Most of the deep sea is characterized by low productivity and low biomass, however there is a patchy distribution of unique habitats that support specialist communities and high biomass. These habitats include hydrothermal vents and cold seeps; geological features that provide reduced compounds like sulfide and methane to fuel chemosynthesis, an alternate form of primary production to photosynthesis. Organic falls like whale carcasses and wood support related but distinct communities of scavengers, grazers, filter feeders, and extreme specialists.

This dissertation examines multiple levels of specialization to deep-sea reducing environments to address the following questions:

1. Is there a common evolutionary path toward specialization in reducing habitats?

2. How have lineages modified their anatomy to specialize in deep-sea habitats?

3. How does variation in sunken wood influence community assembly?

To address the first question, I used a supertree of the Gastropoda, one of the most diverse animal groups in reducing habitats, to ask whether lineages followed similar trajectories toward becoming specialists in these ecosystems. For the second question, I focused on a lineage of limpets (Lepetellidae) that has only been found living on empty Hyalinoecia polychaete tubes, and made hypotheses about how they utilize their substrate based on a detailed 3D reconstruction of the anatomy of Lepetella sierra. The third question focuses on how variation in the substrate can influence diversity and community assembly, particularly in wood fall communities colonizing experimental wood fall substrates of ten different types over the course of two years at 3200m near Monterey, CA. Through the course of exploring these three questions, I have developed collaborations, learned new skills, and contributed new data and perspectives on deep-sea reducing environments.

The birth-death process has been used to study the evolution of a wide variety of biological entities from genes to species. Much recent work has turned to detecting changes in the patterns of lineage splitting by comparing data to birth-death models in which the parameters vary between lineages or over time. Here, I develop methods to investigate how the birth-death process varies under three very different circumstances: changes in the pattern of taxon diversification through time; the effect of whole genome duplications on the pattern of chromosome gain and loss; and changes in the pattern of gene gain and loss on branches of a taxon tree. For all three cases I apply my methods to some real data.

For the last fifteen years researchers have studied the distribution of branching times of a phylogeny of extant taxa in order to detect temporal changes in the process of diversification. Theoretical work on this subject has been based on different implementations of the birth-death process and has proceeded along three basic lines: the comparison of actual branching times to a birth-death process; the inference of the effects of different birth-death processes on the distribution of branching times; and the derivation of analytical results that describe various aspects of different birth-death processes. In chapter 2 I make contributions to all three lines of research for the reconstructed time variable birth-death process.

Previous work had shown how to calculate the distributions of number of lineages and branching times for a reconstructed constant rate birth-death process that started with one or two reconstructed lineages at some time or ended with some number of lineages in the present. In chapter 2 I expand that work to include any time variable birth-death process that starts with any number of reconstructed lineages and/or ends with any number of reconstructed lineages at any time. I also introduce the discrete time birth-death process which operates as an efficient and accurate numerical solution to any time-variable birth-death process and allows for the analytical incorporation of sampling and mass extinctions. Furthermore, I show how to simulate random trees under any of these models.

In order to compare phylogenetic trees to these models, I use these methods to calculate two statistics that describe the effect of a set of branching times to any time variable birth-death model: the maximum likelihood, which can be compared to the distribution of the maximum likelihood for a random sample of trees or to that the maximum likelihood of other birth-death models using the Akaike Information Criterion; and the Komolgorov-Smirnov test, which is based on the fact that the branching times should be independently and identically distributed under many time variable birth-death models. I also demonstrate two new methods for visualizing the distribution of branching times: the lineage through time null plot uses a heat map to show the distribution of the number of lineages at different times; and the waiting time null plot does the same for waiting times between branching times. These plots can be used either to see how different time variable birth-death processes affect these distributions or to compare a data set to any time variable birth-death process. I use all these methods to analyze two data sets of reconstructed taxon branching times.

