THE RELATIVE IMPORTANCE OF HISTORICAL EVENTS AND GENE FLOW ON THE POPULATION STRUCTURE OF A MEDITERRANEAN RAGWORT,SENECIO GALLICUS(ASTERACEAE)

The conservation and ecology of the British Virgin Islands endemic tree, Vachellia anegadensis

Numerous island species have gone extinct and many extant, but threatened, island endemics require ongoing monitoring of their conservation status. The small tree Vachellia anegadensis was formerly thought to occur only on the limestone island of Anegada in the British Virgin Islands and was categorized as Critically Endangered. However, in 2008 it was discovered on the volcanic island of Fallen Jerusalem, c. 35 km from Anegada, and in 2018 it was recategorized as Endangered. To inform conservation interventions, we examined the species’ distribution, genetic population structure, dependency on pollinators and preferred habitat, and documented any threats. We found V. anegadensis to be locally widespread on Anegada but uncommon on Fallen Jerusalem and established that geographical location does not predict genetic differentiation amongst populations. Vachellia anegadensis produces the highest number of seed pods when visited by animal pollinators, in particular Lepidoptera. Introduced animals and disturbance by humans appear to be the main threats to V. anegadensis, and in situ conservation is critical for the species’ long-term survival.

Genetic analysis of Bromus tectorum (Poaceae) in the Mediterranean region: biogeographical pattern of native populations

Genetic diversity within and among 42 native populations of Bromus tectorum (cheatgrass) was characterized within two regions, the eastern Mediterranean and the western Mediterranean. Two hypotheses were tested for the genetic diversity of these populations: (1) populations from the eastern Mediterranean are more genetically diverse compared with populations to the west, a potential consequence of the species' westward dispersal with the spread of agriculture, and (2) populations across the Mediterranean contain comparable genetic diversity but display high genetic differentiation, a potential consequence of both regions having served as refugia during glacial advances in the late Quaternary Period. Populations in the eastern Mediterranean possess 16 polymorphic loci and 37 multilocus genotypes. In contrast, populations from the western Mediterranean include a subset of these polymorphic loci (9) and fewer multilocus genotypes (19), consistent with the dispersal of B. tectorum with the east-west Holocene spread of agriculture. Among the 19 multilocus genotypes identified in populations from the western Mediterranean, 13 are undetected among eastern Mediterranean populations. Average genetic diversity within populations from the eastern Mediterranean is nonetheless comparable to the genetic diversity in populations from the Iberian Peninsula, whereas diversity is the lowest in the populations from southern France. Our results suggest a prominent role for agriculture in the grass's western spread, although glacial history and environmental heterogeneity also could have influenced the grass's genetic diversity. The exceptionally high level of self-pollination (>99%) in B. tectorum has contributed to preserving the genetic signature associated with the species' biogeographical history across the Mediterranean region.

Marked hybridization and introgression in Ophrys sect. Pseudophrys in the western Iberian Peninsula

PREMISE OF THE STUDY

Orchids in the genus Ophrys represent extraordinary cases of tight coevolution between plants and their pollinators, and as a result, they present opportunities for studying hybridization, or a lack thereof, during speciation. However, few studies assess the real effect of hybridization in diversification. The three most representative species of section Pseudophrys in the western Iberian Peninsula-O. dyris, O. fusca, and O. lutea-were chosen to study evolutionary relationships and examine speciation.

METHODS

Using eight specific nuclear microsatellite loci, 357 individuals from 28 locations were studied; 142 of these samples were also studied with four plastid microsatellite loci. Data were analyzed using Bayesian cluster analysis, a median-joint network, and multivariate analysis.

KEY RESULTS

Many O. dyris and O. fusca specimens had three or four alleles and were therefore treated as tetraploid. Ophrys dyris is poorly genetically separated from O. fusca, and pure populations are rare. Ophrys fusca and O. lutea are distinct, but hybrids/introgressed individuals were detected in most of the populations and supported by plastid haplotypes. Ophrys fusca is subdivided into three well-delimited genetic lineages with a strict geographic correspondence confirmed by plastid haplotypes.

CONCLUSIONS

Because postzygotic barriers are weak, leakage in this highly specialized orchid-pollinator system contributes to hybridization and introgression. These leakages may have occurred during periods of past climate change, promoting homogenization and the potential for generations of new biodiversity via production of novel genotypes/phenotypes interacting with pollinators.

Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity

Red deer populations in the Iberian glacial refugium were the main source for postglacial recolonization and subspecific radiation in north-western Europe. However, the phylogenetic history of Iberian red deer (Cervus elaphus hispanicus) and its relationships with northern European populations remain uncertain. Here, we study DNA sequences at the mitochondrial control region along with STR markers for over 680 specimens from all the main red deer populations in Spain and other west European areas. Our results from mitochondrial and genomic DNA show contrasting patterns, likely related to the nature of these types of DNA markers and their specific processes of change over time. The results, taken together, bring support to two distinct, cryptic maternal lineages for Iberian red deer that predated the last glacial maximum and that have maintained geographically well differentiated until present. Haplotype relationships show that only one of them contributed to the northern postglacial recolonization. However, allele frequencies of nuclear markers evidenced one main differentiation between Iberian and northern European subspecies although also supported the structure of both matrilines within Iberia. Thus, our findings reveal a paraphyletic nature for Iberian red deer but also its genetic identity and differentiation with respect to northern subspecies. Finally, we suggest that maintaining the singularity of Iberian red deer requires preventing not only restocking practices with red deer specimens belonging to other European populations but also translocations between both Iberian lineages.

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system, influence of marine currents, and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long-standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present-day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic-Mediterranean refugia after the last glacial period, with leading-edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long-distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life-history and major geographic features interact to shape the distribution of genetic diversity.

The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant-centre hypothesis

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.

Shifting dispersal modes at an expanding species' range margin

While it is generally recognized that noncontiguous (long-distance) dispersal of small numbers of individuals is important for range expansion over large geographic areas, it is often assumed that colonization on more local scales proceeds by population expansion and diffusion dispersal (larger numbers of individuals colonizing adjacent sites). There are few empirical studies of dispersal modes at the front of expanding ranges, and very little information is available on dispersal dynamics at smaller geographic scales where we expect contiguous (diffusion) dispersal to be prevalent. We used highly polymorphic genetic markers to characterize dispersal modes at a local geographic scale for populations at the edge of the range of a newly invasive grass species (Brachypodium sylvaticum) that is undergoing rapid range expansion in the Pacific Northwest of North America. Comparisons of Bayesian clustering of populations, patterns of genetic diversity, and gametic disequilibrium indicate that new populations are colonized ahead of the invasion front by noncontiguous dispersal from source populations, with admixture occurring as populations age. This pattern of noncontiguous colonization was maintained even at a local scale. Absence of evidence for dispersal among adjacent pioneer sites at the edge of the expanding range of this species suggests that pioneer populations undergo an establishment phase during which they do not contribute emigrants for colonization of neighbouring sites. Our data indicate that dispersal modes change as the invasion matures: initial colonization processes appear to be dominated by noncontiguous dispersal from only a few sources, while contiguous dispersal may play a greater role once populations become established.

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

One of the longstanding questions in phylogenetic systematics is how to address incongruence among phylogenies obtained from multiple markers and how to determine the causes. This study presents a detailed analysis of incongruent patterns between plastid and ITS/ETS phylogenies of Tribe Senecioneae (Asteraceae). This approach revealed widespread and strongly supported incongruence, which complicates conclusions about evolutionary relationships at all taxonomic levels. The patterns of incongruence that were resolved suggest that incomplete lineage sorting (ILS) and/or ancient hybridization are the most likely explanations. These phenomena are, however, extremely difficult to distinguish because they may result in similar phylogenetic patterns. We present a novel approach to evaluate whether ILS can be excluded as an explanation for incongruent patterns. This coalescence-based method uses molecular dating estimates of the duration of the putative ILS events to determine if invoking ILS as an explanation for incongruence would require unrealistically high effective population sizes. For four of the incongruent patterns identified within the Senecioneae, this approach indicates that ILS cannot be invoked to explain the observed incongruence. Alternatively, these patterns are more realistically explained by ancient hybridization events.

Population structure of Hypochaeris salzmanniana DC. (Asteraceae), an endemic species to the Atlantic coast on both sides of the Strait of Gibraltar, in relation to Quaternary sea level changes

To detect potential Pleistocene refugia and colonization routes along the Atlantic coast, we analysed amplified fragment length polymorphisms (AFLPs) in 140 individuals from 14 populations of Hypochaeris salzmanniana (Asteraceae), an annual species endemic to the southwestern European and northwestern African coastal areas. Samples covered the total distributional range of the species, with eight populations in southwestern Spain and six populations in northwestern Morocco. Using nine primer combinations, we obtained 546 fragments in H. salzmanniana and its sister species H. arachnoidea of which 487 (89.2%) were polymorphic. The neighbour-joining tree shows that the populations south of the Loukos river in Morocco are clearly differentiated, having more polymorphic, private, and rare fragments, and higher genetic diversity, than all the other populations. The southernmost populations in Morocco, south of the river Sebou, form a large panmictic population. They are probably the oldest populations that have been relatively unaffected by stochastic processes resulting from Pleistocene glaciations. Northward migration of populations during this period may have resulted in loss of genetic diversity in specific regions, perhaps due to bottlenecks caused by rise in sea level during interglacial periods, and, in some cases, by changes in the breeding system.

Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data

In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.

Extensive intraspecific polymorphism detected by SSCP at the nuclear C-mos gene in the endemic Iberian lizard Lacerta schreiberi

C-mos is a highly conserved intronless gene that has proved useful in the analysis of ancient phylogenetic relationships within vertebrates. We selected the Iberian endemic Schreiber's green lizard (Lacerta schreiberi) that persisted in allopatric refugia since the late Pliocene to investigate the utility of the C-mos nuclear gene for intraspecific phylogeographic studies. Our combination of DNA sequencing with the high resolving power of single-strand conformational polymorphism (SSCP) effectively discriminated four common alleles showing strong population structuring (F(ST) = 0.46). In addition, reconstruction of allele phylogenetic relationships further improved our understanding of C-mos spatial patterns of variation and allowed a comparison with previously described mitochondrial DNA data. Finally, limited sequencing of an extended C-mos fragment in six additional Lacerta species showed extensive polymorphism, to our knowledge representing a rare example of variation in a highly conserved nuclear gene.

The origin of a novel form of Senecio (Asteraceae) restricted to sand dunes in southern Sicily

The taxonomy of diploid Mediterranean Senecio sect. Senecio (Asteraceae) is complex, owing to a recent species radiation, high morphological plasticity and occasional interspecific hybridization. A study was conducted to resolve the origin of a novel form of Senecio restricted to sand dunes in southern Sicily, Italy. This has been described previously as morphologically intermediate to Senecio gallicus and Senecio glaucus ssp. coronopifolius, indicating a possible hybrid origin, or as a variant of Senecio leucanthemifolius. Plants of this form grown in a glasshouse were morphologically intermediate to S. glaucus and S. leucanthemifolius, but were also similar to some cultivated individuals of S. gallicus. No evidence for a hybrid origin was obtained from a survey of random amplified polymorphic DNA variation; instead the plants surveyed were most closely allied to Tunisian S. glaucus. They were also polymorphic for the same set of cpDNA haplotypes present in Tunisian S. glaucus. We conclude that the Sicilian Senecio is a variant form of North African S. glaucus ssp. coronopifolius, which most probably dispersed to sand dunes in southern Sicily in the relatively recent past. The presence of several cpDNA haplotypes in this material indicates that there have been multiple introductions of the species to Sicily.

Controlling for the effects of history and nonequilibrium conditions in gene flow estimates in northern bullfrog (Rana catesbeiana) populations

Nonequilibrium conditions due to either allopatry followed by secondary contact or recent range expansion can confound measurements of gene flow among populations in previously glaciated regions. We determined the scale at which gene flow can be estimated among breeding aggregations of bullfrogs (Rana catesbeiana) at the northern limit of their range in Ontario, Canada, using seven highly polymorphic DNA microsatellite loci. We first identified breeding aggregations that likely share a common history, determined from the pattern of allelic richness, factorial correspondence analysis, and a previously published mtDNA phylogeography, and then tested for regional equilibrium by evaluating the association between pairwise F(ST) and geographic distance. Regional breeding aggregations in eastern Ontario separated by <100 km were determined to be at or near equilibrium. High levels of gene flow were measured using traditional F-statistics and likelihood estimates of Nm. Similarly high levels of recent migration (past one to three generations) were estimated among the breeding aggregations using nonequilibrium methods. We also show that, in many cases, breeding aggregations separated by up to tens of kilometers are not genetically distinct enough to be considered separate genetic populations. These results have important implications both for the identification of independent "populations" and in assessing the effect of scale in detecting patterns of genetic equilibrium and gene flow.

