Evolutionary Genetics Research Articles

Perspectives on Modern Synthetic Theory of Evolution

For the past more than a century, evolution has become a corner stone of biology. Different theories have been proposed to explain the mechanisms of evolution such as Lamarckism, Darwinism, germ plasm theory, isolation theory, mutation theory, modern synthetic theory and neutral theory. Among these theories, emphasis is mostly given on single factors. However, modern synthetic theory combines different factors into one theory, particularly natural selection and Mendelian genetics that is why the word synthetic theory is used. Presently, it is the most widely accepted theory to explain the mechanism of evolution although it owes more to Darwin than to any other evolutionary biologist and is essentially built around the concept of natural selection. However, it incorporates much that is post-Darwinian. This theory offers the most widely accepted explanation for the mechanism of evolution and is based on factors such as gene mutations, structural and numerical alterations in chromosomes, genetic recombination, natural selection, random genetic drift, migration, hybridization and reproductive isolation. Further, some recent work in the field of molecular biology have thrown light on the mechanisms of evolution. The new biology goes beyond the modern synthesis, it integrates together genomics, bioinformatics, evolutionary genetics and molecular biology to provide novel explanations, and in the light of these findings, the OMS should be modified or extended. Even there is a suggestion to propose a new theory of evolution as a coherent alternative to modern synthesis

Assessing a Role of Genetic Drift for Deep-Time Evolutionary Events.

Effective population size (Ne) determines the amount of genetic diversity and the fate of genetic variants in a species and thus is an essential parameter in evolutionary genetics. There are standard approaches to determine the Ne of evolving species. For example, the long-term Ne of an extant species is calculated based on its unbiased global mutation rate and the neutral genetic diversity of the species. However, approaches for inferring Ne of ancestral lineages are less known. Here, we introduce an evolutionary genetic statistic and an analytical procedure to assess the efficiency of natural selection for deep nodes by calculating rates of nonsynonymous nucleotide substitutions leading to radical (dR) and conservative (dC) amino acid replacements, respectively. Given that radical variants are more likely to be deleterious than conservative ones, an elevated dR/dC ratio in gene families across the genome means an accelerated genome-wide accumulation of the more deleterious type of mutations (i.e., radical variants), which indicates that natural selection is less efficient and genetic drift becomes more powerful. Earlier approaches that calculate dR/dC do not consider the impact of nucleotide composition (G+C content) on the dR/dC result, which is partially accounted for in more recent methods. Here, we use these methods to demonstrate that genetic drift may have driven the early evolution of Prochlorococcus, the most abundant carbon-fixing photosynthetic bacteria in the ocean.

A cultural evolutionary behavior genetics will need a more sophisticated conceptualization of cultural traits.

A framework that brings together cultural perspectives and behavior genetics has long been needed. To be successful, however, we need sophistication in the conceptualization of culture. Here, we highlight three imperatives to this end: the need for a clear definition of cultural traits, inclusion of the role of societal power, and recognizing the distinction between traits and characteristic adaptations.

Integrating cultural evolution and behavioral genetics.

The 29 commentaries amplified our key arguments; offered extensions, implications, and applications of the framework; and pushed back and clarified. To help forge the path forward for cultural evolutionary behavioral genetics, we (1) focus on conceptual disagreements and misconceptions about the concepts of heritability and culture; (2) further discuss points raised about the intertwined relationship between culture and genes; and (3) address extensions to the proposed framework, particularly as it relates to cultural clusters, development, and power. These commentaries, and the deep engagement they represent, reinforce the importance of integrating cultural evolution and behavioral genetics.

