The Last Glacial Maximum

North Atlantic storm track changes during the Last Glacial Maximum recorded by Alpine speleothems

The European Alps are an effective barrier for meridional moisture transport and are thus uniquely placed to record shifts in the North Atlantic storm track pattern associated with the waxing and waning of Late-Pleistocene Northern Hemisphere ice sheets. The lack of well-dated terrestrial proxy records spanning this time period, however, renders the reconstruction of past atmospheric patterns difficult. Here we present a precisely dated, continuous terrestrial record of meteoric precipitation in Europe between 30 and 14.7 ka. In contrast to present-day conditions, our speleothem data provide strong evidence for preferential advection of moisture from the South across the Alps supporting a southward shift of the storm track during the local Last Glacial Maximum (that is, 26.5–23.5 ka). Moreover, our age control indicates that this circulation pattern preceded the Northern Hemisphere precession maximum by ~3 ka, suggesting that obliquity may have played a considerable role in the Alpine ice aggradation.

Insights into Late-Pleistocene Northern Hemisphere storm track variability are hampered by a lack of well-dated proxy records. Here, the authors present a precisely dated record of meteoric precipitation between 30 and 14.7 ka, and show that obliquity may have played a vital role in Alpine glacier advance.

Fossils reject climate change as the cause of extinction of Caribbean bats

We combined novel radiocarbon dates of bat fossils with time-scaled ecological niche models (ENM) to study bat extinctions in the Caribbean. Radiocarbon-dated fossils show that late Quaternary losses of bat populations took place during the late Holocene (<4 ka) rather than late Pleistocene (>10 ka). All bat radiocarbon dates from Abaco (Bahamas) that represent extirpated populations are younger than 4 ka. We include data on six bat species, three of which are Caribbean endemics, and include nectarivores as well as insectivores. Climate-based ENMs from the Last Glacial Maximum to the present reflect overall stability in distributions, with suitable climatic habitat being present over time. In the absence of radiocarbon dates, bat extinctions had been presumed to take place during the last glacial-interglacial transition (ca. 10 ka). Now we see that extirpation of bats on these tropical islands is more complex than previously thought and primarily postdates the major climate changes that took place during the late Pleistocene-Holocene transition.

Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation

Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South-East Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an Approximate Bayesian Computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.

Anopheles punctulatus group: evolution, distribution, and control

The major malaria vectors of the Southwest Pacific belong to a group of closely related mosquitoes known as the Anopheles punctulatus group. The group comprises 13 co-occurring species that either are isomorphic or carry overlapping morphological features, and today several species remain informally named. The advent of species-diagnostic molecular tools in the 1990s permitted a new raft of studies into the newly differentiated mosquitoes of this group, and these have revealed five species as the region's primary malaria vectors: An. farauti, An. hinesorum, An. farauti 4, An. koliensis, and An. punctulatus. Species' distributions are now well established across Papua New Guinea, northern Australia, and the Solomon Archipelago, but little has been documented thus far in eastern Indonesia. As each species reveals significant differences in distribution and biology, the relative paucity of knowledge of their biology or ecology in relation to malaria transmission is brought into clearer focus. Only three of the species have undergone some form of spatial or population genetics analyses, and this has revealed striking differences in their genetic signatures throughout the region. This review compiles and dissects the key findings for this important mosquito group and points to where future research should focus to maximize the output of field studies in developing relevant knowledge on these malaria vectors.

Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria

To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000-19,000 years ago), when the southern area became re-submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea-level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations.

Coherent changes of southeastern equatorial and northern African rainfall during the last deglaciation

During the last deglaciation, wetter conditions developed abruptly ~14,700 years ago in southeastern equatorial and northern Africa and continued into the Holocene. Explaining the abrupt onset and hemispheric coherence of this early African Humid Period is challenging due to opposing seasonal insolation patterns. In this work, we use a transient simulation with a climate model that provides a mechanistic understanding of deglacial tropical African precipitation changes. Our results show that meltwater-induced reduction in the Atlantic meridional overturning circulation (AMOC) during the early deglaciation suppressed precipitation in both regions. Once the AMOC reestablished, wetter conditions developed north of the equator in response to high summer insolation and increasing greenhouse gas (GHG) concentrations, whereas wetter conditions south of the equator were a response primarily to the GHG increase.

