SINE-derived satellites in scaled reptiles.

BACKGROUND: The genomes of many eukaryotes contain DNA repeats in the form of both tandem and interspersed elements with distinct structure, evolutionary histories, and mechanisms of emergence and amplification. Although there is considerable knowledge regarding their diversity, there is little evidence directly linking these two types. RESULTS: Different tandem repeats derived from portions of short interspersed elements (SINEs) belonging to different families were identified in 56 genomes of squamate reptiles. All loci of SINE-derived satellites (sSats) were thoroughly analyzed. Snake sSats exhibited high similarity in both structure and copy number, while other taxa may have highly diverse (geckos), rare (Darevskia lizards), or missing sSats (agamid lizards). Similar to most satellites associated with heterochromatin, sSats are likely linked to subtelomeric chromosomal regions. CONCLUSIONS: Discovered tandem repeats derived from SINEs exhibit satellite-like properties, although they have not amplified to the same degree as typical satellites. The autonomous emergence of distinct sSats from diverse SINE families in numerous squamate species suggests a nonrandom process of satellite genesis originating from repetitive SINEs.

Interspecific Comparison of Orthologous Short Interspersed Elements Loci Using Whole-Genome Data.

The polymorphism of SINE-containing loci reflects the evolutionary processes that occurred both during the period before the divergence of the taxa and after it. Orthologous loci containing SINE in two or more genomes indicate the relatedness of the taxa, while different copies may have a specific set of mutations and degree of difference. Polymorphic insertion can be interpreted with a high degree of confidence as a shared derived character in the phylogenetic reconstruction of the history of the taxon. The computational comparison of the entire set of SINE-containing loci between genomes is a challenging task, and we propose to consider it in detail using the genomes of representatives of squamate reptiles (lizards) as an example. Our approach allows us to extract copies of SINE from the genomes, find pairwise orthologous loci by using flanking genomic sequences, and analyze the resulting sets of loci for the presence or absence of SINE, the degree of similarity of the flanks, and the similarity of the SINE themselves. The workflow we propose allows us to efficiently extract and analyze orthologous SINE loci for the downstream analysis, as shown in our comparison of species- and genus-level taxa in lacertid lizards.

Evolution of parthenogenetic reproduction in Caucasian rock lizards: A review.

Despite numerous works devoted to hybrid origin of parthenogenesis in reptiles, the causes of hybridization between different species, resulting in the origin of parthenogenetic forms, remain uncertain. Recent studies demonstrate that sexual species considered parental to parthenogenetic rock lizards (Darevskia spp.) avoid interspecific mating in the secondary overlap areas. A specific combination of environmental factors during last glaciation period was critical for ectotherms, which led to a change in their distribution and sex ratio. Biased population structure (e.g., male bias) and limited available distributional range favored the deviation of reproductive behavior when species switched to interspecific mates. To date, at least 7 diploid parthenogenetic species of rock lizards (Darevskia, Lacertidae) originated through interspecific hybridization in the past. The cytogenetic specifics of meiosis, in particular the weak checkpoints of prophase I, may have allowed the formation of hybrid karyotypes in rock lizards. Hybridization and polyploidization are 2 important evolutionary forces in the genus Darevskia. At present, throughout backcrossing between parthenogenetic and parental species, the triploid and tetraploid hybrid individuals appear annually, but no triploid species found among Darevskia spp. on current stage of evolution. The speciation by hybridization with the long-term stage of diploid parthenogenetic species, non-distorted meiosis, together with the high ecological plasticity of Caucasian rock lizards provide us with a new model for considering the pathways and persistence of the evolution of parthenogenesis in vertebrates.

The mixed liver and kidney transcriptome dataset of Darevskia valentini rock lizard.

