Phylogeographic Lineages Research Articles

Phenotypic responses to incubation conditions in ecologically distinct populations of a lacertid lizard: a tale of two phylogeographic lineages

AbstractWe experimentally studied the effects of genetic legacy (eastern vs. western phylogeographic lineage) and population of origin (lowland vs. highland) on the sensitivity of lizard embryos and juveniles to incubation temperature and moisture among four populations of the lacertid Psammodromus algirus. Incubation time was longer at lower temperature, increased slightly at higher moisture, and shorter for highland than for lowland females. Eggs incubated at 24°C produced larger, heavier and shorter tailed hatchlings than those incubated at 32°C. Western juveniles survived better during their first month of life than eastern ones, and juveniles incubated at 32°C survived better than those incubated at 24°C; survivorship was lowest for 24°C hatchlings from the eastern, lowland population. Because juveniles incubated at 32°C grew more rapidly, after 1 month they had compensated their initial size disadvantage. Juveniles incubated at 80% moisture were larger and/or heavier than those incubated at 10% moisture both at hatching and after 1 month. Our results show that although incubation temperature was the main source of phenotypic variation, not all its effects were evident at hatching. Because western juveniles were more tolerant to incubation at low temperature than eastern ones, we suggest that such differences may have limited the westward expansion of the eastern lineage.

Unveiling current Guanaco distribution in chile based upon niche structure of phylogeographic lineages: Andean puna to subpolar forests.

Niche description and differentiation at broad geographic scales have been recent major topics in ecology and evolution. Describing the environmental niche structure of sister taxa with known evolutionary trajectories stands out as a useful exercise in understanding niche requirements. Here we model the environmental niche structure and distribution of the recently resolved phylogeography of guanaco (Lama guanicoe) lineages on the western slope of the southern Andes. Using a maximum entropy framework, field data, and information on climate, topography, human density, and vegetation cover, we identify differences between the two subspecies (L.g.cacsilensis, L.g.guanicoe) and their intermediate-hybrid lineage, that most likely determine the distribution of this species. While aridity seems to be a major factor influencing the distribution at the species-level (annual precipitation <900 mm), we also document important differences in niche specificity for each subspecies, where distribution of Northern lineage is explained mainly by elevation (mean = 3,413 m) and precipitation seasonality (mean = 161 mm), hybrid lineage by annual precipitation (mean = 139 mm), and Southern subspecies by annual precipitation (mean = 553 mm), precipitation seasonality (mean = 21 mm) and grass cover (mean = 8.2%). Among lineages, we detected low levels of niche overlap: I (Similarity Index) = 0.06 and D (Schoener’s Similarity Index) = 0.01; and higher levels when comparing Northern and Southern subspecies with hybrids lineage (I = 0.32-0.10 and D = 0.12-0.03, respectively). This suggests that important ecological and/or evolutionary processes are shaping the niche of guanacos in Chile, producing discrepancies when comparing range distribution at the species-level (81,756 km2) with lineages-level (65,321 km2). The subspecies-specific description of niche structure is provided here based upon detailed spatial distribution of the lineages of guanacos in Chile. Such description provides a scientific tool to further develop large scale plans for habitat conservation and preservation of intraspecific genetic variability for this far ranging South American camelid, which inhabits a diversity of ecoregion types from Andean puna to subpolar forests.

Multilocus phylogeny and biogeography of the New World Pheucticus grosbeaks (Aves: Cardinalidae)

Using a multilocus approach, we investigated the tempo and pattern of diversification in a widely distributed New World songbird, the cardinalid genus Pheucticus. Each of the three geographic groups recovered (North American, Middle American, and South American) was comprised of a pair of currently recognized species, and four, three, and three geographically and genetically distinct phylogeographic lineages respectively. Diversification within Pheucticus appears to have occurred at a relatively constant pace throughout the Pleistocene and evenly across a broad latitudinal distribution. The Isthmus of Panama completion and Pleistocene glacial cycles both appear to have played prominent roles in the diversification of this group.

