Contrasting phylogeographic patterns in Sphagnum fimbriatum and Sphagnum squarrosum (Bryophyta, Sphagnopsida) in Europe

The chloroplast phylogeography of two peat mosses (Sphagnum fimbriatum and Sphagnum squarrosum) with similar distributions but different life history characteristics was investigated in Europe. Our main aim was to test whether similar distributions reflect similar phylogeographic and phylodemographic processes. Accessions covering the European distributions of the species were collected and approx. 2000 bp of the chloroplast genome of each species was sequenced. Maximum parsimony, statistical parsimony and phylodemographic analyses were used to address the question of whether these species with similar distributions show evidence of similar phylogeographic and phylodemographic processes. The chloroplast haplotypes of the currently spreading species S. fimbriatum showed strong geographic structure, whereas those of S. squarrosum, which has stable historical population sizes, showed only very weak geographic affinity and were widely distributed. We hypothesize that S. fimbriatum survived the last glaciations along the Atlantic coast of Europe, whereas S. squarrosum had numerous, scattered refugia in Europe. The dominance of one haplotype of S. fimbriatum across almost all of Europe suggests rapid colonization after the last glacial maximum. We hypothesize that high colonizing ability is an inherent characteristic of the species and its recent expansion in Europe is a response to climate change.     

Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate

Vicariance and dispersal can strongly influence population genetic structure and allopatric speciation, but their importance in the origin of marine biodiversity is unresolved. In transitional estuarine environments, habitat discreteness and dispersal barriers could enhance divergence and provide insight to evolutionary mechanisms underlying marine and freshwater biodiversity. We examined this by assessing phylogeographic structure in the widespread amphipod Gammarus tigrinus across 13 estuaries spanning its northwest Atlantic range from Quebec to Florida. Mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 1 phylogenies supported deep genetic structure consistent with Pliocene separation and cryptic northern and southern species. This break occurred across the Virginian-Carolinian coastal biogeographic zone, where an oceanographic discontinuity may restrict gene flow. Ten estuarine populations of the northern species occurred in four distinct clades, supportive of Pleistocene separation. Glaciation effects on genetic structure of estuarine populations are largely unknown, but analysis of molecular variance (AMOVA) supported a phylogeographic break among clades in formerly glaciated versus nonglaciated areas across Cape Cod, Massachusetts. This finding was concordant with patterns in other coastal species, though there was no significant relationship between latitude and genetic diversity. This supports Pleistocene vicariance events and divergence of clades in different northern glacial refugia. AMOVA results and private haplotypes in most populations support an allopatric distribution across estuaries. Clade mixture zones are consistent with historical colonization and human-mediated transfer. An isolation-by-distance model of divergence was detected after we excluded a suspected invasive haplotype in the St. Lawrence estuary. The occurrence of cryptic species and divergent population structure support limited dispersal, dispersed habitat distribution, and historical factors as important determinants of estuarine speciation and diversification.     

Rangewide phylogeography of a terrestrial slug in Europe: evidence for Alpine refugia and rapid colonization after the Pleistocene glaciations

Intraspecific phylogeographical patterns largely depend on the life history traits of a species. Especially species with a high degree of cold tolerance, limited requirements towards habitat preferences, and relatively low active dispersal capacities may have responded in a different way to the Pleistocene climatological fluctuations than the majority of taxa studied so far. To evaluate this possibility, we studied Arion fuscus (Muller, 1774), a common and widespread European terrestrial slug, from 88 locations (N = 964). Sequence variation was assessed for fragments of the mitochondrial 16S rDNA and COI genes by means of single-strand conformation polymorphisms (SSCP) and subsequent DNA sequencing. Additionally, eight allozyme loci were scored in 843 individuals. Phylogenetic analysis revealed the presence of two major evolutionary lineages, one in the Balkan region and another in the Alps and the rest of Europe. The sequence divergence between the two lineages was limited (3.3%), but gene flow between the regions was absent, suggesting that the two regions have been isolated since the late Pliocene or early Pleistocene. Allozyme differentiation among geographical regions and mitochondrial DNA (mtDNA) lineages was low. The geographical patterns observed in our data showed that (i) haplotype and nucleotide diversities are very low in northern Europe, suggesting that single haplotypes rapidly colonized large areas; (ii) recently expanded haplotype clades have restricted distribution ranges, suggesting that current gene flow is low; and (iii) genetic diversity in the Alps is much higher than in other regions and estimated past gene flow from the Eastern Alps to other regions was high, suggesting that this was a refugial zone during the Pleistocene. This full-range phylogeography suggests the existence of an alternative refugial zone, situated north of the refugial areas currently recognized in most other taxa.     