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

BACKGROUND

Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri].

RESULTS

Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology.

CONCLUSIONS

Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.

Cryptic no more: soil macrofossils uncover Pleistocene forest microrefugia within a periglacial desert

Despite their critical importance for understanding the local effects of global climate change on biodiversity, glacial microrefugia are not well studied because they are difficult to detect by using classical palaeoecological or population genetics approaches. We used soil macrofossil charcoal analysis to uncover the presence of cryptic glacial refugia for European beech (Fagus sylvatica) and other tree species in the Landes de Gascogne (southwestern France). Using botanical identification and direct radiocarbon dating (140 (14) C-dates) of macrofossil charcoal extracted from mineral soils, we reconstructed the glacial and postglacial history of all extant beech stands in the region (n = 11). Soil charcoal macrofossils were found in all sites, allowing the identification of up to at least 14 distinct fire events per site. There was direct evidence of the presence of beech during the last glacial period at three sites. Beech was detected during Heinrich stadial-1, one of the coldest and driest intervals of the last glacial period in Western Europe. Together with previous results on the genetic structure of the species in the region, these findings suggest that beech persisted in situ in several microrefugia through full glacial and interglacial periods up to the present day.

Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl

Gradients of variation--or clines--have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.

Pleistocene paleo-groundwater as a pristine fresh water resource in southern Germany--evidence from stable and radiogenic isotopes

Shallow groundwater aquifers are often influenced by anthropogenic contaminants or increased nutrient levels. In contrast, deeper aquifers hold potentially pristine paleo-waters that are not influenced by modern recharge. They thus represent important water resources, but their recharge history is often unknown. In this study groundwater from two aquifers in southern Germany were analyzed for their hydrogen and oxygen stable isotope compositions. One sampling campaign targeted the upper aquifer that is actively recharged by modern precipitation, whereas the second campaign sampled the confined, deep Benkersandstein aquifer. The groundwater samples from both aquifers were compared to the local meteoric water line to investigate sources and conditions of groundwater recharge. In addition, the deep groundwater was dated by tritium and radiocarbon analyses. Stable and radiogenic isotope data indicate that the deep-aquifer groundwater was not part of the hydrological water cycle in the recent human history. The results show that the groundwater is older than ~20,000 years and most likely originates from isotopically depleted melt waters of the Pleistocene ice age. Today, the use of this aquifer is strictly regulated to preserve the pristine water. Clear identification of such non-renewable paleo-waters by means of isotope geochemistry will help local water authorities to enact and justify measures for conservation of these valuable resources for future generations in the context of a sustainable water management.

Fast evolution from precast bricks: genomics of young freshwater populations of threespine stickleback Gasterosteus aculeatus

Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (Gasterosteus aculeatus) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of G. aculeatus freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci.

Adaptation to novel environments is a keystone of evolution. There is only a handful of natural and experimental systems in which the process of adaptation has been studied in detail, and each studied system brings its own surprises with regard to the number of loci involved, dynamics of adaptation, extent of interactions between loci and of parallelism between different adapting populations. The threespine stickleback is an excellent model organism for evolutionary studies. Marine-derived freshwater populations of this species have consistently acquired a specific set of morphological, physiological and behavioral traits allowing them to reside in freshwater for their whole lifespan. Previous studies identified several genomic regions responsible for this adaptation. Here, using whole-genome sequencing, we compare the allele frequencies at such regions in four derived freshwater populations of known ages: two natural, and two artificially established in 1978. Knowledge of population ages allows us to infer the strength of selection that acted at these loci. Adaptation of threespine stickleback to freshwater is typically fast, and is driven by strong selection favoring pre-existing alleles that are likely present in the ancestral marine population at low frequencies; however, some of the adaptation may also be due to young population-specific alleles.

