Phylogeny, ancestors and anagenesis in the hominin fossil record

2018 ◽  
Author(s):  
Caroline Parins-Fukuchi ◽  
Elliot Greiner ◽  
Laura M. MacLatchy ◽  
Daniel C. Fisher
Keyword(s):  
Probabilistic Models ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Probabilistic Methods ◽  
Evolutionary Divergence ◽  
Temporal Data ◽  
Evolutionary Pattern ◽  
Phylogenetic Methods ◽  
Competing Models ◽  
Fossil Preservation

AbstractProbabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary pattern by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a dataset of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages: Sahelanthropus is ancestral to later hominins; Australopithecus anamensis is ancestral to Au. afarensis; Au. garhi is ancestral to Homo; H. antecessor is ancestral to H. heidelbergensis, which in turn is ancestral to both H. sapiens and H. neanderthalensis. These results show a benefit of accommodating direct ancestry in phylogenetics. By so doing, quantitative results align more closely with previous qualitative expectations.

scholarly journals Phylogeny, ancestors, and anagenesis in the hominin fossil record

Paleobiology ◽  
2019 ◽  
Vol 45 (02) ◽  
pp. 378-393
Author(s):  
Caroline Parins-Fukuchi ◽  
Elliot Greiner ◽  
Laura M. MacLatchy ◽  
Daniel C. Fisher
Keyword(s):  
Homo Sapiens ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Probabilistic Methods ◽  
Evolutionary Divergence ◽  
Temporal Data ◽  
Australopithecus Afarensis ◽  
Homo Heidelbergensis ◽  
Data Set ◽  
Phylogenetic Methods

AbstractProbabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary patterns by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a data set of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages: Sahelanthropus is ancestral to later hominins; Australopithecus anamensis is ancestral to Australopithecus afarensis; Australopithecus garhi is ancestral to Homo; Homo antecessor is ancestral to Homo heidelbergensis, which in turn is ancestral to both Homo sapiens and Homo neanderthalensis. By accommodating direct ancestry in phylogenetics, quantitative results align more closely with previous qualitative expectations.

Segregation and speciation in the Neogene planktonic foraminiferal clade Globoconella

Paleobiology ◽  
1999 ◽  
Vol 25 (3) ◽  
pp. 383-395 ◽  
Author(s):  
Cynthia E. Schneider ◽  
James P. Kennett
Keyword(s):  
Morphological Evolution ◽  
Evolutionary Divergence ◽  
Clinal Variation ◽  
Near Surface ◽  
Surface Warming ◽  
Isotopic Analyses ◽  
Oxygen Isotopic ◽  
Morphological Differences ◽  
Middle Pliocene ◽  
Water Depths

The origin of the Neogene planktonic foraminifer Globorotalia (Globoconella) pliozea in the subtropical southwest Pacific has been attributed to its isolation resulting from intensification of the Subtropical Divergence (Tasman Front). Oxygen isotopic analyses suggest that, although the Subtropical Divergence may have played a role, the evolution of Gr. (G.) pliozea was facilitated by depth segregation of Gr. (G.) conomiozea morphotypes (low and high conical) during an interval of near-surface warming and increasing thermal gradient. Oxygen isotopic analyses suggest that low conical morphotypes of Gr. (G.) conomiozea inhabited greater depths than high conical morphotypes. Low conical forms of Gr. (G.) conomiozea are considered ancestral to the low conical species, Gr. (G.) pliozea. Oxygen isotopes indicate that Gr. (G.) pliozea inhabited greater depths than its ancestor, Gr. (G.) conomiozea.These data are consistent with depth-parapatric and depth-allopatric models, but not with a sympatric model of speciation. In the allopatric model, reproduction at different water depths acts as a barrier between morphotypes. In the parapatric model, clinal variation along a depth gradient acts as a barrier between morphotypes living at the limits of the gradient. Depth segregation in both models results in genetic isolation and evolutionary divergence. Our data support a correlation between morphological evolution and habitat changes in the Globoconella clade, implying separation of populations as a driving force for morphological evolution.Ecological segregation of morphotypes and species may be related to morphology (height of the conical angle), based on the data from Gr. (G.) conomiozea and Gr. (G.) pliozea. However, morphological differences alone do not necessarily produce depth differences. Large morphological differences between Gr. (G.) pliozea and closely related Gr. (G.) puncticulata did not result in isotopic and therefore depth differences between these species. These species coexisted at the same water depths for nearly 1 m.y. Thus, it is unlikely that the extinction of Gr. (G.) pliozea in the middle Pliocene resulted from competition with Gr. (G.) puncticulata, as previously suggested.

