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https://www.readbyqxmd.com/read/28543951/determination-of-genetic-relatedness-from-low-coverage-human-genome-sequences-using-pedigree-simulations
#1
Michael D Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin
We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate, and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination, and sequencing error...
May 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28543226/interactions-within-and-between-clades-shaped-the-diversification-of-terrestrial-carnivores
#2
Mathias M Pires, Daniele Silvestro, Tiago B Quental
A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within-clade diversity dependence suppressing speciation rates and detected between-clade effects increasing extinction rates in six instances...
May 22, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28542710/behavioral-inferences-from-the-high-levels-of-dental-chipping-in-homo-naledi
#3
Ian Towle, Joel D Irish, Isabelle De Groote
OBJECTIVES: A variety of mechanical processes can result in antemortem dental chipping. In this study, chipping data in the teeth of Homo naledi are compared with those of other pertinent dental samples to give insight into their etiology. MATERIALS AND METHODS: Permanent teeth with complete crowns evidencing occlusal wear were examined macroscopically. The location, number, and severity of fractures were recorded and compared to those found in samples of two other South African fossil hominin species and in samples of nonhuman primates (n = 3) and recent humans (n = 7)...
May 24, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28542704/trabecular-and-cortical-bone-structure-of-the-talus-and-distal-tibia-in-pan-and-homo
#4
Zewdi J Tsegai, Matthew M Skinner, Andrew H Gee, Dieter H Pahr, Graham M Treece, Jean-Jacques Hublin, Tracy L Kivell
OBJECTIVES: Internal bone structure, both cortical and trabecular bone, remodels in response to loading and may provide important information regarding behavior. The foot is well suited to analysis of internal bone structure because it experiences the initial substrate reaction forces, due to its proximity to the substrate. Moreover, as humans and apes differ in loading of the foot, this region is relevant to questions concerning arboreal locomotion and bipedality in the hominoid fossil record...
May 24, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28542538/new-evidence-indicates-the-presence-of-barracuda-sphyraenidae-and-supports-a-tropical-marine-environment-in-the-miocene-of-madagascar
#5
Michael D Gottfried, Karen E Samonds, Summer A Ostrowski, Tsiory Harimalala Andrianavalona, Tolotra Niaina Ramihangihajason
Recent exploration of Miocene-age deposits at Nosy Makamby, a small island ~50 km southwest of Mahajanga city in northwestern Madagascar, has led to the recovery of a large sample [82] of isolated barracuda teeth (Sphyraena sp.). in a tropical marine fauna that also includes diverse marine invertebrates, chondrichthyans, bony fishes, turtles, crocodylians, and sirenians. Characteristically for barracudas, the teeth are labiolingually flattened and fang-like with a broadly triangular and blade-like acuminate outline and sharply edged but unserrated cutting margins...
2017: PloS One
https://www.readbyqxmd.com/read/28542468/alveoli-teeth-and-tooth-loss-understanding-the-homology-of-internal-mandibular-structures-in-mysticete-cetaceans
#6
Carlos Mauricio Peredo, Nicholas D Pyenson, Mark D Uhen, Christopher D Marshall
The evolution of filter feeding in baleen whales (Mysticeti) facilitated a wide range of ecological diversity and extreme gigantism. The innovation of filter feeding evolved in a shift from a mineralized upper and lower dentition in stem mysticetes to keratinous baleen plates that hang only from the roof of the mouth in extant species, which are all edentulous as adults. While all extant mysticetes are born with a mandible lacking a specialized feeding structure (i.e., baleen), the bony surface retains small foramina with elongated sulci that often merge together in what has been termed the alveolar gutter...
2017: PloS One
https://www.readbyqxmd.com/read/28542291/the-first-darter-aves-anhingidae-fossils-from-india-late-pliocene
#7
Thomas Stidham, Rajeev Patnaik, Kewal Krishan, Bahadur Singh, Abhik Ghosh, Ankita Singla, Simran S Kotla
New fossils from the latest Pliocene portion of the Tatrot Formation exposed in the Siwalik Hills of northern India represent the first fossil record of a darter (Anhingidae) from India. The darter fossils possibly represent a new species, but the limited information on the fossil record of this group restricts their taxonomic allocation. The Pliocene darter has a deep pit on the distal face of metatarsal trochlea IV not reported in other anhingids, it has an open groove for the m. flexor perforatus et perforans digiti II tendon on the hypotarsus unlike New World anhingid taxa, and these darter specimens are the youngest of the handful of Neogene records of the group from Asia...