Climate refugia: joint inference from fossil records, species distribution models and phylogeography

Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.

Glacial history of the European marine mussels Mytilus, inferred from distribution of mitochondrial DNA lineages

Mussels of the genus Mytilus have been used to assess the circumglacial phylogeography of the intertidal zone. These mussels are representative components of the intertidal zone and have rapidly evolving mitochondrial DNA, suitable for high resolution phylogeographic analyses. In Europe, the three Mytilus species currently share mitochondrial haplotypes, owing to the cases of extensive genetic introgression. Genetic diversity of Mytilus edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using a 900-bp long part of the most variable fragment of the control region from one of their two mitochondrial genomes. To this end, 985 specimens were sampled along the European coasts, at sites ranging from the Black Sea to the White Sea. The relevant DNA fragments were amplified, sequenced and analyzed. Contrary to the earlier findings, our coalescence and nested cladistics results show that only a single M. edulis glacial refugium existed in the Atlantic. Despite that, the species survived the glaciation retaining much of its diversity. Unsurprisingly, M. galloprovincialis survived in the Mediterranean Sea. In a relatively short time period, around the climatic optimum at 10 ky ago, the species underwent rapid expansion coupled with population differentiation. Following the expansion, further contemporary gene flow between populations was limited.

Genome-wide genotype and sequence-based reconstruction of the 140,000 year history of modern human ancestry

We investigated ancestry of 3,528 modern humans from 163 samples. We identified 19 ancestral components, with 94.4% of individuals showing mixed ancestry. After using whole genome sequences to correct for ascertainment biases in genome-wide genotype data, we dated the oldest divergence event to 140,000 years ago. We detected an Out-of-Africa migration 100,000–87,000 years ago, leading to peoples of the Americas, east and north Asia, and Oceania, followed by another migration 61,000–44,000 years ago, leading to peoples of the Caucasus, Europe, the Middle East, and south Asia. We dated eight divergence events to 33,000–20,000 years ago, coincident with the Last Glacial Maximum. We refined understanding of the ancestry of several ethno-linguistic groups, including African Americans, Ethiopians, the Kalash, Latin Americans, Mozabites, Pygmies, and Uygurs, as well as the CEU sample. Ubiquity of mixed ancestry emphasizes the importance of accounting for ancestry in history, forensics, and health.

The early rise and late demise of New Zealand's last glacial maximum

Recent debate on records of southern midlatitude glaciation has focused on reconstructing glacier dynamics during the last glacial termination, with different results supporting both in-phase and out-of-phase correlations with Northern Hemisphere glacial signals. A continuing major weakness in this debate is the lack of robust data, particularly from the early and maximum phase of southern midlatitude glaciation (∼30-20 ka), to verify the competing models. Here we present a suite of 58 cosmogenic exposure ages from 17 last-glacial ice limits in the Rangitata Valley of New Zealand, capturing an extensive record of glacial oscillations between 28-16 ka. The sequence shows that the local last glacial maximum in this region occurred shortly before 28 ka, followed by several successively less extensive ice readvances between 26-19 ka. The onset of Termination 1 and the ensuing glacial retreat is preserved in exceptional detail through numerous recessional moraines, indicating that ice retreat between 19-16 ka was very gradual. Extensive valley glaciers survived in the Rangitata catchment until at least 15.8 ka. These findings preclude the previously inferred rapid climate-driven ice retreat in the Southern Alps after the onset of Termination 1. Our record documents an early last glacial maximum, an overall trend of diminishing ice volume in New Zealand between 28-20 ka, and gradual deglaciation until at least 15 ka.

