10. From Pan to Man the Hunter: Hunting and Meat Sharing by Chimpanzees, Humans, and Our Common Ancestor

Examination of the cranial morphology in Bombina orientalis (Anura: Discoglossidae) revealed the occurrence of additional dermal bones lying: a) between the nasals and frontoparietals, b) between frontoparietals, and c) on the tectum synoticum behind the frontoparietals. The presence of similar bones as well as extra ossifications lying in the midline in the rostral portion of skull was shown to be a rather common event among anurans. Based on the occurrence of bones with similar topology in crossopterygians and different stegocephalians, it was concluded that extra ossifications sporadically appearing in anurans are more likely to be ancient cranial elements than neomorphs. Additional dermal bones found in the anterior portion of the anuran skull are homologous to the postrostrals of crossopterygians; extra ossifications lying between the frontoparietals correspond to the bones with similar topology sporadically appearing in crossopterygians and stegocephalians; and extra bones situated behind the frontoparietals are homologous to the lateral extrascapulars (postparietals of stegocephalians) and the median extrascapular of crossopterygians. These extra bones were proposed to be inherited from the presumed common ancestor of all Gnathostomes and retained in anurans in the state of latent capacities. The sporadic appearance of these bones in anurans results from the phenotypical realization of these latent capacities.

Download Full-text

A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

Mycological Progress ◽

10.1007/s11557-021-01710-y ◽

2021 ◽

Vol 20 (7) ◽

pp. 889-904

Author(s):

M. Prieto ◽

Javier Etayo ◽

I. Olariaga

Keyword(s):

New Species ◽

Common Ancestor ◽

External Surface ◽

Evolutionary Relationships ◽

New Order ◽

Ancestral State ◽

Multigene Phylogeny ◽

State Reconstruction ◽

Distinct Structure ◽

Dark Violet

AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

Download Full-text

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

BMC Genomics ◽

10.1186/s12864-021-07872-z ◽

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.

Download Full-text

Selective Constraints on Intron Evolution in Drosophila

Genetics ◽

10.1093/genetics/165.4.1843 ◽

2003 ◽

Vol 165 (4) ◽

pp. 1843-1851 ◽

Cited By ~ 4

Author(s):

John Parsch

Keyword(s):

Drosophila Melanogaster ◽

Natural Selection ◽

Common Ancestor ◽

Length Distribution ◽

Short Length ◽

Intron Length ◽

Intron Evolution ◽

Intron Size ◽

Duplicated Genes ◽

Selective Constraints

AbstractIntron sizes show an asymmetrical distribution in a number of organisms, with a large number of “short” introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggests that natural selection may play a role in maintaining intron size. A comparison of 15 orthologous introns among species of the D. melanogaster subgroup indicates that, in general, short introns are not under greater DNA sequence or length constraints than long introns. There is a bias toward deletions in all introns (deletion/insertion ratio is 1.66), and the vast majority of indels are of short length (<10 bp). Indels occurring on the internal branches of the phylogenetic tree are significantly longer than those occurring on the terminal branches. These results are consistent with a compensatory model of intron length evolution in which slightly deleterious short deletions are frequently fixed within species by genetic drift, and relatively rare larger insertions that restore intron length are fixed by positive selection. A comparison of paralogous introns shared among duplicated genes suggests that length constraints differ between introns within the same gene. The janusA, janusB, and ocnus genes share two short introns derived from a common ancestor. The first of these introns shows significantly fewer indels than the second intron, although the two introns show a comparable number of substitutions. This indicates that intron-specific selective constraints have been maintained following gene duplication, which preceded the divergence of the D. melanogaster species subgroup.

Download Full-text

Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

Scientific Reports ◽

10.1038/s41598-020-79160-x ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evy van Berlo ◽

Alejandra P. Díaz-Loyo ◽

Oscar E. Juárez-Mora ◽

Mariska E. Kret ◽

Jorg J. M. Massen

Keyword(s):

Experimental Evidence ◽

Common Ancestor ◽

Great Apes ◽

Pongo Pygmaeus ◽

Last Common Ancestor ◽

Contagious Yawning ◽

Proximate Mechanism ◽

Social Species ◽

Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

Download Full-text

Long-Term Experimental Evolution in Escherichia coli. IV. Targets of Selection and the Specificity of Adaptation

Genetics ◽

10.1093/genetics/143.1.15 ◽

1996 ◽

Vol 143 (1) ◽

pp. 15-26 ◽

Cited By ~ 23

Author(s):

Michael Travisano ◽

Richard E Lenski

Keyword(s):

Escherichia Coli ◽

Experimental Evolution ◽

Common Ancestor ◽

The Novel ◽

Physiological Mechanisms ◽

Outer Membranes ◽

Limiting Nutrient ◽

Novel Environments ◽

Uptake Mechanisms

Abstract This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.

Download Full-text

A Chromosome-Based Model for Estimating the Number of Conserved Segments Between Pairs of Species From Comparative Genetic Maps

Genetics ◽

10.1093/genetics/154.1.323 ◽

2000 ◽

Vol 154 (1) ◽

pp. 323-332

Author(s):

David Waddington ◽

Anthea J Springbett ◽

David W Burt

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Common Ancestor ◽

Length Distribution ◽

Genetic Maps ◽

Segment Length ◽

Syntenic Block ◽

Comparative Maps

Abstract Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.

Download Full-text

TRIM32 and Malin in Neurological and Neuromuscular Rare Diseases

Cells ◽

10.3390/cells10040820 ◽

2021 ◽

Vol 10 (4) ◽

pp. 820

Author(s):

Lorena Kumarasinghe ◽

Lu Xiong ◽

Maria Adelaida Garcia-Gimeno ◽

Elisa Lazzari ◽

Pascual Sanz ◽

...

Keyword(s):

Common Ancestor ◽

Genetic Diseases ◽

Ubiquitin Ligases ◽

E3 Ubiquitin Ligases ◽

Lafora Disease ◽

C Terminus ◽

Rare Genetic Diseases ◽

Tripartite Motif ◽

Trim Proteins ◽

Ring E3

Tripartite motif (TRIM) proteins are RING E3 ubiquitin ligases defined by a shared domain structure. Several of them are implicated in rare genetic diseases, and mutations in TRIM32 and TRIM-like malin are associated with Limb-Girdle Muscular Dystrophy R8 and Lafora disease, respectively. These two proteins are evolutionary related, share a common ancestor, and both display NHL repeats at their C-terminus. Here, we revmniew the function of these two related E3 ubiquitin ligases discussing their intrinsic and possible common pathophysiological pathways.

Download Full-text

Allelic Genealogies in Sporophytic Self-Incompatibility Systems in Plants

Genetics ◽

10.1093/genetics/150.3.1187 ◽

1998 ◽

Vol 150 (3) ◽

pp. 1187-1198 ◽

Cited By ~ 9

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.

Download Full-text