Learning and experience shape mate preferences in many species. My thesis investigates the role of experience on mating behavior of male and female sailfin mollies (Poecilia latipinna). In the first chapter I explore whether adult experience influences male sailfin molly mate preference for their sexual parasite, the Amazon molly (Poecilia formosa), and whether experience could account for reproductive character displacement (RCD) of male mate preference in this species. Sailfin males from sympatric populations show a stronger preference for conspecific females over Amazon mollies than do males from allopatric populations. I exposed males from sympatric and allopatric populations to either a sailfin female or an Amazon prior to a mating trial with an Amazon. For the allopatric population, males with recent experience with an Amazon directed fewer mating behaviors towards an Amazon during mating trials than did males with recent experience with a sailfin. Males from the sympatric population, however, performed the same amount of mating behaviors towards an Amazon regardless of experience. Thus adult experience influences mating preferences and suggests that experience may play a role in RCD in this species. In the second chapter I investigate whether a learned sensory bias could influence female mate preferences. Sensory biases that influence mate preferences can arise through selection on the sensory system in foraging and predator detection domains. I tested whether a learned preference originating outside of the mating domain, specifically a color-based food preference, can be transferred to a color-based preference for a male trait. I trained female sailfin mollies to associate either green or blue with food and then tested their preference for animated male sailfins featuring either a blue or green spot. I found that females did not prefer the male with the same color spot to which they had been conditioned. I discuss the problem of learned preference transfer and suggest directions for future research into the role of learning in sensory bias. / text

Speciation, the evolution of morphologically, behaviorally and/or ecologically distinct lineages from a common ancestor, is the fundamental process generating biodiversity. The rapidly developing field of speciation genomics is challenging traditional views of speciation as a gradual, genome-wide process, and highlighting the role of divergent natural selection in the speciation process. This study investigates morphological evolution and the genomic architecture of speciation in a clade of 12 "munias" in the genus Lonchura, one of the most extraordinary cases of recent and rapid diversification in birds. With a diversity of plumage patterns and replicate examples of closely related species living in sympatry, this group is ideally suited
for addressing fundamental questions about the genomics of speciation. In this study, I (1) test for evidence of character displacement between sympatric species using quantitative measurements of plumage coloration and morphology; (2) examine the structure of genome-wide variation using ddRAD-seq (double-digest Restriction Site Associated DNA sequencing); and (3) investigate the genomic structure of divergence using whole-genome sequencing. I find some evidence for character displacement, particularly in morphometrics and crown coloration. There is also a trend, however, for sympatric species to be more similar in coloration than allopatric species, particularly those that have come into contact more recently. Analysis of 7,043 ddRAD-seq loci reveals evidence of introgression among sympatric populations, with overall genomic variation corresponding more closely to geography than species identity. There is also substantial heterogeneity in genetic structure among mitochondrial, autosomal, and Z-linked markers. Finally, whole-genome sequencing reveals low overall genomic divergence while pinpointing "islands of differentiation" that exhibit elevated divergence between species. Two of these islands overlap genes known to be associated with coloration—Agouti signaling protein (ASIP) and Kit ligand (KITLG)—and allelic variation at these genes is associated with phenotypic traits. I also find evidence of a ~26 million base pair inversion on the Z chromosome, which groups the focal species differently than genome-wide variation. A strongly mosaic pattern of population structure among genomic regions supports a genic view of speciation, in which a small fraction of the genome is involved in the initial divergence of species.

