Evolution and Conservation Genetics of Giant Clams Across the Coral Triangle PDF Download
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Author: Timery S. DeBoer
Publisher:
ISBN:
Category :
Languages : en
Pages : 304
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Book Description
Abstract: Understanding how the physical environment shapes patterns of population connectivity is essential to understanding the evolution and conservation of biodiversity. While dispersal barriers that promote regional genetic differentiation are often apparent in terrestrial environments, the relationship between the physical environment and barriers to connectivity in marine populations is less obvious because most species have a dispersive pelagic larval stage capable of traversing long distances. My thesis examines how the abiotic environment shapes genetic structure and population connectivity of marine invertebrates across Indo-West Pacific using Tridacna giant clams as a model. Data from Tridacna crocea indicates strong genetic structure between West Papua, central Indonesia/Philippines, and Sumatra. The estimated average dispersal distance was far below predictions based on passive dispersal via currents and virtually zero between regions. These results indicate potent limits to genetic and demographic connectivity for this species, and are likely related to sea level fluctuations, physical oceanography and larval ecology. Results from mitochondrial DNA were consistent with those from 9 microsatellites. To evaluate the generality of this result, I compared mtDNA phylogeographic patterns in Tridacna crocea, T. maxima, and T. squamosa. Concordant patterns across three congeners suggest the influence of broadly acting oceanographic and/or geological forces in shaping regional genetic structure. Patterns are concordant with a recent global classification of marine environments, suggesting that abiotic processes are structuring marine biodiversity at multiple levels. Finally, I examined the symbiosis between giant clams and their algal symbionts. Results show that symbiont types differ with temperature and that symbiont communities may differ between individuals based on local environmental conditions. Given the well-documented ecological differences among symbionts, these results highlight potential ecological consequences of this symbiosis in the face of global climate change. Combined, these results indicate that patterns of regional divergence are shaped by physical oceanographic and geological processes, but may also be shaped by clam-algal symbiosis. These data have strong conservation implications. Understanding the scale and pattern of population connectivity is critical to effective conservation planning, and the variation of symbiont communities with temperature may prove useful in managing populations of these endangered species in periods of rising ocean temperatures.
Author: Timery S. DeBoer
Publisher:
ISBN:
Category :
Languages : en
Pages : 304
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Book Description
Abstract: Understanding how the physical environment shapes patterns of population connectivity is essential to understanding the evolution and conservation of biodiversity. While dispersal barriers that promote regional genetic differentiation are often apparent in terrestrial environments, the relationship between the physical environment and barriers to connectivity in marine populations is less obvious because most species have a dispersive pelagic larval stage capable of traversing long distances. My thesis examines how the abiotic environment shapes genetic structure and population connectivity of marine invertebrates across Indo-West Pacific using Tridacna giant clams as a model. Data from Tridacna crocea indicates strong genetic structure between West Papua, central Indonesia/Philippines, and Sumatra. The estimated average dispersal distance was far below predictions based on passive dispersal via currents and virtually zero between regions. These results indicate potent limits to genetic and demographic connectivity for this species, and are likely related to sea level fluctuations, physical oceanography and larval ecology. Results from mitochondrial DNA were consistent with those from 9 microsatellites. To evaluate the generality of this result, I compared mtDNA phylogeographic patterns in Tridacna crocea, T. maxima, and T. squamosa. Concordant patterns across three congeners suggest the influence of broadly acting oceanographic and/or geological forces in shaping regional genetic structure. Patterns are concordant with a recent global classification of marine environments, suggesting that abiotic processes are structuring marine biodiversity at multiple levels. Finally, I examined the symbiosis between giant clams and their algal symbionts. Results show that symbiont types differ with temperature and that symbiont communities may differ between individuals based on local environmental conditions. Given the well-documented ecological differences among symbionts, these results highlight potential ecological consequences of this symbiosis in the face of global climate change. Combined, these results indicate that patterns of regional divergence are shaped by physical oceanographic and geological processes, but may also be shaped by clam-algal symbiosis. These data have strong conservation implications. Understanding the scale and pattern of population connectivity is critical to effective conservation planning, and the variation of symbiont communities with temperature may prove useful in managing populations of these endangered species in periods of rising ocean temperatures.