scholarly journals Habitat Partitioning and Overlap by Large Lacertid Lizards in Southern Europe

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 155
Author(s):  
Daniel Escoriza ◽  
Félix Amat
Keyword(s):  
Related Species ◽  
Vegetation Cover ◽  
Western Europe ◽  
Phylogenetic Analyses ◽  
Niche Partitioning ◽  
Probabilistic Methods ◽  
Climate Niche ◽  
Rich Diversity ◽  
Occupancy Patterns ◽  
Lacertid Lizards

South-western Europe has a rich diversity of lacertid lizards. In this study, we evaluated the occupancy patterns and niche segregation of five species of lacertids, focusing on large-bodied species (i.e., adults having >75 mm snout-vent length) that occur in south-western Europe (Italian to the Iberian Peninsula). We characterized the niches occupied by these species based on climate and vegetation cover properties. We expected some commonality among phylogenetically related species, but also patterns of habitat segregation mitigating competition between ecologically equivalent species. We used multivariate ordination and probabilistic methods to describe the occupancy patterns and evaluated niche evolution through phylogenetic analyses. Our results showed climate niche partitioning, but with a wide overlap in transitional zones, where segregation is maintained by species-specific responses to the vegetation cover. The analyses also showed that phylogenetically related species tend to share large parts of their habitat niches. The occurrence of independent evolutionary lineages contributed to the regional species richness favored by a long history of niche divergence.

scholarly journals SATELLITE DNAs IN THE EMBRYOS OF VARIOUS SPECIES OF THE GENUS DROSOPHILA

Genetics ◽  
1972 ◽  
Vol 72 (3) ◽  
pp. 431-439
Author(s):  
E C Travaglini ◽  
J Petrovic ◽  
J Schultz
Keyword(s):  
Buoyant Density ◽  
Gc Content ◽  
Drosophila Species ◽  
Class I ◽  
Evolutionary Divergence ◽  
Dna Molecules ◽  
Class Iii ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Gc Composition

ABSTRACT A tentative evolutionary pattern has been found for two classes of the multiple satellite DNA's found in the genus Drosophila. The satellite DNA's from five Drosophila species (D. melanogaster, D. simulans, D. nasuta, D. virilis and D. hydei) were analyzed and found to fall into three arbitrary CsCl buoyant density classes: Class I, ρ = 1.661-1.669 g cm-3, DNA molecules composed of primarily dA and dT moieties; Class II, ρ = 1.685 and ρ = 1.692, DNA molecules of low GC content; and Class III, ρ = 1.711, a DNA of high GC composition. The dAT satellite DNA's appear in all the species studied except D. hydei, the species of most recent evolutionary divergence, whereas the heavy satellite appears only in the two species of most recent divergence, D. virilis and D. hydei.

Comparison of Probabilistic and Possibility Theory-Based Methods for Design Against Catastrophic Failure Under Uncertainty

1999 ◽  
Author(s):  
Efstratios Nikolaidis ◽  
Harley Cudney ◽  
Sophie Chen ◽  
Raphael T. Haftka ◽  
Raluca Rosca
Keyword(s):  
Probabilistic Models ◽  
Failure Modes ◽  
Possibility Theory ◽  
Probabilistic Methods ◽  
Sufficient Information ◽  
Catastrophic Failure ◽  
Design Problems ◽  
Available Information ◽  
Theoretical Foundations ◽  
Better Than

