Testing models of biological diversification: morphological evolution and cladogenesis in the neotropical furnariidae (Aves: Passeriformes)

In this dissertation I explored the processes that generated high species diversity in a continental adaptive radiation of passerine birds: the family Furnariidae. Although there is a vast amount of information on the microevolutionary mechanisms that generate speciation and adaptation, much less is known about the processes underlying large-scale patterns of diversity. I used new techniques that exploit information contained in phylogenetic trees to investigate the diversification process in Furnariidae at a macroevolutionary scale. First, I conducted the first quantitative study that demonstrated that the Furnariidae constitute a case of rapid diversification in both species numbers and morphology as compared to six closely related families. To evaluate phenotypic diversity, I developed a new multivariate extension of the variance, which I called \u27proper variance\u27, and a new simulation procedure to test for differences in phenotypic diversity when complete phylogenies are not available. I found that the Furnariidae, although not particularly diverse in body size, is unusually diverse in shape. These results support the idea that the Furnariidae constitute a continental adaptive radiation. To explore processes responsible for high species diversity in the Furnariidae, I first investigated the effect of dispersal ability on species proliferation. Assuming that dispersal in birds is highly influenced by flying ability, I used an index of wing shape as a surrogate for flying ability. Using a nearly complete species-level phylogeny of the Furnariidae and a recently developed method, I found a negative correlation between flying ability and speciation rates, suggesting that low dispersal has stimulated species proliferation in Furnariidae. Finally, I investigated the effect of three key innovations on furnariid diversification: adaptations for trunk climbing, spiny-tail morphologies, and skull kinesis. I found that increases in diversification rates are not associated with major morphological changes. In addition, I found that climbing specialization had a negative effect on speciation rates, but that the spiny-tail morphology was positively correlated with speciation rates. These results provide mixed support for a role of key innovations promoting speciation. My results suggest a stronger role of geographic isolation (low dispersal) than ecological opportunities in species diversification in the continental radiation of the Furnariidae

TAXONOMIC AND MOLECULAR STUDIES IN CLERIDAE AND HEMIPTERA

Taxonomic changes are made based on checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH).Lectotypes are designated (and holotypes and paralectotypes recognized) for 44 species of Hydnocerinae, including the type species for Isolemidia, Parmius, Paupris, Allelidea, Blaesiopthalmus and Lemidia, four species of Enoclerus (Clerinae), and 14 species of Cymatodera (Tillinae). Annotations include comments on additional type material, new type locality, previous (type series) locality, and questionable or missing types. Phyllobaenus pallipes(Gorham) and P. rufithorax (Gorham) are synonymized with P. flavifemoratus(Gorham), P. chapini (Wolcott) is synonymized under P. lateralis (Gorham), and P. villosus (Schenkling) is synonymized under P. longus (LeConte), new synonymies. The first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) is presented and compared with the two most recent phylogenetic hypotheses of the group. Phylogenetic relationships of checkered beetles wareere inferred from approximately 5,000 nucleotides amplified from four loci (28S, 16S, 12S, COI). A worldwide sample of ~70 genera is included and phylogenies are reconstructed using Bayesian Inference and Maximum Likelihood. The results are not entirely congruent with either of the current classification systems. Three major lineages are recognized. Tillinae are supported as the sister group to all other subfamilies, whereas Thaneroclerinae, Korynetinae sensu latu and a new subfamily formally described here, Epiclininae, new subfamily, form a sister group to Clerinae + Hydnocerinae. To assess the phylogeny and evolution of Hemiptera, a comprehensive mitogenomic analysis integrating mitogenome-based molecular phylogenetics, fossil-calibrated divergence dating (using BEAST), and ancestral state reconstructions are presented. The 81 sampled mitogenomes represent the most extensive mitogenomic analyses of Hemiptera to date. The putatively primitive “Homoptera” was previously rendered paraphyletic by Heteroptera, whereas the presented results support each group as monophyletic. The results from both diet and habitat ancestral state reconstructions support that 1) Heteroptera (and Homoptera) evolved from a phytophagous ancestor, contrary to the popular hypothesis that the ancestor was predaceous; and 2) family-level radiation of Heteroptera is coincident with the apically-produced labium and the novel hemelytron. It is here proposed these morphological innovations facilitated multiple independent shifts from phytophagy to predation and multiple independent colonizations of aquatic habitats

Historical Examination Of Delayed Plumage Maturation In The Shorebirds (Aves: Charadriiformes)