The noncosmopolitanism paradigm of freshwater zooplankton: insights from the global phylogeography of the predatory cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea,Onychopoda)

A major question in our understanding of eukaryotic biodiversity is whether small bodied taxa have cosmopolitan distributions or consist of geographically localized cryptic taxa. Here, we explore the global phylogeography of the freshwater cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) using two mitochondrial genes, cytochrome c oxidase subunit I and 16s ribosomal RNA, and one nuclear marker, 18s ribosomal RNA. The results of neighbour‐joining and Bayesian phylogenetic analyses reveal an exceptionally pronounced genetic structure at both inter‐ and intra‐continental scales. The presence of well‐supported, deeply divergent phylogroups across the Holarctic suggests that P. pediculus represents an assemblage of at least nine, largely allopatric cryptic species. Interestingly, all phylogenetic analyses support the reciprocal paraphyly of Nearctic and Palaearctic clades. Bayesian inference of ancestral distributions suggests that P. pediculus originated in North America or East Asia and that European lineages of Polyphemus were established by subsequent intercontinental dispersal events from North America. Japan and the Russian Far East harbour exceptionally high levels of genetic diversity at both regional and local scales. In contrast, little genetic subdivision is apparent across the formerly glaciated regions of Europe and North America, areas that historical demographic analyses suggest that were recolonized just 5500–24 000 years ago.     

Genetic divergence and phylogeographic relationships among european perch (Perca fluviatilis) populations reflect glacial refugia and postglacial colonization

We used the widely distributed freshwater fish, perch (Perca fluviatilis), to investigate the postglacial colonization routes of freshwater fishes in Europe. Genetic variability within and among drainages was assessed using mitochondrial DNA (mtDNA) D-loop sequencing and RAPD markers from 55 populations all over Europe as well as one Siberian population. High level of structuring for both markers was observed among drainages and regions, while little differentiation was seen within drainages and regions. Phylogeographic relationships among European perch were determined from the distribution of 35 mtDNA haplotypes detected in the samples. In addition to a distinct southern European group, which includes a Greek and a southern Danubian population, three major groups of perch are observed: the western European drainages, the eastern European drainages including the Siberian population, and Norwegian populations from northern Norway, and western side of Oslofjord. Our data suggest that present perch populations in western and northern Europe were colonized from three main refugia, located in southeastern, northeastern and western Europe. In support of this, nested cladistic analysis of mtDNA clade and nested clade distances suggested historical range expansion as the main factor determining geographical distribution of haplotypes. The Baltic Sea has been colonized from all three refugia, and northeastern Europe harbours descendants from both eastern European refugia. In the upper part of the Danube lineages from the western European and the southern European refugia meet. The southern European refugium probably did not contribute to the recolonization of other western and northern European drainages after the last glaciation. However, phylogenetic analyses suggest that the southern European mtDNA lineage is the most ancient, and therefore likely to be the founder of all present perch lineages. The colonization routes used by perch probably also apply to other freshwater species with similar distribution patterns.     

