jasus edwardsii
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Genome-wide SNP analysis reveals patterns of population differentiation and adaptation of red rock lobster Jasus edwardsii
<p>Declines in global marine finfish catches, which accounts for ~15% of the animal protein consumed by humans, has caused a 6-fold increase in total reported catch of invertebrates since 1950. This has led to the over-exploitation and decline of many marine invertebrate fisheries. The red rock lobster (Jasus edwardsii) fishery is New Zealand’s most economically valuable inshore fishery. The current management strategy relies on the assumption that the stock is comprised of a single panmictic population. However, more recent studies have challenged the genetic homogeneity of Jasus edwardsii across the Tasman sea and described high levels of self-recruitment in a Stewart Island subpopulation. A disregard for the underlying genetic structure in the management of a fishery can lead to excessive removal of individuals from populations contributing to the overall genetic diversity of the stock and thus reduce the species adaptability. The ability to adapt to new environments is particularly important in the context of global climate change and can significantly affect the long-term sustainability of the stock. Thus, the goal of this study was to identify specific patterns of genetic diversity of Jasus edwardsii population and provide an interpretation and assessment of the impact on the NZ fishery. The first objective was to optimize and validate molecular and bioinformatic protocols of Single Nucleotide Polymorphism (SNP) discovery for the red rock lobster Jasus edwardsii. The double digest restriction-site associated DNA (ddRADseq) protocol was optimized for the relatively large red rock lobster genome, which also has a high paralog content. The impact of bioinformatic processing on the population genetic inferences was then assessed by testing three different SNP discovery pipelines with the Rad-loci pipeline producing the most optimal marker discovery rate with a low level of missing data and a low SNP error rate. An analysis of technical replicates confirmed the reproducibility of both the molecular and bioinformatic protocols and also the validated the data generation process suitable for population genetic analyses. The second objective of my thesis was to investigate the genetic structure and population connectivity of adult red rock lobsters. The SNPs discovered were characterised as selectively neutral or under divergent selection (outlier) and both types of markers were analysed using Bayesian model-based clustering (STRUCTURE), non model-based multivariate analysis (Discriminant Analysis of Principal Components (DAPC)) and F-statistics. A lack of population differentiation using neutral genetic markers indicated a high level of gene flow and connectivity between populations. In contrast, there was evidence for selective pressure as a result of the analysis of outlier markers. Three main regions were identified: North-East NZ, North-West NZ and South NZ sub-populations, as part of a larger NZ metapopulation (FST ranged from 0.025 to 0.049, P < 0.001). The results of this study suggested that high levels of gene flow and connectivity are counteracted to some extent by the local selection that promotes the survival and reproduction of locally adapted genotypes. However, the strength of this selective pressure still permits low levels of survival and reproduction of non-optimal genotypes causing allele frequency homogenisation of the new generation of lobsters. The third objective was to investigate the levels of connectivity and adaptive divergence of the red rock lobster pueruli/juvenile lobsters for comparison with pattern of divergence of adult lobster in order to investigate the mechanisms of population structure formation. A suite of Bayesian clustering, non-model multivariate analysis and F-statistics were employed in the assessment of neutral and outlier markers developed for pueruli/juveniles. Similar to adult lobsters, pueruli/juveniles were characterised by a low level of divergence of the neutral markers indicating effective larvae dispersal. Outlier markers detected population differentiation patterns likely to originate from a phenotype – environment mismatch resulting in post-settlement mortality of non-adapted genotypes. The similarity between patterns of genetic divergence of adult lobsters and late juvenile/early juveniles indicates that post-settlement mortality, driven by local environmental conditions, has most likely occurred on earlier developmental stages of Jasus edwardsii, which were not possible to sample in my study. The final objective was to explore environment–genotype associations of Jasus edwardsii. Biological Environment Stepwise (BEST) analyses, redundancy analyses (RDA) and generalized linear modelling (GLM) consistently indicated a correlation between the annual amplitude of sea surface temperature (SST) and adaptive population divergence. In addition, an influence of spatial distribution on the patterns of adaptive population