Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

10.26686/wgtn.16997824 ◽

2021 ◽

Author(s):

◽

Hayden Murray Smith

Keyword(s):

New Zealand ◽

Genetic Structure ◽

Mitochondrial Genome ◽

Control Region ◽

Fish Species ◽

Isolation By Distance ◽

Population Expansion ◽

Phylogeographic Structure ◽

Genetic Population ◽

Biological Trait

This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.

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Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

10.7287/peerj.preprints.3284v1 ◽

2017 ◽

Author(s):

Md Rakeb-Ul Islam ◽

Daniel J Schmidt ◽

David A Crook ◽

Jane M Hughes

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Cryptic Species ◽

Isolation By Distance ◽

Gene Tree ◽

Phylogeographic Structure ◽

Genetic Structuring ◽

River Population ◽

Genetic Population ◽

Eastern Australia

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.

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Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

10.7287/peerj.preprints.3284 ◽

2017 ◽

Author(s):

Md Rakeb-Ul Islam ◽

Daniel J Schmidt ◽

David A Crook ◽

Jane M Hughes

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Cryptic Species ◽

Isolation By Distance ◽

Gene Tree ◽

Phylogeographic Structure ◽

Genetic Structuring ◽

River Population ◽

Genetic Population ◽

Eastern Australia

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.

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Population genetics of Pampus echinogaster along the Pacific coastline of China: insights from the mitochondrial DNA control region and microsatellite molecular markers

Marine and Freshwater Research ◽

10.1071/mf17218 ◽

2018 ◽

Vol 69 (6) ◽

pp. 971 ◽

Cited By ~ 6

Author(s):

Yuan Li ◽

Longshan Lin ◽

Na Song ◽

Yan Zhang ◽

Tianxiang Gao

Keyword(s):

Mitochondrial Dna ◽

Molecular Markers ◽

Genetic Structure ◽

Control Region ◽

Population Expansion ◽

Phylogeographic Structure ◽

Dispersal Ability ◽

Recent Population Expansion ◽

Mitochondrial Dna Control Region ◽

High Dispersal

Genetic variation among seven populations of Pampus echinogaster collected from the coastal waters of China was investigated based on the mitochondrial DNA control region and microsatellite molecular markers. The results revealed a high level of genetic diversity that may be related primarily to the life history traits and diverse habitats of this species. Analysis of the genetic structure and migration of P. echinogaster revealed weak genetic differentiation among populations, with an absence of a phylogeographic structure, indicating relatively high genetic homogeneity that may be associated with a recent population expansion event. The complex migratory and high dispersal ability of ichthyoplankton, as well as China’s offshore circulation, may have played important roles in shaping the current genetic structure of P. echinogaster. Unlike stock division in conventional fisheries, the present study found no significant differences among the P. echinogaster populations, all of which were panmictic. Therefore, in addition to accounting for conventional fishery stocks, a comprehensive assessment should be conducted by considering the phylogenetic structure among different populations.

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Genetic population structure of the monogenean parasite Gyrodactylus thymalli and its host European grayling (Thymallus thymallus) in a large Norwegian lake

Hydrobiologia ◽

10.1007/s10750-020-04431-7 ◽

2020 ◽

Author(s):

Ruben Alexander Pettersen ◽

Claudia Junge ◽

Kjartan Østbye ◽

Tor Atle Mo ◽

Leif Asbjørn Vøllestad

Keyword(s):

Genetic Structure ◽

Evolutionary Biology ◽

Isolation By Distance ◽

Genetic Structuring ◽

Thymallus Thymallus ◽

Homing Behavior ◽

Genetic Population ◽

Monogenean Parasite ◽

European Grayling ◽

Genetic Clusters

Abstract Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.

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Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa033 ◽

2020 ◽

Vol 130 (1) ◽

pp. 49-60

Author(s):

Kirsten M Donald ◽

Graham A McCulloch ◽

Ludovic Dutoit ◽

Hamish G Spencer

Keyword(s):

Population Structure ◽

Gene Flow ◽

New Zealand ◽

Genetic Structure ◽

Geographic Area ◽

Null Alleles ◽

Phylogeographic Structure ◽

Large Geographic Area ◽

Oceanic Currents ◽

Minimal Evidence

Abstract We examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).

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Recent and rapid colonization of the Lesser Sundas Archipelago from adjacent Sundaland by seven amphibian and reptile species

10.1101/571471 ◽

2019 ◽

Author(s):

Sean B. Reilly ◽

Alexander L. Stubbs ◽

Benjamin R. Karin ◽

Evy Arida ◽

Djoko T. Iskandar ◽

...

Keyword(s):

Genetic Structure ◽

Continental Shelf ◽

Population Expansion ◽

Phylogeographic Structure ◽

Recent Common Ancestor ◽

Stepping Stones ◽

Terrestrial Vertebrate ◽

Most Recent Common Ancestor ◽

Short Time Span ◽

Genetic Signatures

AbstractThe Lesser Sundas Archipelago is comprised of two parallel chains of islands that extend between the Asian continental shelf (Sundaland) and Australo-Papuan continental shelf (Sahul). These islands have served as stepping-stones for taxa dispersing between the Asian and Australo-Papuan biogeographic realms. While the oceanic barriers have prevented many species from colonizing the archipelago, a number of terrestrial vertebrate species have colonized the islands either by rafting/swimming or human introduction. Here we examine phylogeographic structure within the Lesser Sundas for three snake, two lizard, and two frog species that each have a Sunda Shelf origin. These species are suspected to have recently colonized the archipelago, though all have inhabited the Lesser Sundas for over 100 years. We sequenced mtDNA from 230 samples to test whether there is sufficiently deep genetic structure within any of these taxa to reject human-mediated introduction. Additionally, we tested for genetic signatures of population expansion consistent with recent introduction, and estimated the ages of Lesser Sundas clades, if any exist. Our results show little to no genetic structure between populations on different islands in five species, and moderate structure in two species. Nucleotide diversity is low for all species, and the ages of the most recent common ancestor for species with monophyletic Lesser Sundas lineages date to the Holocene or late Pleistocene. These results support the hypothesis that these species entered the archipelago relatively recently and either naturally colonized or were introduced by humans to most of the islands within the archipelago within a short time span.

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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 ◽

Population Genetic Structure ◽

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.

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

10.1101/239855 ◽

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.

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

10.26686/wgtn.17009387 ◽

2021 ◽

Author(s):

◽

Clare Louise Gebbie

Keyword(s):

New Zealand ◽

Genetic Structure ◽

Population Genetic Structure ◽

Dna Markers ◽

Microsatellite Dna ◽

Population Genetic ◽

Current Knowledge ◽

Isolation By Distance ◽

Genetic Connectivity ◽

Microsatellite Dna Markers

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.

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