Parallel evolution of auditory genes for echolocation in bats and toothed whales

The ability of bats and toothed whales to echolocate is a remarkable case of convergent evolution. Previous genetic studies have documented parallel evolution of nucleotide sequences in Prestin and KCNQ4, both of which are associated with voltage motility during the cochlear amplification of signals. Echolocation involves complex mechanisms. The most important factors include cochlear amplification, nerve transmission, and signal re-coding. Herein, we screen three genes that play different roles in this auditory system. Cadherin 23 (Cdh23) and its ligand, protocadherin 15 (Pcdh15), are essential for bundling motility in the sensory hair. Otoferlin (Otof) responds to nerve signal transmission in the auditory inner hair cell. Signals of parallel evolution occur in all three genes in the three groups of echolocators--two groups of bats (Yangochiroptera and Rhinolophoidea) plus the dolphin. Significant signals of positive selection also occur in Cdh23 in the Rhinolophoidea and dolphin, and Pcdh15 in Yangochiroptera. In addition, adult echolocating bats have higher levels of Otof expression in the auditory cortex than do their embryos and non-echolocation bats. Cdh23 and Pcdh15 encode the upper and lower parts of tip-links, and both genes show signals of convergent evolution and positive selection in echolocators, implying that they may co-evolve to optimize cochlear amplification. Convergent evolution and expression patterns of Otof suggest the potential role of nerve and brain in echolocation. Our synthesis of gene sequence and gene expression analyses reveals that positive selection, parallel evolution, and perhaps co-evolution and gene expression affect multiple hearing genes that play different roles in audition, including voltage and bundle motility in cochlear amplification, nerve transmission, and brain function.     

Parallel evolution in the major haemoglobin genes of eight species of Andean waterfowl

Theory predicts that parallel evolution should be common when the number of beneficial mutations is limited by selective constraints on protein structure. However, confirmation is scarce in natural populations. Here we studied the major haemoglobin genes of eight Andean duck lineages and compared them to 115 other waterfowl species, including the bar-headed goose ( Anser indicus ) and Abyssinian blue-winged goose ( Cyanochen cyanopterus ), two additional species living at high altitude. One to five amino acid replacements were significantly overrepresented or derived in each highland population, and parallel substitutions were more common than in simulated sequences evolved under a neutral model. Two substitutions evolved in parallel in the αA subunit of two (Ala-α8) and five (Thr-α77) taxa, and five identical βA subunit substitutions were observed in two (Ser-β4, Glu-β94, Met-β133) or three (Ser-β13, Ser-β116) taxa. Substitutions at adjacent sites within the same functional protein region were also observed. Five such replacements were in exterior, solvent-accessible positions on the A helix and AB corner of the αA subunit. Five others were in close proximity to inositolpentaphosphate binding sites, and two pairs of independent replacements occurred at two different α¹β¹ intersubunit contacts. More than half of the substitutions in highland lineages resulted in the acquisition of serine or threonine (18 gains vs. 2 losses), both of which possess a hydroxyl group that can hydrogen bond to a variety of polar substrates. The patterns of parallel evolution observed in these waterfowl suggest that adaptation to high-altitude hypoxia has resulted from selection on unique but overlapping sets of one to five amino acid substitutions in each lineage.     

Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes

The cloverleaf secondary structure of transfer RNA (tRNA) is highly conserved across all forms of life. Here, we provide sequence data and inferred secondary structures for all tRNA genes from 8 new arachnid mitochondrial genomes, including representatives from 6 orders. These data show remarkable reductions in tRNA gene sequences, indicating that T-arms are missing from many of the 22 tRNAs in the genomes of 4 out of 7 orders of arachnids. Additionally, all opisthothele spiders possess some tRNA genes that lack sequences that could form well-paired aminoacyl acceptor stems. We trace the evolution of T-arm loss onto phylogenies of arachnids and show that a genome-wide propensity to lose sequences that encode canonical cloverleaf structures likely evolved multiple times within arachnids. Mapping of structural characters also shows that certain tRNA genes appear more evolutionarily prone to lose the sequence coding for the T-arm and that once a T-arm is lost, it is not regained. We use tRNA structural data to construct a phylogeny of arachnids and find high bootstrap support for a clade that is not supported in phylogenies that are based on more traditional morphological characters. Together, our data demonstrate variability in structural evolution among different tRNAs as well as evidence for parallel evolution of the loss of sequence coding for tRNA arms within an ancient and diverse group of animals.     

