Search

All marine species studied thus far show rhythmic temporal patterns in their behavioural, physiological, and molecular functions, which are collectively known as biological rhythms. Biological rhythms are generated by biological clocks that time biological functions and are synchronized by geophysical cycles, such as the solar light-dark cycle and tidal cycle. On continental margins, behavioural rhythms can be detected by diel (i.e., 24-hour based) or seasonal periodical trawling as a consequence of massive inward and outward displacements of populations to and from the sample areas. As a result, significant errors in population/stock and biodiversity assessments performed by trawling may occur if timing of sampling is not taken into account. The increasing number of cabled and permanent multiparametric seafloor observatories now allows direct, continuous, and long-lasting monitoring of benthic ecosystems and analysis in relation to several habitat cycles. This review describes the adaptation of this technology to investigations of rhythmic behaviour by focusing on automated video imaging. Diel fluctuations in the number of video-observed individuals can be used as a measure of average population rhythmic behaviour. The potential implementation of automated video image analysis in relation to animal tracking and classification procedures based on the combined use of morphometric tools and multivariate statistics is detailed in relation to populational and community studies. Based on video cameras mounted at multiparametric cabled observatories, an integrated time-series analysis protocol using chronobiomedical procedures is proposed to place video-recorded bioinformation in an oceanographic context., Peer Reviewed, Postprint (author’s final draft)

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Includes bibliographical references., The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often chang, by Jonathan N. Blythe., Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008., This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections., Includes bibliographical references., The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often chang, by Jonathan N. Blythe., Ph.D.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2008, The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often chang

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2008, The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often chang

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2008, The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often chang

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2008, The benthic habitat is the terminal destination for marine animals in terms of their reproductive lifecycle. Recruitment dynamics relating to seasonal changes in the benthic habitat may be the best source of information for predicting recruit abundance and for marine resources management. The transition from the pelagic to the benthic phases is the last stage in the connectivity between benthic populations. The transition to the benthos may be a process that dominates recruitment dynamics to the exclusion of other characteristics of larvae such as their quality and their density. Recruitment of benthic marine animals is influenced by two seasonally varying factors of the benthic habitat. First, the availability of suitable habitat for recruitment can in large part determine the survival probability for settlers, a trend that is most pronounced for low or no survival when the settlement substrate is saturated by conspecifics from a recruitment cohort. Preemption is caused by the presence of current occupants from a recruit cohort, and it influences the settlement rate or the survival probability of conspecifics. Descriptive statistics (Chapter 2) and a field experiment (Chapter 4) highlight the role of preemption on barnacle recruitment. The second factor results from seasonal changes in environmental conditions that settlers experience in the benthic habitat, which could affect the physiology and survival probability of barnacle settlers. Highly unpredictable features of recruitment dynamics also play a role, such as wind that enhances wave action in the rocky intertidal that has been linked to the rate of settlement. Day to day variability in wind may cause patterns of settlement to be highly unpredictable. Predator induced mortality is spatially aggregated, and the random pattern of mortality in space is highly unpredictable. In contrast to these high frequency sources of recruitment variability, seasonal factors that vary at lower frequencies and that often chang

Benthic organisms and substrates in the Great Salt Lake, Utah, were sampled during one week in June 2006 to test collection methodologies for biostromes and soft substrates and to get preliminary information on the selenium concentrations of benthic organisms. The sampling was focused on biostromes, as these solid reef-like structures cover 23% of the oxic benthic area of the lake and are the principal habitat for brine fly (Ephydra cinerea) larvae and pupae that are fed upon by some birds utilizing the lake. Samples were taken at depths of 1-5 m along two transects–one near Bridger Bay and another in the southern area of Gilbert Bay. The biostromes were sampled with a pumped-bucket device operated by a SCUBA diver whereas the soft sediments were sampled with a Ponar grab. Water samples and adult brine flies were also collected.