Author: Patricia Munro
Publisher: WorldFish
ISBN: 9718709363
Category : Clam fisheries
Languages : en
Pages : 54
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Author: James W. Fatherree
Publisher: James W Fatherree
ISBN: 0978619463
Category : Pets
Languages : en
Pages : 226
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Book Description
This is an updated edition of the author's "Giant Clams in the Reef Aquarium" (2019), which has been written and photo-illustrated specifically for the interested reef aquarist. Inside you can find information on: the biology of giant clams, detailed information about the common species, how to choose and purchase the best specimens, how to care for them in aquariums, how to deal with problems that may arise, and much more. Table of Contents: Introduction Chapter 1: Tridacnine Biology and More The Shells The Soft Parts Mantle Coloration How They Work Reproduction and Growth Attachments, Self-Righting, and Boring Exposure to Air Chapter 2: The Tridacnine Species Tridacna crocea Tridacna maxima Tridacna noae Tridacna derasa Tridacna squamosa Tridacna gigas Hippopus hippopus Hippopus porcellanus Tridacna mbalavuana, a.k.a. tevoroa Tridacna squamosina, a.k.a. costata Tridacna elongatissima Tridacna rosewateri a.k.a. lorenzi Hybrid Tridacnines Chapter 3: The Aquarium Care and Acquisition of Tridacnines (In)Compatibilities Water Quality and Flow Appropriate Lighting Choosing and Shopping Acclimation and Adaptation Proper Placement Feeding and Foods Chapter 4: Tridacnine Troubles Bleaching Bacterial Infections Protozoans and Pinched Mantle Boring Sponges and Overgrowing Algae Stinging Cnidarians Flatworms and Bristle Worms Predatory Crustaceans Predatory and Parasitic Snails Gas-Bubble Disease Deteriorating Ligaments Spawning Events References and Image Credits Index You can also find James' giant clam photo galleries and supplemental videos at jameswfatherree.com.
Author: Michele Weber
Publisher:
ISBN:
Category :
Languages : en
Pages : 260
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ABSTRACT The Biogeography and Evolution of Symbiodinium in Giant Clams (Tridacnidae) by Michele Weber Doctor of Philosophy in Integrative Biology University of California, Berkeley Professor Jere H. Lipps, Chair Symbiodinium is a diverse lineage of dinoflagellates that forms photoendosymbioses with five phyla of marine invertebrates and protists. The symbiotic relationship provides hosts with a direct source of energetic resources and the dinoflagellates gain access to a safe environment where they can survive in high densities and easily access the raw materials for photosynthesis. In low nutrient, tropical waters, this relationship forms the base of the food web and the reef structure on which diverse communities have evolved. Although many charismatic reef organisms show clear distribution patterns across their ranges, we are still exploring biogeography with respect to symbiosis. Previously biogeographic patterns in marine microbes were largely ignored; microbes were considered pandemic because lineages would not be limited to particular geographic regions as a result of dispersal and connectivity across oceans. More recently, advanced molecular techniques identified multiple scales of genetic variation in Symbiodinium that were not readily apparent from morphological analyses and encouraged investigation of finer scale questions about distributions and evolutionary patterns. We now know that the genus Symbiodinium is diverse and that certain clades are found in unique regions and associate with particular hosts. Distributional data suggests that they were subjected to a selection mosaic and subgeneric clades diverged, geographically and functionally, on various scales but since the data is confined to certain hosts from certain regions, we know little about large-scale patterns. Some host specificity has been observed but since most hosts transmit their symbionts horizontally across generations and symbionts can be exchanged between host lineages, there is limited context for coevolutionary processes to refine particular pairings. I addressed the biogeographic patterns of Symbiodinium from giant clams on two different scales: regionally across their Indo West Pacific distribution and locally in the Northern Red Sea. Finally I analyzed the historical biogeography for the holobiont association between giant clams and Symbiodinium and inferred historical processes to explain the modern symbiont diversity patterns in a region of low host diversity. In the first chapter I documented diversity of Symbiodinium for two species of giant clam, Tridacna maxima and Tridacna squamosa, across their Indo West Pacific distribution. At 25 localities across the Indo-Pacific from French Polynesia to the Red Sea, I collected small pieces of mantle tissue and recorded the depth and reef environment where each sample was collected. A complete distribution of Symbiodinium phylotypes in association with giant clams across their range provided a broad indication of what fraction of total Symbiodinium diversity associates with this host group. Compared to other