Mixed fortunes: ancient expansion and recent decline in population size of a subtropical montane primate, the Arunachal macaque Macaca munzala

Quaternary glacial oscillations are known to have caused population size fluctuations in many temperate species. Species from subtropical and tropical regions are, however, considerably less studied, despite representing most of the biodiversity hotspots in the world including many highly threatened by anthropogenic activities such as hunting. These regions, consequently, pose a significant knowledge gap in terms of how their fauna have typically responded to past climatic changes. We studied an endangered primate, the Arunachal macaque Macaca munzala, from the subtropical southern edge of the Tibetan plateau, a part of the Eastern Himalaya biodiversity hotspot, also known to be highly threatened due to rampant hunting. We employed a 534 bp-long mitochondrial DNA sequence and 22 autosomal microsatellite loci to investigate the factors that have potentially shaped the demographic history of the species. Analysing the genetic data with traditional statistical methods and advance Bayesian inferential approaches, we demonstrate a limited effect of past glacial fluctuations on the demographic history of the species before the last glacial maximum, approximately 20,000 years ago. This was, however, immediately followed by a significant population expansion possibly due to warmer climatic conditions, approximately 15,000 years ago. These changes may thus represent an apparent balance between that displayed by the relatively climatically stable tropics and those of the more severe, temperate environments of the past. This study also draws attention to the possibility that a cold-tolerant species like the Arunachal macaque, which could withstand historical climate fluctuations and grow once the climate became conducive, may actually be extremely vulnerable to anthropogenic exploitation, as is perhaps indicated by its Holocene ca. 30-fold population decline, approximately 3,500 years ago. Our study thus provides a quantitative appraisal of these demographically important events, emphasising the ability to potentially infer the occurrence of two separate historical events from contemporary genetic data.

The influence of Pleistocene climatic changes and ocean currents on the phylogeography of the southern African barnacle, Tetraclita serrata (Thoracica; Cirripedia)

The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041-0.0065, P<0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.

Rapid interhemispheric climate links via the Australasian monsoon during the last deglaciation

Recent studies have proposed that millennial-scale reorganization of the ocean-atmosphere circulation drives increased upwelling in the Southern Ocean, leading to rising atmospheric carbon dioxide levels and ice age terminations. Southward migration of the global monsoon is thought to link the hemispheres during deglaciation, but vital evidence from the southern sector of the vast Australasian monsoon system is yet to emerge. Here we present a 230thorium-dated stalagmite oxygen isotope record of millennial-scale changes in Australian-Indonesian monsoon rainfall over the last 31,000 years. The record shows that abrupt southward shifts of the Australian-Indonesian monsoon were synchronous with North Atlantic cold intervals 17,600-11,500 years ago. The most prominent southward shift occurred in lock-step with Heinrich Stadial 1 (17,600-14,600 years ago), and rising atmospheric carbon dioxide. Our findings show that millennial-scale climate change was transmitted rapidly across Australasia and lend support to the idea that the 3,000-year-long Heinrich 1 interval could have been critical in driving the last deglaciation.

Early maximum extent of paleoglaciers from Mediterranean mountains during the last glaciation

Mountain glaciers respond directly to changes in precipitation and temperature, thus their margin extent is a high-sensitivity climate proxy. Here, we present a robust ¹⁰Be chronology for the glacier maximum areal extent of central Spain paleoglaciers dated at 26.1 ± 1.3 ka BP. These glaciers reached their maximum extent several thousand years earlier than those from central Europe due to the increased precipitation within a cold period between 25 to 29 ka BP, as confirmed by a local speleothem record. These paleoclimate conditions impacted the maximum extent of mountain glaciers along the western and central Mediterranean region. The cause and timing of the enhanced precipitation implies a southward shift of the North Atlantic Polar Front followed by storm tracks in response to changes in insolation via orbital parameters modulation. Thus, these mountain paleoglaciers from the Mediterranean region record an ocean-continent climate interaction triggered by external forcing.

Geographical ancestry is a key determinant of epidermal morphology and dermal composition

BACKGROUND

Geographical ancestry plays a key role in determining the susceptibility of human skin to external insults and dermatological disease. Despite this, studies of skin from individuals of diverse geographical ancestry focus primarily on epidermal pigmentation. Few reports characterize the gross morphology and composition of the dermis and dermal-epidermal junction (DEJ).

