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Phylogeny of Squirrels (Sciurus, Rodentia) Based on Supertrees Reconstruction

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Phylogeny of Squirrels (Sciurus, Rodentia) Based on Supertrees Reconstruction MASARYK UNIVERSITY FACULTY OF SCIENCE DEPARTMENT OF BOTANY AND ZOOLOGY Phylogeny of squirrels (Sciurus, Rodentia) based on supertrees reconstruction Bachelor thesis Patrícia Pečnerová Supervisor: Mgr. NATÁLIA MARTÍNKOVÁ, Ph.D. BRNO 2011 BIBLIOGRAFICKÝ ZÁZNAM Autor: Patrícia Pečnerová Prírodovedecká fakulta, Masarykova univerzita Ústav botaniky a zoológie Názov práce: Fylogenéza veveríc (Sciurus, Rodentia) pomocou rekonštrukcie superstromov Študijný program: Biológia Študijný odbor: Systematická biológia a ekológia Vedúci práce: Mgr. Natália Martínková, Ph.D. Rok obhajoby: 2011 Kľúčové slová: Sciurini, stromové veverice, fylogenéza, superstromy BIBLIOGRAPHIC ENTRY Author: Patrícia Pečnerová Faculty of Science, Masaryk university Department of Botany and Zoology Title of thesis: Phylogeny of squirrels (Sciurus, Rodentia) based on supertrees reconstruction Degree programme: Biology Field of study: Systematic biology and ecology Supervisor: Mgr. Natália Martínková, Ph.D. Year of defence: 2011 Keywords: Sciurini, tree squirrels, phylogeny, supertrees ACKNOWLEDGEMENT I would like to express my thanks to Dr. Natália Martínková, who supervised my thesis, provided me with advise, help and support, dedicated a lot of time to me and has taught me essentials of scientific work. PREHLÁSENIE Prehlasujem, že som túto bakalársku prácu napísala samostatne a výhradne s použitím citovaných prameňov. Súhlasím s uložením tejto bakalárskej práce v knižnici Ústavu botaniky a zoológie Prírodovedeckej fakulty MU v Brne, prípadne v inej knižnici MU, s jej verejným požičiavaním a využitím pre vedecké, vzdelávacie alebo iné verejne prospešné účely, a to za predpokladu, že prevzaté informácie budú riadne citované a nebudú využívané komerčne. Brno 5. mája 2011 ................................................ Patrícia Pečnerová ABSTRACT Since molecular data are used to infer phylogeny, many taxonomic ambiguities have been discussed in the group of tree squirrels of the tribe Sciurini. In this study, I worked with extensive published molecular material to establish phylogenetic relationships and discover where the tribe originated. I used mitochondrial and nuclear DNA sequences and through Bayesian analysis and six different methods of supertree reconstruction, I determined the phylogeny of Sciurini squirrels. A total of 17 included species represented all currently recognized genera and wide geographic distribution of the group. Results of this work supported findings of recent molecular studies. Instead of five currently recognized genera, only two of them were supported and the genus Sciurus was paraphyletic. Species of Microsciurus, Rheithrosciurus and Syntheosciurus occured in lineages with Sciurus species. Originally assigned subgeneric level of these taxa would be more appropriate. Furthermore, supertrees revealed routes of dispersal of the tribe, as species were clustered according to their geographic distribution. Early divergence of palearctic species indicated that the genus Sciurus evolved in Eurasia, crossed land bridge in Beringia and dispersed across North America, entering South America after formation of the Isthmus of Panama. In South America, Microsciurus and Syntheosciurus diversified, while ancestors of Rheithrosciurus colonized Borneo from Eurasia. Relatively recent colonization of the tropics by Sciurini squirrels demonstrates that hypotheses associated with tropical origin as an explanation for latitudinal gradient in species richness were not relevant. Higher diversification rate in the tropics was probably a more accurate explanation. ABSTRAKT Odkedy sa molekulárne dáta využívajú na stanovenie fylogenézy, vrámci skupiny stromových veveríc tribu Sciurini sa pojednáva o mnohých taxonomických nejasnostiach. Pracovala som s rozsiahlym molekulárnym materiálom, aby som stanovila fylogenetické vzťahy a odhalila, kde skupina vznikla. Použila som mitochondriálne a jadrové DNA sekvencie, verejne dostupné, a pomocou Bayesiánskej analýzy a šiestich rôznych metód rekonštrukcie superstromov som určila fylogenézu veveríc tribu Sciurini. Zahrnutých bolo 17 druhov, ktoré reprezentovali všetky súčasne rozoznávané rody a rozsiahle geografické rozšírenie skupiny. Výsledky tejto práce podporili objavy súčasných molekulárnych štúdií. Namiesto piatich aktuálne rozoznávaných rodov boli v našej štúdii potvrdené iba dva a rod Sciurus bol parafyletický. Druhy rodov Microsciurus, Rheithrosciurus a Syntheosciurus sa objavili v líniach spolu s druhmi rodu Sciurus, pôvodne pridelená úroveň podrodov by bola pre tieto taxóny vhodnejšia. Navyše, superstromy odhalili smery, ktorými sa tribus rozširoval, pretože druhy boli zoskupené podľa geografického