differentiation was also detected via RDA. From these results I propose a mechanism underlying the patterns of population differentiation discovered in Chapters 3 and 4: a latitudinal gradient of SST appears to be the selective force promoting the adaptive divergence of the lobster populations with local patterns of connectivity distorting the gradient and thus forming three distinct temperature adapted genotypes (North-West, North-East, and South). An environmental association analysis offered 43 candidate loci, which after alignment of transcriptome-mapped reference catalog sequences to annotated protein databases identified a candidate gene for thermal adaptation - UDP-glycosyltransferase (UGT). UGT is a detoxification enzyme involved in the metabolization of a variety of endogenous and environmental compounds and its activity and gene expression patterns have been linked to temperature. This study provides evidence for the local adaptations of the NZ population of Jasus edwardsii to SST, which together with the efficient mechanism of larval dispersal creates a system likely resilient to changes in temperature. This feature is important in the light of climate change-induced range shifts and supports the long-term sustainability of the red rock lobster fishery. The three genetically distinct regions identified coincide with existing boundaries of the management units and therefore do not require an adjustment of the current management regime.</p>
<p>Declines in global marine finfish catches, which accounts for ~15% of the animal protein consumed by humans, has caused a 6-fold increase in total reported catch of invertebrates since 1950. This has led to the over-exploitation and decline of many marine invertebrate fisheries. The red rock lobster (Jasus edwardsii) fishery is New Zealand’s most economically valuable inshore fishery. The current management strategy relies on the assumption that the stock is comprised of a single panmictic population. However, more recent studies have challenged the genetic homogeneity of Jasus edwardsii across the Tasman sea and described high levels of self-recruitment in a Stewart Island subpopulation. A disregard for the underlying genetic structure in the management of a fishery can lead to excessive removal of individuals from populations contributing to the overall genetic diversity of the stock and thus reduce the species adaptability. The ability to adapt to new environments is particularly important in the context of global climate change and can significantly affect the long-term sustainability of the stock. Thus, the goal of this study was to identify specific patterns of genetic diversity of Jasus edwardsii population and provide an interpretation and assessment of the impact on the NZ fishery. The first objective was to optimize and validate molecular and bioinformatic protocols of Single Nucleotide Polymorphism (SNP) discovery for the red rock lobster Jasus edwardsii. The double digest restriction-site associated DNA (ddRADseq) protocol was optimized for the relatively large red rock lobster genome, which also has a high paralog content. The impact of bioinformatic processing on the population genetic inferences was then assessed by testing three different SNP discovery pipelines with the Rad-loci pipeline producing the most optimal marker discovery rate with a low level of missing data and a low SNP error rate. An analysis of technical replicates confirmed the reproducibility of both the molecular and bioinformatic protocols and also the validated the data generation process suitable for population genetic analyses. The second objective of my thesis was to investigate the genetic structure and population connectivity of adult red rock lobsters. The SNPs discovered were characterised as selectively neutral or under divergent selection (outlier) and both types of markers were analysed using Bayesian model-based clustering (STRUCTURE), non model-based multivariate analysis (Discriminant Analysis of Principal Components (DAPC)) and F-statistics. A lack of population differentiation using neutral genetic markers indicated a high level of gene flow and connectivity between populations. In contrast, there was evidence for selective pressure as a result of the analysis of outlier markers. Three main regions were identified: North-East NZ, North-West NZ and South NZ sub-populations, as part of a larger NZ metapopulation (FST ranged from 0.025 to 0.049, P < 0.001). The results of this study suggested that high levels of gene flow and connectivity are counteracted to some extent by the local selection that promotes the survival and reproduction of locally adapted genotypes. However, the strength of this selective pressure still permits low levels of survival and reproduction of non-optimal genotypes causing allele frequency homogenisation of the new generation of lobsters. The third objective was to investigate the levels of connectivity and adaptive divergence of the red rock lobster pueruli/juvenile lobsters for comparison with pattern of divergence of adult lobster in order to investigate the mechanisms of