The recolonization of Europe by brown bears Ursus arctos Linnaeus, 1758 after the Last Glacial Maximum

1. At the end of the Last Glacial Maximum brown bears Ursus arctos recolonized the glacial landscape of Central and Northern Europe faster than all other carnivorous mammal species of the Holocene fauna. Ursus arctos was recorded in Northern Europe from the beginning of the Late-Glacial. The recolonization of northern Central Europe may have taken place directly after the maximum glaciation. The distribution of the brown bear was restricted to glacial refugia only during the Last Glacial Maximum, for probably no more than 10 000 years. 2. Genetic analyses have suggested three glacial refugia for the brown bear: the Iberian Peninsula, the Italian Peninsula and the Balkans. Subfossil records of Ursus arctos from north-western Moldova as well as reconstructed environmental conditions during the Last Glacial Maximum in this area suggest to us a fourth glacial refuge for the brown bear. Because of its connection to the Carpathians, we designate this as the ‘Carpathian refuge’. 3. Due to the low genetic distance between brown bears of northern Norway, Finland, Estonia, north-eastern Russia and the northern Carpathians (the so-called eastern lineage), the Carpathians were considered the geographical origin of the recolonization of these regions. During the recolonization of northern Europe the brown bear probably reached these areas rapidly from the putative Carpathian refuge.     

Late Pleistocene divergence and postglacial expansion in the Brazilian Atlantic Forest: multilocus phylogeography of Rhopias gularis (Aves: Passeriformes)

In the last decade, phylogeographic studies have revealed a complex evolutionary history of the Brazilian Atlantic Forest (AF) biota. Here, we investigated the evolutionary history of Rhopias gularis, an endemic bird of the AF, based on sequences of two mitochondrial genes and three nuclear introns from 64 specimens from 15 localities. We addressed three main questions: (1) Does the genetic diversity of R. gularis exhibit a distribution pattern congruent with the refuge hypothesis postulated for the AF? (2) Is the population genetic structure of R. gularis congruent with those observed in other AF species? (3) What were the possible historical events responsible for the population structure of this species? Our mtDNA data revealed two phylogroups: (1) phylogroup central‐south, with samples from the central and southern parts of the range; (2) and phylogroup north, which included individuals from southern Bahia. Nevertheless, nuclear loci did not reveal any evidence of population structure. Bottleneck tests indicated that the central‐south lineage experienced demographic expansion, starting around 20 kya, which coincides with the end of the last glacial maximum. However, there was no evidence of population growth in phylogroup north. Isolation with migration analysis indicated that these phylogroups split c.a. 304 kya, with limited gene flow among them. Palaeodistribution models indicated that R. gularis had a reduced distribution in the south and central AF during the last glacial maximum. Our results support a diversification scenario that is in accordance with proposed Pleistocene refugia. The phylogeographic results from our study exhibited spatial and temporal concordances and discordances with previous studies of organisms from the AF. Differences in habitat requirements of these species could be behind this complex scenario. Future studies correlating variables of the niche of these species with the observed phylogeographic patterns may help understand why there are congruent and incongruent results.     

When east met west: the sub-fossil footprints of the west European hedgehog and the northern white-breasted hedgehog during the Late Quaternary in Europe

The distinct distribution of the west European hedgehog Erinaceus europaeus and the northern white-breasted hedgehog Erinaceus roumanicus and their separate refugial origins after the Pleistocene is a well-known example in the zoogeography of the Holarctic. Among the Late Quaternary faunal assemblages, the west European hedgehog is recorded at 269 sites whereas the northern white-breasted hedgehog is recorded only at 52 sites in Europe. The distribution patterns of the temporal and spatial Glacial records of the west European hedgehog show a general trend: a strong restriction to glacial refugia (the Iberian and Italian Peninsulas) during the Weichselian Glacial until the end of the Last Glacial Maximum, and a colonization of southern France during the early Late Glacial between 14 000 and 125 00 ¹⁴C years BP (15 000–12 800 cal. BC). Whereas the British Isles could have already been colonised by the end of the Pre-Boreal, in the rest of Central Europe E. europaeus was clearly distributed there in the Boreal for the first time. The west European hedgehog is an absolute Holocene faunal element in Central Europe. It appears in most parts of Central Europe during the Early Holocene, when the west European hedgehog met its eastern relative, which probably was similarly sensitive. After meeting each other, the distribution limit of both Erinaceus species in Central Europe seems to have been relatively constant in its geographic extent. Because of the clear climatic correlation, E. europaeus should be considered as an indicator species for temperate climatic conditions of the Holocene fauna. This should be considered during the reconstruction of climatic conditions with the help of the analysis of quaternary faunal material.     