OBJECTIVES: This study is performed in the frame of a bigger study dedicated to genomics and transcriptomics of parthenogenesis in vertebrates. Among vertebrates, obligate parthenogenesis was first described in the lizards of the genus Darevskia. In this genus, all found parthenogenetic species originated via interspecific hybridization. It remains unknown which genetic or genomic factors play a key role in the generation of parthenogenetic organisms. Comparative genomic and transcriptomic analysis of parthenogens and their parental species may elucidate this problem. Darevskia valentini is a paternal species for four (of seven) parthenogens of this genus, which we promote as a particularly important species for the generation of parthenogenetic forms. DATA DESCRIPTION: Total cellular RNA was isolated from kidney and liver tissues using the standard Trizol Tissue RNA Extraction protocol. Sequencing of transcriptome libraries prepared by random fragmentation of cDNA samples was performed on an Illumina HiSeq2500. Obtained raw sequences contained 117,6 million reads with the GC content of 47%. After preprocessing, raw data was assembled by Trinity and produced 491,482 contigs.

First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species.

The extant reptiles are one of the most diverse clades among terrestrial vertebrates and one of a few groups with instances of parthenogenesis. Due to the hybrid origin of parthenogenetic species, reference genomes of the parental species as well as of the parthenogenetic progeny are indispensable to explore the genetic foundations of parthenogenetic reproduction. Here, we report on the first genome assembly of rock lizard Darevskia valentini, a paternal species for several parthenogenetic lineages. The novel genome was used in the reconstruction of the comprehensive phylogeny of Squamata inferred independently from 7369 trees of single-copy orthologs and a supermatrix of 378 conserved proteins. We also investigated Hox clusters, the loci that are often regarded as playing an important role in the speciation of animal groups with drastically diverse morphology. We demonstrated that Hox clusters of D. valentini are invaded with transposons and contain the HoxC1 gene that has been considered to be lost in the amniote ancestor. This study provides confirmation for previous works and releases new genomic data that will contribute to future discoveries on the mechanisms of parthenogenesis as well as support comparative studies among reptiles.

De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis.

Darevskia rock lizards include 29 sexual and seven parthenogenetic species of hybrid origin distributed in the Caucasus. All seven parthenogenetic species of the genus Darevskia were formed as a result of interspecific hybridization of only four sexual species. It remains unknown what are the main advantages of interspecific hybridization along with switching on parthenogenetic reproduction in evolution of reptiles. Data on whole transcriptome sequencing of parthenogens and their parental ancestors can provide value impact in solving this problem. Here we have sequenced ovary tissue transcriptomes from unisexual parthenogenetic lizard D. unisexualis and its parental bisexual ancestors to facilitate the subsequent annotation and to obtain the collinear characteristics for comparison with other lizard species. Here we report generated RNAseq data from total mRNA of ovary tissues of D. unisexualis, D. valentini and D. raddei with 58932755, 51634041 and 62788216 reads. Obtained RNA reads were assembled by Trinity assembler and 95141, 62123, 61836 contigs were identified with N50 values of 2409, 2801 and 2827 respectively. For further analysis top Gene Ontology terms were annotated for all species and transcript number was calculated. The raw data were deposited in the NCBI SRA database (BioProject PRJNA773939). The assemblies are available in Mendeley Data and can be accessed via doi:10.17632/rtd8cx7zc3.1.

SLC6A3 (DAT1) as a Novel Candidate Biomarker Gene for Suicidal Behavior.

It has been previously shown that the serotonin and dopamine neurotransmitter systems might influence the predisposition to suicidal behavior. This study aims to estimate the contribution of 11 polymorphisms in the genes SLC6A4 (5HTT), HTR1A, HTR2A, HTR1B, SLC6A3 (DAT1), DRD4, DRD2, COMT, and BDNF to suicidal behavior and severity of symptoms of depression and anxiety in the Russian population. The study was performed on 100 patients with repeated suicide attempts and 154 controls. We first found an association between SLC6A3 (DAT1) 40 bp VNTR locus and suicidal behavior. This association was significant; when using the codominant (p = 0.006), dominant (p = 0.001), overdominant (p = 0.004), and log-additive (p = 0.004) models, LL genotype played a protective role (OR = 0.48, 0.29-0.82, p = 0.005). Difference in the distribution of COMT rs4680 genotypes was significant in the codominant (p = 0.04), dominant (p = 0.013), and log-additive (p = 0.02) models, and AA genotype might protect against suicide (OR = 0.49, 0.26-0.91, p = 0.025). SLC6A4 5-HTTLPR + rs25531 locus was significant in the recessive model (p = 0.024), and also affected the severity of symptoms of depression (p = 0.044) and personal anxiety (p = 0.029). Our results suggest that allelic variants of SLC6A3, COMT, and SLC6A4 genes might be considered as risk factors for suicidal attempts.

