Why are there so many birds in the tropics: using comparative approaches to investigate the confluence of landscape, ecology, and genome in the generation of Neotropical avian diversity

The Neotropics are home to an astonishing level of avian diversity, and thus naturally a focus for the study of the generation of biodiversity. Studies of tropical speciation often focus on large-scale landscape changes, such as the impacts of Pleistocene climate change, the formation of the isthmus of Panama, or the uplift of the Andes. However, the full scope of Neotropical avian diversity is not yet wholly understood, and increasing evidence suggests that other processes beyond these geographical factors contribute to speciation in tropical birds. Here, I examine genetic data, from mitochondrial markers to whole genomes, in a diverse array of Neotropical birds, to better understand the interplay between landscape, genome, and ecology in the development of reproductive isolation. In my first chapter, I use mitochondrial barcodes from over 2,000 birds to detect potential cryptic species across Panama. I find that species-level splits occur in 19% of sampled species, suggesting avian diversity in Panama is substantially underestimated. These disproportionately occurred in species with ecological characteristics associated with low dispersal ability. This is reinforced by the next chapter, in which I use reduced-representation genomic data in ten taxa of lowland Panamanian birds to test whether time is the most important predictor of the outcomes of secondary contact. I find no evidence that time plays a role in determining hybrid zone width in these taxa, and only a partial role in the generation of genomic variation. Instead, diet, which is again linked to dispersal ability as well as demographic changes, is a much better predictor. Finally, I move my focus in Chapter 3 to the Andes, using low-coverage whole genomes to examine the speciation history of the hummingbird genus Aglaeactis. This rapid radiation has significant mitonuclear discord, with completely different phylogenies reconstructed from mitochondrial and nuclear markers. In the two clades defined in the nuclear data, each made of three taxa, I then examined how divergence was distributed across the genome. The three southern taxa, all of which are in allopatry, have overall higher genomic divergence, but it is spread evenly across the genome. In the northern clade, though, I find much lower divergence punctuated by outliers of elevated differentiation. These northern taxa do have contact zones between them, and it is likely that gene flow in that geographic scenario has had a hand in shaping the genomic landscape for the development of reproductive isolation. Taken together, each of these chapters explores how reproductive isolation is the outcome of multiple facets of an organism interacting, and sheds further light on how avian biodiversity is generated

Altitudinalbewegungen von Vögeln in den Anden:mit einer Feldstudie im Nationalpark Carrasco (Bolivien)

Diese Schrift widmet sich den Bewegungen der Vögel der Anden entlang des Höhengradienten (Altitudinalwanderungen) und ihrer öko-ethologischen Steuerung. Daneben leistet sie einen Beitrag zum Naturschutz tropischer Bergwald-Ökosysteme. Umfassende Literaturauswertungen zeigen Forschungs- und Wissensdefizite auf. Eigene ornithologische Felderhebungen im Nationalpark Carrasco und seinem Umland in Bolivien erfolgten in den Jahren 2000-2003 entlang eines Höhentransekts durch tropischen Feuchtwald vom Tiefland zur Waldgrenze. Es wurde unterschieden zwischen altitudinalen jahreszeitlichen Zugvögeln, Vögeln mit kürzerfristigen Pendelbewegungen und dem isolierten Auftreten von Individuen außerhalb des Areals (Vagranten). Altitudinalwanderungen von Vögeln erweisen sich als artspezifisch, orts- und zeitspezifisch. Diese Studie ist ein Beitrag zum Verständnis der Idiosynkrasien und Komplexität der Altitudinalwanderungen von Vögeln in den Anden – und damit des artenreichsten Vogelzugsystems der Erde.The present study investigates the movements of Andean birds along the altitudinal gradient and the eco-ethological control of these movements. In addition, it aims at increasing the effectiveness of conservation of tropical forest ecosystems. A comprehensive literature review reveals considerable gaps in research and knowledge. An ornithological field study was carried out in Carrasco National Park and its surroundings in Bolivia from 2000 to 2003, covering a humid tropical forest transect from the lowlands to timberline. It differentiates between seasonal altitudinal migrant birds, relatively short-term commuters and isolated appearances of individuals outside their range (vagrants). Altitudinal bird movements are shown to be species-specific, but also specific to the spatio-temporal situation. This study contributes to the understanding of the idiosyncracies and complexities of altitudinal movements of Andean birds – and thus of the most bird species-rich migratory system on Earth

The role of physical and ecological barriers in the diversification process of birds in the Guiana Shield, northern Amazonia

