Early divergence dates of demosponges based on mitogenomics and evaluated fossil calibrations

Demosponges are among the most primitive biomineralized metazoans to appear first in the fossil record with hard skeletons; their confirmed earliest fossils are from the lower Cambrian rocks about 520 Ma, with putative demosponge biomarkers reported from 713 to 635 Ma sediments. In this study, we use mitogenomic data to approach the early divergence timescale of demosponges using relaxed molecular clock techniques and likelihood-evaluated fossil calibration strategies. We found that among various molecular dating models, the correlated rate model yielded time estimates of demosponges in this analysis which is most congruent with the fossil appearance dates of demosponges. Our dating analyses show that crown groups of Demospongiae appeared at about 704 (674–741) Ma, and the silicification in demosponges (divergence of spicular sponges) began about 633 (616–648) Ma indicating a gap of over 100 million years between the origin of silicification and their first unequivocal appearance of siliceous spicules in the fossil record (520–525 Ma); demosponges with tetraxon-type spicules (Tetractinellida) are dated here at about 514 (498–530) Ma, an estimate comparable with the earliest tetraxial megasclere fossil records (510–520 Ma, Ordian Age, middle Cambrian).     

Biogeographic relationships of African carnivoran faunas, 7–1.2 Ma

This study analyses the carnivore component of African fossil faunas from three time slices: 7–5 Ma, 4–3 Ma, and 2.5–1.2 Ma, using cluster analysis and principal coordinate analysis (PCO) of presence/absence data on genera. The faunas mostly cluster by time slice, with the exception of Laetoli (Tanzania) and Ahl al Oughlam (Morocco), which differ from all other faunas. The separation during the Late Miocene of a Chado–Libyan bioprovince from the remainder of Africa is supported. No such distinctions are present in the other time slices. Taxonomic distance is not generally correlated with geographic distance, though if Langebaanweg is removed from the 7–5 Ma time slice, the correlation at that time is significant. Comparison of these paleontological results with phylogeographic studies of modern species leads to some general comments on the analytic power of the fossil record with regard to interregional migrations.     

Avian fossil assemblages at the onset of the LGM in the eastern Alps: A palaecological contribution from the Rio Secco Cave (Italy)

The avian fossil assemblages from the late Pleistocene deposits of the Rio Secco Cave (north-eastern Italy) is presented herein. We studied the layers that date back to the end of MIS3 and the beginning of MIS2, which also contain evidence of Gravettian frequentation dated to 33.5–30 ka cal BP. The systematic analysis revealed the presence of 18 species and other supraspecific taxa that supported palaeoenvironmental reconstructions. Taxa indicate that, at the onset of LGM, site surroundings were characterised by conifer or mixed forests, open grasslands, slow-flowing water bodies and mountain meadows with rocky outcrops, as indicated by Lagopus muta. Today, this environment is found above the tree line (beyond 1500–2000 m) and cannot be detected near the site, located at 580 m asl. Noteworthy, is also the finding of the second Italian late Pleistocene fossil record of Picus canus.     

A multilocus coalescent analysis of the speciational history of the Australo-Papuan butcherbirds and their allies