2017: PloS One
https://www.readbyqxmd.com/read/28542238/frutexites-like-structures-formed-by-iron-oxidizing-biofilms-in-the-continental-subsurface-%C3%A3-sp%C3%A3-hard-rock-laboratory-sweden
#8
Christine Heim, Nadia-Valérie Quéric, Danny Ionescu, Nadine Schäfer, Joachim Reitner
Stromatolitic iron-rich structures have been reported from many ancient environments and are often described as Frutexites, a cryptic microfossil. Although microbial formation of such structures is likely, a clear relation to a microbial precursor is lacking so far. Here we report recent iron oxidizing biofilms which resemble the ancient Frutexites structures. The living Frutexites-like biofilms were sampled at 160 m depth in the Äspö Hard Rock Laboratory in Sweden. Investigations using microscopy, 454 pyrosequencing, FISH, Raman spectroscopy, biomarker and trace element analysis allowed a detailed view of the structural components of the mineralized biofilm...
2017: PloS One
https://www.readbyqxmd.com/read/28537283/effects-of-the-capping-ligands-linkers-and-oxide-surface-on-the-electron-injection-mechanism-of-copper-sulfide-quantum-dot-sensitized-solar-cells
#9
Javier Amaya Suárez, Jose J Plata, Antonio M Márquez, Javier Fdez Sanz
Quantum dot-sensitized solar cells, QDSCs, are a clean and effective alternative to fossil fuels to reduce CO2 emissions. However, the different components that constitute the QDSCs and the difficulty of isolating experimentally their effects on the performance of the whole system slow down the development of more efficient devices. In this work, DFT calculations are combined with a bottom-up approach to differentiate the effect of each component on the electronic structure and absorption spectra. First, Cu2S QDs were built including a U parameter to effectively describe the localization of electrons...
May 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28535779/carriers-of-mitochondrial-dna-macrohaplogroup-r-colonized-eurasia-and-australasia-from-a-southeast-asia-core-area
#10
Jose M Larruga, Patricia Marrero, Khaled K Abu-Amero, Maria V Golubenko, Vicente M Cabrera
BACKGROUND: The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia...
May 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28533965/reappraisal-of-the-extinct-seal-phoca-vitulinoides-from-the-neogene-of-the-north-sea-basin-with-bearing-on-its-geological-age-phylogenetic-affinities-and-locomotion
#11
Leonard Dewaele, Eli Amson, Olivier Lambert, Stephen Louwye
BACKGROUND: Discovered on the southern margin of the North Sea Basin, "Phoca" vitulinoides represents one of the best-known extinct species of Phocidae. However, little attention has been given to the species ever since its original 19th century description. Newly discovered material, including the most complete specimen of fossil Phocidae from the North Sea Basin, prompted the redescription of the species. Also, the type material of "Phoca" vitulinoides is lost. METHODS: "Phoca" vitulinoides is redescribed...
2017: PeerJ
https://www.readbyqxmd.com/read/28533964/lygistorrhinidae-diptera-bibionomorpha-sciaroidea-in-early-eocene-cambay-amber
#12
Frauke Stebner, Hukam Singh, Jes Rust, David A Grimaldi
One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina. Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before...
2017: PeerJ
https://www.readbyqxmd.com/read/28533204/diverse-early-dwarf-mistletoes-arceuthobium-ecological-keystones-of-the-eocene-baltic-amber-biota
#13
Eva-Maria Sadowski, Leyla J Seyfullah, Carol A Wilson, Clyde L Calvin, Alexander R Schmidt
PREMISE OF THE STUDY: Extant dwarf mistletoes (Arceuthobium M. Bieb., Viscaceae) are hemiparasites with complex roles in nature. They are one of the most severe pests in northern hemisphere conifer forests, but they also enhance the structural complexity and species diversity of the forests. Here, we describe the first pre-Miocene macrofossils of dwarf mistletoes. The fossils from Eocene Baltic amber provide new insights into the morphological evolution of the Arceuthobium lineage and its paleobiogeography...
May 21, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28531851/comparative-life-cycle-assessment-study-on-environmental-impact-of-oil-production-from-micro-algae-and-terrestrial-oilseed-crops
#14
S Jez, D Spinelli, A Fierro, A Dibenedetto, M Aresta, E Busi, R Basosi
In this study the LCA methodology is applied in order to satisfy two goals: i) to evaluate the hot spots in site-specific production chain of biodiesel from terrestrial and micro-algae feedstock; ii) to compare quantitatively, utilizing primary data, the impacts of the first generation in respect to the third generation bio-fuels. Results show that micro-algae are neither competitive yet with traditional oil crops nor with fossil fuel. The use of renewable technologies as photovoltaics and biogas self production might increase the competitiveness of micro-algae oil...
