Evolutionary Reorganization Research Articles

Evolutionary scaling and cognitive correlates of primate frontal cortex microstructure.

Investigating evolutionary changes in frontal cortex microstructure is crucial to understanding how modifications of neuron and axon distributions contribute to phylogenetic variation in cognition. In the present study, we characterized microstructural components of dorsolateral prefrontal cortex, orbitofrontal cortex, and primary motor cortex from 14 primate species using measurements of neuropil fraction and immunohistochemical markers for fast-spiking inhibitory interneurons, large pyramidal projection neuron subtypes, serotonergic innervation, and dopaminergic innervation. Results revealed that the rate of evolutionary change was similar across these microstructural variables, except for neuropil fraction, which evolves more slowly and displays the strongest correlation with brain size. We also found that neuropil fraction in orbitofrontal cortex layers V-VI was associated with cross-species variation in performance on experimental tasks that measure self-control. These findings provide insight into the evolutionary reorganization of the primate frontal cortex in relation to brain size scaling and its association with cognitive processes.

Frugivore-fruit size relationships between palms and mammals reveal past and future defaunation impacts

Mammalian frugivores are critical seed dispersers, but many are under threat of extinction. Futhermore, the impact of past and future defaunation on plant assemblages has yet to be quantified at the global scale. Here, we integrate palm and mammalian frugivore trait and occurrence data and reveal a global positive relationship between fruit size and frugivore body size. Global variation in fruit size is better explained by present-day frugivore assemblages than by Late Pleistocene assemblages, suggesting ecological and evolutionary reorganization after end-Pleistocene extinctions, except in the Neotropics, where some large-fruited palm species may have outlived their main seed dispersers by thousands of years. Our simulations of frugivore extinction over the next 100 years suggest that the impact of defaunation will be highest in the Old World tropics, and an up to 4% assemblage-level decrease in fruit size would be required to maintain the global body size–fruit size relationship. Overall, our results suggest that while some palm species may be able to keep pace with future defaunation through evolutionary changes in fruit size, large-fruited species may be especially vulnerable to continued defaunation.

Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution.

Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the “repeatome”, remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.

Evolutionary shifts dramatically reorganized the human hippocampal complex.

The hippocampal complex (HC) is central to long-term memory storage and retrieval as well as spatial navigation across many species. Notably, humans appear to have greatly enhanced and possibly unique HC-mediated capacities such as constructive episodic simulation. Key studies have shown that the human HC is disproportionately large amongst hominoids, but much remains unknown at the levels of substructural evolutionary reorganization and ecological selection. Here, we calculated relative sizes of 12 HC subregions in a diverse sample of 44 primate species. We then used a Bayesian phylogenetic method, selective regime analysis, to identify 27 separate evolutionary shifts in HC organization across 65 million years of primate evolution. Additionally, a series of multivariate phylogenetic regressions using HC-related ecological variables as predictors (Diet Breadth, Population Density, Group Size, Home Range Size, and Residual Home Range) revealed that relative fascia dentata and CA1 size were both significantly predicted by species' home range size (after correcting for body size). However, perhaps the most notable finding of this study was that the shifts in HC size and subregional organization in the human lineage were the largest seen in all of primate evolution, rendering modern humans with a HC that is a clear outlier amongst all nonhuman primates investigated here. Given the extensive literature confirming the relationship between HC organization and function, these selective shifts are likely to have played a significant role in the emergence of human-specific capacities, such as constructive episodic simulation.

Skull reconstruction of the late Miocene ape Rudapithecus hungaricus from Rudabánya, Hungary

We report on a computer-based reconstruction of a well-preserved ape skull from late Miocene deposits in Rudabánya, Hungary. Based on micro-computed tomographic scans of the original Rudapithecus hungaricus partial cranium RUD 200 and the associated mandible RUD 212 we realign displaced bone fragments, and reconstruct the shape of the upper and lower jaws guided by occlusal fingerprint analysis of dental wear patterns. We apply geometric morphometric methods based on several hundred landmarks and sliding semilandmarks to estimate missing data, and create multiple reconstructions of the specimen. We then compare the reconstructed overall cranial shape, as well as the volume and shape of the endocast, with extant primates. Multiple reconstructions of RUD 200 yield an average endocranial volume of 234 cc (S.D.: 9 cc; range: 221–247 cc). RUD 200 is most similar to African apes in overall cranial shape, but in a statistical analysis of endocranial shape the specimen falls closest to extant hylobatids. Our data suggest that R. hungaricus from the late Miocene in Europe displays aspects of the overall cranial geometry typical of extant African great apes, but it does not show an evolutionary reorganization of the brain evident in Pan, Gorilla, and Pongo.

