Geographically congruent large‐scale patterns of plastid haplotype variation in the European herbs Silene dioica and S. latifolia (Caryophyllaceae)

The closely related dioecious herbs Silene latifolia and Silene dioica are widespread and predominantly sympatric in Europe. The species are interfertile, but morphologically and ecologically distinct. A study of large‐scale patterns of plastid DNA (polymerase chain reaction–restriction fragment length polymorphism) haplotypes in a sample of 198 populations from most of the European ranges of both species revealed extensive interspecific haplotype sharing. Four of the 28 detected haplotypes were frequent (found in > 40 populations) and widespread. Three of these frequent haplotypes occurred in both species and the geographic distribution of each haplotype was broadly congruent in both species. Each of these three, shared and widespread haplotypes is likely to have colonized central and/or northern Europe after the last glaciation from one or more of refugial areas in southern Europe. Interspecific hybridization and plastid introgression within refugial regions and/or during the early stages of postglacial expansion is the most plausible explanation for the broadly similar distribution patterns of the shared, frequent chloroplast haplotypes in the two species. The fourth frequent, widespread haplotype was absent from S. latifolia and almost entirely restricted to Nordic S. dioica. It is most likely that this haplotype spread into the Nordic countries from a central or northern European source or from a refugial area in Russia. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161 , 153–170.     

Glacial refugia of mammals in Europe: evidence from fossil records

• 1 Glacial refugia were core areas for the survival of temperate species during unfavourable environmental conditions and were the sources of postglacial recolonizations. Unfortunately, the locations of glacial refugia of animals and plants are usually described by models, without reference to facts about real geographical ranges at that time.
• 2 Careful consideration of the faunal assemblages of archaeological sites from the Younger Palaeolithic, which are precisely dated to the Last Glacial Maximum (LGM), gives indications about the distribution of species during the LGM (23 000–16 000 bp ) and provides evidence for the locations of glacial refugia for mammalian species in Europe.
• 3 In Europe, 47 LGM sites, dating from 23 000 to 16 000 bp and containing typical temperate mammal species, have been described. The geographical range of these archaeological sites clearly shows a distribution which differs from the hypothesized traditional refuge areas of the temperate fauna. A considerable number of sites situated in the Dordogne in south‐western France and the Carpathian region contain records of red deer Cervus elaphus, roe deer Capreolus capreolus, wild boar Sus scrofa and red fox Vulpes vulpes.
• 4 The faunal composition of the majority of the evaluated Palaeolithic sites in the southern European peninsulas (with the exception of Greece), as well as France and the Carpathian region, indicates the co‐occurrence of these temperate species with cold‐adapted faunal elements such as mammoth Mammuthus primigenius and/or reindeer Rangifer tarandus.
• 5 The survival of species in Central European refugia would have significant consequences for phylogeography and would be revealed by the dominant distribution of haplotypes, originating from this region. A Carpathian refuge could also be the reason for the very early records of small mammals or mustelids from the Late‐Glacial or Interstadials before the LGM in regions like southern Germany.

     

Late Pleistocene and Holocene development of the felid fauna (Felidae) of Europe: a review

In the fossil deposits of the Late Pleistocene ( c . 115 000–11 500 years ago), five felid species are recorded in Europe: the wildcat Felis silvestris , Eurasian lynx Lynx lynx , Iberian lynx Lynx pardinus , leopard Panthera pardus and cave lion Panthera leo spelaea . In the Holocene, Europe was colonized by F. silvestris , L. lynx and L. pardinus as well as the lion Panthera leo . The status of P. pardus in post-glacial Europe is unknown. So far, only sparse records indicate that P. pardus survived into the early Holocene. During the Late Glacial, both L. lynx and L. pardinus occurred on the Iberian Peninsula. However, from the Holocene, only the Iberian lynx is recorded in this region. There are subfossil records that indicate that L. pardinus also occurred in central and western France until c . 3000 years ago. Surprisingly, with reservations on the determination of the bones (by J. Altuna), both lions and cave lions seem to be recorded in the Iberian Peninsula in the Late Glacial. There are published records of the lion P. leo in the northern Iberian Peninsula from the early Holocene. However, its presence in Europe on the basis of subfossil records was proven initially from the Atlantic period. In Ponto-Mediterranean regions of Europe, the lion is recorded from the Atlantic to the younger sub-Atlantic.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

