A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics

Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates

Satellite mission analysis simulator for Earth Observation

The aim of this final degree project is to study and improve an existing satellite mission simulator software developed using Matlab for Earth observation purposes. Firstly, the characteristics and structure of the existing software is analyzed so that everything is properly understood in order to define appropriate improvements. These improvements are applied to the orbital propagator, the different subsystems of the satellite (power, thermal, data ...), its modes and other important concepts about a satellite mission, so that the simulator is as much approximated as possible to the scenario of a real mission. Once the software improvements are implemented and validated a final satellite mission analysis example is elaborated. This mission consists in observing a geographical zone of the Earth with a real objective and constraints... Finally, the result of the project is a GUIDE application from the Matlab software so that satellite mission analysis simulations can be programmed and studied from it. By analyzing the mission objectives and constraints, the user can try different satellite designs, orbits, modes, ground stations... and realize a comparison between them to obtain the best possible result to achieve their objectives. The methodology used to develop the project is, firstly to develop a study of space mission typical parameters and concepts related to satellites from books and research papers so that a big theoretical background is achieved. With this knowledge acquisition, the existing software can be understand and improved by implementing them to the Matlab Software in the best possible way. The validation of this project is done by comparing the results of every new implementation, by itself and on the whole, with the first version of the simulator and with the theoretical background studied to check its reliability.El principal objectiu d’aquest treball de fi de grau es estudiar i millorar un software de missio espacial amb sat ´ el ` ·lit desenvolupat amb Matlab per a l’observacio de la Terra ´ Primer, las caracteristicas i l’estructra del software existent es analitzat de manera que tot es correctament entes, per tal de definir les millores apropiades. ` Aquestes millores estan aplicades al propagador orbital, als diferents subsistemes del satel ` ·lit com per exemple el de potencia, el t ` ermic o el de dates, als modes i a altres ` conceptes importants sobre una missio amb sat ´ el ` ·lit, de manera que el simulador es el ´ mes aproximat possible a un escenari real de missi ´ o. ´ Un cop s’han implementat i validat les millores de software, un exemple d’analisi de missi ` o´ real amb satel ` ·lit es elaborat. Aquesta missio consisteix a observar una zona geogr ´ afica ` de la Terra amb uns objectius i restriccions... Finalment, el resultat del projecte es una aplicaci ´ o GUIDE a partir del software de Matlab ´ per tal que es puguin programar i estudiar diferents missions. Analitzant els objectius d’una determinada missio juntament amb les restriccions, l’usuari pot provar diferents com- ´ binacions entre el disseny del satel ` ·lit, l’orbita, modes, estacions de terra... i realitzar una ` comparacio entre totes aquestes combinacions per obtenir el millor resultat possible per áconseguir l’objectiu. La metodologia utilitzada per desenvolupar el projecte, primerament es desenvolupar un estudi dels parametres t ` ípics d’una missio espacial i dels conceptes relacionats amb ´ satel ` ·lits a partir de llibres i articles de recerca, per tal d’aconseguir una bona base teorica. ` Amb aquests nous coneixements adquirits, el software existent pot ser entes i millorat ` mitjanc¸ant la implementacio d’aquests nous conceptes, de la millor manera possible. ´ La validacio del projecte es realitza comparant els resultats de cada nova implementaci ´ o,´ tant individualment com en conjunt, amb la primera versio del simulador i la base te ´ orica èstudiada per comprovar la fiabilitat del software

Persistence of a potentially rare mammalian genus (Wyulda) provides evidence for areas of evolutionary refugia within the Kimberley, Australia

Understanding the evolutionary and ecological processes that have shaped current patterns of biodiversity is crucial in the planning and implementation of broad scale conservation management. The temporal and spatial pattern of diversity across a landscape can help identify areas that have acted as climatically stable refugia historically, or do so currently. This has important implications for conservation efforts that try to maximise the evolutionary potential of species, as well as maintaining existing biodiversity. Northern Australia has recently reported catastrophic species decline, particularly in mammals, due to a series of threats. Here we apply an integrative approach utilising molecular analyses and spatial modelling to determine whether disjunct populations of a potentially rare, endemic mammal, the scaly-tailed possum (Wyulda squamicaudata) exhibit differentiation associated with biogeographic barriers or a recent decline. Significant but low genetic differentiation between the east and west Kimberley populations was detected. Principal component analyses indicate potential climatic niche differences that could support recent localised adaptations. Climatic reconstructions back to the last glacial maximum (LGM) indicate areas of suitable habitat have substantially shifted through time for W. squamicaudata and suggest multiple areas of refugia across the Kimberley since the LGM. Further comparative research is required to establish a biogeographical framework that will assist in our understanding of processes that have shaped biodiversity in northern Australia and assist in conservation planning

Evolutionary and natural history of the turtle frog, Myobatrachus gouldii, a bizarre myobatrachid frog in the southwestern Australian biodiversity hotspot

Southwest Australia (SWA) is a global biodiversity hotspot and a centre of diversity and endemism for the Australo-Papuan myobatrachid frogs. Myobatrachus gouldii (the turtle frog) has a highly derived morphology associated with its forward burrowing behaviour, largely subterranean habit, and unusual mode of reproduction. Its sister genera Metacrinia and Arenophryne have restricted distributions in Western Australia with significant phylogeographic structure, leading to the recent description of a new species in the latter. In contrast, Myobatrachus is distributed widely throughout SWA over multiple climatic zones, but little is known of its population structure, geographic variation in morphology, or reproduction. We generated molecular and morphological data to test for genetic and morphological variation, and to assess whether substrate specialisation in this species may have led to phylogeographic structuring similar to that of other plant and animal taxa in SWA. We assembled sequence data for one mitochondrial and four nuclear DNA loci (3628 base pairs) for 42 turtle frogs sampled throughout their range. Likelihood phylogenetic analyses revealed shallow phylogeographic structure in the mtDNA locus (up to 3.3% genetic distance) and little variation in three of the four nDNA loci. The mtDNA haplotype network suggests five geographically allopatric groups, with no shared haplotypes between regions. These geographic patterns are congruent with several other SWA species, with genetic groups restricted to major hydrological divisions, the Swan Coastal Plain, and the Darling Scarp. The geographically structured genetic groups showed no evidence of significant morphological differentiation (242 individuals), and there was little sexual size dimorphism, but subtle differences in reproductive traits suggest more opportunistic breeding in lower rainfall zones. Call data were compared to sister genera Metacrinia and Arenophryne and found to be highly conservative across the three genera. Like many taxa in SWA, topographic variation and Plio-Pleistocene arid fluctuations likely were historic drivers of diversification in M. gouldii