Mitochondrial DNA and Y-Chromosome Variation of Eastern Aleut Populations: Implications for the Genetic Structure and Peopling of the Aleutian Archipelago

The Aleuts are the native inhabitants of the Aleutian archipelago off the southwest coast of Alaska and, since Russian contact in 1741, have experienced a series of demographic transitions. This study investigates the impact of historical events on the genetic structure of the Aleut population through analysis of mitochondrial and Y-chromosome DNA variation in five eastern Aleut communities in relation to previous molecular research conducted on communities located further to the west. Results from HVS-I sequencing and Y-SNP and Y-STR typing reveal patterns of variability that exhibit geographic differentiation in an east-west manner. Mitochondrial haplogroups A and D represent the two major maternal lineages observed in the Aleut samples, with haplogroup D more prevalent in the Pribilofs and island groups located to the west. This distribution pattern is likely the result of founder effect related to the forced population resettlements organized by Russian fur traders in the late 18th and early 19th centuries. In the eastern Aleutian Islands and lower Alaska Peninsula, higher frequencies of haplogroup A and its subclades were observed and based on archaeological and phylogeographic evidence may represent the genetic signature of sustained cultural and demic exchange with neighboring Eskimo and Na-Dene groups. The relationship between geography and mtDNA variation is further evident from the highly significant correlation of geographic and genetic distance matrices (r = 0.717) and the decreasing correlogram of spatial autocorrelation values that present a clinal pattern to mtDNA structure. For the Aleut Y-chromosomes, the vast majority were characterized to European haplogroups (approximately 85%), which contrasts the mtDNA picture that reveals only 6.1% non-native matrilines in the eastern region and thus indicating asymmetrical gene flow between European men and Aleut women. Russian paternal lineages are common in the western islands, whereas the predominantly Scandinavian patriline I1a is observed at elevated frequencies in the eastern communities, a consequence of the American purchase of Alaska and the subsequent influx of Scandinavian and US European fishermen into the region. The application of Monmonier's algorithm and genetic surface interpolations for both genetic systems reveal geographic zones of discontinuity at Umnak and Akutan Islands, underscoring the east-west substructure for the Aleut population. Lastly, phylogeographic analysis of mtDNA data and the results of recent ancient DNA studies suggest that subhaplogroup D2 evolved in Beringia and may represent the ancestral gene pool for both Paleo-Eskimos and Aleuts. Overall, this study identifies a significant relationship between geography and genetic variation in the Aleut population, with a distinct substructure along an east-west axis. These regional differences are due to a combination of historical founder effects, male-biased gene flow from European populations, and the peopling of the Aleutian Archipelago during the postglacial period

Genealogy of the nuclear β-fibrinogen intron 7 in Lissotriton boscai (Caudata, Salamandridae): concordance with mtDNA and implications for phylogeography and speciation

The power of phylogeographic inference resides in its ability to integrate information from multiple sources in an iterative hypothesis- testing framework. In this paper, we build upon previous mtDNA-based hypotheses about the evolutionary history of the Iberian newt Lissotriton boscai using sequences of the highly variable nuclear ß-fibrinogen intron 7. In addition to the nuclear sequences, we produced new mtDNA data across the species range to delineate contact zones and test the congruence between nuclear and mitochondrial datasets at the same level of spatial organization. Through a combination of phylogenetic, phylogeographic continuous diffusion, and genetic landscape modelling analyses, we infer the evolutionary history of the species. We found notable congruence between nuclear and mtDNA datasets, which confirms deep and consistent differentiation between two major lineages that originated in the Miocene. Additionally, we found a new nuclear haplogroup with no mtDNA counterpart, roughly circumscribed to the Iberian Sistema Central mountains, and extensive areas of nuclear admixture across mtDNA lineages. We describe potential historical dispersal routes from an ancestral hypothetical refugium in the western end of the Sistema Central in central Portugal and highlight how deep phylogeographic breaks do not necessarily indicate cryptic speciation events.Peer reviewe

Genealogy of the nuclear β-fibrinogen intron 7 in Lissotriton boscai (Caudata, Salamandridae): concordance with mtDNA and implications for phylogeography and speciation

The power of phylogeographic inference resides in its ability to integrate information from multiple sources in an iterative hypothesis- testing framework. In this paper, we build upon previous mtDNA-based hypotheses about the evolutionary history of the Iberian newt Lissotriton boscai using sequences of the highly variable nuclear ß-fibrinogen intron 7. In addition to the nuclear sequences, we produced new mtDNA data across the species range to delineate contact zones and test the congruence between nuclear and mitochondrial datasets at the same level of spatial organization. Through a combination of phylogenetic, phylogeographic continuous diffusion, and genetic landscape modelling analyses, we infer the evolutionary history of the species. We found notable congruence between nuclear and mtDNA datasets, which confirms deep and consistent differentiation between two major lineages that originated in the Miocene. Additionally, we found a new nuclear haplogroup with no mtDNA counterpart, roughly circumscribed to the Iberian Sistema Central mountains, and extensive areas of nuclear admixture across mtDNA lineages. We describe potential historical dispersal routes from an ancestral hypothetical refugium in the western end of the Sistema Central in central Portugal and highlight how deep phylogeographic breaks do not necessarily indicate cryptic speciation events.Peer reviewe

Contours in Visualization

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

Metrics of Growth Habit Derived from the 3D Tree Point Cloud Used for Species Determination-A New Approach in Botanical Taxonomy Tested on Dragon Tree Group Example

Detailed, three-dimensional modeling of trees is a new approach in botanical taxonomy. Representations of individual trees are a prerequisite for accurate assessments of tree growth and morphological metronomy. This study tests the abilities of 3D modeling of trees to determine the various metrics of growth habit and compare morphological differences. The study included four species of the genus Dracaena: D. draco, D. cinnabari, D. ombet, and D. serrulata. Forty-nine 3D tree point clouds were created, and their morphological metrics were derived and compared. Our results indicate the possible application of 3D tree point clouds to dendrological taxonomy. Basic metrics of growth habit and coefficients derived from the 3D point clouds developed in the present study enable the statistical evaluation of differences among dragon tree species.O

Social Organisation in the Malaysian Peacock Pheasant

This thesis reports a study of the behaviour and morphology of the Malaysian peacock pheasant Polyplectron malacense, an inhabitant of lowland rain forest in Peninsular Malaysia. A total of 21 months was spent in the field and museum collections were visited. Micro-habitat analysis, radio-tracking and contextual analysis of calling behaviour and call playback experiments were used to collect data on the species in the wild. Periods of calling arid display scrape maintenance were infrequent and unpredictable. Not all of the available micro-habitats within the primary forest were used by the birds as some areas were consistently avoided. Within calling periods males used particular micro-habitats to call and maintain display scrapes. Three different call types were heard. There were differences between calling periods in the number of birds calling, the types of calls given and the overall amount of calling. The number of display scrapes maintained also differed. Based on contextual observations, call playback experiments were conducted and stimulus tapes elicited responses and permitted investigation of call function. There are several morphological features of the male which seem likely to be subject to sexual selection. Males appear to possess several sexually-selected traits which show considerable variability among individuals. Several male morphological characters have evolved in. association with particular epigamic display elements, suggesting that they are potentially under selection through female choice. These results suggest that a female is presented with variation among males in several different ornamental traits. A qualitative model, based on food availability, is proposed to explain variation in calling and scrape maintenance among males. It is argued that opportunities for males to display to females may be very rare and that this may explain the evolution of the male's plumage and display. Females lay a single-egg clutch and hence only one male can fertilise a clutch, with the result that competition between males for paternity is likely to be very strong