scholarly journals Inferring the late Quaternary phylogeography of Pseudopanax crassifolius using microsatellite analysis

2021 ◽  
Author(s):  
◽  
Michael Gemmell
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Late Quaternary ◽  
Leading Edge ◽  
The South ◽  
Genetic Structuring ◽  
The North ◽  
Chloroplast Haplotypes ◽  
Patterns And Processes

<p>Geologic processes have shaped the New Zealand archipelago throughout its existence. The last major geologic event was the Pleistocene glaciations beginning around 2.5 million years ago. This cold period left its mark in the phylogeography (the geographic distribution of genetic variation) of New Zealand’s globally significant biota. Studies into the phylogeography of New Zealand have largely focused on species with limited distributions through rarity or ecological preferences. This study focuses on the ubiquitous species Pseudopanax crassifolius (Sol. Ex A. Cunn) K. Koch, also known commonly as Horoeka or Lancewood. This species is widespread and almost continuously distributed throughout New Zealand giving a broad scale look at the patterns and processes that have influenced the formation of New Zealand’s natural history.  Seven microsatellite loci and two rps4 chloroplast haplotypes were utilised to study 247 Pseudopanax crassifolius and nine P. chathamicus individuals sampled from populations from around New Zealand. Pseudopanax crassifolius was found to have levels of genetic diversity and overall differentiation consistent with common widespread trees. The genetic structuring suggests P. crassifolius is not a single homogenous population across a southern cluster. The geographic structuring of genetic variation within these clusters is poor.   The genetic patterns and the spatial distribution of these patterns may reflect the response of Pseudopanax crassifolius to changing environmental conditions during the late Quaternary following the maximum extent of the last glacial maximum (LGM) period. During the maximally cold periods of the LGM, P. crassifolius is likely to have been eliminated or at least greatly reduced in the south and west coast of the South Island. In the remainder of the South Island and throughout the North Island it remained widespread. The heterogeneous pattern of genetic variation with little geographic correlation in the northern cluster may reflect either the extent of the historic distribution of the species or the effect of gene flow between populations acting to inhibit population structuring from establishing. The reduction in genetic diversity and the homogeneity of structure in the south indicate a pattern of leading edge re-colonisation into southern areas as conditions became more favourable following the LGM. The leading edge mode is supported by asymmetric introgression of rps4 haplotype seen between P. crassifolius and P. ferox along the east coast of the South Island.  This study also investigated levels of differentiation between Pseudopanax crassifolius and P. chathamicus. There is limited evidence of differentiation based on microsatellite markers. There is therefore no strong genetic evidence for either the support or rejection of the current species delimitation of the crassifolius group of Pseudopanax species. The two species are morphologically different and geographically isolated. This, alongside evidence from previous studies suggest that P. chathamicus is possibly an example of a group undergoing incipient allopatric speciation. A recent founder event is proposed with enough potential diversity carried in two individual fruit to account for the diversity seen in P. chathamicus.</p>

scholarly journals Inferring the late Quaternary phylogeography of Pseudopanax crassifolius using microsatellite analysis

2021 ◽  
Author(s):  
◽  
Michael Gemmell
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Late Quaternary ◽  
Leading Edge ◽  
The South ◽  
Genetic Structuring ◽  
The North ◽  
Chloroplast Haplotypes ◽  
Patterns And Processes