Late-Pleistocene and early Holocene history of the canid fauna of Europe (Canidae)

In the sub-fossil assemblages of Europe the red fox is clearly the most frequent carnivorous mammalian species with a total of 1553 records. In depositions from the Weichselian Glacial the red fox Vulpes vulpes is, a typical representative of the Holocene fauna, already recorded in 100 assemblages. The Iberian peninsula, Italian peninsula and Balkans were theorised as glacial refugia. Well-founded facts give reason to believe that V. vulpes was also distributed in the Carpathian refuge. Later on, the Crimean peninsula would also appear to be a possible glacial refuge of the red fox.In the last warmer complex of interstadials during the Pleni-Glacial (Hengelo-Denekamp, 38,000–25,000 BC) the red fox was distributed in central Europe. Its distribution during this epoch extended at least in part to southern England. The earliest well-dated records of V. vulpes in central Europe after the Maximum Glaciation lie between 14,000 and 13,500 BC. Already during the early Late-Glacial (13,500 BC) the red fox appeared in typical glacial faunal communities. A separation to glacial refugia was only possible for 10,000 years.During the last warmer Pleni-Glacial complex of interstadials (38,000–25,000 BC) in central Europe a sympatric distribution of the arctic fox (Alopex lagopus) and the red fox probably existed. During the Last Glacial Maximum (22,000–18,000 BC) the arctic fox was exclusively distributed in central Europe, outside of the refuges. The combined distribution of A. lagopus and V. vulpes during the Late-Glacial (15,000–9500 BC) in central Europe, with the probable exception of the Allerød, is precisely documented by sub-fossil assemblages.In the Pleni-Glacial the wolf Canis lupus was distributed in geographic regions that served as glacial refugia of more warm-climate adapted species. Concerning the wolf no drastic decrease of the distribution is assumed. The Holocene presence of C. lupus is probably not caused by recolonisation.

Zusammenfassung

Die Entwicklung der Canidenfauna Europas im Spätpleistozän und frühen HolozänIn den subfossilen Ablagerungen ist Vulpes vulpes in Europa mit 1553 Nachweisen das mit Abstand am häufigsten nachgewiesene Raubsäugetier. Allein in den Ablagerungen des Weichselglazials konnte der Rotfuchs bereits in 100 Fundkomplexen nachgewiesen werden. Als Glazialrefugium des Rotfuchses wird die Iberische Halbinsel sicher identifiziert. Eine Verbreitung der Art während des Kältemaximums wird außerdem auf der Apenninen-Halbinsel sowie der Balkan- Halbinsel vermutet. Außerdem liegen fundierte Fakten für die Annahme vor, dass V. vulpes im Karpatenrefugium verbreitet war. Auf der Halbinsel Krim scheint ein Glazialrefugium für des Fuchses möglich.Während des letzten wärmeren Interstadial-Komplexes im Hochglazial (Hengelo-Denekamp, ca. 38.000–25.000 v. Chr.) war Mitteleuropa vom Rotfuchs besiedelt. Die nördliche Arealgrenze der Art war innerhalb dieses Klimaabschnitts mindestens zeitweise bis nach Südengland ausgedehnt. Die frühesten, zeitlich relativ gut abgesicherten Nachweise von V. vulpes nach der Weichsel-Maximalvereisung in Mitteleuropa liegen etwa zwischen 14.000–13.500 v. Chr. Schon im frühen Spätglazial (ca. 13.500 v. Chr.) kam der Rotfuchs im nördlichen Mitteleuropa in typischen glazialen Faunengemeinschaften vor. Eine Disjunktion des Areals während der letzten Vereisung kann für höchstens 10.000 Jahre stattgefunden haben. Es wird angenommen, dass während des Hengelo-Deenekamp Interstadials ein sympatrisches Vorkommen von Eisfuchs Alopex lagopus und Rotfuchs V. vulpes in Mitteleuropa existierte. Nur zur Zeit des absoluten Kältemaximums (ca. 22.000–18.000 v. Chr.) war außerhalb der Refugialgebiete in Mitteleuropa ausschließlich A. lagopus verbreitet. Das gemeinsame Vorkommen (von A. lagopus und V. vulpes) während des gesamten Spätglazials in Mitteleuropa, wahrscheinlich mit Ausnahme des Allerød-Interstadials, ist präzise belegt.Während des Hochglazials war Canis lupus auch in geografischen Regionen verbreitet, die für an wärmeres Klima gebundene Tierarten den Charakter von Glazialrefugien hatten. Beim Wolf C. lupus kann keine extreme Arealverringerung während der Weichseleiszeit angenommen werden. Das holozäne Vorkommen von C. lupus in Mitteleuropa dürfte daher nicht generell auf eine Rekolonisation zurückzuführen sein.     

Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida

Mechanisms of survival during the Pleistocene glaciation periods have been studied for more than a century. Until now, molecular studies that confirmed animal survival on Alpine nunataks, that is, ice‐free summits surrounded by glaciers, were restricted to peripheral areas. Here, we search for molecular signatures of inner‐Alpine survival of the narrow endemic and putatively parthenogenetic Alpine jumping bristletail Machilis pallida combining mitochondrial and AFLP data from its three known populations. The mitochondrial data indicate survival on both peripheral and central nunataks, the latter suggesting that refugia in the centre of the Alpine main ridge were more widespread than previously recognized. Incongruences between mitochondrial and AFLP patterns suggest a complex evolutionary history of the species and may be explained via parallel fixation of parthenogenesis of different origins during the last glacial maximum. We suggest that the inferred parthenogenesis may have been essential for central nunatak survival, but may pose a serious threat for M. pallida in consideration of the present climatic changes.     

Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears

Models for the development of species distribution in Europe typically invoke restriction in three temperate Mediterranean refugia during glaciations, from where recolonization of central and northern Europe occurred. The brown bear, Ursus arctos, is one of the taxa from which this model is derived. Sequence data generated from brown bear fossils show a complex phylogeographical history for western European populations. Long-term isolation in separate refugia is not required to explain our data when considering the palaeontological distribution of brown bears. We propose continuous gene flow across southern Europe, from which brown bear populations expanded after the last glaciation.     

Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100

Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.     

Sexual dimorphism and cultural evolution in the Late Pleistocene and Holocene of Europe

Dental, cranial and body size data are reviewed for European Upper Paleolithic, Mesolithic and Neolithic males and females. Over these three periods there is a substantial decrease in the level of sexual dimorphism. From separate analysis of trends occurring between males and females, it is shown that the major cause for this decrease in sexual dimorphism is gracilization of the males between the Upper Paleolithic and Mesolithic. Reduction in males is related to shifting technological patterns associated with hunting and changes in the types of animals hunted. Further reduction in sexual dimorphism between the Mesolithic and Neolithic and from the Neolithic to modern European populations is shown to be more closely tied to changes occurring among females. Analysis of changing patterns of sexual dimorphism in Late Pleistocene and Holocene populations of Europe suggests an interrelationship between cultural and biological evolution.     

Deer fauna from Pleistocene and Holocene localities of Ecuador (South America)

Late Pleistocene and Holocene deer remains from Ecuadorian sites have been analysed. Most of the material belongs to Odocoileus virginianus ustus, which is documented in latest Pleistocene deposits, in the Interandean Depression. Coastal sediments referred to the Holocene bear remains of Odocoileus salinae. O. v. ustus and O. salinae differ in size and in the morphology of the antlers and of the dentitions. In the present work, O. salinae is postulated to have derived from O. v. ustus during an arid climatic phase in the latest Pleistocene.     

Phylogeography and niche modelling of the relict plant Amborella trichopoda (Amborellaceae) reveal multiple Pleistocene refugia in New Caledonia

