Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

/pdf/biological-identifications-through-dna-barcodes-2m7h08avvi.pdf

Biological identifications through DNA barcodes

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori , and drift in populations of Drosophila melanogaster . The methods are implemented in a program, structure , version 2.0, which is available at http://pritch.bsd.uchicago.edu.

/pdf/inference-of-population-structure-using-multilocus-genotype-4p91nh3fvr.pdf

Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies

Global climate has fluctuated greatly during the past three million years, leading to the recent major ice ages. An inescapable consequence for most living organisms is great changes in their distribution, which are expressed differently in boreal, temperate and tropical zones. Such range changes can be expected to have genetic consequences, and the advent of DNA technology provides most suitable markers to examine these. Several good data sets are now available, which provide tests of expectations, insights into species colonization and unexpected genetic subdivision and mixture of species. The genetic structure of human populations may be viewed in the same context. The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help our understanding of how organisms were so affected.

http://webpages.icav.up.pt/PTDC/BIA-BEC/105083/2008/hewitt2000.pdf

The genetic legacy of the Quaternary ice ages

The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic information indicate rapid global reversals and changes in ranges of species which would involve elimination with spreading from the edge. Leading edge colonization during a rapid expansion would be leptokurtic and lead to homozygosity and spatial assortment of genomes. In Europe and North America, ice age contractions were into southern refugia, which would promote genome reorganization. (2) The present day genetic structure of species shows frequent geographic subdivision, with parapatric genomes, hybrid zones and suture zones. A survey of recent DNA phylogeographic information supports and extends earlier work. (3) The grasshopperChorthippus parallelusis used to illustrate such data and processes. Its range in Europe is divided on DNA sequences into five parapatric races, with southern genomes showing greater haplotype diversity — probably due to southern mountain blocks acting as refugia and northern expansion reducing diversity. (4) Comparison with other recent studies shows a concordance of such phylogeographic data over pleistocene time scales. (5) The role that ice age range changes may have played in changing adaptations is explored, including the limits of range, rapid change in new invasions and refugial differentiation in a variety of organisms. (6) The effects of these events in causing divergence and speciation are explored usingChorthippusas a paradigm. Repeated contraction and expansion would accumulate genome differences and adaptations, protected from mixing by hybrid zones, and such a composite mode of speciation could apply to many organisms.

https://www.fc.up.pt/mestr_biodiv/aulas/hewitt_1996.pdf

Some genetic consequences of ice ages, and their role in divergence and speciation

An appreciation of the scale and frequency of climatic oscillations in the past few million years is modifying our views on how evolution proceeds. Such major events caused extinction and repeated changes in the ranges of those taxa that survived. Their spatial effects depend on latitude and topography, with extensive extinction and recolonization in higher latitudes and altitudinal shifts and complex refugia nearer the tropics. The associated population dynamics varied with life history and geography, and the present genetic constitution of the populations and species carry attenuated signals of these past dynamics. Phylogeographic studies with DNA have burgeoned recently and studies are reviewed from the arctic, temperate and tropical regions, seeking commonalities of cause in the resulting genetic patterns. Arctic species show distinct shallow genetic clades with common geographical boundaries. Thus Beringia is distinct phylogeographically, but its role as a refugial source is complex. Arctic taxa do not show the common genetic pattern of southern richness and northern purity in north-temperate species. Temperate refugial regions in Europe and North America show relatively deep DNA divergence for many taxa, indicating their presence over several Ice Ages, and suggesting a mode of speciation by repeated allopatry. DNA evidence indicates temperate species in Europe had different patterns of postglacial colonization across the same area and different ones in previous oscillations, whereas the northwest region of North America was colonized from the north, east and south. Tropical montane regions contain deeply diverged lineages, often in a relatively small geographical area, suggesting their survival there from the Pliocene. Our poor understanding of refugial biodiversity would benefit from further combined fossil and genetic studies.

http://webpages.icav.up.pt/PTDC/BIA-BEC/099915/2008/4.Hewitt%202004%20PhilTransRSocLondB.pdf

Genetic consequences of climatic oscillations in the Quaternary.

Hybrid zones are, roughly speaking, narrow regions in which genetically distinct populations meet, mate, and produce hybrids. They are often only a few hundred meters wide and yet may be several hundred kilometers long. They are found in a wide variety of organisms: Tables 1 and 2 list about 150 reasonably clear examples, in which there is a spatial transition between two hybridizing forms. Such a widespread and striking phenomenon requires explanation; more importantly, it offers us several ways of understanding the nature and origin of species. First, hybrid zones pose interesting questions for the taxonomist, for they contrast two views of the species: as a set of populations delimited by genetic barriers to gene exchange; and as a set of populations maintained in a particular stable equilibrium by selection. Second, the wide range of genotypes found in a hybrid zone can be used to analyze the genetic differences and selective forces that separate the taxa involved. This may allow some inferences about the way these differences evolved and, by extrapolation, about the way fully isolated species diverge from each other. Finally, models of parapatric speciation, and of Wright's "shifting balance," involve the formation, move­ ment, and modification of hybrid zones. Hybrid zones must be understood before the plausibility of these models can be judged. After clarifying our terminology, we will summarize the relevant theory and then see how this can be used to make inferences from field data. A notable increase in the number of detailed genetic studies of hybrid zones occurred over

Analysis of Hybrid Zones

Population structure is the result of both present processes and past history. Molecular markers are proving of great value in describing the former, and it is important to similarly determine the latter in order to understand their respective contributions. The study of palaeo-climates has also advanced significantly, and in particular that of the Pleistocene ice ages, which modified species ranges considerably. The last ice age and rapid post-glacial colonization of Europe is summarized. Possible population genetic consequences of expansion northward from southern refugia, and those of remaining in these mountainous regions are discussed. A series of recent case studies are detailed where DNA sequence information has been used to describe species genetic variation and subdivision across Europe. These include a grasshopper, the hedgehog, oak trees, the common beech, the black alder, the brown bear, newts, shrews, water vole, silver fir and house mice. These molecular data confirm southern peninsulas of Europe as major ice age refugia, and in most cases demonstrate that genetically distinct taxa emerged from them. They can thus define genomic differences and so greatly augment previous fossil data. The refugial genomes contributed differently in various species to the re-colonization of Europe, with three broad patterns described as paradigms—«grasshopper», «hedgehog» and «bear». These different expansion patterns produced clusters of hybrid zones where they made contact, and it is argued that many species genomes may be further cryptically subdivided. A reduction in diversity from southern to northern Europe in the extent of allelic variation and species subdivision is seen; this is attributed to rapid expansion northward and the varied topography of southern refugia allowing populations to diverge through several ice ages. The differences in DNA sequence indicate that some species have been diverging in refugial regions for a few ice ages at most, whilst distinct lineages in other species suggest much more ancient separation.

https://www.fc.up.pt/mestr_biodiv/aulas/hewitt_1999.pdf

Godfrey M. Hewitt

Papers

The genetic legacy of the Quaternary ice ages

Some genetic consequences of ice ages, and their role in divergence and speciation

Genetic consequences of climatic oscillations in the Quaternary.

Analysis of Hybrid Zones

Post-glacial re-colonization of European biota