Browsing by Subject "Phylogeography"

Now showing 1 - 9 of 9

Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages
(Public Library of Science, 2009-03-10) Santos, Juan C; Coloma, Luis A; Summers, Kyle; Caldwell, Janalee P; Ree, Richard; Cannatella, David C
The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved.
Diversification and evolution of treefrogs in the Cerrado savanna of South America : from population structure to biogeographic patterns
(2016-05) Vasconcellos, Mariana Mira; Cannatella, David C.; Wilke, C. (Claus); Bolnick, Daniel I.; Simpson, Beryl B.; Young, Kenneth R.; Ryan, Michael J.
Historical and ecological factors underlying population structure and speciation of organisms are fundamental to uncover diversification mechanisms that lead to biogeographic patterns. The main goal of this dissertation is to determine the relative roles of geography and climate promoting diversification in a diverse group of treefrogs in the Cerrado savanna of South America, a hotspot of biodiversity. This dissertation approaches diversification at two different time-scales: from a macro-temporal scale of factors that promote species diversification in the Cerrado region, and from a micro-temporal scale of population divergence and recent cryptic speciation. Three main research goals were developed in separate chapters: (1) Phylogenetic and biogeographic analyses of the species in the Hypsiboas pulchellus group were used to quantify dispersal events between the Cerrado and other dry/open or humid/forested neighboring habitats, and to evaluate how this dynamic historical interchange affected diversification. The evolutionary relationships among the species in this group showed a pattern of multiple recent origins of the endemic Cerrado lineages, indicating recent colonization events. These analyses indicate an interesting pattern of recurrent dispersal among open and forest ecoregions accounting for the accelerated diversification in this group. (2) Species delimitation methods using molecular, morphological and mating call characters were used to study the recent speciation of a small clade of Cerrado endemics. This integrative approach allowed for a better resolution to detect species boundaries and the discovery of cryptic species in spite of conserved morphology and mating calls. (3) Population structure in a widespread Cerrado species was investigated using historical species distribution modeling and next generation sequencing data to evaluate the role of recent climatic fluctuations on population differentiation. Divergence among populations seems strongly affected by Pleistocene climatic instability, a pattern we call isolation-by-instability. In conclusion, this study highlights how diversification and biogeographic patterns in the Cerrado savanna can be affected by its historical dynamic climate and landscape.
Effects of the Distribution of Female Primates on the Number of Males
(Public Library of Science, 2011-05-16) Carnes, Laurel Mariah; Nunn, Charles L.; Lewis, Rebecca J.
The spatiotemporal distribution of females is thought to drive variation in mating systems, and hence plays a central role in understanding animal behavior, ecology and evolution. Previous research has focused on investigating the links between female spatiotemporal distribution and the number of males in haplorhine primates. However, important questions remain concerning the importance of spatial cohesion, the generality of the pattern across haplorhine and strepsirrhine primates, and the consistency of previous findings given phylogenetic uncertainty. To address these issues, we examined how the spatiotemporal distribution of females influences the number of males in primate groups using an expanded comparative dataset and recent advances in Bayesian phylogenetic and statistical methods. Specifically, we investigated the effect of female distributional factors (female number, spatial cohesion, estrous synchrony, breeding season duration and breeding seasonality) on the number of males in primate groups. Using Bayesian approaches to control for uncertainty in phylogeny and the model of trait evolution, we found that the number of females exerted a strong influence on the number of males in primate groups. In a multiple regression model that controlled for female number, we found support for temporal effects, particularly involving female estrous synchrony: the number of males increases when females are more synchronously receptive. Similarly, the number of males increases in species with shorter birth seasons, suggesting that greater breeding seasonality makes defense of females more difficult for male primates. When comparing primate suborders, we found only weak evidence for differences in traits between haplorhines and strepsirrhines, and including suborder in the statistical models did not affect our conclusions or give compelling evidence for different effects in haplorhines and strepsirrhines. Collectively, these results demonstrate that male monopolization is driven primarily by the number of females in groups, and secondarily by synchrony of female reproduction within groups.