host groups, Tridacna are specific hosts; of the hundreds of Symbiodinium genotypes documented in the literature and on GenBank, only ten distinct types live in giant clams and all had been reported from alternative hosts. Giant clams are crown group metazoans and each generation acquires new symbionts from the environment. While other alternative hosts, such as corals and foraminifera, can transfer symbionts between generations and occasionally evolve lineages of specific symbionts, I did not identify novel clam specific lineages. Giant clams host generalist Symbiodinium lineages that are readily available in the water column. Although their distributional range is similar, T. squamosa and T. maxima did not host identical symbionts and I observed gradients in symbiont diversity. Symbionts were most diverse in the Central Indo West Pacific and diversity declined in the Pacific and Indian Oceans. While T. maxima was a generalist across more of its range and hosted diverse symbionts at most localities, T. squamosa was consistently specific for certain symbiont lineages and only in the Central Indo West Pacific did it host more diverse lineages of symbionts. T. squamosa lived on deeper reefs than T. maxima and the symbionts most often associated with T. squamosa exhibited a deeper range than some of the other lineages of Symbiodinium. However, T. maxima were also collected from deep reefs and they hosted different symbiont lineages. These data showed that multiple lineages of Symbiodinium are adapted to depth and they are partitioned between host species. The symbionts were also partitioned between different reef environments. Certain lineages were most common on patch reefs, others on fringing reefs and others from lagoon environments. Phylogenetic systematics indicated that the T. squamosa lineage is younger than the T. maxima lineage and my data on the distribution of Symbiodinium in the two lineages showed that it is also more symbiont specific. This evidence supported the hypothesis that T. squamosa is a less obligate host and can more rigorously select for high performing symbionts than T. maxima. In the second chapter I focused on the lack of Symbiodinium diversity in T. maxima from the Red Sea. Only one phylotype of Symbiodinium was identified from T. maxima in the Red Sea and these sequences were not found in Tridacna samples from other regions. I proposed two hypotheses for the lack of diversity and concluded that multiple symbiont lineages had colonized the Red Sea but only a single lineage was successful and therefore, it replaced the other types and persisted. I compared the Red Sea phylotype to other Symbiodinium from alternative hosts in the Red Sea, the Mediterranean Sea and the West Indian Ocean, to show that the most closely related phylotypes exist along the coast of Kenya. I concluded that the Red Sea lineage originated in the West Indian Ocean and colonized the Red Sea via an alternative host that entered through the straits at Bab al Mandab, after the last glacial maximum, 12,000 years ago. Evidence of an endemic holobiont was evaluated with respect to the evolution of cooperation and transitional associations between partners on a geologic time scale. I suggested that the Red Sea phylotype is dominant because it was an infectious lineage. It easily colonized the new host population soon after the Red Sea reflooded, but the endemic holobiont may be transitional and as conditions stabilize, a more cooperative lineage will out-compete and replace the less efficient phylotype. In the third chapter I addressed a diversity anomaly in the West Indian Ocean. The center of marine biodiversity is the Central Indo West Pacific, which includes Indonesia, the Philippines, Papua New Guinea and the northern Great Barrier Reef in Australia. I sampled more species of giant clam from Papua New Guinea and Australia and observed more symbiont lineages in association with those hosts than any other region within this study. In the West Indian Ocean I only observed two species of host, as was expected based on the marine biodiversity gradient. However, I also identified five lineages of Symbiodinium and while diversity in T. squamosa holobionts was lower in the West Indian Ocean, T. maxima holobionts were equally diverse in both regions. T. squamosa was a generalist in the Central Indo West Pacific and a specialist in the West Indian Ocean but T. maxima was a generalist in both regions. I proposed multiple hypotheses to account for these biogeographic patterns including geologic and oceanographic conditions, niche ecology and historical biogeographic patterns for the hosts. Historical biogeography of a holobiont system provides a new framework that includes the history of associations between partners as well as biogeographic patterns for each individual partner. In this case the history of the association between host and symbiont suggested what modern ecology could not explain. I showed that the holobiont range shifted more slowly than the host ranges and that the modern holobiont diversity in the West Indian Ocean is a legacy of Miocene diversity in that region.
