DNA footprints of European hedgehogs, Erinaceus europaeus and E. concolor: Pleistocene refugia, postglacial expansion and colonization routes

European hedgehogs, Erinaceus europaeus and E. concolor, are among the many European plant and animal taxa that have been subjected to cyclical restriction to glacial refugia and interglacial expansion. An analysis of 95 mitotypes, comprising partial cytochrome b and control region sequences, shows deep divergence between the two hedgehog species. Three europaeus and two concolor clades are clearly identified and are consistent with previously identified refugia for Europe: the Iberian peninsula, Italy, and the Balkans. The degree of mitochondrial divergence among these clades suggests pre-Pleistocene separation of the refugial populations. In contrast, analysis of two nuclear introns clearly separates the two concolor clades, as in the mitochondrial data, but cannot discriminate the three europaeus clades. This discrepancy between nuclear and mitochondrial data is attributed to historical differences in the refugial population size of europaeus and concolor. The geographical distribution of mitotypes is analysed using nested clade analysis. This method, by including unobserved ('missing') mitotypes, can identify mitotype groupings that remain undetected in conventional analyses. However, the application of nested clade analysis to the study of refugial populations may be hampered by such factors as the loss of haplotypes from the refugial areas by repeated contractions of the population and the recent time scale of colonization relative to mutation rate.     

Genome‐wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice‐free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross‐species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south‐central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.     

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.     

Mitochondrial DNA haplotypes indicate two postglacial re‐colonization routes of the spruce bark beetle Ips typographus through northern Europe to Scandinavia

Species in northern Europe re‐colonized the region after the last glacial maximum via several routes, which could have lingering signatures in current intraspecific trait variation. The spruce bark beetle, Ips typographus, occurs across Europe, and biological differences have been found between southern and northern Scandinavian populations. However, the postglacial history of I. typographus in Scandinavia has not been previously studied at a fine geographical scale. Therefore, we collected specimens across northern Europe and analysed the genetic variation in a quite large mitochondrial fragment (698 bp). A high genetic diversity was found in some of the most northern populations, in the Baltic States, Gotland and central Europe. Detected genetic and phylogeographic structures suggest that I. typographus re‐colonized Scandinavia via two pathways, one from the northeast and one from the south. These findings are consistent with the re‐colonization history of its host plant, Picea abies. However, we observed low haplotype and nucleotide diversity in southern Scandinavian populations of I. typographus, indicating that (unlike P. abies) it did not disperse across the Baltic Sea in multiple events. Further, the divergence among Scandinavian populations was shallow, conflicting with a scenario where I. typographus expanded concurrently with its host plant from a ‘cryptic refugium’ in the northwest.     

The Balkans and the colonization of Europe: the post‐glacial range expansion of the wild boar,Sus scrofa

Aim We focus on the biogeographical role of the Balkan Peninsula as a glacial refugium and source of northward post‐glacial dispersal for many European taxa. Specifically, we analysed the genetic structure and variation of wild boar (Sus scrofa) samples primarily from Greece, a region that has repeatedly served as a glacial refugium within the Balkan Peninsula. Location Continental Greece, the Aegean island of Samos and Bulgaria. Methods We analysed wild boar samples from 18 localities. Samples from common domestic breeds were also examined to take into account interactions between wild and domesticated animals. Phylogenetic analyses were carried out on a 637‐bp fragment of the mitochondrial DNA control region in 200 wild boar and 27 domestic pigs. The sequences were also compared with 791 Eurasian wild boar and domestic pig D‐loop sequences obtained from GenBank. Results Ninety‐four haplotypes were identified in the European wild boar data set, of which 68 were found in the Balkan samples and assigned to two previously described clades: the E1 European and Near Eastern clades. All of the continental samples clustered in the E1 clade and the samples from Samos fell into the Near Eastern clade, consistent with the island’s proximity to Asia Minor. Intriguingly, 62 novel haplotypes were identified and are found exclusively in the Balkans. Only six haplotypes were shared between wild boar and domestic pigs. Main conclusions Our data reveal numerous novel and geographically restricted haplotypes in wild boar populations, suggesting the presence of separate refugia in the Balkans. Our analyses support the hypothesis of a post‐glacial wild boar expansion consistent with the leading edge model, north and west from modern day Greece, and suggest little maternal introgression of Near Eastern and domestic haplotypes into wild Balkan populations.     