Dinosaur ossification centres in embryonic birds uncover developmental evolution of the skull.

Radical transformation of the skull characterizes bird evolution. An increase in the relative size of the brain and eyes was presumably related to the loss of two bones surrounding the eye, the prefrontal and postorbital. We report that ossification centres of the prefrontal and postorbital are still formed in bird embryos, which then fuse seamlessly to the developing nasal and frontal bones, respectively, becoming undetectable in the adult. The presence of a dinosaur-like ossification pattern in bird embryos is more than a trace of their evolutionary past: we show how persistent modularity of ossification centres has allowed for evolutionary re-organization of skull architecture in evolution. Our findings also demonstrate that enigmatic mesodermal cells forming the posterior region of the avian frontal correspond to the ossification centre of the postorbital, not the parietal, and link its failure to develop into an adult bone to its incorporation into the expanded braincase of birds.

Understanding Molecular Evolution and Development of the Organ of Corti Can Provide Clues for Hearing Restoration.

The mammalian hearing organ is a stereotyped cellular assembly with orderly innervation: two types of spiral ganglion neurons (SGNs) innervate two types of differentially distributed hair cells (HCs). HCs and SGNs evolved from single neurosensory cells through gene multiplication and diversification. Independent regulation of HCs and neuronal differentiation through expression of basic helix-loop-helix transcription factors (bHLH TFs: Atoh1, Neurog1, Neurod1) led to the evolution of vestibular HC assembly and their unique type of innervation. In ancestral mammals, a vestibular organ was transformed into the organ of Corti (OC) containing a single row of inner HC (IHC), three rows of outer HCs (OHCs), several unique supporting cell types, and a peculiar innervation distribution. Restoring the OC following long-term hearing loss is complicated by the fact that the entire organ is replaced by a flat epithelium and requires reconstructing the organ from uniform undifferentiated cell types, recapitulating both evolution and development. Finding the right sequence of gene activation during development that is useful for regeneration could benefit from an understanding of the OC evolution. Toward this end, we report on Foxg1 and Lmx1a mutants that radically alter the OC cell assembly and its innervation when mutated and may have driven the evolutionary reorganization of the basilar papilla into an OC in ancestral Therapsids. Furthermore, genetically manipulating the level of bHLH TFs changes HC type and distribution and allows inference how transformation of HCs might have happened evolutionarily. We report on how bHLH TFs regulate OHC/IHC and how misexpression (Atoh1-Cre; Atoh1f/kiNeurog1) alters HC fate and supporting cell development. Using mice with altered HC types and distribution, we demonstrate innervation changes driven by HC patterning. Using these insights, we speculate on necessary steps needed to convert a random mixture of post-mitotic precursors into the orderly OC through spatially and temporally regulated critical bHLH genes in the context of other TFs to restore normal innervation patterns.

Decoding system for the AUA codon by tRNA Ile with the UAU anticodon in Mycoplasma mobile

Deciphering the genetic code is a fundamental process in all living organisms. In many bacteria, AUA codons are deciphered by tRNAIle2 bearing lysidine (L) at the wobble position. L is a modified cytidine introduced post-transcriptionally by tRNAIle-lysidine synthetase (TilS). Some bacteria, including Mycoplasma mobile, do not carry the tilS gene, indicating that they have established a different system to decode AUA codons. In this study, tRNAIle2 has been isolated from M. mobile and was found to contain a UAU anticodon without any modification. Mycoplasma mobile isoleucyl-tRNA synthetase (IleRS) recognized the UAU anticodon, whereas Escherichia coli IleRS did not efficiently aminoacylate tRNAIle2UAU. In M. mobile IleRS, a single Arg residue at position 865 was critical for specificity for the UAU anticodon and, when the corresponding site (W905) in E. coli IleRS was substituted with Arg, the W905R mutant efficiently aminoacylated tRNA with UAU anticodon. Mycoplasma mobile tRNAIle2 cannot distinguish between AUA and AUG codon on E. coli ribosome. However, on M. mobile ribosome, M. mobile tRNAIle2UAU specifically recognized AUA codon, and not AUG codon, suggesting M. mobile ribosome has a property that prevents misreading of AUG codon. These findings provide an insight into the evolutionary reorganization of the AUA decoding system.

