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.

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 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.

Plio-pleistocene Hominids: Epistemological and Taxonomic Problems

1970 ◽  
Vol 9 (1) ◽  
pp. 169-202
Author(s):  
Jolanta Koszteyn
Keyword(s):  
Homo Sapiens ◽  
Single Species ◽  
Homo Erectus ◽  
Australopithecus Afarensis ◽  
Homo Heidelbergensis ◽  
Genealogical Tree ◽  
Homo Neanderthalensis ◽  
Homo Habilis ◽  
Homo Antecessor ◽  
Historical Times

Within the historical times, which roughly corresponds with the Holocene epoch, the whole of mankind is believed to be a single species. Homo sapiens. But the human genealogical tree (phylogeny) is populated by a really astounding number of paleontological species and paleontological genera: Ardipithecus ramidus, Australopithecus anamensis, Australopithecus afarensis, Australopithecus africanus, Paranthropus robustus, Paranthropus boisei, Homo habilis, Homo georgicus. Homo erectus, Homo ergaster, Homo antecessor, Homo heidelbergensis, Homo neanderthalensis, Homo sapiens. (cf. Gyula 2002). In fact there are many more (Sahelanthropus tchadensis, Orrorin tugenensis, Kenyanthropus platyops, Australopithecus garhi, Australopithecus aethiopicus) but Foley (2002), quite reasonably, states that the evidence for their existence is, at present, insufficient. The existence of these multiple forms is beyond any doubt. The doubt, however arises concerning the human or „prehuman" status of them. Were they really true specific forms, half-way between the apes and Holocene man? Is it possible that they constitute a number of different ecotypes (or paleoraces) within the same natural species of Homo sapiens?

Hominin transition to Upper Pliocene

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Brain Development ◽  
Late Pleistocene ◽  
Technological Progress ◽  
Homo Sapiens ◽  
Middle Pleistocene ◽  
Evolutionary Significance ◽  
Australopithecus Afarensis ◽  
Phylogenetic Significance ◽  
Homo Neanderthalensis ◽  
Surprising Discovery

This chapter analyzes the transition of the hominins from the Middle Pleistocene to the Late Pleistocene. Two alternative models are explored, the “Multiregional Hypothesis” (MH) and the “Replacement Hypothesis,” and how each model evaluates the existing relationships between the taxa Homo neanderthalensis and Homo sapiens. Next is the investigation of the transitional (or “archaic,” if this grade is taken into account) exemplars found in Europe, Africa, and Asia and their evolutionary significance. In particular, the comparison between H. erectus and H. sapiens in China and Java is investigated, as the main foundation of the MH. The chapter ends with the surprising discovery of Homo floresiensis and its description and interpretations concerning its taxonomic and phylogenetic significance. The correlation between brain development and technological progress is at odds with the attribution of perforators, microblades, and fishing hooks to a hominin with a small cranial volume, similar to that of Australopithecus afarensis.

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 The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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 Measuring Similarity of Deforestation Patterns in Time and Space across Differences in Resolution

Geomatics ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 464-495
Author(s):  
Desi Suyamto ◽  
Lilik Prasetyo ◽  
Yudi Setiawan ◽  
Arief Wijaya ◽  
Kustiyo Kustiyo ◽  
...  
Keyword(s):  
Geometric Feature ◽  
Data Sets ◽  
Temporal Data ◽  
Spatial And Temporal Patterns ◽  
Data Set ◽  
Point Matching ◽  
Point Patterns ◽  
Visual Sensing ◽  
Point Data ◽  
Point To Point

This article demonstrated an easily applicable method for measuring the similarity between a pair of point patterns, which applies to spatial or temporal data sets. Such a measurement was performed using similarity-based pattern analysis as an alternative to conventional approaches, which typically utilize straightforward point-to-point matching. Using our approach, in each point data set, two geometric features (i.e., the distance and angle from the centroid) were calculated and represented as probability density functions (PDFs). The PDF similarity of each geometric feature was measured using nine metrics, with values ranging from zero (very contrasting) to one (exactly the same). The overall similarity was defined as the average of the distance and angle similarities. In terms of sensibility, the method was shown to be capable of measuring, at a human visual sensing level, two pairs of hypothetical patterns, presenting reasonable results. Meanwhile, in terms of the method′s sensitivity to both spatial and temporal displacements from the hypothetical origin, the method is also capable of consistently measuring the similarity of spatial and temporal patterns. The application of the method to assess both spatial and temporal pattern similarities between two deforestation data sets with different resolutions was also discussed.