Refugial races and postglacial colonization history of the freshwater amphipod Gammarus lacustris in Northern Europe

The systematic structure and postglacial population history of the freshwater amphipod Gammarus lacustris were explored in an allozyme survey of 65 populations across Northern Europe. A strong multilocus pattern of differentiation discriminated populations of the north‐east (north‐eastern Norway, northern Finland) from those in the west and the south (southern and central Scandinavia, Denmark, Poland). This principal division is attributed to postglacial colonization of the area by two main refugial races or lineages, one from the east (Russia), the other from the south (north‐western European continent). The strongly diverged Eastern and Western races (Nei's D= 0.3, from 22 loci) now meet in a secondary contact zone across a narrow sector of northernmost Norway. Genetic population compositions in this zone vary in a mosaic pattern, and show no evidence of reproductive incompatibility. Similar contacts of eastern and western lineages, far older than the latest glaciation, are now known from a number of taxa and they constitute a general pattern in Fennoscandian phylogeography. Within the Western Gammarus race, the populations through coastal north‐western Norway are further distinguished from those in southern Scandinavia and Denmark by a set of unique alleles at high frequencies (D = 0.12). This suggests an independent early colonization of the coastal region by another distinct stock, either along an early deglaciated coastal corridor from the south‐west, or directly from the ice‐free continental shelf off the Norwegian coast – a hypothesis that has also previously been presented for G. lacustris, and parallels controversial suggestions of local refugia for other taxa in Scandinavia. The coastal population type only later could come into contact with Gammarus invading over the mountains from the south; these two population types now smoothly intergrade. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 523–542.     

Comparative phylogeography of codistributed aquatic insects in western North America: insights into dispersal and regional patterns of genetic structure

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Postglacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio

Three major phylogeographic lineages of the cottid fish Cottus gobio (bullhead) were identified in northern Europe from mitochondrial DNA sequences and allozyme data. The largely separate freshwater distributions of the lineages demonstrate distinct postglacial colonization histories. West of the Baltic Sea, Swedish lakes were invaded from the southwest (Germany). Another, eastern lineage has colonized the inland waters northeast and east of the Baltic, from refugia in northwest Russia; this lineage comprises a distinct subgroup found only from Estonia. The third lineage, found south and southeast of the Baltic, probably descended from rivers draining to the Black Sea from the north (e.g. Dnepr). In coastal waters of the Baltic Sea, and in near-coast inland waters, the lineages are now found intermixed in various combinations. The alternating fresh- and saltwater phases of the Baltic basin have variously enabled and disabled the use of coastal waters as colonization routes. Hypotheses on the chronology of dispersal and lineage mixing can be based on the distribution of the marker genes and the paleohydrographical record. The diversity of the Fennoscandian bullhead thus comprises anciently diverged (probably mid-Pleistocene) refugial lineages that in their freshwater range constitute distinct evolutionarily significant units. The thorough mixing of the various genomic origins in and around the Baltic, however, refutes the controversial view of distinct species status for the western and eastern ('Cottus koshewnikowi') bullheads. The postglacial contact of the lineages has created new diversity that cannot be interpreted in a conventional hierarchical framework of taxonomic or conservation units.     

Genetic diversity and phylogeography of the Apennine yellow-bellied toad Bombina pachypus, with implications for conservation

Genetic variation was investigated in 17 populations of the Italian endemic Apennine yellow-bellied toad using both mitochondrial (598 bp of the cytochrome b gene) and nuclear (21 allozyme loci) markers. Populations from central Calabria (southern Italy) showed the highest levels of intrapopulation genetic variation, whereas samples located north of this region were nearly lacking in variation. This appears to be a typical pattern of 'southern richness and northern purity', usually attributed to the prolonged population stability within southern refugia coupled with the loss of variation during postglacial northward expansion. However, the overall pattern of genetic variation observed has a strong geographical component, suggesting two Calabrian plains, Catanzaro and Crati-Sibari, as historical barriers to dispersal separating three population groups. These findings cannot be explained by the prolonged stability of southern populations alone, and suggest that the southern richness has been at least in part shaped by allopatric differentiation within the refugial range, followed by intermixing of previously differentiated lineages. From a conservation standpoint, Calabria is the major genetic diversity reservoir for this species, thus deserving particular conservation efforts. Furthermore, although the low intrapopulation genetic variation outside Calabria appears to be of clear historical origin, evidence of a current reduction of gene flow suggests that human disturbance has also played a part, particularly in the anthropogenic impacted Volturno river drainage basin.     

