CURRENT TOPICS IN PHYLOGENETICS AND PHYLOGEOGRAPHY OF TERRESTRIAL AND AQUATIC SYSTEMS ppt

CURRENT TOPICS IN PHYLOGENETICS AND PHYLOGEOGRAPHY OF TERRESTRIAL AND AQUATIC SYSTEMS Edited by Kesara Anamthawat-Jónsson          Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems Edited by Kesara Anamthawat-Jónsson Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Oliver Kurelic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published February, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechweb.org Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems, Edited by Kesara Anamthawat-Jónsson p. cm. ISBN 978-953-51-0217-5   Contents  Preface VII Chapter 1 Ecological Factors that Influence Genetic Structure in Campylobacter coli and Campylobacter jejuni 1 Helen M. L. Wimalarathna and Samuel K. Sheppard Chapter 2 Phylogeography from South-Western Atlantic Ocean: Challenges for the Southern Hemisphere 13 Graciela García Chapter 3 The Generation of a Biodiversity Hotspot: Biogeography and Phylogeography of the Western Indian Ocean Islands 33 Ingi Agnarsson and Matjaž Kuntner Chapter 4 Phylogeography of the Mountain Tapir (Tapirus pinchaque) and the Central American Tapir (Tapirus bairdii) and the Origins of the Three Latin-American Tapirs by Means of mtCyt-B Sequences 83 M. Ruiz-García, C. Vásquez, M. Pinedo-Castro, S. Sandoval, A. Castellanos, F. Kaston, B. de Thoisy and J. Shostell Chapter 5 Hybridisation, Introgression and Phylogeography of Icelandic Birch 117 Kesara Anamthawat-Jónsson  Preface  Changes in the environment, local or global, recent or historical, have evidently shaped the distribution and diversity of organisms seen today, both on land and in the oceans. Plant species migrated from southern refuges and rapidly colonized northern Europe after the last Ice Age retreated, and as a result we have witnessed all possible genetic events, including genetic drift, bottleneck effects, hybridisation, speciation and polyploidisation. Newly formed volcanic islands are colonized rapidly by pioneering species, after which begins a process of successions by further species that eventually results in a stable community of a diverse range of organisms. Surtsey – the 1.4 km 2 southernmost island of the Vestmanneyjar archipelago off the southern coast of Iceland, in the North Atlantic Ocean – was formed as recently as November 1963 from an undersea eruption in the East Volcanic Zone just south of the glacier Eyjafjallajökull. Plant life on Surtsey began only a few years after the island was born; forty years later, the number of higher plant species reached its peak of 69 species, together with numerous species of lower plants, fungi and insects. The island has also become a nesting ground for sea birds. A contrasting example could be the 88-million- years-old Madagascar, a 592,800 km 2 island located in the Indian Ocean off the southeast coast of Africa. In old islands, species radiate, diverge and evolve into lineages distant from the ancestral types but with a variable amount of gene flow in or out of the islands, depending on the means of species dispersal. Island biogeography is one of the most intriguing fields of natural sciences. There is clear evidence that changes in the physical and chemical environment in the oceans, such as temperature displacement, strength of current circulation and diversion rate, post-glacial and recent sea-level rise and ocean acidification due to anthropogenic carbon dioxide from the atmosphere, have affected marine organisms directly and indirectly. Changes in primary production can disturb the balance of marine ecosystems and consequently affect not only the organisms living in the ocean but also life on land. Forage fishes migrate with the ocean currents and inshore, moving around in their life cycle between their spawning, feeding and nursery grounds. Oceans are more productive than freshwaters in temperate latitudes, and anadromous species like salmon and arctic char predominate, whereas catadronous species like freshwater eels generally occur in tropical latitudes where freshwater productivity exceeds that of the ocean. X Preface Overexploitation of key species in the biodiversity-rich tropics, essentially by humans, has caused not only changes in the distribution and diversity of organisms and composition of the ecosystems but is also leading to species extinction at accelerating rates. In Southeast Asia, numerous plants and animals are declared extinct or facing extinction. The Southeast Asian rainforests are the oldest, consistent rainforests on Earth, dating back to the Pleistocene Epoch 70 million years ago. They