Allozyme and mitochondrial DNA variability within the New Zealand damselfly genera Xanthocnemis,Austrolestes, and Ischnura (Odonata)

Abstract

We collected larval damselflies from 17 sites in the North, South and Chatham Islands, and tested the hypotheses that: (1) genetic markers (e.g., allozymes, mtDNA) would successfully discriminate taxa; and (2) the dispersal capabilities of adult damselflies would limit differentiation among locations. Four species from three genera were identified based on available taxonomic keys. Using 11 allozyme loci and the mitochondrial cytochrome c‐oxidase subunit I (COI) gene, we confirmed that all taxa were clearly discernible. We found evidence for low to moderate differentiation among locations based on allozyme (meani F _ST = 0.09) and sequence (COI) divergence (<0.034). No obvious patterns with respect to geographic location were detected, although slight differences were found between New Zealand's main islands (North Island, South Island) and the Chatham Islands for A. colensonis (sequence divergence 0.030–0.034). We also found limited intraspecific genetic variability based on allozyme data (H_exp < 0.06 in all cases). We conclude that levels of gene flow/dispersal on the main islands may have been sufficient to maintain the observed homogeneous population structure, and that genetic techniques, particularly the COI gene locus, will be a useful aid in future identifications.     

Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes

Taxonomic and ecological studies of freshwater harpacticoid copepods are limited globally by the ability to easily and accurately identify specimens. Here, we test the use of the mitochondrial cytochrome c oxidase subunit I (COI) gene locus as a tool for assessing the diversity of freshwater Harpacticoida. We obtained sequences from New Zealand harpacticoid copepods, representing two families, five genera and nine species, including the non-indigenous Elaphoidella sewelli. All species were delineated by the COI gene. However, high intraspecific diversity was evident among populations of Elaphoidella bidens (>12%), and between North and South Island populations of Bryocamptus pygmaeus (>18%), potentially indicating the presence of morphologically cryptic taxa. We suggest that mitochondrial DNA (COI) sequences can provide a useful tool for the routine identification of freshwater harpacticoid copepods. Applications of these data will include assessing species diversity and biogeography as well as assisting with the detection of non-indigenous species.     

Population genetic connectivity of an endemic New Zealand passerine after large‐scale local extirpations: a model of re‐colonization potential

Little is known about how a 70% loss of native forests has affected the genetic connectivity of remnant bird populations in New Zealand. We use the common and widely distributed New Zealand Bellbird Anthornis melanura as an indicator species of population connectivity for well‐flighted birds. Using eight microsatellite loci, we identified five main genetic populations in the North Island, South Island, sub‐Antarctic Auckland Islands and two small remnant island populations adjacent to a large region of avian extirpations in northern North Island. Only one remnant island population, on a 30‐year‐old conservation reserve at Tiritiri Matangi, displayed a clear signature of recent genetic bottleneck. The 7% migration rate at Tiritiri Matangi indicates that bottlenecks can be maintained despite habitat rehabilitation, possibly through behavioural barriers to gene flow. Adjacent to the same extirpation zone, Bellbirds on the Poor Knights Islands were found to have low genetic diversity and low re‐colonization potential. Two gaps concordant with deforestation patterns separated the Kapiti Coast of southern North Island from populations to both the north and the south. In summary, we identified linked avian habitats, as well as isolated and inbred populations and suggest that Bellbirds are good re‐colonizers. We emphasize the importance of genetic studies that assess animal dispersal among newly rehabilitated habitat patches.     

Study of COI sequences from endemic New Zealand aphids highlights high mitochondrial DNA diversity in Rhopalosiphina (Hemiptera: Aphididae)

Focussed searches were made across New Zealand between 2013 and 2016, for endemic aphids from the Schizaphis (Rhopalosiphina) genus, which is currently represented by two putative, undescribed species from the endemic host plants Aciphylla and Dracophyllum. Cytochrome c oxidase I (COI) gene sequences (48 in total) from the Schizaphis were analysed together with those from a broader collection of New Zealand endemic aphids that has been assembled since the year 2000. The bulk of the Schizaphis belonged to two clusters corresponding to the host plant genera. Two aphids from central North Island Dracophyllum represented a much diverged lineage without clear affiliations to other New Zealand Schizaphis. Inter-population variation in the New Zealand Schizaphis was high compared with that seen in international studies of Aphidinae and among populations of other endemic New Zealand Aphidina. Within Schizaphis from Dracophyllum, geography played an apparent role in genetic structuring, with populations from Taranaki (North Island) and especially Mt Lyford (South Island) being divergent from those on the South Island main divide. Two distinct lineages of Schizaphis, which co-occurred at some sites, were found on Aciphylla. Our sequence comparisons, including GMYC analyses, indicated up to five New Zealand Schizaphis lineages, and two newly discovered endemic Aphis species from the host plants Clematis and Hebe.     

