Development and Application of Otolith-Based Methods to Infer Demographic Connections in a Marine Metapopulation

<p>Connectivity between local populations is critical if these are to function as a metapopulation and sustain locally open sink populations. Assessing whether such connections between local populations exist is thus an important step towards understanding coastal metapopulation dynamics as well as assessing the efficacy of spatial management tools such as marine reserve networks. For this thesis, I investigate population connectivity of the common triplefin (Forsterygion lapillum) in Cook Strait, New Zealand, using chemical signatures contained within fish otoliths (ear stones). I concentrate on likely connections between three local marine reserves: Kapiti Island (Kapiti coast), Long Island (Marlborough Sounds) and Taputeranga Marine Reserve (Wellington south coast). To this end I develop and implement new statistical methods to enable stronger inferences from otolith chemistry based approaches. In chapter 2, I evaluate otolith core chemistry as a potential tool (i.e. an environmental fingerprint) for identification of natal source populations of the common triplefin. I sampled otolith chemistry from hatchling fish across a range of hierarchical scales: obtained from individual egg masses within a site; sites within different regions; and regions distributed on the two main islands of New Zealand (North and South Island). This sampling enabled me to construct an “atlas” (or baseline) of otolith core chemistry. I developed and applied a set of novel statistical approaches to examine the characteristics of this natal atlas and optimize its spatial resolution. These analyses allowed me to assess the utility of otolith chemistry as a potential tool to infer patterns of population connectivity in the vicinity of Cook Strait. Chapter 3 develops a new Bayesian approach to facilitate improved clustering and classification of dispersing fish to putative natal populations based on their otolith chemistry. Otolith-based approaches used to infer natal origins of fishes routinely suffer from the (unrealized) requirement to sample all potential natal source populations. An incomplete baseline atlas has greatly limited the application of otolith chemistry as a tool for assessments of connectivity in the marine environment. In this chapter, I develop, evaluate, and implement statistical solutions to this problem. Specifically, I present a clustering model, based on infinite mixtures, which does not require the specification of a potential number of sources. In a second step, I embed this clustering model in a large-scale classification model that allows for classification on scales encompassing a number of potential sources, where recruits are clustered with observations from the baseline or a separate cluster within these regions. This opens the potential for fish that came from an identifiable source other than those sampled to not be assigned to a sampled source. I evaluate the strength of this approach using the well-known weakfish (Cynoscion regalis) dataset. In chapter 4, I apply the statistical methods developed in chapter 3 to the common triplefin. I sampled recent recruits of the common triplefin within each of three marine reserves (Kapiti, Long Island, and Taputeranga) and used otolith chemistry to infer probable natal origins. I then compare these inferred patterns of connectivity with those predicted by a set of hydrodynamic simulations. This comparison enabled me to (qualitatively) assess the likelihood of connectivity (as predicted by otolith chemistry) given local hydrodynamic conditions. For chapter 5, I extend the Bayesian modelling approaches developed in previous chapters to incorporate otolith chemistry data sampled from throughout the life-history of dispersers. As in chapter 3, I develop and evaluate the utility of this approach using a previously published data set (Chinook salmon), and I apply the approach to the common triplefin in a subsequent chapter. Specifically, I propose flexible formulations based on latent state models, and compare these in a series of illustrative simulations and an application to Chinook salmon contingent analysis. In chapter 6, I apply the Bayesian framework (developed in chapter 5) to the common triplefin data set. Specifically, I formulate a model based on putative chemical distinctions between inshore and offshore water-masses. This model allows me to compare dispersal histories among recruits to a set of reserves (evaluated initially in chapter 4), and the approach reveals patterns that appear to be common to all successful recruits. I examine these findings in the light of results obtained in chapter 4 as well as local hydrodynamic conditions. Finally, I conclude my thesis in chapter 7 by discussing the relevance of my findings for the functioning of networks of sub-populations, both in a metapopulation and a reserve network context.</p>

Development and Application of Otolith-Based Methods to Infer Demographic Connections in a Marine Metapopulation