<p>Geologic processes have shaped the New Zealand archipelago throughout its existence. The last major geologic event was the Pleistocene glaciations beginning around 2.5 million years ago. This cold period left its mark in the phylogeography (the geographic distribution of genetic variation) of New Zealand’s globally significant biota. Studies into the phylogeography of New Zealand have largely focused on species with limited distributions through rarity or ecological preferences. This study focuses on the ubiquitous species Pseudopanax crassifolius (Sol. Ex A. Cunn) K. Koch, also known commonly as Horoeka or Lancewood. This species is widespread and almost continuously distributed throughout New Zealand giving a broad scale look at the patterns and processes that have influenced the formation of New Zealand’s natural history.  Seven microsatellite loci and two rps4 chloroplast haplotypes were utilised to study 247 Pseudopanax crassifolius and nine P. chathamicus individuals sampled from populations from around New Zealand. Pseudopanax crassifolius was found to have levels of genetic diversity and overall differentiation consistent with common widespread trees. The genetic structuring suggests P. crassifolius is not a single homogenous population across a southern cluster. The geographic structuring of genetic variation within these clusters is poor.   The genetic patterns and the spatial distribution of these patterns may reflect the response of Pseudopanax crassifolius to changing environmental conditions during the late Quaternary following the maximum extent of the last glacial maximum (LGM) period. During the maximally cold periods of the LGM, P. crassifolius is likely to have been eliminated or at least greatly reduced in the south and west coast of the South Island. In the remainder of the South Island and throughout the North Island it remained widespread. The heterogeneous pattern of genetic variation with little geographic correlation in the northern cluster may reflect either the extent of the historic distribution of the species or the effect of gene flow between populations acting to inhibit population structuring from establishing. The reduction in genetic diversity and the homogeneity of structure in the south indicate a pattern of leading edge re-colonisation into southern areas as conditions became more favourable following the LGM. The leading edge mode is supported by asymmetric introgression of rps4 haplotype seen between P. crassifolius and P. ferox along the east coast of the South Island.  This study also investigated levels of differentiation between Pseudopanax crassifolius and P. chathamicus. There is limited evidence of differentiation based on microsatellite markers. There is therefore no strong genetic evidence for either the support or rejection of the current species delimitation of the crassifolius group of Pseudopanax species. The two species are morphologically different and geographically isolated. This, alongside evidence from previous studies suggest that P. chathamicus is possibly an example of a group undergoing incipient allopatric speciation. A recent founder event is proposed with enough potential diversity carried in two individual fruit to account for the diversity seen in P. chathamicus.</p>

scholarly journals Commensal Rodents in 19th Century Australasia: Diversity, Invasion Routes and the China Connection

2021 ◽  
Author(s):  
Andrew James Veale ◽  
Carolyn King ◽  
Wayne Johnson ◽  
Lara Shepherd
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Dna Sequences ◽  
Archaeological Site ◽  
House Mice ◽  
Mus Musculus Domesticus ◽  
The South ◽  
The North ◽  
Founding Population ◽  
Norway Rats

Abstract The present genetic diversity of commensal rodent populations is often used to inform the invasion histories of these species, and as a proxy for historical events relating to the movement of people and goods. These studies assume that modern genetic diversity generally reflects early colonising events. We investigate this idea by sequencing the mitochondrial DNA of rodent bones found in a 19th-century archaeological site in The Rocks area of Sydney, Australia, the location of the first historical European port. We identified 19th-century bones from two species, Rattus norvegicus and Mus musculus domesticus. We found six genetic haplotypes in the 39 Norway rats, showing either multiple early introductions or a diverse initial founding population. One of them was identical with Norhap01 common in the North Island of New Zealand, but none was like the haplotype Norhap02 found throughout the South Island. We found three haplotypes in seven house mice, all belonging to the dominant subspecies established in Australia, M.m. domesticus. There was no evidence for M. m. castaneus or M. m. musculus having established there. We had few modern R. norvegicus and M. musculus DNA sequences from Sydney, but those we had did tentatively support the hypotheses that (1) modern samples can represent at least a preliminary estimate of historical diversities and origins, and (2) Asian haplotypes of both Norway rats and of house mice reached the South Island of New Zealand early in colonial times direct from China rather than through Port Jackson.

scholarly journals Population Genetics of New Zealand Scampi (Metanephrops challengeri)

2021 ◽  
Author(s):  
◽  
Alexander Verry
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Demographic History ◽  
Eastern Coast ◽  
Genetic Structuring ◽  
The North ◽  
Dispersal Potential