Benthic organisms and substrates in the Great Salt Lake, Utah, were sampled during one week in June 2006 to test collection methodologies for biostromes and soft substrates and to get preliminary information on the selenium concentrations of benthic organisms. The sampling was focused on biostromes, as these solid reef-like structures cover 23% of the oxic benthic area of the lake and are the principal habitat for brine fly (Ephydra cinerea) larvae and pupae that are fed upon by some birds utilizing the lake. Samples were taken at depths of 1-5 m along two transects–one near Bridger Bay and another in the southern area of Gilbert Bay. The biostromes were sampled with a pumped-bucket device operated by a SCUBA diver whereas the soft sediments were sampled with a Ponar grab. Water samples and adult brine flies were also collected.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The goals of this thesis were to quantify the behavior of gastropod larvae (mud snails Ryanassa obsoleta) in turbulence, and to investigate how that behavior affects larval supply in a turbulent coastal inlet. Gastropod larvae retract their velums and sink rapidly in strong turbulence. Turbulence-induced sinking would be an adaptive behavior if it resulted in increased larval supply and enhanced settlement in suitable coastal habitats. In laboratory experiments, mud snail larvae were found to have three behavioral modes: swimming, hovering, and sinking. The proportion of sinking larvae increased exponentially with the turbulence dissipation rate over a range comparable to turbulence in a tidal inlet, and the mean larval vertical velocity shifted from upward to downward in turbulence resembling energetic nearshore areas. The larval response to turbulence was incorporated in a vertical advection-diffusion model to characterize the effects of this behavior on larval supply and settlement in a tidal channel. Compared to passive larvae, larvae that sink in turbulence have higher near-bed concentrations throughout flood and ebb tides. This high larval supply enables behaving larvae to settle more successfully than passive larvae in strong currents characteristic of turbulent tidal inlets. A study was conducted at Barnstable Harbor, MA to estimate the responses of larvae to turbulence in the field. Gastropod larvae from different coastal environments had genus-specific responses to turbulence, suggesting that larvae use turbulence for large-scale habitat selection. On ebb tides, mud snail larvae had a similar response to turbulence as in the laboratory, with greater sinking velocities in strong turbulence. Behavior estimates differed for flood and ebb tides, indicating that additional physical cues influence behavior. Turbulence-induced sinking behavior would enhance retention and promote settlement of mud snail larvae in habitats like Barnstable Harbor., Financial support was provided by a National Science Foundation Graduate Research Fellowship, the WHOI Academic Programs Office, a WHOI Coastal Ocean: Institute grant, a WHOI Mellon independent study grant to L. S. Mullineaux and M; G. Neubert, a Sea Grant New Initiative grant (Grant No. NA16RG2273, project no. R/O-38-PD), the WHOI Biology department, and the Rinehart Coastal Research Center.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The goals of this thesis were to quantify the behavior of gastropod larvae (mud snails Ryanassa obsoleta) in turbulence, and to investigate how that behavior affects larval supply in a turbulent coastal inlet. Gastropod larvae retract their velums and sink rapidly in strong turbulence. Turbulence-induced sinking would be an adaptive behavior if it resulted in increased larval supply and enhanced settlement in suitable coastal habitats. In laboratory experiments, mud snail larvae were found to have three behavioral modes: swimming, hovering, and sinking. The proportion of sinking larvae increased exponentially with the turbulence dissipation rate over a range comparable to turbulence in a tidal inlet, and the mean larval vertical velocity shifted from upward to downward in turbulence resembling energetic nearshore areas. The larval response to turbulence was incorporated in a vertical advection-diffusion model to characterize the effects of this behavior on larval supply and settlement in a tidal channel. Compared to passive larvae, larvae that sink in turbulence have higher near-bed concentrations throughout flood and ebb tides. This high larval supply enables behaving larvae to settle more successfully than passive larvae in strong currents characteristic of turbulent tidal inlets. A study was conducted at Barnstable Harbor, MA to estimate the responses of larvae to turbulence in the field. Gastropod larvae from different coastal environments had genus-specific responses to turbulence, suggesting that larvae use turbulence for large-scale habitat selection. On ebb tides, mud snail larvae had a similar response to turbulence as in the laboratory, with greater sinking velocities in strong turbulence. Behavior estimates differed for flood and ebb tides, indicating that additional physical cues influence behavior. Turbulence-induced sinking behavior would enhance retention and promote settlement of mud snail larvae in habitats like Barnstable Harbor., Financial support was provided by a National Science Foundation Graduate Research Fellowship, the WHOI Academic Programs Office, a WHOI Coastal Ocean: Institute grant, a WHOI Mellon independent study grant to L. S. Mullineaux and M; G. Neubert, a Sea Grant New Initiative grant (Grant No. NA16RG2273, project no. R/O-38-PD), the WHOI Biology department, and the Rinehart Coastal Research Center.