Admixed Phylogenetic Distribution of Drug Resistant Mycobacterium tuberculosis in Saudi Arabia

BackgroundThe phylogeographical structure of Mycobacterium tuberculosis is generally bimodal in low tuberculosis (TB) incidence countries, where genetic lineages of the isolates generally differ with little strain clustering between autochthonous and foreign-born TB patients. However, less is known on this structure in Saudi Arabia—the most important hub of human migration as it hosts a total population of expatriates and pilgrims from all over the world which is equal to that of its citizens.MethodologyWe explored the mycobacterial phylogenetic structure and strain molecular clustering in Saudi Arabia by genotyping 322 drug-resistant clinical isolates collected over a 12-month period in a national drug surveillance survey, using 24 locus-based MIRU-VNTR typing and spoligotyping.Principal FindingsIn contrast to the cosmopolitan population of the country, almost all the known phylogeographic lineages of M. tuberculosis complex (with noticeable exception of Mycobacterium africanum/West-African 1 and 2) were detected, with Delhi/CAS (21.1%), EAI (11.2%), Beijing (11.2%) and main branches of the Euro-American super-lineage such as Ghana (14.9%), Haarlem (10.6%) and Cameroon (7.8%) being represented. Statistically significant associations of strain lineages were observed with poly-drug resistance and multi drug resistance especially among previously treated cases (p value of < = 0.001 for both types of resistance), with relative over-representation of Beijing strains in the latter category. However, there was no significant difference among Saudi and non-Saudi TB patients regarding distribution of phylogenetic lineages (p = 0.311). Moreover, 59.5% (22/37) of the strain molecular clusters were shared between the Saudi born and immigrant TB patients.ConclusionsSpecific distribution of M. tuberculosis phylogeographic lineages is not observed between the autochthonous and foreign-born populations. These observations might reflect both socially favored ongoing TB transmission between the two population groups, and historically deep-rooted, prolonged contacts and trade relations of the peninsula with other world regions. More vigorous surveillance and strict adherence to tuberculosis control policies are urgently needed in the country.

Recipient of the 2012 Molecular Ecology Prize: Craig Moritz

Recipient of the 2012 <i>Molecular Ecology</i> Prize: Craig Moritz

Biogeographically dynamic genetic structure bridging two continents in the monotypic Central American rodentOtotylomys phyllotis

Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 593–610.

Bioactive constituents in Prunus africana: Geographical variation throughout Africa and associations with environmental and genetic parameters

Prunus africana--an evergreen tree found in Afromontane forests--is used in traditional medicine to cure benign prostate hyperplasia. Different bioactive constituents derived from bark extracts from 20 tree populations sampled throughout the species' natural range in Africa were studied by means of GC-MSD. The average concentration [mg/kgw/w] in increasing order was: lauric acid (18), myristic acid (22), n-docosanol (25), ferulic acid (49), β-sitostenone (198), β-sitosterol (490), and ursolic acid (743). The concentrations of many bark constituents were significantly correlated and concentration of n-docosanol was highly significantly correlated with all other analytes. Estimates of variance components revealed the highest variation among populations for ursolic acid (66%) and the lowest for β-sitosterol (20%). In general, environmental parameters recorded (temperature, precipitation, altitude) for the samples sites were not correlated with the concentration of most constituents; however, concentration of ferulic acid was significantly correlated with annual precipitation. Because the concentration of compounds in bark extracts may be affected by tree size, the diameter of sampled plants at 1.3m tree height (as proxy of age) was recorded. The only relationship with tree diameter was a negative correlation with ursolic acid. Under the assumption that genetically less variable populations have less variable concentrations of bark compounds, correlations between variation parameters of the concentration and the respective genetic composition based on chloroplast and nuclear DNA markers were assessed. Only variation of β-sitosterol concentration was significantly correlated with haplotypic diversity. The fixation index (F(IS)) was positively correlated with the variation in concentration of ferulic acid. Principal Components Analysis (PCA) indicated a weak geographic pattern. Mantel tests, however, revealed associations between the geographic patterns of bioactive constituents and the phylogenetic relationship among the populations sampled. This suggests an independent evolution of bark metabolism within different phylogeographical lineages, and the molecular phylogeographic pattern is partly reflected in the variation in concentration of bark constituents. The results have important implications for the design of strategies for the sustainable use and conservation of this important African tree species.

