A Matrilineal Genetic Legacy from the Last Glacial Maximum Confers Susceptibility to Schizophrenia in Han Chinese

Mitochondrial dysfunction has been widely reported in schizophrenia patients. To dissect the matrilineal structure of Han Chinese with or without schizophrenia and to decipher the maternal influence and evolutionary history of schizophrenia, a total of 1212 schizophrenia patients and 1005 matched healthy controls, all of Han Chinese origin, were recruited in Hunan Province, China. We classified haplogroup for each individual based on mitochondrial DNA （mtDNA） sequence variations and compared the haplogroup distribution pattern between cases and controls. Haplogroup B5a presented a higher frequency in cases than in controls （P = 0.02, OR = 1.67, 95% CI = [1.09, 2.56]）, and this result could be confirmed by permutation analysis. Age estimation of haplogroup B5a in cases revealed a much younger age than that of controls, which was coincident with the Northern Hemisphere deglaciation at the end of the Last Glacial Maximum. Analysis of complete mtDNA in five patients belonging to haplogroup B5a showed that this background effect might be caused by haplogroup- defining variants m.8584G〉A and m.10398A〉G. Our results showed that matrilineal risk factor for schizophrenia had an ancient origin and might acquire a predisposing effect on schizophrenia due to the environment change and/or orchestration with other nuclear genetic factors appeared recently in human evolutionary history.     

A Short Guide to the Climatic Variables of the Last Glacial Maximum for Biogeographers

Ecological niche models are widely used for mapping the distribution of species during the last glacial maximum (LGM). Although the selection of the variables and General Circulation Models (GCMs) used for constructing those maps determine the model predictions, we still lack a discussion about which variables and which GCM should be included in the analysis and why. Here, we analyzed the climatic predictions for the LGM of 9 different GCMs in order to help biogeographers to select their GCMs and climatic layers for mapping the species ranges in the LGM. We 1) map the discrepancies between the climatic predictions of the nine GCMs available for the LGM, 2) analyze the similarities and differences between the GCMs and group them to help researchers choose the appropriate GCMs for calibrating and projecting their ecological niche models (ENM) during the LGM, and 3) quantify the agreement of the predictions for each bioclimatic variable to help researchers avoid the environmental variables with a poor consensus between models. Our results indicate that, in absolute values, GCMs have a strong disagreement in their temperature predictions for temperate areas, while the uncertainties for the precipitation variables are in the tropics. In spite of the discrepancies between model predictions, temperature variables (BIO1-BIO11) are highly correlated between models. Precipitation variables (BIO12- BIO19) show no correlation between models, and specifically, BIO14 (precipitation of the driest month) and BIO15 (Precipitation Seasonality (Coefficient of Variation)) show the highest level of discrepancy between GCMs. Following our results, we strongly recommend the use of different GCMs for constructing or projecting ENMs, particularly when predicting the distribution of species that inhabit the tropics and the temperate areas of the Northern and Southern Hemispheres, because climatic predictions for those areas vary greatly among GCMs. We also recommend the exclusion of BIO14 and BIO15 from ENMs because those variables show a high level of discrepancy between GCMs. Thus, by excluding them, we decrease the level of uncertainty of our predictions. All the climatic layers produced for this paper are freely available in http://ecoclimate.org/.     

Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum

The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ～18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates.     

Genetic and palaeo-climatic evidence for widespread persistence of the coastal tree species Eucalyptus gomphocephala (Myrtaceae) during the Last Glacial Maximum

Background and Aims

Few phylogeographic studies have been undertaken of species confined to narrow, linear coastal systems where past sea level and geomorphological changes may have had a profound effect on species population sizes and distributions. In this study, a phylogeographic analysis was conducted of Eucalyptus gomphocephala (tuart), a tree species restricted to a 400 × 10 km band of coastal sand-plain in south west Australia. Here, there is little known about the response of coastal vegetation to glacial/interglacial climate change, and a test was made as to whether this species was likely to have persisted widely through the Last Glacial Maximum (LGM), or conforms to a post-LGM dispersal model of recovery from few refugia.

