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https://www.readbyqxmd.com/read/28196688/biodiversity-and-topographic-complexity-modern-and-geohistorical-perspectives
#1
REVIEW
Catherine Badgley, Tara M Smiley, Rebecca Terry, Edward B Davis, Larisa R G DeSantis, David L Fox, Samantha S B Hopkins, Tereza Jezkova, Marjorie D Matocq, Nick Matzke, Jenny L McGuire, Andreas Mulch, Brett R Riddle, V Louise Roth, Joshua X Samuels, Caroline A E Strömberg, Brian J Yanites
Topographically complex regions on land and in the oceans feature hotspots of biodiversity that reflect geological influences on ecological and evolutionary processes. Over geologic time, topographic diversity gradients wax and wane over millions of years, tracking tectonic or climatic history. Topographic diversity gradients from the present day and the past can result from the generation of species by vicariance or from the accumulation of species from dispersal into a region with strong environmental gradients...
February 11, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28187191/empirical-and-bayesian-approaches-to-fossil-only-divergence-times-a-study-across-three-reptile-clades
#2
Alan H Turner, Adam C Pritchard, Nicholas J Matzke
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time...
2017: PloS One
https://www.readbyqxmd.com/read/28181330/discrete-and-morphometric-traits-reveal-contrasting-patterns-and-processes-in-the-macroevolutionary-history-of-a-clade-of-scorpions
#3
Nicolas Mongiardino Koch, F Sara Ceccarelli, Andrés A Ojanguren-Affilastro, Martín J Ramírez
Many paleontological studies have investigated the evolution of entire body plans, generally relying on discrete character-taxon matrices. In contrast, macroevolutionary studies performed by neontologists have mostly focused on morphometric traits. Although these data types are very different, some studies have suggested that they capture common patterns. Nonetheless, the tests employed to support this claim have not explicitly incorporated a phylogenetic framework, and may therefore be susceptible to confounding effects due to the presence of common phylogenetic structure...
February 9, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28148209/paleontological-studies-integrated-into-a-new-evolutionary-zoology
#4
Shigeru Kuratani, Takema Fukatsu
Zoological Letters, an open access online journal launched in 2015 is entering its third year of publication, and now seeks to drive new insights in evolutionary and comparative zoology by the inclusion of paleontological studies into its scope.
February 2017: Zoological Science
https://www.readbyqxmd.com/read/28111950/expansion-for-the-brachylophosaurus-canadensis-collagen-i-sequence-and-additional-evidence-of-the-preservation-of-cretaceous-protein
#5
Elena R Schroeter, Caroline J DeHart, Timothy P Cleland, Wenxia Zheng, Paul M Thomas, Neil L Kelleher, Marshall Bern, Mary H Schweitzer
Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28107398/integrated-chronology-flora-and-faunas-and-paleoecology-of-the-alajuela-formation-late-miocene-of-panama
#6
Bruce J MacFadden, Douglas S Jones, Nathan A Jud, Jorge W Moreno-Bernal, Gary S Morgan, Roger W Portell, Victor J Perez, Sean M Moran, Aaron R Wood
The late Miocene was an important time to understand the geological, climatic, and biotic evolution of the ancient New World tropics and the context for the Great American Biotic Interchange (GABI). Despite this importance, upper Miocene deposits containing diverse faunas and floras and their associated geological context are rare in Central America. We present an integrated study of the geological and paleontological context and age of a new locality from Lago Alajuela in northern Panama (Caribbean side) containing late Miocene marine and terrestrial fossils (plants, invertebrates, and vertebrates) from the Alajuela Formation...
2017: PloS One
https://www.readbyqxmd.com/read/28073604/morphometric-and-genetic-analysis-of-arcella-intermedia-and-arcella-intermedia-laevis-amoebozoa-arcellinida-illuminate-phenotypic-plasticity-in-microbial-eukaryotes
#7
Alfredo L Porfírio-Sousa, Giulia M Ribeiro, Daniel J G Lahr
Testate amoebae are eukaryotic microorganisms characterized by the presence of an external shell (test). The shell morphology is used as a diagnostic character, but discordance between morphological and molecular data has been demonstrated in groups of arcellinids (Amoebozoa), one of the principal groups of testate amoebae. Morphology of the test is supposed to differentiate genera and species and it is applied in ecological, monitoring and paleontological studies. However, if phenotype does not reflect genotype, conclusions in these types of studies become severely impaired...
November 25, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/28028456/seqenv-linking-sequences-to-environments-through-text-mining
#8
Lucas Sinclair, Umer Z Ijaz, Lars Juhl Jensen, Marco J L Coolen, Cecile Gubry-Rangin, Alica Chroňáková, Anastasis Oulas, Christina Pavloudi, Julia Schnetzer, Aaron Weimann, Ali Ijaz, Alexander Eiler, Christopher Quince, Evangelos Pafilis
Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context...