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The goals of this thesis were to quantify the behavior of gastropod larvae (mud snails Ryanassa obsoleta) in turbulence, and to investigate how that behavior affects larval supply in a turbulent coastal inlet. Gastropod larvae retract their velums and sink rapidly in strong turbulence. Turbulence-induced sinking would be an adaptive behavior if it resulted in increased larval supply and enhanced settlement in suitable coastal habitats. In laboratory experiments, mud snail larvae were found to have three behavioral modes: swimming, hovering, and sinking. The proportion of sinking larvae increased exponentially with the turbulence dissipation rate over a range comparable to turbulence in a tidal inlet, and the mean larval vertical velocity shifted from upward to downward in turbulence resembling energetic nearshore areas. The larval response to turbulence was incorporated in a vertical advection-diffusion model to characterize the effects of this behavior on larval supply and settlement in a tidal channel. Compared to passive larvae, larvae that sink in turbulence have higher near-bed concentrations throughout flood and ebb tides. This high larval supply enables behaving larvae to settle more successfully than passive larvae in strong currents characteristic of turbulent tidal inlets. A study was conducted at Barnstable Harbor, MA to estimate the responses of larvae to turbulence in the field. Gastropod larvae from different coastal environments had genus-specific responses to turbulence, suggesting that larvae use turbulence for large-scale habitat selection. On ebb tides, mud snail larvae had a similar response to turbulence as in the laboratory, with greater sinking velocities in strong turbulence. Behavior estimates differed for flood and ebb tides, indicating that additional physical cues influence behavior. Turbulence-induced sinking behavior would enhance retention and promote settlement of mud snail larvae in habitats like Barnstable Harbor., Financial support was provided by a National Science Foundation Graduate Research Fellowship, the WHOI Academic Programs Office, a WHOI Coastal Ocean: Institute grant, a WHOI Mellon independent study grant to L. S. Mullineaux and M; G. Neubert, a Sea Grant New Initiative grant (Grant No. NA16RG2273, project no. R/O-38-PD), the WHOI Biology department, and the Rinehart Coastal Research Center.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The goals of this thesis were to quantify the behavior of gastropod larvae (mud snails Ryanassa obsoleta) in turbulence, and to investigate how that behavior affects larval supply in a turbulent coastal inlet. Gastropod larvae retract their velums and sink rapidly in strong turbulence. Turbulence-induced sinking would be an adaptive behavior if it resulted in increased larval supply and enhanced settlement in suitable coastal habitats. In laboratory experiments, mud snail larvae were found to have three behavioral modes: swimming, hovering, and sinking. The proportion of sinking larvae increased exponentially with the turbulence dissipation rate over a range comparable to turbulence in a tidal inlet, and the mean larval vertical velocity shifted from upward to downward in turbulence resembling energetic nearshore areas. The larval response to turbulence was incorporated in a vertical advection-diffusion model to characterize the effects of this behavior on larval supply and settlement in a tidal channel. Compared to passive larvae, larvae that sink in turbulence have higher near-bed concentrations throughout flood and ebb tides. This high larval supply enables behaving larvae to settle more successfully than passive larvae in strong currents characteristic of turbulent tidal inlets. A study was conducted at Barnstable Harbor, MA to estimate the responses of larvae to turbulence in the field. Gastropod larvae from different coastal environments had genus-specific responses to turbulence, suggesting that larvae use turbulence for large-scale habitat selection. On ebb tides, mud snail larvae had a similar response to turbulence as in the laboratory, with greater sinking velocities in strong turbulence. Behavior estimates differed for flood and ebb tides, indicating that additional physical cues influence behavior. Turbulence-induced sinking behavior would enhance retention and promote settlement of mud snail larvae in habitats like Barnstable Harbor., Financial support was provided by a National Science Foundation Graduate Research Fellowship, the WHOI Academic Programs Office, a WHOI Coastal Ocean: Institute grant, a WHOI Mellon independent study grant to L. S. Mullineaux and M; G. Neubert, a Sea Grant New Initiative grant (Grant No. NA16RG2273, project no. R/O-38-PD), the WHOI Biology department, and the Rinehart Coastal Research Center.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that se, Financial support was provided by an Academic Programs Office fellowship, a CICOR fellowship and research grant, and a National Science Foundation research grant.