Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog,Nanorana yunnanensis (Dicroglossidae)

Historical drainage patterns adjacent to the Qinghai‐Tibetan Plateau differed markedly from those of today. We examined the relationship between drainage history and geographic patterns of genetic variation in the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base pairs of mitochondrial DNA partial sequences from protein‐coding genes ND1 and ND2, and intervening areas including complete tRNA^Ile, tRNA^Gln and tRNA^Met. Two null hypotheses were tested: (i) that genetic patterns do not correspond to the development of drainage systems and (ii) that populations had been stable and not experienced population expansion, bottlenecking and selection. Genealogical analyses identified three, major, well‐supported maternal lineages, each of which had two sublineages. These divergent lineages were completely concordant with six geographical regions. Genetic structure and divergence were strongly congruent with historical rather than contemporary drainage patterns. Most lineages and sublineages were formed via population fragmentation during the rearrangement of paleodrainage basins in the Early Pliocene and Early Pleistocene. Sympatric lineages occurred only in localities at the boundaries of major drainages, likely reflecting secondary contact of previously allopatric populations. Extensive population expansion probably occurred early in the Middle Pleistocene accompanying dramatic climatic oscillations.     

Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae: Mirbelieae) exhibit different evolutionary history

Genetic structure among disjunct population groups of Pultenaea pauciflora was assessed to determine the evolutionary history of this species as a basis for conservation management strategies. Analysis of individuals from all extant populations using 1737 amplified length polymorphism markers revealed two highly divergent genetic entities with strong geographical structuring. Populations located at Narrogin and Brookton clustered together in Bayesian assignment analysis with every individual optimally placed in a single cluster with complete membership. Genetic differentiation between populations in these two areas was very low. Populations at Boddington were highly divergent from those located at Narrogin and Brookton. All individuals from Boddington populations were optimally placed into a second cluster with complete membership. Populations located at Boddington maintain lower levels of allelic diversity, yet greater levels of mean heterozygosity than populations located at Narrogin and Brookton. The degree of genetic differentiation and different patterns of genetic diversity strongly suggest historical divergence and separate evolutionary influences on the two lineages that occur in different ecological habitat. These Evolutionary Significant Units are likely to represent two cryptic sister taxa in the extant populations currently recognized as P. pauciflora, and the reassessment of taxonomic and conservation status of both lineages is required. © 2013 State of Western Australia. Biological Journal of the Linnean Society © 2013 The Linnean Society of London     

An integrative taxonomic review of the Natal mountain catfish,Amphilius natalensis Boulenger 1917 (Siluriformes,Amphiliidae), with description of four new species

Species delimitation is a permanent issue in systematics. The increasing recognition of geographically isolated populations as independent lineages allowed by new methods of analysis has inflated the species-populations dilemma, which involves deciding whether to consider separate lineages as different species or structured genetic populations. This is commonly observed between fishes of adjacent river basins, with some lineages being considered allopatric sister species and others considered isolated populations or variants of the same species. Pseudocorynopoma doriae is a characid diagnosed from its single congener by the number of anal-fin rays and sexually dimorphic characters of males, including distinct fin colouration. The authors found variation in the colour pattern between isolated populations previously identified as P. doriae but no variation in scale or fin-ray counts. They analysed molecular evidence at the population level and morphological differences related to life history (e.g., colour dimorphism related to inseminating behaviour). The results provide compelling evidence for the recognition of a new species of Pseudocorynopoma despite the lack of discrete differences in meristic data. The recognition of the new species is consistent with biogeographical evidence for the long-term isolation of the respective river drainages and with differences between the ichthyofaunal communities of these rivers.     

Reproductive isolating barriers between colour‐differentiated populations of an African annual killifish,Nothobranchius korthausae (Cyprinodontiformes)

Allopatric populations separated by vicariance events are expected to evolve reproductive isolating mechanisms as a result of disparate selection pressures and genetic drift. The appearance of reproductive isolating mechanisms may vary across taxa with differences in the opportunity for mate choice, and may be asymmetrical. In addition, premating barriers may be affected by individual mating experience. We used choice and no‐choice experiments to investigate reproductive isolation between two allopatric (island and mainland) and colour‐differentiated populations of an African annual fish, Nothobranchius korthausae. Assortative mating under experimental conditions was limited and asymmetrical. Preference for sympatric males was only expressed in nonvirgin females from one population. Virgin fish from both populations mated indiscriminately. No difference in the number of eggs laid, fertilization rate and hatching success was detected in no‐choice experiments. All mating combinations produced viable offspring and no postmating barriers were detected in terms of the performance and fertility of F1 hybrids. Overall, we found little evidence for significant reproductive isolation, which is in contrast with the related killifish taxa in which assortative mating can be strong, even among allopatric populations with no colour differentiation. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 62–72.     