Identifying a contact zone between two phylogeographic lineages of Clematis sibirica (Ranunculeae) in the Tianshan and Altai Mountains

Abstract Clematis sibirica, a woody vine occurring primarily under conifer forests, is widespread in northern Eurasia. In this study, we intend to illustrate how the taxon has responded in the area of the Tianshan and Altai Mountains of Central Asia to the Pleistocene climatic fluctuations. The chloroplast intergenic spacer psbA‐trnH was sequenced for 125 individuals from 28 populations, and a total of eight chlorotypes were identified. The presence of definite phylogeographic structure was detected for the species (NST &gt; GST, P &lt; 0.001), and phylogenetic analysis indicated that the eight chlorotypes were clustered into two divergent lineages. They split at approximately 550–690 ka BP, according to coalescence analysis, coincident with the Pleistocene maximum glacial stage in these mountains, which suggests the restriction of these lineages to separate refugia at that time. Spatial analysis of molecular variance likewise divided the sampled populations into two associations, an Altai and eastern Tianshan group (populations 1–17), and a western Tianshan group (populations 18–28). Low levels of genetic diversity and unimodal mismatch distributions were obtained for both of these groups, suggesting postglacial range expansions. During the course of these expansions, mountain ranges surrounding the Dzungarian Basin probably served as migration corridors. In addition, a contact zone was identified in the central Tianshan and eastern Altai Mountains between the two phylogeographic lineages.

Phylogeographic analysis of avian influenza viruses isolated from Charadriiformes in Belgium confirms intercontinental reassortment in gulls

Nine influenza viruses isolated from gulls and shorebirds in Belgium (2008-2010), including H3N8, H5N2, H6N1, H11N9, H13N6, H13N8, and H16N3 subtypes, were targeted using random amplification and next-generation sequencing. The gene segments of these viruses segregated into three phylogeographic lineage types: (1) segments circulating in waterfowl in Eurasia with sporadic introduction in other species and in the Americas ("Eurasian avian"), (2) segments circulating in American waterfowl with sporadic introduction to other species and regions ("American avian"), and (3) segments circulating exclusively in gulls and shorebirds and having increased connectivity between the two hemispheres ("Charadriiformes specific"). Notably, an H6N1 and an H5N2 isolated from L. argentatus had mainly Eurasian avian genes but shared a matrix segment of American avian origin (first documentation in European gulls of transhemispheric reassortment). These data support the growing evidence of an important role of Charadriiformes birds in the dynamic nature of avian influenza ecology.

Conservation of phylogeographic lineages under climate change

ABSTRACTAim We address the unexplored question of whether the lack of information on intra‐specific diversity inherent in species‐level niche modelling might bias evaluation of the conservation requirements of species and phylogeographic lineages under changing climates. We test for directional biases that might arise due to these methodological differences in ways of assessing risks from climate change.Location The African continent.Methods We identified from peer‐reviewed studies that used both nuclear and plastid markers the distribution of deep phylogeographic divisions within nine species of African mammals and their phylogeographic lineages. We fitted ecological niche models to describe currently suitable, occupied climates and to project the shift of suitable climate to two future time slices. We applied gap analysis to reveal potential changes in the protection of phylogeographic diversity owing to climatic shifts.Results We found that, within species, most phylogeographic lineages differ in the climates they experience and have substantial geographic separation. Models that do not distinguish these subspecific units often fail to identify potential risks of climate change to lineages. Modelled potential effects of climate change on the geographic extent of suitable climate vary in both direction and magnitude. Predictions of the persistence of suitable climate in current protected areas for the resident lineages differ on average by factor of 2 between species and lineage models.Main conclusions Our study develops an original synthetic approach by combining niche modelling, projected climate change, phylogeographic information and gap analysis. We clearly identify the potential benefits of using the new approach to evaluate risks to the conservation of intra‐specific genetic diversity that are posed by climate change. Our results suggest that prudent conservation strategies need to incorporate potential differences in climate tolerance among lineages when planning conservation measures for species confronted with environmental change.