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.     

Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae,Rhodophyta) from New Zealand

Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct “cryptic” species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa.     

The taxonomic identity of a population of terrestrial Leiopelma (Anura: Leiopelmatidae) recently discovered in the northern king country,New Zealand

Abstract

A terrestrial endemic frog resembling Leiopelma archeyi was discovered in the Whareorino Forest, northern King Country, New Zealand, in 1991, where it is broadly sympatric with L. hochstetteri. To clarify its taxonomic status, allozyme electrophoresis of toe tissue was used to compare it genetically with four other populations of terrestrial Leiopelma (L. archeyi from Tapu and Tokatea, Coromandel; L. hamiltoni from Stephens Island; L. pakeka from Maud Island). Thirteen presumed genetic (allozyme) loci could be consistently scored for the five populations. At 11 loci, no genetic differences were found between the Whareorino frog and the two Coromandel L. archeyi populations. Allelic frequencies differed slightly at two loci. We therefore conclude that the terrestrial Whareorino frog represents a western population of L. archeyi. L. hamiltoni from Stephens Island is genetically closer to L. archeyi than is L. pakeka from Maud Island. The Whareorino L. archeyi population is morphologically similar to Coromandel L. archeyi populations, although multivariate analysis suggests subtle morphological differences, including the relative position of the nostril. Size comparisons between Whareorino and three Coromandel sites (Moehau, Tapu, Tokatea) show there were more larger frogs (35–38 mm snout‐vent length) at Whareorino and Tokatea compared with Moehau and Tapu, where maximum snout‐vent lengths were 34 and 36 mm, respectively.     

Closing the gap: Avian lineage splits at a young,narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β‐fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide‐ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.     

One haploid parent contributes 100% of the gene pool for a widespread species in northwest North America

The monoicous peatmoss Sphagnum subnitens has a tripartite distribution that includes disjunct population systems in Europe (including the Azores), northwestern North America and New Zealand. Regional genetic diversity was highest in European S. subnitens but in northwestern North America, a single microsatellite‐based multilocus haploid genotype was detected across 16 sites ranging from Coos County, Oregon, to Kavalga Island in the Western Aleutians (a distance of some 4115 km). Two multilocus haploid genotypes were detected across 14 sites on South Island, New Zealand. The microsatellite‐based regional genetic diversity detected in New Zealand and North American S. subnitens is the lowest reported for any Sphagnum. The low genetic diversity detected in both of these regions most likely resulted from a founder event associated with vegetative propagation and complete selfing, with one founding haploid plant in northwest North America and two in New Zealand. Thus, one plant appears to have contributed 100% of the gene pool for the population systems of S. subnitens occurring in northwest North America, and this is arguably the most genetically uniform group of plants having a widespread distribution yet detected. Although having a distribution spanning 12.5° of latitude and 56° of longitude, there was no evidence of any genetic diversification in S. subnitens in northwest North America. No genetic structure was detected among the three regions, and it appears that European plants of S. subnitens provided the source for New Zealand and northwest North American populations.     

Historical transoceanic dispersal of a freshwater shrimp: the colonization of the South Pacific by the genus Paratya (Atyidae)

Aim To infer the phylogenetic relationships within the freshwater shrimp genus Paratya Miers, 1882 (Atyidae) and to use these data to answer biogeographical questions about the location, timing and form of evolution of this genus in the South Pacific. Location Paratya are spread throughout various freshwater habitats in the western Pacific, with a disjunct northern range in the North Pacific (Japan, Korea, Ryukyu Islands, Siberia) and South Pacific (Australia, New Zealand, New Caledonia, Lord Howe, Norfolk Island). Methods Specimens were obtained from throughout its range. Mitochondrial sequences of cytochrome oxidase subunit I and 16S ribosomal DNA were analysed using phylogenetic techniques to identify whether landmasses are monophyletic and what the relationships are between landmasses. Molecular clock dating methods were used to date divergences between taxa. Results Each landmass was recovered as monophyletic. Japan/Ryukyu Islands is the most basal group, followed by New Zealand. Australian specimens form a sister group to a clade made up of two groups (New Caledonia and Lord Howe/Norfolk Island). The oldest divergence within the genus (between North and South Pacific) took place 12–19 Ma. Main conclusions The geographical origin of the genus (either Gondwana or Laurasia) is unclear. Dispersal occurred between the North and South Pacific long after the split up of Gondwana. Dispersal likely explains the presence of Paratya on each landmass in the South Pacific, from continent to isolated oceanic island. This dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya, given that amphyidromy is plesiomorphic in atyid shrimp.     