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that se, Financial support was provided by an Academic Programs Office fellowship, a CICOR fellowship and research grant, and a National Science Foundation research grant.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The geographic distribution and dynamics of coastal benthic populations are shaped by physical biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short tenn (i.e. days) smallscale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus glandula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation ofnauplii and cyprids. Differences in survival, growth rate,· size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics, I must thank the Chilean MIDEPLAN (Ministerio de Plartificacion y Cooperacion), which provided funds for the first three years of my doctoral studies through a Presidential Fellowship (Beca Presidente de la Republica). Tuition, stipend, and research funds for the rest of my time. as a Joint Program student carne from National Science Foundation grants OCE-0083976 and OCE-9986627 to my thesis supervisor (Jesus Pineda), and through the WHOI Academic Programs Office.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that se, Financial support was provided by an Academic Programs Office fellowship, a CICOR fellowship and research grant, and a National Science Foundation research grant.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The geographic distribution and dynamics of coastal benthic populations are shaped by physical biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short tenn (i.e. days) smallscale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus glandula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation ofnauplii and cyprids. Differences in survival, growth rate,· size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics, I must thank the Chilean MIDEPLAN (Ministerio de Plartificacion y Cooperacion), which provided funds for the first three years of my doctoral studies through a Presidential Fellowship (Beca Presidente de la Republica). Tuition, stipend, and research funds for the rest of my time. as a Joint Program student carne from National Science Foundation grants OCE-0083976 and OCE-9986627 to my thesis supervisor (Jesus Pineda), and through the WHOI Academic Programs Office.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The geographic distribution and dynamics of coastal benthic populations are shaped by physical biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short tenn (i.e. days) smallscale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus glandula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation ofnauplii and cyprids. Differences in survival, growth rate,· size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics, I must thank the Chilean MIDEPLAN (Ministerio de Plartificacion y Cooperacion), which provided funds for the first three years of my doctoral studies through a Presidential Fellowship (Beca Presidente de la Republica). Tuition, stipend, and research funds for the rest of my time. as a Joint Program student carne from National Science Foundation grants OCE-0083976 and OCE-9986627 to my thesis supervisor (Jesus Pineda), and through the WHOI Academic Programs Office.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity of available markers have allowed more complex and fine-scale questions to be asked at a variety of taxonomic levels. At the phylogenetic level, whole mitochondrial genome sequencing of two polychaetes (the deep-sea tubeworm Riftia pachyptila and the intertidal bamboo worm Clymenella torquata) supports the placement of leeches and oligochaetes within the polychaete radiation, in keeping with molecular evidence and morphological reinvestigations. This re-interpretation, first proposed by others, synonomizes "Annelida" and "Polychaeta", and lends further support to the inclusion of echiurids, siboglinids (previously called vestimentiferans) within annelids, and sipunculans as close allies. The complete mt-genome of C. torquata was then rapidly screened to obtain markers useful in short timescale population genetics. Two quickly evolving mitochondrial markers were sequenced from ten populations of C. torquata from the Bay of Fundy to New Jersey to investigate previous hypotheses that the Cape Cod, MA peninsula is a barrier to gene flow in the northwest Atlantic. A barrier to gene flow was found, but displaced south of Cape Cod, between Rhode Island and Long Island, NY. Imposed upon this pattern was a gradient in genetic diversity presumably due to previous glaciation, with northern populations exhibiting greatly reduced diversity relative to southern sites. These trends in C. torquata, combined with other recent short time scale population genetic research, highlight the lack of population genetics models relevant to marine benthic invertebrates. To this end, I constructed a model including a typical benthic invertebrate life cycle, and described the patterns of genetic differentiation at the juvenile and adult stages. Model analysis indicates that se, Financial support was provided by an Academic Programs Office fellowship, a CICOR fellowship and research grant, and a National Science Foundation research grant.