Population genetic structure and diversity of the Apennine endemic stream frog, Rana italica--insights on the Pleistocene evolutionary history of the Italian peninsular biota

For most species in the Western Palaearctic region, southern Mediterranean peninsulas have been identified as major Quaternary refugia and hotspots of intraspecific diversity, and thus, as areas of particular relevance for the conservation of the evolutionary potential. We analysed the patterns of geographical variation among 26 populations of the Italian stream frog, using both nuclear (allozymes) and mitochondrial (partial cytochrome b sequences) markers. Phylogenetic, phylogeographical and population genetic analyses suggested that the species survived the last glacial–interglacial cycles in two distinct refugia, one restricted to the tip of the Calabrian peninsula, at the extreme south of the species' range, the other spanning from central Calabria to central Apennines and showing evidences for further population subdivision therein. Historical demographic tests suggested a significant population expansion from the latter, which most likely began around the last pleniglacial. This expansion would have led to the rapid colonization of the northern Apennines to the north, and to a secondary contact and population admixture with the population from the southern refugium in southern central Calabria. A comparison of the evolutionary history inferred for the Italian stream frog with the data emerging for other codistributed species suggests: (i) the generality of a multiple-refugia scenario for the Italian peninsula, (ii) the possible occurrence of at least one suture zone in southern Italy, and (iii) that for most species, this Pleistocene refugium is not only a hotspot, but also a melting pot of intraspecific genetic diversity. Finally, the conservation implications of these results are also briefly highlighted.     

HOLARCTIC PHYLOGEOGRAPHY OF AN ASEXUAL SPECIES COMPLEX I. MITOCHONDRIAL DNA VARIATION IN ARCTIC DAPHNIA

Pleistocene glacial cycles undoubtedly altered the evolutionary trajectories of many taxa, yet few studies have examined the impact of such events on genetic differentiation and phylogeography at large geographic scales. Here we present the results of a circumarctic survey of mitochondrial DNA diversity in members of the Daphnia pulex complex. The analysis involved the survey of restriction site polymorphisms in a 2100-bp fragment of the NADH-4 (ND4) and NADH-5 (ND5) genes for 276 populations representing the two major groups (tenebrosa and pulicaria) in this complex across their Holarctic range. A comparison of the distribution patterns for seven clades in this complex revealed very clear phylogeographic structuring. Most notably, pulicaria group lineages were restricted primarily to the Nearctic, with some colonization of formerly glaciated portions of northern Europe. This group was not detected from vast expanses of northern Eurasia, including the Beringian glacial refuge. In contrast, tenebrosa group haplotypes showed considerable intercontinental divergence between Eurasian and North American lineages, but were absent from Greenland and Iceland, as well as the Canadian arctic archipelago. Dispersal in Eurasia was primarily in a westerly direction from Beringia, whereas dispersal in the Nearctic followed proglacial drainage patterns. Long-distance dispersal of certain lineages was observed in both groups, and variation in haplotype richness and nucleotide diversity allowed us to make inferences about the positioning of putative glacial refugia. Overall, the phylogeographic pattern of diversification in this arctic complex is characterized by the apparently unique postglacial histories for each clade, indicating that even closely allied taxa can respond independently to the allopatric effects of glacial cycles. This is in sharp contrast to other phylogeographic studies of species assemblages from more southern (unglaciated) latitudes, which are often characterized by concordant patterns.     

Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China

How coniferous trees in northern China changed their distribution ranges in response to Quaternary climatic oscillations remains largely unknown. Here we report a study of the phylogeography of Pinus tabulaeformis, an endemic and dominant species of coniferous forest in northern China. We examined sequence variation of maternally inherited, seed‐dispersed mitochondrial DNA (mtDNA) (nad5 intron 1 and nad4/3–4) and paternally inherited, pollen‐ and seed‐dispersed chloroplast DNA (cpDNA) (rpl16 and trnS‐trnG) within and among 30 natural populations across the entire range of the species. Six mitotypes and five chlorotypes were recovered among 291 trees surveyed. Population divergence was high for mtDNA variation (G_ST = 0.738, N_ST = 0.771) indicating low levels of seed‐based gene flow and significant phylogeographical structure (N_ST > G_ST, P < 0.05). The spatial distribution of mitotypes suggests that five distinct population groups exist in the species: one in the west comprising seven populations, a second with a north–central distribution comprising 15 populations, a third with a southern and easterly distribution comprising five populations, a fourth comprising one central and one western population, and a fifth comprising a single population located in the north‐central part of the species’ range. Each group apart from the fourth group is characterized by a distinct mitotype, with other mitotypes, if present, occurring at low frequency. It is suggested, therefore, that most members of each group apart from Group 4 are derived from ancestors that occupied different isolated refugia in a previous period of range fragmentation of the species, possibly at the time of the Last Glacial Maximum. Possible locations for these refugia are suggested. A comparison of mitotype diversity between northern and southern subgroups within the north‐central group of populations (Group 2) showed much greater uniformity in the northern part of the range both within and between populations. This could indicate a northward migration of the species from a southern refugium in this region during the postglacial period, although alternative explanations cannot be ruled out. Two chlorotypes were distributed across the geographical range of the species, resulting in lower levels of among‐population chlorotype variation. The geographical pattern of variation for all five chlorotypes provided some indication of the species surviving past glaciations in more than one refugium, although differentiation was much less marked, presumably due to the greater dispersal of cpDNA via pollen.     

The evolutionary history of a mammal species with a highly fragmented range: the phylogeography of the European snow vole

The European snow vole Chionomys nivalis has a patchy distribution restricted to rocky habitats across southern Europe and the Near and Middle East. We carried out a phylogeographic study to provide a biogeographic scenario, based on molecular data, outlining the major processes that determined the current distribution of the species. The samples include 26 snow voles from 14 different populations across the entire species range from Spain to Anatolia and Israel. Nearly complete sequences (1037 bp) of the mitochondrial gene for cytochrome b were sequenced. Relationships among haplotypes were inferred with neighbour-joining, maximum likelihood, maximum parsimony analyses and minimum spanning network. An analysis of mismatch distribution was used to cast light on past demographic expansion. We found 22 different haplotypes that fall into six distinct lineages, all but one is supported by high bootstrap values with all methods. Four lineages are allopatric (Tatra Mts., Iberia, Balkans and Middle East) while divergent haplotypes from two lineages show sympatry in the Alps and the Apennines. The basal relationships of these lineages could not be established by any tree. The mean pairwise genetic distance between lineages ranges from 2.4 to 4.2%. The shape of the mismatch distribution indicated a past expansion event dating back to between 158 000 and 84 000 years ago. These data can be interpreted with the existence of southern glacial refugia (Iberia, Balkans, Middle East and Italy) and one additional northern glacial refugium. The lack of phylogenetic resolution among lineages and the shape of mismatch distribution are indicative of a simultaneous and rapid splitting due to a relatively fast initial expansion of populations. Moreover, the analysis supports the hypothesis of the European origin of C. nivalis and its subsequent eastward dispersion during the Middle Pleistocene.     

Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus,based on complete sequencing of the mitochondrial DNA control region

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162-bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well-supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human-mediated stock transfers, parsimony-network-based nested-clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre-dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter- and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.     

Colonization history of the high-arctic pink-footed goose Anser brachyrhynchus

Population structure and phylogeography of the pink-footed goose, Anser brachyrhynchus Baillon 1833, was studied using mtDNA control region sequences (221 bp) from 142 individuals. Present breeding areas of the species in Greenland, Iceland, and Svalbard were largely covered by ice during the late Pleistocene. In pairwise comparisons phiST estimates showed significant differentiation among eastern and western populations, whereas sampling localities within both areas were not differentiated. The mtDNA data indicate that the populations have separated recently (less than 10 000 years ago) and present breeding areas were colonized from one refugial population. The levels of haplotype and nucleotide diversity were approximately five times higher for the eastern population compared to the western population and suggest that the latter was colonized by a subset of eastern birds. Time to the most recent common ancestor of the species is 32 000-46 000 years, i.e. the present mtDNA variation of the pink-footed goose has accumulated during the last 0.1 My. Estimates of the long-term female effective population size (5400-7700 for the eastern population) imply that the refugial population of the pink-footed goose has been large. Tundra habitats were more extensive in cold periods of the late Pleistocene than today and may have sustained population sizes that allowed the accumulation of extant genetic polymorphism. It is not probable that the postulated small refugial areas in the high latitudes had a significant role in maintaining this diversity.     

