Dissertations / Theses on the topic 'Vicariance biogeography'

Diss. (sammanfattning) Stockholm : Stockholms universitet, 2009.<br>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: In press. Paper 5: In press. Härtill 5 uppsatser.

In this thesis, I try to proceed one step further towards an understanding of the biogeographic processes forming the distribution patterns of organisms that we see today. Babblers and warblers are diverse groups of passerines that are phylogenetically intermixed with other groups in the superfamily Sylvioidea. First, the gross phylogeny of the babblers and associated groups was estimated. Five major lineages of a well-supported monophyletic babbler radiation were recovered, and we proposed a new classification at family and subfamily level. Further, the genus Pnoepyga was excluded from Timaliidae, and we proposed the new family Pnoepygidae fam. nov. Second, the systematic position was investigated for the Albertine Rift taxon Hemitesia neumanni, which was found to be nested within the almost entirely Asian family Cettidae, and possible biogeographical scenarios were discussed. We concluded that the most plausible explanation involved late Miocene vicariance in combination with local extinctions. Third, the historical biogeography of a Leiothrichinae subclade, the Turdoides babblers and allies, was inferred. We concluded that the Middle East region probably played an important role in the early history of this clade, followed by local extinctions in this region. Fourth, a Bayesian method to reconstruct the historical biogeography under an event-based model was proposed, where the total biogeographic histories are sampled from its posterior probability distribution using Markov chains. In conclusion, I believe that, especially with more sophisticated methods available, we will see an increasing number of studies inferring biogeographic histories that lead to distribution patterns built up by a combination of dispersals and vicariance, but where these distributions have been extensively reshaped, or litterally demolished, by local extinctions. Therefore, my answer to the frequently asked question dispersal or vicariance? is both, but not the least: extinctions.<br>At the time of the doctoral defence the following papers were unpublished and had a status as follows; Papers 3 and 4: Manuscripts

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among biotic communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to see if phylogeographic breaks in this species were congruent with previously-defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we would find four monophyletic clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographic regions. We generated DNA sequence data (mitochondrial cyt b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analyzed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow, and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographic community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not governed by community province boundaries.

Axelrod (1958) suggested that the late Tertiary shift in regional climate -- the elimination of summer rains -- had a profound influence on the evolution of biotic provinces in the American southwest. In particular, the taxa endemic to biotic provinces characterized by summer drought, e.g., the Mojave Desert, should be derived from ancestors that likely inhabited regions of summer rain, e.g., the Chihuahuan Desert. Further, the derived features of summer-drought taxa should be related to water stress. I examined Axelrod's thesis, using a combination of phylogenetic systematics, physiological ecology, and vicariance biogeography. The first chapter is a cladistic study of the pinyon pines, 13 taxa of small trees that range from the summer-wet regions of Mexico to the summer drought regions of Nevada and California. A parsimony analysis using twenty morphological characters showed that the most recently derived pinyons are from regions of summer drought. The "summer-drought" taxa are characterized by relatively few needles per fascicle. Because fewer needles per fascicle results in a reduction in the needle surface-to-volume ratio, Haller (1965) hypothesized that fewer needles in pines is an adaptation to reduce transpirational water loss. The second chapter reports on a two year study of the xylem pressure potentials of single- and double-needled fascicles of hybrid pinyons in central Arizona. The results showed no significant differences between single- and double-needles. I concluded that either needle morphology does not effect water relations, or that the relatively high precipitation during the study did not allow significant water stress to occur. The third chapter uses the methods of vicariance biogeography to search for a common pattern of relationship between southwestern biotic provinces, as indicated by the relationships of their endemic taxa. Using a biogeographic parsimony analysis, I compared the area cladograms of six taxa -- junipers, pinyon pines, the composite Palafoxia, hedgehog cactus, desert tortoises, and gecko lizards. The most parsimonious area cladogram supports Axelrod's (1958) hypothesis, but also shows that some taxa, notably the junipers, support other patterns of area relationships, e.g., summer-drought primitive. I suggest that there is no single pattern of area relationships because of the effects of the Pleistocene (including dispersal and extinction) and vicariance events other than the Tertiary climatic change, e.g., the separation of the Baja peninsula from mainland Mexico during the Miocene.

