The warbler Prinia inornata (Plain Prinia) is a common songbird found across large parts of southern Asia, and it is currently divided into ten geographically distinct subspecies. It has been suggested by some ornithologists to possibly be a complex of cryptic species, i.e. several species so similar to each other that they have been taxonomically misclassified as being conspecific. This study used audio recordings to compare songs between individuals from different regions in order to see if there are distinct geographical differences, and if so, how these correspond to the current taxonomy. The comparison was made using two methods: A qualitative auditory analysis, and statistical models (NMDS and PCA) based on measurements from spectrograms.  The results show that two main types of song exist that are highly distinct from each other, each taking up roughly half of the geographical range. The two main types can be further divided into a few subtypes, potentially as many as seven in total. The geographical distribution of these subtypes matches that of some of the current subspecies, but the results do not support the current taxonomy as a whole. It is therefore likely that P. inornata comprises at least two species (corresponding to the two main types), possibly more.

Heteromys pictus-spectabilis is a species complex within the subfamily Heteromyinae (Family: Heteromyidae) that is distributed along the western and southern Mexican coast and surrounding environments. Currently, the species complex is accepted as being 2 separate species (H. pictus and H. spectabilis), but this also renders H. pictus paraphyletic. Therefore, the species complex requires re-evaluation in order to resolve the paraphyly. Mitochondrial DNA sequences from a previously existing ~720 specimen database compiled by Victoria Vance were used in conjunction with new nuclear DNA sequences sequenced for the purpose of this study to generate multiple phylogenetic trees via the software programs RAxML, BEAST, and MrBayes to evaluate how different haplotype networks were related to each other. Using these molecular datasets in consideration with Kimura two-parameter values, time calibrations via BEAST, and the relative geographic locations of the haplotype networks, the results strongly indicate this species complex is composed of multiple cryptic species and potentially multiple genera. This was a preliminary exploration into this species complex however, and future research will be required to verify these findings.

In the face of unprecedented anthropogenic change, we increasingly turn to emergent technologies and extensive data sets for solutions that complement much needed systemic changes in our societies. These technological solutions, however, must be approached with care. We must recognize and address biases in the way data has been accumulated. In demographic studies, dormant life stages, such as seed banks, and other cryptic factors have often been neglected. The potential consequences of these omissions have been extensively described in the literature. In the first chapter, I analyze patterns of seed bank omissions in demographic models, finding unjustified omissions are widespread across ecoregions, growth forms, and taxonomic groups. More importantly, studies with longer duration and accounting for a greater range of conditions were less likely to neglect the seed bank. Unfortunately, most demographic studies are conducted for relatively short periods and are limited to one or a few sites. In addition, modeling tools often focus on mean behavior and do not properly characterize variability. In the second chapter, I explore the use of Bayesian generalized linear mixed models to characterize vital rates and compare their variation across growing conditions. Using wild and translocated populations of Dicerandra christmanii,this study tests the ability of this approach to evaluate early translocation success and site suitability.In chapter 3, I expand the demographic analysis of Dicerandra christmaniiand provide an example of the use of Bayesian-fitted Integral Projection Models (IPMs) to combine data sources and incorporate seed dynamics into demographic models. By propagating uncertainty from vital rates to derived population metrics, this study illustrates the consequences of accounting for the seed bank stage and site condition to our assessment of population viability. In the final part of this work, I present potential routes to expand field and modeling tools to help address the inclusion of dormant and cryptic life stages into demographic studies. Among these, I recommend exploring more complex sampling schemes, informed priors, and expanded IPMs.

No description available.

No description available.