The birth of the Acheulian techno-complex in the Caucasus region

The lithic industries of the sites Kermek, Ciscaucasia (2.1–2.0 Ma) and Karakhach, South Caucasus (1.85–1.78 Ma) contain almost all the components of the Acheulian, indicating that this techno-complex appeared in the different areas of the Caucasus region not later than at the end of the Gelasian. Such extremely old ages of these industries as well as a number of their features due to the influence of the local raw material (tabular clasts) suggest that they were formed independently of the Early Acheulian industries known in Africa and the Near East. The very early appearance and further dispersal of Early Acheulian in the Caucasus can be explained by the presence there of raw materials with qualities supporting the production of large tools inherent of Acheulian, and by the very favorable natural conditions of the region in the final Gelazian-initial Calabrian (low or medium altitude terrain with subtropical climate and savanna-like landscape).     

Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution

Class II genes of the human major histocompatibility complex (MHC) are polymorphic. Allelic variation of the coding region of these genes is involved in the antigen presentation and is associated with susceptibility to certain autoimmune diseases. The DR region is unique among human class II regions in that multiple DRB genes are expressed. Differential expression of the different DRB loci has been demonstrated, and we sequenced the proximal promoter region of the HLA-DRB genes, known to be involved in the regulation of nucleotide variations in their regulatory regions and we determined the relationship between the regulatory regions of HLA-DRB genes. This polymorphism found in the regulatory conserved boxes could be involved in the observed differential expression of DRB loci. In addition, we found a polymorphism between the regulatory regions of DRB1 alleles which might be involved in an allele-specific regulation and therefore could be considered as an additional factor in susceptibility to autoimmune diseases.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X64436–X64442, X64544, X64546–X64549, X65558–X65569, and X65585–X65587. Correspondence to: J. F. Eliaou.     

Diversity and evolution of T-cell receptor variable region genes in mammals and birds

 The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes. Received: 20 May 1999 / Revised: 13 July 1999     

Organization and evolution of variable region genes of the human immunoglobulin heavy chain

We have isolated 23 different cosmid clones of the heavy-chain variable region genes (VH) of human immunoglobulin. These clones encompass about 1000 X 10(3) base-pairs of DNA containing 61 VH genes. Characterization of the 23 clones by Southern blot hybridization showed that VH genes belonging to different families were physically linked in many regions. Cluster 71, which was analyzed in detail, comprised seven VH segments arranged in the same orientation with different intervals. This clone contained internal homology regions, each carrying two VH segments of different families. Comparison of the nucleotide sequences of VH segments within each family showed that profiles of accumulation of mutations in framework (FR) and complementarity-determining (CDR) regions were different. CDR had more mutations at amino-acid-substituting positions than at silent positions, whereas FR had the reverse distribution of mutations. Five out of seven VH segments of this cluster were pseudogenes containing various mutations. VH pseudogenes were classified into two distinct groups; one with a few replacement mutations (conserved pseudogenes), and the other with rather extensive mutations (diverged pseudogenes). The possibility that conserved pseudogenes serve as a reservoir of VH segments is discussed.     