The status of a rare phylogeographic lineage of the Vulnerable European souslikSpermophilus citellus,endemic to central Macedonia

AbstractThe conversion of grasslands for agriculture has triggered a serious decline of the European ground squirrel or souslikSpermophilus citellus, categorized as Vulnerable on the IUCN Red List since 1996. The Jakupica phylogeographic lineage of central Macedonia is the smallest of the three major evolutionary lines of the European souslik. This lineage is an important reservoir of within-species diversity and should be regarded as an independent unit for conservation management purposes. It is endemic to Mount Jakupica, where it lives in mountain pastures at 1,500–2,250 m altitude. The total area occupied by sousliks (884 ha) is fragmented and 94% of individuals occur in four colonies. Densities (0.8–5.5 adults ha−1) are lower than those reported elsewhere for the species, with the total population probably &lt;2,000 adults. One large colony, reportedly of c. 1,000 sousliks, was decimated in 2007 by a catastrophic fire and had still not recovered by 2010. A steady decline in livestock grazing, together with the predicted advance of the tree line as a consequence of climate change, will probably reduce the optimal habitat for the souslik and negatively affect population fitness. Monitoring needs to be implemented, at least for the largest colonies, to provide early warning of any declines.

Identification of the barrier to gene flow between phylogeographic lineages of the common hamster Cricetus cricetus

In anthropogenically disturbed habitats, natural barriers still exist and have to be recognized, as they are important for conservation measures. Areas of phylogeographic breaks within a species are often stabilized in inhospitable regions which act as natural barriers. An area of contact between phylogeographic lineages of the common hamster (Cricetus cricetus) was found in the Małopolska Upland in Poland. A total of 142 common hamsters were captured between 2005 and 2009. All hamsters were genotyped at 17 microsatellite loci and partial sequences of the mitochondrial (mtDNA) control region were obtained. No mixed populations with mtDNA haplotypes of both lineages were found. The distance between marginal populations was about 20 km; no hamsters were found in the area between. A principal components analysis (PCA) was performed on microsatellite data and the greatest change in PC1 scores was found between marginal samples. To define the habitat components responsible for the phylogeographic break, we compared the habitat composition of sites occupied by hamsters with those from which hamsters were absent. We found that hamsters avoided forested areas and sandy soils. The area of the potential barrier was characterized by a high proportion of woodland and unfavorable soils in comparison with neighboring areas inhabited by hamsters. They cannot settle in this area due to their high winter mortality in shallow burrows and high predation in the fields adjacent to forests.

STRONG SELECTION AGAINST HYBRIDS MAINTAINS A NARROW CONTACT ZONE BETWEEN MORPHOLOGICALLY CRYPTIC LINEAGES IN A RAINFOREST LIZARD

Phenotypically cryptic lineages comprise an important yet understudied part of biodiversity; in particular, we have much to learn about how these lineages are formed and maintained. To better understand the evolutionary significance of such lineages, we studied a hybrid zone between two morphologically cryptic phylogeographic lineages in the rainforest lizard, Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline inference, individual-based methods and population measures of disequilibrium and using simulations to explore our genetic results in context of theoretical expectations, we inferred the processes maintaining this hybrid zone. We find that these lineages meet in a hybrid zone that is narrow (≈400 m) relative to inferred dispersal rate. Further, the hybrid zone exhibits substantial genetic disequilibrium and sharply coincident and largely concordant clines. Based on our knowledge about the region's biogeography, the species' natural history, and our simulation results, we suggest that strong selection against hybrids structures this system. As all clines show a relatively narrow range of introgression, we posit that this hybrid zone might not yet be in equilibrium. Nonetheless, our results clearly show that phylogeographic lineages can evolve substantial reproductive isolation without concomitant morphological diversification, suggesting that such lineages can constitute a significant component of evolutionary diversity.

