The aim of this thesis is to study phylogeny, species-wide phylogeography and genetic diversity in Formica ants across Eurasia in connection with the history of biotic responses to Quaternary environmental changes. The mitochondrial DNA phylogeny of Palaearctic Formica species supported the subgeneric grouping based on morphological similarity. The exception was that F. uralensis formed a separate phylogenetic group. The mitochondrial DNA phylogeny of the F. rufa group showed the division into three major phylogenetic groups: one with the species F. polyctena and F. rufa, one with F. aquilonia, F. lugubris and F. paralugubris, and the third one with F. pratensis. West-east phylogeographic divisions were found in F. pratensis suggesting post-glacial colonization of western Europe and a wide area from Sweden to the Baikal Lake from separate forest refugia. In contrast, no phylogeographic divisions were detected in either F. lugubris or F. exsecta. Contraction of the distribution range to a single refugial area during the late Pleistocene and the following population expansion could offer a general explanation for the lack of phylogeographic structure across most of Eurasia in these species. Sympatrically distributed and ecologically similar species F. uralensis and F. candida showed clear difference in the phylogeographic structure that reflected difference in their vicariant history. Whereas no phylogeographic divisions were detected in F. uralensis across Europe, F. candida showed a well-supported phylogeographic division between the western, the central and the southern group. In socially polymorphic F. cinerea, the overall level of intrapopulation microsatellite diversity was relatively high and differentiation among populations was low, indicating recent historical connections. The lack of correspondence between genetic affinities and geographic locations of studied populations did not provide any evidence for differentiating between alternative hypotheses concerning the directions and sources of postglacial colonization of Fennoscandia.

The white-tailed eagle is a formerly threatened raptor that is commonly used as a flagship and indicator species in conservation work. This thesis uses molecular genetic methods to study sex determination of nestlings, genetic variability, population structure and phylogeography of the white-tailed eagle. Fourteen microsatellite markers were developed and tested for the white-tailed eagle. A method to sex white-tailed eagle nestlings in the field is presented. The method is based on just one tarsus measure, and is suitable for situations where a single person is handling the nestlings alone in a treetop. Most European white-tailed eagle populations underwent extreme declines during the 20th century. The results presented here show that bottlenecked populations have maintained significant levels of genetic diversity. Gene flow between regions is not a main explanation for this, as indicated by both genetic and ringing data. Instead, the long generation time of white-tailed eagles has acted as an intrinsic buffer against rapid loss of genetic diversity. Additionally, local conservation led to protection of more genetic diversity than if conservation had focused on the large remnant population in Norway. Mitochondrial DNA of white-tailed eagles is structured in two main clades with a predominantly eastern and western Eurasian distribution. The clades likely correspond to separate Ice Age refugia but do not grant classification as evolutionary significant units given their current extensive overlap across large parts of Eurasia. Microsatellite variation was studied in populations across Eurasia. Variability was rather constant across the continent, but clearly lower on Iceland and Greenland. This is best explained by founder effects during their colonisation, but only weak bottlenecks during colonisation of and persistence on the continent. Current population differentiation between Europe and eastern Eurasia is not compatible with a zero gene flow model but requires some amount of gene flow over evolutionary time scales.

Genetic variation within and among populations is a result of past and ongoing processes. Among the most important of such processes are dispersal, habitat fragmentation and selection. This thesis use neutral genetic variation as a tool to investigate these processes in three bird species. In the Siberian jay, the timing of dispersal is dependent on social dominance among siblings. Mark-recapture data, radio-tracking and genetic variation was used to investigate whether timing of dispersal had an effect on dispersal distance. The results show that early dispersing individuals also disperse longer. In the same species, genetic correlation between neighbours was used to find areas with high production of philopatric individuals, which could be indicative of high habitat quality. Great snipe populations in northern Europe have a breeding range divided into two regions. A QST-FST approach was applied to study variation in selection between regions. Differentiation between the regions in neutral molecular markers was low, indicating high gene flow, or short time available for neutral divergence. Morphological divergence between the regions was high, and QST > FST, which indicates divergent selection. Thus, neutral genetic markers can be misleading in identifying evolutionary significant units, and the QST-FST approach might be valuable to identify targets for conservation. Rock ptarmigan, or its ancestors, originated in Beringia, and spread throughout the Holarctic region. Their distribution has subsequently been affected by glaciations, most likely leading to withdrawals and re-colonisations. Neutral genetic variation among five populations around the northern Atlantic was investigated. There was strong genetic structure among the populations, and evidence that Scandinavian rock ptarmigan has been isolated from other populations for considerable time. Rock ptarmigan in Svalbard showed slightly lower genetic variation than others, and comparisons with other studies suggested an eastern colonisation route to Svalbard.