Author: Mei Lin Neo
Publisher: World Scientific
ISBN: 9811274193
Category : Science
Languages : en
Pages : 199
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This book introduces readers to the giant clam's biology, taxonomy and systematics, ecological and cultural significance, threats and challenges, and conservation solutions. The highlight of this book is the species identification guide containing descriptions of 12 known giant clam species accompanied by accurate hand-drawn shell illustrations and live photographs of specimens for comparison. Detailed information is summarised in a visual key on the distinctive features of the individual species, with notes on their ecology, geographic distribution, taxonomy and morphology. This book also includes other useful natural history information to spur the reader's interest in these magnificent animals.With the most comprehensive information presented concisely, this book allows readers to identify a particular giant clam readily and confidently, as well as the other species that it may easily be confused with, confirm that the species occurs in a specific area, and access general information on the biology and ecology of the species. It is a valuable resource for researchers, students, the SCUBA diving community, managers of marine resources, and the public.
Author: Min Hui
Publisher:
ISBN:
Category :
Languages : en
Pages : 170
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Author: Lincoln Rehm
Publisher:
ISBN:
Category : Biophysics
Languages : en
Pages : 0
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Giant clams are known for their unique obligatory symbiosis with the dinoflagellate Family Symbiodiniaceae. Giant clams have enhanced this photosynthesis by developing iridocyte cells to scatter light towards the algae, or zooxanthellae, and by arranging the zooxanthellae in algal pillars. However, giant clams continue to be impacted by both poachers, because of their brightly colored mantle, and changes in their environment. This dissertation focuses on three important areas of giant clam ecology. Here I examine the population demographics of giant clams across the Palauan archipelago, where we found a new record for T. noae. I quantified giant clam mantle hues into three bins: yellow, blue, and green and found that mantle hue varies across a clam's ontogeny. I tested whether there is a relationship between reef habitat and mantle hue. I also compared the absorption of light in clams to a similar system, coral reefs. Finally, I tested whether natural variations in nutrients or light levels can impact the clam's mantle hue and then used a novel approach to characterize the algal pillars within the mantle tissues across the same abiotic variables. The findings of this work suggest that conservation methods in Palau have promoted populations of giant clams and these same clams are among the most photoefficient organisms on the reef. This work developed new methods for large-scale sampling of giant clam hue and algal pillars while also generating new hypotheses for future work on giant clam ecology.
Author: Shashank Keshavmurthy
Publisher: Frontiers Media SA
ISBN: 283250888X
Category : Science
Languages : en
Pages : 256
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Author: Eric James Armstrong
Publisher:
ISBN:
Category :
Languages : en
Pages : 78
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Marine species face several challenges as a result of human activities including direct effects on populations (e.g. overharvesting) and indirect impacts on individuals (e.g. physiological responses to ocean warming and acidification). Ameliorating these impacts requires successful regulation at both the population and physiological levels. One group of critically threatened organisms are the so called “giant clams” (genus Tridacna) of tropical coral reefs. Like corals, giant clams possess calcifying larvae and host symbiotic microalgae and are therefore susceptible to environmentally-driven failure of biomineralization and symbiotic disruption. In addition, giant clams are economically important fisheries species which have been severely overexploited throughout much of their range. While marine reserves have been established to replenish dwindling giant clam stocks, their efficacy in promoting population recovery remains unknown. Similarly, little is known regarding the magnitude of climate-change associated physiological effects on giant clams. This stems, in part, from a lack of knowledge regarding the response of early life-history stages to warming and acidification and because the molecular mechanisms regulating acid-base homeostasis and symbiont photosynthesis in giant clams remain poorly characterized. I addressed these knowledge gaps in populations of the small giant clam, Tridacna maxima, from across a network of marine protected areas (MPAs) on Mo’orea, French Polynesia. I employed a combined physiological and ecological approach to (1) investigate mechanistic processes underlying acid-base regulation within giant clams, specifically in relation to maintenance of host-symbiont homeostasis, (2) measure the effects of increased temperature and elevated pCO2 on giant clam fertilization success, and (3) assess the efficacy of a recently established Marine Protected Area Network in promoting conservation and recovery of this species in an exploitative environment. I demonstrate that giant clams regulate symbiont photosynthesis through the activity of an ion-transport protein, vacuolar-type H+-ATPase (VHA), which is strongly localized in close proximity to symbiotic algae. I further show that clam VHA actively promotes algal photosynthesis, increasing rates of O2 production and holobiont metabolic rate, and likely represents a convergent exaptation for carbon concentration shared by reef-building corals. This process has implications for climate-related responses and may offset the negative impacts of future ocean acidification in these species. I also present the first data demonstrating giant clam early life-history responses to climate change drivers and show that syngamy in giant clams is extremely sensitive to environmental warming. Finally, I demonstrate the significant, positive, effect of MPA establishment in permitting recovery of overharvested giant clam populations. T. maxima populations have increased approximately 3-fold in Mo’orea’s protected sites relative to non-protected controls and this rate of recovery is significantly higher than the global average for marine reserves. Taken together, these results suggest that effective regulation at both the population and physiological level may permit the recovery and persistence of giant clams in the face of anthropogenic challenges.