Partitioning nuclear and chloroplast variation at multiple spatial scales in the neotropical epiphytic orchid, Laelia rubescens

Insights into processes that lead to the distribution of genetic variation within plant species require recognition of the importance of both pollen and seed movement. Here we investigate the contributions of pollen and seed movement to overall gene flow in the Central American epiphytic orchid, Laelia rubescens. Genetic diversity and structure were examined at multiple spatial scales in the tropical dry forest of Costa Rica using nuclear (allozymes) and chloroplast restriction fragment length polymorphism (RFLP) markers, which were found to be diverse (allozymes, P = 73.3%; HE = 0.174; cpDNA, HE = 0.741). Nuclear genetic structure (FSTn) was low at every spatial scale (0.005-0.091). Chloroplast markers displayed more structure (0.073-0.254) but relatively similar patterns. Neither genome displayed significant isolation-by-distance. Pollen and seed dispersal rates did not differ significantly from one another (mp/ms = 1.40) at the broadest geographical scale, among sites throughout Costa Rica. However, relative contributions of pollen and seeds to gene flow were scale-dependent, with different mechanisms determining the dominant mode of gene flow at different spatial scales. Much seed dispersal is highly localized within the maternal population, while some seeds enter the air column and are dispersed over considerable distances. At the intermediate scale (10s to 100s of metres) pollinators are responsible for substantial pollen flow. This species appears capable of distributing its genes across the anthropogenically altered landscape that now characterizes its Costa Rican dry forest habitat.

Patterns of genetic differention between populations of the specialized herbivore Macrosiphoniella tanacetaria (Homoptera, Aphididae)

For herbivorous insects, studies of isolation by distance (IBD) are available for large spatial scales, whereas studies over small geographic distances are relatively rare, in particular for species where population turnover is high. In this study, we investigated IBD and population genetic structure in the aphid Macrosiphoniella tanacetaria, a specialist herbivore of tansy (Tanacetum vulgare). Owing to clonal growth, an individual plant (genet) has one to many shoots (ramets), which can host aphid colonies. Both at the level of ramets and genets, aphid persistence is short, in the order of weeks. Sampling of 17 populations was performed on a logarithmic scale, along the Saale River in Germany in June 2001, with distances between populations ranging from 1 m to 170 km. For the six microsatellites used, allelic and genotypic variability within aphid populations was high, and deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were frequent. Most pairs of populations were significantly differentiated but there was no pattern of IBD. However, including into the analysis four additional populations from Alsace, France, collected at distances of, on average 470 km, resulted in a weak but significant IBD. Aphids are passive dispersers that are known to occasionally disperse over large distances, even though most dispersal is likely to occur over a small spatial scale. We suggest that for the host-specific M. tanacetaria, patterns of genetic variation among populations are, at an ecologically meaningful scale, governed by colonization/extinction dynamics and genetic drift rather than by a drift-dispersal equilibrium.

Cirsium species show disparity in patterns of genetic variation at their range-edge, despite similar patterns of reproduction and isolation

•  Genetic variation was assessed across the UK geographical range of Cirsium acaule and Cirsium heterophyllum. A decline in genetic diversity and increase in population divergence approaching the range edge of these species was predicted based on parallel declines in population density and seed production reported seperately. Patterns were compared with UK populations of the widespread Cirsium arvense. •  Populations were sampled along a latitudinal transect in the UK and genetic variation assessed using microsatellite markers. •  Cirsium acaule shows strong isolation by distance, a significant decline in diversity and an increase in divergence among range-edge populations. Geographical structure is also evident in C. arvense, whereas no such patterns are seen in C. heterophyllum. •  There is a major disparity between patterns of genetic variation in C. acaule and C. heterophyllum despite very similar patterns in seed production and population isolation in these species. This suggests it may be misleading to make assumptions about the geographical structure of genetic variation within species based solely on the present-day reproduction and distribution of populations.

Possible causes of morphological variation in an endemic Moroccan groundsel (Senecio leucanthemifolius var. casablancae): evidence from chloroplast DNA and random amplified polymorphic DNA markers

Genetic variation was assessed in Senecio leucanthemifolius var. casablancae (Compositae), a Moroccan Atlantic coast endemic, in order to examine possible causes of atypical leaf morphology in three populations south of the known range. Evidence for introgression from S. glaucus ssp. coronopifolius and/or divergence was investigated with molecular markers. Both random amplified polymorphic DNA (RAPD) and chloroplast (cp) DNA restriction fragment length polymorphism (RFLP) differentiated the species well. Some evidence that hybridization may have occurred between the two species was provided by cpDNA markers. However, biparentally inherited RAPD markers failed to provide any support for the hypothesis that intermediate leaf morphologies in atypical populations arose through hybridization. Consequently, they are most likely to have arisen via divergence caused by drift and/or selection. Genetic distances among populations of S. leucanthemifolius were significant in all but one case. Isolation by distance was indicated by a significant positive correlation between genetic and geographical distances (r = 0.68, P = 0.01, Mantel test). These results suggest that long-distance achene dispersal is rare, despite the presence of a well-developed pappus. The observed loss of pappus at achene maturity may explain this unexpected result. Due to the morphological distinction of var. casablancae from other varieties of S. leucanthemifolius, we suggest elevation to species rank and treatment of the atypical material at infraspecific rank.

