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

1Department of Genetics, University of Georgia, Athens, Georgia 30602; 2NMFS/ CZES, Genetics, 2725 Montlake Boulevard East, Seattle, Washington 98112; 3Savannah River Ecology Laboratory, Drawer E, Aiken, South Carolina 29801; ~Department of Microbiology and Immunology, School of Medicine, University of California, Los Angeles, California 90024; -SSchool f Veterinary Medicine, Virginia Tech University, Blacksburg, Virginia 24046

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Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics

The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via ‘‘SNP chip’’ microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a major source of information for both population history and genotypephenotype association. Recent developments in reduced-representation genome sequencing experiments on massively parallel sequencers (commonly referred to as RAD-tag or RADseq) have brought direct sequencing to the problem of population genotyping, but increased cost and procedural and analytical complexity have limited their widespread adoption. Here, we describe a complete laboratory protocol, including a custom combinatorial indexing method, and accompanying software tools to facilitate genotyping across large numbers (hundreds or more) of individuals for a range of markers (hundreds to hundreds of thousands). Our method requires no prior genomic knowledge and achieves per-site and per-individual costs below that of current SNP chip technology, while requiring similar hands-on time investment, comparable amounts of input DNA, and downstream analysis times on the order of hours. Finally, we provide empirical results from the application of this method to both genotyping in a laboratory cross and in wild populations. Because of its flexibility, this modified RADseq approach promises to be applicable to a diversity of biological questions in a wide range of organisms.

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Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and ex- tinction. Lineage sorting could also be called deep coalescence, the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host-parasite relation- ships. Each of the processes of discord could yield a different parsimony criterion for reconstruct- ing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the prob- ability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively, phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of inter- breeding. (Biogeography; coalescence; coevolution; evolution; gene duplication; gene genealogy; gene trees; horizontal transfer; hybridization; lineage sorting; parsimony; phylogeny; species con- cepts; species trees; tree reconciliation.)

/pdf/gene-trees-in-species-trees-3saat11ld6.pdf

Gene Trees in Species Trees

Simple repetitive DNA sequences are a widespread and abundant feature of genomic DNA. The following several features characterize such sequences: (1) they typically consist of a variety of repeated motifs of 1-10 bases--but may include much larger repeats as well; (2) larger repeat units often include shorter ones within them; (3) long polypyrimidine and poly-CA tracts are often found; and (4) tandem arrangements of closely related motifs are often found. We propose that slipped-strand mispairing events, in concert with unequal crossing-over, can readily account for all of these features. The frequent occurrence of long tandem repeats of particular motifs (polypyrimidine and poly-CA tracts) appears to result from nonrandom patterns of nucleotide substitution. We argue that the intrahelical process of slipped-strand mispairing is much more likely to be the major factor in the initial expansion of short repeated motifs and that, after initial expansion, simple tandem repeats may be predisposed to further expansion by unequal crossing-over or other interhelical events because of their propensity to mispair. Evidence is presented that single-base repeats (the shortest possible motifs) are represented by longer runs in mammalian introns than would be expected on a random basis, supporting the idea that SSM may be a ubiquitous force in the evolution of the eukaryotic genome. Simple repetitive sequences may therefore represent a natural ground state of DNA unselected for coding functions.

Slipped-strand mispairing: a major mechanism for DNA sequence evolution.

We address the problem of the possible significance of biological speciation to the magnitude and pattern of divergence of asexually transmitted characters in bisexual species. The empirical data for this report consist of restriction endonuclease site variability in maternally transmitted mitochondrial DNA (mtDNA) isolated from 82 samples of Peromyscus polionotus and P. leucopus collected from major portions of the respective species' ranges. Data are analyzed together with previously published information on P. maniculatus, a sibling species to polionotus. Maps of restriction sites indicate that all of the variation observed can be reasonably attributed to base substitutions leading to loss or gain of particular recognition sites. Magnitude of mtDNA sequence divergence within polionotus (maximum approximately equal to 2%) is roughly comparable to that observed within any of five previously identified mtDNA assemblages in maniculatus. Sequence divergence within leucopus (maximum approximately equal to 4%) is somewhat greater than that within polionotus. Consideration of probable evolutionary links among mtDNA restriction site maps allowed estimation of matriarchal phylogenies within polionotus and leucopus. Clustering algorithms and qualitative Wagner procedures were used to generate phenograms and parsimony networks, respectively, for the between-species comparisons. Three simple graphical models are presented to illustrate some conceivable relationships of mtDNA differentiation to speciation. In theoretical case I, each of two reproductively defined species (A and B) is monophyletic in matriarchal genealogy; the common female ancestor of either species can either predate or postdate the speciation. In case II, neither species is monophyletic in matriarchal genotype. In case III, species B is monophyletic but forms a subclade within A which is thus paraphyletic with respect to B. The empirical results for mtDNA in maniculatus and polionotus appear to conform closely to case III. These theoretical and empirical considerations raise a number of questions about the general relationship of the speciation process to the evolution of uniparentally transmitted traits. Some of these considerations are presented, and it is suggested that the distribution patterns of mtDNA sequence variation within and among extant species should be of considerable relevance to the particular demographies of speciation.

Mitochondrial DNA differentiation during the speciation process in Peromyscus.

Restriction endonucleases have recently permitted the detection of extensive intraspecific mitochondrial DNA (mtDNA) sequence heterogeneity in a number of mammalian species (e.g., Potter et al., 1975; Upholt and Dawid, 1977; Avise et al., 1979b; Brown, 1980; Brown and Simpson, 1981; Ferris et al., 1981). Because mtDNA appears to evolve very rapidly (Brown et al., 1979), and because mtDNA seems to be strictly maternally inherited (Hutchison et al., 1974; Lansman et al., 1983), the molecule has been advocated as a potentially useful marker for estimating matriarchal phylogenies within and among conspecific populations and closely related species (Lansman et al., 1981). To date, however, only a small handful of studies have begun to exploit this potential for natural population analysis (Avise et al., 1979b; Brown and Wright, 1979; Brown, 1980; Brown and Simpson, 1981; Ferris et al., 1981a, 1981b). In the first paper of this series, we included a description of mtDNA restriction fragment divergence among three geographically distant samples of the deer mouse, Peromyscus maniculatus (Avise et al., 1979a). Of particular interest was the observation that samples from Colorado and southern Michigan were very similar in mtDNA sequence (estimated nucleotide divergence, P .005), while a sample from North Carolina was very distinct from these (P .040). Here we greatly extend our survey of the deer mouse by analyzing mtDNA sequence variation in 135 animals collected across much of the vast range of the species in North America. Our procedure has been to map restriction sites recognized by eight endonucleases. The restriction maps permit comparisons of the pattern and character of changes in the mtDNA molecule that have occurred during its evolutionary history in P. maniculatus. Thus the data presented in this paper are of considerable significance to two different but closely interrelated aspects of mtDNA evolution: (1) the ' Number IV in the series, "The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations." 2 Current address: Laboratory of Genetics, National Institute of Environmental Health Sciences, Research Triangle Park; North Carolina 27709.

Susan W. Daniel

Papers

Mitochondrial DNA differentiation during the speciation process in Peromyscus.

Extensive genetic variation in mitochondrial dna's among geographic populations of the deer mouse, peromyscus maniculatus.