rank highest in biological richness and diversity, but due to overexploitation and human-associated habitat loss Southeast Asia is losing its rainforests faster than any equatorial region. The last few of Asiatic cheetah in India were shot some 60 years ago. The giant freshwater stingray, weighing half a ton and found only in the Chaophraya and Mekong rivers, has been declared a critically endangered species, due to overfishing and habitat loss from deforestation, dam construction and city development. The white-eyed river martin, a beautiful passerine bird which is known only from a single wintering site in central Thailand, is probably extinct as it has not been seen since 1980. The only thing we scientists can do is to find ways of protecting the species endangered with extinction and preventing other species from entering the endangered stage. In order to manage this effectively, we need to map species distribution, understand essential life-history traits, define genetic variation within species and populations, identify lineages and resolve phylogenetics – especially at the molecular level – and correlate the historical, phylogenetic components with the spatial distributions of gene lineages (phylogeography). In this book, five current topics in phylogenetics and phylogeography of the Earth’s terrestrial and aquatic systems are reviewed: from phylogenetics of microorganisms and the domestication of farm animals (Chapter 1: Wimalarathna & Sheppard), phylogeography of fishes in the Southwest Atlantic Ocean (Chapter 2: García) and island biogeography of the western Indian Ocean (Chapter 3: Agnarsson & Kuntner) to phylogeography of South/Central American mountain tapirs (Chapter 4: Ruiz- García et al.) and hybridisation, introgression and phylogeography of European/Arctic birch tree species from Iceland (Chapter 5: Anamthawat-Jónsson). In Chapter 1, Ecological factors that influence genetic structure in Campylobacter coli and Campylobacter jejuni by HML Wimalarathna and SK Samuel Sheppard, the authors present a thorough overview on the genetic structure of these two bacterial species that cause widespread gastroenteritis in humans. Different methods for genotyping Campylobacter are noted, which together reveal a high degree of genetic structuring and divergence of clonally related lineages. As the vast majority of disease-associated genotypes are also found in other potential disease reservoirs, particular in domesticated/farm animals, there was clearly a need to understand the phylogenetic relationships among these genotypes and the level and mechanism of gene flow between lineages, as well as internal and external factors that can and have influenced the genetic structure of these bacteria. Such knowledge should allow us to foresee what will happen when Campylobacter moves from disease reservoirs to humans, how it becomes pathenogenic and what measures can be adopted to prevent or reduce the Preface XI outbreak. On the evolution of Campylobacter, it is interesting to see indications that the diversification leading to the population structure in extant populations may have occurred around the same time as the development of agriculture and farming some six thousand years ago. Chapter 2, Phylogeography from South-Western Atlantic Ocean: challenges for the Southern Hemisphere by Graciela García, is an excellent review of phylogeographic research on marine and estuarine organisms, mainly fish, from the Southwest Atlantic Ocean (SWA) regions, including the Patagonian Shelf where the warm Brazil current from the north converges with the cold Malvinas current from the south. Different fish models are examined. Both the molecular and genetic data are analysed in relation to geographical distribution of a given species and its genealogical lineages, intra- and interspecific variation, habitats (inshore vs. offshore), feeding behaviours (e.g. pelargic vs. demersal) and certain life-history traits. The molecular markers adopted are mainly from the mitochondrial genome, i.e. the cytochrome b (cyt-b) gene and the D-loop sequences, but genome-wide microsatellite nuclear markers have also been used. The molecular data is then translated into phylogenetics and population structures, both in the past and in recent time. Comparisons are also made between fish and other marine organisms, such as sharks, dolphins and sea lions. The author has summed up the review by contrasting phylogeographic patterns in different marine-estuarine taxa from the SWA Ocean and outlined the future direction of phylogeographic research on marine and estuarine organisms from this region. Chapter 3, The