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

<p>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.</p>

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

<p>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.</p>

Genetic Management of Wild and Translocated Black Rhinoceros in South Africa’s KwaZulu-Natal Region

<p>The African black rhinoceros (Diceros bicornis) is critically endangered. Like other megafauna, the species is managed in parks and is often translocated to expand their range into reserves where they have been extirpated. Management of genetic variation has been identified as an important consideration in long-term management plans for many wild and captive endangered species including black rhino. In this thesis I examined the contemporary levels of genetic variation within the black rhinoceros (D. b. minor) in KwaZulu-Natal (KZN), South Africa, and specifically the relict source population at Hluhluwe-iMfolozi Game Reserve (HiP), and how this information can be incorporated into management decisions to improve the long-term viability and persistence of the population. Previous studies have examined levels of genetic variation and differentiation among the three black rhino subspecies (D. b. minor, D. b. michaeli and D. b. bicornis) in an attempt to resolve their taxonomy and to establish baseline genetic assessments for managing populations. However, there has been a lack of genetic information based on the variable mitochondrial DNA (mtDNA) control region of the KZN metapopulation and a direct comparison of microsatellite variability between the D. b. minor populations of KZN and Zimbabwe. The specific objectives of this study were to: (1) determine the DNA sequence of the mtDNA control region of three subspecies and estimate the level of variation within the HiP source and KZN metapopulation and compare the results with D. b. minor outside KZN and the other two subspecies; (2) use ten microsatellite DNA markers to estimate the levels of heterozygosity and allelic diversity in the HiP source and KZN metapopulation and compare results to previously published microsatellite data (specifically native Zimbabwe D. b. minor; and (3) use VORTEX Population Viability Analysis (PVA) and HiP vital rates to model the effects of increasing population size and supplementation, and investigate what management scenarios would be most effective for minimizing the loss of genetic variation caused by genetic drift with HiP...</p>

Genetic Management of Wild and Translocated Black Rhinoceros in South Africa’s KwaZulu-Natal Region

<p>The African black rhinoceros (Diceros bicornis) is critically endangered. Like other megafauna, the species is managed in parks and is often translocated to expand their range into reserves where they have been extirpated. Management of genetic variation has been identified as an important consideration in long-term management plans for many wild and captive endangered species including black rhino. In this thesis I examined the contemporary levels of genetic variation within the black rhinoceros (D. b. minor) in KwaZulu-Natal (KZN), South Africa, and specifically the relict source population at Hluhluwe-iMfolozi Game Reserve (HiP), and how this information can be incorporated into management decisions to improve the long-term viability and persistence of the population. Previous studies have examined levels of genetic variation and differentiation among the three black rhino subspecies (D. b. minor, D. b. michaeli and D. b. bicornis) in an attempt to resolve their taxonomy and to establish baseline genetic assessments for managing populations. However, there has been a lack of genetic information based on the variable mitochondrial DNA (mtDNA) control region of the KZN metapopulation and a direct comparison of microsatellite variability between the D. b. minor populations of KZN and Zimbabwe. The specific objectives of this study were to: (1) determine the DNA sequence of the mtDNA control region of three subspecies and estimate the level of variation within the HiP source and KZN metapopulation and compare the results with D. b. minor outside KZN and the other two subspecies; (2) use ten microsatellite DNA markers to estimate the levels of heterozygosity and allelic diversity in the HiP source and KZN metapopulation and compare results to previously published microsatellite data (specifically native Zimbabwe D. b. minor; and (3) use VORTEX Population Viability Analysis (PVA) and HiP vital rates to model the effects of increasing population size and supplementation, and investigate what management scenarios would be most effective for minimizing the loss of genetic variation caused by genetic drift with HiP...</p>

Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences

In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.

Identification of the spaghetti eels (Moringua Sp) at Pelabuhan Ratu, Indonesia using mtDNA control region sequences

Eels are economic species of fish. The diversity of eel in the world is essential knowledge that we have to know to manage fisheries in the future. One of the types of eels is Moringua Sp. There are around 11 species of Moringua sp. in the world. In Indonesia, the diversity of Moringua sp. was no information yet. The aim of this study is to the identification of Moringua sp in Indonesia. The method used in this study is a sanger sequence method using the mtDNA control region. Base on this study, we found 726 and 745 base pairs alignment of Moringua by sequencing. The result of BLAST showed identically 87% to Moringua edwardsi and 89% as a Moringua microchir. The low percentage of BLAST yields shows that the sample used for this study is not strong enough to be declared as one of the Moringua species obtained from the results of BLAST analysis. Suspected of being another Moringua species. Thus, to get robust result, further research related to this species identification using COI or Cyt-b.