Reappraisal of the taxonomic status of the cranium Stw 53 from the Plio/Pleistocene of Sterkfontein,in South Africa

A fossil skull, Stw 53, from the Plio/Pleistocene of Sterkfontein, in South Africa, has been referred toHomo habilis Leakey, Napier, andTobias, 1964. Reappraisal of its putative hominine affinity reveals a closer resemblance toAustralopithecus africanus Dart, 1925. The skull, as reconstructed, is too small forH. habilis; with no indication of brain expansion overA. africanus; has a facial angle outside the hominine range, but identical with that ofA. africanus; and whose teeth are not elongated but display buccolingual expansion. Although it was found in the same strata (Member 5) as stone tools, there is no causal connection. It has been dated faunistically at 2–1.5 my BP, but due to an unconformity it is suggested that it could be older. In spite of its late date, Stw 53 shows no intermediate characters which could support a trend towardsH. habilis orA. robustus Broom, 1938. It may, therefore, represent a relict population ofA. africanus.     

A coupled phylogeographical and species distribution modelling approach recovers the demographical history of a Neotropical seasonally dry forest tree species

We investigated here the demographical history of Tabebuia impetiginosa (Bignoniaceae) to understand the dynamics of the disjunct geographical distribution of South American seasonally dry forests (SDFs), based on coupling an ensemble approach encompassing hindcasting species distribution modelling and statistical phylogeographical analysis. We sampled 17 populations (280 individuals) in central Brazil and analysed the polymorphisms at chloroplast (trnS‐trnG, psbA‐trnH, and ycf6‐trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. Phylogenetic analyses based on median‐joining network showed no haplotype sharing among population but strong evidence of incomplete lineage sorting. Coalescent analyses showed historical constant populations size, negligible gene flow among populations, and an ancient time to most recent common ancestor dated from ~4.7 ± 1.1 Myr BP. Most divergences dated from the Lower Pleistocene, and no signal of important population size reduction was found in coalescent tree and tests of demographical expansion. Demographical scenarios were built based on past geographical range dynamic models, using two a priori biogeographical hypotheses (‘Pleistocene Arc’ and ‘Amazonian SDF expansion’) and on two additional hypotheses suggested by the palaeodistribution modelling built with several algorithms for distribution modelling and palaeoclimatic data. The simulation of these demographical scenarios showed that the pattern of diversity found so far for T. impetiginosa is in consonance with a palaeodistribution expansion during the last glacial maximum (LGM, 21 kyr BP), strongly suggesting that the current disjunct distribution of T. impetiginosa in SDFs may represent a climatic relict of a once more wide distribution.     

Revision of fossil hominid jaws from the plio/pleistocene of hadar,in ethiopia including a new species of the genusHomo (hominoidea: homininae)

The assignment of fossil hominoid jaws from the Plio/Pleistocene of Hadar to a single genus,Australopithecus Dart, 1925, is a misnomer. They are morphologically unrestricted to and inconsistent with the diagnosis and evolutionary trend ofAustralopithecus. The morphological pattern of four large jaws is indeed australopithecine and similar toA. africanus Dart, 1925, but six small jaws reveal a pre-habilis stage of dental development early in theHomo lineage. On the basis of their unique hominine dentition, they are reinterpreted as representing a new species,Homo antiquus n.sp.     

Are the photosynthetic membranes of cryptophyte algae inside out?

Summary Cryptomonads are unicellular algae with a unique photosynthetic apparatus, both in structure and pigment composition. A cryptomonad,Rhodomonas lens (R. lens), was studied by conventional electron microscopy, freeze-fracture, and freeze-etch in order to determine whether the thylakoids of this alga are everted with respect to those of other plants, as has been postulated (Gantt et al. 1971,Gantt 1979, 1980) as a means to compensate for the location of the cryptomonad light-harvesting apparatus on the opposite side of the thylakoid membrane from that of related algae. We have characterized the thylakoids of this alga and conclude that they are not everted, but are oriented in the same manner as those of other algae and green plants. Implications for energy transfer are discussed.     