Amborella trichopoda Baill. (Amborellaceae, Amborellales), the sole living member of the sister group to all other extant angiosperms, is endemic to New Caledonia. We addressed the intraspecific phylogeography of Amborella by investigating whether its present population genetic structure could be related to its current and past habitats. We found moderate range‐wide genetic diversity based on nuclear microsatellite data and detected four well‐differentiated, geographically distinct genetic groups using Bayesian clustering analyses. We modelled the ecological niche of Amborella based on the current climatic and environmental conditions. The predictive ability of the model was very good throughout the Central East mainland zone, but Amborella was predicted in the northern part of the island where this plant has not been reported. Furthermore, no significant barrier was detected based on habitat suitability that could explain the genetic differentiation across the area. Conversely, we found that the main genetic clusters could be related to the distribution of the suitable habitat at the last glacial maximum (LGM, c. 21 000 years BP), when Amborella experienced a dramatic 96.5% reduction in suitable area. At least two lineages survived in distinct putative refugia located in the Massif des Lèvres and in the vicinity of Mount Aoupinié. Our findings finally confirmed the importance of LGM rainforest refugia in shaping the current intra‐ and interspecific diversity in New Caledonian plants and revealed the possibility of an as yet unreported refugium. The combination of niche modelling and population genetics thereby offered novel insight into the biogeographical history of an emblematic taxon.     

Phylogeography of red deer (Cervus elaphus) in Europe

Aim To investigate the phylogeographical patterns of red deer (Cervus elaphus) in Europe, and to disentangle the influence of ancient (e.g. Pleistocene ice ages) from more recent processes (e.g. human translocations). Location Europe. Methods In this study we provide by far the most extensive analysis of genetic structure in European red deer, based on analyses of variation at two mitochondrial markers (cyt b and D‐loop) in a large number of individuals from 39 locations. Relationships of mitochondrial DNA haplotypes were determined using minimum spanning networks and phylogenetic analyses. Population structure was examined by analyses of molecular variance. Historical processes shaping the present patterns were inferred from nested clade analysis and nucleotide diversity statistics. Results Within Europe, we detected three deeply divergent mitochondrial DNA lineages. The three lineages displayed a phylogeographical pattern dividing individuals into western European, eastern European and Mediterranean (Sardinia, Spain and Africa) groups, suggesting contraction into three separate refugia during the last glaciation. Few haplotypes were shared among these three groups, a finding also confirmed by F_ST values. Calculations of divergence times suggest that the groups probably split during the Pleistocene. Main conclusions The observed pattern is interpreted to result from isolation in different refugia during the last glaciation. The western and eastern European lineages could be linked to an Iberian and Balkan refugium, respectively. The third lineage might originate from a Sardinian or African refugium. We link local phylogeographical patterns observed in Europe to the post‐glacial recolonization process, shaped by the geographical localization of refugia and barriers to gene flow. Regardless of the importance of red deer as a game species and the tradition of translocating red deer in Europe, we detected few individuals that did not match the trichotomous pattern, suggesting that translocations have occurred mainly at smaller spatial scales.     

The Simulium vernum group (Diptera: Simuliidae) in Europe: multiple character sets for assessing species status

The value of using characters from multiple sources – chromosomes, ecology, gene sequences, and morphology – to evaluate the species status of closely related black flies is demonstrated for three European members of the Simulium vernum group: Simulium crenobium (Knoz, 1961), Simulium juxtacrenobium Bass & Brockhouse, 1990, and Simulium vernum s.s. Macquart, 1826. Simulium juxtacrenobium is a chromosomally, molecularly, and morphologically distinct species that diverged from S. crenobium and S. vernum s.s. about 2 Mya. It is specialized for intermittent streams, is univoltine, and is recorded for the first time from northern Europe, based on collections from Finland and Sweden, representing a range extension of about 1800 km. In contrast, S. crenobium, although confirmed as a distinct species, differs from S. vernum s.s. by only a few larval and chromosomal characters, and by a breeding habitat restricted to mountain spring brooks. Whereas all four character sets independently support the specific distinctness of S. juxtacrenobium and S. vernum s.s., multiple character sets are required to establish the specific validity of S. crenobium.     

The late Pleistocene/Holocene and recent Bosmina (Eubosmina) fauna (Crustacea: Cladocera) of the pre-alpine Starnberger See (FRG)

An analysis of the remains of Bosmina (Eubosmina) in a sedimentcore from the pre-alpine, mesotrophic Starnberger See showedthat the lake was inhabited by B. longispina since the OldestDryas. In the Subatlantic- -1900 years ago — the kesslerimorph of B. coregoni invaded the lake and both taxa have sinceco-existed. Although there was considerable morphological variation,B. longispina clearly differed from Circumbaltic populationsthrough most of the late Pleistocene and Holocene periods. Inthe recent Bosmina fauna of the lake two morphologically wellseparated taxa (B. longispina ruehei and a morph of B. coregoni)occur which differ clearly from the Bosmina remains found inthe core up to the uppermost sample from 7 cm sediment depth.B. coregoni f. kessleri appeared in the lake in a period whenit was supposedly still oligotrophic. The Bosmina successionobserved in the Starnberger See resembles the pattern foundin deep north German lakes.     

