A parasite reveals cryptic phylogeographic history of its host

Sex-biased gene expression (i.e., the differential expression of genes between males and females) is common among sexually reproducing species. However, genes often differ in their sex-bias classification or degree of sex bias between species. There is also an unequal distribution of sex-biased genes (especially male-biased genes) between the X chromosome and the autosomes. We used whole-genome expression data and evolutionary rate estimates for two different Drosophilid lineages, melanogaster and obscura, spanning an evolutionary time scale of around 50 Myr to investigate the influence of sex-biased gene expression and chromosomal location on the rate of molecular evolution. In both lineages, the rate of protein evolution correlated positively with the male/female expression ratio. Genes with highly male-biased expression, genes expressed specifically in male reproductive tissues, and genes with conserved male-biased expression over long evolutionary time scales showed the fastest rates of evolution. An analysis of sex-biased gene evolution in both lineages revealed evidence for a “fast-X” effect in which the rate of evolution was greater for X-linked than for autosomal genes. This pattern was particularly pronounced for male-biased genes. Genes located on the obscura “neo-X” chromosome, which originated from a recent X-autosome fusion, showed rates of evolution that were intermediate between genes located on the ancestral X-chromosome and the autosomes. This suggests that the shift to X-linkage led to an increase in the rate of molecular evolution.

The focus of this dissertation is the relative tempo of molecular evolution among organisms of varying levels of relatedness. Because this is a rapidly expanding area of research, Chapter 1 is devoted to a review of the current state of knowledge on rates of molecular evolution. In Chapter 2, I present an analysis of relative rates of evolution among several distantly related rodents. The heterogeneity in rate of evolution of the cytochrome b gene observed here cannot be explained by metabolic rate, body size, generation time, or nucleotide-generation time. Likewise, there is no evidence that these differences in rate of evolution are due to differential selection. The strongest potential correlate of rate of evolution in these data appears to be population subdivision, a factor long thought to influence heterozygosity of nuclear genes through genetic drift. However, a large number of variables, and complex interactions among variables, may influence rate of evolution of any particular gene; the relative importance of these variables probably differs from gene to gene, even within a species. Therefore, although differences in rate of molecular evolution exist, it likely will remain difficult to predict which species and which genes will show faster (or slower) rates because of the complex interactions among the numerous variables that influence rate of evolution. Cospeciating taxa offer a powerful means to compare rates of evolution between groups of organisms. Congruence in the phylogenies of two symbiotic lineages likely indicates contemporaneous cladogenic events. In Chapter 3, the phylogenies of three symbiotic groups (pocket gophers and two genera of chewing lice) are compared to evaluate their level of phylogenetic congruence, or cospeciation. Although statistical tests indicate a history of widespread cospeciation between these hosts and parasites, analysis of relative rates of evolution in these groups does not indicate the disparity in rates of evolution reported by Hafner et al. (1994).

The phylogeography of Trichuris populations (Nematoda) collected from Cricetidae rodents (Muroidea) from different geographical regions was studied. Ribosomal DNA (Internal Transcribed Spacers 1 and 2, and mitochondrial DNA (cytochrome c- oxidase subunit 1 partial gene) have been used as molecular markers. The nuclear internal transcribed spacers (ITSs) 1 and 2 showed 2 clear-cut geographical and genetic lineages: one of the Nearctic region (Oregon), although the second was widespread throughout the Palaearctic region and appeared as a star-like structure in the minimum spanning network. The mitochondrial results revealed that T. arvicolae populations from the Palaearctic region were separated into 3 clear-cut geographical and genetic lineages: populations from Northern Europe, populations from Southern (Spain) and Eastern Europe (Croatia, Belarus, Kazahstan), and populations from Italy and France (Eastern Pyrénean Mountains). Phylogenetic analysis obtained on the basis of ITS1-5·8S-ITS2 rDNA sequences did not show a differential geographical structure; however, these markers suggest a new Trichuris species parasitizing Chionomys roberti and Cricetulus barabensis. The mitochondrial results revealed that Trichuris populations from arvicolinae rodents show signals of a post-glacial northward population expansion starting from the Pyrenees and Italy. Apparently, the Pyrenees and the Alps were not barriers to the dispersal of Trichuris populations.