Cryptic diversity and unexpected evolutionary patterns in the meadow lizard,Darevskia praticola (Eversmann, 1834)

Darevskia praticola differs from the other species of the genus in having a large but disjunct distribution, covering the Balkan and the Caucasus regions. Furthermore, most Darevskia species occupy saxicolous habitats, whereas D. praticola inhabits meadows and forest environments. Here we determine the phylogeographic and phylogenetic relationships of Darevskia praticola sensu lato and evaluate the current, morphology-based taxonomy. We sequenced two mtDNA genes (Cyt-b and ND4) and two nuclear loci (MC1R and RELN) for samples collected across the species range. Because our sequences amplified with the Cyt-b primers appear to represent a nuclear pseudogene we excluded this marker from the final analysis. Our results support monophyly of D. praticola and show its division into three clades. The first divergence, dated to the Late Pliocene, is between the Balkans and the Caucasus. The Caucasus lineage is further subdivided in a western Greater Caucasus and a Transcaucasia clade, likely due to subsequent differentiation during the Pleistocene. Our findings do not support the current taxonomic arrangement within D. praticola. The main geographic divergence likely happened due to a vicariance event associated with Plio-Pleistocene climatic and vegetation oscillations.     

A new species of the genusHomo (primates: Hominidae) from the Plio/Pleistocene of Koobi Fora,in Kenya

Reassessment of the hominine cranium, KNM-ER 1813, from the Plio/Pleistocene of Koobi Fora, in Kenya, shows that it is not a small-brained, extreme female variant ofH. habilis Leakey, Tobias, & Napier, 1964. Its cranial and dental morphology, morphometrics, and proportions do not conform with eitherH. habilis orH. antiquus Ferguson, 1984. On the basis of its distinctive morphological pattern and mensural gaps which distinguish it fromH. habilis andH. antiquus, the cranium KNM-ER 1813 is described as a common variant representing a male of a small-brained, intermediate population linkingH. habilis 1.83 Myr BP withH. antiquus 2.9 Myr BP, and a new paleospecies of the genusHomo. A key to the Homininae is provided and the phylogenetic relationship of KNM-ER 1813 toH. habilis andH. antiquus is discussed. This paper is dedicated to the memory of my wife,Grace, whose assistance will be sorely missed.     

A long‐standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

Aim Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long‐standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location The sub‐Saharan savanna biome of East and southern Africa. Methods Mitochondrial DNA control‐region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent‐based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr^?1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07–0.37) than for the southern lineage (0.35 Ma; 0.10–0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation‐by‐distance among populations. Main conclusions The data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer‐standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa.     

Late Pleistocene and Holocene whale remains (Cetacea) from Denmark and adjacent countries: Species,distribution, chronology,and trace element concentrations

We describe and review the subfossil whale bones (mammalian order Cetacea) material from the southern Scandinavian area, that is, Skagerrak, Kattegat, the inner Danish waters and the southwestern Baltic Sea. Fifteen species were identified from the subfossil records of which all, except for the bowhead whale (Balaena mysticetus), have also been encountered in the modern times. Fifty-one specimens were radiocarbon dated covering 12 of the subfossil species. The dates fell in three distinct clusters with a few specimens before the last glacial maximum (LGM), a large group between LGM and the Pleistocene/Holocene boundary (ca. 17.0–11.7 cal. kyr BP), and another large group from ca. 8.0 cal. kyr BP onward. Seventeen of the radiocarbon dated specimens have been subjected to trace element analysis by Instrumental Neutron Activation Analysis. Cross plots of the concentrations of Fe and Zn, and Fe and Co show that it is possible to distinguish crayfish eaters from fish/squid eaters. This can be used as a novel and independent method for the determination to species of whale remains of otherwise uncertain speciation.     