Methods

The genetic structure over the entire range of tuart was assessed using seven nuclear (21 populations; n = 595) and four chloroplast (24 populations; n = 238) microsatellite markers designed for eucalypt species. Correlative palaeodistribution modelling was also conducted based on five climatic variables, within two LGM models.

Key Results

The chloroplast markers generated six haplotypes, which were strongly geographically structured (G_ST = 0·86 and R_ST = 0·75). Nuclear microsatellite diversity was high (overall mean H_E 0·75) and uniformly distributed (F_ST = 0·05), with a strong pattern of isolation by distance (r² = 0·362, P = 0·001). Distribution models of E. gomphocephala during the LGM showed a wide distribution that extended at least 30 km westward from the current distribution to the palaeo-coastline.

Conclusions

The chloroplast and nuclear data suggest wide persistence of E. gomphocephala during the LGM. Palaeodistribution modelling supports the conclusions drawn from genetic data and indicates a widespread westward shift of E. gomphocephala onto the exposed continental shelf during the LGM. This study highlights the importance of the inclusion of complementary, non-genetic data (information on geomorphology and palaeoclimate) to interpret phylogeographic patterns.     

Satsurblia: New Insights of Human Response and Survival across the Last Glacial Maximum in the Southern Caucasus

The region of western Georgia (Imereti) has been a major geographic corridor for human migrations during the Middle and Upper Palaeolithic (MP/UP). Knowledge of the MP and UP in this region, however, stems mostly from a small number of recent excavations at the sites of Ortvale Klde, Dzudzuana, Bondi, and Kotias Klde. These provide an absolute chronology for the Late MP and MP–UP transition, but only a partial perspective on the nature and timing of UP occupations, and limited data on how human groups in this region responded to the harsh climatic oscillations between 37,000–11,500 years before present. Here we report new UP archaeological sequences from fieldwork in Satsurblia cavein the same region. A series of living surfaces with combustion features, faunal remains, stone and bone tools, and ornaments provide new information about human occupations in this region (a) prior to the Last Glacial Maximum (LGM) at 25.5–24.4 ka cal. BP and (b) after the LGM at 17.9–16.2 ka cal. BP. The latter provides new evidence in the southern Caucasus for human occupation immediately after the LGM. The results of the campaigns in Satsurblia and Dzudzuana suggest that at present the most plausible scenario is one of a hiatus in the occupation of this region during the LGM (between 24.4–17.9 ka cal. BP). Analysis of the living surfaces at Satsurblia offers information about human activities such as the production and utilisation of lithics and bone tools, butchering, cooking and consumption of meat and wild cereals, the utilisation of fibers, and the use of certain woods. Microfaunal and palynological analyses point to fluctuations in the climate with consequent shifts in vegetation and the faunal spectrum not only before and after the LGM, but also during the two millennia following the end of the LGM.     

Climate and landscape during the Last Glacial Maximum in southwestern Iberia: The small-vertebrate association from the Sala de las Chimeneas,Maltravieso, Extremadura

Here we present the first palaeoenvironmental and palaeoclimatic analysis based on a study of the microvertebates of the Sala de las Chimeneas (Maltravieso Cave, Cáceres). The fauna is ascribed to the end of the Late Pleistocene, as indicated by the presence of Microtus (Iberomys) cabrerae, Microtus agrestis and Arvicola terrestris and by absolute datings of ～ 17 ka BP. The palaeoenvironmental analysis points to a setting within the early part of the Last Glacial Maximum (LGM), with a habitat dominated by woods and humid meadows, a climate (mean annual temperatures) colder than at present (?4 °C), and mean annual precipitation markedly higher (+700 mm) than is currently the case in the area around Cáceres. These data provide new information on the impact of the last cold spells of Marine Isotope Stage 2 (MIS 2) in the Southwest of Europe, in a region where no studies of the microvertebrates of this period had previously been undertaken.     