Glacial history and local adaptation explain differentiation in phenotypic traits in the Alpine grassland herb Campanula barbata

Background: Quaternary glaciations have affected the phylogeographic structure of many widespread plant species of the European Alps. Survival of plants in isolated refugia on the fringes of the Alps has been proposed as a main driver for molecular differentiation within species across the Alps, and could also be responsible for phenotypic differentiation. Aims: To establish if phenotypic differentiation is in accordance with phylogeographic structure and if population differentiation reflects adaptive processes. Methods: In a common garden we measured vegetative and reproductive traits of plants from 15 populations of two phylogeographic lineages of Campanula barbata from subalpine grasslands across the Alps. Results: The two phylogeographic lineages were differentiated in plant height and number of inflorescences, suggesting that glacial history affected phenotypic differentiation, either through neutral processes or adaptation. Furthermore, negative correlations of number of leaves, plant height, number of flowers and above-ground biomass with altitude of population origin indicated that part of the observed differentiation among populations was due to adaptation to current altitude-related conditions either during or after recolonisation. Conclusions: Our results suggest that phenotypic differentiation across the investigated regions may be due to glacial history-related processes as well as due to more recent processes of local adaptation.

Morphological Differentiation in Ouachita Mountain Endemic Salamanders

Morphology of some groups of organisms has been highly conserved over evolutionary time, resulting in genetically divergent taxa with relatively little morphological variation. Genetic studies on salamanders of the genus Plethodon have revealed a high level of morphologically cryptic diversity, and recent ecological and evolutionary studies have suggested that morphology may be informative for taxonomic purposes when combined with genetic data. We examined morphological variation in the Ouachita Mountain endemic salamanders P. fourchensis and P. ouachitae to test whether these sister species, and recently identified phylogeographic lineages within species as defined by genetic data, can be discriminated using morphology. We found that P. fourchensis and P. ouachitae differed significantly in morphology and could be classified correctly with greater than 90% accuracy. Individuals from a previously identified hybrid zone were morphologically intermediate to the two parental species. Phylogeographic lineages within each species (n = 4 for P. fourchensis, n = 7 for P. ouachitae) also exhibited significant morphological differences and were classified correctly in 57–72% of cases. Our results support genetic evidence that showed significant divergence between P. fourchensis and P. ouachitae and among the different lineages within each species. The high levels of diversity within P. fourchensis and P. ouachitae have important implications for conservation because these endemic species have small ranges and lineages are usually restricted to single mountains.

Intraspecific Variation of Reproductive Traits in a Mediterranean Lizard: Clutch, Population, and Lineage Effects

Widely distributed terrestrial ectotherms from the southern European peninsulas show patterns of subdivision (related to isolation in temperate refugia) that allow us to test the relative importance of phylogeographic lineage, population of origin and familial effects as sources of variation for life-history traits. We collected gravid females from 15 geographically separated populations of the lacertid lizard Psammodromus algirus, a widely distributed species with well differentiated eastern and western lineages. We incubated eggs under two treatments of constant (28°C) and fluctuating (28 ± 4°C) temperature, and we examined clutch, population, and lineage effects on several traits of females, eggs, and hatchlings. Incubation time was mainly explained by differences between lineages, but it was also influenced by population and female effects. Within each lineage, incubation was shorter at cooler and wetter sites, and for a given climate it was shorter for eastern than for western populations, suggesting that countergradient variation has evolved independently in the two lineages. Female size, clutch size, and relative fecundity were primarily influenced by inter-population differences, a pattern that seemed attributable to environmental differences in productivity, because mean female size was positively correlated with a gradient of increasing precipitation and decreasing temperature. Clutch size was mainly, but not entirely, dependent on female SVL, suggesting both a proximate effect of local conditions and intrinsic differences among populations. Females from drier and warmer sites produced larger hatchlings. Mean egg mass was mainly determined by familial effects. Eggs incubated at a constant temperature hatched earlier than did their siblings incubated at fluctuating temperatures, a fact that could be explained by considering that in Mediterranean environments developmental rate might increase at a lower speed above average incubation temperature than it does decrease below it.

