Phylogeography: The History and Formation of Species
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Phylogeography: The History and Formation of Species. John C. Avise. Harvard University Press, Cambridge, Massachusetts, 2000, viii + 447 pp., $49.95, (ISBN 0-674-66638-0).
Breakthroughs in DNA sequencing technology in the 1980's revolutionized evolutionary biology, and out of this revolution emerged what has become a highly influential discipline known as phylogeography. Formally introduced a little more than a decade ago by John Avise and his colleagues (Avise et al., 1987), phylogeography is a highly integrative approach used to investigate the relationship between earth history, ecology, and biotic diversification. Phylogeography combines information from population genetics, phylogenetics, geoclimatic history, paleontology, population biology, molecular evolution, and historical biogeography in order to characterize the geographic distributions of genealogical lineages across the geographic landscape (referred to as phylogeographic patterns), and to infer the evolutionary, demographic and biogeographic processes that have shaped these patterns.
In this book, Avise provides an overview of the historical development of phylogeography, from its early stages when animal mitochondrial DNA (mtDNA) was used (almost exclusively) to examine phylogeographic patterns within single species, to today, when an increasingly wider range of additional molecular markers are being used to compare phylogeographic patterns among co-distributed taxa (comparative phylogeography). As the principle founder of the field, no one is better qualified to write a book recounting the history of phylogeography, and Avise excels at providing …Keywords:
Population Genetics
Diversity in Australia’s freshwater fish fauna is relatively depauperate when compared toother landmasses. However the family Melanotaeniidae is one of Australia’s most widespread andspeciose groups of freshwater fishes. As such, they are an ideal group in which to examinefreshwater phylogeography within Australia, as they offer the opportunity to compare species withdifferent niches, but similar evolutionary history. This dissertation investigates patterns of geneticdiversity in three species of Australian freshwater rainbowfishes, two co-distributed species withdistinct niches in undisturbed habitat, and one species in an urban habitat, and explores thehistorical and contemporary processes that have influenced them.In my first chapter I used two co-distributed Melanotaenia species to test the hypothesis thata widespread habitat generalist will have lower levels of genetic diversity and population structurethan a closely related habitat specialist. I used sequence from one mitochondrial gene and onenuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata and todetermine how differences in habitat preference and historical changes in drainage boundaries haveaffected patterns of connectivity and isolation. M. splendida, a widespread species found in the vastmajority of freshwater habitats in northern Australia, showed high levels of genetic diversity, andvery little population structure across its range. Conversely, M. trifasciata, having a greatlycontracted distribution to the northernmost rivers of Queensland and the Northern Territory andhabitat preference for faster flowing, highly oxygenated upland streams, showed extremely highlevels of population structure. While phylogeographic patterns differed, both showed a strongrelationship between stream length and genetic distance. For M. trifasciata genetic distance wasbest explained by stream length within catchments, and an ocean distance at 100x coast length,likely reflecting infrequent dispersal between catchments at times of low sea level (r2 = 0.82). M.splendida had a much shallower relationship with geographic distance, and genetic distance wasbest explained by stream length and a weaker ocean distance (10x coast length), suggesting greaterrates of gene exchange. These results suggest that, although these species are co-distributed theyappear to have experienced different evolutionary histories, with differences in habitat preferencewithin waterways resulting in contrasting scales of genetic patterns.In chapter two I identified hybrid zones between co-distributed M. splendida and M.trifasciata at the periphery of M. trifasciata's distribution. I used morphological identification,mtDNA sequences and two nuclear single nucleotide polymorphism (SNP) diagnostic restrictionassays to characterize incidence, levels and directionality of gene flow between these tworeciprocally monophyletic taxa. Four populations were identified as having undergone extensivehybridization between M. splendida and M. trifasciata. Patterns of gene flow between the two taxawere different in different hybridizing populations with complete mitochondrial capture evident in two populations, uni-directional introgression in a third population, and a complete mixture ofmorphological hybrids and bi-directional gene exchange in the fourth population. This diversity inpatterns of hybridization between two species is unusual and could potentially be due to localenvironmental conditions, although further research is required to determine the processes that aredriving this pattern.In chapter four I investigated how different aspects of habitat degradation affect the geneticdiversity of an Australian native rainbowfish, Rhadinocentrus ornatus, distributed in a highlydeveloped region (southeast Queensland) and what impacts this may have on this species’conservation status. Based on mtDNA sequence data from 327 individuals and 20 populations, Iidentified three distinct genetic lineages that were allopatric at the stream level. Indicators of habitatdegradation had large negative effects on measures of genetic diversity, with close proximity tourban development and alterations to waterways associated with drastically reduced measures ofgenetic diversity across three distinct mtDNA lineages (evolutionary significant units). Loweffective population sizes and low standing genetic variation in degraded habitats may result inreduced adaptive potential in this already threatened narrow range endemic. The only surveyedpopulations with high genetic diversity were found in already protected national parks. Manyhistorical populations of R. ornatus in the highly developed Greater Brisbane Region are alreadyprobably extinct, and without further study and management this may be the fate of presentlygenetically depauperate populations in urban areas.This thesis represents the most comprehensive study to date of rainbowfish populationgenetics. Researching multiple species within the same genus, and sampling a large proportion ofeach species range has provided me with substantial power to infer the evolutionary andcontemporary processes that have shaped genetic diversity and connectivity in three species.Contrasting phylogeographic patterns from two co-distributed species with different environmentalniches occurring in relatively pristine habitats provided insight into long-term evolutionaryprocesses. Sampling large numbers of populations, both in pristine and developed habitats, providedinformation on ecologically relevant forces shaping fine scale connectivity. This work adds togrowing literature on population genetics of Australian freshwater fishes and specifically howhistorical changes in landscape connectivity, hybridization and urban development shape patterns ofgenetic diversity in Australian rainbowfishes.