Evidence for multiple Pleistocene refugia in the postglacial expansion of the eastern tiger salamander, Ambystoma tigrinum tigrinum

Pleistocene glaciations were important determinants of historical migration and, hence, current levels of genetic diversity within and among populations. In many cases, these historical migrations led to the existence of disjunct populations of plants and animals. However, the origin and timing of arrival of these disjunct populations is often debated. In the current study, we identify potential refugia and estimate the timing of vicariance events of the eastern tiger salamander, Ambystoma tigrinum tigrinum, using mitochondrial sequence data. The results suggest a vicariant event 0.75-2 million years ago, separating the tiger salamanders to the east and west of the Apalachicola River Basin. East of the Appalachians, there appear to be multiple independent refugia with little migration among the remaining populations. In particular, populations along the Atlantic Coastal Plain were likely isolated in a coastal plain refugium in the Carolinas. Migrants from this refugium were the likely source of colonists for populations occupying previously glaciated areas along the northeastern Atlantic Coast. A second potential refugium occurs in the Blue Ridge Mountains of western Virginia. This refugium contains a disjunct population of the eastern tiger salamander, as well as a community of nearly 70 other disjunct plant and animal species. The tiger salamanders here have been isolated from other populations for 200,000-500,000 years. These results suggest that disjunct mountain populations of Coastal Plain species may have existed in situ throughout the Pleistocene in Appalachian refugia. Therefore, these disjunct populations are not of recent origin, but rather exist as relicts of a warmer, more widespread fauna and flora that is now restricted to the Coastal Plain.

Mitochondrial DNA variation and GIS analysis confirm a secondary origin of geographical variation in the bushcricket Ephippiger ephippiger (Orthoptera: Tettigonioidea), and resurrect two subspecies

Geographic variation within species can originate through selection and drift in situ (primary variation) or from vicariant episodes (secondary variation). Most patterns of subspecific variation within European flora and fauna are thought to have secondary origins, reflecting isolation in refugia during Quaternary ice ages. The bushcricket Ephippiger ephippiger has an unusual pattern of geographical variability in morphology, behaviour and allozymes in southern France, which has been interpreted as reflecting recent primary origins rather than historical isolation. Re-analysis of this variation using Geographical Information Systems (GIS) suggests a possible zone of hybridization within a complex pattern of geographical variation. Here we produce a genetic distance matrix from restriction fragment length polymorphism (RFLP) bandsharing of an approximately 4.5 kb fragment of mitochondrial DNA (mtDNA), and compare this with predictions resulting from the GIS analysis. The mtDNA variation supports a postglacial origin of geographical variation. Partial Mantel test comparisons of genetic distances with matrices of geographical distance, relevant environmental characteristics and possible refugia show refugia to be the best predictors of genetic distance. There is no evidence to support isolation by distance. However, environmental contrasts do explain significant variation in genetic distance after allowing for the effect of refugial origin. Also, a neighbour-joining tree has a major division separating eastern and western forms. We conclude that the major source of variation within the species is historical isolation in glacial refugia, but that dispersal, hybridization and selection associated with environmental features has influenced patterns of mtDNA introgression. At least two valid subspecies can be defined.

Phylogeography of the European rabbit (Oryctolagus cuniculus) in the Iberian Peninsula inferred from RFLP analysis of the cytochrome b gene

We studied mitochondrial DNA variation in the European rabbit through the examination of restriction fragment length polymorphism in 526 individuals from 20 locations spread across the Iberian Peninsula. Digestion with eight enzymes of a 1120-bp fragment comprising most of the cytochrome b gene resolved 38 different haplotypes. These haplotypes were distributed in two highly divergent clades, with different but overlapping geographical distributions, and with comparable levels of within-clade variation. The overall phylogeographical pattern suggests a history of long-term regional isolation of two groups of rabbit populations, compatible with the recognition of two subspecies within the Iberian Peninsula, followed by recent contact and admixture. The underlying cause is sought in the alternation of glacial and interglacial periods in the late Pleistocene.