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/137446/1/evo01315.pd

Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds

Uncertainties in the phylogeny of birds (Avialae) and their closest relatives have impeded deeper understanding of early theropod flight. To help address this, we produced an updated evolutionary hypothesis through an automated analysis of the Theropod Working Group (TWiG) coelurosaurian phylogenetic data matrix. Our larger, more resolved, and better-evaluated TWiG-based hypothesis supports the grouping of dromaeosaurids + troodontids (Deinonychosauria) as the sister taxon to birds (Paraves) and the recovery of Anchiornithinae as the earliest diverging birds. Although the phylogeny will continue developing, our current results provide a pertinent opportunity to evaluate what we know about early theropod flight. With our results and available data for vaned feathered pennaraptorans, we estimate the potential for powered flight among early birds and their closest relatives. We did this by using an ancestral state reconstruction analysis calculating maximum and minimum estimates of two proxies of powered flight potential—wing loading and specific lift. These results confirm powered flight potential in early birds but its rarity among the ancestors of the closest avialan relatives (select unenlagiine and microraptorine dromaeosaurids). For the first time, we find a broad range of these ancestors neared the wing loading and specific lift thresholds indicative of powered flight potential. This suggests there was greater experimentation with wing-assisted locomotion before theropod flight evolved than previously appreciated. This study adds invaluable support for multiple origins of powered flight potential in theropods (≥3 times), which we now know was from ancestors already nearing associated thresholds, and provides a framework for its further study. Video Abstract: [Figure presented] Pei et al. use an updated phylogeny of early birds and their closest relatives to reconstruct powered flight potential, showing it evolved at least three times. Many ancestors of the closest bird relatives neared thresholds of powered flight potential, suggesting broad experimentation with wing-assisted locomotion before theropod flight evolved.Fil: Pei, Rui. Institute Of Vertebrate Paleontology And Paleoanthropology Chinese Academy Of Sciences; ChinaFil: Pittman, Michael B.. The University Of Hong Kong; Hong KongFil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Dececchi, T. Alexander. Mount Marty College; Estados UnidosFil: Habib, Michael B.. Natural History Museum Of Los Angeles County; Estados UnidosFil: Kaye, Thomas G.. Foundation For Scientific Advancement; Estados UnidosFil: Larsson, Hans C. E.. Mcgill University; CanadáFil: Norell, Mark A.. American Museum of Natural History; Estados UnidosFil: Brusatte, Stephen L.. University of Edinburgh; Reino UnidoFil: Xu, Xing. Institute Of Vertebrate Paleontology And Paleoanthropology Chinese Academy Of Sciences; Chin

Integrating, Developing, and Testing Methods to Generate More Cohesive Approaches to Biogeographic Inference

As a fundamental component of the developing discipline of conservation biogeography, broadscale analyses of biotic assembly and disassembly across multiple temporal and spatial scales provide an enhanced understanding of how geologic transformations and climate oscillations have shaped extant patterns of biodiversity. As with any scientific field, there are limitations in the case of biogeographic historical reconstructions. Historical reconstructions are only as robust as the theoretical underpinnings of the methods of reconstruction (including data collection, quality, analysis, and interpretation). Nevertheless, historical reconstructions of species distributions can help inform our understanding of how species respond to environmental change. My dissertation takes a critical look at the current state of biotic-level biogeographic analyses across an array of spatio-temporal scales and I use the North American warm deserts as a model system to both develop and test biogeographic methods. In particular, I address the biogeographic issue of pseudo-congruence (similar biogeographic patterns produced by historically dissimilar events) and develop potential approaches to reduce the issue of pseudo-congruence in biotic-level analyses. I review potential confounding issues that could produce pseudo-congruence in climate change-based biogeographic analyses and I incorporate temporal components into complex biogeographic theories and methods to reduce pseudo-congruence in biogeographic analysis. My dissertation goals and approaches are described in Chapter 1, which serves as an introduction. In Chapter 2, I provide a summary of paleoclimatic patterns and processes in the North American deserts. A refined understanding of paleoclimatic pattern and process can facilitate the generation of enhanced hypotheses about how biotas are altered by climate change events, particularly in cases where climate change events occurring at different times and scales could produce pseudo-congruent biogeographic patterns. In Chapter 3, I propose a modification to the Phylogenetic Analysis for Comparing Trees (PACT) multi-clade biogeographic analysis, in order to facilitate a modern, integrative biotic-level analysis. I developed a modified PACT (mPACT) protocol that incorporates a temporal component (to reduce pseudo-congruence) and facilitates likelihood-based phylogenetic ancestral area reconstruction. To test the performance of my modification, I conducted modified and standard PACT (mPACT and PACT, respectively) analyses on data previously generated for the North American warm deserts and compared these results to those of a prior analysis that uses Secondary Brooks Parsimony Analysis (Secondary BPA), which is a binary-coded pre-cursor method to PACT. This analysis showed that results from mPACT revealed more diversification compared to Secondary BPA and PACT analyses and that pseudo-congruent patterns were rampant in this dataset. Finally, in Chapter 4, I developed and tested a novel operational approach to exploring evolutionary dynamics of areas of endemism (areas thought by some biogeographers to generate and maintain unique lineages through time). My procedure implements mPACT analyses as well as paleoclimatic and geologic information and I tested my analysis by conducting an analysis on the North American warm deserts. The results of my analysis were congruent with the pre-existing biogeographic hypotheses of the North American warm deserts but also showed that there were more pseudo-congruent events than previously recognized, which may alter the understanding of areas of endemism on a temporal scale. Moreover, I provide novel insights into the potential for areas of endemism to act as both areas of persistence (or stability) as well as areas of transition (ephemeral areas) for biodiversity and I address the issue that diagnosed areas of endemism may not all be equal with respect to biodiversity production and stability through time