population structure formation. A suite of Bayesian clustering, non-model multivariate analysis and F-statistics were employed in the assessment of neutral and outlier markers developed for pueruli/juveniles. Similar to adult lobsters, pueruli/juveniles were characterised by a low level of divergence of the neutral markers indicating effective larvae dispersal. Outlier markers detected population differentiation patterns likely to originate from a phenotype – environment mismatch resulting in post-settlement mortality of non-adapted genotypes. The similarity between patterns of genetic divergence of adult lobsters and late juvenile/early juveniles indicates that post-settlement mortality, driven by local environmental conditions, has most likely occurred on earlier developmental stages of Jasus edwardsii, which were not possible to sample in my study. The final objective was to explore environment–genotype associations of Jasus edwardsii. Biological Environment Stepwise (BEST) analyses, redundancy analyses (RDA) and generalized linear modelling (GLM) consistently indicated a correlation between the annual amplitude of sea surface temperature (SST) and adaptive population divergence. In addition, an influence of spatial distribution on the patterns of adaptive population differentiation was also detected via RDA. From these results I propose a mechanism underlying the patterns of population differentiation discovered in Chapters 3 and 4: a latitudinal gradient of SST appears to be the selective force promoting the adaptive divergence of the lobster populations with local patterns of connectivity distorting the gradient and thus forming three distinct temperature adapted genotypes (North-West, North-East, and South). An environmental association analysis offered 43 candidate loci, which after alignment of transcriptome-mapped reference catalog sequences to annotated protein databases identified a candidate gene for thermal adaptation - UDP-glycosyltransferase (UGT). UGT is a detoxification enzyme involved in the metabolization of a variety of endogenous and environmental compounds and its activity and gene expression patterns have been linked to temperature. This study provides evidence for the local adaptations of the NZ population of Jasus edwardsii to SST, which together with the efficient mechanism of larval dispersal creates a system likely resilient to changes in temperature. This feature is important in the light of climate change-induced range shifts and supports the long-term sustainability of the red rock lobster fishery. The three genetically distinct regions identified coincide with existing boundaries of the management units and therefore do not require an adjustment of the current management regime.</p>
<p>Marine Reserves (MRs) are amongst the most common tools used for marine conservation around the world. New Zealand (NZ) has 34 MRs protecting approximately 7.6% of NZ's territorial seas. In NZ the main purpose of MRs is to allow scientific research to be conducted in the absence of human disturbance. The establishment of MRs around the country produces different biological, social and economic effects in the surrounding communities. However, the majority of previous MR studies have evaluated the biological effects of protection and not the social and economic effects. This thesis investigates how established MRs are performing in terms of social, economic, social and biological goals and contributing to society‘s well-being within New Zealand. For this research I conducted research at two MRs. The Taputeranga MR (TMR) was established in 2008, and is the newest MR established in New Zealand. It is located in the Wellington region, on the Wellington south coast, and extends from Princess Bay to Quarry Bay, protecting 8.54 km² of coastal waters. Kapiti MR (KMR), which is one of the oldest MRs in New Zealand, was established in 1992 in the Wellington region, approximately 50 km north of Wellington city. It is located on the Kapiti coast in front of Paraparaumu beach. The KMR covers 20.90 km² of coastal water, divided into two parts; the largest part is 17.50 km² and the smaller part is 3.4 km². In this thesis I am starting to explore the financial cost of the MRs (chapter 2), where I attempted to estimate all of the costs required to establish a MR. The Taputeranga MR was used as a case study along with an analysis of the management costs for four other MRs. I aimed to find predictor variables across these five MRs to explain differences in their management cost. In addition, I also estimated the displacement cost to fishermen. Results showed that the Taputeranga‘s pre-establishment process cost approximately NZ $508,000, and the establishment process cost approximately NZ $ 354,000. In addition, the average management cost across five MRs per year was around NZ $63,000 year⁻¹. With respect to the predictor variables, the Akaike Information Criterion (AICc) analysis showed that MR size best explains cost, where small MRs are more expensive to maintain than big MRs. The displacement cost was estimated as NZ $22,000 approximately per vessel. I also