The biostratigraphic and palaeoenvironmental significance of Lower Cambrian (Botomian) trilobites from the Ak-Kaya section of the Altai Mountains (southern Siberia,Russia)

The presence of one of the oldest records of polycystine Radiolaria in the Lower Cambrian sedimentary sequence of the Ak-Kaya section (Gorny Altai) requires a biostratigraphic dating. The trilobites found recently a few tens of meters below the radiolarian-bearing level belong to Calodiscus resimus Repina, Serrodiscus fossuliferus Repina and Alacephalus aff. contortus Repina; they suggest that this part of the Shashkunar Formation can be correlated with the lower part of the Botomian stage. The absence of eyes in the two former species suggests a mode of life buried in the fine pelagic sediments. Indications of the presence of a strongly developed musculature on the third species point to a palaeoenvironment characterized by a relatively high hydrodynamic regime.     

Phylogeography of <Emphasis Type="Italic">Littorina sitkana</Emphasis> in the northwestern Pacific Ocean: evidence of eastward trans-Pacific colonization after the Last Glacial Maximum

We investigated genetic diversity and population structure of the Sitka periwinkle Littorina sitkana along the coastlines of the northwestern Pacific (NWP) to evaluate the possibility of trans-Pacific colonization of this species from the NWP to the northeastern Pacific (NEP) after the Last Glacial Maximum. We sampled L. sitkana from 32 populations in the NWP, and sequenced a region of the mitochondrial cytochrome b oxidase gene for population genetic analyses. The results were compared with those of previous reports from the NEP. The genetic diversity of L. sitkana was much higher in the NWP than in the NEP. Genetic connectivity between the NWP and NEP populations was indicated by an extremely abundant haplotype in the NEP that was also present in eastern Hokkaido and the Kuril Islands. To confirm these results, we compared sequences of the longest intron of the aminopeptidase N gene (APN54) in the nuclear genome in four populations of L. sitkana in the NWP with previous results from the NEP. Again, much higher genetic diversity was found in the NWP than in the NEP and genetic connectivity was supported between the Kuril Islands and the NEP. These results imply postglacial colonization of this species from the NWP to the NEP, probably along the Kuril and Aleutian Island chains. This study is the first report of possible trans-Pacific postglacial colonization of a direct-developing gastropod, inferred from genetic data.     

Primary domestication and early uses of the emblematic olive tree: palaeobotanical, historical and molecular evidence from the Middle East

Our knowledge of the origins of olive tree domestication in the Middle East and on the processes governing its extension and persistence in different vegetation types from prehistory through antiquity to modern times derives from diverse sources, spanning the biological sciences to the humanities. Nonetheless, it lacks a robust overview that may lead to floating interpretations. This is especially true in the Middle East, considered as the cradle of agriculture, and where the evolutionary history of this emblematic tree is intertwined with that of civilizations. Olive fruit, oil and wood have been, since Prehistoric times, characteristic products of the lands bordering the Mediterranean Sea. In the domestic economy of these countries, the olive tree gradually became a traditional tree crop since the first oil extraction, through the emergence of regional commerce that accompanied the rise and fall of early Near-Middle Eastern urbanism, until the development of modern trade, with an oil production estimated at circa 3000000 tons per year. The rising importance of the olive tree in human life has turned the tree into an endless source of fascination in the Aegean and Eastern Mediterranean, a symbol and a sacred tree, widely cited in the Bibles, the Koran, and in ancient literature. Here we argue that advances in radiocarbon chronology, palaeobotany, genetics, and archaeology-history have profoundly refined the history of olive trees in the Middle East. This review shows that the heartland of primary olive domestication must be enlarged to the Levant and not only focus on the Jordan Valley. The domestication of the olive tree is a long and ongoing process, linked to the early production of oil and the development of the olive trade. We also suggest that the olive tree became a particular icon, a sacred tree, during the Biblical period in the Levant.     