Changes in geology, sea-level and climate are hypothesised to have been major driving processes of evolutionary diversification (speciation and extinction) in the Australo-Papuan region. Here we use complete species-level sampling and multilocus (one mitochondrial gene, five nuclear loci) coalescent analyses to estimate evolutionary relationships and test hypotheses about the role of changes in climate and landscape in the diversification of the Australo-Papuan butcherbirds and allies (Cracticinae: Cracticus, Strepera, Peltops). Multilocus species trees supported the current classification of the morphologically, ecologically and behaviourally divergent Australian Magpie (Cracticus tibicen (previously Gymnorhina tibicen)) as a member of an expanded genus Cracticus, which includes seven other species with ‘butcherbird’ morphology and behaviour. Non-monophyly of currently recognised species within Peltops and the white-throated butcherbird species-group (C. argenteus, C. mentalis, C. torquatus) at both mtDNA and nuclear loci suggest that a comprehensive taxonomic revision is warranted for both of these groups. The time-calibrated multilocus species tree revealed an early divergence between the New Guinean rainforest-restricted Peltops lineage and the largely open-habitat inhabiting Cracticus (butcherbirds and magpies) plus Strepera (currawongs) lineage around 17–28 Ma, as well as a relatively recent radiation of lineages within Cracticus over the past 8 Ma. Overall, patterns and timings of speciation were consistent with the hypothesis that both the expansion of open sclerophyllous woodlands 25–30 Ma and the formation of extensive grassland-dominated woodlands 6–8 Ma allowed the radiation of lineages adapted to open woodland habitats.     

Earliest occurrence of Puma pardoides (Owen, 1846) (Carnivora,Felidae) at the Plio/Pleistocene transition in western Europe: New evidence from the Middle Villafranchian assemblage of Montopoli,Italy

The puma-like cat Puma pardoides (Owen, 1846) is reported from several Eurasian localities dated to the Late Pliocene–Early Pleistocene, but its Italian fossil record is really poor; in fact, the only possible occurrence comprises some fragmentary postcranial material from the Late Villafranchian locality of Pirro Nord (1.6–1.3 Ma). In the present paper, we describe an isolated left upper carnassial of a medium-sized felid belonging to the collection of fossil mammals from Montopoli (Tuscany, Italy), the type locality of the Middle Villafranchian Faunal Unit (∼2.6 Ma). All the morphological and morphometric characters of the tooth are consistent with an attribution to Puma pardoides (Owen, 1846), which comes out as the second felid species from Montopoli together with Acinonyx pardinensis (Croizet et Jobert, 1828) and is, possibly with the specimens from Perrier-Étouaries, the earliest occurrence in western Europe.     

Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography

With about 400 living species and 82 genera, rodents of the subfamily Sigmodontinae comprise one of the most diverse and more broadly distributed Neotropical mammalian clades. There has been much debate on the origin of the lineage or the lineages of sigmodontines that entered South America, the timing of entrance and different aspects of further diversification within South America. The ages of divergence of the main lineages and the crown age of the subfamily were estimated by using sequences of the interphotoreceptor retinoid binding protein and cytochrome b genes for a dense sigmodontine and muroid sampling. Bayesian inference using three fossil calibration points and a relaxed molecular clock estimated a middle Miocene origin for Sigmodontinae (～12 Ma), with most tribes diversifying throughout the Late Miocene (6.9–9.4 Ma). These estimates together results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution for the most recent common ancestor of Oryzomyalia.     

Cyclestheria hislopi (Crustacea: Branchiopoda): A group of morphologically cryptic species with origins in the Cretaceous

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI > 13%, EF1α > 3% and 28S > 4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian–Australian lineage, with the latter diverging further in the Paleogene. Today’s circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera.     

Late Miocene hominoid from Niger

African Late Miocene hominoids are rare, having been reported from six localities in Kenya, Ethiopia and Chad ranging in age from 10.5 to 5.5 Ma. We here report the occurrence of a hominoid in Niger associated with a vertebrate fauna which indicates an age of between 11–5 Ma. The Niger fossil locality is 940 km north of the nearest known extant hominoids, 1000 km west of the nearest recorded fossil hominoid from Chad.     

