Philosophiae Doctor - PhD / Using two hydrodynamic galaxy formation simulations from the Mufasa project that I helped develop, we aim to better understand the relationship between galaxy evolution and its cold gas content commonly known as the neutral hydrogen or Hi. We first look at the environmental properties of the simulated galaxies and compare to those that are available observationally. As a proxy, we specifically quantify the so-called galactic conf ormity, which is the concordance between the properties of galaxies neighbouring the primaries, in chapter 2. We show that the Hi, the specific star formation rate (sSFR) and the colour of galaxies show galactic conformity in qualitative agreement with previous observed data, i.e. the Hi-rich primary galaxies are surrounded by Hi-richer galaxies than the Hi-poor primary galaxies, and similarly for the sSFR and the colour. We find that environment, quantified by the number of neigbouring galaxies within a fixed aperture, stellar age and molecular hydrogen (H2) also show conformity. Galactic conformity also depends on the dark matter halo mass of the primary galaxy. The galactic conformity signal from the primaries of smaller haloes is weak but extends out to several virial radii of those structures, whereas the signal is very strong for high mass haloes but lowers quickly with distances from the primaries. We also find the galactic conformity only emerges in the later half of cosmic evolution. We next quantify the gas content and star formation depletion timescales in chapter 3. We use two carefully chosen groups of simulated galaxies and find that timescales are affected by both the mass of the virialised structure of the first infall and the galaxy stellar mass at infall: the higher the halo mass or the stellar mass the shorter the timescale. The gas or Hi depletion timescale is concordant to that of the star formation quenching, indicative of direct decrease of SFR due to depletion of the extended cold gas reservoir. The neutral atomic or molecular hydrogen consumption timescale depends on the Hubble time. Galaxies tend to form stars more efficiently at lower redshift. While the halo mass of infall affects the consumption timescale of the Hi, it does not correlate with the H2. We lastly develop machine learning tools to use galaxy photometric data to predict a galaxy’s Hi mass in chapter 4, to allow predictions for Hi from much larger optical photometric surveys. The training and testing of the algorithms are done first with the simulated data from Mufasa. We show that our model performs better than previously done with ad hoc data fitting approaches. Random Forest (RF) followed by the Deep Neural Networks (DNN) perform best among the explored machine learning techniques. Extending the trained models to observed data, namely the Arecibo Legacy Fast ALFA (ALFALFA) and REsolved Spectroscopy Of a Local VolumE (RESOLVE) survey data, we show the overall performance is slightly reduced relative to the simulated testing set owing to the small inconsistency between definition of galaxy properties between simulation and observational data, and DNN perfoms the best in this case. The application of our methods is useful for galaxy-by-galaxy predictions and anticipated to correct for incompletness in the upcoming Hi deep surveys done with MeerKAT and eventually the Square Kilometre Array (SKA).

Caviomorph rodents arrived from Africa as sweepstakes colonists to the South American island continent between 54 and 37 Ma, and subsequently underwent a rapid and widespread adaptive radiation beginning in the middle Eocene. The geographic isolation of South America gave rise to a number of endemic mammal species that filled a wide variety of ecological niches. The resulting size of caviomorph rodents spanned over three orders of magnitude, making them an intriguing lineage to explore the morphological and ecological implications of size evolution. Here, I explore the morphological cranial patterns of extinct and extant caviomorph taxa using 2D landmark-based geometric morphometric analysis. Results are key to advancing our understanding of the effects phylogeny and body size have on cranial morphology of caviomorphs (and more broadly, mammals). This study indicates a deviation from the mammalian modular patterns determined a priori, suggesting unique evolutionary processes at play during the caviomorph adaptive radiation.