The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If researchers could identify the branch of a phylogeny on which a whole genome duplication occurred, before sequencing the genomes of multiple taxa, then they could select taxa that would give them a better picture of that whole genome duplication. In chapter 3 I describe a likelihood model in which the number of chromosomes in a genome evolves according to a Markov process with three stochastic rates: a rate of chromosome duplication and a rate of chromosome loss that are proportional to the number of chromosomes in the genome; and a rate of whole genome duplication that is constant. I implemented software that calculates the maximum likelihood under this model for a phylogeny of taxa in which the chromosome counts are known. I compared the maximum likelihoods of a model in which the genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, in order to determine if a model with whole genome duplications is a good fit for the data. Once it has been determined that the data does fit the model, we infer the phylogenetic position of paleopolyploidies by using this model to calculate the posterior probability that a whole genome duplication occurred on each branch of the taxon tree. I applied this model to a phylogeny of 125 molluscan taxa and inferred three places on that phylogeny where it is very likely that a whole genome duplication occurred: a single branch within the Hypsogastropoda; one of two branches at the base of the Stylommatophora; and one or two branches near the base of Cephalopoda.

Thanks to the wealth of readily available comparative genomic data, it has become apparent that gene family expansion and contraction is critical for the evolution of organisms. Several researchers have developed likelihood methods that use counts of genes in gene families from a number of taxa to deduce on which branches of the phylogenetic tree there has been an unusual amount of gene duplication or gene loss in that gene family. Gene family counts are readily available, but there is a great deal of information in the gene family tree that is unavailable when using gene counts alone. In chapter 4, I develop a method that uses the gene family tree to infer changes in the process of gene gain and loss on a taxonomic tree. This method relies on calculating the probability of a gene tree given a taxon tree and a set of birth-death parameters by which that gene tree evolves on the taxon tree. I use a reversible-jump MCMC to sample from the joint posterior distribution of a set of birth-death parameters and assignments of those parameters to the branches of a taxon tree given a gene tree and a taxon tree. Different assignments are compared using Bayes factors. I use simulations to show that this method has much more power than a method which relies only on counts of gene family members to determine if a gene family evolved by a different process on a pair of taxon branches, and whether that difference is a consequence of differences in the birth rate or the death rate.

In section 4.5 I expand my method to include uncertainty in the gene tree topology, by using a set of gene alignments as my data rather than the fully resolved gene tree. Under this implementation I calculate the probability of those sequences given the gene tree, in addition to the probability of the gene tree given the taxon tree. I modify the reversible-jump MCMC so that it now samples from the posterior distribution of the nucleotide evolution parameters and the gene trees, in addition to the birth-death parameters and their assignments to the branches of the taxon tree. I demonstrate the use of this method on two real gene families found in the Bilateria. I found that a clade of 46 protein tyrosine kinase genes from three taxa is characterized by an increase in the gene duplication rate on the branch leading to Caenorhabditis elegans. Furthermore, a separate analysis of all the posterior hox genes from nine taxa implies that their evolution has been characterized by massive gene loss throughout the Bilateria with a lower rate of turn over in the chordates and at the base of the deuterostomes than is found in the protostomes or in the echinoderms.

It was long thought that dark, nutrient depleted environments, such as the deep sea and subterranean caves, were largely devoid of life and supported low-density assemblages of endemic fauna. The discovery of hydrothermal vents in the 1970s and their subsequent study have revolutionized ecological thinking about lightless, low oxygen ecosystems. Symbiosis between chemosynthetic microbes and their eukaryote hosts has since been demonstrated to fuel a variety of marine foodwebs in extreme environments. We also now know these systems to be highly productive, exhibiting greater macrofaunal biomass than areas devoid of chemosynthetic influx. This dissertation research has revealed chemosynthetic bacteria and crustaceans symbionts that drive another extreme ecosystem - underwater anchialine caves - in which a landlocked, discrete marine layer rests beneath one or more isolated layers of brackish or freshwater.