I used a Hierarchical approach to study historical biogeography in a group of colubrid snakes found in western North America. I combined small regions of mtDNA sequence data from a large number of individuals, with complete mt-genomic data. First, I investigated the relationships among leptodeirines-a presumed subgroup of dipsadines includeng nightsnakes (Pseudoleptodeira, Eridiphas, and Hypsiglena) - using ~1.5 Kb of data (cob and nad4). The relationships differed among parsimony, likelihood, and bayesian analyses. All analyses supported the monophyly of the nightsnakes; however, none supported the monophyly of the leptodeirines. Instead, these data supported a new hypothesis that the dipsadines were ancestrally rear-fanged and preyed on small vertabrates (frogs and lizards), such as the nightsnakes, while the more derived lineages have modified anterior maxillary dentition and prey strictly on invertabrates. Secondly, using an evolutionary species concept, I test species-subspecies boundaries in the wide-ranging hypsiglena, which has over 17 forms described, by collecting ~800 bp of sequence data (nad4 and tRNA) from ~ 175 individuals. Six major clades, concordant with geography, were recognized as species: Chihuahuan Destert (H. jani); central-western Mexico (H. torquata); upland Jalisco (H. Affinis); central California-Cape of Baja ("Coast," H. ochrorhyncha); Sonoran, Mojave, and Great Basin deserts ("Desert" H. chlorophaea), and an undescribed form from the Sonoran-Chihuahuan desert transition zone ("cochise"). The relationships among the major clades were not well resolved. Lastly, I collected complete mt-genome sequence data from 15 individuals including Eridiphas, Pseudoleptodeira, each of the major clades of Hypsiglena, and Sibon and Imantodes. All combined genomic-level analyses contained overwhelming support for a single phylogeny. These data, in conjunction with the phylogeographic data, supported my hypothesis that vicariance associated with the Miocene seperation of the Cape of Baja from mainland Mexico formed the Baja endemic Eridiphas, followed by subsequent range expansion and dispersal of Hypsiglena onto the northern portion of the peninsula and an even later vicariance event associated with the northern inundation of the gulf of California during the Pliocene. Hysiglena later dispersed down the Baja California Peninsula, coming into secondary contact with Eridiphas, forming a ring-like distribution around the Gulf of California.

Since the mid 19th century, the biogeography of island South-East Asia has been the subject of much study. Early researchers explained many of the species distribution patterns by the rise and fall of sea levels and land. This and the work of other researchers culminated in a theory that emphasized the role of Pleistocene sea level low stands in species evolution. With the advent of newly developed molecular techniques, however, it became clear that many species divergence events had taken place before the Pleistocene and a biogeographical theory focusing on Pleistocene sea level changes was inadequate. In this research, I have developed a new biogeographic model that explains present-day distribution patterns and evolutionary relationships between species. I use this new model to explain 10 ‘mammalian riddles’, i.e. evolutionary or distribution patterns in selected mammal species groups that could not be explained with the existing theories. I developed the new model by analyzing the geological literature for this region, and by mapping palaeogeographical and palaeoenvironmental changes for the last 20 million years. In addition I compiled information on the palaeontological record for the region and on divergence times between taxa using a molecular clock assumption. These phylogenetic data were compared with the palaeomaps to assess whether particular divergence events could be correlated with certain palaeogeographical or palaeoenvironmental changes. The combination of these two information sources has resulted in a much-improved understanding of mammalian evolution in island SE Asia. Using this model it is now possible to relate important palaeoenvironmental events, such as the Late Miocene cooling, an Early–Middle Pliocene highstand, or the emergence and submergence of a land bridge between the Malay Peninsula and Java to evolutionary changes in species. I test the accuracy of the new model by analysing the relationships within several mammal groups using craniometric and molecular analysis. The observed relationships and deduced timing of divergence between taxa could in many cases be explained by the model, which indicates that it is relatively accurate. In addition, with the new model I have been able to find solutions to most mammalian riddles, although these results require further testing. Overall, I therefore believe I have made a significant contribution to the biogeographical understanding of island SE Asia.