Understanding the factors that influence the formation and location of distribution boundaries is important for the study of evolutionary processes. These factors can be studied effectively at suture zones, regions containing disproportionally high numbers of contact zones (CZs) and phylogeographic breaks (PBs). Together, CZs and PBs offer complementary views of current and historical factors that separate or bring together populations of closely related taxa. For my dissertation, I studied a suture zone in northern Amazonia, where ~100 pairs of taxa replace one another geographically. I analyzed the Guiana Shield avifauna, using bird distributions to redefine the boundaries of the Guianan area of endemism. I showed that the Rio Branco is an important biogeographical barrier and a natural western limit for this area, although smaller rivers, savannas, and mountains also play a significant role. A multivariate approach revealed that the Branco/Negro interfluvium represents a transitional zone for birds, suggesting that the longstanding view of Amazonia as a mosaic of parapatric areas of endemism likely represents an oversimplification of current patterns. I investigated the role of rivers in maintaining and generating biodiversity by testing predictions of the ‘riverine barrier hypothesis’. Using a comparative phylogeographic approach, I found that phenotypically differentiated populations across rivers are reciprocally monophyletic. The lower Rio Negro represents a stronger barrier to gene flow than does the upper Rio Negro, but no genetic homogenization occurs towards the headwaters. Most ‘riverine barrier hypothesis’ predictions were not supported, suggesting that rivers are key to maintaining biodiversity, but not for its generation. Finally, I explored the role of physical and ecological factors in the location of CZs and PBs. PBs cluster along physical barriers, whereas CZs aggregate at the headwaters of large rivers. Nearly half of the pairs that come into contact hybridize, and show significantly lower genetic distances than pairs that come into contact and do not interbreed, suggesting that time of isolation as inferred from genetic data may predict their likelihood of hybridization. Ecological niche models showed significant levels of niche divergence between pairs, suggesting that environmental variables cannot be ruled out as factors influencing the location of suture zones

Quantifying and categorising the environmental impacts of alien birds

We are faced with a rising tide of alien species introductions across the globe. Some of these species can have significant impacts on native biodiversity. Being able to identify those species that are likely to cause the most damage when introduced to new environments is crucial if we are to minimise the broad range of impacts that they may have. A protocol has recently been developed to quantify and categorise the environmental impacts of alien species: the Environmental Impact Classification for Alien Taxa (EICAT). In Chapter 2, I use EICAT to quantify and categorise the impacts of alien species for an entire taxonomic class (birds). In so doing, I generate the first, directly comparable global dataset on their environmental impacts. The assessment reveals that most alien birds have relatively minor impacts, but that some have population-level impacts that result in native species extirpations and extinctions. The EICAT assessment provides useful information on the ways in which alien birds can adversely affect the environment, and the types of species that have the most severe impacts. It also reveals that we do not have any data on the environmental impacts of over 70% of alien bird species globally: these species are classified as Data Deficient (DD) under EICAT. I use the data generated by the EICAT assessment to answer a number of outstanding questions regarding the environmental impacts of alien birds. In Chapter 3, I examine the factors that influence whether we have impact data for alien birds. I show that many species may be DD because they have minor impacts that do not attract scientific research, but that some species may be DD for reasons unrelated to the severity of their impacts. In Chapter 4, I identify the traits of alien birds that influence the severity of their environmental impacts, finding that widely distributed, generalist birds tend to have the most severe impacts. In Chapter 5, I identify the drivers of spatial variation in the severity of alien bird impacts, finding that factors relating to the duration and frequency of alien bird invasions are key in determining whether the impacts sustained by a region will be damaging. I also produce the first global maps displaying the impacts generated by alien species from an entire taxonomic class. These maps, and the data underpinning them, can be used to identify regions of the world susceptible to the impacts of alien birds. They may therefore assist in directing management interventions to regions where they are most needed

