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• 1. [Article] Demography and the Evolution of Logistic Organization on the Northern Northwest Coast Between 11,000 and 5,000 cal BP

  Focusing on the relationship between demography and sedentary behavior, this thesis explores changes to mobility strategies on the Northern Northwest Coast of North America between 11,000 and 5,000 cal ...

  Citation × Citation Citation Abstract Copy Title: Demography and the Evolution of Logistic Organization on the Northern Northwest Coast Between 11,000 and 5,000 cal BP Author: Brown, Thomas Jay Year: 2016 Focusing on the relationship between demography and sedentary behavior, this thesis explores changes to mobility strategies on the Northern Northwest Coast of North America between 11,000 and 5,000 cal BP. Drawing on a regional database of radiocarbon dates, it uses summed probability distributions (SPDs) of calibrated dates as a proxy for population change, in combination with syntheses of previously published technological, paleo environmental and settlement pattern data to test three hypotheses derived from the literature about the development of logistic mobility among maritime hunter-gatherers on the Northern Coast. In all, each of the hypotheses proposes that early peoples on the coast were foragers that utilized high levels of residential mobility, who later adopted collector (logistic) strategies. Two of the hypotheses emphasize the role of population growth and/or packing and resource distribution in this transformation, while the third emphasizes population replacement. Other issues addressed within this thesis are whether or not the forager-collector continuum, as it is used for terrestrial hunter-gatherers, can be applied to those in aquatic settings. Also explored, is the question of whether the available data is sufficient for making and/or testing claims about early mobility patterns in the region. The results of the demographic models suggest that while population levels were volatile, volatility declined through time and that there is no significant trend in either growth or decline of overall population levels throughout the region. This thesis also confirmed that significant changes to mobility, as evidenced by the emergence of semi-sedentary to sedentary living, begin to appear by ~7,000 cal BP. However, there appears to be little, if any correlation between the advent of more sedentary and logistic behavior and any of the variables tested here. Thus this author suggests, in agreement with Ames (1985; 2004) and Binford (2001) that the distribution of resources and labor organization needs within aquatic environments are sufficient without any other drivers for the development and intensification of logistic mobility. The principle analytic contribution of this research comes from the demographic modeling that relied on the construction of summed probability distributions. Though these methods have become commonplace in other settings (namely Europe), this thesis presents the first application of these methods within the time period and region covered. Moreover, this research is one of the only of its kind to address demographic histories within coastal landscapes that utilizes both marine and terrestrial 14C samples. In order to explore possible biases within the database, comparisons of marine and terrestrial SPDs were made between sub-sections of the region (i.e. Haida Gwaii, Southeast Alaska and the Dundas Islands). Though patterning between each of these areas was consistent, these comparative methods revealed an unexpected finding; a massive population crash throughout the region that began between ~9,000-8,800 cal BP and lasted till around 8,400 cal BP. Importantly, this crash was witnessed within all of the individual sub-areas and within SPDs made from both the marine and terrestrial 14C samples, though the reasons behind this collapse and verification of its existence require future research. However, finding this collapse at all further highlighted the need for use of correctly calibrated 14C dates, as the gap in 14C dates effectively disappears when using uncalibrated dates, which has been a longstanding tradition within Northwest archaeology. Title: Demography and the Evolution of Logistic Organization on the Northern Northwest Coast Between 11,000 and 5,000 cal BP Author: Brown, Thomas Jay Year: 2016 Focusing on the relationship between demography and sedentary behavior, this thesis explores changes to mobility strategies on the Northern Northwest Coast of North America between 11,000 and 5,000 cal BP. Drawing on a regional database of radiocarbon dates, it uses summed probability distributions (SPDs) of calibrated dates as a proxy for population change, in combination with syntheses of previously published technological, paleo environmental and settlement pattern data to test three hypotheses derived from the literature about the development of logistic mobility among maritime hunter-gatherers on the Northern Coast. In all, each of the hypotheses proposes that early peoples on the coast were foragers that utilized high levels of residential mobility, who later adopted collector (logistic) strategies. Two of the hypotheses emphasize the role of population growth and/or packing and resource distribution in this transformation, while the third emphasizes population replacement. Other issues addressed within this thesis are whether or not the forager-collector continuum, as it is used for terrestrial hunter-gatherers, can be applied to those in aquatic settings. Also explored, is the question of whether the available data is sufficient for making and/or testing claims about early mobility patterns in the region. The results of the demographic models suggest that while population levels were volatile, volatility declined through time and that there is no significant trend in either growth or decline of overall population levels throughout the region. This thesis also confirmed that significant changes to mobility, as evidenced by the emergence of semi-sedentary to sedentary living, begin to appear by ~7,000 cal BP. However, there appears to be little, if any correlation between the advent of more sedentary and logistic behavior and any of the variables tested here. Thus this author suggests, in agreement with Ames (1985; 2004) and Binford (2001) that the distribution of resources and labor organization needs within aquatic environments are sufficient without any other drivers for the development and intensification of logistic mobility. The principle analytic contribution of this research comes from the demographic modeling that relied on the construction of summed probability distributions. Though these methods have become commonplace in other settings (namely Europe), this thesis presents the first application of these methods within the time period and region covered. Moreover, this research is one of the only of its kind to address demographic histories within coastal landscapes that utilizes both marine and terrestrial 14C samples. In order to explore possible biases within the database, comparisons of marine and terrestrial SPDs were made between sub-sections of the region (i.e. Haida Gwaii, Southeast Alaska and the Dundas Islands). Though patterning between each of these areas was consistent, these comparative methods revealed an unexpected finding; a massive population crash throughout the region that began between ~9,000-8,800 cal BP and lasted till around 8,400 cal BP. Importantly, this crash was witnessed within all of the individual sub-areas and within SPDs made from both the marine and terrestrial 14C samples, though the reasons behind this collapse and verification of its existence require future research. However, finding this collapse at all further highlighted the need for use of correctly calibrated 14C dates, as the gap in 14C dates effectively disappears when using uncalibrated dates, which has been a longstanding tradition within Northwest archaeology. Close

