O gênero Myotis é extremamente diverso, sendo atualmente reconhecidas 103 espécies, além de 94 subespécies as quais não foram avaliadas satisfatoriamente quanto seu status taxonômico. Para a América do Sul são reconhecidas 12 espécies, das quais cinco são consideradas politípicas, dentre elas Myotis nigricans, táxon considerado um complexo de espécies. Com o objetivo de caracterizar, morfologicamente e molecularmente, os táxons do gênero Myotis que ocorrem no Brasil e aqueles relacionados a Myotis nigricans, examinei 1.018 exemplares depositados em coleções científicas nacionais e internacionais. Analisei 25 caracteres de morfologia externa e craniana, e aferi 13 medidas corporais e 19 cranianas. Submeti as medidas cranianas a testes estatísticos uni e multivariados com o intuito de investigar variações inter e intraespecíficas, e verificar a existência de dimorfismo sexual em cada táxon analisado. Selecionei um gene mitocondrial, citocromo b (402pb), e um gene nuclear, RAG2 (620pb), com a finalidade de caracterizar a diversidade genética intra e interespecífica dos táxons de Myotis, dos quais obtive 78 seqüências: 58 mitocondriais e 20 nucleares. A partir deste conjunto de dados reconheci 8 espécies válidas para o gênero Myotis no Brasil (Myotis albescens, Myotis alter, Myotis levis, Myotis nigricans, Myotis riparius, Myotis ruber, Myotis simus, e Myotis sp.n.). Elevei Myotis osculati ao nível específico, táxon até então considerado uma subespécie de Myotis nigricans; e considerei Myotis punensis e Myotis chiriquensis espécies válidas, as quais eram consideradas sinonímias de Myotis nigricans nigricans. Neste contexto, reconheço 15 espécies sul-americanas do gênero Myotis, o que representa um acréscimo de 25% na diversidade anteriormente reconhecida para o grupo na região. Não encontrei dimorfismo sexual significativo nas medidas cranianas de M. albescens, M. levis, M. nigricans, M. riparius e M. ruber. Para melhor delimitar morfometricamente os táxons estudados, em especial M. nigricans de M. riparius, propus a utilização de dois índices: um craniano e outro maxilar. Os caracteres qualitativos cranianos, como a presença de crista sagital e o posicionamento dos pré-molares superiores, associados aos de morfologia externa, como a disposição de pêlos ao longo do uropatágio, o formato do pavilhão auditivo, e a angularidade da porção distal da maxila inferior, apresentaram-se como os mais robustos na delimitação dos táxons com ocorrência no Brasil. As relações filogenéticas entre as espécies de Myotis após inclusão dos táxons validados neste trabalho, ainda permanecem imprecisas. Através dos métodos de Máxima Parcimônia (MP), de distância de Neighbor-Join (NJ) e análise Bayesiana (B), houve o resgate de dois grandes clados compostos por espécies com crista sagital ausente ou discreta (clado A), e crista sagital presente (clado B). Atribuí a politomia encontrada dentro do clado A à rápida diversificação do grupo na região, com possíveis eventos simultâneos de especiação. Associo a inclusão de M. levis no clado de M nigricans com um evento de introgressão mitocondrial dado a natureza do gene, e ao número de mutações, incompatível com homoplasia do gene. O tempo de divergência estimado em 1,2Ma (±0,8), coincide com os eventos de mudanças climáticas e de retração de florestas durante o Pleistoceno, que propiciariam a hibridização destas duas linhagens. Apliquei o Teste de Mantel nas populações de M. nigricans e M. riparius presente nos domínios da Mata Atlântica, com o intuito de verificar a existência de correlação entre distância genética e distância geográfica entre as populações, testando a hipótese de isolamento por distância, a qual foi rejeitada tanto para M. nigricans (p=0,9449; r=0,23) como para M. riparius (p=0,9997; r=0,60). As populações de Myotis riparius apresentaram uma baixa divergência genética (0,8 a 1,5%) ao longo da distribuição, com compartilhamento de haplótipos entre as populações de Paraíba, São Paulo, Paraná e Paraguai. Em relação à Myotis nigricans destaco o compartilhamento de haplótipos entre as populações da Bahia, São Paulo e Paraná, e a baixa divergência (1,9 a 2,4%) entre as populações ao leste da Serra do Mar. Contudo, os níveis de divergência entre estas populações e as populações provenientes da Serra do Japi e Serra da Mantiqueira são acentuados (5,7 a 8,1%), similares aos níveis interespecíficos para o gênero. Estes dados sugerem um alto fluxo gênico no sentido Norte-Sul da Mata Atlântica ao leste da Serra do Mar, podendo esta atuar como barreira para as populações interioranas. A compreensão dos processos envolvidos na diversificação do grupo será favorecida com a inclusão a estas análises de amostras provenientes de outras populações distribuídas