At broad scales, community ecologists study how biogeographic factors like environmental dissimilarity and geographic distance influence community assembly and composition. At small scales, community ecologists study how one or several species interact to determine habitat partitioning and coexistence. In this dissertation, I present studies at both scales. Chapter One investigates community assembly across the Caribbean, Central, and South American radiations of Anolis lizards and Eleutherodactylid frogs to test whether oceanic islands are unique in their assembly processes. Such uniqueness is suggested by high levels of endemism on islands; however, comparable levels of endemism can be found in mainland communities. I modeled the rate of species turnover between mainland communities, with respect to geographic distance and environmental dissimilarity, and then used the mainland model to predict turnover among islands. Turnover among island communities was significantly higher than predicted from the mainland model, confirming the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts. Chapter Two reviews the evidence for ecological character displacement (ECD), an evolutionary process whereby two resource competitors diverge from one another in phenotype and resource use, facilitating coexistence in a community. I find that, despite current scientific opinion, the evidence for ECD is equivocal; most cases of ECD pattern fail to rule out processes alternative to resource competition that could create the same pattern. I conclude that better evidence may come from real time tests of ECD. Chapters Three and Four describe just such a test in small island populations of Anolis carolinensis. In Chapter Three, I find that small island populations of A. carolinensis that have come into sympatry with a novel competitor, the invasive A. sagrei, shift their habitat use to become more arboreal, compared to allopatric populations. Consistent with prediction, individuals from sympatric populations have larger toepads with additional adhesive scales - a common adaptation to arboreality in Anolis. In Chapter Four, I describe a common garden experiment that finds that the observed toepad divergence is an evolved response, suggesting rates of divergence for toepad area and scale number on par with well known examples of contemporary evolution.

This thesis investigates the ecological and evolutionary implications of a recent secondary contact between two closely related bird species: collared (Ficedula albicollis) and pied (F. hypoleuca) flycatchers. Collared flycatchers started to colonize the Swedish island of Öland, where pied flycatchers were already present, in the late 1950s-early1960s. My major aims were to investigate which factors are acting against versus for long-term coexistence between the two species. Specifically, I investigated the relative importance of allopatric divergence, interspecific competition, hybridization and learning in promoting or inhibiting coexistence. The combined effects of interspecific competition and hybridization drives pied flycatchers towards local extinction in their preferred deciduous habitat. However, my results also show that pied flycatchers are better able to tolerate harsh environmental conditions. This trade-off between competitive ability and resilience in the face of harsh conditions facilitates a regional coexistence between the species. Coexistence is furthermore favoured by competition-mediated divergence in breeding habitat choice, timing of breeding and male breeding plumage colouration. Due to interspecific competition, male pied flycatchers are forced to breed in a more mixed forest type with a later peak in food abundance, which is accompanied by a divergence in breeding time between the two species. In areas shared with collared flycatchers, male pied flycatchers with brown plumage coloration, most divergent from that of collared flycatchers, are favoured by selection. In addition to facilitating coexistence, the observed shift in habitat occupancy increases reproductive isolation between the two species. By using cross-fostering experiments I demonstrate that natal habitat imprinting has the potential to additionally speed up habitat segregation. Finally I show that hybrid nestlings express an intermediate response to harsh environments, indicating that another aspect of ecological-based selection may be important in reproductive isolation between the species. In summary, my results show that adaptations during historic allopatry are important both in facilitating coexistence as well as in providing a foundation for further ecological divergence at secondary contact. This is of relevance today as many species are shifting their distributions in response to habitat disturbance and global warming.

Reproductive isolation can be achieved through multiple types of barriers and is essential for speciation. In flowering plants, pre-pollination barriers (e.g. differentiation in pollination niches) are believed to be the most efficient at preventing gene flow across species boundaries. In closely related species that come into secondary contact, such barriers can evolve to prevent competition for pollinator service and/or interspecific pollen transfer, which can have fitness costs. Hence pollination niche differentiation should be stronger in sympatric populations than in allopatric populations (i.e. character displacement). To investigate the differences in pollination niches and to see if it is consistent with a hypothesis of character displacement, I used the two closely related and phenotypically similar orchid species, Gymnadenia conopsea and G. densiflora. I sampled mixed and pure populations of G. conopsea and G. densiflora on Öland during the summer of 2020. In these populations, I used video cameras and pollinator catches to record pollinator activity and characterize the composition of pollinator communities. Estimation of pollinator efficiency was also assessed by analyzing the number of pollinia carried by each pollinator. Contrary to my expectations, I found that both orchids had their visitation peak during the night and that the most frequent and efficient pollinators were Autographa gamma or Deilephila porcellus for both of them. Furthermore, no increased differentiation between the two species was found in mixed compared to pure populations. My results suggest that plant-pollinator interactions do not act as efficient pre-pollination barriers in these two orchid species, and that competition for pollinator service and through interspecific pollen transfer seem to be too weak to drive pollination niche partitioning.