generation of a biodiversity hotspot: biogeography and phylogeography of the western Indian Ocean islands by Ingi Agnarsson and Matjaz Kuntner is an excellent and comprehensive review on bio- and phylogeography of the terrestrial and freshwater fauna and flora of the western Indian Ocean, together with a thorough introduction to the authors’ own work on spiders. The main point of this review is to demonstrate biogeographical patterns and species dispersal both in and out of the islands, at different geological time scales. The paper begins by describing in detail the paleogeography of the western Indian Ocean and providing relevant background for example on the history and nature of Walacean versus Darwinian islands. This is followed by an extensive overview of biogeographical studies and phylogeographical patterns of the flora and fauna of the islands in this region, with emphasis on Madagascar and smaller islands including the Comoros and the chain of Mascarenes islands. The central body of the chapter is about the group’s own research on molecular phylogeography of spiders of the Indian Ocean, recent discoveries, implications and future directions. Chapter 4, entitled Phylogeography of the mountain tapir (Tapirus pinchaque) and the Central American tapir (Tapirus bairdii) and the origins of the three Latin-American tapirs by means of mtCyt-b sequences is authored by Manuel Ruiz-García et al. Tapirs are the largest terrestrial Amazonian mammal and play an important role in forest dynamics XII Preface as seed dispensers and predators. In this paper, extensive research on the population structure, phylogenetics and phylogeography of the mountain tapir (T. pinchaque of the Andes' central mountains) is described in comparison with the other two neotropical tapir species, the Baird’s tapir (T. bairdii) in Central America and the lowland tapir (T. terrestris), which has the widest distribution and occupies a great diversity of habitats of South America. The study is based on sequence polymorphisms in the functional Cyt-b gene of the mitochondrial genome, the gene most used in studying phylogenetics of mammals, and hence it is possible to compare different species given that the rate of mutation is universally gene-specific. Sample sizes in this study are impressive (ca. 200 individual animals) and the statistics are thorough and appropriate. The authors have interpreted the molecular data in relation to past climatic changes, glacial histories, geological records and fossil finds, coinciding with the patterns of haplotype/species diversification and temporal splits among the extant tapir species. The in-depth discussion is excellent. Western Amazonia is clearly an important area for tapir conservation as it harbours both older and younger lineages and supports a unique diversity. Chapter 5, Hybridisation, introgression and phylogeography of Icelandic birch, by Kesara Anamthawat-Jónsson consists of an overview of research on Icelandic birch, from genecological studies, botanical assessment and species delineation, to cytogenetics and polyploidy, a palynolgical and molecular analysis of introgressive hybridisation, and the origin and phylogeography of birch (Betula) species in Iceland. In contrast to studies on animal phylogenetics, which are mainly built on molecular evolution in the mitochondrial genome, plant molecular phylogenetics is basically measured from changes in the chloroplast genome. Plant chloroplast genomes are stably inherited, sufficiently small and undergo a slow rate of mutational changes. This paper shows that hybridisation occurs between the two birch species that coexist in Iceland, the diploid Arctic dwarf birch Betula nana and tetraploid European tree birch B. pubescens, and that the gene flow between the two species occurs via triploid hybrids. Icelandic birch is most probably postglacial and European in origin, migrating from Western Europe and colonizing Iceland in the early Holocene. Birch woodland is an integral component of the tundra biome which covers expansive areas of the Arctic, amounting to 20% of Earth’s land surface. Arctic tundra is located in the northern hemisphere, encircling the North Pole and extending south to the coniferous forests of the taiga. The present review provides an insight into introgression and phylogeography of Icelandic birch and should lead to a better understanding of Betula in its broader geographical range, together with the bio- and phylogeography of plant species on oceanic islands – especially in the North Atlantic region – and the vegetation ecology of the tundra biome. It is a great honour for me to be designated “book editor” by InTech – Open Access Publisher, and as such it is a pleasure to receive excellent contributions on the subjects [...]