rozšírenia. Ranné odštiepenie palearktických druhov naznačilo, že rod Sciurus sa vyvinul v Eurázii, prekročil pevninský most v Beringii a rozšíril sa cez Severnú Ameriku, vstúpiac do Južnej Ameriky po vytvorení Panamskej šije. V Južnej Amerike sa oddelili rody Microsciurus a Syntheosciurus, zatiaľ čo predkovia rodu Rheithrosciurus kolonizovali Borneo z Eurázie. Pomerne nedávna kolonizácia trópov vevericami tribu Sciurini dokazuje, že neboli platné hypotézy spojené s tropickým pôvodom ako vysvetlením gradientu v druhovej bohatosti podľa nadmorskej výšky. Vyššie diverzifikačné tempo v trópoch bolo, pravdepodobne, vhodnejšie vysvetlenie. TABLE OF CONTENTS 1. Introduction.............................................................................................................9 1.1. Phylogenetics........................................................................................................9 1.2. Ecology and zoogeography of tree squirrels......................................................9 1.3. Taxonomic background.....................................................................................11 1.4. Evolutionary history..........................................................................................12 1.5. Latitudinal gradient in species richness..........................................................13 1.5.1. Geometrical constraints................................................................................13 1.5.2. Origin-related interpretations.......................................................................14 1.5.3. Effects of evolutionary rates.........................................................................15 1.6. Aims.....................................................................................................................19 2. Materials and methods.......................................................................................20 3. Results......................................................................................................................23 4. Discussion................................................................................................................25 4.1. Phylogenetic reconstruction..............................................................................25 4.2. Explanation of recent zoogeography................................................................26 4.3. Tropical species richness...................................................................................26 4.4. Conclusions and implications...........................................................................27 References....................................................................................................................28 Appendix......................................................................................................................36 9 1. INTRODUCTION 1.1. Phylogenetics According to one of the basic principles of biological evolution, all living organisms have evolved from a common ancestor (DARWIN 2006). Lineages of descendants of this single ancestor are depicted in a tree diagram creating basic phylogenetic units, phylogenetic trees (GAUCHER et al. 2010). Tree-like forms with genealogical content have origins in work of Charles Darwin (MOOERS & HEARD 1997, BAUM 2008). HUSON & BRYANT (2005) characterize phylogenetic tree as "a leaflabeled tree that represents the evolutionary history of a set of taxa, possibly with branch lengths, either unrooted or rooted". Root is the point of the oldest common ancestor. With respect to existence or non-existence of a common ancestor, the tree can be rooted or not (GAUCHER et al. 2010). Branches and nodes are of major importance in a phylogenetic tree. Nodes correspond to diversifying events and branches connect them with possibility to indicate the evolutionary time (WHELAN et al. 2001). Longer branches indicate more time of speciation and separation of taxa if mutation rate is similar along branches. The position of a node with respect to root reflects when in evolutionary history the taxon separated. The taxa closer to the root are in a basal position and are more similar to the common ancestor. Meanwhile, the most recently diverged taxa overcame more speciation events and diversified. Terminal nodes (leaves or tips) are specifically identified in a labeled tree (MOOERS & HEARD 1997). Clade, or a lineage, is a monophyletic group in the tree, a group including the ancestor and all its descendants (BAUM 2008). Taxa in this group have common evolutionary history as they all diverged from a single point, the specific node of the tree. 1.2. Ecology and zoogeography of tree squirrels Tribe Sciurini represents a group of tree squirrels found in deciduous, coniferous and tropical forests that are generally diurnal (NOWAK 1999). Sciurini squirrels, in comparison with other
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