Organismic and Evolutionary Biology Graduate Program Dissertations Collection

Phylogenetics and patterns of molecular evolution in amoebozoa

Lahr, Daniel J. G — Mon, 16 Apr 2012 14:14:27 PDT

My dissertation explores several aspects of the relationship between morphological and molecular evolution in amoeboid lineages: ^ Chapter 1—General Introduction. This chapter provides an overview of the most pressing issues in Amoebozoa phylogeny that are dealt with in the remainder of the thesis. ^ Chapter 2—Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new generation high fidelity DNA polymerase. This chapter addresses the methodological difficulty in the study of large gene families, the generation of artifactual sequences by recombination during PCR ^ Chapter 3—Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions. This chapter explores intriging patterns of evolution in the actin gene families of testate amoebae. ^ Chapter 4—Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analysis of SSU-rDNA and actin genes. A deep phylogenetic analyses of the Amoebozoa, enables exploration of well supported taxonomic units within the group. ^ Chapter 5—Interpreting the evolutionary history of the Tubulinea (Amoebozoa), in light of a multigene phylogeny. This chapter explores a more restrict taxonomic unit within the Amoebozoa—the Tubulinea—based on an expanded sample of genes and taxa. ^ Chapter 6—The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms. This chapter asks whether the null-hypothesis that amoebae are asexual is consistent with current phylogenetic evidence. ^

Population dynamics of the Hemlock Woolly Adelgid (Hemiptera: Adelgidae)

Paradis, Annie F — Mon, 16 Apr 2012 14:14:02 PDT

The hemlock woolly adelgid, Adelges tsugae, is an invasive insect from Osaka, Japan threatening populations of eastern hemlock, Tsuga canadensis, and Carolina hemlock, Tsuga caroliniana, in the eastern United States. Previous studies of adelgid population dynamics and hemlock response in the early-1990s suggested that once infested, trees were likely to die within 4 to 6 years; widespread eradication of hemlock throughout the region was expected. However, the vast majority of hemlocks in western Massachusetts are still alive and many are not yet infested, despite the adelgid having been present in the state for 17 years. Many examples of individual trees in Massachusetts harboring adelgid for over ten years have been documented. In order to understand this discrepancy, we conducted detailed lifetable studies of the hemlock woolly adelgid at six locations in Connecticut and Massachusetts from 2004-2008. Adelgid density, fecundity, and survival data as well as temperature and precipitation data were examined to document and understand the apparent stability of adelgid populations in the northeast. These data were also used along with climate projection models to predict the range of suitable habitat for adelgid under two scenarios of carbon emissions through the year 2100.^ In an attempt to regulate adelgid populations, several species of biological control agents have been released, including Laricobius nigrinus Fender (Derodontidae), Sasajiscymnus tsugae Sasaji and McClure (Coccinellidae), and Scymnus ningshanensis Yu and Yao (Coccinellidae). Since few studies have addressed the efficacy of these beetles above the branch level, we conducted an experiment to test their effects on adelgid populations using whole-tree enclosures. These data, in addition to adelgid demography data will be useful in predicting future outbreaks, constructing simulations of adelgid growth and spread, and determining the amount of additional mortality needed from a biological control agent to stabilize adelgid populations.^

Multitrophic effects of bumblebee parasites on plant reproduction

Gillespie, Sandra D — Wed, 18 Jan 2012 12:12:09 PST

Mutualisms are major structuring forces in biological communities. However, the concept of the trophic cascade has rarely been explicitly applied to mutualisms. Antagonists of one mutualist have the potential to negatively affect the second mutualist through effects on their partner, and the magnitude of such effects should vary with mutualism strength. Bumblebees represent an ecologically and economically important mutualist pollinator group. They are attacked by a range of parasites, and visit a variety of plants that vary in reliance on bumblebees for pollination service. Using bumblebees and their parasites, I investigated whether mutualisms can mediate trophic cascades. ^ I surveyed three parasites (Crithidia bombi, Nosema bombi and conopid flies) in Bombus spp. in Massachusetts and found that parasites are more common in wild bumblebees than previously believed (Chapter 1). To test whether infection by these parasites has top-down effects on pollination service to plants, I examined whether site-level parasitism rates correlated with pollination service to greenhouse-raised plants. I used several plant species which varied in their dependence on bumblebees for pollination. The relationship between parasitism and pollination service differed between plants and parasite species, and there was evidence that plants more reliant on bees for pollination experienced stronger negative indirect effects of parasites (Chapter 2). ^ Finally, I developed an ordinary differential equation model of mutualist population dynamics incorporating a producer, its mutualist, and an antagonist of the mutualist. I varied the mutualism from obligate to facultative, and investigated effects of the antagonist on mutualist coexistence. My results highlight how mutualisms differ from traditional trophic cascades, and the importance of considering obligate, facultative, and asymmetric mutualisms in attempting to understand their interactions with the community (Chapter 3). ^ My contributes to conservation issues and extends our theoretical understanding of basic ecology. I provided valuable data about the incidence and multitrophic effects of parasites in an important native pollinator. By combining mutualisms with the theoretical structure of the trophic cascade, two previously independent areas of ecological research that will benefit from integration, my research improves our understanding of how mutualisms structure the community as a whole.^

