cryptic diversity, especially in species complexes whose members are delineated by minor or overlapping morphological variation. We adopt an integrative approach to assess species relationships and resolve species boundaries in the taxonomically difficult Nervilia adolphi/punctata species alliance of N. sect. Linervia, an Old World complex of reduced, one-flowered terrestrial orchids that is both species-rich and poorly known in tropical and warm temperate Asia. We sampled 12 of the 27 known species of the alliance in Asia, including all four species reported from Thailand and a further 20 plants collected in that country that could not be satisfactorily identified using morphology alone. Phylogenetic analyses using one nuclear (ITS) and two plastid (matK and trnL-F) markers confirmed both N. sect. Linervia and the alliance itself as monophyletic, and corroborated 11 of the 12 sampled species; N. punctata proved polyphyletic, with the Thai samples referred to this Indonesian species falling sister to the Himalayan N. mackinnonii. The 20 unidentified Thai samples formed three distinct, strongly supported clades. STACEY, a Bayesian coalescence approach to species delimitation, resolved the same three clusters, but provided evidence suggesting that one comprised two distinct sub-clades. Building on this genetic evidence, we identify subtle morphological differences and invoke a diagnosable species concept to circumscribe three previously unrecognized cryptic species from Thailand. This objective approach to species delimitation validates ostensibly minor morphological differences as a basis for differentiating species within the alliance, paving the way for a global analysis of species boundaries throughout the genus as a whole.     

DNA barcoding Neotropical fishes: recent advances from the Pampa Plain,Argentina

The fish fauna of the Pampa Plain, the southernmost distribution range of many Neotropical species, was barcoded in this study. COI sequences were analysed by means of distance (K2P/NJ) and character‐based (ML) models, as well as the Barcode Index Number (BIN). K2P/NJ analysis was able to discriminate among all previously identified species while also revealing the likely occurrence of two cryptic species that were further supported by BIN and ML analyses. On the other hand, both BIN and ML were not able to discriminate between two species of Rineloricaria. Despite the small genetic divergence between A. cf. pampa and A. eigenmanniorum, a tight array of haplotypes was observed for each species in both the distance and character‐based methods. Deep intraspecific divergences were detected in Cnesterodon decemmaculatus (5%) and Salminus brasiliensis (6%). For Salminus brasiliensis, these findings were further supported by character‐based (ML) evidence and meristic and morphological data. Our results also showed that Pampa Plain representatives of Salminus brasiliensis, Rhamdia quelen, Hoplias malabaricus, Synbranchus marmoratus, Australoheros facetus, Oligosarcus jenynsii and Corydoras paleatus differed by more than 3% from their conspecifics from other parts of South America. Overall, this study was able to highlight the likely occurrence of a cryptic species in Salminus brasiliensis and also illustrate the strong geographical structure in the COI sequence composition of seven fish species from South America.     

The blackburni/murchisona species complex in Australian Pseudotetracha (Coleoptera: Carabidae: Cicindelinae: Megacephalini): evaluating molecular and karyological evidence

Our phylogenetic analysis of three endemic species of the Australian tiger beetle genus Pseudotetracha (Fleutiaux, 1864) from South Australia used sequences of two fragments of the mitochondrial genes 16S rRNA and cytochrome oxidase III. A matrix for each gene and two combined matrices were constructed. We compared these three riparian species, together with data from nine taxa of this genus available in GenBank, using parsimony and Bayesian methods. These molecular results are in agreement with the phylogenetic hypothesis for the blackburni/murchisona species complex previously proposed based on morphology, whereas other recent molecular analyses have questioned the existence of this species complex. In all of our analyses, samples of P. blackburni divided into two statistically supported clades, one of which is more closely related to P. mendacia and P. pulchra than to the other P. blackburni clade. This suggests the existence of a cryptic new species. Additionally, we analysed chromosomes of the second metaphase cells of members of the two clades. The observations showed different karyotypes as blackburni‐1 has two types of second meiotic metaphase cells with 11 and 12 chromosomes, whereas in blackburni‐2, all cells have 12 chromosomes, adding evidence for the putative existence of two species.     