<p>Connectivity between local populations is critical if these are to function as a metapopulation and sustain locally open sink populations. Assessing whether such connections between local populations exist is thus an important step towards understanding coastal metapopulation dynamics as well as assessing the efficacy of spatial management tools such as marine reserve networks. For this thesis, I investigate population connectivity of the common triplefin (Forsterygion lapillum) in Cook Strait, New Zealand, using chemical signatures contained within fish otoliths (ear stones). I concentrate on likely connections between three local marine reserves: Kapiti Island (Kapiti coast), Long Island (Marlborough Sounds) and Taputeranga Marine Reserve (Wellington south coast). To this end I develop and implement new statistical methods to enable stronger inferences from otolith chemistry based approaches. In chapter 2, I evaluate otolith core chemistry as a potential tool (i.e. an environmental fingerprint) for identification of natal source populations of the common triplefin. I sampled otolith chemistry from hatchling fish across a range of hierarchical scales: obtained from individual egg masses within a site; sites within different regions; and regions distributed on the two main islands of New Zealand (North and South Island). This sampling enabled me to construct an “atlas” (or baseline) of otolith core chemistry. I developed and applied a set of novel statistical approaches to examine the characteristics of this natal atlas and optimize its spatial resolution. These analyses allowed me to assess the utility of otolith chemistry as a potential tool to infer patterns of population connectivity in the vicinity of Cook Strait. Chapter 3 develops a new Bayesian approach to facilitate improved clustering and classification of dispersing fish to putative natal populations based on their otolith chemistry. Otolith-based approaches used to infer natal origins of fishes routinely suffer from the (unrealized) requirement to sample all potential natal source populations. An incomplete baseline atlas has greatly limited the application of otolith chemistry as a tool for assessments of connectivity in the marine environment. In this chapter, I develop, evaluate, and implement statistical solutions to this problem. Specifically, I present a clustering model, based on infinite mixtures, which does not require the specification of a potential number of sources. In a second step, I embed this clustering model in a large-scale classification model that allows for classification on scales encompassing a number of potential sources, where recruits are clustered with observations from the baseline or a separate cluster within these regions. This opens the potential for fish that came from an identifiable source other than those sampled to not be assigned to a sampled source. I evaluate the strength of this approach using the well-known weakfish (Cynoscion regalis) dataset. In chapter 4, I apply the statistical methods developed in chapter 3 to the common triplefin. I sampled recent recruits of the common triplefin within each of three marine reserves (Kapiti, Long Island, and Taputeranga) and used otolith chemistry to infer probable natal origins. I then compare these inferred patterns of connectivity with those predicted by a set of hydrodynamic simulations. This comparison enabled me to (qualitatively) assess the likelihood of connectivity (as predicted by otolith chemistry) given local hydrodynamic conditions. For chapter 5, I extend the Bayesian modelling approaches developed in previous chapters to incorporate otolith chemistry data sampled from throughout the life-history of dispersers. As in chapter 3, I develop and evaluate the utility of this approach using a previously published data set (Chinook salmon), and I apply the approach to the common triplefin in a subsequent chapter. Specifically, I propose flexible formulations based on latent state models, and compare these in a series of illustrative simulations and an application to Chinook salmon contingent analysis. In chapter 6, I apply the Bayesian framework (developed in chapter 5) to the common triplefin data set. Specifically, I formulate a model based on putative chemical distinctions between inshore and offshore water-masses. This model allows me to compare dispersal histories among recruits to a set of reserves (evaluated initially in chapter 4), and the approach reveals patterns that appear to be common to all successful recruits. I examine these findings in the light of results obtained in chapter 4 as well as local hydrodynamic conditions. Finally, I conclude my thesis in chapter 7 by discussing the relevance of my findings for the functioning of networks of sub-populations, both in a metapopulation and a reserve network context.</p>

Application of otolith chemistry at multiple life history stages to assess population structure of Warsaw grouper in the Gulf of Mexico

Chemical markers in otoliths have been used to assess the stock structure of many marine fishes, but these natural markers have yet to be widely evaluated or applied to demersal fishes in offshore habitats where physicochemical gradients are generally less pronounced relative to nearshore waters. To address this, we quantified trace elements (Li, Mg, Mn, Co, Cu, Zn, Sr, Ba) and stable isotopes (δ13C and δ18O) in otoliths of Warsaw grouper Hyporthodus nigritus from 4 regions in the Gulf of Mexico (Texas, Louisiana, Alabama-NW Florida, and SW Florida). Region-specific differences in otolith chemistry were observed, and notable differences in several influential markers (Mn:Ca, Sr:Ca, and Ba:Ca ratios and δ18O) were present, particularly between the most distant regions investigated (Texas/Louisiana and SW Florida). Distinct regional signatures were observed for Warsaw grouper across 3 life history stages: first year (otolith core), most recent years (otolith edge), and lifetime (whole otolith), suggesting that individuals within certain regions share common environmental histories that may represent unique contingents or sub-populations. Findings also demonstrate that spatial variability within these markers was consistent enough to overcome any temporal variability within the geographic domains investigated for all 3 life history stages, highlighting their potential value for assessing the natal origin, exchange, and population structure of this species and potentially other members of the deepwater fish assemblage.