researched and examined the social impacts of MRs (chapter 3). The aim of this chapter was to explore the human dimensions of the TMR and KMR and a hypothetical MR as a control area. I used a series of questionnaires with five main groups affected by the establishment of the MRs. Results showed that of the people who conducted activities close to the TMR and KMR, nobody selected either area specifically because there was a MR in the vicinity. With respect to MR knowledge, the majority of people at both MRs and at the hypothetical MR believed they knew what a MR was, however, nobody could provide a correct description of the main reasons for MR designation in New Zealand. Most groups surveyed at KMR indicated that its establishment had not personally affected them. At TMR, all groups believed they had experienced direct (personal) and indirect problems since the establishment of the MR. At the hypothetical MR, the majority of respondents perceived that its establishment would not cause any personal or family problems. I found that respondents at both MRs and the hypothetical MR believed that MRs are a good tool for protecting the environment. I also develop a framework to understand and estimate MR goods and services by using the Millennium Ecosystem Assessment framework (chapter 4). The aim of this study was to identify and determine use and non-use values of the Taputeranga MR and Kapiti MR. At KMR and TMR I identified eight main value-categories: (1) Commercial fishing benefits from MR, (2) Nature-based tourism, (3) Education, (4) Research, (5) Public recreation, (6) Recreational fishing benefit from MR, (7) Ecosystem health, and (8) Existence – Bequest value. The existence-bequest values (non-use values) were estimated based on the public‘s willingness to pay (WTP) and found to have a mean value of NZ $61.54 at the TMR and NZ $31.45 at the KMR per household/year. After being exploring cost of MRs, social effects of MRs and MR goods and services, I researched the biological effects of MRs. For this I examined the effect of MRs on rock lobster (Jasus edwardsii) biomass and abundance (chapter 5). I investigated how rock lobsters (RLs) (Jasus edwardsii) have responded to the protection afforded by the TMR and KMR by comparing rock lobster Catch Per Unit Effort (CPUE) between reserve and nonreserve areas. The average CPUE was higher inside both MRs than outside. Also bigger RLs were caught inside both MRs'. In addition, the TMR catches were twice as high compared with historical catches, and the KMR compared with historical catches were 1.93 times higher. By integrating all these different chapters and methodologies I have been able to provide insights that will help in the future of conservation of MRs, by improving the level of information for better decision-making, improving the communication between decision makers and stakeholders and to build better relationships between researchers and nonextractive users of MRs. Moreover, I provide recommendations that could be useful to include within the current Marine Protected Area Policy and potentially improve it. These recommendations also attempt to minimize the time and costs involved in MRs from the pre-establishment stages, by creating effective and formal alliances between different groups of stakeholders.</p>
<p>Marine Reserves (MRs) are amongst the most common tools used for marine conservation around the world. New Zealand (NZ) has 34 MRs protecting approximately 7.6% of NZ's territorial seas. In NZ the main purpose of MRs is to allow scientific research to be conducted in the absence of human disturbance. The establishment of MRs around the country produces different biological, social and economic effects in the surrounding communities. However, the majority of previous MR studies have evaluated the biological effects of protection and not the social and economic effects. This thesis investigates how established MRs are performing in terms of social, economic, social and biological goals and contributing to society‘s well-being within New Zealand. For this research I conducted research at two MRs. The Taputeranga MR (TMR) was established in 2008, and is the newest MR established in New Zealand. It is located in the Wellington region, on the Wellington south coast, and extends from Princess Bay to Quarry Bay, protecting 8.54 km² of coastal waters. Kapiti MR (KMR), which is one of the oldest MRs in New Zealand, was established in 1992 in the Wellington region, approximately 50 km north of Wellington city. It is located on the Kapiti coast in front of Paraparaumu beach. The KMR covers 20.90 km² of coastal water, divided into two parts; the largest part is 17.50 km² and the smaller part is 3.4 km². In this thesis I am starting to explore the financial cost of the MRs (chapter 2), where I attempted to estimate all of the costs required to establish a MR. The Taputeranga MR was used as a case study along with an analysis of the management costs for four other MRs. I aimed to find predictor variables across these five MRs to explain differences in their management cost. In addition, I also estimated