The genetic diversity and phylogeography of brown bear maternal lineages have been studied extensively over the last two decades. In this study the genetic diversity and maternal phylogeography of non-invasively sampled 35 brown bears, including 5 captive individuals were reported from Turkey. In addition to the optimization of DNA extraction from hair, faeces and old skin samples and their PCRs, Bayesian phylogenetic analyses based on a 269 bp long piece of bear mitochondrial DNA were conducted and 14 novel haplotypes belonging to three major lineages were revealed. The most widespread lineage was found to be the &ldquo / Eastern&rdquo / clade 3a, while geographically more restricted &ldquo / Western&rdquo / and &ldquo / Middle Eastern&rdquo / lineages were reported for the country for the first time. A specimen from the Taurus range (southern Turkey) was shown to be closely related to the presumably extinct bears in Lebanon. Moreover, a unique novel lineage that appears to have split early within the Middle Eastern clade was defined. Despite limited sampling, this study demonstrates a high level of mitochondrial diversity in Turkish brown bears, extends the ranges of both European and Middle Eastern clades into Turkey, and identifies a new divergent lineage of possibly wider historical occurrence while demonstrating the significance of non-invasive genetic sampling for such analysis.

The island of Gotland houses a number of terrestrial mammalian species even though it was covered with ice during the last glacial period. The purpose of this study is to genetically analyse the mountain hare (Lepus timidus) to deduce its origin and genetic structure during different time periods, and also to discuss how it reached the island. A 130 base pair sequence of mitochondrial DNA from 38 prehistoric hares was analysed and compared to modern hares from different locations in Europe. The result shows a discrepancy among the samples creating two populations with different origin.

<p>Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. Sometimes, placement of certain groups within Hookeriales remains challenging even at the molecular level. That is the case of the genus <italic>Calyptrochaeta</italic>. We study diversification dynamics in this genus to elucidate possible mechanisms obscuring its placement and we address biogeographic questions using the Tropical Conservatism scenario as our null hypothesis. Furthermore, to better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns are compared in two species of the genus <italic>Calyptrochaeta</italic> (i.e., <italic>C. apiculata</italic> and <italic>C. asplenioides</italic>) and vicariance and recent long distance dispersal are tested to explain the disjunct distributions observed in these species. </p><p>In this study we reconstruct relationships among pleurocarpous mosses in or associated to the Hookeriales, in <italic>Calyptrochaeta</italic>, and within <italic>Calyptrochaeta</italic>. Six molecular markers are explored in total from all three genome compartments to reconstruct the evolution of morphological characters and habitat preferences in our phylogenies. Divergence times are estimated in a Bayesian framework using a relaxed molecular clock, and diversification rates are calculated on the chronograms resulting from these estimations. </p><p>As a result, we found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. We show that diversification rates in <italic>Calyptrochaeta</italic> have changed through its history. Also, though we lack support to clearly reject the tropical conservatism hypothesis, our data point to a more complex scenario where both temperate and tropical species can be ancient and give rise to one another, since shifts between tropical and temperate regions seem to be possible in any direction. Finally, we have show that recent long distance dispersal best explains the distribution of both <italic>C. apiculata</italic> and <italic>C. asplenioides</italic> in the Southern Hemisphere.</p> / Dissertation

Summarized the results of previous studies, the body size of Niviventer coxingi seemed to be correlated with altitude. For more exact evidence, geographic variations of body lengths and appendage sizes among areas were examined. Moreover, Freckleton et al. (2003) indicated that phylogenetic relationships may affect the results of one¡¦s study while variation of body size is discussed. Therefore, the phylogeographic variation among different areas was also examined in this study. The body lengths of N. coxingi in higher altitude (Fong-gang, 1700 m) were shorter than in lower altitude (Shan-ping 700 m). Body lengths of N. coxingi in Shan-ping were longer than other areas but Wu-shih-kang; and N. coxingi in Fong-gang were longer than those in Wu-tou Mountain; but no significant differences were found among other areas. No significant differences were found in appendage sizes but hind-foot length. Significant differences of the hind-foot length were only found between Shan-ping which had the longest hind-foot lengths in average and those in Wu-tou Mountain which had the shortest. No correlations were found between altitudes and the body length or appendage sizes of N. coxingi. The phylogenetic relationships based on D-loop region of N. coxingi were reconstructed by neighbor-joining, maximum parsimony and maximum-likelihood methods. An N. culturatus was used to be an outgroup. All three trees represented similar patterns. Although some individuals from neighborhood grouped together, some individuals from the same area represented distantly. Moreover, many branches represented in the root of the consensus trees because of the low bootstrap value. The results revealed the geographic variations did not correlated with their phylogenetic relationships and the heat conservation/ dissipation mechanism, which was the traditional explanation of Bergmann¡¦s rule, was not appropriate for N. coxingi, either.

