Population Genetics of New Zealand Pagrus auratus and Genetic Variation of an Aquaculture Broodstock

<p>Fisheries and aquaculture are major contributors of nutrition and animal protein worldwide. Understanding the genetic variation and differentiation within and between wild populations is important for both sustainable fisheries management and selection of aquaculture broodstock. This study determined the genetic variation and differentiation of New Zealand Pagrus auratus based on mitochondrial DNA control region sequencing and microsatellite DNA genotyping. Low but significant differentiation was measured between several sample sites, but otherwise the population was genetically panmictic. The M-ratio test and Fu’s Fs statistics indicate that there may have been historical bottlenecks at all sample sites and a more recent bottleneck in the Tasman Bay. Two South Island sites were identified that had not been through recent bottlenecks and were not significantly differentiated from the Tasman Bay, which may provide a source of gene flow to aid its genetic recovery. Comparison of the broodstock and wild genetic variation indicate that the broodstock represented most of the genetic variation found in high frequency in wild populations, but further wild-caught individuals may be needed, based on the criteria used in several previous studies. Simulations indicate that adding approximately 20 and 48 wild-caught individuals from multiple populations to the current broodstock was needed to represent all genetic variation above a target frequency of 0.05 in the Tasman Bay and all sample sites, respectively.</p>

Population Genetics of New Zealand Pagrus auratus and Genetic Variation of an Aquaculture Broodstock

<p>Fisheries and aquaculture are major contributors of nutrition and animal protein worldwide. Understanding the genetic variation and differentiation within and between wild populations is important for both sustainable fisheries management and selection of aquaculture broodstock. This study determined the genetic variation and differentiation of New Zealand Pagrus auratus based on mitochondrial DNA control region sequencing and microsatellite DNA genotyping. Low but significant differentiation was measured between several sample sites, but otherwise the population was genetically panmictic. The M-ratio test and Fu’s Fs statistics indicate that there may have been historical bottlenecks at all sample sites and a more recent bottleneck in the Tasman Bay. Two South Island sites were identified that had not been through recent bottlenecks and were not significantly differentiated from the Tasman Bay, which may provide a source of gene flow to aid its genetic recovery. Comparison of the broodstock and wild genetic variation indicate that the broodstock represented most of the genetic variation found in high frequency in wild populations, but further wild-caught individuals may be needed, based on the criteria used in several previous studies. Simulations indicate that adding approximately 20 and 48 wild-caught individuals from multiple populations to the current broodstock was needed to represent all genetic variation above a target frequency of 0.05 in the Tasman Bay and all sample sites, respectively.</p>

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Unrestricted gene flow between two subspecies of translocated brushtail possums (Trichosurus vulpecula) in Aotearoa New Zealand

Two lineages of brushtail possums (Trichosurus vulpecula) were historically introduced to Aotearoa New Zealand, and these two subspecies have different phenotypic forms. Despite over 100 years of potential interbreeding, they appear to retain morphological differences, which may indicate reproductive isolation. We examined this using population samples from a confined landscape and scored each specimen for phenotype using a number of fur colour traits. This resulted in a bimodal trait distribution expected for segregated grey and black lineages. We also sought evidence for genetic partitioning based on spatial and temporal effects. Genetic structure and rates of genetic mixing were determined using seven neutral, species-specific nuclear microsatellite markers and mitochondrial DNA control region sequence. Genotype analyses indicated high levels of variation and mtDNA sequences formed two major haplogroups. Pairwise tests for population differentiation of these markers found no evidence of subdivision, indicating that these brushtail possums behave as a single randomly mating unit. Despite maintenance of two main colour phenotypes with relatively few intermediates, previous inference of assortative mating and anecdotes of distinct races, our data indicate that New Zealand brushtail possums can freely interbreed, and that in some locations they have formed completely mixed populations where neutral genetic markers are unrelated to phenotype. This has implications for effective pest management towards eradication.

Molecular identification of the first Galapagos fur seal (Arctocephalus galapagoensis) reported on the central coast of Oaxaca

Several sightings of different pinniped species have been recorded outside their typical areas of distribution. In May 2019, pinniped yearlings were sighted on 4 occasions on the central coast of Oaxaca, Mexico. One of them was found injured in La Escobilla (Oaxaca, Mexico) and was transported immediately to the Centro Mexicano de la Tortuga for rehabilitation. Visual identification of the species was inconclusive, as young individuals of several fur seal species can be very similar. A molecular analysis was thus performed to confirm the species. DNA was extracted from the individual, and a fragment of the mitochondrial DNA control region was sequenced and aligned with several sequences of other fur seal species. A parsimony analysis was performed, and the tree revealed that the individual was a Galapagos fur seal, Arctocephalus galapagoensis. This is the first record of this species on the central coast of Oaxaca. The atypical presence of this species in the country could be related to high sea surface temperatures associated with events such as El Niño.

First Record of a Novel Mitochondrial DNA Haplotype of a Marble Trout Lineage of Salmo Trutta in Turkey

A new record of a marble trout mtDNA haplotype known to be restricted to Adriatic basin (called marmoratus lineage within Salmo trutta complex) has been reported from Eşen Stream in the Aegean Sea basin of southeastern Turkey, based on sequence data of the mitochondrial DNA control region. The results of this study showed a single unique haplotype from this population, called MATR1. Phylogenetic analyses of this haplotype along with other haplotypes belonging to different mitochondrial DNA lineages of the S. trutta complex confirmed the existence of the marmoratus lineage in Turkey, suggesting a possible river capture between the Adriatic and Aegean Sea basins until the last (Würmian) marine regression.

Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep (Ovis aries) Breeds

To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.