OBJECTIVES

To characterize epidermal morphology and dermal composition in skin from individuals of diverse geographical ancestry.

METHODS

Immunohistochemical techniques were used to assess epidermal morphology and protein composition of the DEJ and dermal extracellular matrix in photoprotected skin from young African, Eurasian and Far East Asian individuals (n = 7 per group; age 18-30 years).

RESULTS

The epidermis of African skin was thicker, with deeper rete ridges and a more convoluted DEJ than Eurasian and Far East Asian skin. Compared with Eurasians, protein composition of the DEJ was collagen VII poor in African and Far East Asian skin (P < 0·001 and P < 0·01, respectively); the dermis of African skin was enriched in fibrillar collagens (P < 0·05), but was relatively elastin poor (P < 0·05). African dermis was abundant in fibrillin-rich microfibrils and fibulin-5 (P < 0·001 and P < 0·001, respectively) compared with Eurasian and Far East Asian skin.

CONCLUSIONS

We demonstrate that fundamental differences exist in skin structure and composition in individuals of diverse geographical ancestry. Disparate environmental pressures encountered by ancestral human populations living at different latitudes may have driven adaptations in skin structure and composition. Further research into the functional significance and clinical consequences of these differences is warranted.

Craniometric analysis of European Upper Palaeolithic and Mesolithic samples supports discontinuity at the Last Glacial Maximum

The Last Glacial Maximum (LGM) represents the most significant climatic event since the emergence of anatomically modern humans (AMH). In Europe, the LGM may have played a role in changing morphological features as a result of adaptive and stochastic processes. We use craniometric data to examine morphological diversity in pre- and post-LGM specimens. Craniometric variation is assessed across four periods--pre-LGM, late glacial, Early Holocene and Middle Holocene--using a large, well-dated, data set. Our results show significant differences across the four periods, using a MANOVA on size-adjusted cranial measurements. A discriminant function analysis shows separation between pre-LGM and later groups. Analyses repeated on a subsample, controlled for time and location, yield similar results. The results are largely influenced by facial measurements and are most consistent with neutral demographic processes. These findings suggest that the LGM had a major impact on AMH populations in Europe prior to the Neolithic.

Genome-wide analysis of cold adaptation in indigenous Siberian populations

Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels and increased blood pressure that have been attributed to adaptation to the extreme cold climate. In this study we introduce a dataset of 200 individuals from ten indigenous Siberian populations that were genotyped for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. A region on chromosome 11 (chr11:66–69 Mb) contained the largest amount of clustering of significant signals and also the strongest signals in all the different selection tests performed. We present a list of candidate cold adaption genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.

Orbital control of western North America atmospheric circulation and climate over two glacial cycles

The now arid Great Basin of western North America hosted expansive late Quaternary pluvial lakes, yet the climate forcings that sustained large ice age hydrologic variations remain controversial. Here we present a 175,000 year oxygen isotope record from precisely-dated speleothems that documents a previously unrecognized and highly sensitive link between Great Basin climate and orbital forcing. Our data match the phasing and amplitudes of 65°N summer insolation, including the classic saw-tooth pattern of global ice volume and on-time terminations. Together with the observation of cold conditions during the marine isotope substage 5d glacial inception, our data document a strong precessional-scale Milankovitch forcing of southwestern paleoclimate. Because the expansion of pluvial lakes was associated with cold glacial conditions, the reappearance of large lakes in the Great Basin is unlikely until ca. 55,000 years into the future as climate remains in a mild non-glacial state over the next half eccentricity cycle.