nas porções Leste Oeste da Mata Atlântica. / Myotis is a highly diverse genus, with 103 species recognized so far, in addition to another 94 subspecies whose taxonomical status has not yet been completely evaluated. Twelve species are known to South America, among which five are considered polytypic, including Myotis nigricans. This taxon in considered a species complex. In order to characterize, both morphologically and molecularly, the taxa of the genus Myotis, I examined 1,018 individuals from national and foreign scientific collections. Twenty-five characters from external and cranial morphology were analyzed and 13 body and 19 cranial measures were checked. In order to investigate inter and intraspecific variations and the existence of sexual dimorphism in each taxon analyzed, I submitted the cranial measures to uni and multivariate statistic tests. To characterize intra and interspecific genetic diversity of the taxa in the genus Myotis, I selected one mitochondrial gene, cytochrome b (402pb), and a nuclear gene, RAG2 (602pb). From these two genes, I obtained 78 sequences: 58 mitochondrial and 20 nuclear. From the data obtained, I recognized as valid eight Brazilian species in the genus Myotis (Myotis albescens, Myotis alter, Myotis levis, Myotis nigricans, Myotis riparius, Myotis ruber, Myotis simus, and Myotis sp.n.). I elevated Myotis osculati, a taxon hitherto considered a subspecies of Myotis nigricans, to specific level and diagnosed Myotis punensis and Myotis chiriquensis as valid species, which were previously considered synonyms of Myotis nigricans nigricans. In this context, I recognize 15 species for the genus Myotis in South America, representing an increase of 25% in the previously known diversity for the group in the continent. I have not found significant sexual dimorphism in the cranial measures for M. albescens, M. levis, M. nigricans, M. riparius and M. ruber. To better delimitate morphometricaly the taxa herein studied, specially M. nigricans from M. riparius, I proposed the use of two indexes: one cranial and one maxillary. Qualitative characters from skull, such as presence or absence of a sagittal crest and the arrangement of upper premolars, associated to those from external morphology, such as the arrangement of the hair along the uropatagium, the shape of external ear, and the angling from the distal portion of the lower maxillae, were fundamental for diagnosing the taxa occurring in Brazil. The phylogenetic relationship among the species of genus Myotis is still imprecise, even after the inclusion of those taxa diagnosed as valid in this thesis. Through Maximum Likelihood (ML), Neighbor-Join (NJ) and Bayesian analysis methods, two clades were defined, one formed by species with absent or shallow sagittal crest (clade A), and another (clade B) with the presence of sagittal crest. I correlate the polytomy found within clade A with a fast diversification of this group in the region, possibly with simultaneous events of speciation. I correlate the inclusion of M. levis in the clade of M. nigricans with an event of mitochondrial introgression, given the nature of this gene and the number of mutations, which are not compatible with the homoplasy for this gene. The estimated divergence time of 1.2 Ma (±0.8), coincides with climatical changes and forest retraction during the Pleistocene, which allowed the hybridization of these two lineages. I ran the Test of Mantel for the populations of M. nigricans and M. riparius from the Atlantic Forest dominium, aiming at verifying the existence of a correlation between genetic distance and geographical distance in the populations, testing the hypothesis of isolation by distance, which was rejected both for M. nigricans (p=0.9449; r=0.23) and for M. riparius (p=0.9997; r=0.60). The populations of Myotis riparius showed a low genetic divergence (0.8 to 1.5%) along their distribution, with the populations from Paraíba, São Paulo, Paraná and Paraguay sharing haplotypes. Regarding Myotis nigricans, I point out that populations from Bahia, São Paulo and Paraná share haplotypes and low divergence (1.9 to 2.4%) between the populations from the western portion of Serra do Mar. Yet, the level of divergence between such populations and those from Serra do Japi and Serra da Mantiqueira is high (5.7 to 8.1%), therefore similar to the interspecific levels for the genus. These data suggest a high gene flow from the North-South direction to eastern Serra do Mar, which may be acting as a barrier to interior populations. The understanding of the processes involved in the diversification of the group will be favored by the inclusion of samples of other populations distributed in the East-West portions of the Atlantic Forest.