Rhaetian magneto-biostratigraphy from the Southern Alps (Italy): Constraints on Triassic chronology

New Late Triassic–earliest Jurassic magneto-biostratigraphic data have been obtained from three overlapping sections in the Southern Alps, Italy (Costa Imagna, Brumano, Italcementi Quarry), composed of ~ 520 m of shallow-marine carbonates outcropping in stratigraphic continuity. Characteristic magnetic components of presumed depositional age record a sequence of 9 normal and reverse polarity magnetozones (as defined by at least three stratigraphically superposed samples) linked by conodont and palynofloral evidence from this study and the literature to Rhaetian to Triassic–Jurassic boundary age. This represents a significantly larger number of polarity zones than previously recognized in more condensed Rhaetian sections from the literature, and by inference represents more time. These data are placed in a broader Late Triassic temporal framework by means of correlations to published magneto-biostratigraphic data from the Tethyan marine Pizzo Mondello section and the Newark astronomical polarity time scale (APTS). This framework is consistent with a position of the Norian–Rhaetian boundary (as defined at Brumano and Pizzo Mondello by the first appearance of Misikella posthernsteini) within Newark magnetozones E17r–E19r in the ~ 207–210 Ma time interval, in basic agreement with the position originally estimated in the Newark using pollen biostratigraphy (E18 at 208–209 Ma). This framework is also consistent with the position of the Triassic–Jurassic boundary interval (placed at Italcementi Quarry at the acme of Kraeuselisporites reissingeri coincident with a negative carbon isotope excursion) correlative to just above Newark magnetozone E23r and just below the oldest CAMP lavas dated at ~ 202 Ma. Hence, we estimate the duration of the Rhaetian to be ~ 5.5–8.5 Myr (or even longer if the Triassic–Jurassic boundary is instead placed above the negative carbon isotope excursion as at Kuhjoch, which is the designated GSSP for the base of the Hettangian), and encompassing 9 magnetozones. This duration contrasts with a duration of ~ 2 Myr and only ~ 4 magnetozones in several alternative published magneto-biostratigraphic schemes.     

The Eocene Juncitarsus – its phylogenetic position and significance for the evolution and higher-level affinities of flamingos and grebes

The Early Eocene Juncitarsus was described as one of the earliest fossil flamingos, and played a critical role in the hypothesis of a charadriiform origin of Phoenicopteriformes. It has been noted that phoenicopteriform affinities of Juncitarsus conflict with the recently proposed sister group relationship between flamingos and the morphologically very divergent grebes (Podicipediformes), but a detailed assessment of the evolutionary significance of Juncitarsus in light of this new hypothesis has not yet been performed. Here, the affinities of Juncitarsus are reviewed, and its position as sister group of the clade (Phoenicopteriformes + Podicipediformes) is affirmed. The osteology of Juncitarsus suggests that swimming adaptations evolved in the stem lineage of this latter clade after the divergence of Juncitarsus. Charadriiformes remain among the candidate taxa for the closest extant relatives of flamingos and grebes, but more data are needed for well-supported phylogenetic hypotheses.     

Historical dendroarchaeology of two log structures in the Valles Caldera National Preserve,New Mexico,USA

We used dendroarchaeological techniques to determine the year of construction of two historic structures in the Valles Caldera National Preserve of New Mexico, USA. Historical documents date some structures in the headquarters area of the Preserve, but the Commissary Cabin and Salt Barn were lacking conclusive construction dates. Both structures were originally thought to have been built by the Otero family who bought the property in 1899. We found that the structures were built from two tree species, white fir (Abies concolor (Gordon) Lindl. ex Hildebr.) and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), surprising given that ponderosa pines are also found in great numbers in the adjacent forest. Tree rings from 20 logs were confidently crossdated both graphically and statistically and provided cutting dates of trees in both structures of 1940 and 1941 when compared against the Fenton Lake reference chronology (Commissary Cabin: r = 0.69, t = 15.54, p < 0.0001, n = 263 years; Salt Barn: r = 0.77, t = 11.7, p < 0.0001, n = 232 years). By combining the cutting date years and terminal ring attributes, we suggest that both structures were built in the spring or early summer of 1941 using freshly cut logs and logs that had been cut the previous spring (1940, before or during the growing season) and stockpiled. The cutting dates of 1940 and 1941 indicate that these buildings were constructed during the Franklin Bond (1939–1945) era and associated with the transition from sheep ranching to more modern cattle grazing. These new dates provide a more distinct understanding of the cultural resources at the Valles Caldera National Preserve and provide interpretative staff with more accurate information that can be given to the public.     