Most anchialine caves contain low invertebrate abundances, yet some have inexplicably large biomasses of shrimp and remipedes, a rare crustacean class endemic to caves. Since only anecdotal evidence of remipede feeding in the field has been published and little ecological information about anchialine organisms is known, in situ studies are crucial to understanding whether there are direct or indirect links between chemosynthetic input into anchialine foodwebs and remipede abundance. This dissertation research integrates studies of geochemistry, microbiology, invertebrate food web dynamics, and behavior in these extreme ecosystems. Findings include the following: 1) highly stratified anchialine caves support communities of freeliving chemosynthetic bacteria, 2) Typhlatya pearsei, an anchialine shrimp, harbors chemosynthetic endosymbiotic bacteria, 3) the remipede, S. tulumensis, may also harbor chemosynthetic symbionts ectobiotically 4) food webs in the cave are complex and vary spatially, driving community structure changes 5) remipedes likely use chemical gradients and specialized chemosensory receptors to navigate in their lightless environment.

This combined body of research provides the first systematic study into anchialine ecology and has found them to be rich in taxa for comparative study with other chemosynthetic systems. For example, the finding of the first chemosynthetic endosymbiosis in a crustacean, T. pearsei, and the first chemosynthetic epibiosis in a remipede, S. tulumensis, allows for a variety of comparative coevolutionary studies. Typhlatya, a genus of troglobytic shrimp, are found in anchialine systems across the Caribbean and Bermuda and likely all contain chemoendosymbiotic bacteria. As such this discovery provides a springboard for comparative research into the transmission and evolution of chemosynthetic symbiotic associations. The most interesting outcomes, however, may result from comparing ecological and ecosystem function patterns described in caves to those known for deepwater as well as molluscan and annelid systems. Furthermore, anchialine systems, a primary source for agricultural, domestic, and industrial water use, are especially susceptible to climate change. Therefore, not only are studies of ecosystem function such as this imperative to conserving endemic cave fauna and their suitable habitat, but they may also help in the preservation of clean water caches for future generations.

Harmful blooms of green macroalgae, known as green tides, have been increasing in frequency and intensity world-wide over the last decade. Composed mainly of the macroalgae, Ulva, these blooms occur in areas of low wave energy and high nutrient input from anthropogenic sources; they often result in massive die-offs in the impacted ecosystem. My dissertation addressed three key questions concerning the potential for green tides to occur in central San Francisco Bay: 1) what species of Ulva inhabit the bay and which of them have been identified as bloom-forming taxa in other locations? 2) does an overwintering, benthic bank of dormant propagules contribute to the rapid growth of spring Ulva populations? 3) does waterborne spore availability limit the recruitment of Ulva populations? Within central San Francisco Bay, I identified six species of Ulva using genetic barcoding, only four of which were previously reported within the bay. Several of these species are known to produce economically costly green tides in other regions of the world. While previous studies on the control of algal blooms focused on post-recruitment processes such as herbivory and space competition, I investigated two pre-recruitment processes: banks of benthic microscopic forms and supply of waterborne propagules. A multifactorial lab experiment demonstrated that banks of dormant benthic microscopic Ulva forms (i.e. gametes, zoospores or thallus fragments) survive winter incubation periods (12 weeks of darkness undisturbed at 11°C), but at a depressed growth rate. Successful recruitment from these banks is strongly influenced by seasonal increases in water temperature. A regular regime of water column sampling and laboratory culturing demonstrated that waterborne propagule supply varied with location within the central bay, and that the abundance of propagules in the water column varied strongly with season. Although water samples from all sites yielded recruits, sites north of the bay mouth yielded more Ulva recruits than southern sites during the spring recruitment period while sites south of the bay mouth yielded more recruits in fall. Together, this information indicates that propagule supply, hydrographic patterns that mediate dispersal, and environmental and physiological constraints on juvenile development impose important limitations on dynamics of green tide algae in the central San Francisco Bay. These interacting factors must be included in management as future global climate change is expected to stimulate more rapid development of spring green algal blooms.