The latest-Permian mass extinction was the greatest biotic crisis of the Phanerozoic. The extinction decimated both marine and terrestrial communities, and changed the evolutionary trajectory of multicellular life on the planet. The unique nature of the extinction’s aftermath has prompted attention from paleontologists seeking to understand the timing and pattern of the Triassic recovery. With this dissertation I have sought to shed additional light on the terrestrial side of the extinction by examining different patterns by which its survivors responded to the extinction. Temnospondyl amphibians were one of the few tetrapod clades that were able to take advantage of the extinction to expand their diversity. In Chapter 1 I examine the relationship between taxonomic and ecological diversity of temnospondyls across the Permian-Triassic (P-Tr) boundary in the Karoo Basin of South Africa. Ecomorphological diversity, as implied by differences in cranial shape, was incorporated into the study by the use of a landmark-based geometric morphometric analysis. Both taxonomic diversity and cranial disparity were low during the Permian and increased across the Permian-Triassic boundary. Taxonomic diversity was stable through the Triassic, but disparity showed subsequent increases during the Olenekian and Anisian. Temnospondyls were restricted in size immediately following the extinction, but size range fully rebounded by the Olenekian. Tests of phylogenetic signal demonstrate that cranial shape was heavily influenced by phylogenetic relatedness, and the observed increases in disparity may be partly the result of decreases in the net relatedness of coeval Karoo stereospondylomorph temnospondyls in younger faunas. The increase in community-level taxonomic diversity for temnospondyls in the Karoo following the latest-Permian mass extinction was likely facilitated by an influx of distantly related and ecologically distinct species from other parts of Pangea. In Chapter 2, I discuss the merits of different potential methods for quantifying rates of dispersal within clades. I then apply some of these methods to two very different scenarios, first the dispersal of crocodylians across oceanic barriers during the Late Cretaceous and Cenozoic, and second the dispersal of different groups of tetrapods across Pangea during the Permo-Triassic interval. For crocodylians, because they were dispersing across substantial geographic obstacles, I opted for a direct measurement approach utilizing the optimization of discrete dispersals onto phylogenies. I examined the history of crocodylian biogeography using both parsimony and maximum likelihood on three distinct topologies with several different methods for estimating branch lengths. Across all analyses, members of the clade Alligatoroidea consistently dispersed across oceanic barriers less frequently than did non-alligatoroids. This is consistent with the hypothesis that the greater degree of salt tolerance observed in extant crocodyloids and gavialoids played a role in shaping crocodylian biogeography. The phylogenetic and temporal distribution of high dispersal rates points to an acquisition of greater salt tolerance early in the history of Crocodyloidea and Gavialoidea, potentially near the base of Longirostres if the combined evidence topology is correct. Patterns observed for changes in dispersal rate within individual clades can be largely attributed to changes in global climate and continental configuration over their history. The greater geographic ambiguity represented by the Permo-Triassic continental configuration makes a direct measurement approach inappropriate. For this study I instead opted for a proxy measurement approach, using the phylogenetic clustering of taxa within a community, measured using the Net Relatedness Index. I examined temporal changes in the phylogenetic clustering of five major tetrapod clades that span the Permian-Triassic boundary (Stereospondylomorpha, Parareptilia, Neodiapsida, Anomodontia, and Eutheriodontia) in order to examine patterns of extinction and origination through time, as well as rates of geographic dispersal. Some clades (Stereospondylomorpha, Parareptilia, and Neodiapsida) show evidence of phylogenetically selective extinction across the boundary, but this is not a universal pattern. Only one clade, Stereospondylomorpha, shows an unambiguous increase in dispersal rate following the mass extinction event. Other clades either show no change in dispersal rate, or have results that are mixed, depending on the parameters used in the analysis. These results show that stereospondylomorph temnospondyls were dispersing between geographical regions at increased rates during the Early Triassic, and this may explain much of their apparent increase in diversity following the latest-Permian mass extinction. In Chapter 3, I perform a comparison between the timing of the Triassic recovery with that following the Cretaceous-Paleogene (K-Pg) mass extinction. Three terrestrial fossil-bearing