Competition has long been recognized as a central force in shaping evolution, particularly through character displacement. Yet research on character displacement is biased as it has focused almost exclusively on pairs of interacting species while ignoring multispecies interactions. Unfortunately, communities are seldom so simple that only pairs of species interact, and it is not clear if inferences from pairwise interactions are sufficient to explain patterns in nature. A more realistic approach is to ask how traits evolve when multiple species interact. Here I explore the importance of multispecies competitive interactions on trait evolution in four congeneric species of livebearing fishes in the genus Poeciliopsis (P. prolifica, P. viriosa, P. latidens, and P. presidionis). These species are found co-occurring throughout northwestern Mexico: My first chapter builds a framework for multispecies character displacement research by hypothesizing three effects that an unconsidered competitor, termed a hidden competitor, can have on pairwise interactions and the resulting pattern of character displacement. I show through these effects that research focused solely on pairwise interactions can be misleading for character displacement. I also provide suggestions on how to address character displacement research that incorporates more complexity. In chapter two, I test for character displacement in body shape in the four congeneric species. I found evidence for convergent character displacement in populations of P. prolifica, P. viriosa, and P. latidens. I also found that the convergence in body shape was not consistently in the same direction, meaning that when more than two species co-occurred I did not find a more extreme body shape that when only two species co-occurred. On the contrary, body shape when more than two competitors co-occurred seemed to be intermediate between the shape of two competitors and no competitor. This intermediate shape suggests that evolution in multispecies communities may occur in response to several competitors, rather than pairwise interactions. Finally, in chapter three, I test the effect of several hypothetical selective pressures on life history of P. prolifica, including intraspecies and interspecies competition, factors not often considered in life history evolution. I found that competition, both intraspecific and interspecific, was the most important factor in explaining variation in life history. I also found that the best models were those that included these selective pressures as direct effects as opposed to indirect effects through resource availability. However, it is not clear why competition was supported as a direct effect and future studies are needed to fully understand this aspect. Overall, my research suggests that competition plays an important role in shaping trait evolution, even in traits where it has not been considered. Thus, competition should be included in future studies as it may be an important factor in shaping several traits. I also found that competition in multispecies interactions is more complex than in a simple pairwise interactions, and can be harder to detect due to confounding effects acting in conjunction with competition. My study highlights the importance of competition and of considering multispecies competition to better understand the effects of competition.

ABSTRACT One cause of declines and extinctions of island species is carnivore introduction. Four carnivores, including the small Indian mongoose (Herpestes auropunctatus), are on the IUCN’s list of 100 of the World's Worst Invasive Alien Species. My thesis summarizes global patterns of carnivore introductions and examines ecological, evolutionary, and management impacts of this mongoose. I study abundances of reptiles and amphibians on mongoose-infested and mongoose-free islands in the Adriatic Sea to determine if factors other than mongoose presence can account for abundance differences. For several reptiles and amphibians, the mongoose is implicated as causing differences. Additionally, I assess species abundance in the small mammal community and activity times of introduced ship rats (Rattus rattus) on the same islands. The mongoose is implicated in a shift in rat activity times, but it is difficult to separate mongoose impacts on small mammal abundance from rat impacts. To manage introduced carnivores, we can exclude, control, or eradicate them. I review literature data on mongoose eradication and control campaigns. I compiled a list of all islands with known mongoose populations and focused on assessing successes, failures, and challenges. The mongoose has been eradicated only on six very small islands. Management at low levels by various techniques has been attempted on many islands, with variable success. On almost all islands of introduction, the mongoose has no potential competitors of similar size. However, on three Adriatic islands where the mongoose was introduced, a similar-sized native carnivore, the stone marten (Martes foina), is present, while on one Adriatic island the small Indian mongoose is the sole carnivore. To see if character displacement occurs in the mongoose when the marten is present, and vice-versa, I examined size variation in the diameter of the upper canine tooth (the prey-killing organ) and skull length in these two species on these islands. Character displacement in both traits was evident for the mongoose but not the marten. Lastly, I developed a simulation model to examine genetic consequences of serial introductions of the small Indian mongoose and found that the potential for population genetic data to determine introduction pathways and sequences is limited.

No description available.