Infestation of urban populations of the Northern white‐breasted hedgehog,Erinaceus roumanicus,by Ixodes spp. ticks in Poland

Infestation by the nest‐dwelling Ixodes hexagonus Leach and the exophilic Ixodes ricinus (Linnaeus) (Ixodida: Ixodidae) on the Northern white‐breasted hedgehog, Erinaceus roumanicus (Erinaceomorpha: Erinaceidae), was investigated during a 4‐year study in residential areas of the city of Poznań, west‐central Poland. Of 341 hedgehogs, 303 (88.9%) hosted 10 061 Ixodes spp. ticks encompassing all parasitic life stages (larvae, nymphs, females). Ixodes hexagonus accounted for 73% and I. ricinus for 27% of the collected ticks. Male hedgehogs carried significantly higher tick burdens than females. Analyses of seasonal prevalence and abundance of I. hexagonus revealed relatively stable levels of infestation of all parasitic stages, with a modest summer peak in tick abundance noted only on male hosts. By contrast, I. ricinus females and nymphs peaked in spring and declined steadily thereafter in summer and autumn, whereas the less abundant larvae peaked in summer. This is the first longterm study to evaluate the seasonal dynamics of both tick species on populations of wild hedgehogs inhabiting urban residential areas.     

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.     

A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer

Jack pine (Pinus banksiana Lamb.) is a broadly distributed North American conifer and its current range was covered by the Laurentian ice sheet during the last glacial maximum. To infer about the history and postglacial colonization of this boreal species, range-wide genetic variation was assessed using a new and highly variable minisatellite-like marker of the mitochondrial genome. Among the 543 trees analysed, 14 distinct haplotypes were detected, which corresponded to different repeat numbers of the 32-nucleotide minisatellite-like motif. Several haplotypes were rare with limited distribution, suggesting recent mutation events during the Holocene. At the population level, an average of 2.6 haplotypes and a mean haplotype diversity (H) of 0.328 were estimated. Population subdivision of genetic diversity was quite high with G(ST) and R(ST) values of 0.569 and 0.472, respectively. Spatial analyses identified three relatively homogeneous groups of populations presumably representative of genetically distinct glacial populations, one west and one east of the Appalachian Mountains in the United States and a third one presumably on the unglaciated northeastern coastal area in Canada. These results indicate the significant role of the northern part of the US Appalachian Mountains as a factor of vicariance during the ice age. A fourth distinct group of populations was observed in central Québec where the continental glacier retreated last. It included populations harbouring haplotypes present into the three previous groups, and it had higher level of haplotype diversity per population (H = 0.548) and lower population differentiation (G(ST) = 0.265), which indicates a zone of suture or secondary contact between the migration fronts of the three glacial populations. Introgression from Pinus contorta Dougl. var. latifolia Engelm. was apparent in one western population from Alberta. Altogether, these results indicate that the mitochondrial DNA variation of jack pine is geographically highly structured and it correlates well with large-scale patterns emerging from recent phylogeographical studies of other tree boreal species in North America.     

European common frog (Rana temporaria) recolonized Switzerland from multiple glacial refugia in northern Italy via trans‐ and circum‐Alpine routes

The high mountain ranges of Western Europe had a profound effect on the biotic recolonization of Europe from glacial refugia. The Alps present a particularly interesting case because they form an absolute barrier to dispersal for most taxa, obstructing recolonization from multiple refugia in northern Italy. Here, we investigate the effect of the European Alps on the phylogeographic history of the European common frog Rana temporaria. Based on partial cytochrome b and COXI sequences from Switzerland, we find two mitochondrial lineages roughly north and south of the Alpine ridge, with contact zones between them in eastern and western Switzerland. The northern haplogroup falls within the previously identified Western European haplogroup, while the southern haplogroup is unique to Switzerland. We find that the lineages diverged ~110 kya, at approximately the onset of the last glacial glaciation; this indicates that they are from different glacial refugia. Phylogenetic analyses suggest that the northern and southern haplogroups colonized Switzerland via trans‐ and circum‐Alpine routes from at least two separate refugia in northern Italy. Our results illustrate how a complex recolonization history of the central European Alps can arise from the semi‐permeable barrier created by high mountains.     

Refugia, differentiation and postglacial migration in arctic-alpine Eurasia, exemplified by the mountain avens (Dryas octopetala L.)