• 2. [Article] Evaluating the Influence of Policy and Technology in Driving Aquaculture Land Use Patterns in Thailand, 1990-2013

  Since the 1980's shrimp aquaculture has been one of Thailand's largest industries and has created cultivation ponds as a dominant feature on the landscape. While shrimp farming has been economically successful, ...

  Citation × Citation Citation Abstract Copy Title: Evaluating the Influence of Policy and Technology in Driving Aquaculture Land Use Patterns in Thailand, 1990-2013 Author: Mosurinjohn, Nathan Year: 2014 Since the 1980's shrimp aquaculture has been one of Thailand's largest industries and has created cultivation ponds as a dominant feature on the landscape. While shrimp farming has been economically successful, it has received criticism for being environmentally harmful, most notably because of farms replacing mangrove forests. Legislation regulating aquaculture development and technological responses to disease outbreak have had a large influence on the land use of the Thai coast. The objective of this research is to provide a systematic examination of how regulation and technology development have influenced land use in this region. To accomplish this, Landsat derived data were analyzed at the national and provincial scale to determine how Thai coastal land use systems change over time. I found that interrelated changes in technology and legislation have had complex influences on the landscape, which encourage both the restriction and expansion of aquaculture growth depending on time and location. Title: Evaluating the Influence of Policy and Technology in Driving Aquaculture Land Use Patterns in Thailand, 1990-2013 Author: Mosurinjohn, Nathan Year: 2014 Since the 1980's shrimp aquaculture has been one of Thailand's largest industries and has created cultivation ponds as a dominant feature on the landscape. While shrimp farming has been economically successful, it has received criticism for being environmentally harmful, most notably because of farms replacing mangrove forests. Legislation regulating aquaculture development and technological responses to disease outbreak have had a large influence on the land use of the Thai coast. The objective of this research is to provide a systematic examination of how regulation and technology development have influenced land use in this region. To accomplish this, Landsat derived data were analyzed at the national and provincial scale to determine how Thai coastal land use systems change over time. I found that interrelated changes in technology and legislation have had complex influences on the landscape, which encourage both the restriction and expansion of aquaculture growth depending on time and location. Close

• 3. [Article] Channel Shallowing as Mitigation of Coastal Flooding

  Here, we demonstrate that reductions in the depth of inlets or estuary channels can be used to reduce or prevent coastal flooding. A validated hydrodynamic model of Jamaica Bay, New York City (NYC), is ...