Glacial forcing of central Indonesian hydroclimate since 60,000 y B.P

The Indo-Pacific warm pool houses the largest zone of deep atmospheric convection on Earth and plays a critical role in global climate variations. Despite the region's importance, changes in Indo-Pacific hydroclimate on orbital timescales remain poorly constrained. Here we present high-resolution geochemical records of surface runoff and vegetation from sediment cores from Lake Towuti, on the island of Sulawesi in central Indonesia, that continuously span the past 60,000 y. We show that wet conditions and rainforest ecosystems on Sulawesi present during marine isotope stage 3 (MIS3) and the Holocene were interrupted by severe drying between ∼33,000 and 16,000 y B.P. when Northern Hemisphere ice sheets expanded and global temperatures cooled. Our record reveals little direct influence of precessional orbital forcing on regional climate, and the similarity between MIS3 and Holocene climates observed in Lake Towuti suggests that exposure of the Sunda Shelf has a weaker influence on regional hydroclimate and terrestrial ecosystems than suggested previously. We infer that hydrological variability in this part of Indonesia varies strongly in response to high-latitude climate forcing, likely through reorganizations of the monsoons and the position of the intertropical convergence zone. These findings suggest an important role for the tropical western Pacific in amplifying glacial-interglacial climate variability.

A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene

Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.

Microsatellite and mitochondrial markers reveal strong gene flow barriers for Anopheles farauti in the Solomon Archipelago: implications for malaria vector control

Anopheles farauti is the primary malaria vector throughout the coastal regions of the Southwest Pacific. A shift in peak biting time from late to early in the night occurred following widespread indoor residue spraying of dichlorodiphenyltrichloro-ethane (DDT) and has persisted in some island populations despite the intervention ending decades ago. We used mitochondrial cytochrome oxidase I (COI) sequence data and 12 newly developed microsatellite markers to assess the population genetic structure of this malaria vector in the Solomon Archipelago. With geographically distinct differences in peak A. farauti night biting time observed in the Solomon Archipelago, we tested the hypothesis that strong barriers to gene flow exist in this region. Significant and often large fixation index (FST) values were found between different island populations for the mitochondrial and nuclear markers, suggesting highly restricted gene flow between islands. Some discordance in the location and strength of genetic breaks was observed between the mitochondrial and microsatellite markers. Since early night biting A. farauti individuals occur naturally in all populations, the strong gene flow barriers that we have identified in the Solomon Archipelago lend weight to the hypothesis that the shifts in peak biting time from late to early night have appeared independently in these disconnected island populations. For this reason, we suggest that insecticide impregnated bed nets and indoor residue spraying are unlikely to be effective as control tools against A. farauti occurring elsewhere, and if used, will probably result in peak biting time behavioural shifts similar to that observed in the Solomon Islands.

Periglacial fires and trees in a continental setting of Central Canada, Upper Pleistocene

Fire is a key factor controlling global vegetation patterns and carbon cycling. It mostly occurs under warm periods during which fuel builds up with sufficient moisture, whereas such conditions stimulate fire ignition and spread. Biomass burning increased globally with warming periods since the last glacial era. Data confirming periglacial fires during glacial periods are very sparse because such climates are likely too cold to favour fires. Here, tree occurrence and fires during the Upper Pleistocene glacial periods in Central Canada are inferred from botanical identification and calibrated radiocarbon dates of charcoal fragments. Charcoal fragments were archived in sandy dunes of central Saskatchewan and were dated >50000-26600 cal BP. Fragments were mostly gymnosperms. Parallels between radiocarbon dates and GISP2-δ¹⁸O records deciphered relationships between fire and climate. Fires occurred either hundreds to thousands of years after Dansgaard-Oeschger (DO) interstadial warming events (i.e., the time needed to build enough fuel for fire ignition and spread) or at the onset of the DO event. The chronological uncertainties result from the dated material not precisely matching the fires and from the low residual ¹⁴C associated with old sample material. Dominance of high-pressure systems and low effective moisture during post-DO coolings likely triggered flammable periglacial ecosystems, while lower moisture and the relative abundance of fuel overshadowed lower temperatures for fire spread. Laurentide ice sheet (LIS) limits during DO events are difficult to assess in Central Canada due to sparse radiocarbon dates. Our radiocarbon data set constrains the extent of LIS. Central Saskatchewan was not covered by LIS throughout the Upper Pleistocene and was not a continental desert. Instead, our results suggest long-lasting periods where fluctuations of the northern tree limits and fires after interstadials occurred persistently.