Characterization of Xenopus Tissue Inhibitor of Metalloproteinases-2: A Role in Regulating Matrix Metalloproteinase Activity during Development

BackgroundFrog metamorphosis is totally dependent on thyroid hormone (T3) and mimics the postembryonic period around birth in mammals. It is an excellent model to study the molecular basis of postembryonic development in vertebrate. We and others have shown that many, if not all, matrix metalloproteinases (MMPs), which cleave proteins of the extracellular matrix as well as other substrates, are induced by T3 and important for metamorphosis. MMP activity can be inhibited by tissue inhibitors of metalloproteinase (TIMPs). There are 4 TIMPs in vertebrates and their roles in postembryonic development are poorly studied.Methodology/Principal FindingsWe analyzed the TIMP2 genes in Xenopus laevis and the highly related species Xenopus tropicalis and discovered that TIMP2 is a single copy gene in Xenopus tropicalis as in mammals but is duplicated in Xenopus laevis. Furthermore, the TIMP2 locus in Xenopus tropicalis genome is different from that in human, suggesting an evolutionary reorganization of the locus. More importantly, we found that the duplicated TIMP2 genes were similarly regulated in the developing limb, remodeling intestine, resorbing tail during metamorphosis. Unexpectedly, like its MMP target genes, the TIMP2 genes were upregulated by T3 during both natural and T3-induced metamorphosis.Conclusions/SignificanceOur results indicate that TIMP2 is highly conserved among vertebrates and that the TIMP2 locus underwent a chromosomal reorganization during evolution. Furthermore, the unexpected upregulation of TIMP2 genes during metamorphosis suggests that proper balance of MMP activity is important for metamorphosis.

Structure and molecular evolution of the ribosomal DNA external transcribed spacer in the cockroach genusBlattella

The ribosomal DNA (rDNA) cluster of insects contains several hundred repeating structural-functional units and, therefore, is a typical example of a multigene family. Eukaryotic ribosomal RNA (rRNA) genes (18S, 5.8S, and 28S like) are arranged in tandemly repeated clusters in the nucleolus organizers, separated by several spacers, namely the nontranscribed spacer, the external transcribed spacer (ETS), and the internal transcribed spacers. The nucleotide sequences of the ETS of the three closely related Blattella cockroach species, Blattella germanica (Linnaeus, 1767), Blattella asahinai (Mizukubo, 1981), and Blattella lituricollis (Walker, 1868), were determined and compared. The three species had relatively similar ETS lengths, and sequence differences among them could be explained by two types of rearrangements, namely deletions of subrepeats and nucleotide substitutions. Minor ETS variants in B. germanica differed from the major variant in the same way that the major ETS variants of the three Blattella species differed from each other. Concerted evolution and the birth-and-death models, which are often invoked to explain the diversity and evolution of the multigene families of rDNA clusters, are discussed in the light of our data. A new model is proposed to explain the evolutionary reorganization of the ETS region: evolution of rDNA by "magnification-and-fixation" is characterized by magnification of minor subrepeats, which become adaptive in a new rapidly changed environment, and subsequent fixation of this variant type as a major component of the multigene family of a new species.

Evolutionary reorganizations of ontogenesis in related frog species of the family Myobatrachidae

Literary data on the comparative embryology of Australian endemic frogs of the family Myobatrachidae have been considered. Six main types of development have been recognized, the important criteria for which are egg size, the site of embryo and tadpole development (in water or on land), the character of larval nutrition (exotrophic or endotrophic), the occurrence of direct development, brooding, etc. An attention has been also paid to the character of the early cleavage process in the embryos of various species. The peculiarities of ontogeny in Myobatrachidae are compared with those in representatives of other families in the order Anura. The perspectives of some further embryological studies of this Australian frog family have been outlined.

The evolutionary reorganization of ontogeny and origin of multicellularity

The formation of morphogenetic mechanisms during emergence of multicellularity is discussed in this article.

