Origin and early evolution of the amniote occiput

2000 ◽  
Vol 74 (5) ◽  
pp. 938-956 ◽  
Author(s):  
David S Berman
Keyword(s):  
Common Ancestor ◽  
Cladistic Analysis ◽  
Early Evolution ◽  
Recent Common Ancestor ◽  
Phylogenetic Study ◽  
Basic Approach ◽  
Skull Roof ◽  
Anatomical Data ◽  
Paleozoic Tetrapods

Reinterpretation of cranial materials of the diadectomorphs Limnoscelis and Diadectes has prompted a reconsideration of the origin and early evolution of the amniote occiput. The basic approach is a phylogenetic study of major groups of Paleozoic tetrapods based on the occiput and closely associated elements of the skull roof. A lack of adequate anatomical data has forced the elimination of only a few relevant higher-level taxa from consideration, and, using Acanthostega as the reference outgroup, a cladistic analysis of the interrelationships of the Lepospondyli, Temnospondyli, Seymouriamorpha, Baphetidae (= Loxommatidae), Anthracosauria, Diadectomorpha, Synapsida, and Reptilia has produced the following results: 1) the ingroup taxa exhibit a basal dichotomy in which one division consists of the unresolved relationships of Lepospondyli, Temnospondyli, and Seymouriamorpha; 2) the pattern of relationships of the second division of the ingroup taxa is a series of nested clades, terminating with the Diadectomorpha and Synapsida as sister taxa sharing a more recent common ancestor than either does with Reptilia. This relationship requires assignment of Diadectomorpha to Amniota; and 3) the Anthracosauria and Baphetidae are progressively more distant clades or sister taxa. On the basis of the cladistic analysis, the attainment of the amniote occiput is described as passing through four morphological grades of organization. Each grade of the series is characterized by a set of derived character states that defines the progressively more-derived nodes and from which branch a clade containing the unresolved trichotomy of Lepospondyli, Temnospondyli, and Seymouriamorpha; the Baphetidae clade; the Anthracosauria clade; and the Diadectomorpha + Synapsida and Reptilia clades, respectively.

Huehuecanauhtlus tiquichensis, a new hadrosauroid dinosaur (Ornithischia: Ornithopoda) from the Santonian (Late Cretaceous) of Michoacán, Mexico

2012 ◽  
Vol 49 (2) ◽  
pp. 379-395 ◽  
Author(s):  
Angel Alejandro Ramírez-Velasco ◽  
Mouloud Benammi ◽  
Albert Prieto-Márquez ◽  
Jesús Alvarado Ortega ◽  
René Hernández-Rivera
Keyword(s):  
North America ◽  
Late Cretaceous ◽  
Common Ancestor ◽  
Cladistic Analysis ◽  
Lateral View ◽  
Occlusal Plane ◽  
Recent Common Ancestor ◽  
Vicariant Event ◽  
Most Recent Common Ancestor ◽  
Caudal Vertebrae

Huehuecanauhtlus tiquichensis gen. et sp. nov. is the southernmost diagnostic basal hadrosauroid in the Americas. The holotype and referred material of this taxon came from Santonian strata in the Michoacán State, southwestern Mexico. Huehuecanauhtlus tiquichensis is diagnosed on the basis of a combination of dental, axial, and appendicular characters, including the following: at least two teeth exposed on the occlusal plane of the dentary and maxilla; seven sacral vertebrae; tall neural spines of caudal vertebrae; supraacetabular process long; and short and trapezoidal (in lateral view) postacetabular process. It differs from other hadrosauroids in having an ilium with extreme ventral deflection of the preacetabular process. Maximum parsimony cladistic analysis placed H. tiquichensis as a closely related outgroup to Hadrosauridae. The occurrence of H. tiquichensis in the Santonian of North America may be explained as a dispersal event from Asia to North America that occurred no later than the Albian or, alternatively, as a vicariant event of a most recent common ancestor widespread in both landmasses.