Hyalella azteca, an amphipod crustacean, is frequently used in freshwater toxicity tests. Since the mid-1980s, numerous organizations have collected and established cultures of H. azteca originating from localities across North America. However, H. azteca is actually a large cryptic species complex whose members satisfy both the biological and the phylogenetic species concepts. Recently, two publications reported that members of the H. azteca cryptic species complex have different toxicity responses to anions and an insecticide. In this study, four members of the H. azteca species complex were identified with DNA barcoding. The genetic variation among the four clades was consistent with interspecific distances between species. These lineages (clades 1, 3, 6, and 8) were cultured in identical conditions and monitored on a weekly basis to determine two life history traits: adult mortality and juvenile production. The large-bodied clades had significantly better survival and juvenile production compared to the small-bodied clade 3. Clade 6 had very low juvenile production and high mortality; therefore, was not included in this study. Unique culture protocols may be required for each clade to optimize growth, survival, and juvenile production in laboratory conditions. Genetic barcoding has identified only two clades in a survey of 17 laboratories. Therefore these two clades (1 and 8) were compared after exposure to copper and nickel 14-day toxicity tests. Clade 8 was 2.3-2.6 times more tolerant to copper exposure than clade 1 based on their LC50 and LC25. Similarly, clade 8 was more tolerant to nickel exposure than clade 1: LC50 was 1.8 times higher for the former. Nickel LBC50 and LBC25 were significantly different between clades by a factor of 2.1-2-8. Mortality (relative to copper concentrations in tissue), growth, and bioaccumulation responses were not significantly different based on overlapping confidence intervals. Although clades 1 and 8 are both large-bodied ecomorphs, these lineages had significantly different body mass (i.e., dry weight) after 14 days. The results of this study indicate that genetically characterized cultures of H. azteca should be used in toxicity tests.

Les expériences de séquençage à haut débit ont permis de démontrer que la transcription ne se limite pas aux régions codantes et qu’une grande partie du génome est transcrite en ARN non-codants (ARNnc). Parmi eux, les transcrits cryptiques sont initiés à l’intérieur des régions codantes. Des études faites chez la levure Saccharomyces cerevisiae, ont pu identifier plusieurs facteurs qui répriment la transcription cryptique. Un de ces facteurs est Spt6, une chaperonne d’histones requise pour le maintien d’un bon niveau de nucléosomes le long des gènes transcrits. Lorsque Spt6 est muté, on observe une déplétion des nucléosomes conduisant à l’activation des promoteurs cryptiques. Cependant, le mécanisme par lequel ces transcrits cryptiques sont régulés n’est pas encore clair. Dans ce mémoire, nous présentons un travail dans lequel nous avons développé une méthode probabiliste dans le but de caractériser les transcrits cryptiques à partir de données de RNA-Seq. Cette méthode est basée sur une cumulation des données et permet de tenir compte des variations dans l’expression et dans la longueur des gènes, grâce à une étape de randomisation des données. Les résultats démontrent que notre méthode est au moins aussi efficace que les méthodes précédemment décrites dans la littérature et offre un bon compromis entre le taux de faux positifs et de faux négatifs. Enfin, le plus important est que cette méthode permet de prédire les régions génomiques où les transcrits cryptiques sont initiés. Nous avons mis en évidence la présence de transcrits cryptiques sur les brins sens et antisens par rapport au gène. Nous avons également montré que les promoteurs cryptiques sens et antisens sont enrichis en motif TATA et que les transcrits cryptiques sont polyadénylés, ce qui suggère qu’ils peuvent être régulés par les mêmes mécanismes qui régulent les gènes. Alors que les transcrits cryptiques sur le brin sens se terminent à la même position que les gènes dont ils sont issus, les transcrits cryptiques sur le brin antisens terminent préférablement aux extrémités 3’ des gènes situés en amont. Nous proposons donc que les terminateurs chez S. cerevisiae ont évolué pour terminer la transcription de manière bidirectionnelle afin d’empêcher une transcription aberrante qui pourrait envahir les gènes voisins. / High throughout sequencing experiments have shown that transcription in not limited to coding regions and that most of the genome is transcribed into non-coding RNA (ncRNA). Among them, cryptic transcripts are aberrantly initiated from within the coding regions. Several studies in Saccharomyces cerevisiae have identified many factors that suppress cryptic transcription. One such factor is Spt6, a histone chaperone required for maintaining appropriate nucleosome levels on transcribed genes. In Spt6 mutant cells, nucleosomes are depleted, leading to activation of cryptic promoters. However, the mechanism by which these cryptic transcripts are regulated remains unclear. In this thesis, we present the development of a probabilistic method for the characterization of cryptic transcripts from RNA-Seq data. The method is used to characterize cryptic transcription in spt6-1004 cells. The method is based on a cumulative distribution function, thus taking into account variations in gene expression and gene length thanks to a data randomization step. Results show that our method is at least as good as previously published methods and provides a good compromise between false positives and false negatives. Importantly, this method allows for the prediction of genomic regions where cryptic transcripts are initiated. We have demonstrated the presence of cryptic transcripts running on the sense and antisense strands relative to genes. We also showed that, both sense and antisense cryptic promoters are enriched for TATA-like sequences and that cryptic transcripts are polyadenylated, suggesting that they may be regulated by the same mechanism that occurs on genes. While the cryptic transcripts on the sense strand terminate at the same position as the genes from which they are derived, cryptic transcripts on the antisense strand preferentially terminate at the 3’-end of upstream genes. We therefore propose that S. cerevisiae terminators have evolved to terminate transcription bidirectionally in order to prevent an aberrant transcription that could invade neighboring genes.