Effect of founding events on coat colour polymorphism of Apodemus speciosus (Rodentia: Muridae) on the Izu Islands

To infer the evolutionary mechanism of phenotypic variation among isolated island populations, we investigated coat colour and genetic variation in the large Japanese field mouse (Apodemus speciosus) on the Izu Islands (Ohshima, Niijima, Kouzushima, and Miyakejima). Coat colour in the most remote population (Miyakejima) was unique and significantly darker than that in the other populations. Ohshima that is closest to the source population showed variation in coat colour within its population. Phylogeographical analyses using mitochondrial and microsatellite markers suggested that the island populations (except Kouzushima) were founded sequentially from the closest Ohshima to remote Niijima and Miyakejima during or before the penultimate interglacial period. Secondary gene flow from the source population was rare and occurred only for the closest (Ohshima) population. In addition, we found that an amino acid mutation in the Agouti signalling protein gene (Asip) was associated with coat colour variation among the island populations. The mutation was rare in the source population but completely fixed in the Miyakejima population. The phenotypic and genetic variation suggested that severe reduction of genetic variation and changes in allele frequency as a result of sequential colonization (i.e. the founder effect) had significant effects on colour polymorphism. The findings of the present study suggest that the founder effect, in addition to natural selection, facilitated the morphological changes below the species level over a relatively long time scale. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 522–535.     

Apochromic populations of Dactylorhiza incarnata s.l. (Orchidaceae): diversity and systematic significance as revealed by allozyme markers and morphology

Apochromic forms of the Eurasian Dactylorhiza incarnata s.l. were studied in northern Europe to reveal their genetic (allozyme) and morphological diversity and to assess their systematic significance. The study included eight localities with sympatric populations of plants with anthocyanin‐pigmented and apochromic flowers. Parallel samples of the two morphs were taken from each locality. Genetic variation was only found at the allozyme loci pgd, pgi and ugpp. Statistically significant differences in allele frequencies between the two colour morphs were found in two localities and demonstrate that the occurrence of apochromic individuals in D. incarnata s.l. is not always because of spontaneous mutation. At least in some localities the apochromic plants form distinct breeding groups (but local populations of different colour morphs may also be composed of several more or less distinct breeding groups). Based on molecular and morphometric data, it is proposed that the apochromic study populations from calcareous fens should be referred to D. incarnata var. ochroleuca, whereas the apochromic study populations from non‐calcareous fens are better treated as aberrant local populations of var. incarnata s.l. Possible evolutionary patterns and processes are discussed and guidelines for identification of var. ochroleuca from morphological features are given. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 396–407.     

Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data

Cryptic species have been increasingly revealed in the marine realm through an analytical approach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes and morphology). Illustrations of cryptic taxa improve our understanding of species diversity and evolutionary histories within marine animals. The pen shell Atrina pectinata is known to exhibit extensive morphological variations that may harbour cryptic diversity. In this study, we investigated A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial (cytochrome c oxidase subunit I, mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well as morphology. Phylogenetic analyses of mtCOI ‘DNA barcoding gene’ sequences resolved six divergent lineages with intralineage divergences between 0.4% and 0.8%. Interlineage sequence differences ranged from 4.3% to 22.0%, suggesting that six candidate cryptic species are present. The nrITS gene revealed five deep lineages with Kimura 2‐parameter distances of 3.7–30.3%. The five nuclear lineages generally corresponded to mtCOI lineages 1–4 and (5 + 6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences of significant variance were found within an individual, clearly implying recent hybridization events between/among the evolutionary lineages, which contributed to cytonuclear discordance. Morphologically, five morphotypes matched the five genetic lineages, although the intermediates may well blur the boundaries of different morphotypes. This study demonstrates the importance of combining multiple lines of evidence to explore species cryptic diversity and past evolutionary histories.     

Patterns and processes in the evolutionary history of parrotfishes (Family Labridae)

Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well‐supported clades with mid Pliocene/Pleistocene diversification. Twenty‐two reciprocally monophyletic sister‐species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 529–557.     