The biogeography of Central America is considered a classical case study in understanding the impact of vicariant events on patterns of biotic dispersal. While many biogeographers have focused on community composition and geographic limits of species at broad scales across Central America, much less work has focused on post-colonization diversification patterns at finer scales. The livebearing freshwater fish Xenophallus umbratilis presents an ideal system for determining the impact of recent earth history events on biodiversity in northern Costa Rica. Here, we test the hypothesis that marine inundation of the San Carlos and Northern Limón basins during the Miocene has caused genetic fragmentation among X. umbratilis populations, despite contemporary freshwater connections across this region. To test this idea, we collected mitochondrial (cytb) and nuclear (Xmrk-2) DNA sequence data from up to 162 individuals taken from 27 localities across northern Costa Rica. We employed a variety of analytical approaches, including: maximum parsimony (MP) and maximum likelihood (ML), analysis of molecular variance (AMOVA), nested clade phylogeographic analysis (NCPA), and demographic analysis of population size through time. We found four major clades within X. umbratilis, each geographically isolated with no shared haplotypes across drainages. Oddly, clades that occupy adjacent drainages are not always sister taxa in the phylogeny, suggesting that colonization in this species is more complex than a simple model of isolation by distance. All our results are consistent with the hypothesis that changes in sea level associated with glacial eustatic cycles have had an important effect in shaping diversification patterns in this species.

Submitted by Maria de Lourdes Mariano (lmariano@ufscar.br) on 2017-01-09T12:40:50Z No. of bitstreams: 1 VIDALJR_JoãodeDeus_2014.pdf: 5289373 bytes, checksum: 071875c19c5148dc61481da7f8ee7095 (MD5)<br>Approved for entry into archive by Maria de Lourdes Mariano (lmariano@ufscar.br) on 2017-01-09T12:40:58Z (GMT) No. of bitstreams: 1 VIDALJR_JoãodeDeus_2014.pdf: 5289373 bytes, checksum: 071875c19c5148dc61481da7f8ee7095 (MD5)<br>Approved for entry into archive by Maria de Lourdes Mariano (lmariano@ufscar.br) on 2017-01-09T12:41:06Z (GMT) No. of bitstreams: 1 VIDALJR_JoãodeDeus_2014.pdf: 5289373 bytes, checksum: 071875c19c5148dc61481da7f8ee7095 (MD5)<br>Made available in DSpace on 2017-01-09T12:41:13Z (GMT). No. of bitstreams: 1 VIDALJR_JoãodeDeus_2014.pdf: 5289373 bytes, checksum: 071875c19c5148dc61481da7f8ee7095 (MD5) Previous issue date: 2014-02-26<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)<br>Rauvolfia L. is a pantropical genus with 70 species distributed throughout America, Africa and Asia, also being present in several remote islands like Hawaii and French Polynesia. Although having an estimated age of 34 million years, the genus has a wide distribution as a result of its remarkable dispersal capacity, given its distribution associated with water bodies and the fact that its fruits are a food source for many bird species, placing Rauvolfia as a highly interesting group for biogeographical studies. Based on this, we produced distribution maps for the 70 species of the genus from occurrence data obtained from herbarium sheets and revision articles, which were digitalized and georeferenced. Species with similar distribution patterns were grouped and their maps were produced and compared with maps of topography and hydrography. We analyzed this distribution together with the most recent phylogenetic hypothesis for the group to infer the distribution of ancestral nodes and to identify barriers in the distribution among sister groups. The phylogeny used was based on chloroplast markers, while divergence timing was estimated by molecular clock, calculated for the whole tribe Vinceae Duby in a parallel study. Softwares S-DIVA and VIP were used for biogeographical reconstructions, which were interpreted within the context of current biogeographical hypotheses. The genus Rauvolfia is mainly limited by climatic and geographic factors. Moreover, while some vicariance episodes were identified, much of the patterns observed for Rauvolfia present distribution were attributed to long-distance dispersal events, reinforcing the role of dispersal in current discussions about angiosperm biogeography.<br>Rauvolfia L. é um gênero pantropical, composto por 70 espécies distribuídas ao longo de América, África e Ásia, além de estar presente em diversas ilhas remotas como Havaí e Polinésia Francesa. Apesar de possuir uma idade estimada em 34 milhões de anos, o gênero apresenta uma distribuição ampla resultante de uma notável capacidade de dispersão, atribuída a sua distribuição associada a corpos d’água e ao fato de seus frutos serem uma fonte de alimentos para muitas espécies de pássaros, situando Rauvolfia como um grupo altamente interessante para estudos biogeográficos. Partindo deste princípio, nós produzimos mapas de distribuição para as 70 espécies do gênero a partir de dados de ocorrência obtidos de etiquetas de pranchas de herbários e de trabalhos de revisão, que foram digitalizados e georreferenciados. As espécies com padrões similares de distribuição foram agrupadas e seus mapas foram produzidos e comparados com mapas de relevo e hidrografia. Analisou-se então esta distribuição em conjunto com a mais recente hipótese filogenética para o grupo para se inferir a distribuição dos ramos ancestrais e localizar barreiras na distribuição de táxons irmãos. A filogenia utilizada foi baseada em marcadores cloroplastidiais, enquanto a datação foi estimada através de relógio molecular, inferida para toda a tribo Vinceae Duby em um estudo paralelo. Foram utilizados os softwares S-DIVA e VIP para as reconstruções biogeográficas, que foram interpretadas dentro do contexto de hipóteses biogeográficas atuais. O gênero Rauvolfia se apresentou delimitado principalmente por fatores climáticos e geográficos. Além disso, apesar da identificação de alguns episódios de vicariância, grande parte dos padrões observados para a distribuição atual de Rauvolfia foi atribuído a eventos de dispersão a longas distâncias, reforçando o papel desses eventos nas atuais discussões sobre biogeografia de Angiospermas.