Late Quaternary biomes of Canada and the eastern United States

Pollen data have been used to construct biome maps for today, 6000 ¹⁴C yr bp and 18,000 ¹⁴C yr bp for Canada and the eastern United States. The inferred modern biome distributions agree well with independent reconstructions of North American vegetation prior to European settlement. Some discrepancies between the pollen data and the modern potential vegetation are caused by post‐settlement clearing of the landscape and the consequent increase of herbaceous types in the recent pollen record. Biome distributions at 6000 ¹⁴C yr bp reflected the warmer and drier conditions then prevalent in the continental interior, but the overall position of biomes was similar to that of today. The boreal treeline in North America was not significantly north of its present position, in contrast to the 100–200 km shift reported for Siberia. At the last glacial maximum (18,000 ¹⁴C yr bp ), steppe and tundra were prevalent in the Midwest and north‐western Canada, and coniferous forests and woodlands grew in eastern North America. The open vegetation at 18,000 ¹⁴C yr bp was probably due to drier conditions and/or lower concentrations of atmospheric CO₂. The composition and physical structure of biomes is not constant over time. Mid‐Holocene biomes were similar in structure to those of today, but shifts in the relative importance of individual plant functional types are large enough that the physical properties of biomes, such as albedo, canopy conductance and surface roughness, are likely to have varied even during the Holocene. Last glacial maximum biomes were structurally different from their modern counterparts. The biome maps therefore may obscure significant vegetational changes in space and time during the late Quaternary. The difference between the highest and next highest affinity scores for each sample measures how strongly affinity scores discriminate among biomes. For many biomes, the difference is not large, and affinity score ties are not uncommon, highlighting the importance of tie‐break procedures when using the biomization method.     

The biogeography of the western Mediterranean: elucidating contradictory distribution patterns of differentiation in Maniola jurtina (Lepidoptera: Nymphalidae)

In the western Palaearctic, the Mediterranean zone is an important region where taxa and genes of thermophilous organisms are preserved during glacial stages and new clades are generated. This is achieved through the existence of refugia over Mediterranean Europe and North Africa, where organisms persisted and continued to evolve during the cold phases. However, it is not clear in detail how these refugia function for the maintenance of ancestral taxa, the evolution of new taxa, and as launching pads during postglacial colonizations of northern Europe. One outstanding issue is the incongruence of findings from different marker systems. For the butterfly Maniola jurtina, morphometry and allozyme data analyzed for populations scattered over Europe and North Africa show congruent patterns for Sicily and the Maghreb but produce discrepant results for the Italian mainland. This discrepancy between allozyme and morphological data can be explained by recent gene flow in the wake of postglacial range expansions and shifts. It is evident that colonization histories are far more complex than originally considered. We highlight different aspects of colonization and evolutionary history emerging from the joint use of different marker systems and advocate multiple uses of different markers in paleobiogeographic reconstructions to explore evolutionary events and colonization pathways. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 571–577.     

Genetic structure,phylogeography, and demography of Anadara tuberculosa (Bivalvia) from East Pacific as revealed by mtDNA: Implications to conservation

Wild populations of the pustulose ark, Anadara tuberculosa (Bivalvia), an emblematic species of the East Pacific mangrove ecosystem declined in South American countries (Colombia, Ecuador, and Peru) mainly due to overharvesting and habitat loss or degradation. Understanding the genetic aspects of geographic variations and population structure of A. tuberculosa, currently unknown, appears as a priority to fishery authorities in order to elaborate integrated and collaborative conservation policies for fishery management, aquaculture, and stock enhancement programs. We used mtDNA sequence data to investigate haplotype diversity, genetic structure, and demography of A. tuberculosa. Results indicate genetic homogeneity of populations distributed north and south of the equator, respectively. However, statistically significant differentiation emerged between northern and southern populations with pairwise ф_ST values ranging between 0.036 and 0.092. The oceanic current system acting in the area (Panama Current and Humboldt Current) might play a role in limiting the larval dispersal of the species, still poorly understood. Demography reconstruction supported recent population expansion, possibly started after last glacial maximum. Our results would suggest separate and independent management of populations north and south of the equator.