Extensive genetic divergence in the East Asian natricine snake,Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations

We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I‐A, I‐B, and I‐C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 395–408.     

On glacial refugia,genetic diversity,and microevolutionary processes: deep phylogeographical structure in the endemic newt Lissotriton italicus1

We investigated the phylogeographical patterns of Lissotriton italcus, a newt endemic to the Italian peninsula, aiming to determine why hotspots of intraspecific diversity so ‘hot’. We found two main mitochindrial DNA lineages (net sequence divergence of 6.8% at two fragments of total length of 1897 bp): one restricted to part of the Calabrian peninsula (i.e the southernmost portion of the species range) and the other widespread throughout the rest of the species range. Both lineages, which had a parapatric distribution, showed evidence of further subdivisions, with an overall number of eight terminal haplogroups, most of whose times to the most recent common ancestors were estimated at the Late Pleistocene. Analysis of molecular variance suggested that partitioning populations according to the geographical distribution of these haplogroups can explain 97% of the observed genetic variation. These results suggest that L. italicus underwent repeated cycles of allopatric fragmentation throughout the Pleistocene, and that it likely survived the Late Pleistocene paleoenvironmental changes within eight separate refugia. Thus, the current hotspot of intraspecific diversity of L. italicus (within the Calabrian peninsula) has not been moulded by long‐term stability of large populations but rather by multiple events of allopatric fragmentation and divergence. When compared with the patterns recently identified in other species, these results suggest that the occurrence of phases of allopatric divergence (eventually followed by secondary admixture) could be a common, albeit probably underrated feature in the history of formation of hotspots of intraspecific diversity. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 42–55.     

Nuclear DNA recapitulates the cryptic mitochondrial lineages of Lumbricus rubellus and suggests the existence of cryptic species in an ecotoxological soil sentinel

Mitochondrial DNA analysis has revealed two distinct phylogenetic lineages within the ecotoxological sentinel earthworm model Lumbricus rubellus Hoffmeister, 1843. The existence of these lineages could complicate ecotoxicological studies that use the species as a sentinel for soil contamination testing, as they may respond differently to contamination; however, as mitochondrial haplotypes are not always expected to segregate in the same way as chromosomal DNA in natural populations, we further investigated this issue by using nuclear DNA markers (microsatellites) to measure genetic diversity, differentiation, and gene flow in sympatric populations of the two L. rubellus lineages at two sites in South Wales. Our results show that sympatric populations of the two lineages are more genetically differentiated than geographically distant populations of the same lineage, and Bayesian clustering analysis revealed no evidence of gene flow between the lineages at either site. Additionally, DNA sequencing of these microsatellite loci uncovered substantial differentiation between lineages at homologous flanking regions. Overall our findings indicate a high degree of nuclear genetic differentiation between the two lineages of L. rubellus, implying reproductive isolation at the two study sites and therefore the potential existence of cryptic species. The existence of two cryptic taxa has major implications for the application of L. rubellus as an ecotoxicological sentinel. It may therefore be necessary to consider the lineages as separate taxa during future ecotoxicological studies. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 780–795.     

Secondary contact followed by gene flow between divergent mitochondrial lineages of a widespread Neotropical songbird (Zonotrichia capensis)

Understanding how genetic and phenotypic differences that arise in geographically isolated populations influence the outcome of secondary contact advances our knowledge of speciation. In the present study, we investigate the secondary contact between divergent lineages of a widespread Neotropical songbird, the Rufous‐collared sparrow (Zonotrichia capensis). Zonotrichia capensis is morphologically and behaviourally diverse, and shows a pattern of lineage diversification produced by a Pleistocene expansion and colonization of South America from a probable Central American origin. Consistent with previous results, we find three lineages throughout the species range, showing between 1.5% and 2.5% divergence in mitochondrial control region sequences. These lineages come into secondary contact in the Dominican Republic, La Paz (Bolivia), and North‐eastern Argentina. We use DNA microsatellite data to study a broad secondary contact zone in North‐eastern Argentina, finding that Bayesian clustering analyses do not assign individuals to their respective mitochondrial lineages. Overall, we did not observe nuclear genetic discontinuities in the study area. We conclude that, if genetic, morphological, and/or cultural differences accumulated among lineages during isolation, they were insufficient to prevent gene flow after secondary contact. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 863–868.     