Many arctic-alpine organisms have vast present-day ranges across Eurasia, but their history of refugial isolation, differentiation and postglacial expansion is poorly understood. The mountain avens, Dryas octopetala sensu lato, is a long-lived, wind-dispersed, diploid shrub forming one of the most important components of Eurasian tundras and heaths in terms of biomass. We address differentiation and migration history of the species with emphasis on the western and northern Eurasian parts of its distribution area, also including some East Greenlandic and North American populations (partly referred to as the closely related D. integrifolia M. Vahl). We analysed 459 plants from 52 populations for 155 amplified fragment length polymorphisms (AFLP) markers. The Eurasian plants were separated into two main groups, probably reflecting isolation and expansion from two major glacial refugia, situated south and east of the North European ice sheets, respectively. Virtually all of northwestern Europe as well as East Greenland have been colonized by the Southern lineage, whereas northwest Russia, the Tatra Mountains and the arctic archipelago of Svalbard have been colonized by the Eastern lineage. The data indicate a contact zone between the two lineages in northern Scandinavia and possibly in the Tatra Mountains. The two single populations analysed from the Caucasus and Altai Mountains were most closely related to the Eastern lineage but were strongly divergent from the remaining eastern populations, suggesting survival in separate refugia at least during the last glaciation. The North American populations grouped with those from East Greenland, irrespective of their taxonomic affiliation, but this may be caused by independent hybridization with D. integrifolia and therefore not reflect the true relationship between populations from these areas.     

Polymorphic microsatellite DNA markers for the white‐breasted thrasher,Ramphocinclus brachyurus

We isolated and characterized six polymorphic microsatellite markers for the white‐breasted thrasher from genomic libraries enriched for (AC)_n, (GT)_n, (CAAA)_n, (TTTC)_n, (GAC)_n, (CT)_n and (TTTG)_n microsatellites. The number of alleles per locus ranged from two to seven. Observed heterozygosity (H_O) ranged from 0.30 to 0.85.     

Scattered late‐glacial and early Holocene tree populations as dispersal nuclei for forest development in north‐eastern European Russia

Aim Concepts about patterns and rates of post‐glacial tree population migration are changing as a result of the increasing amount of palaeobotanical information being provided by macroscopic plant remains. Here we combine macrofossil, pollen and stomata records from five sites in north‐eastern European Russia and summarize the results for the late‐glacial–early Holocene transition. The late‐glacial–early Holocene transition encompasses the first indications of trees (tree‐type Betula, Picea abies, Abies sibirica and Larix sibirica) and subsequent forest development. Considerable time‐lags between the first macrobotanical and/or stomata finds of spruce (Picea abies) and the establishment of a closed forest are reconsidered. Location Pechora basin, north‐eastern European Russia. Methods We used plant macrofossil, stomata, pollen and radiocarbon analyses to reconstruct late‐glacial and early Holocene tree establishment and forest development. The data were derived from lake sediment and peat archives. Results Palaeobotanical data reveal an early Holocene presence (11,500–10,000 cal. yr bp ) of arboreal taxa at all five sites. One site presently located in the northernmost taiga zone, shows the presence of spruce and reproducing tree birch during the late‐glacial. Given the current view of post‐glacial population dynamics and migration rates, it seems likely that the source area of these early tree populations in north‐eastern European Russia was not located in southern Europe but that these populations had local origins. Results thus support the emerging view that the first post‐glacial population expansions in non‐glaciated regions at high latitudes do not reflect migration from the south but were a result of an increase in the size and density of small persisting outlying tree populations. Main conclusions Results suggest that the area east of the margin of the Scandinavian ice sheet to the Ural Mountains had isolated patches of trees during the late‐glacial and early Holocene and that these small populations acted as initial nuclei for population expansion and forest development in the early Holocene.     

Post‐glacial colonization of eastern Europe from the Carpathian refugium: evidence from mitochondrial DNA of the common vole Microtus arvalis

There is now considerable evidence for the survival of temperate species within glacial refugia that were situated at relatively high latitudes, notably the Carpathian Basin and Dordogne region in Europe. However, the prevalence of fossil remains in such locations is rarely matched by molecular evidence for their contribution to subsequent geographical and demographic expansion of the species in question. One obstacle to this has been insufficient analysis of modern samples from the relevant areas, in particular the parts of eastern Europe that surround the Carpathian refugium. In the present study, we examine the patterns of variation in mitochondrial DNA of the common vole (Microtus arvalis), obtained from existing museum specimens and from newly‐collected samples obtained in this area. We show that common voles from one of six extant mitochondrial DNA lineages have colonized most of the species' range in eastern Europe. We contend that the post‐glacial dispersal of this lineage most likely originated from the Carpathian refugium, adding support to the argument that such northern refugia made an important contribution to existing genetic diversity in Europe. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●● , ●●–●●.     

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.     