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Together with the heterosporous lycophytes, the clubmoss family (Lycopodiaceae) is the sister lineage to all other vascular land plants. Given the family’s important position in the land-plant phylogeny, studying the evolutionary history of this group is an important step towards a better understanding of plant evolution. Despite this, little is known about the Lycopodiaceae, and a well-sampled, robust phylogeny of the group is lacking. The goal of this dissertation is to resolve the relationships among evolutionary lineages in the Lycopodiaceae and provide insight into the timing and drivers of diversification in the family. First, to place the evolution of the family within a global and historical context, I generated a densely sampled, time-calibrated phylogeny of the family. I sampled 50% of the estimated 400 extant species in the Lycopodiaceae and used eight fossils to calibrate the age of major divergence events in the family and across the land-plant phylogeny. Further, we used a probabilistic biogeographic model to infer the historical biogeography of the family. Together, these analyses indicate that the Lycopodiaceae originated in the late Devonian, began its early diversification in the Carboniferous, and accumulated much of its extant diversity during the Cenozoic. From a geographical perspective, major cladogenesis events in the family’s history appear to be linked to the breakup of the Pangaean and Gondwanan supercontinents, with long-distance dispersal playing a role in the establishment of younger evolutionary lineages. Second, I examined the drivers of diversification in the species-rich genus Phlegmariurus in the Neotropics. This clade includes an estimated 150 species and is most diverse in high-elevation habitats in the tropical Andes of South America. Using a time-calibrated phylogeny of the group and species distribution and niche data, I demonstrate a strong positive association between lineage diversification rates and the mean elevation of species’ distributions as well as a strong negative correlation between diversification rates and the size of species’ ranges. Further, we employ a paleoelevation-dependent diversification model to test for an association between the uplift of the Andes and diversification in the clade and demonstrate that speciation rates in Neotropical Phlegmariurus are positively associated with increasing elevations in the Andes. Third, I use a phylogenetic framework to test the monophyly of morphology-based species groups in Neotropical Phlegmariurus. I demonstrate that most groups are not monophyletic, and that convergent evolution is widespread in the genus. We use ancestral character-state reconstruction methods for six morphological traits to elucidate patterns of trait evolution and to circumscribe new species groups. A total of eleven new monophyletic species groups are proposed and defined.

Gene duplications generate critical components of genetic variation that can be selected upon to affect phenotypic evolution. The angiosperm GATA transcription factor family has undergone both ancient and recent gene duplications, with the HAN-like clade displaying divergent functions in organ boundary establishment and lateral organ growth. To better determine the ancestral function within core eudicots, and to investigate their potential role in floral diversification, I conducted HAN-like gene expression and partial silencing analyses in the asterid species petunia (Petunia x hybrida). My results indicate duplication of HAN-like genes at the base of Solanaceae followed by expression diversification within the flower. Although no aberrant phenotypes were apparent following single gene knockdowns, silencing of both paralogs lead to leaf senescence. Together with other functional studies, these data suggest a possible ancestral role for HAN-like genes in core eudicot shoot apical meristem development, followed by functional diversification following both speciation and duplication.

This thesis is concerned with the role the rich cluster environment plays in the evolution of its galaxy population. We approach this issue from two angles, first we use deep wide-field imaging to investigate the effect of the cluster environment on the spatial and luminosity distribution of galaxies. Secondly, we focus on one particularly interesting class of galaxy, the enigmatic E+A galaxies, using a combination of state-of-the-art telescopes and novel instrumentation to elucidate the physical mechanisms and environmental influences causing the rapid change in star-formation activity in these galaxies. We present results from a deep photometric study of the rich galaxy cluster Abell 2218 (z=0.18) based on Hubble Space Telescope images. These have been used to derive the cluster luminosity function to extremely faint limits. We find the faint-end slope of the luminosity function to vary with environment within the cluster - in the sense that the ratio of `dwarf' galaxies to `giant' galaxies increases in the lower-density outskirt regions. Using imaging obtained with the Isaac Newton Telescope (INT) we confirm the presence of luminosity segregation in Abell 2218. However, luminosity segregation in clusters does not appear to be ubiquitous, with two other clusters studied with the INT (A119 at z=0.04 and A2443 at z=0.11) showing no sign of luminosity segregation of their galaxy populations. We use integral field spectroscopy of a sample of E+A galaxies in intermediate redshift clusters, obtained with the FLAMES system on the European Southern Observatory's VLT and the GMOS instrument on Gemini-North, to determine the radial variation in the strength of Hdelta absorption in these galaxies, and hence map out the distribution of the recently formed stellar population. We find a diversity of behaviour amongst these galaxies in terms of the radial variation in Hdelta absorption: with gradients that are either negative, flat, or positive. By comparing with numerical simulations we suggest that the first of these different types of radial behaviour provides evidence for a merger/interaction origin, whereas the latter two types of behaviour are more consistent with the truncation of star formation in normal disk galaxies.

