Population genetic structure of New Zealand blue cod (Parapercis colias) based on mitochondrial and microsatellite DNA markers

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Current Knowledge ◽

Isolation By Distance ◽

Genetic Connectivity ◽

Parapercis colias (blue cod) is an endemic temperate reef fish that supports an important commercial and recreational fishery in New Zealand. However, concerns have been raised about localized stock depletion, and multiple lines of evidence have suggested P. colias may form several biologically distinct populations within the New Zealand Exclusive Economic Zone. Mark and recapture studies along with otolith and stable isotope studies have indicated that individuals are sedentary with very limited movement beyond the scale of 10-20km. The primary goal of this research was to advance the current knowledge of P. colias population genetic structure. This information can be incorporated into stock assessment models with the aim of improving the management of the P. colias fishery. This study made use of 454 pyrosequencing technology to isolate and develop the first set of microsatellite DNA markers for P. colias. These seven microsatellite loci, along with mitochondrial control region sequences, were used to determine the levels of genetic variation and differentiation between sites around the New Zealand coastline, including the Chatham Islands. Significant differentiation was observed between the Chatham Islands and mainland New Zealand sample sites, indicating that these two regions form distinct populations. Interpretation of the results for the mainland sites was more complex. Mitochondrial sequence data detected no significant pairwise differentiation between mainland sites, although a pattern of isolation-by-distance was observed. However, evidence for genetic differentiation among mainland sites was weak based on the microsatellite DNA analysis. Although pairwise Gѕт levels were significant in some sites, this was not reflected in principal component analysis or Bayesian structure analysis. It is likely that through long range dispersal, migration is at or above the threshold for genetic connectivity, but below a level necessary for demographic connectivity. This is indicated by both the genetic structure reported here, along with previous studies showing limited dispersal of P. colias.

Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.)

Genome ◽

10.1139/gen-43-1-15 ◽

2000 ◽

Vol 43 (1) ◽

pp. 15-21 ◽

Cited By ~ 5

Author(s):

L. Perera ◽

J.R. Russell ◽

J. Provan ◽

W. Powell

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Cocos Nucifera ◽

Population genetic structure of Catla catla (Hamilton) revealed by microsatellite DNA markers

Aquaculture ◽

10.1016/j.aquaculture.2005.02.012 ◽

2005 ◽

Vol 246 (1-4) ◽

pp. 151-160 ◽

Cited By ~ 33

Author(s):

Md. Samsul Alam ◽

Md. Shahidul Islam

Keyword(s):

Genetic Structure ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Catla Catla ◽

Population genetic structure of Central African Trypanosoma brucei gambiense isolates using microsatellite DNA markers

Infection Genetics and Evolution ◽

10.1016/j.meegid.2009.09.019 ◽

2010 ◽

Vol 10 (1) ◽

pp. 68-76 ◽

Cited By ~ 30

Author(s):

Gustave Simo ◽

Flobert Njiokou ◽

Christopher Tume ◽

Smiths Lueong ◽

Thierry De Meeûs ◽

...

Keyword(s):

Genetic Structure ◽

Trypanosoma Brucei ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Trypanosoma Brucei Gambiense ◽

Population genetic structure of three major river Populations of rohu,Labeo rohita (Cyprinidae: Cypriniformes) using microsatellite DNA markers

Genes & Genomics ◽

10.1007/bf03191137 ◽

2009 ◽

Vol 31 (1) ◽

pp. 43-51 ◽

Cited By ~ 9

Author(s):

Md. Samsul Alam ◽

Marya Jahan ◽

Md. Mokarrom Hossain ◽

Md. Shahidul Islam

Keyword(s):

Genetic Structure ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Labeo Rohita ◽

Microsatellite Dna Markers ◽

Major River

POPULATION GENETIC STRUCTURE OF AN ENDANGERED KALIBAUS, Labeo calbasu (HAMILTON, 1822) REVEALED BY MICROSATELLITE DNA MARKERS

Croatian Journal of Fisheries ◽

10.14798/71.2.648 ◽

2013 ◽

Vol 71 (2) ◽

pp. 65-73

Author(s):

Mohammad Robiul Hasan ◽

Mohammad Nahiduzzaman ◽

Mostafa Ali Reza Hossain ◽

Mohammad Samsul Alam

Keyword(s):

Genetic Structure ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Characterisation of the Mitochondrial Genome and the Population Genetics of Polyprion Oxygeneios (Hapuku) from Around New Zealand

10.26686/wgtn.17011832.v1 ◽

2021 ◽

Author(s):