Reconstruction of temperature experienced by Pacific bluefin tuna Thunnus orientalis larvae using SIMS and microvolume CF-IRMS otolith oxygen isotope analyses

This study aimed to reconstruct temperatures experienced during the larval period by adult Pacific bluefin tuna Thunnus orientalis using high-resolution otolith stable oxygen isotope (δ18O) analysis. A novel otolith sample preparation protocol for secondary ion mass spectrometry (SIMS) analysis developed in this study reduced the background noise of SIMS measurements, enabling analyses of >10 times higher resolution around the otolith core compared to previous studies using conventional isotope ratio mass spectrometry (IRMS). The values obtained from SIMS were compared to those obtained by microvolume δ18Ootolith analysis using micromilling and conventional continuous-flow IRMS (CF-IRMS). There was a systematic offset (average 0.41‰ with SIMS resulting in lower values) most likely caused by matrix effects on SIMS δ18Ootolith values that can be calibrated using a strong linear relationship between SIMS and CF-IRMS measurements (r2 = 0.78, p < 0.001). The core-to-edge δ18Ootolith of 5 Pacific bluefin tuna revealed fine-scale seasonal variations in water temperature agreeing with known migration patterns. In addition, the ambient water temperature experienced during larval stages (about 10-20 d post hatch) estimated from otolith core δ18O ranged from 26.7 to 30.7°C, overlapping with temperatures associated with the occurrence of larval Pacific bluefin tuna. Combining SIMS and microvolume CF-IRMS δ18O otolith analyses offers a microscale examination of fish ecology that is not possible with conventional IRMS techniques. This novel method is particularly useful for understanding the early life history of fish that may be affected by climate change and reconstructing a well-resolved migration history for fish species that have small otoliths and/or narrow growth increments.

Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus)

Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ13C and δ18O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12–18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ18O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ18O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.

Use of fresh water by an estuarine-resident marine catfish: evidence from gonadal and otolith chemistry analyses

In this study, we examine how the Guri catfish Genidens genidens uses estuarine and freshwater habitats along the largest South American coastal lagoon, through the chemical analysis of otoliths and microscopic analysis of gonads. Chemical composition (Sr:Ca) of otolith edges allowed distinguishing between individuals who used the estuarine or freshwater compartments of the lagoon. The analysis of core-to-edge chemical profiles of each individual otolith revealed that the population may present two different patterns of habitat use along the lagoon. The ‘type 1’ pattern (89.5%) includes fish who appear to have been born in estuarine waters, whereas ‘type 2’ (9.5%) includes those fish born in fresh water. Nevertheless, juveniles from both patterns appear to migrate to estuarine waters. The gonad analysis shows G. genidens may reproduce in fresh water, as nearly 57% of all sampled fish were found to spawn in the freshwater portion of the lagoon. Also, the otolith core of many adult fish presented freshwater signatures, thus suggesting consistent fresh water use during early life. Our findings based on otolith and gonadal analyses challenge the previous classification of G. genidens as an estuarine resident. Rather, our results allow the suggestion that this species should be placed in the ‘estuarine and fresh water’ guild, which includes both fish completing their life cycles within the estuary and fish who consistently use freshwater habitats.