The postcranial skeletal anatomy of the carboniferous tetrapod Greererpeton burkemorani Romer, 1969

1989 ◽  
Vol 323 (1213) ◽  
pp. 75-133 ◽  
Keyword(s):  
West Virginia ◽  
Common Ancestor ◽  
Cladistic Analysis ◽  
Skeletal Remains ◽  
Uncinate Process ◽  
Recent Common Ancestor ◽  
Pectoral Girdle ◽  
Neural Arch

The discovery of well-preserved skeletal remains of Greererpeton burkemorani Romer, 1969, from the Upper Mississippian at Greer, West Virginia, has prompted a redescription of its postcranial skeletal anatomy. The vertebrae are rhachitomous, more specifically schizomerous. The presacral count is approximately 41. Neural arch elements of the atlas-axis complex consist of paired pro- and atlas arches and a relatively massive axis arch. All presacral vertebrae appear to have borne short, gently curved ribs, most of which developed a flange or stiletto-like uncinate process. The sacral rib is long. In adults, the scapulocoracoid and the dermal pectoral girdle are large and well ossified. The ascending iliac blade is undivided and the pubis is poorly ossified. A cladistic analysis indicates that Greererpeton burkemorani shares a more recent common ancestor with the anthracosaur Proterogyrinus scheelei than it does with either Crassigyrinus scoticus or Ichthyostega sp.

Reinterpretation of the temporal and occipital regions in Diadectes and the relationships of diadectomorphs

1992 ◽  
Vol 66 (3) ◽  
pp. 481-499 ◽  
Author(s):  
David S Berman ◽  
Stuart S. Sumida ◽  
R. Eric Lombard
Keyword(s):  
New Mexico ◽  
Common Ancestor ◽  
Cladistic Analysis ◽  
Recent Common Ancestor ◽  
New Materials ◽  
Natural Group ◽  
North Central ◽  
The Third ◽  
Sister Clade ◽  
Loss Of Contact

New materials from the Permo-Pennsylvanian of north-central New Mexico permit a new description of the temporal and occipital regions of the diadectomorph Diadectes. The important issue of the fate of the intertemporal bone is resolved by demonstrating its absence and apparent incorporation into the parietal as a lateral lappet. Four cranial autapomorphies of Diadectes are recognized: 1) loss of contact between postparietal and tabular; 2) supratemporal greatly enlarged with well-developed occipital process; 3) tabular no longer exposed on skull roof, but greatly reduced and incorporated into occipital plate, with a coarse, posteromedially facing surface; and 4) skull roofing bones thick and porous, with a consistent network of U-shaped grooves. The temporal–occipital region of Diadectes is compared with those of holotypic and recently collected specimens of Limnoscelis and Tseajaia, the type genera of the other two recognized diadectomorph families, Limnoscelidae and Tseajaiidae. On the basis of the literature the comparisons are extended to include certain late Paleozoic amniotes: synapsid Pelycosauria, Captorhinomorpha, and the primitive diapsid Petrolacosaurus. The results are subjected to a cladistic analysis, which supports the following hypotheses of relationships: 1) Diadectidae, Tseajaiidae, and Limnoscelidae form a natural group, the Diadectomorpha; 2) Diadectes and Tseajaia share a more recent common ancestor than either does with Limnoscelis; 3) Diadectomorpha, Pelycosauria, and their descendants form an unnamed, primitive sister clade to that consisting of Captorhinomorpha, Petrolacosaurus, and their descendants; and 4) the taxon Cotylosauria (sensu Heaton, 1980), consisting of Diadectomorpha and Seymouriamorpha, is paraphyletic and invalid. The third hypothesis dictates the assignment of Diadectomorpha to Amniota.

scholarly journals Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pattarapol Sumreddee ◽  
El Hamidi Hay ◽  
Sajjad Toghiani ◽  
Andrew Roberts ◽  
Samuel E. Aggrey ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Recent Common Ancestor ◽  
Pedigree Information ◽  
Grid Search ◽  
Genomic Information ◽  
The Impact ◽  
Daily Gain ◽  
Harmful Effects

Abstract Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.

scholarly journals Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 1187-1198 ◽  
Author(s):  
Mikkel H Schierup ◽  
Xavier Vekemans ◽  
Freddy B Christiansen
Keyword(s):  
Dominance Hierarchy ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Self Incompatibility ◽  
Most Recent Common Ancestor ◽  
Dominance Interactions ◽  
Turnover Process ◽  
Neutral Gene ◽  
Interspecific Comparisons ◽  
Coalescence Times

Abstract Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

scholarly journals Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018

2021 ◽  
Author(s):  
Wenjun Cheng ◽  
Tianjiao Ji ◽  
Shuaifeng Zhou ◽  
Yong Shi ◽  
Lili Jiang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Mainland China ◽  
Recent Common Ancestor ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Significant Difference ◽  
Echovirus 6 ◽  
Epidemiological Characteristics ◽  
Highest Posterior Density ◽  
Genotype F

AbstractEchovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.

scholarly journals The Ancestry of a Sample of Sequences Subject to Recombination

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1217-1228 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Genetic Distance ◽  
Population Size ◽  
Upper Bound ◽  
Recombination Rate ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Sequence Length ◽  
Most Recent Common Ancestor ◽  
The Mean ◽  
Mean Time

Abstract In this article we discuss the ancestry of sequences sampled from the coalescent with recombination with constant population size 2N. We have studied a number of variables based on simulations of sample histories, and some analytical results are derived. Consider the leftmost nucleotide in the sequences. We show that the number of nucleotides sharing a most recent common ancestor (MRCA) with the leftmost nucleotide is ≈log(1 + 4N Lr)/4Nr when two sequences are compared, where L denotes sequence length in nucleotides, and r the recombination rate between any two neighboring nucleotides per generation. For larger samples, the number of nucleotides sharing MRCA with the leftmost nucleotide decreases and becomes almost independent of 4N Lr. Further, we show that a segment of the sequences sharing a MRCA consists in mean of 3/8Nr nucleotides, when two sequences are compared, and that this decreases toward 1/4Nr nucleotides when the whole population is sampled. A measure of the correlation between the genealogies of two nucleotides on two sequences is introduced. We show analytically that even when the nucleotides are separated by a large genetic distance, but share MRCA, the genealogies will show only little correlation. This is surprising, because the time until the two nucleotides shared MRCA is reciprocal to the genetic distance. Using simulations, the mean time until all positions in the sample have found a MRCA increases logarithmically with increasing sequence length and is considerably lower than a theoretically predicted upper bound. On the basis of simulations, it turns out that important properties of the coalescent with recombinations of the whole population are reflected in the properties of a sample of low size.

The evolutionary history and conservation value of disjunct Bartonia paniculata subsp. paniculata (Branched Bartonia) populations in Canada

Botany ◽  
2013 ◽  
Vol 91 (9) ◽  
pp. 605-613 ◽  
Author(s):  
Claudia Ciotir ◽  
Chris Yesson ◽  
Joanna Freeland
Keyword(s):  
Great Lakes ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Great Lakes Region ◽  
Conservation Value ◽  
Most Recent Common Ancestor ◽  
Disjunct Populations ◽  
Management Plans ◽  
Global Status

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species’ global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial–interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value.

Whole-genome analysis-based phylogeographic investigation of Streptococcus pneumoniae serotype 19A sequence type 320 isolates in Japan.

2021 ◽  
Author(s):  
Satoshi Nakano ◽  
Takao Fujisawa ◽  
Bin Chang ◽  
Yutaka Ito ◽  
Hideki Akeda ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Sampling Bias ◽  
Health Concern ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Identification Rate ◽  
Most Recent Common Ancestor ◽  
The Common ◽  
The U.S

After the introduction of the seven-valent pneumococcal conjugate vaccine, the global spread of multidrug resistant serotype 19A-ST320 strains became a public health concern. In Japan, the main genotype of serotype 19A was ST3111, and the identification rate of ST320 was low. Although the isolates were sporadically detected in both adults and children, their origin remains unknown. Thus, by combining pneumococcal isolates collected in three nationwide pneumococcal surveillance studies conducted in Japan between 2008 and 2020, we analyzed 56 serotype 19A-ST320 isolates along with 931 global isolates, using whole-genome sequencing to uncover the transmission route of the globally distributed clone in Japan. The clone was frequently detected in Okinawa Prefecture, where the U.S. returned to Japan in 1972. Phylogenetic analysis demonstrated that the isolates from Japan were genetically related to those from the U.S.; therefore, the common ancestor may have originated in the U.S. In addition, Bayesian analysis suggested that the time to the most recent common ancestor of the isolates form Japan and the U.S. was approximately the 1990s to 2000, suggesting the possibility that the common ancestor could have already spread in the U.S. before the Taiwan 19F-14 isolate was first identified in a Taiwanese hospital in 1997. The phylogeographical analysis supported the transmission of the clone from the U.S. to Japan, but the analysis could be influenced by sampling bias. These results suggested the possibility that the serotype 19A-ST320 clone had already spread in the U.S. before being imported into Japan.

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