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ABSTRACT: The role of larval dispersal in ecology and evolution is still largely undescribed in many marine organisms. Larval recruitment has long been viewed as being dominated by unpredictable, highly variable processes but also as a significant driver of population ecology and genetics. Without any knowledge about the directionality and magnitudes of larval recruitment, understanding marine species population dynamics remains a highly uncertain endeavor. Unfortunately, given the need for extensive management and conservation of many fishery species, this uncertainty can directly affect our ability to implement effective management policy. Gag, Mycteroperca microlepis, in the Gulf of Mexico are a perfect example of this conundrum where larval dispersal appears to be important, but we have a very limited understanding of how it is affecting populations. In this dissertation, I describe a series of studies pointed at describing the role of larval dispersal in patterns of population genetics of gag across the Gulf of Mexico as well as examining its relationship to the population ecology of the system. In Chapter Two, I examined patterns of genetic variation across life stages (adult and juvenile), space, and time to explore the role of larval dispersal in the effective population size of gag. Typically, marine systems are believed to exhibit low effective size to census size ratios due to large variation among individuals in reproductive success. While gag do exhibit this low ratio, there is little evidence to support "sweepstakes"--Like reproductive success. I found little support for significant genetic differentiation among post-settlement juveniles both in space and time or for juvenile gag being a sample of a subset of adult genetic diversity. Also, adult gag did not exhibit any consistent spatial bias in contributions to juvenile cohorts. Overall, across the entire West Florida Shelf, juvenile gag appeared to be a well-mixed sample of adult gag offspring. The results suggest that larval dispersal has little effect on the population genetics of gag and the patterns of reproductive success among individuals.
Understanding how speciation occurs in the ocean is challenging because the high dispersal potential of marine larvae, and the scarcity of absolute physical barriers to their dispersal, suggest that gene flow should slow or prevent the evolution of divergence among populations. However, spatial heterogeneity in gene flow and localized sexual selection are two potential drivers of divergence among marine populations. Here I investigate how gene flow and sexual selection contribute to reproductive divergence in a coastal seastar with a long larval pelagic phase, Patiria miniata. I first use microsatellite markers to assess genetic population structure across the species range along the west coast of North America, and find a genetic disjunction near the central coast of British Columbia consistent with two hypotheses about the effects of historical climate events and contemporary gene flow. I next use an oceanographic dispersal model to assess the extent to which variation in larval dispersal can account for this structure. I find that oceanographic features predict the genetic structure observed better than dispersal distance between populations alone. Given this genetic structure, I next test the hypothesis that fertilization proteins of this broadcast spawner have diversified among the two (northern and southern) populations, as predicted under a hypothesis of sexual conflict. My findings reveal divergent, positive selection in the sperm protein bindin, which suggest that sexual selection has lead to localized divergence at this fertilization compatibility gene. Finally, I test fertilization compatibility between males and females as a function of population source and male bindin genotype. I find that localized coevolution has occurred in the southern population, and that southern females have a greater affinity than northern females for male bindin genotypes found in the south. Together, these findings provide evidence that patterns in larval dispersal and sexual selection can lead to reproductive divergence in a marine species in spite of its high dispersal potential. Characterizing both genetic structure and adaptive molecular evolution among populations is a powerful approach for understanding incipient speciation in the sea.
Abstract: Larval dispersal in marine species allows gene flow across broad expanses of pelagic ocean, and can potentially provide genetic cohesion within widespread species. However, genetic connectivity across discontinuous ranges spanning thousands of kilometers must also rely on the availability of intermediate habitat. Here, I use comparative phylogeography and coalescent modeling to explore the interplay between habitat requirements and gene flow in eight pelagically dispersing species. First, I test the hypothesis that periods of lowered sea levels during glacial maxima promoted allopatric differentiation across the Indonesian-Australian Archipelago by comparing phylogeographic patterns in six species co-distributed across this region. Mitochondrial COI datasets from all six species are discordant in the degree and location of genetic structure across the archipelago, ranging from near reciprocal monophyly to admixtures between divergent clades, to a nearly complete absence of structure. However, all six species show strong departures from the neutral Wright-Fisher model, and a coalescent model of demography suggests that each species has expanded its range in response to sea- level rise and restoration of habitat on the Sunda and Sahul shelves at the end of the Pleistocene. Discordant phylogeographic patterns among species may arise from different habitat requirements, which could determine the degree to which local populations were impacted by sea level fluctuations. I then examine genetic structure across the South Pacific in two species of amphidromous freshwater Neritid gastropods that have retained marine pelagically dispersing larvae. Results show surprisingly low levels of genetic structure among Western Pacific archipelagos, despite the rarity of their freshwater habitat. Finally, I compare gene flow across the South Pacific in marine and amphidromous Neritid gastropods to test the hypothesis that intermediate atoll stepping-stones facilitate genetic connectivity in the marine species. Under a model of the structured coalescent, all four species have high levels of gene flow in the Western Pacific. In the Central Pacific, where a biophysical model of larval dispersal predicts connectivity through atoll stepping-stones, gene flow was significantly lower in the marine species, and negligible in the amphidromous species.