Genetic admixture of burbot (Teleostei: Lota lota) in Lake Constance from two European glacial refugia

The burbot, Lota lota, is the only freshwater species of the codfish family and has a Holarctic distribution. Pleistocene glaciations caused significant geographical differentiation in the past, but its life history characterized by winter spawning migrations over large distances is likely to homogenize populations by contemporary gene flow. We investigated the population genetic structure of 541 burbots from Lake Constance and adjacent Rhine and Danube tributaries in Europe using the entire mitochondrial DNA (mtDNA) control region and 11 microsatellites. Microsatellites revealed considerable population divergence (F(ST) = 0.26) and evidenced recent bottlenecks in two Central European rivers. In accordance to previous evidence two main phylogeographic lineages (Atlantic and Danubian) were found co-occurring at similar frequencies in Lake Constance, where they currently undergo random mating as indicated by microsatellites. The Danubian lineage contributed only a small proportion to the lake's mtDNA diversity, and probably expanded within the lake shortly after its formation approximately 10,000-15,000 BP. The larger Atlantic haplotype diversity suggested a population expansion older than the lake itself. Levels of admixture at microsatellite loci were less obvious due to their high variability, and coalescence methods were used to estimate past admixture proportions. Our results reinforce a model of a two-step colonization of Europe by burbot from an ancestral Danubian refuge, and confirm the persistence of a secondary Atlantic refuge, as proposed to exist for other freshwater fish. We conclude that the present-day burbot population in Lake Constance bears the genetic signature of both contemporary gene flow and historical separation events.     

Multiple ice‐age refugia in Pacific cod,Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (F_ST = 0.028, r² = 0.33) and mtDNA (F_ST = 0.027, r² = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.     

Prioritizing refugia for freshwater biodiversity conservation in highly seasonal ecosystems

Aim

Refugia play a key ecological role for the persistence of biodiversity in areas subject to natural or human disturbance. Temporary freshwater ecosystems regularly experience dry periods, which constrain the availability of suitable habitats. Current and future threats (e.g. water extraction and climate change) can exacerbate the negative effects of drying conditions. This could compromise the persistence of a large proportion of global freshwater biodiversity, so the identification and protection of refugia seems an urgent task.

Location

Northern Australia.

Methods

We demonstrate a new approach to identify and prioritize the selection of refugia and apply it to the conservation of freshwater fish biodiversity. We identified refugia using estimates of water residency time derived from satellite imagery and used a systematic approach to prioritize areas that provide all the fish species inhabiting the catchment with access to a minimum number of refugia while maximizing the length of stream potentially accessible for recolonization after the dry period. These priority refugia were locked into a broader systematic conservation plan with area‐based targets and direct connectivity. We accounted for current threats during the prioritization process to ensure degraded areas were avoided, thus maximizing the ecological role of priority refugia.

Results

Priority refugia were located in lowland reaches, where the incidence of threats was less prominent in our study area and headwaters in good condition. An additional set of 106 planning units (6500 km²) were required to represent 10% of each species' distribution in the broad conservation plan. A hierarchical management zoning scheme was applied to demonstrate how these key ecological features could be effectively protected from the major threats caused by aquatic invasive species and grazing.

Main conclusions

This new approach to identifying priority refugia and incorporating them into the conservation planning process in a systematic way would help enhance the resilience of freshwater biodiversity in temporary systems.

     

Competitive exclusion: phylogeography’s ‘elephant in the room’?