successions were examined, the Lower Triassic Beaufort Group in South Africa and Cis-Ural succession in Russia, and the Paleocene faunas of the American northern Great Plains. A comparison of generic diversity of tetrapods through time for the post-extinction intervals reveals a temporal disparity between the length of terrestrial recovery after the latest-Permian and K-Pg extinctions. Both Permo-Triassic successions show a period of low taxonomic richness (4-5Myr) after the extinction event, followed by an eventual rise in richness. The North American K-Pg succession shows a different pattern, with an immediate rise in richness culminating in a plateau shortly after the extinction (1-3 Myr). This disparity in recovery times may result from prolonged deleterious environmental conditions following the P-Tr events, although several important differences exist between these sequential fossil assemblages that may be affecting the apparent speed of recovery.

The North American Astereae clade (Asteraceae: Astereae) represents an ecologically important lineage whose species frequently comprise early to mid-successional ecosystems primarily throughout the United States. In the eastern U.S., most species are perennial suffrutescent herbs whereas many in the western U.S. are shrubs or subshrubs, particularly in the Solidagininae s.l. The delimitation of this subtribe, however, has remained unclear as molecular phylogenetics have not resolved whether the Solidagininae s.s. and another clade, the Gutierrezia lineage, collectively form the Solidagininae s.l. To evaluate the relationships among and within these lineages, high-throughput sequencing was employed across the North American Astereae. Highthroughput sequencing was also used to clarify relationships of one taxonomically contentious genus within the Gutierrezia lineage, Euthamia. Additional Euthamia specimens were amplified via polymerase chain reactions for sequencing two loci to increase phylogenetic sampling within the genus. Subsequent species delimitations based on molecular phylogenetics and morphological evaluations from literature were used to model species distributions through ecological niche modeling. Niche comparisons via the R package ‘Humboldt’ further assessed whether the most closely related species differed considerably in their environmental niche occupation. These collectively outlined the distributions of all nine Euthamia species and indicated that hypothetical sister taxa have diverged environmentally for both allopatric and sympatric species.

Biodiversity of coral reefs is higher than in any other marine ecosystem, and significant research has focused on studying coral taxonomy, physiology, ecology, and coral-associated fauna. Yet little is known about symbiotic copepods, abundant and numerous microscopic crustaceans inhabiting almost every living coral colony. In this thesis, I investigate the genetic diversity of different groups of copepods associated with reef-building corals in distinct parts of the Indo-Pacific; determine species boundaries; and reveal patterns of biogeography, endemism, and host-specificity in these symbiotic systems. A non-destructive method of DNA extraction allowed me to use an integrated approach to conduct a diversity assessment of different groups of copepods and to determine species boundaries using molecular and taxonomical methods. Overall, for this thesis, I processed and analyzed 1850 copepod specimens, representing 269 MOTUs collected from 125 colonies of 43 species of scleractinian corals from 11 locations in the Indo-Pacific. The genetic assessment of the most abundant copepod morphotypes associated with hermatypic corals in Lizard Island (Great Barrier Reef) revealed a large number of species previously unknown for this region. Analyses of diversity and patterns of biogeographical distribution of copepods associated with Galaxea corals throughout the Indo-Pacific showed that the species diversity of this group is high and appears to be regionally specific, an uncommon pattern in most coral reef-associated invertebrates. Results for the symbiotic copepod fauna of Red Sea pocilloporid corals, a family of corals with a high level of morphological variability within and among its members, showed that the majority of the discovered poecilostomatoid copepods belong to the genus Spaniomolgus, which demonstrated a significant genetic diversity of morphologically-similar species. Assessment of the diversity of copepods associated with the Red Sea mushroom corals revealed several undescribed species and showed no evidence of specificity to the hosts neither on species nor on the family level, which contradicts a modern assumption of high host-specificity of copepods. Overall, this dissertation is a first study of genetic diversity of copepods associated with invertebrates, and it provides substantial insight into the diversity of coral-associated microcrustaceans and insight to patterns of their host-specificity as well as distribution around the Indo-Pacific.