New Ther1-derived SINE Squam3 in scaled reptiles.

BACKGROUND: SINEs comprise a significant part of animal genomes and are used to study the evolution of diverse taxa. Despite significant advances in SINE studies in vertebrates and higher eukaryotes in general, their own evolution is poorly understood. RESULTS: We have discovered and described in detail a new Squam3 SINE specific for scaled reptiles (Squamata). The subfamilies of this SINE demonstrate different distribution in the genomes of squamates, which together with the data on similar SINEs in the tuatara allowed us to propose a scenario of their evolution in the context of reptilian evolution. CONCLUSIONS: Ancestral SINEs preserved in small numbers in most genomes can give rise to taxa-specific SINE families. Analysis of this aspect of SINEs can shed light on the history and mechanisms of SINE variation in reptilian genomes.

Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis.

BACKGROUND: The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three species yields estimates of clonal diversity and tests the hypothesis of a single origin for D. unisexualis. RESULTS: Genotyping and sequencing of four microsatellite-containing loci for 109 specimens of D. unisexualis, 17 D. valentini, and 45 D. raddei nairensis identified 12 presumptive clones, including one widespread and 11 rare clones. Most individuals in some localities had a rare clone. Clone-specific alleles in D. unisexualis were compared with those of the parental species. The results inferred a single hybridization event. Post-formation mutations best explain the less common clones. CONCLUSIONS: Interspecific analyses identify alleles inherited by D. unisexualis from its bisexual ancestors. SNP analyses fail to reject the hypothesis of a single interspecific origin of D. unisexualis, followed by microsatellite mutations in this initial clone. Microsatellites detect higher clonal diversity in D. unisexualis compared to allozymes and identify the likely origins of clones. Our approach may be applicable to other unisexual species whose origins involve interspecific hybridization.

Multiple interspecific hybridization and microsatellite mutations provide clonal diversity in the parthenogenetic rock lizard Darevskia armeniaca.

BACKGROUND: The parthenogenetic Caucasian rock lizard Darevskia armeniaca, like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual Darevskia mixta and Darevskia valentini. Darevskia armeniaca was shown to consist of one widespread allozyme clone and a few rare ones, but notwithstanding the origin of clonal diversity remains unclear. We conduct genomic analysis of D. armeniaca and its parental sexual species using microsatellite and SNP markers to identify the origin of parthenogenetic clonal lineages. RESULTS: Four microsatellite-containing loci were genotyped for 111 specimens of D. armeniaca, 17 D. valentini, and four D. mixta. For these species, a total of 47 alleles were isolated and sequenced. Analysis of the data revealed 13 genotypes or presumptive clones in parthenogenetic D. armeniaca, including one widespread clone, two apparently geographically restricted clones, and ten rare clones. Comparisons of genotype-specific markers in D. armeniaca with those of its parental species revealed three founder-events including a common and two rare clones. All other clones appeared to have originated via post-formation microsatellite mutations in the course of evolutionary history of D. armeniaca. CONCLUSION: Our new approach to microsatellite genotyping reveals allele-specific microsatellite and SNP markers for each locus studied. Interspecies comparison of these markers identifies alleles inherited by parthenospecies from parental species, and provides new information on origin and evolution of clonal diversity in D. armeniaca. SNP analyses reveal at least three interspecific origins of D. armeniaca, and microsatellite mutations in these initial clones give rise to new clones. Thus, we first establish multiple origins of D. armeniaca. Our study identifies the most effective molecular markers for elucidating the origins of clonal diversity in other unisexual species that arose via interspecific hybridization.