10.1007/s11174-008-2009-x

A concept of evolution of ontogeny based on the original data on the comparative biology of Volvox development and published paleoclimatic data is presented. Previously, we have demonstrated that evolutionary reorganizations of asexual development in Volvox are related to the changes in the rate, diel rhythms, and light/dark control of cell divisions. Here, we propose that such rearrangements could take place during much of Cenozoic time (e.g., in Eocene and Miocene) as adaptations to short and warm winter day in high latitudes. This proposal is confirmed by experimental data on culturing Volvox species with different types of development under short photoperiod.

Adaptive Evolution of 5'HoxD Genes in the Origin and Diversification of the Cetacean Flipper

The homeobox (Hox) genes Hoxd12 and Hoxd13 control digit patterning and limb formation in tetrapods. Both show strong expression in the limb bud during embryonic development, are highly conserved across vertebrates, and show mutations that are associated with carpal, metacarpal, and phalangeal deformities. The most dramatic evolutionary reorganization of the mammalian limb has occurred in cetaceans (whales, dolphins, and porpoises), in which the hind limbs have been lost and the forelimbs have evolved into paddle-shaped flippers. We reconstructed the phylogeny of digit patterning in mammals and inferred that digit number has changed twice in the evolution of the cetacean forelimb. First, the divergence of the early cetaceans from their even-toed relatives coincided with the reacquisition of the pentadactyl forelimb, whereas the ancestors of tetradactyl baleen whales (Mysticeti) later lost a digit again. To test whether the evolution of the cetacean forelimb is associated with positive selection or relaxation of Hoxd12 and Hoxd13, we sequenced these genes in a wide range of mammals. In Hoxd12, we found evidence of Darwinian selection associated with both episodes of cetacean forelimb reorganization. In Hoxd13, we found a novel expansion of a polyalanine tract in cetaceans compared with other mammals (17/18 residues vs. 14/15 residues, respectively), lengthening of which has previously been shown to be linked to synpolydactyly in humans and mice. Both genes also show much greater sequence variation among cetaceans than across other mammalian lineages. Our results strongly implicate 5'HoxD genes in the modulation of digit number, web forming, and the high morphological diversity of the cetacean manus.

On the problem of ecological evolution in Volvox

A concept of evolution of ontogeny based on the original data on the comparative biology of volvox development and published paleoclimatic data is presented. Previously, we have demonstrated that evolutionary reorganizations of asexual development in Volvox are related to the changes in the rate, diel rhythms, and light/dark control of cell divisions. Here, we propose that such rearrangements could take place during much of Cenozoic time (e.g., in Eocene and Miocene) as adaptations to short and warm winter day in high latitudes. This proposal is confirmed by experimental data on culturing volvox species with different types of development under short photoperiod.

Evolutionary reorganizations of ontogenesis in related species of coenobial volvocine algae

The evolutionary aspects of ontogenesis in green volvocine algae have been considered on the basis of the author's and published data, as well as the information on taxonomy, phylogeny, and ecology of this group. Analysis of the rate, diurnal rhythm, and light/dark control of cell divisions in various species, as well as experiments with the nucleic acid and protein synthesis inhibitors made it possible to elucidate cellular mechanisms underlying evolutionary rearrangements of asexual development in the genus Volvox.

Evolutionary reorganizations of ontogenesis in ascidians of the genus Molgula

The data on comparative, experimental, and molecular embryology of ascidians (genus Molgula) published during the last 15 years have been reviewed. Some representatives of this genus evolved from development with a tailed larva (tadpole) to direct development associated with the loss of larval structures, such as tail, notochord, sensory organs, and differentiated muscles. The data on evolutionary reorganizations of ontogenesis in ascidians of the genus Molgula have been compared with those in sea urchins, anuran amphibians, and some other organisms.

Evolutionary Reorganizations of Ontogenesis in Sea Urchins

The data published during recent 15-20 years on comparative, experimental and molecular embryology of unusually developing sea urchins have been reviewed. These animals are characterized by large lipidrich eggs, highly modified embryogenesis, and the absence of a planktotrophic larva. Such a type of development is evolutionary advanced and arose independently in various phylogenetic lineages of the sea urchins.