A series of loams in north Kent, ranging in date from earliest Late Glacial times to the middle of the Sub-boreal period, and their contained molluscan and archaeological evidences

The loams, forming the source of the results recorded below, range in date from earliest Late Glacial times to the middle part of the Sub-boreal period. These loams are to be divided, on the basis of colour, into seven distinct groups.
The molluscan fauna contained in the loams show an absence of both marsh and freshwater species.
Contrary to the generally accepted view the shells Helicella striata (Muller) and Helicella geyeri (Soøs)–both now extinct in this country–continued to flourish in north Kent well into the post-glacial climatic optimum.
This optimum reached its apogee in Atlantic/Sub-boreal times. Before this occurred these two species had ceased to occupy the neighbourhood in question.
Reference has been made previously to the relative distribution, in certain deposits, of Hel. striata and Hel. geyeri, on the one hand, and of Hygromia hispida (Muller) on the other (Burchell, 1971).     

A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide

Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.     

A critical review of the protracted domestication model for Near-Eastern founder crops: linear regression, long-distance gene flow, archaeological, and archaeobotanical evidence

The recent review by Fuller et al. (2012a) in this journal is part of a series of papers maintaining that plant domestication in the Near East was a slow process lasting circa 4000?years and occurring independently in different locations across the Fertile Crescent. Their protracted domestication scenario is based entirely on linear regression derived from the percentage of domesticated plant remains at specific archaeological sites and the age of these sites themselves. This paper discusses why estimates like haldanes and darwins cannot be applied to the seven founder crops in the Near East (einkorn and emmer wheat, barley, peas, chickpeas, lentils, and bitter vetch). All of these crops are self-fertilizing plants and for this reason they do not fulfil the requirements for performing calculations of this kind. In addition, the percentage of domesticates at any site may be the result of factors other than those that affect the selection for domesticates growing in the surrounding area. These factors are unlikely to have been similar across prehistoric sites of habitation, societies, and millennia. The conclusion here is that single crop analyses are necessary rather than general reviews drawing on regression analyses based on erroneous assumptions. The fact that all seven of these founder crops are self-fertilizers should be incorporated into a comprehensive domestication scenario for the Near East, as self-fertilization naturally isolates domesticates from their wild progenitors.     

The occurrence of thermophilous trees in the Scandes Mountains during the early Holocene: evidence for a diverse tree flora from macroscopic remains

1 Macroscopic remains of the fairly thermophilous tree species Alnus glutinosa , Tilia cordata and Betula pendula were recovered in subalpine and adjacent boreal environments far above and beyond their present-day distributional limits. This establishes that the early Holocene tree flora of the Scandes Mountains in northern Sweden was indeed richer than it is today.
2 Dates ranged between c . 8600 and 7000 radiocarbon years bp . These are much earlier than previous estimates by conventional pollen stratigraphical analyses of the arrival of these species at their maximum geographical limits. This highlights problems in using only pollen data for vegetation reconstruction, and suggests re-evaluation of earlier records.
3 The results, together with similar macrofossils for Picea abies and Larix sibirica in northern Sweden, suggest that many tree species spread rapidly and became established at their most extended range limits during the early Holocene. Abundances have subsequently varied in accordance with the ecology of individual species as well as with climatic change.
4 Palaeoclimatic inferences may suggest a strongly continental climate, i.e. warmer and drier summers and possibly fairly cold winters between 8600 and 7000 bp relative to the present. Some change towards a more oceanic climate regime with less pronounced seasonal contrasts may have occurred towards the end of the period.     

A long-living species of the hydrophiloid beetles: Helophorus sibiricus from the early Miocene deposits of Kartashevo (Siberia, Russia)

The recent hydrophiloid species Helophorus (Gephelophorus) sibiricus (Motschulsky, 1860) is recorded from the early Miocene deposits of Kartashevo assigned to the Ombinsk Formation. A detailed comparison with recent specimens allowed a confident identification of the fossil specimen, which is therefore the oldest record of a recent species for the Hydrophiloidea. The paleodistribution as well as recent distribution of the species is summarized, and the relevance of the fossil is discussed. In addition, the complex geological settings of the Kartashevo area are briefly summarized.     

Hedyotis ouachitana (Rubiaceae): A new species from the Ouachita Mountains of Arkansas and Oklahoma

AHedyotis from the Ouachita Mountain region of Arkansas and Oklahoma is superficially similar toH. longifolia (Gaertn.) Hook., but differs consistently in pubescence of the inner corolla and pubescence of the lower stem. It occupies a different habitat and apparently does not hybridize withH. longifolia var.longifolia when the two occur in close proximity. It is described asH. ouachitana.     