  Citation × Citation Citation Abstract Copy Title: Channel Shallowing as Mitigation of Coastal Flooding Author: Orton, Philip M., Talke, Stefan A., Jay, David A., Yin, Larry, Blumberg, Alan F., Georgas, Nickitas, Zhao, Haihong, Roberts, Hugh J., MacManus, Kytt Year: 2015 Here, we demonstrate that reductions in the depth of inlets or estuary channels can be used to reduce or prevent coastal flooding. A validated hydrodynamic model of Jamaica Bay, New York City (NYC), is used to test nature-based adaptation measures in ameliorating flooding for NYC’s two largest historical coastal flood events. In addition to control runs with modern bathymetry, three altered landscape scenarios are tested: (1) increasing the area of wetlands to their 1879 footprint and bathymetry, but leaving deep shipping channels unaltered; (2) shallowing all areas deeper than 2 m in the bay to be 2 m below Mean Low Water; (3) shallowing only the narrowest part of the inlet to the bay. These three scenarios are deliberately extreme and designed to evaluate the leverage each approach exerts on water levels. They result in peak water level reductions of 0.3%, 15%, and 6.8% for Hurricane Sandy, and 2.4%, 46% and 30% for the Category-3 hurricane of 1821, respectively (bay-wide averages). These results suggest that shallowing can provide greater flood protection than wetland restoration, and it is particularly effective at reducing "fast-pulse" storm surges that rise and fall quickly over several hours, like that of the 1821 storm. Nonetheless, the goal of flood mitigation must be weighed against economic, navigation, and ecological needs, and practical concerns such as the availability of sediment. Title: Channel Shallowing as Mitigation of Coastal Flooding Author: Orton, Philip M., Talke, Stefan A., Jay, David A., Yin, Larry, Blumberg, Alan F., Georgas, Nickitas, Zhao, Haihong, Roberts, Hugh J., MacManus, Kytt Year: 2015 Here, we demonstrate that reductions in the depth of inlets or estuary channels can be used to reduce or prevent coastal flooding. A validated hydrodynamic model of Jamaica Bay, New York City (NYC), is used to test nature-based adaptation measures in ameliorating flooding for NYC’s two largest historical coastal flood events. In addition to control runs with modern bathymetry, three altered landscape scenarios are tested: (1) increasing the area of wetlands to their 1879 footprint and bathymetry, but leaving deep shipping channels unaltered; (2) shallowing all areas deeper than 2 m in the bay to be 2 m below Mean Low Water; (3) shallowing only the narrowest part of the inlet to the bay. These three scenarios are deliberately extreme and designed to evaluate the leverage each approach exerts on water levels. They result in peak water level reductions of 0.3%, 15%, and 6.8% for Hurricane Sandy, and 2.4%, 46% and 30% for the Category-3 hurricane of 1821, respectively (bay-wide averages). These results suggest that shallowing can provide greater flood protection than wetland restoration, and it is particularly effective at reducing "fast-pulse" storm surges that rise and fall quickly over several hours, like that of the 1821 storm. Nonetheless, the goal of flood mitigation must be weighed against economic, navigation, and ecological needs, and practical concerns such as the availability of sediment. Close

• 4. [Article] Woven Into the Community: Resilience and Tsunami Evacuation Route Configuration in Neskowin, Oregon

  89 pages. Examining committee chair: Chris Enright

  Citation × Citation Citation Abstract Copy Title: Woven Into the Community: Resilience and Tsunami Evacuation Route Configuration in Neskowin, Oregon Author: Davis, Bryn Year: 2017 89 pages. Examining committee chair: Chris Enright Title: Woven Into the Community: Resilience and Tsunami Evacuation Route Configuration in Neskowin, Oregon Author: Davis, Bryn Year: 2017 89 pages. Examining committee chair: Chris Enright Close

• 5. [Article] A Morphologic Proxy for Debris Flow Erosion With Application to the Earthquake Deformation Cycle, Cascadia Subduction Zone, USA

  In unglaciated steeplands, valley reaches dominated by debris flow scour and incision set landscape form as they often account for > 80% of valley network length and relief. While hillslope and fluvial ...