Abstract This paper compares probabilistic and possibility-based methods for design against catastrophic failure under uncertainty. It studies the effect of the amount of information on the effectiveness of each method. The study is confined to problems where the boundary between survival and failure is sharp. First, the paper examines the theoretical foundations of probability and possibility. It also compares the two methods when they are used to assess the risk of a system. Finally, it compares the two methods on two design problems. A major difference between probability and possibility is in the axioms about the union of events. Because of this difference, probability and possibility calculi are fundamentally different and one cannot simulate possibility calculus using probabilistic models. It is shown that possibility-based methods can be less conservative than probability-based methods in systems with many failure modes. On the other hand, possibility-based methods tend to be more conservative than probability-based methods in systems that fail only if many unfavorable events occur simultaneously. Probabilistic methods are better than possibility-based methods if sufficient information is available. However, the latter can be better if little information is available. A principal reason is that it is easier to identify the most conservative possibilistic model than the most conservative probabilistic model that is consistent with the available information.

scholarly journals Micromorphological, anatomical and molecular study of Hedera species (Araliaceae) in Iran

2020 ◽  
Vol 63 (2) ◽  
pp. 91-101
Author(s):  
Elham Amini ◽  
Fatemeh Nasrollahi ◽  
Ali Sattarian ◽  
Mahboobeh Haji Moradkhani ◽  
Sohrab Boozarpour ◽  
...  
Keyword(s):  
North Africa ◽  
Phylogenetic Analyses ◽  
Molecular Study ◽  
Molecular Characteristics ◽  
Nrdna Its ◽  
Anticlinal Wall ◽  
Data Set ◽  
Phylogenetic Methods ◽  
Extant Species ◽  
Qualitative Characters

Hedera, with 12 extant species, is a genus of evergreen climbers native to Europe, north Africa, and south Asia. In this study, the micromorphological, anatomical structure and molecular evidences of 11 populations from two species of Hedera (H. helix and H. pastuchovii) have been considered to evaluate the relationships in Hedera. In total, seven quantitative and qualitative characters of pollen were selected and measured. Based on this study, the anticlinal wall and surface sculpturing of seed support for separation of two species of Hedera. Micromorphology of epidermis illustrated two types of epidermal cells: puzzle-shaped and polygonal cells. Using nuclear (nrDNA ITS) marker, we reconstructed phylogenetic relationships within two species of Hedera. This data set was analyzed by phylogenetic methods including Bayesian inference, maximum likelihood, and maximum parsimony. In phylogenetic analyses, all members of two species formed a well-supported clade (PP = 1; ML/BS = 100/100) and divided into two major clades (A and B). Neighbor Net diagram demonstrated separation of the studied populations. The results showed that these taxa differ in taxonomically important micromorphological, anatomical and molecular characteristics and these data provide reliable evidence for separation of these two species.

Comparative phylogeography of two co-distributed species of lizards of the genus Liolaemus (Squamata: Tropiduridae) from Southern Chile

2012 ◽  
Vol 33 (1) ◽  
pp. 55-67 ◽  
Author(s):  
Marcela A. Vidal ◽  
Juan Carlos Ortiz ◽  
Juan Carlos Marín ◽  
Elie Poulin ◽  
Patricio I. Moreno
Keyword(s):  
Dna Sequences ◽  
Middle Pleistocene ◽  
Phylogeographic Structure ◽  
Evolutionary Divergence ◽  
Southern Chile ◽  
Historical Events ◽  
Lizard Species ◽  
Comparative Phylogeography ◽  
Evolutionary Pattern ◽  
The Times