Migration patterns of subgenus Alnus in Europe since the last glacial maximum: a systematic review

Background/Aims

Recently, new palaeoecological records supported by molecular analyses and palaeodistributional modelling have provided more comprehensive insights into plant behaviour during the last Quaternary cycle. We reviewed the migration history of species of subgenus Alnus during the last 50,000 years in Europe with a focus on (1) a general revision of Alnus history since the Last Glacial Maximum (LGM), (2) evidence of northern refugia of Alnus populations during the LGM and (3) the specific history of Alnus in particular European regions.

Methodology

We determined changes in Alnus distribution on the basis of 811 and 68 radiocarbon-dated pollen and macrofossil sites, respectively. We compiled data from the European Pollen Database, the Czech Quaternary Palynological Database, the Eurasian Macrofossil Database and additional literature. Pollen percentage thresholds indicating expansions or retreats were used to describe patterns of past Alnus occurrence.

Principal Findings

An expansion of Alnus during the Late Glacial and early Holocene periods supports the presence of alders during the LGM in southern peninsulas and northerly areas in western Europe, the foothills of the Alps, the Carpathians and northeastern Europe. After glaciers withdrew, the ice-free area of Europe was likely colonized from several regional refugia; the deglaciated area of Scandinavia was likely colonized from a single refugium in northeastern Europe. In the more northerly parts of Europe, we found a scale-dependent pattern of Alnus expansion characterised by a synchronous increase of Alnus within individual regions, though with regional differences in the times of the expansion. In southern peninsulas, the Alps and the Carpathians, by contrast, it seems that Alnus expanded differently at individual sites rather than synchronously in whole regions.

Conclusions

Our synthesis supports the idea that northern LGM populations were important sources of postglacial Alnus expansion. The delayed Alnus expansion apparent in some regions was likely a result of environmental limitations.

Greece: a Balkan subrefuge for a remnant red deer (cervus elaphus) population

A number of phylogeographic studies have revealed the existence of multiple ice age refugia within the Balkan Peninsula, marking it as a biodiversity hotspot. Greece has been reported to harbor genetically differentiated lineages from the rest of Balkans for a number of mammal species. We therefore searched for distinct red deer lineages in Greece, by analyzing 78 samples originating from its last population in Parnitha Mountain (Central Greece). Additionally, we tested the impact of human-induced practices on this population. The presence of 2 discrete mtDNA lineages was inferred: 1) an abundant one not previously sampled in the Balkans and 2) a more restricted one shared with other Balkan populations, possibly the result of successful translocations of Eastern European individuals. Microsatellite-based analyses of 14 loci strongly support the existence of 2 subpopulations with relative frequencies similar to mitochondrial analyses. This study stresses the biogeographic importance of Central Greece as a separate Last Glacial Maximum period refugium within the Balkans. It also delineates the possible effects that recent translocations of red deer populations had on the genetic structuring within Parnitha. We suggest that the Greek red deer population of Parnitha is genetically distinct, and restocking programs should take this genetic evidence into consideration.

Mitochondrial phylogeography of a Beringian relict: the endemic freshwater genus of blackfish Dallia (Esociformes)

Mitochondrial genetic variability among populations of the blackfish genus Dallia (Esociformes) across Beringia was examined. Levels of divergence and patterns of geographic distribution of mitochondrial DNA lineages were characterized using phylogenetic inference, median-joining haplotype networks, Bayesian skyline plots, mismatch analysis and spatial analysis of molecular variance (SAMOVA) to infer genealogical relationships and to assess patterns of phylogeography among extant mitochondrial lineages in populations of species of Dallia. The observed variation includes extensive standing mitochondrial genetic diversity and patterns of distinct spatial segregation corresponding to historical and contemporary barriers with minimal or no mixing of mitochondrial haplotypes between geographic areas. Mitochondrial diversity is highest in the common delta formed by the Yukon and Kuskokwim Rivers where they meet the Bering Sea. Other regions sampled in this study host comparatively low levels of mitochondrial diversity. The observed levels of mitochondrial diversity and the spatial distribution of that diversity are consistent with persistence of mitochondrial lineages in multiple refugia through the last glacial maximum.

