scholarly journals A first investigation into the evolutionary relationships, population structure and demographic history of New Zealand Trevally (Pseudocaranx georgianus) and its implications for fisheries management

2021 ◽  
Author(s):  
◽  
Leah Kemp
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Western Australia ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Whole Genome Sequence ◽  
Coi Gene ◽  
P Value

<p>Pseudocaranx georgianus is a commercially important fishery in New Zealand. Currently, the management of this fishery assumes that Quota Management Areas comprise single biological stocks of a single species. However, little is known regarding the population structure of New Zealand P. georgianus and morphological data suggests that a cryptic Pseudocaranx species is included within these fisheries.  Whole genome sequence data was used to assemble and describe the first P. georgianus mitogenome. Primers were developed to produce the first genetic sequence data for New Zealand P. georgianus. The cytochrome c oxidase subunit I (COI) gene was sequenced for fourteen P. georgianus from New Zealand waters. These were compared phylogenetically with existing COI sequence data for P. georgianus from Australia and other Pseudocaranx species from a world-wide distribution. The hyper-variable control region of 304 P. georgianus sampled throughout New Zealand’s North Island and 68 P. georgianus from three locations in Western Australia were also sequenced. These sequences were used to explore the population structure and demographic history of New Zealand P. georgianus using haplotype networks, AMOVA’s, genetic diversity measures, Tajima’s D, Fu’s F and Bayesian migration analyses.  The P. georgianus mitogenome is typical of Cartilaginous fish species showing no major gene rearrangements, typical gene region lengths and stop and start codons. While assembling the P. georgianus mitogenome, this thesis demonstrates the importance of key methodological choices made when assembling mitogenomes from whole genome sequence data in silco in Geneious version 11.1. The choice of reference mitogenome has the largest influence on the quality of the assembly, impacting the annotation of the final mitogenome and the resolution of uncertain DNA regions. Increasing the number of mapping iterations increased the quality of the assembly but has a limited ability to mitigate the effects of using a poor reference mitogenome. Overall, I demonstrate the need to investigate and report the quality of published mitogenomes.   All Pseudocaranx species were monophyletic on the COI gene, supporting the current taxonomy of the Pseudocaranx complex. P. georgianus from Western Australia and New Zealand’s North Island represent a monophyletic clade pending a taxonomic verification that two Pseudocaranx dentex sampled in Australia are in fact P. georgianus.   No evidence was found to suggest that either of the New Zealand or Western Australian populations of P. georgianus are isolated by distance or clearly structured as distinct stocks. However, some populations of New Zealand P. georgianus were genetically distinct, including fish sampled from Raglan and the Bay of Plenty (FST of 0.02698 (p-value: 0.00901+-0.0091) as well as the North Cape and North Taranaki Bight (FST: 0.02698, p-value: 0.00901+-0.0091).   Some evidence was found to support the claim that P. georgianus along the west coast of New Zealand’s North Island is structured and no evidence was found to refute the claim that fish from the Bay of Plenty are the same biological stock as fish from TRE2. Highly divergent control region sequences of fish sampled from Three Kings Islands and the Kermadec Islands suggest that these fish could be a species distinct from P. georgianus. Two genetically distinct populations of P. georgianus were identified in New Zealand’s North Island and Western Australia (FST: 0.03517, p-value < 0.001), but further research would be required to determine if they are distinct species or populations. One juvenile population sampled in Whangarei had a high level of genetic connectivity with adult P. georgianus throughout New Zealand’s North Island, likely reflecting the batch spawning and occasional long-distance migration behaviour of P. georgianus.  Negative Tajima’s D and Fu’s F statistics (D: -1.50612, p-value: 0.018; F: -23.54376, p-value: 0.011), unimodal mismatch distributions and skyline plots indicate that the New Zealand P. georgianus population has undergone a population expansion, possibly resulting from a geographic range expansion.The Western Australian population may also have undergone a population expansion (D: -1.27903, p-value: 0.086; F: -24.11497, p-value < 0.00001). However, a multimodal mismatch distribution (Harpending’s Raggedness index: 0.00454591, p-value: 0.02) indicated that there is some stability in the size of this population.   This thesis is a first genetic investigation into New Zealand P. georgianus and has provided important biological insights into this species. Valuable information is revealed which will inform the management of New Zealand P. georgianus fisheries as inputs for stock assessment models. Additionally, several future research directions have been revealed which will further extend our knowledge of this taonga. For example, future genetic and taxonomic analyses may reveal a cryptic Pseudocaranx species occurring in the Three Kings and Kermadec Islands.</p>

scholarly journals A first investigation into the evolutionary relationships, population structure and demographic history of New Zealand Trevally (Pseudocaranx georgianus) and its implications for fisheries management

2021 ◽  
Author(s):  
◽  
Leah Kemp
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Western Australia ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Whole Genome Sequence ◽  
Coi Gene ◽  
P Value

