Comparative phylogeography reveals pre‐decline population structure of New Zealand Cyclodina (Reptilia: Scincidae) species

We examined the comparative phylogeography of all species within the endemic New Zealand skink genus Cyclodina to gain insight into the influence of historical processes on the biogeography of the North Island fauna. Until 1–2 kya, six Cyclodina species occurred sympatrically across the North Island of New Zealand. However, most species have undergone dramatic distributional declines subsequent to the introduction of mammals and the arrival of humans. We compare the phylogeographic patterns evident in Cyclodina species in three biogeographic categories: widespread species (Cyclodina aenea, Cyclodina ornata), North Island disjunct relics (Cyclodina macgregori, Cyclodina whitakeri), and northeastern island relics (Cyclodina alani, Cyclodina oliveri, Cyclodina townsi). Mitochondrial DNA (ND2) sequence data was obtained from across the entire range of each Cyclodina species. We used Neighbour‐joining, maximum likelihood and Bayesian methods to examine the phylogeographic patterns present in each species. Phylogeographic patterns varied among species in different biogeographic categories. Substantial phylogeographic structure was evident in the two widespread species (C. aenea, C. ornata), with Pliocene and Pleistocene divergences between clades evident. Divergences among island groups in the three northeastern island relic species (C. alani, C. oliveri, C. townsi) occurred during the late Pliocene–Pleistocene. By contrast, relatively shallow structure, indicative of late Pleistocene divergences, was present in the two North Island disjunct species (C. macgregori, C. whitakeri). The results strongly suggest that the Poor Knights Islands population of C. ornata represents a new species. We suggest that the contrasting phylogeographic patterns exhibited by Cyclodina species in different biogeographic categories might be related to body size, ecology, and habitat preferences. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 388–408.     

Comparative phylogeography of two closely related <Emphasis Type="Italic">Viola</Emphasis> species occurring in contrasting habitats in the Japanese archipelago

Similar distribution ranges shared by closely related plant species may have been shaped through different migration histories if those species have differing habitat preference. To test this hypothesis, phylogeographical patterns and population genetic structures were compared between two sister Viola species: Viola eizanensis preferring woodland and V. chaerophylloides var. sieboldiana preferring grassland, both being native to the Japanese Archipelago. Amplified fragment length polymorphism (AFLP) was used for phylogenetic reconstruction, together with Bayesian ancestry analysis, AMOVA, analysis of genetic diversity statistics, and analysis of the relative contribution of each population to total diversity. The results indicated that V. eizanensis had two distinct lineages occurring in the western and eastern part of Japan, but such lineages are not distinct in V. chaerophylloides var. sieboldiana. Both species exhibited the low genetic diversity and high between-population differentiation typical of selfing plants. In V. chaerophylloides var. sieboldiana, one particular population made a significantly higher contribution to the total heterozygosity (H _T), whereas in V. eizanensis, no population was identified as making a particularly higher contribution to H _T. These findings suggest that V. eizanensis had been isolated in two large glacial refugia, whereas populations of V. chaerophylloides var. sieboldiana were restricted to a single small refuge. Different light requirements between these two closely related species probably caused these differing responses to climatic change during the last ice age. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparative phylogeography and demographic history of two marsupials of the Atlantic Forest in eastern Brazil

The Atlantic Forest biodiversity hotspot in eastern South America has been the focus of several phylogeographic studies concerning relationships between populations and areas and how taxa respond to environmental changes. We infer and compare the demographic and biogeographic histories of two didelphid marsupial species, Gracilinanus microtarsus and Marmosops incanus, from the Atlantic Forest of eastern Brazil to determine how these species responded to environmental changes over time, using mitochondrial and nuclear DNA sequences. We found great intraspecific genetic divergence in both species and a strong geographic structure related to similar and spatially cohesive groups within each species. These groups are consistent with the same topographical barriers, such as mountains and river valleys. Intraspecific clades are very old, dating back to a period of tectonic activities in the Neogene (5.39–8.57 Mya). Changes in the environment over the last 7 million years lead to fairly concordant demographic changes in both marsupial species, including population expansion during the last glacial maximum (ca. 21,000 years ago) or last interglacial (ca. 120,000 years ago) or both. These results do not fit the Pleistocene refuge hypothesis as an explanation of the historical biogeography and diversification of both species in the Atlantic Forest, but are compatible with the Atlantis Forest hypothesis.     

Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai‐Tibetan plateau

Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai‐Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai‐Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford’s snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros). Our results revealed the three species mostly distributed on the platform region of the plateau that experienced population expansion following the retreat of the extensive glaciation period (0.5–0.175 Ma). These results are at odds with the results from avian species of Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023–0.018 Ma). A single refugium was identified in a restricted semi‐continuous area around the eastern margin of the plateau, instead of multiple independent refugia for European and North American species. For the other two species distributed on the edges of the plateau (the twite and black redstart), populations were maintained at stable levels. Edge areas are located on the eastern margin, which might have had little or no ice cover during the glaciation period. Thus, milder climate may have mitigated demographic stresses for edge species relative to the extremes experienced by platform counterparts, the present‐day ranges of which were heavily ice covered during the glaciation period. Finally, various behavioural and ecological characteristics, including dispersal capacities, habitat preference and altitude specificity along with evolutionary history might have helped to shape different phylogeographical structures appearing in these five species.     