Das tropische Südostasien, und besonders der Indo-Australische Archipel, ist bekannt für seine bemerkenswerte floristische und faunistische Diversität, besonders konzentriert in vier der identifizierten Biodiversitäts-Hotspots (Indochina, Sundaland, die Philippinen und Wallacea). In dieser Arbeit wird die biogeographische Geschichte Südostasiens beleuchtet, um Regionen mit einer erhöhten Biodiversität zu identifizieren und zu testen, ob dies mit Diversifikationen innerhalb der Region und Einwanderungen und/oder Auswanderungen korreliert und ob sich diese Faktoren über die Zeit hinweg ausgleichen. Ein besonderer Augenmerk wird auf Sulawesi und seine besondere Fauna gelegt, um zu testen, ob ein Ursprung durch Vikarianz für verschiedene Tiergruppen plausibel erscheint und wann Diversifikationen innerhalb der Fisch- und Schnecken-Radiationen im Malili-Seensystem begannen. Dabei wird auf Meta-Analysen und mehrere Disziplinen zurückgegriffen für eine integrative biogeographische Geschichte Südoastasiens und seiner Fauna, indem molekulare Uhr-Analysen, Berechnungen zur Ermittlung des Ursprungsortes mit tektonischen, paläogeographischen und klimatischen Rekonstruktionen verbunden werden, um potentielle Ursachen für die heutige Verbreitung zu finden.<br>Tropical Southeast Asia, and particularly the Indo-Australian Archipelago, is known for its tremendous floral and faunal biodiversity, mainly accumulated in four of the world’s biodiversity hotspots identified (Indochina, Sundaland, the Philippines, and Wallacea). Here, Southeast Asia’s biogeographic history is examined to identify areas being characterized by high levels of biodiversity (number of lineages, species richness) through time and to test whether the respective biota is mainly due to in situ diversification, immigration and/or emigration, or equilibrium dynamics. Moreover, this thesis focuses particularly on Sulawesi and its peculiar fauna to test if a vicariant origin appears plausible for certain groups and when the remarkable fish and snail radiations found in the Malili Lakes system started to diversify. To achieve this, meta-analytical and multi-disciplinary approaches are considered for an integrative historical biogeographic history of Southeast Asia and its biota by using molecular clock analyses and ancestral area estimations together with tectonic, palaeogeographic and climatic reconstructions to reveal potential causes for present-day distribution.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