Endoparasitoids of herbivorous lepidopterans have intimate relationships with their host species as well as the plant on which their host develops. Characteristics of both hosts and plants can affect parasitoid success in tri-trophic systems and thus, drive diversification. Genetic differentiation was estimated for Cotesia congregata (Say) collected from two distinct host-plant complexes, Manduca sexta L. on tobacco (Nicotiana tabacum L.) and Ceratomia catalpae, (Haworth) on catalpa (Catalpa bignonioides Walker), in the mid-Atlantic region of North America using seven microsatellite loci and the mitochondrial COI locus. Microsatellite allele frequencies were differentiated based on host-plant complex, and COI haplotypes from individuals on the same host-plant were identical despite geographic distances between catalpa sites of up to 830 km and distances between tobacco sites of up to 294 km. Results indicate genetic differentiation of subpopulations of C. congregata based on host-plant complex and not geographic distance, and were designated as host races. Cotesia congregata is a gregarious parasitoid, meaning that many individuals develop in a single host larva. Superparasitism, or repeated egg-laying events in the same host larva, is likely to occur in gregarious species. Brood size was not a good predictor of superparasitism in C. congregata, but within-brood male allele diversity indicates either superparasitism or multiple mating by female wasps.

Estudo da termitofauna (Insecta, Isoptera) da região do alto Rio Madeira, Rondônia. Na região conhecida como alto Rio Madeira, no município de Porto Velho, Rondônia, estão sendo criadas as Usinas Hidrelétricas (UHEs) de Santo Antônio e Jirau. As construções das represas das UHEs estão inundando grandes porções de floresta ao longo das duas margens do rio Madeira. Desta forma o conhecimento da biota local, especialmente de sua distribuição no espaço, é extremamente importante, ainda mais porque o alinhamento dos rios Amazonas-Madeira-Mamoré separa a região Neotropical em duas áreas de endemismo para diversos grupos de animais. Essa tese tem por objetivo apresentar os resultados gerais obtidos ao longo de três anos de monitoramento de cupins nas áreas de influência da UHE de Jirau e dois anos nas áreas de influência da UHE de Santo Antônio, assim como desenvolver um estudo de comunidades e análise da distribuição espacial dos cupins presentes nas áreas de influência da UHE de Jirau (Capítulo 1). Outro objetivo é o estudo da estrutura genética das populações de Heterotermes tenuis (Rhinotermitidae) ao longo das áreas de influência das duas UHEs, visando investigar a existência de fluxo gênico entre as populações de cada margem do Rio Madeira (Capítulo 2). Foram amostrados doze módulos, sete na margem esquerda do rio e cinco na margem direita. Cada um era compostos por transectos de 3 ou 4 km e parcelas perpendiculares a cada 1km, e as amostragens foram realizadas em subparcelas de 5x2m dentro das parcelas. Durante um total de 20 campanhas foram investigadas 1121 subparcelas, totalizando 7875 amostras de cupins e pelo menos 169 espécies. Esse é provavelmente o trabalho com maior esforço amostral já empregado e também o que registrou o maior número de espécies de cupins até hoje. Para o estudo de comunidades, foram aleatorizadas 20 subparcelas nos seis módulos da UHE de Jirau, sendo cinco subparcelas dentro das parcelas marcadas nas seguintes distâncias em relação à margem do rio: P1 - 50 m, P2 - 1 km, P3 - 2 km e P4 - 3 km. A composição de cupins não está relacionada com o lado do rio. O estimador que mais se aproximou do provável número real de espécies foi o Jackknife 2. Como resultado das análises de diversidade beta utilizando a composição de espécies de cupins houve um agrupamento dos módulos com o mesmo tipo de solo, sugerindo que algumas espécies de cupins estejam distribuídas de acordo com esta variável. Em relação à distância para o rio, a parcela mais próxima do rio foi a mais singular, tanto em relação à composição de espécies quanto à riqueza e abundância, sendo que existem espécies restritas à P1 e outras praticamente ausentes nessas parcelas. Das dez variáveis ambientais analisadas, a riqueza de cupins se mostrou correlacionada com a altitude, concentração de argila e silte no solo e estratificação vegetal entre 1 e 5 m. Para o estudo da estrutura genética das populações de H. tenuis foram