Analiza varijabilnosti L1 gena humanog papiloma virusa tipa 16 u našoj populaciji

Introduction: Human papilloma viruses (HPV) have been identified as a major etiological factor in the pathogenesis of cervical cancer. High-risk type HPV16 has the greatest medical significance. Based on differences in the nucleotide sequence of the type 16 genome, the existence of 16 variants of this type with different geographical distribution has been shown. Aim: Examination of the nucleotide sequence variability of the L1 gene presented in HPV16 variants in our territory. Material and methods: The paper includes 37 sequences of HPV16 L1 genes taken from the database of the Institute of Microbiology and Immunology of the Faculty of Medicine, University of Belgrade. The sequences were compared with the reference sequences of the HPV16 variants and the construction of the phylogenetic tree was done using the MEGA (Molecular Evolutionary Genetics Analysis, version X) software package. Results: Out of the 37 HPV16 L1 analyzed gene sequences, 23 were grouped with European variants. Other isolates were grouped with non-European HPV16 variants. The nucleotide distance was less than 1%, that is, at the level of subvariants. Conclusion: The results of this study indicate that the European variants of the HPV16 virus are the most common in our population, but they also indicate the presence of non-European variants. Further analysis is necessary in order to monitor the circulation of HPV16 variants in our population.

1010 – CONVERGENT SOMATIC EVOLUTION FROM EARLY LIFE IN A GERMLINE RIBOSOMOPATHY

Clonal tracking of stem cells and their progeny by whole genome sequencing permits exploration of evolutionary genetics in human disease. We performed phylogenetic reconstruction of haematopoiesis using somatically acquired mutations in 323 single haematopoietic stem and progenitor cell-derived colonies from 10 individuals with an inherited disorder of ribosome assembly, Shwachman-Diamond syndrome. We observed numerous clonal expansions, with recurrent acquisition of mutually exclusive mutations (EIF6, TP53, RPL5, RPL22, PRPF8, chromosomes 7 and 15) in multiple different clones in utero or early childhood converging on the p53-dependent nucleolar surveillance pathway that monitors ribosome integrity. In contrast to clones carrying biallelic TP53 mutations, genomes derived from colonies carrying mono-allelic TP53 mutations displayed no increase in mutation burden or specific mutational signatures. Our study highlights striking loss of clonal diversity with convergent somatic evolution on the p53-dependent nucleolar surveillance pathway from early life to offset the deleterious effects of a germline mutation in a Mendelian haematopoietic disorder. Clonal tracking of stem cells and their progeny by whole genome sequencing permits exploration of evolutionary genetics in human disease. We performed phylogenetic reconstruction of haematopoiesis using somatically acquired mutations in 323 single haematopoietic stem and progenitor cell-derived colonies from 10 individuals with an inherited disorder of ribosome assembly, Shwachman-Diamond syndrome. We observed numerous clonal expansions, with recurrent acquisition of mutually exclusive mutations (EIF6, TP53, RPL5, RPL22, PRPF8, chromosomes 7 and 15) in multiple different clones in utero or early childhood converging on the p53-dependent nucleolar surveillance pathway that monitors ribosome integrity. In contrast to clones carrying biallelic TP53 mutations, genomes derived from colonies carrying mono-allelic TP53 mutations displayed no increase in mutation burden or specific mutational signatures. Our study highlights striking loss of clonal diversity with convergent somatic evolution on the p53-dependent nucleolar surveillance pathway from early life to offset the deleterious effects of a germline mutation in a Mendelian haematopoietic disorder.

Mathematical Analyses in Genetics and Evolution

Evolution is the phenomenon of the development organisms from more simple earlier forms to more advanced forms in the course of a long period of time. The Genetics refers to inheritance of characters from the parental generation and to the changes in the characters that occur between the offspring of the parents. Mendelian heredity principles forms the foundation over which the modern understanding of the evolutionary process, i.e., “Modern Synthesis” was built. Mathematical derivations, equations and models were used by geneticists and evolutionists as tools to understand the Evolutionary Genetics over the period of time.