Late Pliocene grassland from Olduvai Gorge,Tanzania

The Olduvai fossil plants documented by us in this paper are the first direct evidence for open grassland in the late Neogene of Africa based on macroplant remains. Silicified remains of herbaceous ground cover are exceptionally well preserved in situ within Late Pliocene sediments below the initial pyroclastic ash surge unit of Tuff IF in the uppermost part of Bed I, Olduvai Gorge, northern Tanzania. Published radiometric and palaeomagnetic dates place this grass layer between 1.839 + 0.005 Ma and 1.785 + 0.01 Ma. Exposed at localities on the south side of the Gorge this herbaceous ground cover grew on a floodplain developed on a dried out lake bed, following pronounced lake retreat of saline–alkaline palaeo-Lake Olduvai during a developing dry climatic phase. Sheathed basal culms, rhizomes and roots are interpreted as those of one or more small mat-forming grasses or less likely, sedges. Small dicotyledonous herbs were probably also present. The proximity of adjacent plants indicates a relatively dense ground cover. Roots extended at least 8 cm below the ground surface. Aerial parts of the plants were absent or were not preserved when the weathered basal culms were covered by a thin layer of brown waxy clay, followed by fallout of pyroclastic ash. Both units were mostly eroded away prior to emplacement of a wet, cool pyroclastic surge which then buried and preserved in situ remnants of the herbaceous ground cover. Preservation of the semi-woody rhizomes implies well-drained soils, otherwise the plant material would have quickly rotted. Collections from discontinuous exposures indicate the grassland covered an area of at least a few hectares. This open grassland would have provided grazing for the Late Pliocene fauna.     

New insights into the pattern,timing, and duration of the evolutionary origin of the foraminiferal genus Hantkenina

A high-resolution study of the Tethyan Contessa Highway reference section (Gubbio, Italy) has produced a detailed, well-constrained and more complete pattern of the gradual evolutionary origin of the foraminiferal genus Hantkenina from Clavigerinella than hitherto shown. A nine-stage pattern is presented for this evolutionary lineage. The related time frame and duration are assessed using the astronomical calibration of the Contessa Highway record. The evolution of Clavigerinella caucasica to Hantkenina gohrbandti, the real ancestor of Hantkenina, leads in 333 kyr. The H. gohrbandti first appearance is dated at 45.564 Ma. Our findings show that during the middle Eocene, from 46 to 45.5 Ma and with a major pulse centered at 45.521 Ma deep-mesopelagic planktonic foraminifera may have developed different morphological modifications to tolerate temporary exceptionally stressful environmental conditions. These conditions are principally related to poorly oxygenated and usually food-poor waters. This suggests that sustained and expanded oxygen minimum zone conditions and associated enhanced eutrophication might have occurred during that time.     

Stature,body mass,and brain size: A two-million-year odyssey

Physical size has been critical in the evolutionary success of the genus Homo over the past 2.4 million-years. An acceleration in the expansion of savannah grasslands in Africa from 1.6 Ma to 1.2 Ma witnessed concomitant increases in physical stature (150–170 cm), weight (50–70 kg), and brain size (750–900 cm³). With the onset of 100,000 year Middle Pleistocene glacial cycles (“ice ages”) some 780,000 years ago, large-bodied Homo groups had reached modern size and had successfully dispersed from equatorial Africa, Central, and Southeast Asia to high-latitude localities in Atlantic Europe and North East Asia. While there is support for incursions of multiple Homo lineages to West Asia and Continental Europe at this time, data does not favour a persistence of Homo erectus beyond ～400,000 years ago in Africa, west and Central Asia, and Europe. Novel Middle Pleistocene Homo forms (780,000–400,000 years) may not have been substantially taller (150–170 cm) than earlier Homo (1.6 Ma–800,000 years), yet brain size exceeded 1000 cm³ and body mass approached 80 kg in some males. Later Pleistocene Homo (400,000–138,000 years) were ‘massive’ in their height (160–190 cm) and mass (70–90 kg) and consistently exceed recent humans. Relative brain size exceeds earlier Homo, yet is substantially lower than in final glacial H. sapiens and Homo neanderthalensis. A final leap in absolute and relative brain size in Homo (300,000–138,000 years) occurred independent of any observed increase in body mass and implies a different selective mediator to that operating on brain size increases observed in earlier Homo.     