◽

Henry Somerset Lane

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

New Zealand ◽

Genetic Structure ◽

Mitochondrial Genome ◽

Microsatellite Dna ◽

Population Genetic ◽

The West ◽

Polyprion Oxygeneios

Polyprion oxygeneios (hapuku) is an important commercial and recreational fishery species within New Zealand. Moreover, P. oxygeneios are currently being developed as a high-value New Zealand aquaculture species. There have been no previous studies on New Zealand’s P. oxygeneios that have been able to detect genetic differences among samples, which may be of use to either broodstock or fisheries managers. An understanding of the genetic structure of commercially harvested species maximises the potential for sustainable harvesting through effective management schemes. The primary goal of this thesis was to investigate the population genetic structure of P. oxygeneios using molecular markers to analyse samples collected from sites within New Zealand’s Exclusive Economic Zone (EEZ). The DNA sequence of the whole mitochondrial genome of P. oxygeneios was determined and it showed a similar structure and gene organisation to that of other species across a wide range of taxa. A set of species-specific control region primers was developed for P. oxygeneios and Polyprion americanus, and additional primers were designed for the 16S and ND6 genes of P. oxygeneios. A ~488 bp portion of the mitochondrial DNA (mtDNA) control region sequence from 274 individuals, and genotypes from 259 individuals using nine polymorphic microsatellite loci, were used to investigate the phylogeography and population genetic structure of P. oxygeneios. The mitochondrial DNA data failed to detect any significant differentiation between sample sites. However, the microsatellite DNA analyses showed that individuals sampled from the west coast of the South Island (Hokitika) were genetically distinct from individuals sampled at all other New Zealand sites. These two groups might be representative of two discrete populations of P. oxygeneios within New Zealand’s EEZ. These results suggest that the west coast South Island P. oxygeneios fishery should continue to be managed as a separate stock, with some possible revision of the Cook Strait fishery required. Analyses of the mtDNA and microsatellite DNA data of P. oxygeneios broodstock held at NIWA’s Bream Bay Aquaculture Park showed that they were not significantly differentiated from the wild populations (excluding Hokitika). Simulations also described the appropriate sampling efforts required to capture an appropriate level of genetic diversity when either establishing a new broodstock or supplementing an existing broodstock with new individuals. Continued management of the broodstock will be required to maintain the high levels of genetic diversity that have been captured in the founding broodstock in future generations.

A population genetic analysis of the New Zealand spotty (Notolabrus celidotus) using mitochondrial DNA and microsatellite DNA markers

10.26686/wgtn.17012603.v1 ◽

2021 ◽

Author(s):

◽

Rachel Zoe Wilcox

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

New Zealand ◽

Control Region ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Mtdna Control Region ◽

Mtdna Sequences ◽

Notolabrus celidotus (the New Zealand spotty) is a common rocky reef species that is endemic to New Zealand. This species is the most abundant demersal reef fish in New Zealand, and is distributed throughout the North and South Islands, and Stewart Island. Notolabrus celidotus consumes a wide variety of small invertebrates, and juveniles are reliant on coastal kelp forests as nursery habitats. Because N. celidotus is such a common species on New Zealand rocky reefs it is a good model species for population genetic studies. The primary goal of this research was to investigate new genetic markers and add new sample locations to bolster previous genetic population data from N. celidotus. The thesis research utilised DNA sequences obtained from a 454 massively parallel DNA sequencer and reports six new microsatellite loci for N. celidotus. These loci are the first microsatellite DNA markers to be developed for this species. Additional mitochondrial DNA (mtDNA) control region sequences were obtained from new samples of N. celidotus and combined with previously reported mtDNA sequences. Increasing the sample size improved the genetic coverage of N. celidotus populations around coastal New Zealand. The mtDNA sequences were analysed to examine the population connectivity and demographic history of N. celidotus. The microsatellite DNA loci reported in this study were also used to examine the levels of genetic diversity and population structure in N. celidotus. Results of the combined genetic analyses revealed extremely high levels of genetic diversity among the population sample of the mtDNA control region. Both the mitochondrial DNA and microsatellite DNA analyses showed a distinct lack of population genetic structuring, which suggests there is constant mixing of N. celidotus among sites. The results of this study have the potential to inform the expectations about the genetic structure of closely related wrasse species, such as Notolabrus fucicola, as well as other coastal species that have a similar life history, dispersal power, and New Zealand-wide distribution.