Morphological, phytochemical and molecular characterization of five common Jatropha species in the Niger Delta Region of Nigeria

The economic and medicinal important genus Jatropha contains many distinctly different species. To elucidate the genetic relationship of five common occurring Jatropha species namely J. multifida, J. podagrica, J.tanjorernsis, J. curcas, and J. gossypifolia, thirty-nine morphological, six phytochemical features and one arbitrary marker was used to screen and explore their similarity. Morphological data was obtained from the measurement of vegetative and reproductive parts while the presence of five phytochemicals was determined using differentphytochemical tests. The DNA of all five Jatropha species were amplified and sequenced using Ribolose 1, 5- biphosphate carboxylase molecular marker. The DNA sequences were then aligned using the Basic Local Alignment Search Tool for nucleotide 2.8.0 version of the National Center for Biotechnology Information database and phylogenetic trees were constructed using Paleontological Statistical software and Molecular Evolutionary Genetics Analysis version 7.0.26 software. From the results of the classical and phylogenetic cluster analysis, the five Jatropha species was separated into two major clusters. The highly distinctive J. gossypifolia was the only species that clustered separately from the other Jatropha species. Although, J. tanjorensis has been reported to be a hybrid from J. curcas and J. gossypifolia, the species did not segregate and cluster with these species, but segregated with J. multifida, and J.podagrica, indicating that this species is more closely related to J. multifida, and J. podagrica than J. curcas and J.gossypifolia. The result therefore provide information that would be useful in the plant improvement programs for the genus Jatropha.

The emerging complexity of Open Science: assessing Intelligent Data Openness in Genomic Anthropology and Human Genomics.

In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the "intelligent data openness" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.

Complementary square wave voltammetry and tandem mass spectrometry analysis to identify and detect compensatory genomic changes in nematodes due to nickel (II) exposure

Nickel is a toxic heavy metal that may cause negative health outcomes including cancer upon exposure [1]. Square wave voltammetry was used to assay DNA directly extracted from nickel-exposed nematodes that had originated from either high or low Ni-containing environments in order to assess the role of evolutionary genetics in the Ni toxicity process. Extracted DNA was immobilized on pyrolytic graphite (PG) electrodes following layer by layer (LbL) protocols and then electrochemically oxidized in the presence of Ru(bpy)3+ to generate electrocatalytic oxidative currents at ∼+1.05 V vs. SCE. Both C. elegans and P. pacificus nematodes were utilized, each with a volcanic or cosmopolitan soil source strain. DNA oxidative peak currents (Ip) increased for all nematode strains upon exposure to 50 μg/L Ni2+, but those originating from volcanic soils exhibited significantly (40–50%) lower Ip upon Ni2+ exposure compared to similarly exposed nematodes from cosmopolitan soils. Further SWV analysis was performed on DNA from a series of C. elegans N2xCB4856 recombinant inbred advanced intercross line populations (RIALs). A continuum of Ip magnitude was seen as a function of Ni2+ exposure among the RIAL strains indicating Ni-tolerance is complex and affected by multiple loci. The majority of the DNA from Ni-exposed individual RIAL strain cultures produced an increase in oxidative current in comparison to DNA from analogous Ni-unexposed cultures of the same RIAL strains. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis on acid hydrolyzed nematode DNA provided validation of the electrochemical findings. Guanine and oxidatively damaged guanine content were monitored via appropriate m/z mass transitions. Guanine content in all Ni-exposed RIAL DNA was lower, while oxidatively damaged guanine was elevated compared to unexposed nematodes in all but one analyzed RIAL. Combined, the complementary electrochemical and MS/MS data provide evidence that evolutionary genetics leads to genetic protection from environmental toxicants, suggesting a possibility that multiple genes are involved in the protection of the organism from Ni exposure.