ABSTRACT A major focus in biology is understanding the diversification of life and the processes that cause it. Much of this diversity is in the form of phenotypic variation among populations and species. In this thesis, I investigate two separate aspects of such phenotypic divergence. The first is the divergence of male mate preferences and their potential contribution to precopulatory sexual isolation and speciation. The second is the divergence of postcopulatory phenotypic divergence in the form of seminal fluid protein expression. With respect to the first aspect, in two separate experiments I investigated the contribution of male mate preferences to sexual isolation between two closely related fruit fly species experiencing differential costs to hybridization, Drosophila recens and Drosophila subquinaria. Male mate preferences are of particular interest because of their potential contribution to sexual isolation, a form of reproductive isolation which can contribute to speciation in sexually reproducing species. In the first experiment, I test for the presence of male mate preferences in each of the two species and whether the relative strength of the preference is concordant with the cost of hybridization. I found that that D. subquinaria males indiscriminately courted both their own (i.e. homospecific) females and heterospecific D. recens females. While D. recens from allopatry showed a similar pattern, those from sympatry courted their own females more than heterospecific females, indicating a pattern of reproductive character displacement. In the second experiment I test the role of learning in the context of these male mate preference in D. recens, and whether learning also showed a pattern of reproductive characteristic. I did not find evidence of learning in that D. recens males did not reduce their courting intensity towards heterospecific females after experiencing rejection by similar females. Consequently, I did not find an indication of reproductive character displacement. Finally, with respect to postcopulatory phenotypic divergence, I studied differences in seminal fluid protein expression between experimental populations of D. melanogaster experiencing one of three mating environments allowing for differing opportunities of mate competition and the environment in which it took place. These three mating environments include one in which mate competition was absent (MCabsent,), one in which mate competition occurred in a small, structurally simple environment (MCsimple), and one in which mate competition occurred in a larger, somewhat more complex environment (MCcomplex,). Male seminal fluids are of particular interest due to their ability to mediate postcopulatory competition between males and, therefore, can be used to manipulate females to a male’s own fitness benefit, potentially at her expense (i.e. sexual conflict). I investigated divergence in one particular seminal fluid protein implicated in sexual conflict, sex peptide (Acp70A). Whereas, gene expression levels among males from the three-mating treatment did not differ on average, relative stored quantities did, with MCcomplex males carrying significantly less sex peptide than either of MCabsent or MCsimple males (which did not differ from one another). This result suggests that mate competition and the environment in which it occurs play a significant role in the divergence of sex peptide phenotypes. ABSTRAIT Un objectif majeur de la biologie est de comprendre la diversification de la vie et les processus qui la provoquent. Une grande partie de cette diversité se présente sous la forme de variations phénotypiques entre les populations et les espèces. Dans cette thèse, j'étudie deux aspects distincts d'une telle divergence phénotypique. Le premier est la divergence des préférences des mâles et leurs contributions potentielles à l'isolement sexuel pré-copulatoire et à la spéciation. Le second est la différence de la divergence phénotypique post-copulatoire sous la forme de l'expression des protéines du liquide séminal. En ce qui concerne le premier aspect, dans deux expériences distinctes, j'ai étudié la contribution des préférences de compagnon mâle à l'isolement sexuel entre deux espèces de mouches des fruits étroitement liées subissant des coûts différentiels d'hybridation, Drosophila recens et Drosophila subquinaria. Les préférences des mâles sont particulièrement intéressantes en raison de leurs contributions potentielles à l'isolement sexuel, une forme d'isolement reproductif qui peut contribuer à la spéciation des espèces se reproduisant sexuellement. Dans la première expérience, je teste la présence de préférences de compagnon mâle dans chacune des deux espèces et si la force relative de la préférence est concordante avec le coût de l'hybridation. J'ai constaté que les mâles de D. subquinaria courtisaient sans discernement à la fois leurs propres femelles (c'est-à-dire homospécifiques) et les femelles hétérospécifiques de D. recens. Alors que D. recens de l'allopatrie a montré un modèle similaire, ceux de la sympatrie courtisaient leurs propres femelles plus que les femelles hétérospécifiques, indiquant un modèle de déplacement du caractère reproducteur. Dans la deuxième expérience, je teste le rôle de l'apprentissage dans le contexte de ces préférences de compagnon masculin dans D. recens, et si l'apprentissage a également montré un modèle de caractéristique de reproduction. Je n'ai pas trouvé de preuve d'apprentissage dans la mesure où les mâles D. recens ne réduisaient pas leur intensité de fréquentation envers les femelles hétérospécifiques après avoir été rejetés par des femelles similaires. Par conséquent, je n'ai pas trouvé d'indication de déplacement du caractère reproducteur. Enfin, en ce qui concerne la divergence phénotypique post-copulatoire, j'ai étudié les différences dans l'expression des protéines du liquide séminal entre les populations expérimentales de D. melanogaster connaissant l'un des trois environnements d'accouplement, permettant différentes possibilités de compétition de compagnon et l'environnement dans lequel elle a eu lieu. Ces trois environnements d'accouplement incluent un environnement dans lequel la compétition entre partenaires était absente (MCabsent,), un dans lequel la compétition entre partenaires se produisait dans un petit environnement structurellement simple (MCsimple) et un dans lequel la compétition entre partenaires se produisait dans un environnement plus grand et un peu plus complexe (MCcomplexe,). Les fluides séminaux mâles sont particulièrement intéressants en raison de leur capacité à négocier la compétition post-copulatoire entre les mâles et, par conséquent, peuvent être utilisés pour manipuler les femelles dans l'intérêt de la forme physique d'un mâle, potentiellement à ses dépens (c'est-à-dire conflit sexuel). J'ai étudié la divergence dans une protéine du liquide séminal particulière impliquée dans un conflit sexuel, le peptide sexuel (Acp70A). Alors que les niveaux d'expression génique chez les mâles du traitement à trois accouplements ne différaient pas en moyenne, les quantités relatives stockées le faisaient, les mâles MCcomplexe portant significativement moins de peptide sexuel que les mâles MCabsent ou MCsimple (qui ne différaient pas les uns des autres). Ce résultat suggère que la compétition de partenaire et l'environnement dans lequel elle se produit jouent un rôle important dans la divergence des phénotypes des peptides sexuels.