<p>A fundamental goal of fisheries management is sustainable harvesting and the preservation of properly functioning populations. Therefore, an important aspect of management is the identification of demographically independent populations (stocks), which is achieved by estimating the movement of individuals between areas. A range of methods have been developed to determine the level of connectivity among populations; some measure this directly (e.g. mark-recapture) while others use indirect measures (e.g. population genetics). Each species presents a different set of challenges for methods that estimate levels of connectivity. Metanephrops challengeri is a species of nephropid lobster that supports a commercial fishery and inhabits the continental shelf and slope of New Zealand. Very little research on population structure has been reported for this species and it presents a unique set of challenges compared to finfish species. M. challengeri have a short pelagic larval duration lasting up to five days which limits the dispersal potential of larvae, potentially leading to low levels of connectivity among populations. The aim of this study was to examine the genetic population structure of the New Zealand M. challengeri fishery.  DNA was extracted from M. challengeri samples collected from the eastern coast of the North Island (from the Bay of Plenty to the Wairarapa), the Chatham Rise, and near the Auckland Islands. DNA from the mitochondrial CO1 gene and nuclear ITS-1 region was amplified and sequenced. The aligned dataset of DNA sequences was then used to estimate levels of both genetic diversity and differentiation, and examine demographic history. Analyses of population structure indicate that M. challengeri from the Auckland Islands region are genetically distinct from M. challengeri inhabiting the Chatham Rise, and those collected from waters off the eastern coast of the North Island. There appears to be gene flow among the sampling sites off the eastern coast of the North Island and on the Chatham Rise, but some isolation by distance was detected. These results indicate that some of these populations may be demographically uncoupled. Genetic diversity estimates combined with Bayesian skyline plots and demographic history parameters suggest that M. challengeri populations have recently undergone a size expansion.  The genetic structuring between the Auckland Islands site and all others may be due to a putative habitat disjunction off the Otago shelf. In contrast, a largely continuously distributed population along the eastern coast of the North Island and the Chatham Rise most likely promotes gene flow as larvae can be transported limited distances by oceanic currents. Historical changes in climate may have influenced the patterns of present-day structure and genetic diversity of M. challengeri, by altering habitat availability and other characteristics of their environment. This study provides evidence that species which appear to have limited dispersal potential can still maintain connected populations, but there are situations where large breaks in suitable habitat appear to limit gene flow. The results of this study will help inform stock structure of the M. challengeri fishery, which will enable stock assessments to be more precisely aligned to natural population boundaries.</p>

scholarly journals Population Genetics of New Zealand Scampi (Metanephrops challengeri)

2021 ◽  
Author(s):  
◽  
Alexander Verry
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Demographic History ◽  
Eastern Coast ◽  
Genetic Structuring ◽  
The North ◽  
Dispersal Potential