Polymorphisms of dopamine receptor genes DRD2 and DRD4 in African populations of Hadza and Datoga differing in the level of culturally permitted aggression.

The key regulator in the control of aggressive behavior is dopamine receptors. Association of variants in these genes with aggression has been shown in modern populations. However, these studies have not been conducted in traditional cultures. The aim of our study was to investigate population features in distributions of allele and genotype frequencies of DRD2 rs1800497, DRD4 120 bp Ins, and DRD4 exon III polymorphisms and their associations with aggressive behavior in the traditional African populations of Hadza and Datoga, which display a contrast in their culturally permitted aggression. Overall, 820 healthy unrelated Hadza and Datoga individuals were studied. Self-rated scores of aggression were collected using Buss and Perry's Aggression Questionnaire. Polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP) was used to determine the genotype of each individual. We show that the Hadza and the Datoga differed significantly in allele and genotype frequencies of all studied loci. Our association analysis detected that only ethnicity and sex of individuals significantly influenced their aggression rank, but we failed to identify any associations of DRD2 rs1800497, DRD4 120 bp Ins, or DRD4 exon III polymorphisms with aggression. Thus, our data have no strong evidence to support the involvement of polymorphisms of DRD2 and DRD4 in controlling aggressive behavior.

Serotonergic gene polymorphisms (5-HTTLPR, 5HTR1A, 5HTR2A), and population differences in aggression: traditional (Hadza and Datoga) and industrial (Russians) populations compared.

BACKGROUND: Current knowledge on genetic basis of aggressive behavior is still contradictory. This may be due to the fact that the majority of studies targeting associations between candidate genes and aggression are conducted on industrial societies and mainly dealing with various types of psychopathology and disorders. Because of that, our study was carried on healthy adult individuals of both sex (n = 853). METHODS: Three populations were examined: two traditional (Hadza and Datoga) and one industrial (Russians), and the association of aggression with the following polymorphisms 5-HTTLPR, rs6295 (5HTR1A gene), and rs6311 (5HTR2A gene) were tested. Aggression was measured as total self-ratings on Buss-Perry Aggression Questionnaire. RESULTS: Distributions of allelic frequencies of 5-HTTLPR and 5HTR1A polymorphisms were significantly different among the three populations. Consequently, the association analyses for these two candidate genes were carried out separately for each population, while for the 5HTR2A polymorphism, it was conducted on the pooled data that made possible to introduce ethnic factor in the ANOVA model. The traditional biometrical approach revealed no sex differences in total aggression in all three samples. The three-way ANOVA (µ + 5-HTTLPR + 5HTR1A + 5HTR2A +ε) with measures of self-reported total aggression as dependent variable revealed significant effect of the second serotonin receptor gene polymorphism for the Hadza sample. For the Datoga, the interaction effect between 5-HTTLPR and 5HTR1A was significant. No significant effects of the used polymorphisms were obtained for Russians. The results of two-way ANOVA with ethnicity and the 5HTR2A polymorphism as main effects and their interactions revealed the highly significant effect of ethnicity, 5HTR2A polymorphism, and their interaction on total aggression. CONCLUSIONS: Our data provided obvious confirmation for the necessity to consider the population origin, as well as cultural background of tested individuals, while searching for associations between genes and behavior, and demonstrated the role of cultural attitudes towards the use of in-group aggression. Our data partly explained the reasons for disagreement in results of different teams, searching for candidate-gene associations with behavior without considerations of culturally desirable norms. Previous studies suggested that the 5HTR2A gene polymorphism associates with aggression and criminality. Our data extended these findings, demonstrating the role of rs6311 (5HTR2A gene) in aggression in adult healthy men and women from our samples. We found that G-allele carriers were rated higher on total aggression.

The origin of multiple clones in the parthenogenetic lizard species Darevskia rostombekowi.