Offshore fresh groundwater reserves as a global phenomenon

The flow of terrestrial groundwater to the sea is an important natural component of the hydrological cycle. This process, however, does not explain the large volumes of low-salinity groundwater that are found below continental shelves. There is mounting evidence for the global occurrence of offshore fresh and brackish groundwater reserves. The potential use of these non-renewable reserves as a freshwater resource provides a clear incentive for future research. But the scope for continental shelf hydrogeology is broader and we envisage that it can contribute to the advancement of other scientific disciplines, in particular sedimentology and marine geochemistry.

Genetic and morphometric divergence in threespine stickleback in the Chignik catchment, Alaska

Divergent selection pressures induced by different environmental conditions typically lead to variation in life history, behavior, and morphology. When populations are locally adapted to their current environment, selection may limit movement into novel sites, leading to neutral and adaptive genetic divergence in allopatric populations. Subsequently, divergence can be reinforced by development of pre-or postzygotic barriers to gene flow. The threespine stickleback, Gasterosteus aculeatus, is a primarily marine fish that has invaded freshwater repeatedly in postglacial times. After invasion, the established freshwater populations typically show rapid diversification of several traits as they become reproductively isolated from their ancestral marine population. In this study, we examine the genetic and morphometric differentiation between sticklebacks living in an open system comprising a brackish water lagoon, two freshwater lakes, and connecting rivers. By applying a set of microsatellite markers, we disentangled the genetic relationship of the individuals across the diverse environments and identified two genetic populations: one associated with brackish and the other with the freshwater environments. The “brackish” sticklebacks were larger and had a different body shape than those in freshwater. However, we found evidence for upstream migration from the brackish lagoon into the freshwater environments, as fish that were genetically and morphometrically similar to the lagoon fish were found in all freshwater sampling sites. Regardless, few F1-hybrids were identified, and it therefore appears that some pre-and/or postzygotic barriers to gene flow rather than geographic distance are causing the divergence in this system.

On the biogeography of Centipeda: a species-tree diffusion approach

Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.

Responses of ocean circulation and carbon cycle to changes in the position of the Southern Hemisphere westerlies at Last Glacial Maximum

We explore the impact of a latitudinal shift in the westerly wind belt over the Southern Ocean on the Atlantic meridional overturning circulation (AMOC) and on the carbon cycle for Last Glacial Maximum background conditions using a state-of-the-art ocean general circulation model. We find that a southward (northward) shift in the westerly winds leads to an intensification (weakening) of no more than 10% of the AMOC. This response of the ocean physics to shifting winds agrees with other studies starting from preindustrial background climate, but the responsible processes are different. In our setup changes in AMOC seemed to be more pulled by upwelling in the south than pushed by downwelling in the north, opposite to what previous studies with different background climate are suggesting. The net effects of the changes in ocean circulation lead to a rise in atmospheric pCO₂ of less than 10 μatm for both northward and southward shift in the winds. For northward shifted winds the zone of upwelling of carbon- and nutrient-rich waters in the Southern Ocean is expanded, leading to more CO₂outgassing to the atmosphere but also to an enhanced biological pump in the subpolar region. For southward shifted winds the upwelling region contracts around Antarctica, leading to less nutrient export northward and thus a weakening of the biological pump. These model results do not support the idea that shifts in the westerly wind belt play a dominant role in coupling atmospheric CO₂ rise and Antarctic temperature during deglaciation suggested by the ice core data.