Phylogeographic and evolutionary research programmes have successfully elucidated compelling genetic signatures of earth history. Particularly influential achievements include the demonstration of postglacial recolonization patterns for high-latitude taxa and phylogenetic demonstration of the 'progression rule' along oceanic island chains such as Hawaii. While both of these major biogeographic patterns clearly rely on rapid dispersal over long distances, their phylogeographic detection also apparently relies on the competitive exclusion of secondary dispersers. Such exclusion could occur either between or within species and might reflect fitness differences between lineages or, alternatively, neutral demographic processes (e.g. 'high-density blocking'). Regardless, such spatial genetic patterns would be rapidly eroded were it not for the failure of subsequent dispersers to contribute genetically to newly colonized populations. In addition to its role in revealing colonization patterns, competitive exclusion may also explain the maintenance of historic phylogeographic disjunctions long after the original physical barriers to dispersal have ceased to exist. Additionally, some of the most persuasive evidence of competitive exclusion comes from studies of anthropogenic extinction, where surviving lineages have subsequently expanded their ranges, apparently benefitting from the demise of their prehistoric sisters. Broadly, these biogeographic paradigms are united by the 'disconnect' between dispersal and colonization success, the latter being heavily influenced by inter- and intraspecific competition. Despite its apparent importance, such exclusion (especially within species) has received virtually no attention in the phylogeographic literature. Future studies should aim to test directly for the role of competitive exclusion in constraining the biogeography of highly dispersive taxa.     

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

The Alpine lake whitefish (Coregonus lavaretus) species complex is a classic example of a recent radiation, associated with colonization of the Alpine lakes following the glacial retreat (less than 15 kyr BP). They have formed a unique array of endemic lake flocks, each with one to six described sympatric species differing in morphology, diet and reproductive ecology. Here, we present a genomic investigation of the relationships between and within the lake flocks. Comparing the signal between over 1000 AFLP loci and mitochondrial control region sequence data, we use phylogenetic tree-based and population genetic methods to reconstruct the phylogenetic history of the group and to delineate the principal centres of genetic diversity within the radiation. We find significant cytonuclear discordance showing that the genomically monophyletic Alpine whitefish clade arose from a hybrid swarm of at least two glacial refugial lineages. Within this radiation, we find seven extant genetic clusters centred on seven lake systems. Most interestingly, we find evidence of sympatric speciation within and parallel evolution of equivalent phenotypes among these lake systems. However, we also find the genetic signature of human-mediated gene flow and diversity loss within many lakes, highlighting the fragility of recent radiations.     

A re-appraisal of nunatak survival in arctic-alpine phylogeography

A long standing and at times fervid debate in biogeography revolves around the question whether arctic and high alpine organisms survived Pleistocene ice ages on small island-like areas protruding above the ice-sheet, socalled nunataks, or whether they did so in peripheral nonglaciated refugial areas. A common picture emerging from a plethora of molecular phylogeographic studies in the last decade is that both in the Arctic and in temperate mountain ranges such as the European Alps nunatak survival needs to be only rarely invoked to explain observed genetic patterns (for a rare example see Stehlik et al. 2002). As two studies in this issue show, depreciation of the nunatak hypothesis is, however, not warranted. In this issue of Molecular Ecology Westergaard et al. (2011) investigate genetic patterns of two arctic-alpine plant species distributed on both sides of the Atlantic exclusively in areas that were mostly covered by ice-sheets during Pleistocene glacial advances. In both species, amplified fragment length polymorphism (AFLP) data identified divergent and partly genetically diverse groups east and west of the Atlantic. This suggests, for the first time in Arctic plants, in situ survival on nunataks. In an entirely different geographic setting and on a different geographic scale, Lohse et al. (2011, this issue) study the colonization of high alpine areas in the Orobian Alps, situated within and adjacent to a prominent peripheral refugial area (massif de refuge) in the Southern Alps of northern Italy, by dispersal-limited carabid ground beetles. Using explicit hypothesis testing and inference of ancestral locations in a Bayesian framework, stepwise colonization from two separate southern refugia is found to shape the genetic pattern of these beetles, but at the northern edge, populations survived at least parts of the last glaciation in situ on nunataks.