Comprehensive Analysis and Assessment on Codon Usage Pattern of Hemolytic Genes from Different Strains of Leptospira interrogans

Background: Leptospirosis is a disease that is zoonotic in nature. It is easily able to survive in the environment and gets transmitted from the reservoir hosts such as rat to humans. Though the cause of Leptospira interrogans virulency is not determined, these studies expresses that the product of a Leptospira interrogans gene sphH is hemolytic in nature and is capable of lysing the erythrocyte cells and also few epithelial cell membranes.
 Aim: In this study, we have analyzed the codon usage bias of the gene sphH, taken from 49 strains of Leptospira interrogans.
 Materials and Methods: Data Collection: The full CDSs nucleotide of the gene sphH from 49 Leptospira interrogans was downloaded separately in FASTA format from the NCBI nucleotide database. Molecular Evolutionary Genetics Analysis (MEGA) program was used to edit and align the coding sequences. With the help of statistical techniques such as RSCU and ENC we have determined the codons mostly used to express the gene sphH and source of the bias with methods such as parity rule 2, neutrality plots.
 Result: The nucleotide content of the , gene across 49 variants of leptospira divulged that the usage of A (36.03% ± 0.74) and T (31.81% ± 0.65) occurred more frequently than the usage of G (17.88% ± 0.57) and C (14.28% ± 0.66) making the gene composition AT more than GC. The composition of bases in the 3rd position saw base T most frequent than base A.
 Conclusion: The codon and amino acid use patterns reflect this bias in genetic composition. Leptospiral strains have a similar general codon usage pattern and are slightly biassed. The majority of the frequently occurring codons are A- and U-ending, showing that mutational bias is the primary driver determining codon usage in this bacterium. There were significant changes in synonymous codon usage frequencies between Leptospira interrogans and with other virulent strains. Codon use preferences to account for these differences.

Gavin Ortlund. Retrieving Augustine’s Doctrine of Creation: Ancient Wisdom for Current Controversy.

Gavin Ortlund. <i>Retrieving Augustine’s Doctrine of Creation: Ancient Wisdom for Current Controversy</i>.

Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes.

Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments.

MotivationCRISPR/Cas9-based technology allows for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context. This approach, known as saturation genome editing (SGE), a form of deep mutational scanning, systematically alters each position in a target region to explore its function. SGE experiments require the design and synthesis of oligonucleotide variant libraries which are introduced into the genome. This technology is applicable to diverse fields such as disease variant identification, drug development, structure–function studies, synthetic biology, evolutionary genetics and host–pathogen interactions. Here, we present the Variant Library Annotation Tool (VaLiAnT) which can be used to generate variant libraries from user-defined genomic coordinates and standard input files. The software can accommodate user-specified species, reference sequences and transcript annotations.ResultsCoordinates for a genomic range are provided by the user to retrieve a corresponding oligonucleotide reference sequence. A user-specified range within this sequence is then subject to systematic, nucleotide and/or amino acid saturating mutator functions. VaLiAnT provides a novel way to retrieve, mutate and annotate genomic sequences for oligonucleotide library generation. Specific features for SGE library generation can be employed. In addition, VaLiAnT is configurable, allowing for cDNA and prime editing saturation library generation, with other diverse applications possible.Availability and implementationVaLiAnT is a command line tool written in Python. Source code, testing data, example input and output files and executables are available (https://github.com/cancerit/VaLiAnT) in addition to a detailed user manual (https://github.com/cancerit/VaLiAnT/wiki). VaLiAnT is licensed under AGPLv3.Supplementary information Supplementary data are available at Bioinformatics online.

The complete chloroplast genome sequence of the medicinal plant Cercis chinensis and phylogenetic analysis

Cercis chinensis is a deciduous shrub or small landscape tree with exceptional ornamental characteristics. Here, we report the complete chloroplast genome of C. chinensis to provide a foundation for further phylogenetic studies of the Leguminosae. The chloroplast (cp) genome was 158,999 bp in size containing a large single-copy (LSC) region 88,176 bp in length, a small single-copy (SSC) region 19,583 bp in length, and two inverted repeat (IR) regions that were 25,620 bp each. The total GC content of the cp genome was 42.9% with the LSC, SSC, and IR regions 36.2, 33.8, and 29.4%, respectively. The cp genome contains 129 genes, including 85 protein-coding, 36 tRNA, and 8 rRNA genes. The phylogenetic analysis revealed that C. chinensis is closely related to Cercis glabra. These results provide valuable information about the evolutionary processes and conservation genetics of C. chinensis.