Evolution of Jatropha : phylogenetics, biogeography, and phylogeography
(2019-06-13) LeClear, Nathan Michael; Simpson, Beryl Brintnall; Linder, C. Randal; Cannatella, David; Mauseth, James; Roux, Stanley; Jha, Shalene
The genus Jatropha (Euphorbiaceae) is comprised of approximately 180 species of flowering plants adapted to arid and semi arid climates in tropical regions around the world. As the evolutionary relationships within this group have not been tested using molecular phylogenetic approaches, I used a combination of traditional molecular markers and genomic data generated from restriction site-associated DNA sequencing (RADseq) for this purpose. Using this phylogeny, I answered questions of trends in morphological evolution in the neotropical species of Jatropha, and explored potential causes of missing data in RADseq datasets. I reconstructed the biogeographic history of Jatropha at the global scale to test hypotheses of vicariance and dispersal pertaining to pantropical disjunct groups. I also investigated the impact of tectonic events on diversification of Jatropha within Mesoamerica, and tested standing hypotheses about geographic structure in lineages endemic to seasonally dry tropical forests. Using J. cardiophylla as a model, I looked for evidence of Pleistocene refugia in the interior Sonoran Desert using RADseq and ecological niche modeling. Jatropha was found to be monophyletic based upon traditional markers, and relationships within Jatropha were resolved with RADseq data. Evolutionary analyses indicated the ancestor of Jatropha was a shrub bearing a tricarpellate fruit. Jatropha originated in the Neotropics and arrived in Africa via at least two long distance dispersal events. Tectonic events in Mesoamerica impacted diversification of Jatropha through both vicariance events and by preventing dispersal between areas. Mixed evidence was found in support of the hypothesis that seasonally dry tropical forest lineages are dispersal limited and primarily experience in situ diversification. Genetic analysis of J. cardiophylla showed that this species consists of two genetically distinct, yet geographically overlapping lineages. Ages of coalescence for each lineage predate the Last Glacial Maximum. Niche modeling did not identify obvious Pleistocene refugia, but somewhat aligned with spatial patterns of genetic variation. It appears that J. cardiophylla has responded to multiple rounds of climate change in the Sonoran Desert, and that different lineages may have responded differently. The sum of this work represents a significant contribution to our understanding of the evolution of Jatropha at multiple scales.
Evolutionary history of Lost World frogs
(2014-08) Salerno, Patricia Elena; Cannatella, David C.; Hillis, David M; Wilke, Claus; Simpson, Beryl B; Perez, Francisco L
The Lost World of South America is a unique landscape of flattop mountains that are home to hundreds of endemic species. These flattop mountains, or tepuis, were formed after millions of years of erosion of the high-altitude Guiana Shield plateau. The tepui summits, isolated by their surrounding cliffs that can be up to 1000 m tall, are thought of as “islands in the sky,” harboring relict flora and fauna that underwent vicariant speciation due to plateau fragmentation. High endemicity atop tepui summits supports the idea of an ancient “Lost World” biota. However, recent work suggests dispersal between lowlands and summits occurred long after tepui formation, but neither view (i.e., ancient vicariance vs. recent dispersal) has strong empirical support owing to a lack of studies. I tested diversification hypotheses of the Guiana Shield highlands by estimating divergence times of Tepuihyla, a Guiana Shield endemic genus. Diversification among the different species did not support the Lost World Hypothesis of summit diversification, but rather recent dispersal approximately 50 million years after tepuis formed. This study was the first to explicitly test these hypotheses with a tepui endemic vertebrate, and as such a significant contribution to our understanding of the evolutionary history of this region. After increasing sampling, I focused on three of the most recently diverged lineages of Tepuihyla, in order to examine population genetics, phylogeography, and species delimitation atop these summits. I found high levels of lineage sorting in spite of low divergences in both nuclear and mitochondrial genes. I also found an unexpected pattern of nuclear versus mitochondrial diversity, suggesting the possibility of a recent mitochondrial selective sweep. Species delimitation analyses support the existence of a cryptic, undescribed summit species. Finally, I obtained a Single Nucleotide Polymorphism matrix with next-generation sequencing in order to observe more fine-scale population structure atop the Chimantá massif, a formation composed of ten tepui summits and intermediate altitudes separating them. I found high levels of population structure and assignment atop different tepui summits on the massif, indicating that even at extremely low levels of divergence the landscape complexity may be fomenting population isolation even at the smaller scale of within-massif divergences.
Evolutionary patterns and processes of the high Andean genera Demosthenesia, Pellegrinia, Polyclita, Rusbya, and Siphonandra (Vaccinieae: Ericaceae)
(2024-02-05) Ortiz Valencia, Edgardo Manuel Martín; Simpson, Beryl Brintnall; Juenger, Thomas; Hillis, David M; Jansen, Robert K; Mauseth, James D; Young, Kenneth R
The Andean uplift is arguably the most important geologic event that led to the diversification of the richest biota in the planet. By the end of the Miocene, the Andes reached almost half their current elevation and their eastern slopes intercepted, condensed, and precipitated enough westward-moving moist air from the Amazon to cause the formation of montane forests. Later, climatic oscillations during the Pleistocene heavily affected the distribution of upper montane forests. Today, the upper belt of these forests, also known as cloud forest, possesses the highest levels of endemism in the world, however, the processes that drove this diversification are still poorly understood. To investigate these processes, I selected the blueberry tribe, Vaccinieae, that contains ~1,760 species mostly concentrated in the Neotropics and particularly abundant in the montane forests of the eastern Andean slopes. In chapter 1, I focus on a group of five endemic genera (Demosthenesia, Pellegrinia, Polyclita, Rusbya, and Siphonandra) that inhabit the cloud forest up to timberline at ~3000-3500 masl. I investigate if they share a single or multiple evolutionary origins by constructing the largest and most robust time-calibrated phylogeny of the tribe to date and performing diversification and historical biogeographic analyses. In chapter 2, I use a phylogenomic approach seeking to further resolve the relationships of the most recently diverged groups, Demosthenesia and Rusbya. Finally, in chapter 3, I explore the effects of Pleistocene climatic oscillations on the present geographic and genetic structure of the widespread blueberry species Demosthenesia mandonii, and attempt to locate areas that might have served as Pleistocene refugia. My results indicate that the five genera do not share a single origin, however their divergence dates are contemporaneous at ~6 Ma. At a larger scale, the Neotropical blueberries have multiple evolutionary origins, with a main radiation influenced by both the uplift of the Andes and Cenozoic temperatures. Lastly, the population analysis of D. mandonii, suggests a severe contraction of its range during the last glacial maximum followed by re-expansion towards the present, this species most likely survived the las glaciation in a single Pleistocene refugium located in the Urubamba valley (Cusco, Peru).