Genetic subdivision, glacial refugia and postglacial recolonization in the golden-striped salamander, Chioglossa lusitanica (Amphibia: urodela)

The golden-striped salamander (Chioglossa lusitanica) is an ecologically specialized species, endemic to north-western Iberia. Patterns of genetic variation were assessed at seven polymorphic enzyme loci and one mitochondrial DNA (mtDNA) marker (cytochrome b) in 17 populations across its range. Estimates of enzyme genetic diversity revealed a high degree of genetic subdivision (FST = 0.68), mainly attributable to the existence of two groups of populations. The groups were located, respectively, north and south of the Mondego River, indicating that this river coincided with a major historical barrier to gene flow. A significant decrease in genetic variability from the Mondego northwards was associated with the Douro and Minho rivers. mtDNA sequence variation revealed a congruent pattern of two haplotype groups (d = 2.2%), with a geographical distribution resembling that of allozymes. The pattern and depth of genetic variation is consistent with the following hypotheses: (i) subdivision of an ancestral range of the species prior to the middle Pleistocene; (ii) secondary contact between populations representing historical refugia; (iii) relatively recent range expansion giving rise to the northern part of the species range; and (iv) loss of genetic variation through founder effects during range expansion across major rivers.

Random amplified polymorphic DNA (RAPD) and quantitative trait analyses across a major phylogeographical break in the Mediterranean ragwort Senecio gallicus Vill. (Asteraceae)

Random amplified polymorphic DNA (RAPD) and quantitative trait variation of the widespread and ephemeral Senecio gallicus were surveyed in 11 populations sampled from the Iberian Peninsula and southern France. The aim of the study was to compare population relationships and levels of geographical differentiation with chloroplast (cp) DNA and allozyme variation assessed previously in the same populations. Employing multivariate statistics, a moderate level of intraspecific differentiation was observed among populations from Iberian coastal and inland regions for both RAPDs and quantitative traits. However, RAPDs provided greater resolution in identifying additional population structure within the hypothesized, Pleistocene refugial source area of the species in coastal Iberia. A major part of the geographical subdivision in RAPD and quantitative traits was concordant with the coastal vs. inland divergence as previously inferred from cpDNA haplotype frequencies, but strongly contrasted with the geographical uniformity of the species for allozymes. This concordance across various nuclear and cytoplasmic markers (RAPDs/quantitative traits, cpDNA) suggests that geographical uniformity for allozymes is more attributable to low rates of evolution and/or small genome sampling rather than high rates of pollen dispersal, slow rates of nuclear lineage sorting, or indirect balancing selection. The present study underscores the value of using additional classes of nuclear markers for narrowing the numbers of competing causal hypotheses about intraspecific cpDNA-allozyme discrepancies and their underlying evolutionary processes.

Fine-scale genetic structure and clinal variation in silene acaulis despite high gene flow

We investigated whether the distribution of genes reflects the patchy distribution of individuals of Silene acaulis on Pennsylvania Mountain in central Colorado. Five polymorphic protein loci were analysed using both F-statistics and spatial autocorrelation. Low thetaPOP (FST) indicated little genetic differentiation between populations approximately 1 km apart. This indicates high gene flow within our study site, perhaps as a result of long-distance pollen dispersal. Despite little differentiation between populations, there was clinal variation at the 6-Pgd-1 locus and significant within-population genetic structure (indicated by both thetaPATCH and spatial autocorrelation). We infer that this fine-scale genetic structure is the result of limited seed dispersal combined with genetic drift. The level of genetic structure varied markedly among populations, with the greatest genetic structure (highest Moran's I and thetaPATCH values) in two low-altitude, small, low-density populations. Intensive sampling such as used in this study may reveal similar patterns of fine-scale genetic differentiation in other patchily distributed plant species, particularly those with limited seed dispersal.

Population differentiation in mediterranean plants: insights into colonization history and the evolution and conservation of endemic species

Colonization and isolation are critical events in the evolutionary dynamics of plant populations. In this paper I review how spatial population structure of genetic markers provides insights into the evolutionary significance of episodes of colonization and isolation in the Mediterranean flora. I use as themes to structure my review the following topics: spatial structure induced by historical associations among populations of widespread species; population differentiation in relation to the evolution of closely related species with disjunct distributions; the potential effect of founder events during colonization on character evolution; and the conservation implications of spatial population structure. My review illustrates that the Mediterranean flora is full of examples that provide key insights into such evolutionary and conservation issues.