utilizadas 84 sequências dessa espécie dos 12 módulos de monitoramento, seis de colônias do Cerrado e três do GenBank (de Manaus, Guiana Francesa, e Equador), além de uma de H. longiceps como grupo externo. Nas análises iniciais, foi encontrada uma forte estruturação genética entre as sequências: todas as análises filogenéticas (máxima parcimônia, máxima verossimilhança e inferência bayesiana), assim como a rede de haplótipos, formaram dois grupos consistentes, mas sem qualquer relação espacial. A partir disso, passou-se a trabalhar com a hipótese de que há duas espécies crípticas (chamadas Ht. A e Ht. B). Desta forma, todas as análises para testar se o Rio Madeira funcionava como barreira biogeográfica foram testadas separadamente para cada uma das supostas duas espécies crípticas, entretanto, não foi constatada qualquer influência do rio como barreira ao fluxo gênico entre as populações de cada margem. / The Santo Antônio and Jirau hydroelectrics plants (HP) are being built in the Madeira River region, in Porto Velho, RO, Brazil. The HPs will flood large portions of native forest, and thus knowledge of the local biota and its distribution in space is extremely important for the formulation of management plans for creation of protected areas. This region in particular is unique, since the alignment of Amazonas-Madeira-Mamoré Rivers divides the Neotropical region into two areas of endemism for a diversity of taxa. The main objective of this thesis was to monitor termites for three years in areas near the Jirau HP and two years in areas near the Santo Antônio HP. As well as conduct a community level study and analyze the spatial distributions of termites from the areas influenced by Jirau HP (Chapter 1); and investigate the population genetic structure of Heterotermes tenuis (Rhinotermitidae), for the two areas influenced by the HPs, to test whether there is genetic flow between the populations on either bank of the Madeira River (Chapter 2). Twelve modules were marked, seven on the left bank of the river and five on the right bank. Each module was composed of 3 or 4 km transects and perpendicular parcels every 1 km. The sampling was conducted in sub parcels of 5 x 2 m inside each main parcels. During 20 expeditions, 1121 subparcels were investigated and a total of 7875 samples were collected and identified to 169 species. This study incorporates greater sampling effort than already employed by other published studies to date and also registered the highest number of termites species of any similar study. For the community study, 20 subparcels were randomized in the six modules of the Jirau HP, with five subparcels marked in relation to distance from the river margin (P1 - 50 m, P2 - 1 km, P3 - 2 km, and P4 - 3 km). The termite species composition was not related to side of the river bank. The richness estimator Jackknife 2 was the best estimator of the real number of species diversity. The beta diversity analysis with termite species composition clustered for modules with the same soil type, suggesting that some termite species may be distributed according to the soil type. Parcels closest to the river were the most unique, both in terms of termite species composition and abundance patterns, with some species restricted to the P1 and others absent. Of the ten environmental variables measured, termite species richness was correlated with altitude, clay and silt concentration in the soil, and vegetation stratification between 1 and 5 m, among. For the study of the genetic structure of Heterotermes tenuis, 84 sequences of this species were used from the 12 monitoring modules, six from colonies from the Cerrado (Brazilian Savanna), three from GeneBank (from Manaus, French Guiana and Ecuador), and one of H. longiceps as outgroup. In the initial analysis, relatively strong genetic structure within the samples was found: all phylogenetic analysis (maximum parsimony and likelihood, and Bayesian inference), and haplotype networks, consistently clustered two groups of haplotypes, but without any spatial relationships. Thus was assumed that there were two cryptic species (here called Ht. A and Ht. B), and all the analysis to test whether the Madeira River was a biogeographic barrier were conducted separately for each putative species. However, it was not possible to detect any influence of the river to genetic flow between the populations from either side of the river.