Multiple Pleistocene refugia and post‐glacial colonization in the European chub (Squalius cephalus) revealed by combined use of nuclear and mitochondrial markers

Aim To analyse patterns of nuclear and mitochondrial genetic variation in the European chub, Squalius cephalus (Linnaeus, 1758), in order to understand the evolutionary history of this species and to test biogeographical hypotheses for the existence of co‐distributed European freshwater fish species. Location Rivers in Europe (Finland, Poland, Czech Republic, France, Bulgaria, Spain, Italy). Methods We genotyped 12 polymorphic microsatellite markers derived from 310 individuals collected from across the distribution of S. cephalus in Europe (including a total of 15 populations) and sequenced mitochondrial DNA (mtDNA) from a subset of 75 individuals. Sequences of mtDNA cytochrome b were analysed using both phylogenetic (median‐joining networks) and population genetic methods (tests for demographic history, mismatch distributions, Bayesian coalescent analysis). Geographical structure in microsatellite loci was examined using a distance method (F_ST), factorial correspondence analysis (FCA) and a Bayesian clustering method (structure ). Results The mtDNA network showed a clear split into four different haplogroup lineages: Western (separated into Atlantic and Danubian sublineages), Eastern, Aegean (occurring in two distinct sublineages in the Balkans and in Spain) and Adriatic. Our results indicate recent population expansion in the Eastern and Western Atlantic lineages and the admixture of two previously separate sublineages (Atlantic and Danubian) in the Western lineage. Bayesian structure analysis as well as FCA results roughly corresponded to the mtDNA‐based structure, separating the sampled individuals into almost non‐overlapping groups. Main conclusions Our results support hypotheses suggesting origins of extant lineages of freshwater fishes in multiple refugia and the subsequent post‐glacial colonization of Europe via different routes. We confirmed the previously proposed two‐step expansion scenario from the Danube refuge, the existence of a secondary (Atlantic) refuge during the last glaciation (probably in the Rhone River) and population expansion of this lineage. Conspicuous divergences among Mediterranean populations reflect their different origin, as well as their low contribution to the recent genetic pool of chub in central Europe.     

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.     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

Microsatellite variation and genetic structure of brook trout (Salvelinus fontinalis) populations in Labrador and neighboring Atlantic Canada: evidence for ongoing gene flow and dual routes of post-Wisconsinan colonization

In conservation genetics and management, it is important to understand the contribution of historical and contemporary processes to geographic patterns of genetic structure in order to characterize and preserve diversity. As part of a 10-year monitoring program by the Government of Newfoundland and Labrador, Canada, we measured the population genetic structure of the world's most northern native populations of brook trout (Salvelinus fontinalis) in Labrador to gather baseline data to facilitate monitoring of future impacts of the recently opened Trans-Labrador Highway. Six-locus microsatellite profiles were obtained from 1130 fish representing 32 populations from six local regions. Genetic diversity in brook trout populations in Labrador (average H(E)= 0.620) is within the spectrum of variability found in other brook trout across their northeastern range, with limited ongoing gene flow occurring between populations (average pairwise F(ST)= 0.139). Evidence for some contribution of historical processes shaping genetic structure was inferred from an isolation-by-distance analysis, while dual routes of post-Wisconsinan recolonization were indicated by STRUCTURE analysis: K= 2 was the most likely number of genetic groups, revealing a separation between northern and west-central Labrador from all remaining populations. Our results represent the first data from the nuclear genome of brook trout in Labrador and emphasize the usefulness of microsatellite data for revealing the extent to which genetic structure is shaped by both historical and contemporary processes.     

Anthropogenic changes to the landscape resulted in colonization of koalas in north‐east New South Wales,Australia

Significant changes in the distribution and persistence of species have been driven by Pleistocene cyclical climate changes and, more recently, by human modification of the environment. In eastern Australia, Pleistocene cyclical patterns in temperature and aridity led to the expansion and retraction of rainforest and likely affected the distribution of the koala (Phascolarctos cinereus, family Phascolarctidae), a species preferring dry or open woodland. More recently, anthropogenic landscape modification has led to a large‐scale change in distribution of the koala following the destruction of approx. 75 000 ha of subtropical rainforest in north‐east New South Wales termed the ‘Big Scrub’. Sharing of the control region haplotypes to the north and south of this region indicate historical connectivity of coastal koala populations. However, the majority (110/115) of sampled koalas from this region shared a single mitochondrial control region haplotype, suggesting that koalas did not persist in multiple refugial pockets within a heterogenous rainforest but expanded into the region following deforestation. Bayesian cluster analysis of microsatellite data consistently identified two clusters of koalas. One cluster, in the north of the area, had high microsatellite diversity (10 alleles per locus, He = 0.79) and clustered with koalas further to the north, thus suggesting a southerly expansion into the cleared area. To the south was a cluster with significantly lower diversity (six alleles per locus, He = 0.59, P < 0.001). It is possible there has been restricted or filtered movement of koalas between these clusters, which coincides with a cleared river valley and associated roads or immigration from populations both to the north and to the south. This study gives an insight into the timescale of changes in species distribution following rapid alterations to suitable habitat.