A population genetic analysis of the New Zealand spotty (Notolabrus celidotus) using mitochondrial DNA and microsatellite DNA markers

10.26686/wgtn.17012603 ◽

2021 ◽

Author(s):

◽

Rachel Zoe Wilcox

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

New Zealand ◽

Control Region ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Mtdna Control Region ◽

Mtdna Sequences ◽

Notolabrus celidotus (the New Zealand spotty) is a common rocky reef species that is endemic to New Zealand. This species is the most abundant demersal reef fish in New Zealand, and is distributed throughout the North and South Islands, and Stewart Island. Notolabrus celidotus consumes a wide variety of small invertebrates, and juveniles are reliant on coastal kelp forests as nursery habitats. Because N. celidotus is such a common species on New Zealand rocky reefs it is a good model species for population genetic studies. The primary goal of this research was to investigate new genetic markers and add new sample locations to bolster previous genetic population data from N. celidotus. The thesis research utilised DNA sequences obtained from a 454 massively parallel DNA sequencer and reports six new microsatellite loci for N. celidotus. These loci are the first microsatellite DNA markers to be developed for this species. Additional mitochondrial DNA (mtDNA) control region sequences were obtained from new samples of N. celidotus and combined with previously reported mtDNA sequences. Increasing the sample size improved the genetic coverage of N. celidotus populations around coastal New Zealand. The mtDNA sequences were analysed to examine the population connectivity and demographic history of N. celidotus. The microsatellite DNA loci reported in this study were also used to examine the levels of genetic diversity and population structure in N. celidotus. Results of the combined genetic analyses revealed extremely high levels of genetic diversity among the population sample of the mtDNA control region. Both the mitochondrial DNA and microsatellite DNA analyses showed a distinct lack of population genetic structuring, which suggests there is constant mixing of N. celidotus among sites. The results of this study have the potential to inform the expectations about the genetic structure of closely related wrasse species, such as Notolabrus fucicola, as well as other coastal species that have a similar life history, dispersal power, and New Zealand-wide distribution.

Characterisation of the Mitochondrial Genome and the Population Genetics of Polyprion Oxygeneios (Hapuku) from Around New Zealand

10.26686/wgtn.17011832 ◽

2021 ◽

Author(s):

◽

Henry Somerset Lane

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

New Zealand ◽

Genetic Structure ◽

Mitochondrial Genome ◽

Microsatellite Dna ◽

Population Genetic ◽

The West ◽

Polyprion Oxygeneios

Polyprion oxygeneios (hapuku) is an important commercial and recreational fishery species within New Zealand. Moreover, P. oxygeneios are currently being developed as a high-value New Zealand aquaculture species. There have been no previous studies on New Zealand’s P. oxygeneios that have been able to detect genetic differences among samples, which may be of use to either broodstock or fisheries managers. An understanding of the genetic structure of commercially harvested species maximises the potential for sustainable harvesting through effective management schemes. The primary goal of this thesis was to investigate the population genetic structure of P. oxygeneios using molecular markers to analyse samples collected from sites within New Zealand’s Exclusive Economic Zone (EEZ). The DNA sequence of the whole mitochondrial genome of P. oxygeneios was determined and it showed a similar structure and gene organisation to that of other species across a wide range of taxa. A set of species-specific control region primers was developed for P. oxygeneios and Polyprion americanus, and additional primers were designed for the 16S and ND6 genes of P. oxygeneios. A ~488 bp portion of the mitochondrial DNA (mtDNA) control region sequence from 274 individuals, and genotypes from 259 individuals using nine polymorphic microsatellite loci, were used to investigate the phylogeography and population genetic structure of P. oxygeneios. The mitochondrial DNA data failed to detect any significant differentiation between sample sites. However, the microsatellite DNA analyses showed that individuals sampled from the west coast of the South Island (Hokitika) were genetically distinct from individuals sampled at all other New Zealand sites. These two groups might be representative of two discrete populations of P. oxygeneios within New Zealand’s EEZ. These results suggest that the west coast South Island P. oxygeneios fishery should continue to be managed as a separate stock, with some possible revision of the Cook Strait fishery required. Analyses of the mtDNA and microsatellite DNA data of P. oxygeneios broodstock held at NIWA’s Bream Bay Aquaculture Park showed that they were not significantly differentiated from the wild populations (excluding Hokitika). Simulations also described the appropriate sampling efforts required to capture an appropriate level of genetic diversity when either establishing a new broodstock or supplementing an existing broodstock with new individuals. Continued management of the broodstock will be required to maintain the high levels of genetic diversity that have been captured in the founding broodstock in future generations.