Genetic Structure of Populations

The genetic structure of populations may be studied at different scales. The combination of genetic information from populations through a species' range leads to a knowledge of the spatial aspects of population genetics (Fig. 3). While investigating the population genetics of wild species, several indices may be used (Box 1). The most common for each population are the expected heterozygosity and the allelic richness. When the investigation concerns the structure of the populations, then F statistics and their derivatives are the most common indices (Wallis 1994), but the application of geostatistical techniques indicates that these traditional values might not be the best indicators of population differentiation (Joost et al. 2007, 2008).

Each of these genetic indices has its own objectives. The allelic richness is very sensitive to population bottlenecks and to population admixture. In the diploid beech tree Fagus sylvatica (W & C Europe, 0-2,000 m), the area of the highest heterozygosity in Europe corresponds to the area which was colonized between 4,000 and 2,000 years ago, which corresponds to the area of admixture of colonization fronts coming from different glacial refugia (Comps et al. 2001). On the other hand, the highest allelic richness is still found near refugia, i.e., the Balkan Peninsula and S Italy.

The process of colonization leads thus to a decrease of allelic richness, due to multiple foundation events, while colonization from different areas may lead to high heterozygosities, because of the admixture from refugia with different alleles (Widmer and Lexer 2001; Petit et al. 2001). For species which have colonized N Europe from a Southern refugium, their heterozygosity decreases with increasing

Fig. 3 Isolation by distance effect in Carabus solieri.The slope depends on the time since colonization. The northernmost zones (4-6), i.e., the most recently colonized, show a more level slope than the areas close to the refugia (1), with a gradient of slopes for in between zones. Redrawn from Garnier et al. (2004)

Fig. 3 Isolation by distance effect in Carabus solieri.The slope depends on the time since colonization. The northernmost zones (4-6), i.e., the most recently colonized, show a more level slope than the areas close to the refugia (1), with a gradient of slopes for in between zones. Redrawn from Garnier et al. (2004)

Box 1 Indices Used in Population Genetics

H Expected Heterozygosity Probability that two alleles sampled at random from a population are different. It is a function of the allelic frequencies. The expected heterozygosity is basically calculated for each locus, and a mean (or sometimes a median) value is presented for a number of loci. This index is particularly sensitive to bottlenecks having occurred in the population previously. This index is also called the Nei's gene diversity.

Allelic Richness The number of alleles per locus is a good index of diversity. It is highly sensitive to past population bottlenecks (Luikart et al. 1998) and investigated loci. As it depends on the number of sampled individuals, this index has to be normalised to a given sample size (El Mousadik and Petit 1996).

Fixation Index FST is an index of the way two or more populations are differentiated from each other. It depends on the difference of allele frequencies among the populations. It is usually estimated from allele frequencies in the concerned populations, as follows:

fst = (ht - h)/ht with Hs the mean expected heterozygosity of an individual in each population mating randomly, and HT the expected heterozygosity of an individual in a total population mating randomly (e.g., Hartl and Clark 1989).

Isolation by distance The strength of any isolation by distance effect is measured as the slope of the regression of an index of genetic distance as a function of the geographic distance, both axes being expressed in logarithmic scale. The genetic distance is expressed either as FST or as FST /(1-FST) for each pair of populations. The steeper the slope is, the stronger the isolation by distance effect would be.

Neighborhood Size Individuals often do not reproduce at the location of their parents. The genetic neighborhood has been defined as the area within which most of the individual will reproduce. Dispersal is the movement from the birth or parents' locations to the reproduction location. Wright (1943) defined the genetic neighborhood of an individual as the population of the area within the variance (c2) of the dispersal distance. With d the density of individuals, the neighborhood size is given by Ne = 4ndc2. As the dispersal distance is usually difficult to measure, the neighborhood size is

Box 1 (continued)

often estimated from the differentiation between populations, using FST values estimated by pairs of populations to estimate the gene flow

4 fst

The y-intercept of the log-log plot of the estimated MST against geographic distance gives an approximation of the local effective population size (Slatkin 1993; example in Neve et al. 2008).

distances from their refugia. This has been called the "leading edge" effect, where the front (here North) part of the distribution moves, and the northernmost populations are the results of multiple colonization events (Hewitt 1993, 1996; Nichols and Hewitt 1994). The slope of the decrease of this heterozygosity depends on the rate of the loss of genetic diversity through the stepping stone colonization process.

During shifts of species range, the newly occupied area is the result of multiple colonization events. If this colonization is the result of rare events involving individuals only at the front edge of the distribution, a strong isolation by distance will follow together with a reduction of allelic diversity due to the repetitive colonization effect (Ibrahim et al. 1996). This resulted in a series of genetic hotspots distributed in the S Europe. Climate warming led to a gradual upward range shift, with little loss of genetic diversity, while the Northwards range shift involved long distance migration and multiple colonization bottleneck events. In the Frangula alnus, Eurosiberian diploid (0-1,400 m), the Iberian Peninsula and Turkey still harbor by far most of the genetic diversity. These probably correspond to the two main refugia for this species, and the colonization of the plains of central Europe was possible only by crossing severe barriers to dispersal (and hence gene flow) caused by the Pyrenees and the Black Sea (Hampe et al. 2003). In the arctic-alpine diploid species Ranunculus glacialis (1,700-4,000 m), populations from N Europe show a much lower genetic diversity than Alpine populations, as they resulted from a colonization from E Alps, where populations have retained a high genetic diversity (Schönswetter et al. 2003). In Gentiana ligustica, tetraploid endemic to the Ligurian Alps, the Shannon's Diversity index, computed on AFLP fragments, decreases with increasing distance from putative Würm refugia (Diadema 2006).