  Citation × Citation Citation Abstract Copy Title: A Morphologic Proxy for Debris Flow Erosion With Application to the Earthquake Deformation Cycle, Cascadia Subduction Zone, USA Author: Penserini, Brian D., Roering, Joshua J., Strieg, Ashley Year: 2017 In unglaciated steeplands, valley reaches dominated by debris flow scour and incision set landscape form as they often account for > 80% of valley network length and relief. While hillslope and fluvial process models have frequently been combined with digital topography to develop morphologic proxies for erosion rate and drainage divide migration, debris-flow-dominated networks, despite their ubiquity, have not been exploited for this purpose. Here, we applied an empirical function that describes how slope-area data systematically deviate from so-called fluvial power-law behavior at small drainage areas. Using airborne LiDAR data for 83 small (~ 1 km2) catchments in the western Oregon Coast Range, we quantified variation in model parameters and observed that the curvature of the power-law scaling deviation varies with catchment-averaged erosion rate estimated from cosmogenic nuclides in stream sediments. Given consistent climate and lithology across our study area and assuming steady erosion, we used this calibrated denudation-morphology relationship to map spatial patterns of long-term uplift for our study catchments. By combining our predicted pattern of long-term uplift rate with paleoseismic and geodetic (tide gauge, GPS, and leveling) data, we estimated the spatial distribution of coseismic subsidence experienced during megathrust earthquakes along the Cascadia Subduction Zone. Our estimates of coseismic subsidence near the coast (0.4 to 0.7 m for earthquake recurrence intervals of 300 to 500 years) agree with field measurements from numerous stratigraphic studies. Our results also demonstrate that coseismic subsidence decreases inland to negligible values > 25 km from the coast, reflecting the diminishing influence of the earthquake deformation cycle on vertical changes of the interior coastal ranges. More generally, our results demonstrate that debris flow valley networks serve as highly localized, yet broadly distributed indicators of erosion (and rock uplift), making them invaluable for mapping crustal deformation and landscape adjustment. © 2017 Elsevier B.V. Title: A Morphologic Proxy for Debris Flow Erosion With Application to the Earthquake Deformation Cycle, Cascadia Subduction Zone, USA Author: Penserini, Brian D., Roering, Joshua J., Strieg, Ashley Year: 2017 In unglaciated steeplands, valley reaches dominated by debris flow scour and incision set landscape form as they often account for > 80% of valley network length and relief. While hillslope and fluvial process models have frequently been combined with digital topography to develop morphologic proxies for erosion rate and drainage divide migration, debris-flow-dominated networks, despite their ubiquity, have not been exploited for this purpose. Here, we applied an empirical function that describes how slope-area data systematically deviate from so-called fluvial power-law behavior at small drainage areas. Using airborne LiDAR data for 83 small (~ 1 km2) catchments in the western Oregon Coast Range, we quantified variation in model parameters and observed that the curvature of the power-law scaling deviation varies with catchment-averaged erosion rate estimated from cosmogenic nuclides in stream sediments. Given consistent climate and lithology across our study area and assuming steady erosion, we used this calibrated denudation-morphology relationship to map spatial patterns of long-term uplift for our study catchments. By combining our predicted pattern of long-term uplift rate with paleoseismic and geodetic (tide gauge, GPS, and leveling) data, we estimated the spatial distribution of coseismic subsidence experienced during megathrust earthquakes along the Cascadia Subduction Zone. Our estimates of coseismic subsidence near the coast (0.4 to 0.7 m for earthquake recurrence intervals of 300 to 500 years) agree with field measurements from numerous stratigraphic studies. Our results also demonstrate that coseismic subsidence decreases inland to negligible values > 25 km from the coast, reflecting the diminishing influence of the earthquake deformation cycle on vertical changes of the interior coastal ranges. More generally, our results demonstrate that debris flow valley networks serve as highly localized, yet broadly distributed indicators of erosion (and rock uplift), making them invaluable for mapping crustal deformation and landscape adjustment. © 2017 Elsevier B.V. Close

• 6. [Article] Impacts of Permafrost Degradation on a Stream in Taylor Valley, Antarctica

  The McMurdo Dry Valleys (MDV) of Antarctica are an ice-free landscape that supports a complex, microbially dominated ecosystem despite a severely arid, cold environment (< 5 cm water equivalent/y, − 18 ...