Genetic analysis of sable (<Emphasis Type="Italic">Martes zibellina</Emphasis>) and pine marten (<Emphasis Type="Italic">M. martes</Emphasis>) populations in sympatric part of distribution area in the northern Urals

Analysis of nucleotide sequences of the mitochondrial DNA (mtDNA) control region (495 bp) of sables (Martes zibellina) and pine martens (M. martes) from allopatric parts of the species ranges has shown a considerable interspecific genetic distance (>3%). In sympatric populations of these species in the northern Urals, differences between two species-specific mtDNA lineages are still large; however, classification of each individual nucleotide sequence with one of the two lineages is not correlated with whether the given animal is phenotypically a sable, a pine marten, or a potential hybrid (the so-called “kidas”). This indicates a high degree of reciprocal introgression of the sable and pine marten mtDNA in the northern Urals and suggests that their interspecific hybridization is common in the sympatric zone.     

Genetic and chaetal variation in Nais worms (Annelida,Clitellata, Naididae)

The genus Nais is a group of oligochaetous clitellates, common in eutrophic freshwater habitats. About 30 species are described. Species identification is based primarily on chaetal characters, which are often subtle, inconsistent, and even overlapping between nominal species. We investigated the correlation between genetic variation and chaetal morphology in this genus. Eighty‐one individuals from Europe, North America, and China were included in the study. Seventy‐five of these were preserved as vouchers. They were scrutinized with regard to chaetal morphology, and ten different morphotypes were identified. Three molecular markers, two mitochondrial (the COI gene and 16S rDNA) and one nuclear (the ITS region), were used to establish the genetic lineages in the material. Genetic variation was found to be largely congruent with chaetal character patterns. However, at least nine separately evolving lineages (all supported by mitochondrial as well as nuclear data) correspond to at most six nominal species. Four morphotypes/lineages are recognized as Nais barbata, Nais christinae, Nais elinguis, and Nais stolci, respectively, whereas five, or possibly more, lineages represent a morphological continuum covering the variation of the Nais communis/variabilis complex. Thus, cryptic speciation is revealed. Our results indicate that a taxonomic revision of the genus will be needed in the future.     

Complex patterns of morphological and mtDNA variation in Lacerta perspicillata (Reptilia; Lacertidae)

Lacerta perspicillata is a north-west African lacertid lizard that shows considerable intraspecific variation, with three subspecies described on the basis of colour pattern and body size. Recent observations of a population containing two morphological forms and more than one deep genetic lineage, as well as an apparent lack of concordance between forms and genetic lineages, suggest that the complexity is greater than previously thought. To analyse and quantify this variation, we studied the variability within this species at two levels: (1) external morphology (multivariate analysis of scalation, body dimensions, and colour pattern) and (2) mtDNA (sequencing and single-strand confirmation polymorphism analysis). Fifty-two individuals were studied at Taza, northern Morocco. Two morphological groupings (ostensibly representing two previously described subspecies) and two deep mtDNA lineages were detected at this site, with complete correspondence between the two. This, together with an apparent lack of hybrids, would normally support respective full species recognition. However, analysis of 98 individuals from other populations demonstrated that the situation is highly complex with the same genetic lineages having reversed morphotypes in other areas, making such a designation difficult. Across the other studied populations, we found no support for any of the currently recognized subspecies. The lack of congruence between mtDNA lineages and morphometric patterns (in some cases) and the morphological similarity among lizards from different lineages suggest ecophenotypic convergence or multiple introgressive hybridization. The study highlights the tremendous complexity that may exist within a taxon and the inadequacy of older alpha-taxonomy based designations in describing it.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 479–490.     

Divergence between passerine populations from the Malvinas – Falkland Islands and their continental counterparts: a comparative phylogeographical study

Bursts of speciation have followed colonization of remote oceanic islands by diverse taxa, a process evidenced by island endemics around the world. The present study explores whether the Malvinas – Falkland Islands (MFI), a relatively understudied archipelago off the South Atlantic coast of Patagonia, harbour endemic genetic lineages of passerine birds. Nine passerine species nest regularly in the MFI (Cinclodes antarcticus, Muscisaxicola maclovianus, Troglodytes cobbi, Cistothorus platensis, Turdus falcklandii, Anthus correndera, Melanodera melanodera, Sturnella loyca, and Carduelis barbata). Mitochondrial DNA (cytochrome c oxidase I sequences) are used to quantify and compare divergence between insular and continental populations, finding genetic patterns to vary across these nine species. Most MFI passerines do not show significant genetic differentiation from continental populations, whereas C. platensis, M. melanodera, and T. falcklandii are modestly diverged. Finally, T. cobbi differes markedly from its closest continental relative Troglodytes aedon, a result that is confirmed using nuclear and vocal data. The study also identifies broadly divergent lineages within continental populations of C. platensis and T. aedon. Taken together, these results suggest that the land bird populations of the MFI were established at different times. Troglodytes cobbi is the oldest MFI land bird, splitting from continental T. aedon during the Great Patagonian Glaciation of the Pleistocene. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, •• , ••–••.     