<p>Pseudocaranx georgianus is a commercially important fishery in New Zealand. Currently, the management of this fishery assumes that Quota Management Areas comprise single biological stocks of a single species. However, little is known regarding the population structure of New Zealand P. georgianus and morphological data suggests that a cryptic Pseudocaranx species is included within these fisheries.  Whole genome sequence data was used to assemble and describe the first P. georgianus mitogenome. Primers were developed to produce the first genetic sequence data for New Zealand P. georgianus. The cytochrome c oxidase subunit I (COI) gene was sequenced for fourteen P. georgianus from New Zealand waters. These were compared phylogenetically with existing COI sequence data for P. georgianus from Australia and other Pseudocaranx species from a world-wide distribution. The hyper-variable control region of 304 P. georgianus sampled throughout New Zealand’s North Island and 68 P. georgianus from three locations in Western Australia were also sequenced. These sequences were used to explore the population structure and demographic history of New Zealand P. georgianus using haplotype networks, AMOVA’s, genetic diversity measures, Tajima’s D, Fu’s F and Bayesian migration analyses.  The P. georgianus mitogenome is typical of Cartilaginous fish species showing no major gene rearrangements, typical gene region lengths and stop and start codons. While assembling the P. georgianus mitogenome, this thesis demonstrates the importance of key methodological choices made when assembling mitogenomes from whole genome sequence data in silco in Geneious version 11.1. The choice of reference mitogenome has the largest influence on the quality of the assembly, impacting the annotation of the final mitogenome and the resolution of uncertain DNA regions. Increasing the number of mapping iterations increased the quality of the assembly but has a limited ability to mitigate the effects of using a poor reference mitogenome. Overall, I demonstrate the need to investigate and report the quality of published mitogenomes.   All Pseudocaranx species were monophyletic on the COI gene, supporting the current taxonomy of the Pseudocaranx complex. P. georgianus from Western Australia and New Zealand’s North Island represent a monophyletic clade pending a taxonomic verification that two Pseudocaranx dentex sampled in Australia are in fact P. georgianus.   No evidence was found to suggest that either of the New Zealand or Western Australian populations of P. georgianus are isolated by distance or clearly structured as distinct stocks. However, some populations of New Zealand P. georgianus were genetically distinct, including fish sampled from Raglan and the Bay of Plenty (FST of 0.02698 (p-value: 0.00901+-0.0091) as well as the North Cape and North Taranaki Bight (FST: 0.02698, p-value: 0.00901+-0.0091).   Some evidence was found to support the claim that P. georgianus along the west coast of New Zealand’s North Island is structured and no evidence was found to refute the claim that fish from the Bay of Plenty are the same biological stock as fish from TRE2. Highly divergent control region sequences of fish sampled from Three Kings Islands and the Kermadec Islands suggest that these fish could be a species distinct from P. georgianus. Two genetically distinct populations of P. georgianus were identified in New Zealand’s North Island and Western Australia (FST: 0.03517, p-value < 0.001), but further research would be required to determine if they are distinct species or populations. One juvenile population sampled in Whangarei had a high level of genetic connectivity with adult P. georgianus throughout New Zealand’s North Island, likely reflecting the batch spawning and occasional long-distance migration behaviour of P. georgianus.  Negative Tajima’s D and Fu’s F statistics (D: -1.50612, p-value: 0.018; F: -23.54376, p-value: 0.011), unimodal mismatch distributions and skyline plots indicate that the New Zealand P. georgianus population has undergone a population expansion, possibly resulting from a geographic range expansion.The Western Australian population may also have undergone a population expansion (D: -1.27903, p-value: 0.086; F: -24.11497, p-value < 0.00001). However, a multimodal mismatch distribution (Harpending’s Raggedness index: 0.00454591, p-value: 0.02) indicated that there is some stability in the size of this population.   This thesis is a first genetic investigation into New Zealand P. georgianus and has provided important biological insights into this species. Valuable information is revealed which will inform the management of New Zealand P. georgianus fisheries as inputs for stock assessment models. Additionally, several future research directions have been revealed which will further extend our knowledge of this taonga. For example, future genetic and taxonomic analyses may reveal a cryptic Pseudocaranx species occurring in the Three Kings and Kermadec Islands.</p>

scholarly journals Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

2017 ◽  
Author(s):  
Yeşerin Yıldırım ◽  
Marti J. Anderson ◽  
Selina Patel ◽  
Craig D. Millar ◽  
Paul B. Rainey
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Haplotype Network ◽  
Founding Population ◽  
Mtdna Sequence ◽  
Expansion Time ◽  
History Of