On the systematic position of the large-sized deer from Apollonia,Early Pleistocene,Greece

The revision of the large-sized deer association from the early Pleistocene site Apollonia (Early Pleistocene; Greece), revealed the presence of two species,Praemegaceros pliotarandoides (De Alessandri, 1903) and a giant representative of the genusArvernoceros. P. pliotarandoides (=Psekupsoceros orientalis Radulesco & Samson, 1967) is characterized by advanced dental morphology, lack of the middle antler tine, and dichotomously branched distal part of the antlers and is regarded as the direct forerunner of middle PleistoceneP. verticornis. The species attribution of the ApollonianArvernoceros is not clear enough because of the incomplete data, and for this reason we keep this form under the nameArvernoceros cf.verestchagini. The presence ofArvernoceros in Apollonia certainly extends its chronological occurrence to early Pleistocene and a new generic definition is proposed. Several taxonomic and systematic questions on early Pleistocene large-sized deer of Europe are also discussed.     

PINUS × CRITCHFIELDII,A LATE PLEISTOCENE HYBRID PINE FROM COASTAL SOUTHERN CALIFORNIA

Fossil cones buried in an old landslide at San Clemente are dated at 30,000–34,000 BP (years before present). They generally resemble cones of the natural hybrid Pinus radiata × P. attenuata at Año Nuevo, and also the artificial hybrid P. × attenuradiata. But differences in cone shape, size, and apophyses suggest that the fossil P. × critchfieldii Axelrod and T. G. Hill represents a hybrid of populations of P. radiata and P. attenuata then in coastal southern California. This agrees with population differences between these species in central and southern California during the Pleistocene. Regional comparisons of Late Pleistocene floras indicate that at San Clemente mean annual rainfall was about 580–635 mm, or twice that of today, mean annual temperature was about 2.5 C cooler (13.5 vs. 16.0 C), the mean monthly range was lower (5.9 vs. 7.7 C), the growing season was about 40 days shorter (170 vs. 210 days), and equability was higher (M 72 vs. M 67). Forest was replaced by coastal sage scrub and grassland along the San Clemente coast as drier, warmer climate developed after 12,000 BP.     

Hominin teeth from the early Late Pleistocene site of Xujiayao,Northern China

It is generally accepted that from the late Middle to the early Late Pleistocene (～340–90 ka BP), Neanderthals were occupying Europe and Western Asia, whereas anatomically modern humans were present in the African continent. In contrast, the paucity of hominin fossil evidence from East Asia from this period impedes a complete evolutionary picture of the genus Homo, as well as assessment of the possible contribution of or interaction with Asian hominins in the evolution of Homo sapiens and Homo neanderthalensis. Here we present a comparative study of a hominin dental sample recovered from the Xujiayao site, in Northern China, attributed to the early Late Pleistocene (MIS 5 to 4). Our dental study reveals a mosaic of primitive and derived dental features for the Xujiayao hominins that can be summarized as follows: i) they are different from archaic and recent modern humans, ii) they present some features that are common but not exclusive to the Neanderthal lineage, and iii) they retain some primitive conformations classically found in East Asian Early and Middle Pleistocene hominins despite their young geological age. Thus, our study evinces the existence in China of a population of unclear taxonomic status with regard to other contemporary populations such as H. sapiens and H. neanderthalensis. The morphological and metric studies of the Xujiayao teeth expand the variability known for early Late Pleistocene hominin fossils and suggest the possibility that a primitive hominin lineage may have survived late into the Late Pleistocene in China. Am J Phys Anthropol 156:224–240, 2015. © 2014 Wiley Periodicals, Inc.     

Temporal dynamics of invertebrate community assembly in Lake Victoria since the late Pleistocene based on chitinous remains

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Phylogenetic relationships among Palearctic and Nearctic burbot (Lota lota): Pleistocene extinctions and recolonization

The burbot (Lota lota Linnaeus, 1758) is the only freshwater species from the cod family. Various taxonomic hypotheses were tested against molecular data by sequencing the mitochondrial cytochrome b locus of 120 burbot from 41 populations together with the related species Molva molva (ling) and Brosme brosme (tusk), which represented the other Lotinae genera. Within the genus Lota two distinct phylogroups were observed: one in North America south of the Great Slave Lakes (Lota lota maculosa) and one in Eurasia and the remainder of the Nearctic region (Lota lota lota). The burbot lineage separated 10 Myr BP from the other Lotinae, while the genetic variation within burbot appeared to be approximately 1 Myr old. However, fossil evidence suggested that burbot already existed in the Early Pliocene in Europe, from were it probably colonized North America in the Early Pleistocene. While Nearctic burbot survived climatic oscillations and diverged in several refugia, the Eurasian form became extinct or was reduced to a very small population. In the Late Pleistocene the species recolonized the Palearctic region to establish its present distribution range.     