Alleles of sAAT-1,2* isoloci in brown trout: potential diagnostic marker for tracking routes of post-glacial colonization in northern Europe

Distribution alleles of sAAT-1,2 * isoloci in brown trout Salmo trutta populations of northern Europe revealed two glacial refugia, 'Baltic' and 'Atlantic'.     

Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-pleistocene recolonization of northern Europe

Mitochondrial haplotype diversity in seven Portuguese populations of brown trout, Salmo trutta L., was investigated by sequencing the 5' end of the mitochondrial DNA (mtDNA) control region. Five new haplotypes were described for this species, each two to three mutational steps distant from the common north Atlantic haplotype. Significant population subdivision of mtDNA haplotypes was also apparent. Based on these results, as well as on published data describing the distribution of both mtDNA haplotypes and allozyme alleles throughout Europe, the postglacial recolonization of northern Europe was re-evaluated. It is argued that the available data do not support the contribution of two major glacial refugia (southwest Atlantic and Ponto-Caspian Basin) to this postglacial recolonization, as proposed in a recently published model. The unique genetic architecture of Portuguese brown trout within the Atlantic-basin clade of this species represents a highly valuable genetic resource that should be protected from introgression with nonendemic strains of hatchery fish.     

Mitochondrial DNA variation in North American populations of Daphnia obtusa: continentalism or cryptic endemism?

The morphological stasis of many freshwater crustaceans has resulted in the prior delineation of cosmopolitan species and has been explained by their capacity for long-distance dispersal. This study examines the phylogeography of Daphnia obtusa, a cladoceran thought to be widespread in North America. However, sequence variation of the mitochondrial cytochrome c oxidase subunit I gene indicates that this taxon is composed of two morphologically cryptic species, designated D. obtusa NA1 and NA2. NA2 is restricted to the east, whereas NA1 is broadly distributed across the United States, and is subdivided into four phylogroups that show weak genetic differentiation over broad geographical areas, which likely reflects recent long-distance dispersal. The current distributions of the four phylogroups in NA1 can be explained by recent range expansion from different refugia following the last Pleistocene glacial advance. Interestingly, the mitochondrial phylogroups identified in this study do not correspond to lineages detected in a previous allozyme analysis. However, the latter groups are associated with a habitat shift suggesting that natural selection may have played a role in their divergence. The results of this and previous studies illustrate the complicated biogeographical history of freshwater cladocerans.     

Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long-distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration-drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these species, Brachionus manjavacas, in the Iberian Peninsula, where it often co-occurs with the morphologically similar species B. plicatilis sensu stricto. We obtained sequences from 233 individuals from diapausing eggs and clonal cultures from 16 lakes in the Iberian Peninsula, and a Tunisian lake. Two strongly supported deep mitochondrial DNA clades were found (A and B). Phylogenetic and nested clade analysis showed that clade A has a strong phylogeographical structure, with a strong similarity of phylogeographical patterns between B. manjavacas clade A and B. plicatilis s.s. These include (i) signatures of allopatric fragmentation between central and southern populations, and (ii) range expansions in the Iberian Peninsula, both likely to have occurred during the Pleistocene. We find evidence for a glacial refugium in the Guadiana basin. Clades A and B co-occurred in several of these lakes because of range expansion and secondary contact between both clades. The co-occurrence between B. plicatilis s.s. and B. manjavacas is not recent, and both species might have experienced similar environmental challenges during the Pleistocene. The strong correlation of genetic and geographical distance found suggests that historical events can lead to such correlation, mirroring the effects of 'isolation by distance' in equilibrium populations.