O canto de anúncio dos anuros apresenta importância fundamental como mecanismo primário de isolamento reprodutivo. Em decorrência disto, estes cantos têm se mostrado altamente valiosos para a determinação da identidade das espécies, para assegurar uma diagnose confiável, e adicionalmente, têm contribuído para revelar espécies crípticas nos mais variados complexos de espécies. Apesar de alguns estudos na literatura terem investigado o padrão de evolução do canto com uma abordagem comparada incorporando a estrutura filogenética do grupo estudado, apenas na última década têm emergido os primeiros estudos utilizando uma abordagem filogenética para a investigação da evolução do canto em anuros. Pererecas do gênero Scinax Wagler, 1830 são um dos mais abundantes e conspícuos grupos de anuros dos Neotrópicos, sendo reconhecido atualmente como o segundo gênero mais especioso dentre os hilídeos (Hylidae), i.e. 111 spp. descritas. O monofiletismo, a ampla distribuição geográfica, riqueza de espécies, heterogeneidade de ambientes ocupados e a variação morfológica e acústica das espécies de Scinax faz deste um clado interessante para o estudo da evolução da comunicação acústica. No presente estudo os principais objetivos foram contribuir com a taxonomia e zoogeografia do gênero Scinax através da descrição detalhada dos caracteres do canto de anúncio de espécies dos clados S. ruber e S. catharinae, melhorando assim a caracterização biológica (diagnose) destas espécies, e identificar e caracterizar a variação acústica intra-específica para parte das espécies estudadas. Como consequência desta primeira etapa do trabalho, era esperada a produção de uma base de dados acústicos de alta qualidade, de maneira padronizada e detalhada para seu uso subsequente em estudos comparados utilizando uma abordagem comparada filogenética (i.e. segunda etapa do trabalho). Espécies/populações de Scinax foram acusticamente amostradas em 60 localidades (dados inéditos), concentrando-se principalmente nas regiões sudeste, central e sul do Brasil, dentro dos biomas Mata Atlântica e Cerrado. No total, foram analisados cerca de 3.500 cantos de anúncio, pertencentes a 387 indivíduos - 332 indivíduos do clado Scinax ruber e 55 indivíduos do clado S. catharinae (grupo S. catharinae), a maior parte consistindo de dados inéditos (aprox. 75% dos dados). A análise destes dados permitiu a caracterização acústica detalhada de 40 espécies nominais do clado Scinax (i.e. 32 spp. clado S. ruber; 8 spp. clado S. catharinae) - o que corresponde a 36% das espécies atualmente conhecidas do gênero. Diferenças inter-específicas reportadas nas características do canto de anúncio destas espécies forneceram suporte robusto para a diagnose acústica de quase todas as espécies estudadas. Adicionalmente, esta amostragem acústica intensiva para o gênero revelou elevados níveis de diversidade críptica em Scinax, i.e. 33 espécies não descritas. A maior parte dessa diversidade críptica encontrada está oculta sob os nomes S. squalirostris (7 espécies crípticas) e S. fuscomarginatus (4 espécies crípticas). Desta forma, a análise acurada e detalhada dos dados acústicos do canto de anúncio revelaram um profundo impacto sobre a taxonomia do grupo. A base de dados interespecíficos de alta qualidade produzidos e a disponibilidade de hipóteses filogenéticas para Scinax na literatura permitiram a investigação da evolução dos sinais acústicos no grupo, e.g. reconhecer e diferenciar a magnitude de fatores filogenéticos sobre a diversificação inter-específica do canto de anúncio, avaliar se caracteres acústicos associados a morfologia ou comportamento-fisiologia apresentam diferentes níveis de sinal filogenético e investigar o padrão evolutivo dos caracteres acústicos (canto de anúncio) e do CRC em Scinax através do procedimentos de otimização/mapeamento. Estas análises conduzidas revelaram altos níveis de sinal filogenético para a maioria dos caracteres do canto de anúncio investigados (i.e. 16 de 21 caracteres, com ? não diferindo de 1 nesses caracteres), sobre uma topologia de 31 spp. do gênero. A intensidade elevada de sinal filogenético encontrado foi similar aos níveis observados em caracteres morfológicos na literatura, não confirmando a hipótese de que caracteres comportamentais seriam mais lábeis em relação a caracteres morfológicos. As análises de mapeamento de caráter evidenciaram dois padrões principais de canto de anúncio em Scinax, cada padrão