AbstractPleurobranchaea maculatais a rarely studied species of the Heterobranchia found throughout the south and western Pacific – and recently recorded in Argentina – whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history ofP. maculatapopulations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and theCOIandCytBregions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence from Argentinian sea slugs did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

scholarly journals Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

2020 ◽  
Author(s):  
P.C. Pretorius ◽  
T.B. Hoareau
Keyword(s):  
Population Size ◽  
Sea Level ◽  
Environmental Changes ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Population Level ◽  
Sea Level Changes ◽  
Reef Development ◽  
Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

Phylogeny and biogeography of the Australasian centipede Henicops (Chilopoda: Lithobiomorpha): A combined morphological and molecular approach

2006 ◽  
Vol 37 (3) ◽  
pp. 241-256 ◽  
Author(s):  
Donald Colgan ◽  
Gregory Edgecombe ◽  
Deirdre Sharkey
Keyword(s):  
New Zealand ◽  
Western Australia ◽  
New Caledonia ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
28S Rrna ◽  
Southeastern Australia ◽  
Lord Howe Island ◽  
Eastern Australia

AbstractThe lithobiomorph centipede Henicops is widely distributed in Australia and New Zealand, with five described species, as well as two species in New Caledonia and Lord Howe Island. Parsimony, maximum likelihood and Bayesian analyses of ca. 800 aligned bases of sequence data from 16S rRNA and 28S rRNA were conducted on a dataset including multiple individuals of Henicops species from populations sampled from different parts of species' geographic ranges, together with the allied henicopines Lamyctes and Easonobius. Morphological characters are included in parsimony analyses. Molecular and combined datasets unite species from eastern Australia and New Zealand to the exclusion of species from Western Australia, New Caledonia and Lord Howe Island. The molecular data favour these two geographic groupings as clades, whereas inclusion of morphology resolves New Caledonia, Lord Howe Island, southwest Western Australia and Queensland as successive sisters to southeastern Australia and New Zealand. The basal position of the Lord Howe Island species in the phylogeny favours a diversification of Australasian Henicops since the late Miocene unless the Lord Howe species originated in a biota that pre-dates the island. The molecular and combined data resolve the widespread morphospecies H. maculatus as paraphyletic, with its populations contributing to the geographic groupings New South Wales + New Zealand and Tasmania + Victoria.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

scholarly journals Molecular and morphological characterisation of new species in the trapdoor spider genus Aname (Araneae: Mygalomorphae: Nemesiidae) from the Pilbara bioregion of Western Australia

Zootaxa ◽  
2012 ◽  
Vol 3383 (1) ◽  
pp. 15 ◽  
Author(s):  
FRANCES S. B. HARVEY ◽  
VOLKER W. FRAMENAU ◽  
JANINE M. WOJCIESZEK ◽  
MICHAEL G. RIX ◽  
MARK S. HARVEY
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Western Australia ◽  
Adult Male ◽  
Sequence Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Morphological Characterisation ◽  
Mitochondrial Sequence

A study of selected species in the nemesiid spider genus Aname L. Koch, 1873 from the Pilbara bioregion of Western Australia was undertaken using molecular and morphological techniques. Bayesian and parsimony analyses of mitochondrial sequence data from the Cytochrome c Oxidase subunit I (COI) gene found evidence for four species, confirming our initial morphological examination of adult male specimens. These four species are here described as A. mellosa n. sp., A. aragog n. sp., A. ellenae n. sp. and A. marae n. sp. Only the female of A. mellosa n. sp. is described.

scholarly journals Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12639
Author(s):  
Hsiu-Chin Lin ◽  
Chia-Jung Tsai ◽  
Hui-Yu Wang
Keyword(s):  
Population Structure ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Demographic History ◽  
Ice Age ◽  
Fish Stock ◽  
Ecological Niches ◽  
Specific Information ◽  
Similar Species ◽  
Haplotype Networks

Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22–39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these differences, a single well-mixing fish stock, thus one management unit, was identified in each of the four species, presumably due to expansion of their population sizes predated the Last Glacial Maximum and a lack of distribution barrier. The most dominant T. japonicus, which have at least one magnitude higher effective population size than the others, show a unique abrupt size expansion event at 75 to 50-kilo years ago when the low sea level occurred during the ice age. Main conclusions The demographic history revealed by our genetic analyses advances understanding of the current distribution and population structure for these congeneric species. Moreover, the uncovered population structure provides insight into the assessment and management of these species. Such information complements contemporary knowledge about these species and enables us to forecast their ability to resist future environmental and anthropogenic disturbances.

scholarly journals Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data

Plant Disease ◽  
2017 ◽  
Vol 101 (5) ◽  
pp. 666-673 ◽  
Author(s):  
Marie-Claude Gagnon ◽  
Nicolas Feau ◽  
Angela L. Dale ◽  
Braham Dhillon ◽  
Richard C. Hamelin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Sequence ◽  
Sequence Data ◽  
Ornamental Plants ◽  
Phytophthora Ramorum ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
And Migration

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.

Sign in / Sign up

Export Citation Format

Share Document