Paleodistributions and Comparative Molecular Phylogeography of Leafcutter Ants (Atta spp.) Provide New Insight into the Origins of Amazonian Diversity
(Public Library of Science, 2008-07-23) Solomon, Scott E.; Bacci, Mauricio Jr; Martins, Joaquim Jr; Vinha, Giovanna Gonçalves; Mueller, Ulrich G.
The evolutionary basis for high species diversity in tropical regions of the world remains unresolved. Much research has focused on the biogeography of speciation in the Amazon Basin, which harbors the greatest diversity of terrestrial life. The leading hypotheses on allopatric diversification of Amazonian taxa are the Pleistocene refugia, marine incursion, and riverine barrier hypotheses. Recent advances in the fields of phylogeography and species-distribution modeling permit a modern re-evaluation of these hypotheses. Our approach combines comparative, molecular phylogeographic analyses using mitochondrial DNA sequence data with paleodistribution modeling of species ranges at the last glacial maximum (LGM) to test these hypotheses for three co-distributed species of leafcutter ants (Atta spp.). The cumulative results of all tests reject every prediction of the riverine barrier hypothesis, but are unable to reject several predictions of the Pleistocene refugia and marine incursion hypotheses. Coalescent dating analyses suggest that population structure formed recently (Pleistocene-Pliocene), but are unable to reject the possibility that Miocene events may be responsible for structuring populations in two of the three species examined. The available data therefore suggest that either marine incursions in the Miocene or climate changes during the Pleistocene—or both—have shaped the population structure of the three species examined. Our results also reconceptualize the traditional Pleistocene refugia hypothesis, and offer a novel framework for future research into the area.
Population Dynamics Constrain the Cooperative Evolution of Cross-Feeding
(Public Library of Science, 2009-01-05) Bull, James J.; Harcombe, William R.
Cross-feeding is the exchange of nutrients among species of microbes. It has two potential evolutionary origins, one as an exchange of metabolic wastes or byproducts among species, the other as a form of cooperation known as reciprocal altruism. This paper explores the conditions favoring the origin of cooperative cross-feeding between two species. There is an extensive literature on the evolution of cooperation, and some of the requirements for the evolution of cooperative cross-feeding follow from this prior work–specifically the requirement that interactions be limited to small groups of individuals, such as colonies in a spatially structured environment. Evolution of cooperative cross-feeding by a species also requires that cross-feeding from the partner species already exists, so that the cooperating mutant will automatically be reciprocated for its actions. Beyond these considerations, some unintuitive dynamical constraints apply. In particular, the benefit of cooperative cross-feeding applies only in the range of intermediate cell densities. At low density, resource concentrations are too low to offset the cost of cooperation. At high density, resources shared by both species become limiting, and the two species become competitors. These considerations suggest that the evolution of cooperative cross-feeding in nature may be more challenging than for other types of cooperation. However, the principles identified here may enable the experimental evolution of cross-feeding, as born out by a recent study.
Wing Patterns in the Mist
(Public Library of Science, 2010-02-05) Martin, Arnaud; Kapan, Durrell D.; Gilbert, Lawrence E.
The aesthetic appeal of butterfly wing patterns has been costly to their status as a tool of fundamental scientific inquiry. Thus, while mimetic convergence in wing patterns between edible “Batesian” mimics and distasteful models, or between different distasteful “Müllerian” mimics (species that cooperate to educate predators) has long been the subject of genetic analysis [1] and field experiments [2], most biology text books confine mimicry to sections on striking adaptations without applying these examples to broader topics of evolution. Meanwhile, the study of color patterns in animals, often tucked into the same sections of texts, is undergoing a revolution in this age of evo-devo and genomics [3]. Among insect models for studying color pattern, the genus Heliconius is gaining the attention of an ever-widening audience.