<p>A fundamental goal of fisheries management is sustainable harvesting and the preservation of properly functioning populations. Therefore, an important aspect of management is the identification of demographically independent populations (stocks), which is achieved by estimating the movement of individuals between areas. A range of methods have been developed to determine the level of connectivity among populations; some measure this directly (e.g. mark-recapture) while others use indirect measures (e.g. population genetics). Each species presents a different set of challenges for methods that estimate levels of connectivity. Metanephrops challengeri is a species of nephropid lobster that supports a commercial fishery and inhabits the continental shelf and slope of New Zealand. Very little research on population structure has been reported for this species and it presents a unique set of challenges compared to finfish species. M. challengeri have a short pelagic larval duration lasting up to five days which limits the dispersal potential of larvae, potentially leading to low levels of connectivity among populations. The aim of this study was to examine the genetic population structure of the New Zealand M. challengeri fishery.  DNA was extracted from M. challengeri samples collected from the eastern coast of the North Island (from the Bay of Plenty to the Wairarapa), the Chatham Rise, and near the Auckland Islands. DNA from the mitochondrial CO1 gene and nuclear ITS-1 region was amplified and sequenced. The aligned dataset of DNA sequences was then used to estimate levels of both genetic diversity and differentiation, and examine demographic history. Analyses of population structure indicate that M. challengeri from the Auckland Islands region are genetically distinct from M. challengeri inhabiting the Chatham Rise, and those collected from waters off the eastern coast of the North Island. There appears to be gene flow among the sampling sites off the eastern coast of the North Island and on the Chatham Rise, but some isolation by distance was detected. These results indicate that some of these populations may be demographically uncoupled. Genetic diversity estimates combined with Bayesian skyline plots and demographic history parameters suggest that M. challengeri populations have recently undergone a size expansion.  The genetic structuring between the Auckland Islands site and all others may be due to a putative habitat disjunction off the Otago shelf. In contrast, a largely continuously distributed population along the eastern coast of the North Island and the Chatham Rise most likely promotes gene flow as larvae can be transported limited distances by oceanic currents. Historical changes in climate may have influenced the patterns of present-day structure and genetic diversity of M. challengeri, by altering habitat availability and other characteristics of their environment. This study provides evidence that species which appear to have limited dispersal potential can still maintain connected populations, but there are situations where large breaks in suitable habitat appear to limit gene flow. The results of this study will help inform stock structure of the M. challengeri fishery, which will enable stock assessments to be more precisely aligned to natural population boundaries.</p>

Inherited and Environmentally Induced Differences in Mutation Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 87-99
Author(s):  
Bernard C Lamb ◽  
Muhammad Saleem ◽  
William Scott ◽  
Nina Thapa ◽  
Eviatar Nevo
Keyword(s):  
Genetic Variation ◽  
Spontaneous Mutation ◽  
The South ◽  
Natural Genetic Variation ◽  
The North ◽  
Ascospore Germination ◽  
Evolution Canyon ◽  
Two Generations ◽  
Wild Strains ◽  
Sordaria Fimicola

Abstract We have studied whether there is natural genetic variation for mutation frequencies, and whether any such variation is environment-related. Mutation frequencies differed significantly between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. Strains from the harsher, drier, south-facing slope had higher frequencies of new spontaneous mutations and of accumulated mutations than strains from the milder, lusher, north-facing slope. Collective total mutation frequencies over many loci for ascospore pigmentation were 2.3, 3.5 and 4.4% for three strains from the south-facing slope, and 0.9, 1.1, 1.2, 1.3 and 1.3% for five strains from the north-facing slope. Some of this between-slope difference was inherited through two generations of selfing, with average spontaneous mutation frequencies of 1.9% for south-facing slope strains and 0.8% for north-facing slope strains. The remainder was caused by different frequencies of mutations arising in the original environments. There was also significant heritable genetic variation in mutation frequencies within slopes. Similar between-slope differences were found for ascospore germination-resistance to acriflavine, with much higher frequencies in strains from the south-facing slope. Such inherited variation provides a basis for natural selection for optimum mutation rates in each environment.

Late Quaternary change in the mountains of New Guinea

Antiquity ◽  
1995 ◽  
Vol 69 (265) ◽  
pp. 818-830 ◽  
Author(s):  
Geoff Hope ◽  
Jack Golson
Keyword(s):  
Late Quaternary ◽  
New Guinea ◽  
Mountainous Areas ◽  
The South ◽  
Environmental Sequence ◽  
The North ◽  
Australian Continent

At the south and north limits of our region are mountainous areas very different from the open arid spaces of the Australian continent between. In the north, the high country of New Guinea offers a complex and well-studied environmental sequence as the arena for early and puzzling human adaptations, precursor of the extraordinary societies of the island today.