From ‘cryptic species’ to integrative taxonomy: an iterative process involving DNA sequences,morphology, and behaviour leads to the resurrection of Sepsis pyrrhosoma (Sepsidae: Diptera)

Tan, D. S. H., Ang, Y., Lim, G. S., Ismail, M. R. B. & Meier, R. (2010). From ‘cryptic species’ to integrative taxonomy: an iterative process involving DNA sequences, morphology, and behaviour leads to the resurrection of Sepsis pyrrhosoma (Sepsidae: Diptera). —Zoologica Scripta, 39, 51–61. The increased availability of DNA sequences has led to a surge of ‘cryptic species’ in the literature. These units are usually proposed based on finding genetically distinct lineages within species that were initially defined based on morphological characters. However, few authors attempt to confirm whether these ‘cryptic’ units are species and even fewer authors are explicit about which species concept is applied. Here, we use an example from Sepsidae (Diptera) to demonstrate how cryptic species can be validated by an iterative process involving several data sources and an evaluation of the data under different species concepts. A phylogeographic analysis based on 50 specimens for five species of the flavimana group revealed deep mitochondrial splits within Sepsis flavimana which was suggestive of a cryptic species. We resolve the initial conflict between DNA sequences and morphology by adding new morphological data as well as behavioural evidence and tests for reproductive isolation. One cryptic species is confirmed and Sepsis pyrrhosoma, a former synonym of S. flavimana, is here shown to be a valid species under most species concepts. We can thus document that the same data can lead to similar conclusions under conflicting concepts once different kinds of data are integrated.     

Cryptic Genetic Diversity Is Paramount in Small-Bodied Amphibians of the Genus Euparkerella (Anura: Craugastoridae) Endemic to the Brazilian Atlantic Forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.     

Cryptic species in the Neotropical fish genus Curimatopsis (Teleostei,Characiformes)

Detritivores of the fish family Curimatidae are assigned to eight genera, one of which, the Curimatopsis, with only five species, is the least speciose genus and sister to other seven genera in the family. Ongoing morphological investigations reveal, however, the likely existence of additional species. In this study, fifty‐one specimens of Curimatopsis from multiple rivers of the Amazon, Paraguay and Suriname drainages were identified morphologically according to the present species concepts and then barcoded using the universal cytochrome c oxidase subunit I (COI) mitochondrial marker. Species delimitation analyses were conducted using Bayesian methods through the general mixed Yule‐coalescent analysis combined with conventional likelihood, genetic distance and haplotypic diversity approaches. We found eleven well‐supported clusters that represent four of the named species and seven cryptic, undescribed species of Curimatopsis. Our results show a clear delimitation of species boundaries constrained by distinct Amazonian river ecotones that may have promoted intrageneric lineage diversification. This is the first of a series of genetic studies applicable to future taxonomic, phylogenetic and evolutionary studies across the Curimatidae.     

Divergence and species discrimination in freshwater bryozoans (Bryozoa: Phylactolaemata)

We explored the suitability of nuclear and mitochondrial ribosomal markers [small subunit nuclear ribosomal RNA gene, large subunit nuclear ribosomal RNA gene, and a region spanning partial small mitochondrial ribosomal RNA subunit, four transfer RNA genes, and partial large mitochondrial ribosomal RNA subunit (referred to as rrnS‐rrnL)] for resolving patterns of diversification of 27 freshwater bryozoan species (class: Phylactolaemata) and evaluated the utility of statoblast ultrastructural features and molecular phylogenies for species discrimination in the Fredericellidae and Plumatellidae. Molecular data identified Plumatella fruticosa as distinct from the rest of the plumatellids, rendering the latter polyphyletic. rrnS‐rrnL was the most suitable marker for species discrimination and identified two undescribed species of Plumatella and at least two undescribed species of Fredericella. Lack of wide dispersal by fredericellid statoblasts may underlie the observed propensity for cryptic speciation and phylogeographical structure in Fredericella. Conversely, the strong dispersal potential of plumatellid statoblasts may mediate efficient gene flow between distant populations and explain the relatively low intraspecific divergence and lack of evidence for cryptic speciation. We show that species identification based on external features of statoblasts can be problematic in both genera, including for a putatively highly invasive, biofouling species, Plumatella vaihiriae, thereby highlighting the utility of rrnS‐rrnL sequences for species barcoding. © 2013 The Linnean Society of London     

DNA barcoding of genus Toxoptera Koch (Hemiptera: Aphididae): Identification and molecular phylogeny inferred from mitochondrial COI sequences