To reveal the relationship between organismal evolution and the molecular evolutionary rate, the temporal pattern of evolutionary rates were investigated for various genes during the course of deuterostome evolution. Deuterostome lineage leading to extant mammals was tentatively divided into two periods (the First and the Latter periods) by the time of divergence of bony fishes and mammals. For each of the First and the Latter period, evolutionary rates of 207 gene sets were calculated. In the Latter period, the evolutionary rate was significantly reduced in such informational genes as transcription factors and cytoplasmic ribosomal RNAs and proteins. In contrast, a variety of enzymes and mitochondrial ribosomal proteins evolve at nearly constant rate throughout the First and the Latter periods. The present result suggests that the increase of gene number by extensive gene duplications in the early evolution of vertebrates is responsible for the decrease of evolutionary rate.

To reconstruct the climatic conditions of the Lagar Velho rockshelter during the late Pleistocene, we applied the bioclimatic model to the rodent assemblages, mainly composed of the vole species Arvicola sapidus, Microtus arvalis, Microtus agrestis, Microtus (Terricola) lusitanicus and Microtus (Iberomys) cabrerae and the field mouse Apodemus sylvaticus. Based on the distribution of these species by layers and percentages, considering different climate-types, and applying a series of functions, it was possible to estimate the mean annual temperature (MAT), the mean temperature of the coldest month (MTC), the mean temperature of the warmest month (MTW) and the mean annual precipitation (MAP). For comparative purposes, the resulting parameters were compared with climate data obtained for the last 30 years from nearby meteorological stations in order to attain averages and observe climatic fluctuations. The climatic parameters were then compared with the Koppen-Geiger classification in order to contrast our data with the current climate-types. Finally, we combined the results with chronological and environmental information to produce a climate framework within Marine Isotope Stage 2 (MIS 2).

Iceland is an isolated island situated in the North Atlantic Ocean, south of the polar circle, between Norway and Greenland. In 1997, Iceland had approximately 275 000 inhabitants. First to live in Iceland were Irish hermits. It is generally believed that they were living on the island during the eighth and ninth centuries but disappeared when Norse people started to arrive in Iceland in 874. In 930 Iceland is believed to have been fully settled with a rural population of at least 20 000 inhabitants. The majority of the settlers came from Norway but some came from Sweden, Ireland, and Scotland. Already, during the settlement period livestock (sheep, horses, cattle, pigs, and poultry), pets (dogs and cats), and accidentally probably also house mouse Mus musculus and field mouse Apodemus sylvaticus were imported from one or more of these countries. Certainly, both the settlers and the animals carried their parasites to Iceland. Until the twentieth century most foreign connections (travel and trade) were with countries in northern Europe. Therefore, it is expected that the Icelandic parasite fauna has, through the centuries, resembled the endemic fauna of Scandinavia and the British Isles.

This paper presents new evidence to challenge the accepted view that both the house mouse Mus musculus domesticus and the field mouse Apodemus sylvaticus were introduced to Shetland by the Vikings. Archaeological remains of both Mus and Apodemus have been recovered from the site of Old Scatness Broch. While both mice were present in deposits dating to around the period of early Viking incursions, Apodemus has also been identified in a number of deposits dated to the middle Iron Age (200 BC–AD 400), while Mus bones have also been recovered from two well sealed contexts also of middle Iron Age date.

Spirocerca lupi and dogs: the role of nematodes in carcinogenesis

Using an appropriately designed and replicated study of a latitudinal influence on rates of evolution, we test the prediction by K. Rohde [(1992) Oikos 65, 514-527] that the tempo of molecular evolution in the tropics is greater than at higher latitudes. Consistent with this prediction we found tropical plant species had more than twice the rate of molecular evolution as closely related temperate congeners. Rohde's climate-speciation hypothesis constitutes one explanation for the cause of that relationship. This hypothesis suggests that mutagenesis occurs more frequently as productivity and metabolic rates increase toward the equator. More rapid mutagenesis was then proposed as the mechanism that increases evolutionary tempo and rates of speciation. A second possible explanation is that faster rates of molecular evolution result from higher tropical speciation rates [e.g., Bromham, L. & Cardillo, M. (2003) J. Evol. Biol. 16, 200-207]. However, we found the relationship continued to hold for genera with the same number of, or more, species in temperate latitudes. This finding suggests that greater rates of speciation in the tropics do not cause higher rates of molecular evolution. A third explanation is that more rapid genetic drift might have occurred in smaller tropical species populations [Stevens, G. C. (1989) Am. Nat. 133, 240-256]. However, we targeted common species to limit the influence of genetic drift, and many of the tropical species we used, despite occurring in abundant populations, had much higher rates of molecular evolution. Nonetheless, this issue is not completely resolved by that precaution and requires further examination.

Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.