Isolation by distance
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Mantel test
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Biogeography is the study of the patterns and causes of the distribution of living things. There are a number of approaches to solving biogeographical issues, including historical biogeography, ecological biogeography and phylogeography. Phylogeography is the study of the genetic and geographic structure of populations and species. Phylogeography usually uses genetic information to examine genealogical history and patterning within species and populations. This information is used to determine the relationships of biogeographical regions and species histories. Utilized genetic markers are often unitarily inherited, for instance, mitochondrial or chloroplast DNA sequences and such they track the genealogical history of either the maternal or the paternal lineage. In article was discussed the role of phylogeography in historical biogeography and some of its connecting functions within the framework of the biodiversity sciences.
Environmental niche modelling
Vicariance
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ANALYSES OF POPULATION GENETICS: GUIDELINES AND DEVELOPMENTS Analyzing intraspecific genetic variation: a practical guide using mitochondrial DNA and microsatellites Florian Leese and Christoph Held Detecting and measuring genetic differentiation Christopher E. Bird, Stephen A. Karl, Peter E. Smouse, and Robert J. Toonen Rethinking the mechanisms that shape marine decapod population structure Bree K. Yednock and Joseph E. Neigel Causes of chaos: spatial and temporal genetic heterogeneity in the intertidal anomuran crab Petrolisthes cinctipes Robert J. Toonen and Richard K. Grosberg POPULATION GENETICS AND PHYLOGEOGRAPHY OF MARINE CRUSTACEANS Comparative phylogeography of Indo-West Pacific intertidal barnacles Ling Ming Tsang, Tsz Huen Wu, Wai Chuen Ng, Gray A. Williams, Benny K. K. Chan, and Ka Hou Chu Evolution and conservation of marine biodiversity in the Coral Triangle: insights from stomatopod Crustacea Paul H. Barber, Samantha H. Cheng, Mark V. Erdmann, Kimberly Tenggardjaja, and Ambariyanto Comparative phylogeography of three achelate lobster species from Macaronesia (northeast Atlantic) Elsa Froufe, Patricia Cabezas, Paulo Alexandrino, and Marcos Perez-Losada Genetic variation and differentiation of Fenneropenaeus merguiensis in the Thai Peninsula Warapond Wanna and Amornrat Phongdara Population genetics in the rocky shore crab Pachygrapsus marmoratus from the western Mediterranean and eastern Atlantic: complementary results from mtDNA and microsatellites at different geographic scales Sara Fratini, Christoph D. Schubart, and Lapo Ragionieri POPULATION GENETICS AND PHYLOGEOGRAPHY OF LIMNIC CRUSTACEANS The history of the Daphnia pulex complex: asexuality, hybridization, and polyploidy France Dufresne Phylogeographic patterns in Artemia: a model organism for hypersaline crustaceans Ilias Kappas, Athanasios D. Baxevanis, and Theodore J. Abatzopoulos Intraspecific geographic differentiation and patterns of endemism in freshwater shrimp species flocks in ancient lakes of Sulawesi Kristina Von Rintelen Molecular and conservation biogeography of freshwater caridean shrimps in north-western Australia Benjamin D. Cook, Timothy J. Page, and Jane M. Hughes Comparing phylogeographic patterns across the Patagonian Andes in two freshwater crabs of the genus Aegla (Decapoda: Aeglidae) Marcos Perez-Losada, Jiawu Xu, Carlos G. Jara, and Keith A. Crandall Molecular diversity of river versus lake freshwater anomurans in southern Chile (Decapoda: Aeglidae) and morphometric differentiation between species and sexes Heather D. Bracken-Grissom, Tiffany Enders, Carlos G. Jara, and Keith A. Crandall Population structure of two crayfish with diverse physiological requirements Jesse W. Breinholt, Paul E. Moler, and Keith A. Crandall Shallow phylogeographic structure of Puerto Rico freshwater crabs: an evolutionary explanation for low species diversity compared to Jamaica Christoph D. Schubart, Nicole T. Rivera, Keith A. Crandall, and Tobias Santl
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Over the past two decades, phylogeography has become an increasingly popular approach to investigating the geography of genetic variation within and among populations, species, and groups of closely related species. Phylogeographic research is uniquely positioned between historical and ecological biogeography, but to date has not incorporated many of the fundamental concepts of the former and, therefore, is susceptible to criticism that it is not a legitimate method in area-based historical biogeography. Here, we review the similarities and differences between phylogeography and area-based historical biogeography; and review concerns regarding the differences. We then summarize one recent approach to reconciling differences that highlights the synergistic and reciprocal strengths of each approach at different stages in the analysis of historical structure within populations, species, and young biotas.
Reciprocal
Vicariance
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Insular biogeography
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