I used a Hierarchical approach to study historical biogeography in a group of colubrid snakes found in western North America. I combined small regions of mtDNA sequence data from a large number of individuals, with complete mt-genomic data. First, I investigated the relationships among leptodeirines-a presumed subgroup of dipsadines includeng nightsnakes (Pseudoleptodeira, Eridiphas, and Hypsiglena) - using ~1.5 Kb of data (cob and nad4). The relationships differed among parsimony, likelihood, and bayesian analyses. All analyses supported the monophyly of the nightsnakes; however, none supported the monophyly of the leptodeirines. Instead, these data supported a new hypothesis that the dipsadines were ancestrally rear-fanged and preyed on small vertabrates (frogs and lizards), such as the nightsnakes, while the more derived lineages have modified anterior maxillary dentition and prey strictly on invertabrates. Secondly, using an evolutionary species concept, I test species-subspecies boundaries in the wide-ranging hypsiglena, which has over 17 forms described, by collecting ~800 bp of sequence data (nad4 and tRNA) from ~ 175 individuals. Six major clades, concordant with geography, were recognized as species: Chihuahuan Destert (H. jani); central-western Mexico (H. torquata); upland Jalisco (H. Affinis); central California-Cape of Baja ("Coast," H. ochrorhyncha); Sonoran, Mojave, and Great Basin deserts ("Desert" H. chlorophaea), and an undescribed form from the Sonoran-Chihuahuan desert transition zone ("cochise"). The relationships among the major clades were not well resolved. Lastly, I collected complete mt-genome sequence data from 15 individuals including Eridiphas, Pseudoleptodeira, each of the major clades of Hypsiglena, and Sibon and Imantodes. All combined genomic-level analyses contained overwhelming support for a single phylogeny. These data, in conjunction with the phylogeographic data, supported my hypothesis that vicariance associated with the Miocene seperation of the Cape of Baja from mainland Mexico formed the Baja endemic Eridiphas, followed by subsequent range expansion and dispersal of Hypsiglena onto the northern portion of the peninsula and an even later vicariance event associated with the northern inundation of the gulf of California during the Pliocene. Hysiglena later dispersed down the Baja California Peninsula, coming into secondary contact with Eridiphas, forming a ring-like distribution around the Gulf of California.

Deserts are interesting places due to the large number of plants and animals that live there. Nocturnal wasps are extremely abundant in deserts, but they are difficult to identify and their life cycles are not well known especially the families of Chyphotidae, Tiphiidae (Brachycistidinae), and Mutillidae (velvet ants). In this dissertation, I determine how to correctly identify a particularly difficult group of species that all have black heads from the family Chyphotidae. This is important because these species make up a large proportion of specimens collected. Also, I expanded our knowledge on the distribution of the species of these three families of wasps by conducting a trap-transect study in Joshua Tree National Park catching 22 species of Brachyscistidinae based on the collection of 13,960 specimens, 11 species of Chyphotes based on the collection of 1,513 specimens and 35 species of velvet ants based on 8,447 specimens. From this study, three new species of velvet ants are described: Odontophotopsis dalyi Sadler and Pitts, sp. nov., O. odontoloxia Sadler and Pitts, sp. nov., and Photomorphus schoenwerthi Sadler and Pitts, sp. nov. Lastly, I used new molecular methods to determine relationships of the species of Brachyscistis, Chyphotes, and Odontophotopsis. These relationships suggest that the species are young, which is contradictory to evidence based on birds and mammals. These relationships also support dates for the inundation of southern California by the Boues Sea Embayment and confirm a hypothesized Baja Inner Peninsular Seaway.