A Record of the Weevil Anthonomus dudkoi Legalov (Coleoptera,Curculionidae: Anthonomini) from Katon-Karagay National Park (South-Western Altai)

Entomological Review - The recently described from the Russian Altai and Kazakh Altai Anthonomus dudkoi Legalov is found in the Katon-Karagay National Park in Eastern Kazakhstan (South-Western...     

Sea level and faunal change during the late Wenlock and earliest Ludlow (Silurian): A point of view from the Algerian Sahara

A late Wenlock transgression (C. rigidus zone) affecting a large area of the Algerian Sahara has been known for the last thirty years; in this case there is no break at the Wenlock‐Ludlow boundary and the sedimentation is continuous to the earliest Ludlow. But in many other areas of Sahara a late Wenlock regression is observed. This regression may or may not be followed by a latest Wenlock or an early Ludlow transgression. A sedimentary model is proposed in despite of several problems. In order to compare what happens in each region a schematic diagram is used showing the tendencies to shallowing and deepening. Differences observed between the North Sahara basin and the other parts of the Algerian Sahara and comparison between local sea‐level curves and the global sea‐level curve proposed by Johnson et al. (1991) lead to reconsider the evidence of an eustatic early Ludlow event. To end the problem of the disappearance of nearly all graptolites at the end of Wenlock is discussed. The influence of land emergence in the evolution of marine fossil groups in the disturbance that it can bring to the development of the microplankton and the chemistry of the sea seems to have been too neglected.     

Phase behavior of membranes reconstituted from dipentadecanoylphosphatidylcholine and the Mg2+-dependent, Ca2+-stimulated adenosinetriphosphatase of sarcoplasmic reticulum: evidence for a disrupted lipid domain surrounding protein

A new method was used for reconstituting active sodium deoxycholate solubilized Ca2+-ATPase of rabbit skeletal muscle sarcoplasmic reticulum. Removal of the detergent by dialysis at the pretransition temperature of the pure lipid (22 degrees C) favored the formation of sheet-like structures with a lipid and protein content close to that of the detergent-solubilized sample. Freeze-fracture electron micrographs revealed the Ca2+-ATPase to be organized in rows corresponding to the typical banded pattern seen in low-temperature freeze-fracture micrographs of pure lipid bilayers. Incubation of the sheetlike structures at a temperature (38 degrees C) above the pure lipid main phase transition (33.5 degrees C) caused closure of the sheets into vesicles displaying homogeneous intramembranous particle distributions, at least for membranes containing less than 150 lipids per Ca2+-ATPase. However, in membranes of higher lipid content, free lipid patches were seen both above and below the lipid phase transition. By use of high-sensitivity differential scanning calorimetry, three classes of excess heat capacity peaks were observed in the vesiculated samples. A broadened "free lipid" peak occurred for samples containing between 550 and 200 lipids per protein (Tm = 33.5 degrees C, as for the order-disorder transition in pure lipid vesicles). Between 200 and 150 lipids per Ca2+-ATPase, a broad shoulder became apparent in the range of 29-32 degrees C. Below 150 lipids per Ca2+-ATPase, a peak at 26-28 degrees C became increasingly prominent with lower lipid content. At a lipid to protein ratio of about 30, no peaks in heat capacity were observed. The temperature dependence of diphenylhexatriene fluorescence anisotropy revealed a similar pattern of membrane phase behavior, except that a phase transition was detected at 33.5 degrees C in all membranes studied. On the basis of these observations, we propose that the Ca2+-ATPase is surrounded by a "lipid annulus" of motionally inhibited lipid molecules that do not contribute to a calorimetrically detectable phase transition. Beyond the annulus, "secondary domains" of disrupted lipid packing account for the peak at 26-28 degrees C and the 29-32 degrees C shoulders. At high lipid to protein ratios, the secondary domains coexist with protein-free, lipid-bilayer patches, which account for the peak at 33.5 degrees C.