2016: PeerJ
https://www.readbyqxmd.com/read/28012461/ten-years-in-the-dump-an-updated-review-of-the-miocene-primate-bearing-localities-from-abocador-de-can-mata-ne-iberian-peninsula
#9
David M Alba, Isaac Casanovas-Vilar, Miguel Garcés, Josep M Robles
More than ten years of paleontological fieldwork during the enlargement of the Can Mata Landfill (Abocador de Can Mata [ACM]), in els Hostalets de Pierola (Vallès-Penedès Basin, NE Iberian Peninsula) led to the recovery of >60,000 Miocene vertebrate remains. The huge sampling effort (due to continuous surveillance of heavy machinery digging activity, coupled with manual excavation and screen-washing of sediments) enabled generally rare faunal elements such as pliopithecoid and hominoid primates to be found...
January 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28004894/explanations-for-adaptations-just-so-stories-and-limitations-on-evidence-in-evolutionary-biology
#10
Richard J Smith
Explanations of the historical origin of specific individual traits are a key part of the research program in paleontology and evolutionary biology. Why did bipedalism evolve in the human lineage? Why did some dinosaurs and related species have head crests? Why did viviparity evolve in some reptiles? Why did the common ancestor of primates evolve stereoscopic vision, grasping hands and feet, nails instead of claws, and large brains? These are difficult questions. To varying degrees, an explanation must grapple with (1) judgments about changes in fitness that might follow from a change in morphology - without actually observing behavior or measuring reproductive success, (2) the relationship between genes and traits, (3) limitations on doing relevant experiments, (4) the interpretation of causes that are almost certainly contingent, multifactorial, interactive, hierarchical, nonlinear, emergent, and probabilistic rather than deterministic, (5) limited information about variation and ontogeny, (6) a dataset based on the random fortunes of the historical record, including only partial hard-tissue morphology and no soft-tissue morphology, (7) an equally partial and problematic (for example, time-averaged) record of the environment, (8) the compression of all data into a geological time scale that is likely to miss biologically important events or fluctuations, (9) dependence on a process that can only be inferred ("form and even behavior may leave fossil traces, but forces like natural selection do not", (1:130) ) and finally, (10) the assumption of the "adaptationist programme"(2) that the trait in question is in fact an adaptation rather than a consequence of genetic drift, correlated evolution, pleiotropy, exaptation, or other mechanisms...
November 2016: Evolutionary Anthropology
https://www.readbyqxmd.com/read/28003534/dental-data-perform-relatively-poorly-in-reconstructing-mammal-phylogenies-morphological-partitions-evaluated-with-molecular-benchmarks
#11
Robert S Sansom, Matthew Albion Wills, Tamara Williams
Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and non-independence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 datasets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, and that osteological characters are significantly more compatible with molecular trees...
December 20, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28000409/the-evolution-of-the-zygomatic-bone-from-agnatha-to-tetrapoda
#12
Zhikun Gai, Xiaobo Yu, Min Zhu
Establishing the homology of the zygomatic or jugal bone and tracing its origin and early evolution represents a complex issue because of large morphological gaps between various groups of vertebrates. Using recent paleontological findings, we discuss the deep homology of the zygomatic or jugal bone in stem gnathostomes (placoderms) and examine its homology and modifications in crown gnathostomes (acanthodians, chondrichthyans and osteichthyans). The discovery of the placoderm Entelognathus from the Silurian of China (∼423 million years ago) established that the large dermal plates in placoderms and osteichthyans are homologous...
January 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/27940618/from-teeth-to-baleen-and-raptorial-to-bulk-filter-feeding-in-mysticete-cetaceans-the-role-of-paleontological-genetic-and-geochemical-data-in-feeding-evolution-and-ecology
#13
Annalisa Berta, Agnese Lanzetti, Eric G Ekdale, Thomas A Deméré
The origin of baleen and filter feeding in mysticete cetaceans occurred sometime between approximately 34 and 24 million years ago and represents a major macroevolutionary shift in cetacean morphology (teeth to baleen) and ecology (raptorial to filter feeding). We explore this dramatic change in feeding strategy by employing a diversity of tools and approaches: morphology, molecules, development, and stable isotopes from the geological record. Adaptations for raptorial feeding in extinct toothed mysticetes provide the phylogenetic context for evaluating morphological apomorphies preserved in the skeletons of stem and crown edentulous mysticetes...
December 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/27939713/incorporating-fossils-into-hypotheses-of-insect-phylogeny
#14
REVIEW
Jessica L Ware, Phillip Barden
Fossils represent stem and crown lineages, and their inclusion in phylogenetic reconstruction influences branch lengths, topology, and divergence time estimation. In addition, paleontological data may inform trends in morphological evolution as well as biogeographic history. Here we review the incorporation of fossils in studies of insect evolution, from morphological analyses to combined 'total evidence' node dating analyses. We discuss challenges associated with fossil based phylogenetics, and suggest best practices for use in tree reconstruction...