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005, The geographic distribution and dynamics of coastal benthic populations are shaped by physical biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short tenn (i.e. days) smallscale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus glandula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation ofnauplii and cyprids. Differences in survival, growth rate,· size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics, I must thank the Chilean MIDEPLAN (Ministerio de Plartificacion y Cooperacion), which provided funds for the first three years of my doctoral studies through a Presidential Fellowship (Beca Presidente de la Republica). Tuition, stipend, and research funds for the rest of my time. as a Joint Program student carne from National Science Foundation grants OCE-0083976 and OCE-9986627 to my thesis supervisor (Jesus Pineda), and through the WHOI Academic Programs Office.

River improvement and maintenance works can play an important role in conserving rivers and restoring them to a more natural state. This paper focuses on aquatic organisms (specifically, benthic animals) as indicators of river conditions, toward clarifying the relationship between inhabitation by these animals and the physical conditions of a river channel (flow velocity, water depth, bottom materials) and the food environment (i. e., periphyton and particulate organic matter). The relationship was examined by comparing pools and riffles in various types of river channels, such as those with and without river improvement works. The examination found that improved sections have less storage of organic matter than unimproved sections have. We also confirmed our findings on restoring a river to its natural state by varying the physical conditions and food environment in the improved section.

The youngest major turnover in deep-sea benthic foraminifera (termed the Stilostomella extinction) is documented in two ODP sites in the South Atlantic Ocean. This study is the first detailed investigation of its kind in this region, and reveals the pulsed decline and eventual extinction of 33 species of elongate, cylindrical benthic foraminifera belonging to the families Stilostomellidae, Pleurostomellidae, and part of the Nodosariidae during the mid-Pleistocene climatic transition (MPT, ~1200 - 600ka). Furthermore, the Stilostomella extinction is limited to elongate species with highly specific apertural characteristics (e.g. cribrate, slit lunate, and hooded with secondary teeth), such as Chrysalogonium, Ellipsoglandulina, and Pleurostomella species, respectively. Micropaleontological and sedimentological data from lower bathyal Sites 1082 and 1088 (1290 m and 2082 m water depth, respectively) provide a proxy record of oceanographic changes in the South Atlantic Ocean through the MPT. This study compares the timing and causes of the Stilostomella extinction between two highly contrasting environmental settings in relation to paleoceanographic history, sediment regime and paleoproductivity. In the South Atlantic, the abundance and accumulation rate of Extinction Group (EG) taxa began to decline between ~ 1070 and 1000 ka at both core sites. The rate of decline was pulsed, with major declines usually associated with cool periods, and partial recoveries during intervening warm periods. The timing of highest occurrences (HOs) was diachronous between sites, and the final Stilostomella extinction datum is marked by the uppermost occurrence of Myllostomella matanzana and Siphonodosaria sagrinensis at ~705 ka in Site 1082, and Myllostomella matanzana and Pleurostomella alternans at ~600 ka in Site 1088. This corresponds with the previously documented global Stilostomella extinction datum within the period of 700 and 570 ka. Detailed comparisons with North Atlantic and So

This study examines the effect of the hydrological regime and landscape characteristics on benthic stream macroinvertebrate communities in the Whanganui Catchment, New Zealand, using a variety of statistical techniques. A total of 36 hydrological variables were considered. Thirteen of these were calculated from long-term flow and rainfall records, and interpolated using geographic information systems (GIS) to cover the area of interest. Ten hydrological variables were derived from topographical maps though GIS, with a further 13 hydrological variables determined from rainfall information relating to the timing since the last event. Catchment and riparian landscape variables (land cover, geology and soil type) were derived from New Zealand's land classification database and land resource inventory using GIS. Community structure was measured using an ordination, species richness, total number of animals and the densities of 22 common taxa. Biological data was also quantified with a variety of diversity and water quality indices including Simpson's, Margalef's and Macroinvertebrate Community Index. Individual links between biological and all environmental data were explored through Pearson's correlations. Multiple regression was used to examine the combination of the environmental variables that were best in determining individual characteristics of community structure. Canonical correlation was utilized to assess overall concurrent patterns between landscape and biotic data. Stepwise logistic regression and classification trees were used to explore occurrence of the 22 selected taxa in relation to environmental variables. Of the modelling techniques assessed for prediction of taxa occurrence classification trees gave as good or better predictions than the other models and tended to produce simpler models, suggesting that it is probably a better modelling technique for this data. Of the environmental variables, FRE3 (number of flood events per year over 3 times the med