Abstract Sequence variation of the atpB-rbcL noncoding spacer region of the chloroplast DNA was used to reconstruct the phylogeography of Tetraena mongolica.T. mongolica (Zogophylaceae) is a relict species of a monotypic genus of in Inner Mongolia of China. It has been listed as seriously endangered plants that only distributed on the Ordos plateau of Inner Mongolic. The area is a refuge of many relict Asian Plants. Reproduction of T. mongolica is mainly by seed but a reproduction is anther way under the stress. A total of 880 bp of the atpB-rbcL spacer of cpDNA was sequenced from 8 populations of T. Mongolic. According to the cpDNA data, the level of gene flow (Nm:0.04-2.01), and population differentiation (Fst:0.199-0.895) were indicated, and the ¡§isolation by distance¡¨ model was not supported (R2 =0.0024). Based on minimum spanning network and nested clade analysis, the past fragmentation is the main phylogeographic factor affecting the population structure of T. mongolica .We suggested the deluges of Yellow River and isolation of Gianlishan Mountain cased the population fragmentation of T. mongolica. Keywords: phylogeography, Tetraena mongolica, gene flow, population differentiation, nested clade analysis, past fragmentation

This study presents evidence from mitochondrial and nuclear loci that there is genetic divergence among and within geographic populations of Lagenorhynchus obscurus. The effect of seasonal variation on the genetic structure within New Zealand was examined with mitochondrial DNA control region sequences from 4 localities. Analysis of nested haplotype clades indicated genetic fragmentation and at least 1 historical population expansion within New Zealand. AMOVA and Fst values from nuclear and mitochondrial DNA sequences suggested significant divergence between New Zealand, South Africa, Argentina, and Peru. Dispersal via the west-wind drift was not supported by patterns of population structure among regions. Alternatively, these data support reciprocal exchange among all four regions with 100% posterior probability for a root of origin in the Indian/Atlantic Oceans. The degree of divergence between Peru and other regions indicates the isolation of Peruvian stock is temporally correlated with the constriction of Drake’s passage in the Plio-Pleistocene. There is evidence that the Plio-Pliestocene paleoceanography of the Indian and Southern Atlantic Oceans influenced phylogeography with shifts of temperate sea surface temperatures northward ~5º of latitude, disrupting the dispersal corridor between New Zealand and Atlantic populations. A preference for temperate waters along continental shelves is proposed as an explanation for lack of contemporary genetic exchange among regions. This study supports the polyphyly of the genus Lagenorhynchus. North Atlantic species form a monophyletic Lagenorhynchus. In the Southern Hemisphere, L. australis/L. cruciger and L. obliquidens/L. obscurus do not form a monophyletic group. I discuss the taxonomic implications and propose taxonomic revision of the genus based on these results. Measures of character interaction indicate that combined evidence from nuclear and mitochondrial genes provide better phylogenetic resolution among delphinid lineages than any data partition independently, despite some indications of conflict among mitochondrial and nuclear data.

<p>Islands have been the inspiration for some of evolutionary biology's most important advances. This is largely due to the unique properties of islands that promote the differentiation of island species from their mainland counterparts. Rodents are widely distributed across even the most remote islands, a rarity among mammals, making them uniquely suited to study the factors leading to the divergence of insular species. In this dissertation, I use two case studies to examine the morphological and genetic divergences that take place in an insular environment.</p><p>In chapters one and two, I examine how different factors influence insular body size change in rodents. In chapter one, I examine factors influencing the direction of island body size change using classification tree and random forest (CART) analyses. I observe strong consistency in the direction of size change within islands and within species, but little consistency at broader taxonomic scales. Including island and species traits in the CART analyses, I find mainland body mass to be the most important factor influencing size change. Other variables are significant, though their roles seem to be context-dependent.</p><p>In chapter two, I use the distributions of mainland rodent population body sizes to identify `extreme' insular rodent populations and compare traits associated with those populations and their islands with those island populations of a more typical size. I find that althought there is no trend among all insular rodents towards a larger or smaller size, `extreme' populations are more likely to increase in size. Using CART methods, I develop a predictive model for insular size change that identifies resource limitations as the main driver when insular rodent populations become `extremely small'. </p><p>Chapters three and four shift their focus to a single rodent species, the deer mouse <italic>Peromyscus maniculatus</italic>, as they examine the genetic differentiation of deer mice across the California Channel Islands and the nearby mainland. In chapter three, I sequence a region of the mitochondrial control region for individuals from 8 populations across the northern Channel Islands and two mainland sites, and I analyze these sequences by calculating population genetics parameters and creating a Bayesian inference tree and a statistical parsimony haplotype network. All of these analyses reveal significant divergences between island and mainland populations. Among the islands, Santa Barbara and Anacapa islands both display unique genetic signatures, but the other northern islands remain relatively undifferentiated.</p><p>In chapter four, I genotype individuals from the previous chapter at 5 microsatellite loci, I calculate additional population genetics parameters and I utilize a Bayesian clustering algorithm to examine the similarities and differences between nuclear and mitochondrial analyses. I find the nuclear data to be largely congruent with the mitochondrial analyses; there are significant differences between island and mainland populations, and Anacapa Island is significantly differentiated from the other islands. Unlike the previous analyses, Santa Barbara Island is not significantly different from the northern islands, yet San Miguel Island has a unique genetic signature. </p><p>These studies underscore the importance of ecological processes and historical biogeography in the generation of diversity, and they highlight the role of islands as drivers of evolutionary divergence.</p> / Dissertation