Discovery of cryptic species diversity in North American pine-feeding chionaspis scale insects (Hemiptera: Diaspididae)

Gwiazdowski, Rodger A — Wed, 18 Jan 2012 12:11:35 PST

The pine-needle scale insects; Chionaspis pinifoliae and C. heterophyllae are armored scale insects (Hemiptera: Diaspididae) with extensive native ranges throughout North America. In particular, C. pinifoliae is found on almost every species in the genus Pinus. Both species are economically important pests on pines, and over a century of scientific literature has considered these as only two morphological species. The life history of scale insects suggests they may form strongly structured metapopulations, resulting in high rates of host race formation and possibly speciation. Such newly originated species are likely to be morphologically similar. The geographic distribution and host use of these two species suggests they may represent a group of species that have gone unsampled due to their broad distribution or unrecognized due to their similar morphology.^ To explore the potential for species diversity in pine-needle scale insects I collected 366 individual insects from 320 localities across North America, representing 51 host species within the Pinaceae. I estimated species diversity by inferring species boundaries using genealogical concordance across allele genealogies of two nuclear loci and one mitochondrial locus. Using Maximum Likelihood allele genealogies in a majority-rule consensus to assess congruence, I conservatively detect 10 species in this group. However some of these 10 species contain morphological subgroups that conventional taxonomy would recognize as their own species. I explored alternate species delimitations using a range of species delimitation schemes based on genealogical concordance and mitochondrial divergence. I analyzed these delimitation schemes as species in a Bayesian species tree analysis, and infer that a delimitation of 26 species is the optimum scheme. This 26-species scheme also recognizes most of the aforementioned unique morphological subgroups, as species. Additionally, the genetic analyses for the above work occasionally recovered parasitoid sequences, from the 28S D2 and D3 subunits of ribosomal RNA. I included these sequences in a phylogeny of over 500 specimens from 18 of 19 families within the Chalcidoidea. I compared the phylogenetic results against a comprehensive list of parasitoids recorded from C. pinifoliae and C. heterophyllae, and find the 28s sequences indicate the parasitoid diversity utilizing these pine-feeding scale insects is much higher than previously thought. ^

Movin' & groovin' salamanders: Conservation implications of large scales and quirky sex

Charney, Noah — Wed, 18 Jan 2012 12:10:43 PST

Mole salamanders (Ambystoma) and woodfrogs ( Lithobates sylvaticus) are abundant in New England and depend on ephemeral wetlands for breeding. Their aquatic habitats have been well studied and are protected by several local and regional regulations. State endangered species laws also protect mabled salamanders (A. opacum), Jefferson salamanders (A. jeffersonianum), and blue-spotted salamanders (A. laterale). However, these amphibians spend most of their adult lives in terrestrial habitats that remain poorly protected and elusive to researchers. ^ In chapter 1, I developed a novel technique using passive integrated transponders for tracking small animals. I used this technique to track marbled salamanders walking up to 200 m from their breeding pond during post-breeding migrations. ^ In Chapter 2, I examined the importance of multiple habitat variables for controlling the distributions of woodfrogs and spotted salamanders at 455 ponds in western Massachusetts. Based on a variable-comparison technique I developed, the best predictor for either species of amphibian was the amount of forest in the surrounding landscape. Both species were found more frequently in upland forests where the ponds are least protected by state and federal wetland regulations. ^ In chapter 3, I used my data from chapter 2 and three other similar data sets to conduct an analysis of spatial scale and to parameterize a recently published resistant kernel model. The complex model parameterized by an expert panel did significantly worse than the null model. The distributions of both amphibians were best predicted by measuring the landscape at very large scales (over 1000 m). The most effective scales for conservation may be largest for organisms of intermediate dispersal capability. ^ In chapter 4, I explored the evolution and genetics of the Jefferson/blue-spotted/unisexual salamander complex. I framed research into the fascinating unisexual reproductive system with a model that relates nuclear genome replacement, positive selection on hybrids, and biogeography of the species complex. I parameterized this model using genetic data taken from salamanders spanning Massachusetts and an individual-based breeding simulation. If paternal genomes are transmitted to offspring with the frequencies reported from laboratory experiments, then my model suggests that there must be strong selection favoring unisexuals with hybrid nuclei. ^