the displacement cost to fishermen. Results showed that the Taputeranga‘s pre-establishment process cost approximately NZ $508,000, and the establishment process cost approximately NZ $ 354,000. In addition, the average management cost across five MRs per year was around NZ $63,000 year⁻¹. With respect to the predictor variables, the Akaike Information Criterion (AICc) analysis showed that MR size best explains cost, where small MRs are more expensive to maintain than big MRs. The displacement cost was estimated as NZ $22,000 approximately per vessel. I also researched and examined the social impacts of MRs (chapter 3). The aim of this chapter was to explore the human dimensions of the TMR and KMR and a hypothetical MR as a control area. I used a series of questionnaires with five main groups affected by the establishment of the MRs. Results showed that of the people who conducted activities close to the TMR and KMR, nobody selected either area specifically because there was a MR in the vicinity. With respect to MR knowledge, the majority of people at both MRs and at the hypothetical MR believed they knew what a MR was, however, nobody could provide a correct description of the main reasons for MR designation in New Zealand. Most groups surveyed at KMR indicated that its establishment had not personally affected them. At TMR, all groups believed they had experienced direct (personal) and indirect problems since the establishment of the MR. At the hypothetical MR, the majority of respondents perceived that its establishment would not cause any personal or family problems. I found that respondents at both MRs and the hypothetical MR believed that MRs are a good tool for protecting the environment. I also develop a framework to understand and estimate MR goods and services by using the Millennium Ecosystem Assessment framework (chapter 4). The aim of this study was to identify and determine use and non-use values of the Taputeranga MR and Kapiti MR. At KMR and TMR I identified eight main value-categories: (1) Commercial fishing benefits from MR, (2) Nature-based tourism, (3) Education, (4) Research, (5) Public recreation, (6) Recreational fishing benefit from MR, (7) Ecosystem health, and (8) Existence – Bequest value. The existence-bequest values (non-use values) were estimated based on the public‘s willingness to pay (WTP) and found to have a mean value of NZ $61.54 at the TMR and NZ $31.45 at the KMR per household/year. After being exploring cost of MRs, social effects of MRs and MR goods and services, I researched the biological effects of MRs. For this I examined the effect of MRs on rock lobster (Jasus edwardsii) biomass and abundance (chapter 5). I investigated how rock lobsters (RLs) (Jasus edwardsii) have responded to the protection afforded by the TMR and KMR by comparing rock lobster Catch Per Unit Effort (CPUE) between reserve and nonreserve areas. The average CPUE was higher inside both MRs than outside. Also bigger RLs were caught inside both MRs'. In addition, the TMR catches were twice as high compared with historical catches, and the KMR compared with historical catches were 1.93 times higher. By integrating all these different chapters and methodologies I have been able to provide insights that will help in the future of conservation of MRs, by improving the level of information for better decision-making, improving the communication between decision makers and stakeholders and to build better relationships between researchers and nonextractive users of MRs. Moreover, I provide recommendations that could be useful to include within the current Marine Protected Area Policy and potentially improve it. These recommendations also attempt to minimize the time and costs involved in MRs from the pre-establishment stages, by creating effective and formal alliances between different groups of stakeholders.</p>
<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>
<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>
Abstract The Western Kangaroo Island Marine Park (WKIMP) was declared as part of South Australia's representative system of Marine Protected Areas in 2009. Sanctuary Zone 3 (SZ-3) of the WKIMP is a no-take area protected from fishing since 1 October 2014 and is located within the Northern Zone Rock Lobster Fishery (NZRLF). In February 2017, a dedicated survey was undertaken to estimate the relative abundance (catch per unit effort (CPUE), kg/potlift) and size of southern rock lobster (Jasus edwardsii) inside and outside SZ-3. Survey results were then compared with historical estimates of abundance and size obtained from commercial fishery-dependent data. Survey estimates of relative abundance of legal-size lobsters were 4.4 times greater inside SZ-3 compared with outside in 2017. Since 2014, when fishing was last permitted inside SZ-3, the relative abundance of lobsters increased by 75%. The mean size of legal-size female and male lobsters also increased by 4.1% and 12.5%, respectively. The population responses recorded are consistent with the results recorded for southern rock lobster stocks in marine parks in other jurisdictions.