First report of mitochondrial COI in foraminifera and implications for DNA barcoding

Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in many marine environments and play a major role in global carbon cycling. Species recognition in Foraminifera is mainly based on morphological characters and nuclear 18S ribosomal RNA barcoding. The 18S rRNA contains variable sequence regions that allow for the identification of most foraminiferal species. Still, some species show limited variability, while others contain high levels of intragenomic polymorphisms, thereby complicating species identification. The use of additional, easily obtainable molecular markers other than 18S rRNA will enable more detailed investigation of evolutionary history, population genetics and speciation in Foraminifera. Here we present the first mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences (“barcodes”) of Foraminifera. We applied shotgun sequencing to single foraminiferal specimens, assembled COI, and developed primers that allow amplification of COI in a wide range of foraminiferal species. We obtained COI sequences of 49 specimens from 17 species from the orders Rotaliida and Miliolida. Phylogenetic analysis showed that the COI tree is largely congruent with previously published 18S rRNA phylogenies. Furthermore, species delimitation with ASAP and ABGD algorithms showed that foraminiferal species can be identified based on COI barcodes.

Genomic prediction in the wild: A case study in Soay sheep.

Genomic prediction, the technique whereby an individual's genetic component of their phenotype is estimated from its genome, has revolutionised animal and plant breeding and medical genetics. However, despite being first introduced nearly two decades ago, it has hardly been adopted by the evolutionary genetics community studying wild organisms. Here, genomic prediction is performed on eight traits in a wild population of Soay sheep. The population has been the focus of a >30year evolutionary ecology study and there is already considerable understanding of the genetic architecture of the focal Mendelian and quantitative traits. We show that the accuracy of genomic prediction is high for all traits, but especially those with loci of large effect segregating. Five different methods are compared, and the two methods that can accommodate zero-effect and large-effect loci in the same model tend to perform best. If the accuracy of genomic prediction is similar in other wild populations, then there is a real opportunity for pedigree-free molecular quantitative genetics research to be enabled in many more wild populations; currently the literature is dominated by studies that have required decades of field data collection to generate sufficiently deep pedigrees. Finally, some of the potential applications of genomic prediction in wild populations are discussed.

A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913.

Simple SummaryThe scaly rockcod (Trematomus loennbergii) is distributed in the Antarctic Ocean and this area is isolated by the Antarctic Circumpolar Current. It is important region to study evolutionary diversity. Trematomus is the main genus, having 11 species, and their habit distribution is well known. However, their genetic and genomic information is not studied. In addition, some species have similar morphology. In this study, a genome survey of T. loennbergii and microsatellite motif analysis were conducted to obtain genomic profile. The fundamental data such as genome size, heterozygosity ratio, duplication ration and microsatellite motifs were obtained. These data will provide a foundation for further whole-genome sequencing and the development of new molecular markers of T. loennbergii.Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

Evolvability: A Quantitative-Genetics Perspective

The concept of evolvability emerged in the early 1990s and soon became fashionable as a label for different streams of research in evolutionary biology. In evolutionary quantitative genetics, evolvability is defined as the ability of a population to respond to directional selection. This differs from other fields by treating evolvability as a property of populations rather than organisms or lineages and in being focused on quantification and short-term prediction rather than on macroevolution. While the term evolvability is new to quantitative genetics, many of the associated ideas and research questions have been with the field from its inception as biometry. Recent research on evolvability is more than a relabeling of old questions, however. New operational measures of evolvability have opened possibilities for understanding adaptation to rapid environmental change, assessing genetic constraints, and linking micro- and macroevolution.