The Conservation Value of Residential Landscapes for Native Bird Communities: Patterns, Processes, and Management Implications

Lerman, Susannah Beth — Thu, 08 Dec 2011 11:08:55 PST

Urbanization, as it transforms natural biotic systems into human-dominated landscapes, is recognized as one of the greatest threats to biodiversity throughout the world. Furthermore, urban dwellers are becoming increasingly disconnected with the natural world. Here I investigate whether residential landscape designs that mimic the natural environment can provide habitat for native birds. First I uncover some of the patterns of bird distribution in residential yards by incorporating habitat features, urbanization measurements and socioeconomic factors with bird monitoring data into a multivariate analysis. The results indicate that native birds associate with neighborhoods with native plants and shrubs, neighborhoods closer to desert tracts, and higher income neighborhoods. Very few bird species associate with low income and predominantly Hispanic neighborhoods. Additional analyses based on social survey data demonstrate that residents notice the varying levels of bird variety in their neighborhood. Second, I address whether perceived habitat quality differs between residential landscape designs by testing foraging decisions at artificial food patches. Birds foraging in yards landscaped with native plants consume fewer resources than birds foraging in exotic landscaped yards. This suggests that alternative food sources are more available in the native landscaped yards, indicating better quality habitat. Third, I investigate the relationship between native bird diversity and neighborhoods with a Homeowner Association (HOA). Neighborhoods with an HOA have higher native bird diversity, perhaps due to an active and enforceable landscape maintenance plan. I suggest an HOA adapt features from the Sustainable Sites Initiative to further improve habitat conditions for native birds and other wildlife. Results from the Dissertation support the implementation of native landscaping in residential yards to help reverse the loss of urban biodiversity. Consequentially, these landscapes will provide positive opportunities for urban dwellers to reconnect with the natural world.

Phylogenics and Patterns of Molecular Evolution in Amoebozoa

Lahr, Daniel J.G. — Tue, 06 Dec 2011 08:35:44 PST

My dissertation explores several aspects of the relationship between morphological and molecular evolution in amoeboid lineages:

Chapter 1 - General Introduction: This chapter provides an overview of the most pressing issues in Amoebozoa phylogeny that are dealt with in the remainder of the thesis

Chapter 2 - Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new generation high fidelity DNA polymerase: This chapter addresses the methodological difficulty in the study of large gene families, the generation of artifactual sequences by recombination during PCR.

Chapter 3 - Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions: This chapter explores intriging patterns of evolution in the actin gene families of testate amoebae.

Chapter 4 - Comprehensive phylogenetic reconstruction of Amoebozoa based on concatenated analysis of SSU-rDNA and actin genes: A deep phylogenetic analyses of the Amoebozoa, enables exploration of well supported taxonomic units within the group.

Chapter 5 - Interpreting the evolutionary history of the Tubulinea (Amoebozoa), in light of a multigene phylogeny: This chapter explores a more restrict taxonomic unit within the Amoebozoa - the Tubulinea - based on an expanded sample of genes and taxa.

Chapter 6 - The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms: This chapter asks whether the null-hypothesis that amoebae are asexual is consistent with current phylogenetic evidence

The evolution of cranial morphology, feeding performance and behavior in neotropical leaf-nosed bats (Chiroptera: Phyllostomidae)