May 10, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28531204/messinian-age-and-savannah-environment-of-the-possible-hominin-graecopithecus-from-europe
#15
Madelaine Böhme, Nikolai Spassov, Martin Ebner, Denis Geraads, Latinka Hristova, Uwe Kirscher, Sabine Kötter, Ulf Linnemann, Jérôme Prieto, Socrates Roussiakis, George Theodorou, Gregor Uhlig, Michael Winklhofer
Dating fossil hominids and reconstructing their environments is critically important for understanding human evolution. Here we date the potentially oldest hominin, Graecopithecus freybergi from Europe and constrain the environmental conditions under which it thrived. For the Graecopithecus-bearing Pikermi Formation of Attica/Greece, a saline aeolian dust deposit of North African (Sahara) provenance, we obtain an age of 7.37-7.11 Ma, which is coeval with a dramatic cooling in the Mediterranean region at the Tortonian-Messinian transition...
2017: PloS One
https://www.readbyqxmd.com/read/28531170/potential-hominin-affinities-of-graecopithecus-from-the-late-miocene-of-europe
#16
Jochen Fuss, Nikolai Spassov, David R Begun, Madelaine Böhme
The split of our own clade from the Panini is undocumented in the fossil record. To fill this gap we investigated the dentognathic morphology of Graecopithecus freybergi from Pyrgos Vassilissis (Greece) and cf. Graecopithecus sp. from Azmaka (Bulgaria), using new μCT and 3D reconstructions of the two known specimens. Pyrgos Vassilissis and Azmaka are currently dated to the early Messinian at 7.175 Ma and 7.24 Ma. Mainly based on its external preservation and the previously vague dating, Graecopithecus is often referred to as nomen dubium...
2017: PloS One
https://www.readbyqxmd.com/read/28530240/controlling-for-the-species-area-effect-supports-constrained-long-term-mesozoic-terrestrial-vertebrate-diversification
#17
Roger A Close, Roger B J Benson, Paul Upchurch, Richard J Butler
Variation in the geographic spread of fossil localities strongly biases inferences about the evolution of biodiversity, due to the ubiquitous scaling of species richness with area. This obscures answers to key questions, such as how tetrapods attained their tremendous extant diversity. Here, we address this problem by applying sampling standardization methods to spatial regions of equal size, within a global Mesozoic-early Palaeogene data set of non-flying terrestrial tetrapods. We recover no significant increase in species richness between the Late Triassic and the Cretaceous/Palaeogene (K/Pg) boundary, strongly supporting bounded diversification in Mesozoic tetrapods...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28528908/the-new-red-algal-subphylum-proteorhodophytina-comprises-the-largest-and-most-divergent-plastid-genomes-known
#18
Sergio A Muñoz-Gómez, Fabián G Mejía-Franco, Keira Durnin, Morgan Colp, Cameron J Grisdale, John M Archibald, Claudio H Slamovits
Red algal plastid genomes are often considered ancestral and evolutionarily stable, and thus more closely resembling the last common ancestral plastid genome of all photosynthetic eukaryotes [1, 2]. However, sampling of red algal diversity is still quite limited (e.g., [2-5]). We aimed to remedy this problem. To this end, we sequenced six new plastid genomes from four undersampled and phylogenetically disparate red algal classes (Porphyridiophyceae, Stylonematophyceae, Compsopogonophyceae, and Rhodellophyceae) and discovered an unprecedented degree of genomic diversity among them...
May 17, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28528757/temporal-and-seasonal-variations-of-black-carbon-in-a-highly-polluted-european-city-apportionment-of-potential-sources-and-the-effect-of-meteorological-conditions
#19
Marek Kucbel, Agnieszka Corsaro, Barbora Švédová, Helena Raclavská, Konstantin Raclavský, Dagmar Juchelková
Black carbon - a primary component of particulate matter emitted from an incomplete combustion of fossil fuels, biomass, and biofuels - has been found to have a detrimental effect on human health and the environment. Since black carbon emissions data are not readily available, no measures are implemented to reduce black carbon emissions. The temporal and seasonal variations of black carbon concentrations were evaluated during 2012-2014. The data were collected in the highly polluted European city - Ostrava, Czech Republic, surrounded by major highways and large industries...
May 18, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28528483/fossil-record-of-ephedra-in-the-lower-cretaceous-aptian-argentina
#20
Gabriela G Puebla, Ari Iglesias, María A Gómez, Mercedes B Prámparo
Fossil plants from the Lower Cretaceous (upper Aptian) of the La Cantera Formation, Argentina, are described. The fossils studied represent a leafy shooting system with several orders of articulated and striated axes and attached leaves with unequivocal ephedroid affinity. We also found associated remains of ovulate cones with four whorls of sterile bracts, which contain two female reproductive units (FRU). Ovulate cone characters fit well within the genus Ephedra. Special characters in the ovulate cones including an outer seed envelope with two types of trichomes, allowed us to consider our remains as a new Ephedra species...
May 20, 2017: Journal of Plant Research
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