Infidelity in romantic relationships can be devastating, and can cause many complex emotional reactions. The Jealousy as a Specific Innate Module (JSIM) hypothesis posits that due to differing reproductive pressures over evolutionary history, men and women have evolved different mechanisms to respond to infidelity. JSIM proposes that men, due to fears of cuckoldry, will respond with intense jealousy to a partner's sexual infidelity. It proposes that women, who are certain of their maternity but may suffer severe consequences if their mate falls in love with another and diverts his resources elsewhere, will respond with intense jealousy to emotional infidelity. These gender effects were examined in a study of participants who had recently been cheated on sexually, emotionally, or both, by romantic partners. Distress, forgiveness, and couple identity were measured. Results among actual victims of infidelity failed to support the JSIM hypotheses. Men and women responded with similar levels of distress to both types of infidelity. Both men and women were less forgiving as sexual infidelity severity increased, yet the severity of sexual infidelity was associated positively and significantly with less forgiveness for women, and it was associated less positively and non-significantly with less forgiveness for men. Men reported more couple identity after infidelity than did women. In a larger sample that used hypothetical scenarios, it was found that men responded with more upset to sexual infidelity and women responded with more upset to emotional infidelity when using a forced choice method.

Oxygen has been assumed to be a vital trigger for the evolution of multicellular life forms on Earth, partly based on its power to promote substantial energy flux in cell respiration and partly as biosynthesis of compounds like collagen require oxygen. However, the co-evolution of large life and the Earth’s chemical environment is not well understood at present, and there is particular disagreement in the field about whether the Cambrian explosion of animal life forms was a chemical or biological event. Here, I discuss the evolution of multicellularity, divided in simple or complex forms, in light of the evolution of ocean water column chemistry in both the Proterozoic and the early Paleozoic. Even if the appearance of animals is confined to the Ediacaran, other fossil evidence of complex multicellularity can be argued to occur in the Paleo-, Meso- and Neoproterozic. These finds are, if anything, reason enough to keep searching for early experiments in complex multicellularity. In this search, we may have to expand our toolbox by looking at e.g. trace element aggregations and the isotopic composition of key elements.  Research over the last couple of years have accentuated that much of the interval between the Ediacaran and the Devonian was dramatic with transitional ocean chemistry at the same time that large forms of animal life experienced dynamic radiation and ecological expansion. Results presented here describe some aspects of this time, including geochemistry from Chengjiang and a mechanism for preserving non-mineralized Cambrian animals that was partly dependent on specific ocean chemistry. Also, geochemical proxies using iron and molybdenum are used to infer a Paleozoic atmosphere with less than 50% of present levels of oxygen. The possibility that the subsequent rise is due to terrestrial plants and linked to the appearance of large predatory fish is discussed. Finally, the first mass extinction in the end-Ordovician is linked to low oxygen concentrations in the water column. It appears that more than oxygen was critical to allow the radiation of large life forms on Earth, but that chemistry and tectonic activity were intimately intertwined to biology, in a dance of permitting and being determined by certain aspects of ecology. / Under lång tid har vi sett atmosfärens syrehalt som avgörande för att stora livsformer skulle börja utvecklas på jorden, delvis eftersom syre är ett energirikt bränsle men också för att det krävs vid sammansättningen av vissa ämnen som djur behöver, till exempel proteinet kollagen. Men, i själva verket, har vi inte lyckats reda ut detaljerna om hur utvecklingen av tidigt, stort liv och miljö satt samman, och om den kambriska explosionen framförallt var en biologisk eller kemiskt händelse. I den här avhandlingen diskuterar jag hur utvecklingen av flercellighet, då uppdelat i enkla och komplexa former, kan vara kopplad till hur havens kemi förändrats både i proterozoikum (2.5-0.5 miljarder år sedan) och paleozoikum (0.5-0 miljarder år sedan. Även om fossil från moderna djur dyker upp runt ediacaran och kambrium, så finns det långt äldre fossil som kan påvisa flercellighet. Dessa fossil ger, om inte annat, anledning att leta vidare efter fler spår av pre-kambrisk flercellighet och kanske kan vi utöka våra sökmetoder till att också tolka ansamlingar, eller isotopsammansättningar, av spårmetaller. Den kambriska explosinen av djurliv (med startskott för 543 miljoner år sedan) är ett etablerat begrepp, men den senaste årens forskning har satt fokus på att en längre period, från ediacaran till devon, var en dynamisk tid med skiftande havskemi, nya djurarter och experimentella ekologiska nätverk. I den här avhandlingen presenteras några resultat som belyser just denna övergångstid, som geokemin i Chengjiang som beskriver hur havets kemi skiftar från syrefritt till sulfatfritt till syrerikt, och hur djur utan skal och ben kunde bli bevarade genom att flera unika förhållanden sammanföll. En annan studie visar hur molybden använts för att påvisa att atmosfärens syrehalt, under den här perioden, var högst hälften av vår moderna nivå. Vi hävdar att stigningen som skedde i devon, delvis tack vare växternas intåg på land, och att stigningen kan speglas i att fiskar först då hade råd att jaga och växa sig stora. Slutligen visar jag också på hur det första stora massutdöendet kan vara sammankopplat med syrefria hav, snarare än kyla och mer syre än djuren klarade av. Ett komplext samspel mellan flera kemiska ämnen, utöver syre, tektonisk aktivitet och biologi ser ut att höra samman med den dramatiska uvecklingen för stora livsformer på jorden.