Abstract Identification of aphid species is always difficult due to the shortage of easily distinguishable morphological characters. Aphid genus Toxoptera consists of species with similar morphology and similar to Aphis in most morphological characters except the stridulatory apparatus. DNA barcodes with 1 145 bp sequences of partial mitochondrial cytochrome‐coxidase I (COI) genes were used for accurate identification of Toxoptera. Results indicated mean intraspecific sequence divergences were 1.33%, whereas mean interspecific divergences were greater at 8.29% (0.13% and 7.79% if T. aurantii 3 and T. aurantii 4 are cryptic species). Sixteen samples were distinguished to four species correctly by COI barcodes, which implied that DNA barcoding was successful in discrimination of aphid species with similar morphology. Phylogenetic relationships among species of this genus were tested based on this portion of COI sequences. Four species of Toxoptera assembled a clade with low support in maximum‐parsimony (MP) analysis, maximum‐likelihood (ML) analysis and Bayesian phylogenetic trees, the genus Toxoptera was not monophyletic, and there were two sister groups, such as T. citricidus and T. victoriae, and two clades of T. aurantii which probably presented cryptic species in the genus.     

Aphis (Hemiptera: Aphididae) species groups found in the Midwestern United States and their contribution to the phylogenetic knowledge of the genus

A phylogeny of the genus Aphis Linnaeus, 1 758 was built primarily from specimens collected in the Midwest of the United States. A data matrix was constructed with 68 species and 41 morphological characters with respective character states of alate and apterous viviparous females. Dendrogram topologies of analyses performed using UPGMA (Unweighted Pair Group Method with Arithmetic Mean), Maximum Parsimony and Bayesian analysis of Cytochrome Oxidase I, Elongation Factor 1‐α and primary endosymbiont Buchnera aphidicola 16S sequences were not congruent. Bayesian analysis strongly supported most terminal nodes of the phylogenetic trees. The phylogeny was strongly supported by EF1‐α, and analysis of COI and EF1‐α molecular data combined with morphological characters. It was not supported by single analysis of COI or Buchnera aphidicola 16S. Results from the Bayesian phylogeny show 4 main species groups: asclepiadis, fabae, gossypii, and middletonii. Results place Aphis and species of the genera Protaphis Börner, 1952, Toxoptera Koch, 1856 and Xerobion Nevsky, 1928 in a monophyletic clade. Morphological characters support this monophyly as well. The phylogeny shows that the monophyletic clade of the North American middletonii species group belong to the genus Protaphis: P. debilicornis (Gillette & Palmer, 1929 ), comb. nov., P. echinaceae (Lagos and Voegtlin, 2009 ), comb. nov., and P. middletonii (Thomas, 1879 ). The genus Toxoptera should be considered a subgenus of Aphis (stat. nov.). The analysis also indicates that the current genus Iowana Frison, 1954 should be considered a subgenus of Aphis (stat. nov.).     

Relationships within Podocarpaceae based on DNA sequence,anatomical, morphological,and biogeographical data

Despite considerable recent progress in understanding intergeneric relationships, a comprehensive analysis of Podocarpaceae at the species level using molecular data, biogeography, anatomy, and morphology has not been previously attempted. Here we present sequence analyses of rbcL, nrITS1 and NEEDLY intron 2 for two‐thirds (183 accessions of 145 taxa) of all Podocarpaceae species representing all genera except Parasitaxus. These analyses include many more species and accessions than previous studies and result in a more resolved phylogeny. The comprehensive anatomical and morphological study ensures that the identification of taxa is correct and also provides clade support. Bayesian and parsimony analyses were used to resolve 20 well‐supported monophyletic groups including 11 groups of the formerly poorly resolved subgenera Podocarpus and Foliolatus. The well‐resolved topology is supported by anatomical and morphological features and is highly congruent with geographical distribution. © The Willi Hennig Society 2011.     

Historical biogeography and cryptic diversity in the Callichthyinae (Siluriformes,Callichthyidae)

The family Callichthyidae, divided into the subfamilies Corydoradinae and Callichthyinae, contains more than 200 species of armoured catfishes distributed throughout the Neotropics, as well as fossil species dating from the Palaeocene. Both subfamilies are very widely distributed throughout the continent, with some species ranges extending across multiple hypothesized biogeographical barriers. Species with such vast geographical ranges could be made up of multiple cryptic populations that are genetically distinct and have diverged over time. Although relationships among Callichthyinae genera have been thoroughly investigated, the historical biogeography of the Callichthyinae and the presence of species complexes have yet to be examined. Furthermore, there is a lack of fossil‐calibrated molecular phylogenies providing a time frame for the evolution of the Callichthyinae. Here, we present a novel molecular data set for all Callichthyinae genera composed of partial sequences of mitochondrial and nuclear markers. These data were used to construct a fossil‐calibrated tree for the Callichthyinae and to reconstruct patterns of spatiotemporal evolution. All phylogenetic analyses [Bayesian, maximum likelihood and maximum parsimony (MP)] resulted in a single fully resolved and well‐supported hypothesis for the Callichthyinae, where Dianema is the sister group of all the remaining genera. Results suggest that the ancestry of most Callichthyinae genera originated in the Amazonas basin, with a number of subsequent ancestral dispersal events between adjacent basins. High divergences in sequences and time were observed for several samples of Hoplosternum littorale, Megalechis picta and Callichthys callichthys, suggesting that these species may contain cryptic diversity. The results highlight the need for a taxonomic revision of species complexes within the Callichthyinae, which may reveal more diversity within this relatively species‐poor lineage.     