Geodetic strain and the deformational history of the North Island of New Zealand during the late Cainozoic

1987 ◽  
Vol 321 (1557) ◽  
pp. 163-181 ◽  
Keyword(s):  
New Zealand ◽  
Subduction Zone ◽  
East Coast ◽  
Late Quaternary ◽  
Plate Boundary ◽  
Boundary Zone ◽  
Metamorphic Belt ◽  
Volcanic Region ◽  
The North ◽  
Plate Boundary Zone

The subduction zone under the east coast of the North Island of New Zealand comprises, from east to west, a frontal wedge, a fore-arc basin, uplifted basement forming the arc and the Central Volcanic Region. Reconstructions of the plate boundary zone for the Cainozoic from seafloor spreading data require the fore-arc basin to have rotated through 60° in the last 20 Ma which is confirmed by palaeomagnetic declination studies. Estimates of shear strain from geodetic data show that the fore-arc basin is rotating today and that it is under extension in the direction normal to the trend of the plate boundary zone. The extension is apparently achieved by normal faulting. Estimates of the amount of sediments accreted to the subduction zone exceed the volume of the frontal wedge: underplating by the excess sediments is suggested to be the cause of late Quaternary uplift of the fore-arc basin. Low-temperature—high-pressure metamorphism may therefore be occurring at depth on the east coast and high-temperature—low-pressure metamorphism is probable in the Central Volcanic Region. The North Island of New Zealand is therefore a likely setting for a paired metamorphic belt in the making.

scholarly journals Ecological impact and spread of an invasive paper wasp in New Zealand (Hymenoptera: Vespidae)

2021 ◽  
Author(s):  
Matthew Howse
Keyword(s):  
At Risk ◽  
Invasive Species ◽  
New Zealand ◽  
Ecological Impact ◽  
Diet Analysis ◽  
Paper Wasp ◽  
Gut Contents ◽  
Suitable Habitat ◽  
The South ◽  
The North

<p><b>Social wasps are considered among the most successful and impactful invasive species in the world. One species, Polistes dominula has spread from its native Mediterranean range to every continent except Antarctica. This wasp reached New Zealand in the last decade where it has established in the north of the South Island, however, reports of its presence are increasing throughout the country. Due to its recent arrival in New Zealand, little is known about where this species is likely to establish or what impacts it may have on local insect communities. In this thesis, I conducted two studies to investigate these questions, providing valuable information that may inform future management of this invasive species. </b></p><p>In chapter 2, I used two bioclimatic modelling methods to predict areas of suitable habitat across four regions in the southern hemisphere. These models were informed by global temperature and precipitation data as well as global distribution occurrence data of P. dominula. These data were used to estimate conditions most highly correlated with the presence of this wasp. The models identified large areas across the target regions that were climatically suitable for the establishment of P. dominula. Many of these areas are not known to currently contain populations of this species, representing habitat potentially vulnerable to further invasion by P. dominula. Areas across South America, South Africa and Australia were predicted to be climatically suitable. In New Zealand, much of the North Island and eastern parts of the South Island were predicted to be suitable habitat for this wasp. These results suggest that P. dominula could potentially establish across more of the country and expand its invaded range. Information provided by these models may guide conservation and biosecurity management by highlighting key areas where prevention and mitigation should be prioritized. </p><p>In chapter 3, I used molecular diet analysis to investigate the range of prey being utilised by P. dominula in New Zealand. Using DNA barcoding, larval gut contents of P. dominula and another closely related species, Polistes chinensis, were analysed to identify what species were present in the diet of both wasps. Butterflies and moths (Lepidoptera) were found to be the most highly represented order in both species’ diets. True bugs (Hemiptera) and flies (Diptera) were also abundant. Both wasps were shown to consume a range of native and introduced species including a number of agricultural pests. P. dominula was found to utilise a wider range of prey than P. chinensis. This more diverse prey range, combined with known differences in nesting behaviour, suggest that P. dominula may represent a more significant threat to invertebrate diversity than the already well-established P. chinensis. These results may inform conservation and biosecurity managers on which species are most at risk where this new invasive wasp becomes established. </p><p>This thesis provides insights into the potential impacts of a new invasive species to New Zealand. Both chapters represent the first time that these methods have been used to study P. dominula. This work highlights the need for continued monitoring of wasp populations throughout New Zealand, especially in regions highlighted as vulnerable to P. dominula establishment. We also suggest the need to prioritise the conservation of ‘at-risk’ species in coastal and human-altered habitats. Increased public engagement through the citizen-science initiatives should be encouraged while more research into management and control methods is recommended.</p>