Morphing of the phylogeographic lineages of the Balkan alpine newts ( Ichthyosaura alpestris, Caudata, Salamandridae): In situ morphological diversification

Numerous alpine newt ( Ichthyosaura alpestris) populations from the Balkans, representing all the previously established phylogeographic lineages, were studied for variations in various morphological characteristics (body size and shape, skull qualitative traits and number of trunk vertebrae). Here, we present a decoupling of morphological and mtDNA phylogeographic substructuring in the alpine newt on the Balkan Peninsula. In sharp contrast to other European newts ( Triturus spp., Lissotriton spp.), the vast majority of morphological variation in the alpine newt is concentrated at the population level indicating an in situ morphological diversification. We found that the rate of morphological change is similar to the rate of mtDNA change. We hypothesize that the alpine newts are characterized by non-adaptive morphological evolution.

Historical biogeography of the Brazilian Atlantic forest and the Carnaval-Moritz model of Pleistocene refugia: what do phylogeographical studies tell us?

The present study uses published phylogeographical studies to test the Carnaval–Moritz (CM) model of forest dynamics in the Atlantic forest of Brazil. The model predicts that a large forested area in the north–central region of this biome has remained stable during the last glacial maximum, and only relicts in its current southernmost distributions. All available sequences for phylogeographical studies on vertebrates on the Atlantic forest were obtained from GenBank. All datasets consisted of mitochondrial sequences and were submitted to the same analyses, including time of divergence and migration rates between phylogeographical lineages, as well as historical demography analyses, including neutrality tests and Ne estimates. The species studied showed different degrees of phylogeographical structure. Two contact zones are defined: one very heterogeneous in south-east Brazil that was largely congruent with the CM model and one around the Doce river further north. Population genetics analyses showed a smaller effective number on southern population, and most of these southern populations showed evidence for recent demographic expansion. These features are also in agreement with the CM model. Additionally, divergence/expansion events dated back to the Pleistocene epoch in all but one organism. According to hierarchical approximate Bayesian computation analysis, most of the data can be attributed to a single event. The results highlight the need for more finescale studies in the Atlantic forest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 499–509.

Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii)

We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species' extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make-up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.

Could Betula humilis have survived the last glaciation at a current margin of its distribution? Testing the hypothesis of a glacial refugium using nuclear microsatellites

The probability of population extinction seems to differ within the species range. Populations occupying former glacial refugia could harbor substantial genetic resources, hence they should be less prone to extirpation. It was hypothesized that the shrub birch Betula humilis could have survived the Last Glacial Maximum (LGM) at the current southwestern margin of its range. Using ten nuclear microsatellites, we studied genetic variation within and between 18 localities of B. humilis situated in marginal and subcentral areas. Six marginal populations were located in areas covered by an ice sheet during the LGM, and the remaining samples came from unglaciated areas. Analysis of private allele frequencies as well as hierarchical AMOVAs conducted for geographical regions, marginal versus central populations, and glaciated versus unglaciated areas did not confirm the hypothesis of glacial isolate of the shrub birch in southeastern Poland. On the other hand, very high genetic variation in some localities in northeastern Poland was found. Survival in periglacial areas followed by broad-fronted colonization or the existence of an admixture zone of phylogeographic lineages was proposed to explain this phenomenon.