The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species. All individuals are heterozygous at the loci. The major clone occurs in 24 individuals and involves three populations. Four rare clones involve one or several individuals from one or two populations. Most variation owes to parent-specific single nucleotide polymorphisms, which occur as heterozygotes. This result fails to reject the hypothesis of a single hybridization founder event that resulted in the initial formation of one major clone. The other clones appear to have originated via post-formation microsatellite mutations of the major clone.

The complete mitochondrial genome of the causative agent of the human cercarial dermatitis, the visceral bird schistosome species Trichobilharzia szidati (platyhelminthes: Trematoda: Schistosomatidae).

We report the first complete mitochondrial genome of visceral bird schistosome Trichobilharzia szidati (Platyhelminthes, Trematoda: Schistosomatidae). The circular genome is 14293 bp in length and contains 12 protein-coding genes, 12S and 16S rRNAs genes, 22 tRNAs and one non-coding region (202 bp) (accession number MF136777). Phylogenetic relationships based on 12 protein-coding gene sequences (PCG) of mitogenomes of a number of trematode and cestode species have shown that T. szidati is the closest genetic relative to nasal bird schistosome T. regenti. The complete mitogenome sequence of T. szidati may serve as a resource for comparative mitogenomics and trematode evolution studies.

Polymorphisms of two loci at the oxytocin receptor gene in populations of Africa, Asia and South Europe.

BACKGROUND: The oxytocin (OT) system is known to be implicated in the regulation of complex social behavior, particularly empathy and parenting. The goal of this study was to estimate the gender and population differences in polymorphisms of two oxytocin receptor gene SNPs, rs53576 and rs2254298, in four populations. RESULTS: These data were compared with each other and with 14 samples from the corresponding regions retrieved from the 1000 Genomes database. Low level of heterozygosity was observed for both SNPs in all populations in this study (rs53576: Catalonian, Hobs = 0.413; Hadza, Hobs = 0.556; sr2254698: Khanty-Mansi, Hobs = 0.250; Datoga, Hobs = 0.550). The amount of variance due to regional variability was almost equal for both SNPs (rs53576: FRT = 0.086, rs2554298: FRT = 0.072), whereas variance for the population level of variability was twice bigger for rs2554298 (rs53576: FST = 0.127, rs2554298: FST = 0.162). Pairwise coefficients of fixation demonstrate that the Hadza were well differentiated from other African populations except of Datoga, the Datoga were weakly differentiated from other African origin populations, the Ob Ugric people were extremely differentiated from all other populations. Catalans were extremely differentiated of Asian populations. CONCLUSIONS: It is hypothesized on the base of spatial distribution of the evolutionary novel A alleles of the both OXTR gene loci, that the spread of alleles of rs22542298 and rs53376 SNPs may be associated to some extant with manipulation of parental investment in humans.

The complete mitochondrial genome of the parthenogenetic Caucasian rock lizard Darevskia unisexualis (Squamata: lacertidae) contains long tandem repeat formed by 59 bp monomer.

The first complete mitochondrial genome sequence of parthenogenetic Caucasian rock lizard Darevskia unisexualis (Lacertidae family) is determined by hybrid assembly with Illumina HiSeq and PacBio RS II platforms. The circular 21.4 kbp mitogenome contains 13 protein-coding genes, 12S and 16S rRNA genes, 20 tRNAs, two pseudogenized tRNAs, and one long tandem repeats with 4.1 kbp length formed by 59 bp monomer repeated x70.6 times located before control region. This finding represents a new example of mitogenome variation in lizards of hybrid origin, providing fundamental data for following study of a unique hybridization system formed by parthenogenetic and bisexual species in the mountain steppe of central Armenia.

Androgen Receptor Gene Polymorphism, Aggression, and Reproduction in Tanzanian Foragers and Pastoralists.