Genetic variation in Trithuria inconspicua and T. filamentosa (Hydatellaceae): a new subspecies and a hypothesis of apomixis arising within a predominantly selfing lineage

2019 ◽  
Author(s):  
Rob D. Smissen ◽  
Kerry A. Ford ◽  
Paul D. Champion ◽  
Peter B. Heenan
Keyword(s):  
Genetic Variation ◽  
New Zealand ◽  
Morphological Variation ◽  
Genetic Distances ◽  
Herbarium Specimens ◽  
Minimum Evolution ◽  
The North ◽  
Genetic Groups ◽  
Morphological Differences ◽  
High Level

While examining herbarium specimens of Trithuria inconspicua Cheeseman, we observed differences in the stigmatic hairs among plants from New Zealand’s North and South Islands. This motivated us to assess genetic and morphological variation within this species and its sister T. filamentosa Rodway from Tasmania. Samples were collected from lakes in the three disjunct geographic areas where the two species occur. Genetic variation in both species was assessed with simple sequence-repeat (SSR, microsatellite) markers and analyses of genetic distances. We also compared the morphology of northern and southern New Zealand T. inconspicua using fresh material. Samples of each species clustered together in a minimum evolution tree built from genetic distances. Trithuria filamentosa had more genetic diversity than did T. inconspicua. Within T. inconspicua, plants from lakes in the North Island and the South Island formed discrete genetic groups diagnosable by subtle morphological differences. Low levels of heterozygosity in both species are consistent with a high level of selfing, as suggested for other co-sexual Trithuria species, but unusual for a putative apomict. On the basis of genetic and morphological variation, we propose recognition of the northern New Zealand and southern New Zealand lineages of T. inconspicua at subspecies rank.

scholarly journals The stratigraphy of the Neogene-Quaternary succession in the southwest Netherlands from the Schelphoek borehole (42G4-11/42G0022) – a sequence-stratigraphic approach

2007 ◽  
Vol 86 (4) ◽  
pp. 317-332 ◽  
Author(s):  
A.A. Slupik ◽  
F.P. Wesselingh ◽  
A.C. Janse ◽  
J.W.F. Reumer
Keyword(s):  
The Netherlands ◽  
Coastal Area ◽  
Late Quaternary ◽  
Tidal Channel ◽  
The South ◽  
Glacial Cycles ◽  
Sequence Stratigraphic ◽  
The North ◽  
Mammal Fauna

AbstractWe investigate the stratigraphy of Neogene and Quaternary intervals of the Schelphoek borehole (Schouwen, Zeeland, the Netherlands). The Breda Formation (Miocene-Zanclean) contains three sequences separated by hiatuses. The Oosterhout Formation (Zanclean-Piacenzian) contains at least two sequences. This formation is overlain by seven sequences of the Gelasian Maassluis Formation that almost certainly represent glacial cycles. The three lowermost sequences are provisionally assigned to the Praetiglian (MIS 96, MIS 98 and MIS 100). A large hiatus exists between the top of the Maassluis Formation and the base of the late Middle to Late Quaternary succession. Due to extensivein situreworking of older strata (including fossils) at the base of several of the formations, their exact boundaries are difficult to establish. The Neogene succession in the Schelphoek borehole is compared to the stratigraphic successions in the Antwerp area to the south and the Dutch coastal area and continental platform to the north. Finally, the stratigraphic context of the Gelasian (‘Tiglian’) mammal fauna dredged from the bottom of a major tidal channel in the adjacent Oosterschelde is assessed by comparison with the Schelphoek borehole.

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