Genetic polymorphisms ofQ region genes from wild-derived mice: Implications forQ region evolution

Both serological and DNA sequence analyses were performed to determine the extent of genetic polymorphism inQ region genes. A panel of Qa-2-specific monoclonal antibodies (mAbs) was tested on 35 wildderived and inbred mouse strains. Members of this reagent panel recognize multiple and distinct epitopes on the Qa-2-bearing molecule(s). Although quantitative variations in Qa-2 levels were observed, no structural polymorphisms were detected. All strains were either entirely positive or entirely negative with the complete set of reagents. Moreover, cell surface Qa-2 expression was not significantly affected by differences in age or sex of the mouse or cell cycle status. To confirm this apparent lack of genetic polymorphism, the polymerase chain reaction (PCR) technique was used to amplify a portion of the 3 end of theQ region genes,Q4 toQ9, from several independent wild-derived strains of mice. Sequence analysis of the amplified material revealed very little evidence of nucleotide divergence. All strains tested had aQ even DNA sequence identical to that ofQ6/Q8 in the B10 strain. Likewise, all tested strains had aQ odd DNA sequence identical toQ7/Q9 in the B10 strain. Two strains showed additionalQ even sequences, while all strains tested possessed additionalQ odd sequences. The observed lack of polymorphism suggests that theQ genes have evolved in a different manner fromH-2K andH-2D. Moreover, duplications of these genes appear to have arisen prior to nucleotide sequence divergence.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M30896-30902.     

Parallel evolution in the hominoid trunk and forelimb

The evolutionary history of the living hominoids has remained elusive despite years of exploration and the discovery of numerous Miocene fossil ape species. Part of the difficulty can be attributed to the changing nature of our views about the course of hominoid evolution. In the 1950s and 1960s, individual Miocene taxa were commonly viewed as the direct ancestors of specific living ape species, suggesting an early divergence of the modern lineages.^1–5 However, in most cases, the Miocene forms were essentially “dental apes,” resembling extant species in dental and a few cranial features, but possessing more primitive postcranial features that suggested arboreal quadrupedalism rather than suspensory habits. With the introduction of molecular methods of phylogenetic reconstruction and the increasing use of cladistic analysis, it has become apparent that the radiation leading to the modern hominoids was somewhat more recent than had been believed, and that most of the Miocene hominoid species had little to do with the evolutionary history of the living apes. © 1998 Wiley-Liss, Inc.     

Genotype diversity of the Bacillus anthracis strains isolated from the Caucasus region

The study of the genotypes of Bacillus anthracis strains isolated from the Caucasus region was performed using MLVA. Among 149 strains, 32 distinctive MLVA-8 genotypes belonging to Ala, A3a, A4 and B1 molecular diversity groups were identified. 9 genotypes were not described previously; 6 genotypes were not found in other geographic regions and could be considered as endemic for Caucasus. The majority of the identified genotypes are widespread not only in Caucasus, but also throughout Eurasia, Africa, and America. Molecular diversity of Caucasian isolates is comparable to the worldwide diversity. This represents historical relations of this region, proximity to ancient trade routes and intensity of the anthrax epizootic in Caucasus. The obtained results are of interest from the theoretical point of view, as well as for the application in epidemiological research of the anthrax outbreaks.     

The role of genetic biases in shaping the correlations between languages and genes

It has recently been proposed [Dediu, D., Ladd, D.R., 2007. Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin. Proc. Natl Acad. Sci. USA 104(26), 10944-10949] that genetically coded linguistic biases can influence the trajectory of language change. However, the nature of such biases and the conditions under which they can become manifest have remained vague. The present paper explores computationally two plausible types of linguistic acquisition biases in a population of agents implementing realistic genetic, linguistic and demographic processes. One type of bias represents an innate asymmetric initial state (initial expectation bias) while the other an innate asymmetric facility of acquisition (rate of learning bias). It was found that only the second type of bias produces detectable effects on language through cultural transmission across generations and that such effects are produced even by weak biases present at low frequencies in the population. This suggests that learning preference asymmetries, very small at the individual level and not very frequent at the population level, can bias the trajectory of language change through the process of cultural transmission.     