Major Histocompatibility Complex (MHC) class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Determining how intra-specific genetic diversity is apportioned among natural populations is essential for detecting local adaptation and identifying populations with inherently low levels of extant diversity which may become a conservation concern. Sequence polymorphism at two adaptive loci (MHC DRA and DQB) was investigated in long-finned pilot whales (Globicephala melas) from four regions in the North Atlantic and compared with previous data from New Zealand (South Pacific). Three alleles were resolved at each locus, with trans-species allele sharing and higher levels of non-synonymous to synonymous substitution, especially in the DQB locus. Overall nucleotide diversities of 0.49?±?0.38% and 4.60?±?2.39% were identified for the DRA and DQB loci, respectively, which are relatively low for MHC loci in the North Atlantic, but comparable to levels previously described in New Zealand (South Pacific). There were significant differences in allele frequencies within the North Atlantic and between the North Atlantic and New Zealand. Patterns of diversity and divergence are consistent with the long-term effects of balancing selection operating on the MHC loci, potentially mediated through the effects of host-parasite coevolution. Differences in allele frequency may reflect variation in pathogen communities, coupled with the effects of differential drift and gene flow.     

Evolution and phylogeny of the New Zealand cicada genus Kikihia Dugdale (Homoptera: Auchenorrhyncha: Cicadidae) with special reference to the origin of the Kermadec and Norfolk Islands' species

Aim Determine the phylogeny and dispersal patterns of the cicada genus Kikihia in New Zealand and the origin of the Norfolk, Kermadec, and Chatham Island cicadas. Location New Zealand, Norfolk Island, Kermadec Islands and Chatham Island. Methods DNA sequences from 16 species and four soon to be described species of cicadas from New Zealand and Norfolk Island (Australia) were examined. A total of 1401 base pairs were analysed from whole genome extraction of three mitochondrial genes (cytochrome oxidase subunit II, ATPase6 and ATPase8). These DNA sequences were aligned and analysed using standard likelihood approaches to phylogenetic analysis. Dates of divergences between clades were determined using a molecular clock based on Bayesian statistics. Results Most species in the genus Kikihia diverged between 3 and 5 million years ago (Ma) coincident with a period of rapid mountain building in New Zealand. Cicada species on the Kermadec and Norfolk Islands invaded recently from New Zealand and are closely related to the New Zealand North Island species Kikihia cutora. Main conclusions Speciation in the genus Kikihia was likely due in large part to the appearance of new habitats associated with the rise of the Southern Alps, starting c. 5 Ma. Dispersal of Kikihia species within mainland New Zealand probably occurred gradually rather than through long‐distance jumps. However, invasion of Norfolk, the Kermadecs and Chatham Islands had to have occurred through long‐distance dispersal.     

Crossing the Tasman Sea: Inferring the introduction history of Litoria aurea and Litoria raniformis (Anura: Hylidae) from Australia into New Zealand

Abstract The amphibian fauna of New Zealand consists of three native species (Leiopelma spp.), and three Litoria species introduced from Australia in the last 140 years. We conducted a molecular phylogeographical study that aimed to identify the Australian origins of two species, Litoria aurea and Litoria raniformis. We used partial sequences of the mitochondrial cytochrome oxidase I (cox1) gene from 59 specimens sampled from across the range of both species to identify the probable source populations for the New Zealand introductions, and to describe the current genetic diversity among New Zealand Litoria populations. Our genetic data suggest that L. aurea was introduced into the North Island of New Zealand from two regions in Australia, once from the northern part of coastal New South Wales and once from the southern part of coastal New South Wales. Our data indicate that L. raniformis introductions originated from the Melbourne region of southern Victoria and once established in the South Island of New Zealand, the species subsequently spread throughout both islands. In addition, we found a distinct haplotype in L. raniformis from Tasmania that strongly suggests, contrary to earlier reports, that this species was not introduced into New Zealand from Tasmania. Finally, we identified two very distinctive mitochondrial lineages of L. raniformis within the mainland Australia distribution, which may be previously unrecognized species.     

Variation in habitat use along the freshwater–marine continuum by grey mullet Mugil cephalus at the southern limits of its distribution

In this study, habitat use by Mugil cephalus was investigated in the waters of the west coast of the North Island of New Zealand by analysing microchemical composition of otoliths (laser‐ablation inductively coupled plasma mass spectrometry) obtained from individuals from commercial fish stocks and research surveys. Results of this study show that M. cephalus at the southern limits of its distribution display highly flexible migratory behaviour with extensive use of freshwater and brackish habitats, potentially enabling them to maximize foraging opportunities. Mugil cephalus can tolerate a wide range of salinities and can therefore utilize higher productivity areas, such as estuaries and eutrophic riverine lakes. Finally, M. cephalus populations across a range of climates and latitudes appear to differ in the extent to which they utilize freshwater and brackish habitats, possibly with increasing penetration of fresh waters with increasing latitude.     