scholarly journals Coastal Change Patterns from Time Series Clustering of Permanent Laser Scan Data

2020 ◽  
Author(s):  
Mieke Kuschnerus ◽  
Roderik Lindenbergh ◽  
Sander Vos
Keyword(s):  
Time Series ◽  
Laser Scanning ◽  
Clustering Algorithm ◽  
Coastal Areas ◽  
Small Scale ◽  
Temporal Data ◽  
Agglomerative Clustering ◽  
Data Set ◽  
Deformation Processes ◽  
Spatio Temporal

Abstract. Sandy coasts are constantly changing environments governed by complex interacting processes. Permanent laser scanning is a promising technique to monitor such coastal areas and support analysis of geomorphological deformation processes. This novel technique delivers 3D representations of a part of the coast at hourly temporal and centimetre spatial resolution and allows to observe small scale changes in elevation over extended periods of time. These observations have the potential to improve understanding and modelling of coastal deformation processes. However, to be of use to coastal researchers and coastal management, an efficient way to find and extract deformation processes from the large spatio-temporal data set is needed. In order to allow data mining in an automated way, we extract time series in elevation or range and use unsupervised learning algorithms to derive a partitioning of the observed area according to change patterns. We compare three well known clustering algorithms, k-means, agglomerative clustering and DBSCAN, and identify areas that undergo similar evolution during one month. We test if they fulfil our criteria for a suitable clustering algorithm on our exemplary data set. The three clustering methods are applied to time series of 30 epochs (during one month) extracted from a data set of daily scans covering a part of the coast at Kijkduin, the Netherlands. A small section of the beach, where a pile of sand was accumulated by a bulldozer is used to evaluate the performance of the algorithms against a ground truth. The k-means algorithm and agglomerative clustering deliver similar clusters, and both allow to identify a fixed number of dominant deformation processes in sandy coastal areas, such as sand accumulation by a bulldozer or erosion in the intertidal area. The DBSCAN algorithm finds clusters for only about 44 % of the area and turns out to be more suitable for the detection of outliers, caused for example by temporary objects on the beach. Our study provides a methodology to efficiently mine a spatio-temporal data set for predominant deformation patterns with the associated regions, where they occur.

scholarly journals Evolutionary divergence reveals the molecular basis of EMRE dependence of the human MCU

2020 ◽  
Vol 3 (10) ◽  
pp. e202000718 ◽  
Author(s):  
Melissa JS MacEwen ◽  
Andrew L Markhard ◽  
Mert Bozbeyoglu ◽  
Forrest Bradford ◽  
Olga Goldberger ◽  
...  
Keyword(s):  
Calcium Channel ◽  
Molecular Basis ◽  
Homo Sapiens ◽  
Transmembrane Domains ◽  
Chimeric Proteins ◽  
Evolutionary Divergence ◽  
Mitochondrial Calcium Uniporter ◽  
Calcium Uniporter ◽  
Channel Opening ◽  
Strict Requirement

The mitochondrial calcium uniporter (MCU) is a calcium-activated calcium channel critical for signaling and bioenergetics. MCU, the pore-forming subunit of the uniporter, contains two transmembrane domains and is found in all major eukaryotic taxa. In amoeba and fungi, MCU homologs are sufficient to form a functional calcium channel, whereas human MCU exhibits a strict requirement for the metazoan protein essential MCU regulator (EMRE) for conductance. Here, we exploit this evolutionary divergence to decipher the molecular basis of human MCU’s dependence on EMRE. By systematically generating chimeric proteins that consist of EMRE-independent Dictyostelium discoideum MCU and Homo sapiens MCU (HsMCU), we converged on a stretch of 10 amino acids in D. discoideum MCU that can be transplanted to HsMCU to render it EMRE independent. We call this region in human MCU the EMRE dependence domain (EDD). Crosslinking experiments show that EMRE directly interacts with HsMCU at its transmembrane domains as well as the EDD. Our results suggest that EMRE stabilizes the EDD of MCU, permitting both channel opening and calcium conductance, consistent with recently published structures of MCU-EMRE.

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