Temperate grasslands belong to the most diverse plant communities of Central Europe. However, there is still a lack of information about glacial refugia and migration processes of herbaceous grassland and especially steppe species in Central Europe. Therefore, we analyzed the survival and postglacial immigration of Scorzonera purpurea to Central Europe. We investigated 348 individuals from 37 populations in Europe using amplified fragment length polymorphisms and chloroplast microsatellite analyses. Our study revealed two major genetic groups along the European distribution range consisting of western populations on the one hand and closely related central and (south)eastern populations on the other hand. Genetic variation was highest within populations from the Pannonian basin and decreased toward Western and Central Europe. Our study gives evidence for the long-term survival of S. purpurea in Western Europe and the postglacial immigration from the southeastern parts of Europe, maybe by domestic livestock of migrating farmers during the Neolithic age to Central Europe. Immigration presumably followed two routes from Pannonia along the river Danube into Southern Germany and from Pannonia along the northern border of the Carpathians to Northern Germany. In Central Germany, the different genetic lineages may have met and formed contact zones. Our data show that steppe species may both have survived in and immigrated to Western and Central Europe. Further and more detailed studies on other steppe species are, therefore, needed to investigate the origin of these rare and often endangered species more generally.

The introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand during the 1990s as a means of controlling feral rabbits is an important case study in viral emergence. Both epidemics are exceptional in that the founder viruses share an origin and the timing of their release is known, providing a unique opportunity to compare the evolution of a single virus in distinct naive populations. We examined the evolution and spread of RHDV in Australia and New Zealand through a genome-wide evolutionary analysis, including data from 28 newly sequenced RHDV field isolates. Following the release of the Australian inoculum strain into New Zealand, no subsequent mixing of the populations occurred, with viruses from both countries forming distinct groups. Strikingly, the rate of evolution in the capsid gene was higher in the Australian viruses than in those from New Zealand, most likely due to the presence of transient deleterious mutations in the former. However, estimates of both substitution rates and population dynamics were strongly sample dependent, such that small changes in sample composition had an important impact on evolutionary parameters. Phylogeographic analysis revealed a clear spatial structure in the Australian RHDV strains, with a major division between those viruses from western and eastern states. Importantly, RHDV sequences from the state where the virus was first released, South Australia, had the greatest diversity and were diffuse throughout both geographic lineages, such that this region was likely a source population for the subsequent spread of the virus across the country. Most studies of viral emergence lack detailed knowledge about which strains were founders for the outbreak or when these events occurred. Hence, the human-mediated introduction of rabbit hemorrhagic disease virus (RHDV) into Australia and New Zealand from known starting stocks provides a unique opportunity to understand viral evolution and emergence. Within Australia, we revealed a major phylogenetic division between viruses sampled from the east and west of the country, with both regions likely seeded by viruses from South Australia. Despite their common origins, marked differences in evolutionary rates were observed between the Australian and New Zealand RHDV, which led to conflicting conclusions about population growth rates. An analysis of mutational patterns suggested that evolutionary rates have been elevated in the Australian viruses, at least in part due to the presence of low-fitness (deleterious) variants that have yet to be selectively purged.

Erratic rates of molecular evolution and incongruence of fossil and molecular divergence time estimates in Ostracoda (Crustacea)

We report the presence of four nuclear paralogs of a 380-bp segment of cytochrome b in callitrichine primates (marmosets and tamarins). The mitochondrial cytochrome b sequence and each nuclear paralog were obtained from several species, allowing multiple comparisons of rates and patterns of substitution both between mitochondrial and nuclear sequences and among nuclear sequences. The mitochondrial DNA had high overall rates of molecular evolution and a strong bias toward substitutions at third codon positions. Rates of molecular evolution among the nuclear sequences were low and constant, and there were small differences in substitution patterns among the nuclear clades which were probably attributable to the small number of sites involved. A novel method of phylogenetic reconstruction based on the large difference in rates of evolution at different codon positions among mitochondrial and nuclear clades was used to determine whether different nuclear paralogs represent independent transposition events or duplications following a single insertion. This method is generally applicable in cases where differences in pattern of molecular evolution are known, and it showed that at least three of the four nuclear clades represent independent transposition events. The insertion events giving rise to two of the nuclear clades predate the divergence of the callitrichines, whereas those leading to the other two nuclear clades may have occurred in the common ancestor of marmosets.

Variation in Modes and Rates of Evolution in Nuclear and Mitochondrial Ribosomal DNA in the Mushroom Genus Amanita (Agaricales, Basidiomycota): Phylogenetic Implications