associado a um dos grandes clados do grupo, além fornecerem evidência robusta para o suporte de sinapomorfias acústicas para cada clado. / The advertisement call of frogs presents fundamental importance as a primary mechanism of reproductive isolation. As a result, these calls have proven to be highly valuable in determining the species identity, to ensure reliable diagnosis, and additionally, the advertisement calls has helped to reveal cryptic species in various species groups. Although some studies in the literature have investigated the pattern of evolution of the calls with a comparative approach incorporating information about the group phylogeny under study, only in the last decade studies using a phylogenetic approach to investigate the evolution of anurans calls have emerged. Treefrogs of the genus Scinax Wagler, 1830 is one of the most abundant and conspicuous groups of frogs in the Neotropics, actually being recognized as the second most specious genus among the hylids (Hylidae), i.e .111 spp described. The monophyletism, wide geographic distribution, richness of species, heterogeneity of environments occupied and the morphological and acoustic variation makes Scinax an interesting group to the investigation of the evolution of acoustic communication. The main aims of the present study were to contribute to the taxonomy and zoogeography knowledge of the genus Scinax through a detailed description of the characters of the advertisement calls of the species from the clades S. ruber and S. catharinae. Thus, it was possible make better the biological characterization (diagnosis) of these species and allowed to identify and characterize the intra-specific acoustic variation to part of the genus. As a consequence, the first part of this study permitted to produce a high-quality acoustic database, in a detailed and standardized manner to being used in a subsequent comparative phylogenetic approach (second part of the study). Species/populations of Scinax were acoustically sampled at 60 locatilies (original data), mainly concentrated in the southeastern, central, and southern of Brazil, in Atlantic Rain forest and Cerrado biomes. In total, about 3,500 advertisement calls were analyzed from 387 individuals (332 of Scinax ruber clade; and 55 of S. catharinae clade) - the most part consisting of new data (ca. 75%). Data analysis allowed the detailed acoustic characterization of 40 nominal species of the clade Scinax (i.e. 32 spp. of S. ruber clade; 8 spp. of S. catharinae clade), what correponds to 36% of currently known diversity of the genus. Inter-specific differences in the reported characteristics of the advertisement calls provided robust support to acoustic diagnosis for almost all species. Additionally, this intensive acoustic sampling to the genus revealed high levels of cryptic diversity in Scinax, i.e. 33 undescribed species. Most part of these cryptic diversity were under the nominal species S. squalirostris (7 cryptic species) and S. fuscomarginatus (4 cryptic species). Thus, accurate and detailed analysis of acoustic data of the advertisement call revealed a profound impact on the group taxonomy. The interspecific high-quality database here generated, and the availability of phylogenetic hypotheses for Scinax in the literature allowed the investigation of the evolution of acoustic signals in the genus, e.g. to recognize and differentiate the magnitude of phylogenetic factors on the inter-specific diversification of advertisement calls; to assess if acoustic characters related to morphology or behavior-physiology present different levels of phylogenetic signal; and to investigate the pattern of evolution of acoustic characters (advertisement call) and SVL in Scinax through optimization/mapping procedures. These analyses revealed high levels of phylogenetic signal for most of the characters of the advertisement call investigated (i.e. 16 of 21 characters with ?=1), based on a topology of 31 terminals species. The high intensity of phylogenetic signal found was similar to the levels observed for morphological characters in the literature, what is in disagree with the hypothesis that behavioral characters would be more labile than morphological characters. The character mapping analysis revealed two main patterns in Scinax, each one associated with one of the main clades of the genus, besides provide strong evidence to support acoustic synapomorphies for each clade.