Application of UV-cured resin as embedding/mounting media for practical, time-saving otolith specimen preparation

Otoliths are calcified structures located in the inner ears of fish, as in most vertebrates, that are responsible primarily for the perception of gravity, balance and movement, and secondarily of sound detection. Microstructural and chemical analyzes of the inner otolith growth layers, called increments, constitute powerful tools to estimate fish age and elucidate many life history and demographic traits of fish populations. Otolith analyzes often require the production of a thin cross section that includes in the same plane of view the otolith core and all microscopic layers formed from birth until the moment of collection (otolith edge). Here we report on the usefulness of UV-cured resins that have become recently popular among nail artists and hobbyists for otolith specimen preparation. We show that single-component UV-cured resins can replace successfully and advantageously the commonly used two-component Epoxy resins to obtain otolith cross sections suitable for both microstructural examination and chemical analysis by electron probe microanalysis. UV-cured resins provide on-demand, extremely rapid (minute-order) hardening and high transparency, while providing similar adhesion and mechanical support for the otoliths during processing and analysis as Epoxy resins. UV-cured resins may revolutionize otolith specimen preparation practically- and time-wise, and may be particularly useful in teaching and workshop situations in which time for otolith embedding is a constraint.

Inter-annual variability in otolith chemistry of catfish Genidens barbus from South-western Atlantic estuaries

The catfish Genidens barbus is a commercial species from South America. The aim of the present study was to examine the inter-annual variability in estuary-specific chemical signatures of otolith cores (Ba:Ca, Mg:Ca, Mn:Ca, Sr:Ca and Zn:Ca ratios) for three estuaries from Argentina and Brazil where adults were collected over multiple years. Secondarily, we evaluated whether the percentages of classification of individuals to their natal origin place are affected by the grouping of several cohorts. Most element:Ca ratios were not significantly different among year cohorts. Results from PERMANOVA revealed significant differences in the multi-element signatures of the otolith core between cohorts for the Plata River estuary (PR) (P = 0.006) and the Patos Lagoon (PL) (P = 0.03), while no significant differences (P = 0.9) were found for Paranaguá Bay (PB). The percentages of spatial classification (discriminant function analyses) decreased to between 15.5 and 25% for PR and PL when cohorts were grouped. This work makes it clear that the temporal variation in the chemical signature of the adult catfish otolith core can greatly affect the percentages of spatial classification.

Another New Zealand centenarian: age validation of black cardinalfish (Epigonus telescopus) using lead–radium and bomb radiocarbon dating

Black cardinalfish (Epigonus telescopus, Apogonidae) is an important component of deepsea commercial fishing activity in the New Zealand region. It is estimated to live longer than 100 years on the basis of counts of unvalidated annual growth zones in otoliths. Age-validation procedures for long-lived fishes are often one of the following two techniques: (1) lead–radium disequilibria, which uses the natural decay of radium-226 into lead-210 as a natural clock; or (2) bomb radiocarbon (Δ14C) dating, which relies on the marine signal created by nuclear testing. The high estimated lifespan, as well as the large size of the otolith core region, make E. telescopus an excellent candidate for a combined application of these two independent age-validation techniques. The lead–radium dating using otolith cores indicated that growth-zone counts less than ~60 years were consistent with radiometric ages, whereas higher counts appeared to be under-estimates. There was 95% confidence that maximum age was at least 95 years. The validation indicated that fish aged over 60 years tended to be under-aged by up to 30%. The bomb radiocarbon levels in otolith cores supported age estimates up to ~40 years made from zone counts, and by inference from the zone counts validated with lead–radium dating, longevity exceeds 100 years.

Nursery areas and connectivity of the adults anadromous catfish (Genidens barbus) revealed by otolith-core microchemistry in the south-western Atlantic Ocean

The anadromous catfish, Genidens barbus, is a commercial and vulnerable species from South America. The aims of the present study were to assess whether the nursery areas can be discriminated by using microchemical signatures of lapillus otoliths, to assess the accuracy of classifying fish in relation to natal nursery area and to discuss the possibility of existence of homing behaviour. Thus, the otolith-core chemical signatures (barium (Ba):calcium (Ca), lithium (Li):Ca, magnesium (Mg):Ca, manganese (Mn):Ca, strontium (Sr):Ca, and zinc (Zn):Ca ratios) of adult fish were compared among different estuaries (De La Plata River in Argentina, and Patos Lagoon, Paranaguá Bay and Guanabara Bay in Brazil). PERMANOVA analysis showed significant differences in the multi-element signatures of the otolith core among sampling sites for all cohorts (2002, 2003, 2006 and 2007), indicating that the technique has considerable potential for use in future assessments of population connectivity and nursery areas of G. barbus. Via quadratic discriminant function analysis, fish were classified to natal nursery areas with 80–100% cross-validation classification accuracies. These results suggested that a high level of spatial segregation exists in adult catfish life and homing behaviour could not be ruled out on the basis of our data.