Santana Mata, Sharlene E — Thu, 17 Nov 2011 13:18:15 PST

Morphology can play a major role in ecological diversification and adaptive radiation when it consistently enhances performance and behavior. Here I investigate how cranial and dental morphology, feeding performance and behavior relate to one another and to the dietary radiation in Neotropical leaf-nosed bats (Family Phyllostomidae). First, I build a 3D biomechanical model to investigate the mechanism connecting cranial morphology and bite performance (bite force) and how bats with different diets vary in biomechanical parameters predicting bite force. The model demonstrates that cranial morphology is a strong predictor of bite force variation, and that bats differ in biomechanical predictors of bite force when they are classified according to dietary hardness. Second, I investigate the relationship between biting behavior and bite force across phyllostomids. My results indicate that bats modulate their performance by changing their biting behaviors to maximize bite force when feeding on hard foods. Using phylogenetic correlations and ancestral state reconstructions, I provide evidence for correlated evolution of behavior and performance, and rapid evolution in these traits that coincided with the use of plant resources. Third, I investigate the trends in molar complexity, chewing behavior and efficiency in breaking down prey across phyllostomids with different diets. My results illustrate that frugivores exhibit a higher dental complexity than insectivores and omnivores, and that the latter groups achieve higher performance in insect breakdown through higher molar complexity and chewing behavior. Finally, I investigate if other behavioral traits relevant to fitness have shaped the evolution of the skull morphology, using roost excavation in Lophostoma silvicolum as a model system. Through finite element analysis, I provide support for the prediction that the skull of L. silvicolum presents adaptations for roost excavation, in the form of a stronger skull. When all my findings are considered there is evidence that, although morphology can strongly predict performance, behavior plays an important role in modulating performance, and selection on this ability could have contributed to the ecological diversification of phyllostomids. Overall, the dietary radiation of phyllostomids, in particular the use of plant resources, was associated with dramatic changes in cranial and dental morphology, feeding performance and behavior.^

Movin' & Groovin' Salamanders: Conservation Implications of Large Scales and Quirky Sex

Charney, Noah D. — Fri, 19 Aug 2011 08:52:03 PDT

Mole salamanders (Ambystoma) and woodfrogs (Lithobates sylvaticus) are abundant in New England and depend on ephemeral wetlands for breeding. Their aquatic habitats have been well studied and are protected by several local and regional regulations. State endangered species laws also protect mabled salamanders (A. opacum), Jefferson salamanders (A. jeffersonianum), and blue-spotted salamanders (A. laterale). However, these amphbibians spend most of their adult lives in terrestrial habitats that remain poorly protected and elusive to researchers.

In chapter 1, I developed a novel technique using passive integrated transponders for tracking small animals. I used this technique to track marbled salamanders walking up to 200 m from their breeding pond during post-breeding migrations.

In Chapter 2, I examined the importance of multiple habitat variables for predicting the distributions of woodfrogs and spotted salamanders at 455 ponds in western Massachusetts. Based on a variable-comparison technique I developed, the best predictor for either species of amphibian was the amount of forest in the surrounding vii landscape. Both species were found more frequently in upland forests where the ponds are least protected by state and federal wetland regulations.

In chapter 3, I used my data from chapter 2 and three other similar data sets to conduct an analysis of spatial scale and to parameterize a recently published resistant kernel model. The complex model parameterized by an expert panel did significantly worse than the null model. The distributions of both amphibians were best predicted by measuring the landscape at very large scales (over 1000 m). The most effective scales for conservation may be largest for organisms of intermediate dispersal capability.

In chapter 4, I explored the evolution and genetics of the Jefferson/blue-spotted/unisexual salamander complex. I framed research into the fascinating unisexual reproductive system with a model that relates nuclear genome replacement, positive selection on hybrids, and biogeography of the species complex. I parameterized this model using genetic data taken from salamanders spanning Massachusetts and an individual-based breeding simulation. If paternal genomes are transmitted to offspring with the frequencies reported from laboratory experiments, then my model suggests that there must be strong selection favoring unisexuals with hybrid nuclei.

Diversity of eukaryotes and their genomes

Wegener Parfrey, Laura E — Thu, 16 Jun 2011 13:15:39 PDT

My dissertation addresses two aspects of eukaryotic evolution, (1) the organization of eukaryotic diversity and (2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life. Relaxed molecular clock analyses of this taxon-rich dataset place the origin on eukaryotes in the Paleoproterozoic, and suggest that all of the major lineages of eukaryotes diverged before the Neoproterozoic. This robust scaffold of the tree of eukaryotes is also used to elucidate common themes in genome evolution across eukaryotes. Mapping dynamic genome features onto this tree demonstrates that they are widespread in eukaryotes, and suggests that a common mechanism underlies genome plasticity. Foraminifera, a diverse lineage of marine amoebae, provide a good model system for investigating genome dynamics because they amplify portions of their genome and go through ploidy cycles during their life cycle. Assessment of nuclear dynamics in one species of Foraminifera, Allogromia laticollaris strain CSH, reveals that genome content varies according the life cycle stage and food source, which may differentially impact organismal fitness. The inclusion of diverse microbial eukaryotes enables better resolution of eukaryotic relationships and improves our understanding the dynamic nature of eukaryotic genomes. ^