Phylogeography of Phrynocephalus erythrurus from the Qiangtang Plateau of the Tibetan Plateau

Phrynocephalus erythrurus of the Qiangtang Plateau occupies the highest regions of any reptile on earth. Here, we report mitochondrial DNA haplotypes sampled throughout the distribution of P. erythrurus and analyze patterns of genetic divergence among populations. The species diverged into two major lineages/subspecies at 3.67 mya corresponding to the Northern and Southern Qiangtang Plateau. The Northern Qiangtang lineage diverged into two subpopulations at 2.76 mya separated by the Beilu River Region and Wulanwula Mountains. Haplotypes from the southern Qiangtang lineage diverged 0.98 mya as a star-shaped pattern. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruptions to gene flow. There was no evidence of sudden recent range expansions within any of the clades/lineages. NCPA infers allopatric fragmentation and restricted gene flow as the most likely mechanisms of population differentiation. Our results also indicate the presence of at least three refugia since the Hongya glaciation. Mountain movement and glaciations since mid-Pliocene are considered to have shaped phylogenetic patterns of P. erythrurus. P. erythrurus parva is suggested as a valid subspecies of P. erythrurus. Using four calibration points, we estimate an evolutionary rate of 0.762% divergence per lineage per million years for a mitochondrial genomic segment comprising the genes encoding ND2, tRNA^Trp and tRNA^Ala.     

Cenozoic long-term terrestrial climatic evolution in Germany tracked by δ18O of rodent tooth phosphate

Even though the Cenozoic has been recognized as a period of important climate change, long-term climatic changes that took place in the continental domain are still questioned. For an area, southern Germany, for which other long-term palaeoclimatic records exist, analysis of oxygen isotope composition of small mammal teeth has been carried out for localities ranging in age from the late Eocene (c.36 Ma) to the middle Miocene (c.10 Ma). Comparison of this long-term continental δ¹⁸O record with the marine record reveals comparable trends. The major Cenozoic climatic events are thus recognized in the continental oxygen isotope record.Through comparison with other quantitative palaeoclimatic reconstructions available for the studied area, temperatures in southern Germany are broadly estimated to have fluctuated between 12 °C and 25 °C from late Eocene to early late Miocene. According to the different available chronological frameworks, either a ～ 2 °C (considering the classical biostratigraphy) or a ～ 6 °C (considering a revised biostratigraphy) decrease in mean air temperature is estimated for the Eocene/Oligocene boundary.     

Evaluating the dendroclimatological potential of Taxus baccata (yew) in southwest Ireland

Tree-ring research in Ireland has typically been dominated by Quercus species, particularly Quercus petraea and Quercus robur. Recent years have seen a greater focus on multi-species reconstructions in Ireland but, due to difficulties with the hardness of the wood, missing/pinched rings and fused stems, Taxus baccata has not been included in these investigations. Despite these difficulties, a 31-tree, 204-year T. baccata chronology was successfully constructed from Killarney National Park, southwest Ireland. The chronology exhibits promising dendroclimatological potential, with climatic responsiveness equivalent to that of the other major Irish tree taxa, including Quercus. The chronology shows the strongest relationship with May–June precipitation from Muckross House synoptic station (1970–2007; r = 0.521, p < 0.01) and Valentia Observatory (1941–2007; r = 0.545, p < 0.01). November–April temperatures also exhibited a strong relationship with the chronology post-1970 (r = 0.605, p < 0.01 for Muckross House, r = 0.567, p < 0.01 for Valentia Observatory), but this relationship is not time stable and breaks down for the pre-1970 Valentia Observatory record. The long-lived nature of T. baccata, the exceptional preservation of wood and rings in this hard softwood species, as well as its prominence in Irish archaeology, all point to the potential to expand this chronology both spatially and temporally, and demonstrate T. baccata's potential in multi-site and multi-species tree-ring studies in the region.     