Revisão taxonômica e filogenia de Cheirodontinae (Characiformes: Characidae) : integrando evidência morfológica e molecular

A ictiofauna neotropical de água doce é taxonomicamente a mais diversa do planeta, porém sua diversidade ainda é amplamente subestimada. A evidência para essa subestimativa vem do acúmulo de formas morfologicamente distintas, mas não descritas, depositadas em coleções de museus e dos resultados de estudos baseados em DNA (por exemplo, delimitação de espécies) que identificam consistentemente um número maior de linhagens divergentes do que o atualmente é aceito, mesmo dentro de grupos bem estudados. Investigamos a diversidade de linhagens dentro de Cheirodontinae, sequenciamos a subunidade I do citocromo c oxidase mitocondrial (COI) e delineamos linhagens usando 8 diferentes métodos de delimitação de espécies de lócus único. Os resultados fornecem evidências fortes e consistentes para a existência de uma diversidade adicional e não descrita dentro de Cheirodontinae. Dentro de Cheirodontinae, encontramos hipóteses divergentes (morfológicas vs. moleculares) sobre as relações filogenéticas dentro da subfamília. Testamos essas duas hipóteses, usando dados integrados (morfológicos e moleculares: COI, 16S, 12S, RAG1, RAG2, Myh6) propomos uma nova hipótese de relações filogenéticas dentro da subfamília, e subdividimos a subfamília, em 8 clados, que são corroborados pelas diferentes metodologias (parcimônia e modelos). Com esta informação morfológica e molecular, estimamos o tempo de divergência dentro da subfamília usando Evidencia-total com datação FBD, o que nos levou a determinar que Cheirodontinae se diversificou de Aphyocharacinae, aproximadamente 28 Ma. Com esses resultados reconstruímos a história biogeográfica dos Cheirodontinae na região neotropical e testamos a influência do tamanho e sua capacidade de inseminação em sua diversificação.The neotropical freshwater fish fauna is taxonomically the most diverse vertebrate on the planet, however its diversity is still largely underestimated. Evidence for this underestimation comes from the accumulation of morphologically distinct but undescribed forms deposited in museum collections, and from the results of various DNA-based studies (eg, species delimitation) that consistently identify a larger number of divergent lineages than currently accepted, even within well-studied species, we investigated the diversity of lineages within the Cheirodontinae. To investigate this diversity, we sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delineated lineages using 8 different single-locus species delimitation methods. The results provide strong and consistent evidence for additional and undescribed taxonomic diversity in Cheirodontinae. Within the Cheirodontinae, we find divergent hypotheses (morphological vs. molecular) about phylogenetic relationships within the subfamily. We test these two hypotheses, using integrated data (morphological and molecular: COI, 16S, 12S, RAG1, RAG2, Myh6) we propose a new hypothesis of phylogenetic relationships within the subfamily, and we subdivide the subfamily, into 8 clades, which are corroborated by the different methodologies (parsimony and models). With this morphological and molecular information, we estimated the time of divergence within the subfamily using Total-evidence with FBD dating, this led us to determine that the Cheirodontinae diversified from the Aphyocharacinae, approximately 28 Ma. With these results we reconstruct the biogeographical history of the Cheirodontinae in the neotropical region and we test the influence of the size and its insemination capacity in its diversification