Comparative molecular phylogeography of two Xenopus species, X. gilli and X. laevis, in the south-western Cape Province, South Africa

Xenopus gilli is a vulnerable anuran with a patchy distribution along the south-western coast of the Cape Province, South Africa. This species is sympatric with Xenopus laevis laevis , a widespread relative found over much of southern Africa. We examined the molecular phylogeography and population structure of the contact zone between these species to obtain information about historical biogeography and conservation management of this region. Analyses of the distribution, frequency, and cladistic and phenetic relationships among mitochondrial DNA haplotypes indicate that population subdivision is present in both taxa but that long-term isolation of sets of populations has occurred in X. gilli only. Haplotype and nucleotide diversity are also considerably higher within and among X. gilli ponds than X. l. laevis ponds in this region. We attribute the genetic segregation of X. gilli populations to ancient habitat fragmentation by ocean transgression into X. gilli habitat and to continued habitat alteration by human activity. The lower level of genetic diversity in X. l. laevis in this region is likely a result of a recent arrival of this taxon to the south-western Cape region relative to X. gilli . Population structure in X. l. laevis may be a result of isolation by distance. Clear evidence exists for at least two management units within X. gilli and strongly supports the establishment of protective measures east of False Bay in order to conserve a substantial portion of this species' extant genetic diversity.     

Molecular assessment of Ulva (Ulvales,Chlorophyta) diversity in Vietnam including the new species U. vietnamensis

Species diversity of Ulva in Vietnam was investigated using three commonly used genetic markers, the nuclear encoded rDNA ITS region and the plastid encoded rbcL and tufA genes. Single locus species delimitation methods, complemented with morphological and ecological information resulted in the delimitation of 19 species. This diversity is largely incongruent with the traditional understanding of Ulva diversity in Vietnam. Only four species identified in this study, U. lactuca, U. reticulata, U. spinulosa, and U. flexuosa, have been previously reported, and seven species, U. ohnoi, U. tepida, U. chaugulii, U. kraftiorum, U. meridionalis, U. limnetica, and U. aragoënsis, are recorded for the first time from Vietnam. Seven genetic clusters could not be associated with species names with certainty. A new species, U. vietnamensis, is described from marine to brackish coastal areas from southern Vietnam based on its morphological and molecular distinctiveness from the currently known Ulva species. A comparison with recent molecular-based studies of Ulva diversity showed that species composition in Vietnam is similar to that of adjacent countries, including Japan, China, as well as Australia. Our study emphasizes the importance of molecular data in the assessment of Ulva diversity, and indicates that a lot of diversity may still remain to be discovered, especially in tropical regions.     

Morphological and molecular concordance for the recognition of two species in the New ZealandPolystichum richardii (Hook.) J. Smith complex

The New Zealand fernPolystichum richardii is shown to comprise at least two evolutionary lineages. A narrow-scaled morphological form and a wide-scaled morphological form are recognised. Principal Component Analysis of a set of frond, soral and spore characters supports this morphological separation. Amplified Fragment Length Polymorphism (AFLP) DNA fingerprinting shows that the two morphological forms are also genetically distinct. They are sympatric across a broad area of central New Zealand, and often grow together without apparent ecological separation at the local level. Both are known to form sterile hybrids withP. vestitum, suggesting that both morphological forms ofP. richardii are at least partially outcrossing. The morphological and genetic distinctiveness of these two morphological forms, combined with their sympatric distributions and their (at least partially) outcrossing mating systems, merits their recognition as separate species.     

The genus Scapheremaeus (Acari,Oribatida, Cymbaeremaeidae) in the oribatid mite fauna of New Zealand,with description of two new species

Two new species of oribatid mites of the genus Scapheremaeus (Oribatida, Cymbaeremaeidae), Scapheremaeus gibbus sp. n. and Scapheremaeus luxtoni sp. n., are described from New Zealand. Scapheremaeus gibbus sp. n. is morphologically most similar to Scapheremaeus humeratus Balogh & Mahunka, 1967, but differs from the latter by the number of notogastral, genital and adanal setae, morphology of bothridial setae, position of adanal lyrifissures and absence of humeral processes. Scapheremaeus luxtoni sp. n. is morphologically most similar to Scapheremaeus yamashitai Aoki, 1970, but differs from the latter by the morphology of notogastral and rostral setae, morphology of leg solenidia φ₂ and development of humeral processes. The species Scapheremaeus zephyrus Colloff, 2010 is recorded for the first time in New Zealand. An identification key to the known New Zealand species of Scapheremaeus is provided.