Nuclear microsatellite DNA markers for New Zealand kiwi (Apteryx spp.)

Kiwi (Apterygidae) is an endemic New Zealand avian family comprising five species whose conservation is actively managed. We present five polymorphic microsatellite DNA loci isolated from North Island brown kiwi (Apteryx mantelli). In addition, we demonstrate cross‐amplification, and in some cases, polymorphism, of these microsatellite DNA loci in four other kiwi species. Therefore, these markers may be broadly applicable to conservation genetic studies within this family.     

Incidence, importance and virulence of Puccinia hordei on barley in New Zealand

Brown rust of barley (Puccinia hordei) is widespread in New Zealand and causes crop losses in some years. The cultivars presently grown lack adequate genetic resistance but a highly resistant line has been produced. Twelve different virulence combinations were identified in the pathogen population using the Welsh differential lines; there were differences between North Island and South Island isolates; and no virulence was observed for resistance conferred by factors Pa 3 and Pa 7.     

Gondwanan radiation of the Southern Hemisphere crayfishes (Decapoda: Parastacidae): evidence from fossils and molecules

Aim The sequential break‐up of Gondwana is thought to be a dominant process in the establishment of shared biota across landmasses of the Southern Hemisphere. Yet similar distributions are shared by taxa whose radiations clearly post‐date the Gondwanan break‐up. Thus, determining the contribution of vicariance versus dispersal to seemingly Gondwanan biota is complex. The southern freshwater crayfishes (family Parastacidae) are distributed on Australia and New Guinea, South America, Madagascar and New Zealand and are unlikely to have dispersed via oceans, owing to strict freshwater limitations. We test the hypotheses that the break‐up of Gondwana has led to (1) a predominately east–west (((Australia, New Zealand: 80 Ma) Madagascar: 160–121 Ma) South America: 165–140 Ma), or (2) a southern (((Australia, South America: 52–35 Ma) New Zealand: 80 Ma) Madagascar: 160–121 Ma) pattern for parastacid crayfish. Further, we examine the evidence for a complete drowning of New Zealand and subsequent colonization by freshwater crayfish. Location Southern Hemisphere. Methods The evolutionary relationships among the 15 genera of Parastacidae were reconstructed using mitochondrial [16S, cytochrome c oxidase subunit I (COI)] and nuclear (18S, 28S) sequence data and maximum likelihood and Bayesian methods of phylogenetic reconstruction. A Bayesian (multidivtime ) molecular dating method using six fossil calibrations and phylogenetic inference was used to estimate divergence time among crayfish clades on Gondwanan landmasses. Results The South American crayfish are monophyletic and a sister group to all other southern crayfish. Australian crayfish are not monophyletic, with two Tasmanian genera, Spinastacoides and Ombrastacoides, forming a clade with New Zealand and Malagasy crayfish (both monophyletic). Divergence of crayfish among southern landmasses is estimated to have occurred around the Late Jurassic to Early Cretaceous (109–178 Ma). Main conclusions The estimated phylogenetic relationships and time of divergence among the Southern Hemisphere crayfishes were consistent with an east–west pattern of Gondwanan divergence. The divergence between Australia and New Zealand (109–160 Ma) pre‐dated the rifting at around 80 Ma, suggesting that these lineages were established prior to the break‐up. Owing to the age of the New Zealand crayfish, we reject the hypothesis that there was a complete drowning of New Zealand crayfish habitat.     

Genetic variation in island populations of tuatara (<Emphasis Type="Italic">Sphenodon</Emphasis> spp) inferred from microsatellite markers

Tuatara (Sphenodon spp) populations are restricted to 35 offshore islands in the Hauraki Gulf, Bay of Plenty and Cook Strait of New Zealand. Low levels of genetic variation have previously been revealed by allozyme and mtDNA analyses. In this new study, we show that six polymorphic microsatellite loci display high levels of genetic variation in 14 populations across the geographic range of tuatara. These populations are characterised by disjunct allele frequency spectra with high numbers of private alleles. High F _ST (0.26) values indicate marked population structure and assignment tests allocate 96% of all individuals to their source populations. These genetic data confirm that islands support genetically distinct populations. Principal component analysis and allelic sequence data supplied information about genetic relationships between populations. Low numbers of rare alleles and low allelic richness identified populations with reduced genetic diversity. Little Barrier Island has very low numbers of old tuatara which have retained some relictual diversity. North Brother Island’s tuatara population is inbred with fixed alleles at 5 of the 6 loci.     

Fin whale MDH‐1 and MPI allozyme variation is not reflected in the corresponding DNA sequences

The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH‐1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH‐1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.