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

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

It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is M∘=(1/FST-1)/4, which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if FST is replaced by NST . In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1993.tb01215.x

Isolation by distance in equilibrium and non-equilibrium populations.

▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...

Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

A. method for estimating the average level of gene flow in a subdivided population, as measured by the average number of migrants exchanged between local populations, Nm, is presented. The results from a computer simulation model show that the logarithm of Nm is approximately linearly related to the logarithm of the average frequency of private alleles, p(1), in a sample of alleles from the population. It is shown that this result is relatively insensitive to changes in parameters of the model other than Nm and the number of individuals sampled per population. The dependence of the value of p(1) on the numbers of individuals sampled provides a rough way to correct for differences in sample size. This method was applied to data from 16 species, showing that estimated values of Nm range from much greater than 1 to less than 0.1. These results confirm the qualitative analysis of Slatkin (1981). This method was also applied to subsamples from a population to show how to measure the extent of isolation of local populations.

Rare alleles as indicators of gene flow

Phylogenetic relationships based on 801 base pairs (bp) of the mitochondrial cytochrome b gene are examined for eight genera and 28 species of the akodontine tribe of South American murid rodents. The akodontine tribe comprises some 35% of the total diversity of the subfamily Sigmodontinae, but the current taxonomy at virtually all levels is uncertain because of inadequate generic diagnoses and assessments of variation and trends in traditional morphological characters. Monophyly of the tribe cannot be resolved by the sequence data, based on comparisons to outgroup taxa in three other tribes (Oryzomyini, Phyllotini, and Thomasomyini). However, highly corroborated monophyletic units within the group are obtained in a variety of both parsimony and distance analyses. These include a redefined and numerically dominant genus Akodon (with Microxus and Hypsimys as synonyms), Bolomys, Lenoxus, Oxymycterus , and a strongly supported assemblage that includes the central Andean Chroeomys and 'Akodon' andinus and the southern Abrothrix, 'Akodon' olivaceus, and the long-clawed mice of the genera Notiomys, Geoxus, and Chelemys. Sequence divergence within species is typically less than 5%, although levels can reach 10% for some highly polytypic forms. Divergence among genera within the tribe reaches 35% in corrected estimates, a level that is as great as that among representatives of different tribes. Changes in the current classification of akodontines are suggested based on these data, and the timing and place of origin of the tribe and its radiation is discussed.

The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for the akodontine tribe

Phylogenetic relationships among South American sigmodontine rodents were examined based on the complete sequence for the mitochondrial cytochrome b gene [1140 base pairs (bp)] for 66 species and between 759 and 1140 bp for an additional 19 species. Thirty-eight South American genera were represented, coming from eight of nine tribes. Outgroups included the North American murid rodents Peromyscus, Reithrodontomys, Scotinomys, and Neotoma, the Old World murine rodents Mus and Rattus, and the geomyoid genera Thomomys, Geomys, Dipodomys, and Perognathus as the most distant outgroup. The South American sigmodontines were supported as a monophyletic lineage. Within this radiation several clear-cut suprageneric groupings were identified. Many of the currently recognized tribal groupings of genera were found fairly consistently, although not always with high levels of bootstrap support. The various tribes could not be linked hierarchically with any confidence. In addition, several genera stand out as unique entities, without any apparent close relatives. The overall pattern suggests a rapid radiation of the sigmodontines in South America, followed by differentiation at the tribal and generic levels.

Phylogenetic Relationships and the Radiation of Sigmodontine Rodents in South America: Evidence from Cytochrome b

A 401-bp fragment of the mitochondrial cytochrome b gene was sequenced from polymerase chain reaction-amplified products for 20 natural populations representing 12 species of South American akodontine rodents (Muridae). Variation among these taxa increased with their hierarchical position, from comparisons within local populations to those among different genera. Two individuals from the same local population differed by less than 1% sequence divergence. Sequence divergence among geographic samples within a species was 0.25%-8%, while that among species was 3%-21%. Comparisons of the akodontine sequences with that for the house mouse show 21%-25% sequence difference. A parsimony-based phylogenetic analysis of the data supports the placement of the taxon Microxus within Akodon (sensu stricto), of Bolomys just outside the Akodon cluster, and of Chroeomys as a separate genus quite distinct from the other members of this group. This phylogenetic hypothesis is identical to that determined from electrophoretic data but is quite divergent from the present taxonomy of the group.

Variation in mitochondrial cytochrome b sequence in natural populations of South American akodontine rodents (Muridae: Sigmodontinae).

Parapatric speciation across sharp ecological gradients is an alternative to the more usual allopatric model as both a general explanation of organismal diversification and as an explicit statement regarding differentiation of tropical forest biotas (Endler, 1977, 1982a, 1982b). The relevance of this model to species of small mammals distributed across a 3,000 meter gradient on the eastern flank of the Peruvian Andes is examined here by phylogenetic analysis of comparative mitochondrial DNA sequences, relying on both freshly collected samples and extracts taken from skins preserved in museum collections. These analyses falsify the applicability of the gradient model in this case. Moreover, the phylogenetic approach employed here provides an explicit test of the feasibility of the gradient model for any other taxon, either plant or animal, of the lowland Amazonian forest.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1992.tb01992.x

mtDNA PHYLOGENY OF ANDEAN MICE: A TEST OF DIVERSIFICATION ACROSS ECOLOGICAL GRADIENTS.

Species definitions are commonly based on documentation either of genetic or ecologic cohesion (biological species models) or of phylogenetic relationship (phylogenetic spe? cies concept). However, these philosophical positions are often incompatible with data on ge? nealogical relationship of and genetic/reproductive interactions among member populations. The difficulty in defining species in nature based on either viewpoint is exacerbated when times between divergence events are short, when differentiation among populations prior to speciation is extensive, and when reticulation events persist subsequent to speciation. We illustrate this set of problems with data on mitochondrial DNA sequences and both nuclear sequences and allozyme electromorphs for sets of populations of two currently recognized species of pocket gophers, Thomomys bottae and T. townsendii in the western United States. These molecular per? spectives give somewhat conflicting views of polyphyly, paraphyly, and monophyly at the population and species level due, in part, to probable differences in times to monophyly, dif? ferential lineage sorting, retention of ancestral polymorphisms, and/or episodes of asymmetrical introgressive hybridization. As a consequence, strict adherence to any species concept in the objective recognition of evolutionary units within this complex is difficult at best. (Species concepts; paraphyly; polyphyly; allozymes; mtDNA sequence; 0-globin sequence; pocket go? phers; Thomomys.)

Margaret F. Smith

Papers

The diversification of South American murid rodents: evidence from mitochondrial DNA sequence data for the akodontine tribe

Phylogenetic Relationships and the Radiation of Sigmodontine Rodents in South America: Evidence from Cytochrome b

Variation in mitochondrial cytochrome b sequence in natural populations of South American akodontine rodents (Muridae: Sigmodontinae).

mtDNA PHYLOGENY OF ANDEAN MICE: A TEST OF DIVERSIFICATION ACROSS ECOLOGICAL GRADIENTS.

Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (Genus Thomomys)