  Citation × Citation Citation Abstract Copy Title: Impacts of Permafrost Degradation on a Stream in Taylor Valley, Antarctica Author: Sudman, Zachary, Gooseff, Michael N., Fountain, Andrew G., Levy, Joseph S. Year: 2017 The McMurdo Dry Valleys (MDV) of Antarctica are an ice-free landscape that supports a complex, microbially dominated ecosystem despite a severely arid, cold environment (< 5 cm water equivalent/y, − 18 °C mean annual air temperature). Recent observations of permafrost degradation in the coastal zones of the MDV suggest that this region is nearing a threshold of rapid landscape change. In 2012, substantial thermokarst development was observed along several kilometers of the west branch of Crescent Stream in Taylor Valley mostly in the form of bank failures, whereas the adjacent east branch was unaffected. The objective of this study was to quantify the changes to the stream banks of the west branch of Crescent Stream and to determine the impacts on the composition of the stream bed material. Three annually repeated terrestrial LiDAR scans were compared to determine the rates of ground surface change caused by thermokarst formation on the stream bank. The areal extent of the thermokarst was shown to be decreasing; however, the average vertical rate of retreat remained constant. Field measurements of bed materials indicated that the west branch and the reach downstream of the confluence (of east and west branches) consistently contained more fines than the unaffected east branch. This suggests that the finer bed material is a result of the thermokarst development on the west branch. These finer bed material compositions are likely to increase the mobility of the bed material, which will have implications for stream morphology, stream algal mat communities, and downstream aquatic ecosystems. Title: Impacts of Permafrost Degradation on a Stream in Taylor Valley, Antarctica Author: Sudman, Zachary, Gooseff, Michael N., Fountain, Andrew G., Levy, Joseph S. Year: 2017 The McMurdo Dry Valleys (MDV) of Antarctica are an ice-free landscape that supports a complex, microbially dominated ecosystem despite a severely arid, cold environment (< 5 cm water equivalent/y, − 18 °C mean annual air temperature). Recent observations of permafrost degradation in the coastal zones of the MDV suggest that this region is nearing a threshold of rapid landscape change. In 2012, substantial thermokarst development was observed along several kilometers of the west branch of Crescent Stream in Taylor Valley mostly in the form of bank failures, whereas the adjacent east branch was unaffected. The objective of this study was to quantify the changes to the stream banks of the west branch of Crescent Stream and to determine the impacts on the composition of the stream bed material. Three annually repeated terrestrial LiDAR scans were compared to determine the rates of ground surface change caused by thermokarst formation on the stream bank. The areal extent of the thermokarst was shown to be decreasing; however, the average vertical rate of retreat remained constant. Field measurements of bed materials indicated that the west branch and the reach downstream of the confluence (of east and west branches) consistently contained more fines than the unaffected east branch. This suggests that the finer bed material is a result of the thermokarst development on the west branch. These finer bed material compositions are likely to increase the mobility of the bed material, which will have implications for stream morphology, stream algal mat communities, and downstream aquatic ecosystems. Close

• 7. [Article] Recombination Rate Heterogeneity Compartmentalizes Genomic Variation and Facilitates Adaptive Evolution in the Threespine Stickleback

  72 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2...

  Citation × Citation Citation Abstract Copy Title: Recombination Rate Heterogeneity Compartmentalizes Genomic Variation and Facilitates Adaptive Evolution in the Threespine Stickleback Author: Crandall, Johnathan Gage Williams Year: 2017 72 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Title: Recombination Rate Heterogeneity Compartmentalizes Genomic Variation and Facilitates Adaptive Evolution in the Threespine Stickleback Author: Crandall, Johnathan Gage Williams Year: 2017 72 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Close

• 8. [Article] THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus)

  Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary ...

  Citation × Citation Citation Abstract Copy Title: THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus) Author: Nelson, Thomas Year: 2017 Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species. Title: THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus) Author: Nelson, Thomas Year: 2017 Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species. Close