Structure, regulation, and evolution of Passerine molt

[eng] Molt is the process of plumage renewal by which birds maintain and adjust its functionality throughout their lifecycle. Multiple elements have been tackled in bird molt research (timing, duration, sequence, intensity, extent, feather growth rate, and plumage quality), but major gaps still exist on molt regulation, and especially on molt evolution. This thesis focuses on one molt element extensively recorded since mid-20th century but seldom studied as an individual trait: the set of feathers replaced after a given molt episode by one individual (here referred to as final molt phenotype). This is surprising because feathers differ in their function (e.g. signaling, thermoregulation, contribution to different flight functions, durability), costs of production, and morphology (e.g. exposure, mass, shape), all of which can be targeted by natural selection. Therefore, the final molt phenotype should be under strong selective pressures, suggesting that its regulation has been shaped during evolution to optimize plumage performance throughout the bird’s lifecycle. This thesis explores the potential of analyzing final molt phenotypes as is (instead of being analyzed partially or indirectly) to uncover underlying mechanisms of molt regulation and to provide insights on the evolution of molt in passerine birds. Following are the main findings presented in this thesis. Final molt phenotypes differed between the post-juvenile and the pre-breeding molts along the passerine phylogeny. A nested organization of final molt phenotypes suggested a rank of feather molt importance as underlying rule of molt. However, deviations from perfect nestedness were largely associated with the pre-breeding molt. Shared ancestry explained a large portion of final molt phenotype variation, likely due to constraints associated to plumage morphology, which is highly conserved in passerines. Phylogenetic analyses confirmed the phylogenetic independence of the pre-breeding molt and the strong phylogenetic signal of the post-juvenile molt. Further, they showed the overlooked relevance of environmental factors on the evolution of passerine molt, although their effect varied among taxonomic groups and molt episodes, thus highlighting the flexibility and adaptiveness of molt. Findings exposed in this thesis confirm the relevance of the final molt phenotype as a promising element to advance in our understanding of bird molt.[cat] La muda és el procés de renovació del plomatge mitjançant el qual els ocells mantenen i ajusten la seva funcionalitat durant tot el seu cicle vital. S’han abordat diversos elements en la investigació de la muda dels ocells (calendari, durada, extensió, intensitat, seqüència, qualitat del plomatge i velocitat de creixement de la ploma), però encara hi ha importants llacunes sobre la regulació de la muda i, sobretot, sobre la seva evolució. Aquesta tesi se centra en un element de la muda àmpliament registrat des de mitjan segle XX, però que encara no ha estat estudiat com a tret individual: el conjunt de plomes substituïdes després d’un determinat episodi de muda per un individu (aquí anomenat fenotip final de muda). Això és sorprenent perquè les plomes difereixen en la seva funció (e.g. senyalització, termoregulació, contribució al vol, durabilitat), costos de producció i morfologia (e.g. exposició, massa, forma), que poden ser objecte de selecció natural. Per tant, el fenotip de muda final hauria d’estar sota fortes pressions selectives, cosa que suggereix que la seva regulació s’ha configurat durant l’evolució per optimitzar el rendiment del plomatge al llarg del cicle de vida de l’ocell. Aquesta tesi explora el potencial d'analitzar el fenotip de muda final tal com és (en lloc d'analitzar-lo parcialment o indirectament) per descobrir els mecanismes subjacents de regulació de la muda i proporcionar informació sobre l'evolució de la muda en els passeriformes. A continuació es mostren les principals conclusions presentades en aquesta tesi. El fenotip de muda final diferia entre la muda post-juvenil i la pre-nupcial al llarg de la filogènia dels passeriformes. Una organització aniuada del fenotip de muda final va suggerir l’existència d’un rang d'importància en la muda de les plomes com a regla subjacent. Tanmateix, les desviacions de l’aniuament perfecte es van associar en gran mesura amb la muda pre-nupcial. L'ascendència compartida explicava una gran part de la variació del fenotip de muda final, probablement a causa de restriccions associades a la morfologia del plomatge, la qual està molt conservada en els passeriformes. Les anàlisis filogenètiques van confirmar la independència filogenètica de la muda pre- nupcial i l’elevat senyal filogenètic de la muda post-juvenil. A més, van mostrar la rellevància que han tingut els factors ambientals en l’evolució de la muda dels passeriformes, tot i que el seu efecte varia entre els grups taxonòmics i també entre els episodis de muda, destacant així la flexibilitat i la naturalesa adaptativa de la muda. Les troballes exposades en aquesta tesi confirmen la rellevància del fenotip de muda final com un element prometedor per avançar en la nostra comprensió de la muda dels ocells

Origin and dynamics of a hybrid zone between Ramphocelus tanagers (Thraupidae) in Colombia

Characterizations of hybrid zones are of importance in evolutionary biology because they can give insights about the characters and processes implied in population divergence. Here, we characterize a hybrid zone between tanagers in the genus Ramphocelus (Thraupidae) located in Western Colombia. We tested whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using molecular, morphological, and plumage coloration data in combination with palaeodistribution modeling. Models of potential historical distributions based on climate data and genetic signatures of population expansion suggest that the hybrid zone originated following secondary contact between two populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Comparisons between historical and current specimens suggest the zone has moved towards the east, possibly as a result of sexual selection or of asymmetric gene flow.Magíster en Ciencias BiológicasMaestrí