scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Geography is more important than life history in the recent diversification of the tiger salamander complex

2021 ◽  
Vol 118 (17) ◽  
pp. e2014719118
Author(s):  
Kathryn M. Everson ◽  
Levi N. Gray ◽  
Angela G. Jones ◽  
Nicolette M. Lawrence ◽  
Mary E. Foley ◽  
...  
Keyword(s):  
Life History ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Tiger Salamander ◽  
Life History Variation ◽  
Mexican Axolotl ◽  
Population Genetic Differentiation ◽  
Wide Range ◽  
Lineage Divergence

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

scholarly journals A differential expression of pyrethroid resistance genes in the malaria vector Anopheles funestus across Uganda is associated with patterns of gene flow

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0240743
Author(s):  
Maurice Marcel Sandeu ◽  
Charles Mulamba ◽  
Gareth D. Weedall ◽  
Charles S. Wondji
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Insecticide Resistance ◽  
Pyrethroid Resistance ◽  
Anopheles Funestus ◽  
Metabolic Resistance ◽  
Transcription Analysis ◽  
Genome Wide

Background Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya. Methods Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation. Results Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley. Conclusion The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.

Survival and behaviour of juvenile red rock lobster, Jasus edwardsii, on rocky reefs with varying predation pressure and habitat complexity

2008 ◽  
Vol 59 (3) ◽  
pp. 246 ◽  
Author(s):  
K. A. S. Mislan ◽  
Russ C. Babcock
Keyword(s):  
New Zealand ◽  
Kelp Forest ◽  
Predatory Fish ◽  
Rocky Reef ◽  
Rocky Reefs ◽  
Jasus Edwardsii ◽  
Fish Predators ◽  
Two Factors ◽  
Direct And Indirect Impacts ◽  
Indirect Impacts

The role of large predatory fish in coastal communities is generally unknown because of overfishing. In order to understand the direct and indirect impacts of these increased population sizes on coastal food chains, the effect of areas with more fish predators on the survival and behaviour of potential prey was assessed. Juvenile lobsters, Jasus edwardsii (10–20 mm carapace length), were tethered on rocky reefs inside and outside marine reserves in northeastern New Zealand to assess survival under differing predator densities. Since rocky reef habitats in northeastern New Zealand include zones of kelp forest and barren reef, a two-way factorial design was used to determine the effects of predators, habitat, and the interaction of these two factors on juvenile lobster survival. Overall, the results indicated that neither varying large fish density nor varying kelp density had direct impacts on the survival rate of juvenile lobsters. Laboratory manipulations demonstrated behavioural changes by juvenile lobsters such that when a large predatory fish was present, juvenile lobsters spent significantly less time moving, even when separated from the predator by a porous barrier. Thus areas with more fish predators may increase juvenile lobster survival but potentially at the cost of reduced feeding opportunities.

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

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).

Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

2012 ◽  
Vol 60 (2) ◽  
pp. 133
Author(s):  
Fiona E. Hogan ◽  
Marian Weaving ◽  
Gregory R. Johnston
Keyword(s):  
Population Genetics ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Reproductive Ecology ◽  
454 Sequencing ◽  
Urban Environments ◽  
Shotgun Sequencing ◽  
Target Species ◽  
Single Population ◽  
Polymorphic Microsatellite

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

scholarly journals Development and characterisation of microsatellite markers for the fungus Lasiodiplodia theobromae

2008 ◽  
Vol 34 (1) ◽  
pp. 55-57 ◽  
Author(s):  
José Emilson Cardoso ◽  
Michael James Wilkinson
Keyword(s):  
Microsatellite Markers ◽  
Fungal Pathogen ◽  
Population Studies ◽  
Higher Plants ◽  
Epidemiologic Studies ◽  
Preliminary Evaluation ◽  
Lasiodiplodia Theobromae ◽  
Tropical Regions ◽  
Wide Range ◽  
Polymorphic Microsatellite

Lasiodiplodia theobromae is an important fungal pathogen of higher plants from tropical and sub-tropical regions. The fungus infects divergent hosts in a wide range of environmental conditions, suggesting that it is highly variable. The aim of this study was to develop new polymorphic microsatellite markers from a Brazilian isolate of L. theobromae that can be used in population studies of this and related fungi. The nine microsatellite markers developed included six that revealed allelic polymorphisms among nine isolates of the disease collected from infected plants in Brazil. Preliminary evaluation of the markers suggested substantial genetic variability among Brazilian L. theobromae populations. These markers have potential utility for evolutionary and epidemiologic studies of this fungus.

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