This study focuses on a secondary contact zone between two sister species of woodrat, Neotoma fuscipes (dusky-footed woodrat) and N. macrotis (big-eared woodrat). Along the Nacimiento River, on the border of southern Monterey and northern San Luis Obispo counties, the ranges of these sister species of woodrats meet and overlap forming a secondary contact zone. The zone of secondary contact is estimated to include a 500-meter (~1,650 linear feet) portion of the Nacimiento River riparian corridor. This research examines quantifiable morphological change that is likely associated with heightened inter-specific competition within the contact zone. When in sympatry the sister species may compete for resources indirectly through exploitative competition, or directly through contest competition, or through a combination of these two processes. The prediction that heightened competition has resulted in distinctive morphological character shifts between allopatric and sympatric populations was tested my examining size and shape of adult woodrats along a 20-kilometer transect. It was confirmed that adults woodrats of the two sister taxa are morphologically distinct (N = 602) and that the phallus morphology was indeed a reliable means to identify adult male woodrats as to species (p < 0.0001, N = 331). A two model approach was used to examine convergence and divergence in size and shape of woodrats across the transect. Neotoma fuscipes exhibited a statistically significant divergerence from N. macrotis with regard to breadth of rostrum (p < 0.0001, N = 414) in a region of sympatry along the Nacimiento River. Based on the results on one statistical model, N. macrotis exhibited a statistically significant convergence with regard to body-size (p = 0.0240, N = 587) and length of hind foot (p < 0.0001, N = 563) towards those of N. fuscipes between zones of sympatry and allopatry. Alternatively, based on the results of a second statistical model that accounted for environmental variation within the system both species exhibited a statistically significant divergence with regard to body-size (p = 0.0054, N = 587) and towards that of N. fuscipes between zones of sympatry and allopatry. Also, N. macrotis exhibited a statistically significant convergence with regard to length of ear (p = 0.0022, N = 563) towards that of N. fuscipes. Based on the results of both models, detectable re-patterning of size-independent traits was observed to varying degrees. The morphological character shifts between sympatric populations and allopatric populations of woodrats suggest that ecological interactions between the species are occuring. Specifically, across the contact zone, patterns of variation in body-size and other morphological character traits are consistent with expectations of a combination of contest and exploitative competition.