Species interactions restrict or promote population growth, structure communities, and contribute to evolution of diverse taxa. I seek to understand how multiple species interactions are maintained, how human altered species interactions influence evolution, and explore factors that contribute to variation in species interactions. In Chapter 1, I examine how plants interact with multiple guilds of mutualists, many of which are costly interactions. The evolution of traits used to attract different mutualist guilds may be constrained due to ecological or genetic mechanisms. I asked if two sets of plant traits that mediate interactions with two guilds of mutualists, pollinators and ant bodyguards, were positively or negatively correlated across 36 species of Gossypium (cotton). Traits to attract pollinators were positively correlated with traits to attract ant bodyguards. Rather than interaction with one mutualist guild limiting interactions with another mutualist guild, traits have evolved to increase attraction of multiple mutualist guilds simultaneously. In Chapters 2 and 3, motivated by the fact that agriculture covers nearly 50% of the global vegetated land surface, I explore the consequences of changes in plant mutualist and antagonist guilds in agriculture for selection on plant traits. I first explore how agriculture alters abundance and community structure of mutualist pollinators and antagonist seed predators of wild Helianthus annuus texanus. Mutualists were more abundant near crops, whereas antagonists were more abundant far from crops near natural habitat. In addition, mutualist pollinator communities were more diverse near sunflower crops. Plant mutualists and antagonists respond differently to agriculture. Next, I explore how these changes in abundance and community structure of mutualists and antagonists influenced natural selection on H. a. texanus floral traits. Natural selection on heritable floral traits differed near versus far from crop sunflowers, and overall selection was more heterogeneous near crop sunflowers. Furthermore, mutualist pollinators and antagonist seed predators mediated these differences in selection. Finally, in Chapter 4, I ask if variation in interaction outcomes differs across types of species interactions. Furthermore, I examined the relative importance of factors that create context-dependency in species interactions. Using meta-analysis of 353 papers, we found that mutualisms were more likely to change sign of the interaction outcome when compared across contexts than competition, and predation was the least likely to change sign. Overall, species identity caused the greatest variation in interaction outcomes: whom you interact with is more important for context-dependency than where or when the interaction occurs. Additionally, the most important factors driving context-dependency differed significantly among species interaction types. Altogether, my work makes progress in understanding how species maintain interactions with multiple guilds of mutualists, how agriculture alters species interactions and subsequent natural selection, and the variation in species interaction outcomes and their causes.