Study of a temporal bone of Homo heildelbergensis

ConclusionsThe characteristic features of the Hh specimen conformed to those of other Pleistocene human fossils, indicating strong cranial structures and a heavy mandible. The mastoid was large and suggested a powerful sternocleidomastoid muscle. The inner ear and tympanic cavities were similar in size and orientation, suggesting that their functions were probably similar. Our observations suggest that the left ear of this Hh specimen was healthy. The large canaliculo–fenestral angle confirms that this ancestor was bipedal. It also strongly suggests that Hh individuals were predisposed to develop certain pathologies of the labyrinth capsule associated with bipedalism, in particular otosclerosis.ObjectiveWe studied a temporal bone of Homo heidelbergensis (Hh) in order to investigate the clinical and physiological implications of certain morphological features, especially those associated with the evolutionary reorganization of the inner ear.Material and methodsThe bone, found in a breach of a cave near Málaga in southern Spain, together with Middle–Upper Pleistocene faunal remains, is >300 000 years old. Four analytical methods were employed. A 3D high-resolution surface laser scan was used for anatomical measurements. For the sectional analysis of the middle and inner ears of Hh we used high-resolution CT, simultaneously studying a normal temporal bone from Homo sapiens sapiens (Hss). To study the middle and inner ear spaces we used 3D reconstruction CT preceded by an intra-bone air shielding technique. To examine the tympanic cavities and measure the canaliculo–fenestral angle, we used a special minimally invasive endoscopic procedure.ResultsThe surface, sectional and 3D CT examinations showed that the Hh specimen was generally more robust and larger than the Hss specimen. It had a large glenoid fossa. The external meatus was wide and deep. The middle ear, and especially the mastoid, was large and widely pneumatized. There were no appreciable differences in the position and size of the labyrinthine spaces and tympanic cavity. The dimensions of the semicircular canals were similar to those of the Hss specimen. Endoscopy revealed normal, healthy tympanic walls and an ossicle fragment in the atticum that probably belonged to the body of the malleus. The diameters of the fallopian duct and the tympanic opening of the Eustachian tube were large. The canaliculo–fenestral angle was ≈114°.

Characteristics of paravertebral muscles - fibre type distribution pattern in the pika, Ochotona rufescens (Mammalia: Lagomorpha)

The evolution of the locomotor apparatus in vertebrates is marked by major reorganizations in trunk’s musculature. The hypothesized functions of mammalian back muscles in the literature are discussed under consideration of the distribution and proportion of oxidative, type-I-fibres, oxidativeglycolytic, type-IIa-fibres and glycolytic, type-IIb-fibres in paravertebral muscles of a small mammal. The fibre type distribution was examined fro ma complete series of histological sections maintaining topographical relationships between the muscles as well as within the muscle, in order to establish the overall distribution pattern. The deep and short muscles showed the highest percentage of oxidative fibres. The larger, superficial paravertebral muscles contained the highest percentage of glycolytic fibres. Two muscles were intermediate in their proportion of fibre types. All epaxial muscles together can be interpreted as an antigravity muscle–complex counteracting enduringly against the rebound tendency caused by gravitation, comparable with antigravity muscles in limbs. A gradient from deep to superficial, or a clear regionalization of oxidative muscle fibres in central deep regions around a large intramuscular tendon was found in the m. spinalis and the m. quadratus lumborum, respectively. Concepts of the function of human back muscles as those of A. Bergmark (1989: Acta Orthop. Scand. 230, 1) or S.G.T. Gibbons & M.J. Comerford (2001: Orthop. Division Rev. March/April, 21) were exposed to be more general within mammals. Functional specializations of different muscles and muscle parts are discussed under the consideration of evolutionary reorganization of the paravertebral musculature in tetrapods.Along the cranio-caudal axis, the percentage of oxidative fibres was decreased in caudal direction within the same muscles, whereas the proportion of glycolytic fibres was increased. Therefore, classifications of muscles as glycolytic or oxidative based on biopsies or analyses of single cross-sections may result in wrong interpretations. Changes in the proportions of the fibre type distribution pattern were mostly due to oxidative and glycolytic fibre types, whereas the percentage of oxidative-glycolytic fibres had only minor influence. A significant positive correlation between the cross-sectional area of the single fibre and its percentage in the area investigated were observed for oxidative fibres, whereby the size was positive correlated to the proportion of the oxidative fibres.