Adaptive evolution of variable region genes encoding an unusual type of immunoglobulin in camelids

A typical immunoglobulin (Ig) molecule is composed of four polypeptide chains: two identical heavy (H) chains and two identical light (L) chains. This tetrameric structure is conserved in almost all jawed vertebrate species. However, it has been discovered that camels and llamas (family: Camelidae) possess a type of dimeric Ig that consists of two H chains only. These H chains do not associate with L chains, and they do not have the first constant region (CH1), which is present in the conventional Ig. In spite of these changes, the dimeric Ig maintains the normal immune function. To understand the evolution of the dimeric Ig, we studied the phylogenetic relationships of the variable region (V(H)H) genes of the dimeric Ig from Camelidae and those (V(H)) of the conventional Ig from mammals. The results showed that the V(H)H genes form a monophyletic cluster within one of the mammalian V(H) groups, group C. We examined the type of selective force in complementarity-determining regions (CDRs) and framework regions (FRs) by comparing the rate of synonymous (dS) and nonsynonymous (dN) substitutions. We found that the results obtained from V(H)H genes were similar to those from V(H) genes in that CDRs showed an excess of dN over dS (indicating positive selection), whereas the reverse was true for FRs (purifying selection). However, when the extent of positive selection or purifying selection was investigated at each codon site, three major differences between V(H)H and V(H) genes were found. That is, very different types of selective force were observed between V(H)H and V(H) genes (1) at the sites that contact the L chain in the conventional Ig, (2) at the sites that interact with the CH1 region in the conventional Ig, and (3) in the H1 loop. Our findings suggest that adaptive evolution has occurred in the functionally important sites of the V(H)H genes to maintain the normal immune function in the dimeric Ig.     

Analysing Betula litwinowii encroachment and reforestation in the Kazbegi region,Greater Caucasus,Georgia

Aims

The encroachment of tree and shrub species in high mountains is an increasing worldwide phenomenon, which is expected to dramatically alter high‐mountain ecosystems and their functioning. Moreover it indicates in some cases a reforestation process, which will result in important ecological and social benefits, including carbon sequestration and protection against landslides. We therefore examined the spatial extent of forest growth and shrub encroachment mainly of birch (Betula litwinowii) in the sub‐alpine belt of the Central Greater Caucasus between 1987 and 2010 and its relation to topographic site conditions.

Location

Kazbegi district, Central Greater Caucasus, Georgia.

Methods

We analysed 155 vegetation relevés sampled in 2009, 2011 and 2015, mainly derived from the Caucasus Vegetation Database, to obtain information about topographic site conditions and structure of B. litwinowii stands. B. litwinowii forest growth was assessed by digitizing the forest outlines from aerial and space‐borne imagery (1987, 2005 and 2010). To identify areas of B. litwinowii encroachment as an indicator for different encroachment stages, we modelled the tree and shrub cover using the Random Forest algorithm.

Results

We found four types of B. litwinowii stands, characterized by different tree and shrub coverage (initial Bromus variegatus–Betula litwinowii encroachment indicating the first stage of succession, Aconitum nasutum–Betula litwinowii forest, Rubus idaeus–Betula litwinowii forest and Rhododendron caucasicum–Betula litwinowii tree line scrubs). B. litwinowii forest increased 25% compared to 1987 mainly in an uphill direction. Furthermore the modelled tree and shrub cover (R² = .69) could be related to the four vegetation types.

Conclusions

Our results indicate a recent trend towards shrub encroachment and consequently reforestation in the Kazbegi region.     