What is the effect of isolation in the formation of new lineages? Volcanic islands provide an ideal scenario to explore this question due to their various degrees of isolation, environmental variability and generally understood geology. On the other hand, the dispersal abilities, diverse ecology, and known natural history of spiders make them a suitable group of study to address this big question.

Because, the formation of new clades on islands start with a colonization event, I first studied long distance dispersal across different Pacific archipelagoes for spiders of the genus Tetragnatha. Then, I focused on the early stages of diversification for this group in the Hawaiian archipelago using population genetics studies combining Sanger sequencing of mitochondrial genes and Exon Capture for nuclear markers. Finally, I studied the effect of isolation at the morphological level. In particular, by looking the convergent evolution of color polymorphisms among species present on islands and continental areas. For this I examine the case of the family Theridiidae.

Colonization of remote archipelagoes corresponds to a very rare event. The Long- jawed spiders, genus Tetragnatha, are widely distributed around the world including oceanic islands. In Hawai'i there are 37 species of one or two colonization events from North America. In the Marquesas there are 5 species and phylogenetic evidence suggests an origin somewhere in the Asia. For the species present in the Society Islands, Rapa Nui and D. raptor (Hawai'i), their biogeographic origin is still unsolved. In order to examine colonization patterns across the Pacific Rim, I used freshly collected and museum specimens for phylogenetic analysis. The DNA from historic collections was sequenced using newly design primer pairs to amplify overlapping short fragments of COI. The phylogenetic reconstruction shows two of the species from the Society Islands (T. rava and T. tuamoaa) and D. raptor in the same clade as other species from Asia. T. moua (Society Islands) is sister to T. nitens, which has a circumtropical distribution making strong biogeographic statements difficult. The species from the Marquesas appear linked to a basal polytomy, while the one from Rapa Nui is in the same clade as the Hawaiian species. Other new species from Hawai'i were added into the analysis, but their phylogenetic position within the Web building clade is not conclusive. The first chapter provides preliminary information about origin of Tetragnatha spiders in Pacific islands. The implementation of Next Generation Sequencing technologies and inclusion of more species could improve this understanding.

Once the founder event occurs lineages could follow different diversification trajectories. Adaptive radiation is one of them in which many species evolve on a short period of time occupying different ecological niches. The study of their temporal dynamic it is not a simple problem to address in natural conditions. However, the chronosequence of the Hawaiian Islands provides "snapshots" of different stages of the diversification process. Here, I propose a population-based mechanism, which associated with the changes on the landscape attempts to explain the patterns of species diversity. By comparing species present on the young (Big Island: T. anuenue and T. brevignatha) and middle age islands (Maui: T. waikamoi and T. brevignatha), I tested the following predictions: (1) higher genetic structure in the young island populations and (2) lower genetic structure in populations from the middle age island. To test these hypotheses I sequenced three mitochondrial genes (COI, ND1 and Cytb). For my first prediction I found that the mitochondrial haplotype distribution is not related to the specific volcano configuration, but rather with breaks in forest types associated with rain regimens. The second prediction was not supported. Instead, I found strong genetic isolation between populations on Maui. Finally, a time calibrated coalescent reconstruction of T. brevignatha provided evidence for a population expansion during Pleistocene glacial periods. It also suggests that the Windward/Leeward population break is related to more recent events than the original colonization of the island. Species evolving in Hawai'i seem to be affected not only by the geologic development of the islands, but also by more recent climatic events.

On this context, I studied the genetic structure of newly formed species. In the third chapter I examined the genetic signatures of young speciation events by applying the transcriptome-based Exon Capture approach to the study of three closely related species (T. brevignatha, T. waikamoi and T. macracantha) from Maui Nui and Big Island. The combined data showed the existence of 5 clades: T. brevignatha Big Island, T. brevignatha Maui, T. macracantha, T. waikamoi and a WaikBrevMac clade. The last one includes specimens from all three nominal species. For T. brevignatha, the molecular divergence between the populations of Maui and Big Island are similar to "species level" comparisons. The Big Island population shows a strong break between the Leeward and Windward populations. For T. waikamoi nuclear data suggests that the population break between Haleakalā and West Maui is less pronounced than the break based on mitochondrial data. In the case of T. macracantha, we found a separation between the Maui and Lana'i populations. Moreover, there are two very divergent lineages co- existing in Kīpahulu Valley. Lastly, the finding of the WaikBrevMac group adds a new layer of complexity where recent speciation events suggest divergent lineages with convergent (or are the ancestral) morphologies and no genetic admixture. The addition of species with different eco-morphologies will complement these findings and also inform about the genetic signatures of ecological speciation.