The bed movement of 42 streams in the Ruahine Forest Park, Urewera National Park, and Cass-Craigiebum region was predicted from each stream's channel and catchment characteristics. While a stepwise regression was relatively unsuccessful in predicting tracer particle movement, an artificial neural network analysis achieved strong correlations with measured tracer particle data. Forty-three streams in the Ruahine and Tararua Forest Parks were sampled in the summers of 1996 and 2001, and the macroinvertebrate communities compared. Changes in community structure between the two surveys did not correlate with any measured environmental characteristics including stream bed movement and change in periphyton biomass. MCI scores changed by a mean of 12.8 points between the two surveys, and the number of sites attaining an MCI score indicative of a 'pristine' stream dropped from 40 to 29. This appears to be related to a change in stream temperature, with streams that were cooler in 2001 than in 1996 showing an increase in MCI, while those which were warmer showed a decrease. Changes such as these could have a marked effect on biomonitoring programmes that use reference sites similar to these streams. In both 1996 and 2001, a greater number of taxa were collected from sites with more periphyton - taxon richness appears to asymptote at chlorophyll a concentrations greater than 5 μg/cm² Twelve streams within the Ruahine Forest Park were sampled every three months between June 2000 and May 2001. Both periphyton biomass and macroinvertebrate taxon richness tended to decrease with bed movement. While macroinvertebrate community structure showed marked changes over the study period, these changes were not linked to bed movement or variation in periphyton level. The seasonal changes observed in these streams are not significantly different to the changes seen between the summers of 1996 and 2001 - community structure was no more stable between two summers separated by five years than

In this study different sampling methodology and strategy was explored to develop an efficient inventory protocol for assessing biodiversity of stream macroinvertebrates in New Zealand. In a preliminary study 3 benthic invertebrate sampling techniques (Surber, kicknet and individual stone sampling) were compared to examine which maximised collected biodiversity per unit effort. Kicknet samples collected a higher number of taxa than either Surber or individual stone samples. Three-minute kicknets collected significantly more taxa than the other techniques, although 30-second kicknets collected the most taxa per unit effort. Detrended correspondence analysis of sampling techniques showed groupings of 30-second and 1-minute kicknets, 5 or more Surber samples, or individual stones samples collected the best representation of the community. Three strategies of sample collection using kicknet samples were investigated in 54 streams, in 3 conservation regions in the South Island, to see which collected greater taxa richness per unit effort. These strategies examined taxa accumulation in three samples in a) the same stream, b) different streams within one region, c) different streams in each of the 3 regions. Collected taxa richness was higher when sampling effort was spread over more habitats and a larger area i.e., strategy b and c. Environmental characteristics measured at each stream, were assessed to examine links between community structure and habitat characteristics. Community structure was most strongly linked with altitude, canopy cover, moss cover, stream width, and temperature. Five groups of communities were identified ranging from small high altitude streams with moss and high canopy cover, to larger more open low altitude streams. These groups had a common core of invertebrate taxa that differed in density and relative abundance. To test for the presence of indicator taxa of biodiversity, individual taxa densities were correlated with total taxa richness. Sev

Surber samples from the benthos and T-bar samples (14 mm PVC pipe diameter) from the hyporheos were collected from 8 Southern Hawkes Bay rivers, differing in environmental conditions and geological age, and 8 rivers of the Cass/Craigieburn region of Canterbury that had differing physical stability and hyporheic physicochemical characteristics. Gravel bedded rivers of the Southern Hawkes Bay (North Island) and Cass/Craigieburn region (South Island) were sampled to examine the spatial distribution of the hyporheos in relation to physicochemical factors, bed stability and the significance of the hyporheic zone as a refuge and/or source of invertebrate colonists to the benthos. Physical bed movement, the duration of channel dewatering and flow variance were used to measure disturbance to the hyporheos and benthos, respectively. Benthic invertebrate communities of many streams are subject to constant disturbance from fluctuations in flow, temperature, and bed movement. In contrast, the hyporheos residing in the hyporheic zone may not experience the same disturbance regimes because bed movement occurs less often in the hyporheic zone and there is less diel temperature, dissolved oxygen and flow fluctuations. In the rivers investigated, broad (between river) and finer (within river) scale environmental factors influenced the composition of the hyporheos. Local geomorphology appeared to have a significant effect on the hyporheos by markedly increasing the proportion of epigean animals (benthic animals resident in the hyporheos) at sites of young geomorphology (less that 0.05 mya). In contrast, hypogean animals (animals seldom encountered from the benthos) dominated geologically older sites (greater than 0.4 mya). Species diversity in the hyporheic zone was highest with intermediate levels of bed movement where both hypogean and epigean animals were present. The greater abundance of epigean fauna with increasing bed movement may reflect differences in disturbance regime betw