Resistance of winter wheat varieties to tan spot in the North Caucasus region of Russia

Tan spot caused by Pyrenophora tritici-repentis (Died.) Drechsler, in recent years, occupies an increasingly large area on the territory of Russia. Due to the wide distribution and economic significance of this disease, the search for resistant plants to the pathogen is relevant. This paper presents the results of a field assessment for 2017–2019 of 34 regionally distributed winter wheat varieties of Russian selection for resistance to P. tritici-repentis in the North Caucasus region of Russia. Field resistance - the development of the disease up to 30% against the background of artificial infection for three years was shown by 20.5% of the studied varieties. Wheat varieties were assessed for resistance to isolates of tan spot identified as races 1, 3, and 4 in the greenhouse at the seedling stage. The number of resistant accessions for each race was different and ranged from 12 to 20. The 12 varieties showed resistance to race 1, 14 varieties to race 3, 20 varieties to race 4. This research showed that the resistance to tan spot of studied varieties was race-specific. A functional allele of the susceptibility gene Tsn1 to P. tritici-repentis isolates, producing the toxin Ptr ToxA, was diagnosed by PCR method. Of the analyzed 34 varieties, 13 had a dominant allele of the Tsn1 (Tsn1⁺), and 21 had a recessive allele in the tsn1tsn1 homozygous state. All Tsn1⁺ varieties, and most varieties with recessive alleles tsn1tsn1, were susceptible to tan spot in the field. Varieties Dolya, Gurt, Lebed and Sila, which showed field resistance, had the tsn1tsn1 genotype. The expected reaction of varieties with different allelic composition of the Tsn1 gene to inoculation with the isolate of race 1, according to the generally accepted model of “gene-to-gene” interaction, did not coincide with that observed in reality, which confirms the results obtained by other authors. Research results demonstrate the effect of weather conditions on the susceptibility of wheat varieties to tan spot. In years with higher humidity and higher average air temperatures, the susceptibility response to the disease was observed in more varieties than in drier years. The studies show that the main part (79.5%) of winter wheat varieties of Russian selection widely zoned in the North Caucasus region of Russia are susceptible to P. tritici-repentis. Varieties that have been resistant to the pathogen in the adult phase in the field for three years and to the pathogen races in which the recessive allele of the tsn1 gene has been identified may be of interest as sources of resistance for developing new disease-resistant varieties.     

Redeployment of the Six genes in evolution

It has become clear that during evolution, efficient molecular mechanisms are used over and over again to achieve various patterning tasks. The Six gene story illustrates a new aspect of the molecular conservation during embryogenesis. Members of the Six gene family have been identified on the basis of sequence homology with Drosophila sine oculis gene, which acts within a network of genes including eyeless (Pax family), eyes absent (Eya family) and dachshund (Dach family) to trigger compound eye organogenesis. Some aspects of the regulatory complex operating in Drosophila appear to be conserved during vertebrate eye patterning, but also for other differentiation processes. In this regard, Six1 is required nonetheless during myogenesis, but also for kidney, thymus, inner ear, nose, lacrimal and salivary gland organogenesis. These phenotypes are reminiscent of those previously described for Eya and Pax mutants, suggesting a functional link between these factors during mammalian organogenesis.     

Numerical phytosociology of the subalpine belt of the Kazbegi region,Caucasus, USSR

A vegetational transect across a glacial valley was investigated. Structure and species composition, as well as influence of disturbance by biotic factors (grazing of sheep and cattle) and abiotic factors (topography, wind, water) are discussed.According to species composition and community structure, 4 main vegetation types were distinguished by comparing field data from phytosociological relevés with results of numerical treatments (3 methods of numerical classification and DCA ordination): 1) Chamaesciadium acaule-Polygonum viviparum, 2) Festuca cf. woronowii-Carex tristis, 3) Veratrum lobelianum-Taraxacum stevenii and 4) Rhododendron caucasicum-Vaccinium myrtillus communities.Species diversity (evenness, and number of species) was low in the ungrazed dwarf-shrub alpine communities, which were dominated by Rhododendron caucasicum, in comparison with the grazed meadow. The highest values of these characteristics were found in the transitions among the types.