Phylogenetic resolution and systematics of the Asian tree frogs,Rhacophorus (Rhacophoridae,Amphibia)

Li, J.T., Li, Y., Murphy, R.W., Rao, D.‐Q. & Zhang, Y.‐P. (2012). Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia). —Zoologica Scripta, 41, 557–570. The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, South‐east Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well‐supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.     

Another example of cryptic diversity in lichen-forming fungi: the new species <Emphasis Type="Italic">Parmelia mayi</Emphasis> (Ascomycota: Parmeliaceae)

In the last decade, a number of cryptic species have been discovered in lichenized fungi, especially in species with a cosmopolitan or disjunctive distribution. Parmelia saxatilis is one of the most common and widely distributed species. Recent molecular studies have detected two species, P. ernstiae and P. serrana, within P. saxatilis s. lat., suggesting the existence of considerable genetic diversity that may not yet be expressed at the phenotypic level. Due to the complexity in the P. saxatilis s. lat. group, we used this as a model to study the species boundary and identify cryptic lineages. We used Phylogenetic (Bayes, ML and MP) and genetic distance approaches to analyze ITS and β-tubulin sequences. Our results confirm the existence of another cryptic lineage within P. saxatilis s. lat. This lineage is described herein as a new species, P. mayi. It forms an independent, strongly supported, monophyletic lineage, distantly related to the morphologically similar species P. ernstiae, P. saxatilis and P. serrana. Morphologically, it is indistinguishable from P. saxatilis but the new species is separated by molecular, bioclimatic, biogeographic and chemical characters. At present, P. mayi appears to have a restricted distribution in the northern Appalachian mountain territories of North America. It is found in climatic conditions ranging from hemiboreal and orotemperate to cryorotemperate ultrahyperhumid bioclimates.     

A classification of Danaus butterflies (Lepidoptera: Nymphalidae) based upon data from morphology and DNA

Classification of the cosmopolitan butterfly genus Danaus (Nymphalidae: Danainae) is revised at subgeneric, specific and subspecific levels, combining for the first time mitochondrial and nuclear DNA sequence information with morphological data. Tree topologies based on the nuclear genome (allozymes, pheromone components, the morphology of all life history stages and nuclear DNA sequences), on the one hand, and mitochondrial DNA, on the other, are incongruent and challenge the current taxonomy of the genus. Although earlier classifications, based on adult morphology alone, are, in general, well supported by an analysis of total evidence, the mitochondrial phylogeny shows that the species D. chrysippus and its subgenus Anosia are deeply paraphyletic. Subspecies dorippus of D. chrysippus is the basal clade of the genus and is reinstated as the species D. dorippus. The former species D. plexaure is demoted to a subspecies of D. eresimus. The specific status of D. erippus, as distinct from D. plexippus, is tentatively supported. On the strength of the new data, division of the monophyletic genus Danaus s.l. into three subgenera Danaus s.s., Salatura and Anosia is unsustainable and is abandoned. Of the 15 terminal clades (taxa) of Danaus s.l. included in the study, 11 are species that broadly conform to the biological species concept. (The West Indian species D. cleophile, missing from our analysis, is the twelfth species). The remaining terminal clades are subspecies of D. chrysippus comb. nov. and D. dorippus stat. rev. Two sympatric Neotropical species, D. eresimus and D. gilippus, are morphologically distinct and sexually isolated but have nearly identical mitochondrial genomes. In contrast, two partially sympatric Palaeotropical species, D. chrysippus and D. dorippus, are cryptic species that share structural morphology and hybridize but have highly differentiated mitochondrial genomes. D. dorippus is polymorphic for two anciently diverged haplotypes and its history has possibly involved recombinational speciation and/or hybridism. © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society, 2005, 144 , 191?212.