The retreating range margin is also subject to important changes in the population structure. As the area becomes generally unsuitable to the species of interest, its local suitable habitat patches become scarce and far between. The populations which used to be part of large networks of populations exchanging individuals with their neighbors become more isolated. These "trailing edge" populations are then reduced in their effective size, and are subject to drift, independently of other populations (Hampe and Petit 2005). The populations within the different mountain massifs of S Europe have been present in these areas often for several glacial cycles, resulting in levels of population exchanges to have occurred roughly according to the geographic distance. As at the continental scale the population exchanges have been rare, and as this process ended up being leveled over a very long time span (Slatkin 1993), the populations now found in the S European mountains often end up showing a very strong isolation by distance effect. If the North of Europe has been colonized from an Eastern refugium ("Chorthippus pattern," Hewitt 1999), the populations of the mountains of S Europe may have been isolated from the Northern populations at least since the Riss glaciation (ca. 130-240 ky BP). In this case their long isolation resulted in a strong differentiation. The Capercaillie Tetrao urogallus of the Cordillera Cantabrica and the Pyrenees is an old lineage different from the rest of the species' distribution, from the Alps and Scandinavia into Siberia (Duriez et al. 2007), which is the result of populations from the Iberian refugium not colonizing the lowlands North of the Pyrenees.

Within a given mountain massif, populations may also show a high differentiation, as they are separated by strong barriers such as valleys and rivers. If populations survived in nunataks during the last glaciation, the differentiation between these is the result of a pre-glacial isolation. In such cases, the populations now found at high altitudes of the Alps are the result of in situ survival during the Würm glaciation rather than post-glacial recolonization from peripheral areas. The perennial tetraploid cushion plant Eritrichium nanum most probably survived in at least three nunatak areas of the Alps (above 2,500 m), as these populations are the most variable (high number of private AFLP fragments) and the whole data set form three distinct clades (Stehlik et al. 2001). In other cases such as the artic-alpine diploid Saxifraga oppositifolia, genetics studies do not allow the identification of nunatak survival in the Alps, presumably because any surviving nunatak population would have been swamped by colonization from the main refugia (Holderegger et al. 2002). Sometimes a single pre-glacial population may end up being split: the tetraploid SW Alpine endemic Senecio halleri survived in two nunataks in the South part of its distribution, SW and NE of the Aosta valley, Italy. These two populations are not significantly different from each other, resulting probably from a single pre-glaciation colonization event (Bettin et al. 2007). Survival in and around mountain massifs during the last glaciation favoured the development of genetic differentiation between populations. In the widespread diploid Arabis alpina, the high among population variation in the mountains of S Europe (Alps, Tatra and Carpathians) suggests several refugia for this species, whereas all over the North of its distribution (Scandinavia, Iceland, Greenland and Newfoundland) it shows very low genetic variation, as these populations probably result from the recolonization from a single refugium closely following the retreating glaciers (Ehrich et al. 2007). Notably the populations in the East African mountains show high inter-populations variation, an evidence of their old age.

The carabid beetle Carabus solieri is an endemic species to the SW Alps near the Italian-French border. Garnier et al. (2004) sampled the whole distribution of this species, and performed genotypic identification of ten microsatellite loci in 1,080 individuals. Globally these populations show a strong isolation by distance, which is not surprising for a wingless species living in the mountain forests, in an area with many barriers to dispersal such as non-forested areas, roads, rivers etc. The 41 studied populations were grouped into three clusters, from South to North. Each cluster was then cut into two parts to have a series of six subclusters. Analysing these clusters separately for isolation by distance effect yielded a strong cline in the slope of the relationship between genetic distance and geographic distance. The slope is the steepest nearest to the refugium, and the most gradual in the recolonized area, i.e., northernmost set of populations (Fig. 3).

Other patterns of postglacial colonization have been described, from the refugia in central Asia or N Europe. The rare Alpine populations of the tetraploid Carex atro-fusca originate from a central Asian refugium, while Siberia and Greenland populations form a sister clade (Schonswetter et al. 2006a). The diploid Ranunculus pygmaeus provides even a more extreme case as the Alpine populations probably originate from a refugium on the Taymyr Peninsula, East of the last glacial ice sheet (Schonswetter et al. 2006b). In Norway, the high nucleotide diversity of the populations of the root vole Microtus oeconomus from the island of And0ya strongly suggests in situ glacial survival for this species (Brunhoff et al. 2006). These examples show that the recoloniza-tion of the European ice sheet, after the last glacial maximum, took part from all directions, even if the contribution of the Southern refugia was prevalent (Fig. 4).

Fig. 4 Map of Eurasia showing the Last Glacial Maximum (LGM; ca. 20 ky BP), with the main identified refugia of European taxa (LGM from Svendsen et al. 2004; Ivy-Ochs et al. 2008). Small glaciated areas in Mediterranean mountains (not shown here) are discussed in Hughes et al. (2006). Filled circles: main refugia; Open circles: nunatak refugia

Lgm Eurasia

Fig. 4 Map of Eurasia showing the Last Glacial Maximum (LGM; ca. 20 ky BP), with the main identified refugia of European taxa (LGM from Svendsen et al. 2004; Ivy-Ochs et al. 2008). Small glaciated areas in Mediterranean mountains (not shown here) are discussed in Hughes et al. (2006). Filled circles: main refugia; Open circles: nunatak refugia

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