Author: Kathryn Stankiewicz
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Coral reefs are some of the most diverse ecosystems on the planet. While corals are ecologically and economically important, many species are in sharp decline due to the impacts of anthropogenic climate change. As members of the class Anthozoa, they also represent one of the oldest clades of metazoans. Thus, there is a pressing need to study the biology of these organisms from the standpoint of conservation and, at the same time, we may gain novel insight into ancient features of basal animals to better understand evolution of the higher metazoans. A critical underpinning of effective conservation is to delineate barriers to gene flow that may prevent the spread of adaptive alleles. The discovery of such barriers relies on theoretical population genetic models with assumptions that are frequently violated in real world datasets. Here, we investigated the impact of different population genetic methodologies through a re-estimation of genetic structure in empirical microsatellite datasets from both coral and non-coral species. Recent work showed that the [delta]K statistic, when applied to the output of the program STRUCTURE, often underestimates the true number of populations and proposed four alternative estimators. In comparing these newer K estimators with traditional ([delta]K and posterior probability) estimates in the empirical datasets re-analyzed here, we found widespread disagreement between estimators. Thus, we determined that a multi-tool approach, including a combination of all estimators and visual inspection of STRUCTURE plots, is always warranted in inferring the number of populations. Scleractinian corals have successfully adapted to a wide range of habitats from sunlit, tropical shallow waters to the dark and cold of the deep sea. By comparing genomic features of species from diverse habitats, we can gain insights into coral evolution. While several genomes of tropical corals now exist, temperate species remain understudied. I, thus, focused on developing a chromosome-scale genome assembly for the facultatively symbiotic, temperate coral Astrangia poculata. In comparison to the tropical coral Acropora millepora, we discovered a gene family with putative functions in circadian sleep/wake cycle, feeding suppression, and sleep promotion that was significantly bigger in Astrangia poculata. This finding highlights the potential role of gene expansion in the remarkable dormancy state A. poculata enters to survive the harsh, cold conditions of winter in the northern part of its range. In contrast, gene families that were significantly larger in Acropora millepora had functions relating to meiosis and sperm hyperactivation, consistent with the extreme requirements of sperm competition during mass spawning events in this species. Finally, in the fourth and fifth chapter, I studied how existing genetic variation is recombined and passed on from the current generation to the next -- a critical step in how corals may adapt to changing environments. We built a genetic linkage map for Acropora palmata and characterized the recombination landscape in a coral for the first time. We discovered pronounced heterochiasmy in A. palmata and suggest this may be due to female meiotic drive. We further confirm that coral recombination rates are high compared to other animals, which is a necessary prerequisite for fast adaptation to changing conditions. We then turned to studying how the genome of A. palmata recombines with the genome of its sister species, A. cervicornis when they form an F1 hybrid. We profiled the local ancestry of F1 hybrids between the two species and found regions of loss of heterozygosity (LOH) despite the expectation of heterozygosity at all loci in an F1 interspecific hybrid. These LOH regions were biased for the A. palmata ancestry and could contribute to the commonly observed sterility of the F1 hybrid. However, we did not find an association between local recombination in A. palmata and the LOH regions in the F1 hybrids, therefore the mechanisms underlying excess parentage of A. palmata in F1 hybrids remains unknown and deserves further study. Overall, this dissertation aims to develop and implement genomic resources and population genetic approaches to aid conservation efforts and to enhance our understanding of these threatened animals at the base of the Tree of Life. The results found here emphasize the importance of including genomic resources for a diversity of taxa during the study of core concepts in biology. Particularly, these findings demonstrate the value of high-quality genomic resources in non-model systems, such as corals.