Pliocene–Pleistocene ecological niche evolution shapes the phylogeography of a Mediterranean plant group

Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean Basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here, we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean Basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation. We carried out a dated phylogenetic–phylogeographic study based on seven DNA regions (nDNA and ptDNA) and fingerprinting data (AFLPs), and modelled ecological niches and species distributions for the Pliocene, Pleistocene and present. Phylogenetic and divergence time analyses revealed that both species form a monophyletic lineage originated in the late Pliocene–early Pleistocene. We detected clear genetic differentiation between both species with distinct genetic clusters in disjunct areas, indicating the predominant role of geographic barriers limiting gene flow. We found a remarkable shift in the climatic requirements between Pliocene and extant populations, although the niche seems to have been relatively conserved since the Pleistocene split of both species. This study highlights how an integrative approach combining different data sources and analyses, including fossils, allows solid and robust inferences about the evolutionary history of a plant group since the Pliocene.     

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade-dwelling species

Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA-sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well-known refugia. We hypothesize that low light requirements evolved when species persisting in cold-stage refugia were forced into marginal habitats by more competitive warm-stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.     

Variability of Nucleotide Sequences of Mitochondrial DNA Cytochrome b Gene in Chars of the Genus Salvelinus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome b gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus–S. malma malmacomplex group. Within the S. alpinus–S. m. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma–Chukotka group includes lake S. taranetzi, S. boganidae, andS. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northernS. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene–Pleistocene.     

Rock art at the pleistocene/holocene boundary in Eastern South America

Background

Most investigations regarding the First Americans have primarily focused on four themes: when the New World was settled by humans; where they came from; how many migrations or colonization pulses from elsewhere were involved in the process; and what kinds of subsistence patterns and material culture they developed during the first millennia of colonization. Little is known, however, about the symbolic world of the first humans who settled the New World, because artistic manifestations either as rock-art, ornaments, and portable art objects dated to the Pleistocene/Holocene transition are exceedingly rare in the Americas.

Methodology/Principal Findings

Here we report a pecked anthropomorphic figure engraved in the bedrock of Lapa do Santo, an archaeological site located in Central Brazil. The horizontal projection of the radiocarbon ages obtained at the north profile suggests a minimum age of 9,370±40 BP, (cal BP 10,700 to 10,500) for the petroglyph that is further supported by optically stimulated luminescence (OSL) dates from sediment in the same stratigraphic unit, located between two ages from 11.7±0.8 ka BP to 9.9±0.7 ka BP.

Conclusions

These data allow us to suggest that the anthropomorphic figure is the oldest reliably dated figurative petroglyph ever found in the New World, indicating that cultural variability during the Pleistocene/Holocene boundary in South America was not restricted to stone tools and subsistence, but also encompassed the symbolic dimension.     

River islands,refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura,Ranidae) of the Qinghai‐Tibetan Plateau

Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai‐Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re‐treat to south‐eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG‐1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north‐eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.     

Atherurus karnuliensis Lydekker, 1886, a Pleistocene brush-tailed porcupine from India, China and Vietnam

Pleistocene porcupine remains from China allocated toAtherurus sp.,Atherurus cf.macrourus andTrichys cf.fasciculata, and from Vietnam toAtherurus macrourus have been studied. These fossils have been compared with the type material of the PleistoceneA. karnuliensis Lydekker, 1886 from India and with the extant speciesA. macrourus (Linnaeus, 1758) andTrichys fasciculata (Shaw, 1801). As a result, all fossil specimens studied are allocated toA. karnuliensis.