Many marine fish populations are severely declining due to over-fishing, loss of both juvenile and adult habitats, and accelerating environmental degradation. Fisheries management and the implementation of marine protected areas (MPAs) and other conservation tools are currently hindered by large gaps in knowledge about larval dispersal and its subsequent effects on population dynamics and regulation. This lack of knowledge is due to the inherent difficulty associated with tracking miniscule marine fish larvae. Population genetics approaches are particularly promising, but current methods have been of limited use for inferring ecologically relevant rates of population connectivity because of the large population sizes and high amounts of gene flow present in most marine species. To address these issues, I developed novel genetic methods of identifying parent-offspring pairs to directly track the origin and settlement of larvae in natural populations. These parentage methods fully account for large numbers of pair-wise comparisons and do not require any demographic assumptions or observational data. Furthermore, these methods can be used when only a small proportion of candidate parents can be sampled, which is often the case in large marine populations. I also employed Bayes' theorem to take into account the frequencies of shared alleles in putative parent-offspring pairs, which can maximize statistical power when faced with fixed numbers of loci. I accounted for genotyping errors by introducing a quantitative method to determine the number of loci to allow to mismatch based upon study-specific error rates. These novel parentage methods were applied to yellow tang (Zebrasoma flavescens, Acanthuridae) sampled around the Island of Hawai'i (measuring 140 km by 129 km) during the summer of 2006. We identified four parent-offspring pairs, which documented dispersal distances ranging from 15 to 184 kilometers. Two of the parents were located within MPAs and their offspring dispersed to unprotected areas. This observation provided direct evidence that MPAs can successfully seed unprotected sites with larvae that survive to become established juveniles. All four offspring were found to the north of their parents and a detailed oceanographic analysis from relevant time periods demonstrated that passive transport initially explained the documented dispersal patterns. However, passive dispersal could not explain how larvae eventually settled on the same island from which they were spawned, indicating a role for larval behavior interacting with fine-scale oceanographic features. Two findings together suggested that sampled reefs did not contribute equally to successful recruitment: (1) low levels of genetic differentiation among all recruit samples, and (2) the fact that the 4 documented parents occurred at only 2 sites. These findings empirically demonstrated the effectiveness of MPAs as useful conservation and management tools and highlighted the value of identifying both the sources and successful settlement sites of marine larvae. I next examined patterns of larval dispersal in bicolor damselfish (Stegastes partitus, Pomacentridae) collected during the summers of 2004 and 2005 from reefs lining the Exuma Sound, Bahamas (measuring 205 km by 85 km). Parentage analysis directly documented two parent-offspring pairs located within the two northern-most sites, which indicated self-recruitment at these sites. Multivariate analyses of pair-wise relatedness values confirmed that self-recruitment was common at all sampled populations. I also found evidence of "sweepstakes events", whereby only a small proportion of mature adults contributed to subsequent generations. Independent sweepstakes events were indentified in both space and time, bolstering the direct observations of self-recruitment and suggesting a role for sweepstakes analyses to identify the scale of larval dispersal events. This dissertation provides insights into the patterns of larval dispersal in coral-reef fishes. The coupling of direct (e.g., parentage) and indirect (e.g., assignment methods, sweepstakes analyses) methods in conjunction with continued technological and methodological advances will soon provide large-scale, ecologically relevant, rates of larval exchange. By uncovering the dynamics of these enigmatic processes, the implementation of conservation and management strategies for marine fishes in general will undoubtedly experience greater success.
This is the first book to provide a detailed treatment of the field of larval ecology. The 13 chapters use state-of-the-art reviews and critiques of nearly all of the major topics in this diverse and rapidly growing field. Topics include: patterns of larval diversity, reproductive energetics, spawning ecology, life history theory, larval feeding and nutrition, larval mortality, behavior and locomotion, larval transport, dispersal, population genetics, recruitment dynamics and larval evolution. Written by the leading new scientists in the field, chapters define the current state of larval ecology and outline the important questions for future research.
The spatial distribution of genetic variation across landscapes is influenced by physical features that facilitate or restrict movement and natural selection driven by environmental heterogeneity. Many marine organisms undergo a pelagic larval stage, during which time ocean currents influence dispersal and the degree of gene flow. Furthermore, gradients in temperature, salinity, and other environmental conditions produce spatially varying selection pressures across species ranges. In the first part of my thesis, I offer a novel perspective for marine conservation that emphasizes the importance of considering both connectivity (where connectivity is maintained by dispersal) and the potential for marine populations to adapt to their environment. To do so, I highlight how genomic data can be used to infer population connectivity (i.e. based on neutral genetic variation) and environmental selection (i.e. based on putatively adaptive genetic variation) in the context of marine reserve networks. Next, using a genomic dataset derived from restriction-site associated DNA sequencing (RADseq), I investigated the impact of ocean currents and environmental variables on spatial patterns of neutral and adaptive genetic variation in the commercially harvested giant California sea cucumber (P. californicus) along the northeastern Pacific coast. The results showed evidence for population structure despite the potential for widespread gene flow, and demonstrated that accounting for directionality of ocean currents explained genetic variation better than between-site geographic distances. Strong associations between sea bottom temperature and putatively adaptive loci were identified at a broad spatial scale, as well as moderate evidence that surface salinity and bottom current velocities contribute to regional patterns of adaptive differentiation. In a study using simulations of larval dispersal coupled with demo-genetic simulations, I found that potential dispersal was spatially restricted with shorter pelagic larval duration (PLD), but there was no difference between a model of diffusive (isotropic) larval transport and oceanographic (anisotropic) transport. However, several important caveats were highlighted that should be addressed in future work. Collectively, my thesis integrates genomic, environmental, and oceanographic data to understand the role of seascape features on connectivity and adaptation, with implications for marine conservation plans that aim to connect marine populations and support adaptive responses to environmental change.