Finally, to examine the effects of isolation in morphology I addressed the phenomena of convergent evolution in a color polymorphism on island and continental species. This kind of convergence has been widely studied, as it corresponds to a unique situation where the convergence leads to diversity. In the spider family Theridiidae, the independent evolution of the abdominal color polymorphism has been well described in at least four species (Enoplognatha ovata, E. latimana, Theridion grallator and T. californicum). Among the shared characteristics on these cases of color polymorphism are: (1) the presence of "Yellow" as the double recessive and more common variant, (2) single loci Mendelian inheritance (except in Big Island population of T. grallator), (3) constant frequencies of variants among poorly connected populations and (4) evidence of the action of natural selection. The genus Selkirlkiella from the temperate rainforest of southern South America has several species with some degree of color polymorphism. Here, I documented the color polymorphisms of S. alboguttata (Robinson Crusoe Island) and S. luisi (Valdivia, Chile). Selkirlkiella alboguttata displays 6 morphs and S. luisi two morphs. The "Yellow" morph was the more common in both species. Based on a molecular phylogeny, we confirm that this genus is closely related to Enoplognatha. The presence of color polymorphism in this genus appears to be an event of convergent evolution at the family level, while between species it is likely due to common ancestry. There is also evidence of other cases of color polymorphism in the family. Finally, this phenomenon seems to be associated with the "under leaf community".

Spiders are a very diverse group of organisms. Due to their exceptional dispersal abilities, they have colonized even the most remote islands on the planet. The implementation of new genetic methods as well as the collection of specimens from remote areas will reveal even more insights about the biology of these organisms. This knowledge will extremely valuable to expand the understanding of the effects of isolation in the generation of biodiversity.

In order to fully understand the processes that influence phenotypic evolution, it is necessary to explore the role that developmental channeling plays in shaping morphology. In my doctoral research, I have investigated how an increased understanding of ontogenetic patterns gives insight into the evolution of birds. Here, I present the results of an integrative study combining material from multiple levels of the biological hierarchy (clade, individual organism, and cell), using both paleontological and neontological data. Specifically, I studied post-natal gross morphological change and cellular growth in a phylogenetically broad sampling of Cretaceous and modern avians, using ontogenetic series when available.

A three-dimensional geometric morphometric analysis of ontogenetic cranial shape change indicates that a relatively high level of developmental constraint governs the evolution of the skull, although shape at onset of growth is a more variable characteristic, in large part because hatchling chicks already have cranial morphology very similar to that of adults. Histological study of extant bird skeletons also indicates high variability in onset of growth among taxa and reveals a common pattern of greater skeletal maturity of the femur relative to the humerus at the time of hatching. This is interpreted as an example of a ‘spandrel,’ later exapted by semi-precocial taxa in which pelvic limbs appear to achieve functional maturity before pectoral limbs for adaptive reasons. Histological analysis of Cretaceous avians indicates this trait of differential maturity between limb elements may have a very deep evolutionary origin, and could explain substantial microstructural differences that persist into adulthood in some extinct taxa. I focused in particular on growth in members of the Enantiornithes, and further conclude that this group exhibits a greater diversity of growth strategies than originally hypothesized, although with no apparent relationship to body size or geological age, and that this clade had a unique developmental mode not directly comparable that of to any crown-group birds. Finally, phylogenetic and functional constraints appear to have a much greater influence on cellular growth of long bones than on cranial shape change, for which developmental channeling is a primary influence.