Divergence and molecular variation in common whelk Buccinum undatum (Gastropoda: Buccinidae) in Iceland: a trans‐Atlantic comparison

The dispersal and history of species affects their genetic population structure at both small and large geographical scales. The common whelk, Buccinum undatum, is a widespread subtidal gastropod in the North Atlantic that has no planktonic larvae and has thus limited dispersal capacity. The snail, which has been harvested by humans for centuries, is highly variable in morphology. To evaluate the population structure in the rich fishing grounds in western Iceland and its divergence from samples across the Atlantic, genetic patterns based on sequence variation in two mitochondrial (mt)DNA genes (COI and 16S) and five microsatellites were studied and compared with variation in populations from both sides of the Atlantic. Significant differences in allele and haplotype frequencies were found among samples separated by short distances along the coast of Iceland. Partition of the variation showed larger variance among samples obtained from distant regions than from neighbouring sites and genetic distances were correlated with geographical distance among populations in Europe. Phylogeographic patterns in mtDNA reveal different monophyletic lineages on both sides of the Atlantic, which predate the onset of the Ice Age and which may constitute cryptic species. Similar micro‐ and macrogeographical patterns were observed for the mtDNA and microsatellite markers, despite high frequencies of null alleles. Bayesian skyline reconstructions of the demographic history and mismatch distributions suggest that, although sizes of some populations were unaffected by Ice Age glaciations, others show signs of expansion after the Last Glacial Maximum. These phylogeographical patterns are consistent with patterns expected for low dispersal species that have survived in allopatric glacial refugial populations on both sides of the Atlantic and in deep‐sea refugia within each continent. The observed genetic structure has implications for conservation and sustainable management of the harvested populations. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 145–159.     

Y‐chromosomal variation confirms independent domestications of swamp and river buffalo

Y‐chromosomal variation in the water buffalo was analysed by sequencing of DBY, ZFY and SRY gene segments. A clear separation of the paternal lineages of the river and swamp types parallels the differences between their maternal lineages and nuclear DNA. Sequence divergence was found to be comparable to the divergence of taurine cattle and zebu, and this divergence predated domestication, confirming that river and swamp buffalo originated from different wild populations. Within a sample of 23 Thai swamp buffaloes, we identified four haplotypes with different geographical distributions, two of which were shared by Thai wild buffaloes.     

The role of vicariance and dispersal on New Zealand's estuarine biodiversity: the case of Paracorophium (Crustacea: Amphipoda)

To investigate the role of vicariance and dispersal on New Zealand's estuarine biodiversity, we examined variability in mitochondrial cytochrome c oxidase subunit I (COI) gene sequences for the amphipod genus Paracorophium. Individuals from the two nominate endemic species (Paracorophium excavatum and Paracorophium lucasi) were collected from sites throughout the North and South Islands. Sequence divergences of 12.8% were detected among the species. However, divergences of up to 11.7% were also observed between well supported clades, suggesting the possibility of cryptic species. Nested clade analyses identified four distinct lineages from within both P. excavatum and P. lucasi, with boundaries between clades corresponding to topographical features (e.g. Cook Straight, North and East Cape). Sequence divergences of 3.7–4.9% were also observed within geographic regions (e.g. east and west coasts of the upper North Island). Genetic structure in Paracorophium appears to represent prolonged isolation and allopatric evolutionary processes dating back to the Upper Miocene and continuing through the Pliocene and early Pleistocene. On the basis of molecular clock estimates from sequence divergences and reconstructions of New Zealand's geological past, we suggest that sea level and landmass changes during the early Pleistocene (2 Mya) resulted in the isolation of previously contiguous populations leading to the present‐day patterns. COI genetic structure was largely congruent with previously observed allozyme patterns and highlights the utility of COI as an appropriate marker for phylogeographic studies of the New Zealand estuarine fauna. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 863–874.