Holocene and Late Pleistocene climate in the sub-Mediterranean continental environment: A speleothem record from Poleva Cave (Southern Carpathians,Romania)

The PP10 stalagmite from Poleva Cave provides a Late Pleistocene and Holocene isotopic record characteristic for the SW of Romania, a sub-Mediterranean climatic region. The speleothem was dated by eight TIMS and one alpha U-series dates which showed that it was precipitated between ∼ 75 ka and ∼ 2 ka with at least two hiatuses. The basal sector of the stalagmite showed a slow-growing regime of ∼ 0.26 cm/ka, while the upper one grew relatively fast with about 5 cm/ka. The temporal resolution for the isotopic sampling is thus ∼ 2 ka/sample for the lower sector, and ∼ 150 years/sample for the upper one. The relationship between δ¹⁸O and temperature was found positive. The isotopic record of the lower sector shows two marked cold intervals during ∼ 67 and 58 ka and ∼ 40–35 ka, respectively, which correlate well with the Villars and Soreq records. The upper sector record is so far the most detailed Holocene isotopic record in Romania and the only one available for the regions located at the exterior of the Carpathians Range. The signal shows a gradual warming after the GS1 event punctuated by several cold events at ∼ 8, 7.2 and 4.2 ka and also by warm oscillations centered at about 5.2 and 3.3 ka. The results seem to indicate that if the North-Atlantic first-order signals may extend well to the south-eastern Europe, their amplitude and general trend may be diminished by the interferences with the Mediterranean circulation.     

A multilocus phylogeny of archiheterodont bivalves (Mollusca,Bivalvia, Archiheterodonta)

The bivalve clade Heterodonta encompasses more than half of the extant bivalve species and is presently considered a derived group of the modern bivalves (Newell 1965 ; Waller 1998 ). Heterodonta is subdivided into two major lineages, the hyperdiverse Euheterodonta and Archiheterodonta. The latter comprises four relatively small extant families: Astartidae, Carditidae, Condylocardiidae and Crassatellidae, whose relationships and internal phylogeny are poorly understood. We assessed the phylogeny of archiheterodont bivalves using a multilocus data set comprised of molecular sequence data from six loci (18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, cytochrome b, internal transcribed spacer 2 and histone H3). Resultant data sets of ~4 Kb of concatenated molecular sequence data were analysed using probabilistic approaches (maximum likelihood and Bayesian inference) and parsimony direct optimization. We recovered strong support for the monophyly of Archiheterodonta, within which Astartidae is the sister group of Crassatellidae, and these two constitute the sister clade of Carditidae, which is paraphyletic with respect to Condylocardiidae. The relationships among the constituent species groups were evaluated in the context of the archiheterodont fossil record through the estimation of divergence times. Diversification times of archiheterodont families were congruent with bounded estimates of origins based on palaeontological data: Archiheterodonta diversified during the Devonian, 373.1 Ma (95% highest posterior density interval [HPD] 325.8–428.2); Crassatelloidea around the Carboniferous, 330.1 Ma (95% HPD 291.0–372.7); Crassatellidae around the Triassic, 224.0 (95% HPD 140.6–320.2); Astartidae around the Permian, 288.2 Ma (95% HPD 269.2–307.3); and Carditoidea around the Jurassic, 178.8 Ma (95% HPD 120.9–228.3).