Turtles are important components of ecosystems around the world, with diverse ecological niches and adaptations. However, there are few detailed studies of how turtle community structure reflects local environments. This project applied techniques of community structure analysis to sites across the United States to infer past ecosystem and environmental conditions of the early Pliocene Gray Fossil Site (GFS) in northeastern Tennessee based on the ancient turtle community. Results indicate extant turtle community structure closely reflects environmental conditions, and that ancient turtle communities can be used to infer climate and habitat conditions of past ecosystems. Application to the GFS turtle community shows similarity to modern communities of the southern Gulf Coast and subtropical southeastern United States. These findings are consistent with previous interpretations of the GFS environment as warmer and wetter than the southern Appalachian climate of today, and demonstrate the utility of fossil turtle assemblage data in determining past environmental conditions.

Platanthera is one of the largest genera of temperate orchids and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are western North America and eastern Asia. The diversity in floral morphological traits such as floral color, shape and the length of nectar spur is associated with numerous pollination syndromes, making Platanthera an ideal system to study the evolution of floral traits and pollination biology. Despite its diversity, a thorough phylogenetic hypothesis for the genus is lacking because no studies have yet sampled taxa exhaustively or developed a robust molecular toolkit. Nevertheless, in past phylogenetic studies some intrageneric groups of species appear to be monophyletic. One of these groups is subgenus Limnorchis, but the majority of taxa in this group have not been included in a phylogenetic analysis. In this study, I developed a new toolkit for Platanthera consisting of genomic information from 617 low-copy nuclear loci. Using a targeted enrichment approach, I collected high-throughput sequence data from these loci in 23 accessions, including nine of the 12 diploids of subgenus Limnorchis and nine outgroup Platanthera species. A maximum likelihood search was performed on a 570,818 nucleotide supermatrix to generate a phylogeny. This analysis resolved a strongly supported monophyletic clade for subgenus Limnorchis. This phylogeny was then used to test hypotheses of biogeographic diversification and floral trait evolution of subgenus Limnorchis. Ancestral biogeographic reconstruction indicated that subgenus Limnorchis originated in western North America ca. 3 – 4.5 Mya from an ancestor that was widespread in western North America and eastern Asia and subsequently diversified in western North America, followed by dispersal of some species to eastern North America. Floral macro and micro-morphological traits were characterized across the subgenus. Ancestral character reconstruction suggests convergent evolution of spur length, spur shape and viscidium shape, possibly in response to selection by similar pollinators. Understanding the biogeographic history and morphological diversification of subgenus Limnorchis within a phylogenetic context will contribute to an updated taxonomy for the subgenus.

No description available.

This study analyzes tree, soil, and microtopographic patterns present within the Cranberry Glades, a bog wetland complex located in the mountains of West Virginia. The Cranberry Glades are comprised of four open bog meadows, which provide unique habitat to several rare and endangered plant species. However, these meadows are filling in with trees and alder. This research is a study on the factors that may be involved in the processes and patterns influencing tree encroachment into the bog meadows across the open meadow – bog forest ecotone. To determine the patterns of infilling and the potential relationships among the trees, microtopography, and soil conditions, I collected and analyzed data on each of these factors within nine belt transects located across the ecotone. I gathered tree data on the following: location within transect, species, diameter at breast height or diameter at ground level, height class, associated microtopography, and growing conditions on 1,389 trees. Soil samples were gathered across the ecotone and analyzed for percent moisture, pH, and various nutrients and metals. I assessed historical aerial photographs to gain a temporal history on the patterns of infilling. The results indicate that trees decrease in density across the ecotone towards the peatland interior, and that trees are likely to be growing on hummock features and within tree islands. Soil properties resulted in mixed conclusions. The aerial photograph assessment revealed that trees and alders have been steadily encroaching into the open peatlands for at least the past 52 years. The finding of this research lend to increased knowledge on southern peatlands, wetland succession, and the Cranberry Glades Botanical Area. / Master of Science