The androgen receptor (AR) gene polymorphism in humans is linked to aggression and may also be linked to reproduction. Here we report associations between AR gene polymorphism and aggression and reproduction in two small-scale societies in northern Tanzania (Africa)--the Hadza (monogamous foragers) and the Datoga (polygynous pastoralists). We secured self-reports of aggression and assessed genetic polymorphism of the number of CAG repeats for the AR gene for 210 Hadza men and 229 Datoga men (aged 17-70 years). We conducted structural equation modeling to identify links between AR gene polymorphism, aggression, and number of children born, and included age and ethnicity as covariates. Fewer AR CAG repeats predicted greater aggression, and Datoga men reported more aggression than did Hadza men. In addition, aggression mediated the identified negative relationship between CAG repeats and number of children born.

Clonal diversity and clone formation in the parthenogenetic Caucasian rock Lizard Darevskia dahli [corrected].

The all-female Caucasian rock lizard species Darevskia dahli and other parthenogenetic species of this genus reproduce normally via true parthenogenesis. Previously, the genetic diversity of this species was analyzed using allozymes, mitochondrial DNA, and DNA fingerprint markers. In the present study, variation at three microsatellite loci was studied in 111 specimens of D. dahli from five populations from Armenia, and new information regarding clonal diversity and clone formation in D. dahli was obtained that suggests a multiple hybridization origin. All individuals but one were heterozygous at the loci studied. Based on specific allele combinations, 11 genotypes were identified among the individuals studied. Individuals with the same genotypes formed distinct clonal lineages: one major clone was represented by 72 individuals, an intermediate clone was represented by 21 individuals, and nine other clones were rare and represented by one or several individuals. A new approach based on the detection and comparison of genotype-specific markers formed by combinations of parental-specific markers was developed and used to identify at least three hybridization founder events that resulted in the initial formation of one major and two rare clones. All other clones, including the intermediate and seven rare clones, probably arose through postformation microsatellite mutations of the major clone. This approach can be used to identify hybridization founder events and to study clone formation in other unisexual taxa.

Clonal diversity and clone formation in the parthenogenetic Caucasian rock lizard Darevskia dahlia.

The all-female Caucasian rock lizard species Darevskia dahli and other parthenogenetic species of this genus reproduce normally via true parthenogenesis. Previously, the genetic diversity of this species was analyzed using allozymes, mitochondrial DNA, and DNA fingerprint markers. In the present study, variation at three microsatellite loci was studied in 111 specimens of D. dahli from five populations from Armenia, and new information regarding clonal diversity and clone formation in D. dahli was obtained that suggests a multiple hybridization origin. All individuals but one were heterozygous at the loci studied. Based on specific allele combinations, 11 genotypes were identified among the individuals studied. Individuals with the same genotypes formed distinct clonal lineages: one major clone was represented by 72 individuals, an intermediate clone was represented by 21 individuals, and nine other clones were rare and represented by one or several individuals. A new approach based on the detection and comparison of genotype-specific markers formed by combinations of parental-specific markers was developed and used to identify at least three hybridization founder events that resulted in the initial formation of one major and two rare clones. All other clones, including the intermediate and seven rare clones, probably arose through postformation microsatellite mutations of the major clone. This approach can be used to identify hybridization founder events and to study clone formation in other unisexual taxa.

Aggression and polymorphisms in AR, DAT1, DRD2, and COMT genes in Datoga pastoralists of Tanzania.

The aim of this study was to analyse the relationships between polymorphisms in four candidate genes (AR, DAT1, DRD2, and COMT) and aggression in men from a traditional society of East African pastoralists, the Datoga. Buss and Perry's Aggression Questionnaire was used to measure aggression. The number of CAG repeats in the AR gene was negatively correlated with physical aggression, anger, and hostility. Among the genes of the dopaminergic system, a significant single-gene effect was detected only for DRD2 with regard to anger. At the level of a two-gene model, a significant effect for DRD2 and a tendency for DAT1 were observed for the DAT1-DRD2 gene pair regarding hostility, and two tendencies were observed for the interaction effect of the DAT1-COMT pair regarding anger and hostility. These data suggest a probable link between physical aggression and direct fitness caused by strong sexual selection in Datoga men.