December 2016: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/27917244/la-images-a-software-for-elemental-distribution-bioimaging-using-la-icp-ms-data
#15
Hugo López-Fernández, Gustavo de S Pessôa, Marco A Z Arruda, José L Capelo-Martínez, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato
The spatial distribution of chemical elements in different types of samples is an important field in several research areas such as biology, paleontology or biomedicine, among others. Elemental distribution imaging by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is an effective technique for qualitative and quantitative imaging due to its high spatial resolution and sensitivity. By applying this technique, vast amounts of raw data are generated to obtain high-quality images, essentially making the use of specific LA-ICP-MS imaging software that can process such data absolutely mandatory...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27897168/stepwise-onset-of-the-icehouse-world-and-its-impact-on-oligo-miocene-central-asian-mammals
#16
Mathias Harzhauser, Gudrun Daxner-Höck, Paloma López-Guerrero, Olivier Maridet, Adriana Oliver, Werner E Piller, Sylvain Richoz, Margarita A Erbajeva, Thomas A Neubauer, Ursula B Göhlich
Central Asia is a key area to study the impact of Cenozoic climate cooling on continental ecosystems. One of the best places to search for rather continuous paleontological records is the Valley of Lakes in Mongolia with its outstandingly fossil-rich Oligocene and Miocene terrestrial sediments. Here, we investigate the response by mammal communities during the early stage of Earth's icehouse climate in Central Asia. Based on statistical analyses of occurrence and abundance data of 18608 specimens representing 175 mammal species and geochemical (carbon isotopes) and geophysical (magnetic susceptibility) data we link shifts in diversities with major climatic variations...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27886207/characteristic-tetrapod-musculoskeletal-limb-phenotype-emerged-more-than-400-mya-in-basal-lobe-finned-fishes
#17
Rui Diogo, Peter Johnston, Julia L Molnar, Borja Esteve-Altava
Previous accounts of the origin of tetrapod limbs have postulated a relatively sudden change, after the split between extant lobe-finned fish and tetrapods, from a very simple fin phenotype with only two muscles to the highly complex tetrapod condition. The evolutionary changes that led to the muscular anatomy of tetrapod limbs have therefore remained relatively unexplored. We performed dissections, histological sections, and MRI scans of the closest living relatives of tetrapods: coelacanths and lungfish. Combined with previous comparative, developmental and paleontological information, our findings suggest that the characteristic tetrapod musculoskeletal limb phenotype was already present in the Silurian last common ancestor of extant sarcopterygians, with the exception of the autopod (hand/foot) structures, which have no clear correspondence with fish structures...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27804976/tetrapod-limb-and-sarcopterygian-fin-regeneration-share-a-core-genetic-programme
#18
Acacio F Nogueira, Carinne M Costa, Jamily Lorena, Rodrigo N Moreira, Gabriela N Frota-Lima, Carolina Furtado, Mark Robinson, Chris T Amemiya, Sylvain Darnet, Igor Schneider
Salamanders are the only living tetrapods capable of fully regenerating limbs. The discovery of salamander lineage-specific genes (LSGs) expressed during limb regeneration suggests that this capacity is a salamander novelty. Conversely, recent paleontological evidence supports a deeper evolutionary origin, before the occurrence of salamanders in the fossil record. Here we show that lungfishes, the sister group of tetrapods, regenerate their fins through morphological steps equivalent to those seen in salamanders...
November 2, 2016: Nature Communications
https://www.readbyqxmd.com/read/27725256/segmentation-in-tardigrada-and-diversification-of-segmental-patterns-in-panarthropoda
#19
Frank W Smith, Bob Goldstein
The origin and diversification of segmented metazoan body plans has fascinated biologists for over a century. The superphylum Panarthropoda includes three phyla of segmented animals-Euarthropoda, Onychophora, and Tardigrada. This superphylum includes representatives with relatively simple and representatives with relatively complex segmented body plans. At one extreme of this continuum, euarthropods exhibit an incredible diversity of serially homologous segments. Furthermore, distinct tagmosis patterns are exhibited by different classes of euarthropods...
October 7, 2016: Arthropod Structure & Development
https://www.readbyqxmd.com/read/27717134/ontogeny-of-modern-human-longitudinal-body-and-transverse-shoulder-proportions
#20
Mélanie A Frelat, Michael Coquerelle, Erik Trinkaus
OBJECTIVES: Whereas variation of modern human adult body size and shape has been widely studied in the context of ecogeographical clines, little is known about the differential growth patterns of transverse and longitudinal dimensions among human populations. Our study explored the ontogenetic variation of those body proportions in modern humans. METHODS: We compared results from four different approaches to study cross-sectional skeletal samples of Africans (n = 43), Amerindians (n = 69) and Europeans (n = 40) from 0 to 14 years of age...
September 26, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
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