Comparative phylogeography describes the patterns of evolutionary divergence and whether or not they are congruent, in co-distributed populations of different taxa. If the populations of these taxa have been co-distributed for a prolonged time, and if the times between processes of perturbation or vicariance have been more or less stable, it is expected that patterns of divergence will be congruent in closely related species, for example because of similar biological and demographic characteristics. Liolaemus pictus and L. cyanogaster are widely co-distributed lizard species in southern Chile, occurring in a region with a complex topology. We analyzed the phylogeographic structure of the two lizard species using Cytochrome b DNA sequences to estimate their genetic structure in response to historical events. Our results suggest an evolutionary pattern of genetic diversity for each species that is consistent with the geomorphological history of the region, suggesting a complex phylogeographic history in Liolaemus species. Also, the high levels of divergence among haplotypes in several populations suggest the possibility that their origin might predate the middle Pleistocene in both species. Finally, our results are consistent with our hypothesis that two species have responded to historical events in parallel, where historical process have been sufficient to influence their phylogeographical structure (0.80 congruency between topologies).

Darwin and evolutionary tales in leukemia

Hematology ◽  
2009 ◽  
Vol 2009 (1) ◽  
pp. 3-12 ◽  
Author(s):  
Mel Greaves
Keyword(s):  
Charles Darwin ◽  
Single Cell Analysis ◽  
Lymphoblastic Leukemia ◽  
Gene Copy Number ◽  
Monozygotic Twins ◽  
Chromosome Translocation ◽  
Gene Copy ◽  
Clinical Samples ◽  
Evolutionary Divergence ◽  
Evolutionary Pattern

AbstractAll cancers evolve by a process of genetic diversification and “natural selection” akin to the process first described by Charles Darwin for species evolution. The evolutionary, natural history of childhood acute lymphoblastic leukemia (ALL) is almost entirely covert, clinically silent and well advanced by the point of diagnosis. It has, however, been possible to backtrack this process by molecular scrutiny of appropriate clinical samples: (i) leukemic clones in monozygotic twins that are either concordant or discordant for ALL; (ii) archived neonatal blood spots or Guthrie cards from individuals who later developed leukemia; and (iii) stored, viable cord blood cells. These studies indicate prenatal initiation of leukemia by chromosome translocation and gene fusion (or hyperdiploidy) and the post-natal acquisition of multiple, gene copy number alterations (CNAs), mostly deletions. The prenatal or first “hit” occurs very commonly, exceeding the clinical rate of ALL by some 100× and indicating a low rate of penetrance or evolutionary progression. The acquisition of the critical, secondary CNAs requires some Darwinian selective advantage to expand numbers of cells at risk, and the cytokine TGF beta is able to exercise this function. The clonal architecture of ALL has been investigated by single cell analysis with multicolor probes to mutant genes. The data reveal not a linear sequence of mutation acquisition with clonal succession but rather considerable complexity with a tree-like or branching structure of genetically distinct subclones very reminiscent of Darwin’s original 1837 evolutionary divergence diagram. This evolutionary pattern has important implications for stem cells in ALL, for the origins of relapse and for therapeutic targeting.

Vehicle Risk Level Estimation by Using Experimental Trajectories in Bend

2011 ◽  
Author(s):  
Abdourahmane Koita ◽  
Dimitri Daucher ◽  
Michel Fogli
Keyword(s):  
Probability Density ◽  
Reliability Analysis ◽  
Probabilistic Models ◽  
Hermite Polynomials ◽  
Probabilistic Methods ◽  
Risk Level ◽  
General Context ◽  
Risk Levels ◽  
Modelling Uncertainties ◽  
Non Gaussian

This paper tackles the general context of road safety, focussing on the light vehicles safety in bends. It consists to use a reliability analysis in order to estimate the failure probability of vehicle trajectories. Firstly, we build probabilistic models able to describe measured trajectories in a given bend. The models are transforms of scalar normalized second order stochastic processes which are stationary, ergodic and non-Gaussian. The process is characterized by its probability density function and its power spectral density estimated starting from the experimental trajectories. The probability density is approximated by a development on the Hermite polynomials basis. The second part is devoted to apply a reliability strategy intended to associate a risk level to each class of trajectories. Based on the joint use of probabilistic methods for modelling uncertainties, reliability analysis for assessing risk levels and statistics for classifying the trajectories, this approach provides a realistic answer to the tackled problem.

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