Complex interactions between topographic heterogeneity and steep gradients in climate and environmental conditions are commonly assumed to promote biotic diversification. Using tropical frogs as a model, I investigate the nature of these interactions that disrupt migration between populations, causing genetic divergence and speciation. I determine the role of several putative factors that affect gene flow (Euclidean distances, Least Cost Path (LCP) distances, topographic complexity, and elevation difference) and promote genetic structure (FST) between populations of three tropical Andean frog species. Moreover, I investigate, from an intraspecific perspective, whether montane frog species display on average larger genetic distances per kilometer relative to lowland species. Finally, I test if recent genetic divergence caused by topographic barriers to gene flow is paralleled by independent character systems such as acoustics and morphological traits in the high Andean frog Dendropsophus labialis. Even though the effect of geographic features on migration (and conversely, FST) was species-specific, LCP and Euclidean distances had the strongest effect on migration rate. Topographic complexity also reduced migration rate whereas elevation difference did not have an effect. I found that indeed highland species show larger genetic distances per kilometer between haplotypes than do lowland species. Also, genetic divergence is strongly associated with topographic heterogeneity, which is an intrinsic characteristic of montane regions. Finally, I found that acoustic variation in D. labialis diverges according to genealogical history, but external morphology does not follow this relationship. Stochastic processes due to genetic drift appear to be a better explanatory mechanism for the divergence in calls than adaptive variation. The strong and congruent divergence observed in acoustic and genetic characters indicates that these two groups correspond to morphologically cryptic parapatric species. Overall, the results of this study suggest some of the mechanisms that allow tropical mountains to promote intraspecific genetic divergence. The combined effect of ridges (promoting allopatric differentiation) and environmental gradients across elevation (promoting parapatric differentiation) are effective forces that are present mostly in highland biomes. Unfortunately, such biomes are critically threatened by habitat destruction and climate change, possibly more than any other biome on earth.<br>text

abstract: Here I present a phylogeographic study of at least six reproductively isolated lineages of harvester ants within the Pogonomyrmex barbatus and P. rugosus species group. The genetic and geographic relationships within this clade are complex: four of the identified lineages are divided into two pairs, and each pair has evolved under a mutualistic system that necessitates sympatry. These paired lineages are dependent upon one another because interlineage matings within each pair are the sole source of hybrid F1 workers; these workers build and sustain the colonies, facilitating the production of the reproductive caste, which results solely from intralineage fertilizations. This system of genetic caste determination (GCD) maintains genetic isolation among these closely related lineages, while simultaneously requiring co-expansion and emigration as their distributions have changed over time. Previous studies have also demonstrated that three of the four lineages displaying this unique genetic caste determination phenotype are of hybrid origin. Thus, reconstructing the phylogenetic and geographic history of this group allows us to evaluate past insights and plan future inquiries in a more complete historical biogeographic context. Using mitochondrial DNA sequences sampled across most of the morphospecies' ranges in the U.S. and Mexico, I employed several methods of phylogenetic and DNA sequence analysis, along with comparisons to geological, biogeographic, and phylogeographic studies throughout the sampled regions. These analyses on Pogonomyrmex harvester ants reveal a complex pattern of vicariance and dispersal that is largely concordant with models of late Miocene, Pliocene, and Pleistocene range shifts among various arid-adapted taxa in North America.<br>Dissertation/Thesis<br>M.S. Biology 2012