...Preface of the book I would like to express my deepest appreciation to all authors for accepting the invitation and for your willingness to share the knowledge and research results I hope that the book will be an inspiration and find applications in research in the field of phylogenetics and phylogeography of terrestrial and aquatic systems in general Kesara Anamthawat-Jónsson Institute of Life and Environmental... coli clade 3 and being acquired by C jejuni, all genetic exchange events identified involved C coli clade 1 as either donor or recipient 6 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems The existence of hybrids and the maintenance of alleles of C jejuni origin within the C coli gene pool demonstrates that mechanistic barriers are not preventing interspecies gene... infections in Norway Scand J Infect Dis 24, 741-749 Kessel AS, Gillespie IA, O'Brien SJ, et al (2001) General outbreaks of infectious intestinal disease linked with poultry, England and Wales, 1992-1999 Commun Dis Public Health 4, 171-177 10 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems Kittl S, Kuhnert P, Hachler H, Korczak BM (2011) Comparison of genotypes and antibiotic... those of nuclear genes, 2) 16 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems mitochondrial DNA do not undergo recombination, and hence clear genealogical patterns can be reconstructed 2.1 Current knowledge in the phylogeography of different endemics marine-estuarine fish ecotypes from SWA Ocean Estuaries and lagoons are discrete habitats separated by physical and/ or... associated estuarine environments of the SWA Ocean represented a sister clade of Engraulis However, a non overlapping in their respective environments and niches was reported 20 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems Lycengraulis grossidens The Atlantic sabretooth anchovy occurs in brackish estuaries and adjacent marine areas, penetrating freshwater environments... understanding of the evolution of the genus can be obtained if the time scale for the divergence of lineages can be overlaid upon the tree of genetic relatedness By cross-referencing estimated dates of divergence within the genus Campylobacter with ecological data it is possible to make 8 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems inferences about the conditions... Atlantic continental shelf, an ecosystem largely influenced by both Malvinas and Brazilian currents, which conform a confluence in this area These two water masses 14 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems have distinct characteristics and constitute a sharp transition zone referred as the subtropical shelf front (Piola et al., 2000) Fig 1.1 Map of bathymetry... African estuaries (Durand et al 2005) B aurea shows significant negative values in the Mantel test 18 Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems corroborating a non-association between genetic and geographic distances and excluding the aforementioned possible scenarios (García et al., 2008) Species Haplotype Parsimony Number of Variable Diversity informative Sites... remains distinct from clades 2 & 3, there is evidence of gene flow between C jejuni and C coli clade 1 Analysis of 1738 alleles from a total of 2953 Sequence Types identified 31 mosaic alleles, of which 25 had demonstrably been acquired by C coli from C jejuni, and the remaining 6 had originated in C coli and been acquired by C jejuni With the exception of a single mosaic allele, having originated in. .. those lineages that are found in a niche to which humans are routinely exposed have acquired the necessary colonisation factors to persist in this environment, and opportunistically to infect humans 6 Dating lineage divergence Genotyping isolates from various sources can offer insight into the causes of the genetic structuring in Campylobacter populations However, a more comprehensive understanding of . CURRENT TOPICS IN PHYLOGENETICS AND PHYLOGEOGRAPHY OF TERRESTRIAL AND AQUATIC SYSTEMS Edited by Kesara Anamthawat-Jónsson          Current Topics in Phylogenetics and Phylogeography. distributions of gene lineages (phylogeography) . In this book, five current topics in phylogenetics and phylogeography of the Earth’s terrestrial and aquatic systems are reviewed: from phylogenetics of. sub- populations, and the variation between sub-populations can be exploited in order to Current Topics in Phylogenetics and Phylogeography of Terrestrial and Aquatic Systems 2 determine the source of