Molecular Population Genetics Research Articles

First report on the molecular phylogenetics and population genetics of Aedes aegypti in Iran

BackgroundAedes aegypti, the primary vector of various human arboviral diseases, is a significant public health threat. Aedes aegypti was detected in Iran in 2018, in Hormozgan province, but comprehensive information regarding its genetic diversity and origin within the country remains scarce. This study aimed to determine the origin and genetic diversity of Ae. aegypti in southern Iran.MethodsAedes aegypti mosquitoes were collected from Bandar Abbas City, Hormozgan Province, southern Iran, between May and July 2022. Specimens were morphologically identified. Origin and assess genetic diversity were assessed based on the mitochondrial DNA-encoded cytochrome c oxidase subunit I (mtDNA-COI) gene.ResultsBLAST (basic local alignment search tool) analysis confirmed the accuracy of the morphological identification of all specimens as Ae. aegypti, with 100% similarity to GenBank sequences. Calculated variance and haplotype diversity were 0.502 and 0.00157, respectively. Among the 604 examined nucleotide sequences, only a single site was non-synonymous. Total nucleotide diversity and average pairwise nucleotides were determined as 0.00083 and 0.502, respectively. Fu and Li's D test values were not statistically significant. Strobeck’s S statistic value was 0.487, and Tajima’s D value was 1.53395; both were not statistically significant (P > 0.10).ConclusionsPhylogenetic analysis revealed two distinct clades with minimal nucleotide differences and low haplotype diversity, suggesting the recent establishment of Ae. Aegypti in the southern region of Iran. The phylogenetic analysis also indicated an association between Ae. aegypti populations and mosquitoes from Saudi Arabia and Pakistan.Graphical

Unraveling the Molecular Basis of Stabilizing Selection by Experimental Evolution

Abstract Stabilizing selection provides a challenge to molecular population genetics. Although stabilizing selection is ubiquitous, its genomic signature is difficult to distinguish from demographic signals. Experimental evolution provides a promising approach to characterize genomic regions exposed to stabilizing selection. A recent experimental evolution study of Aedes aegypti populations evolving either with or without sexual selection found a pattern of genetic differentiation suggestive of relaxed stabilizing selection. I argue that this study could not have detected the signal of relaxed stabilizing selection. I highlight why incorrect statistical methods resulted in a high number of false positive candidate single nucleotide polymorphism (SNPs) and discuss the fallacy of functional validation of candidate SNPs for polygenic traits by RNA-mediated knockdown.

Intron Regions as Genetic Markers for Population Genetic Investigations of Opisthorchis viverrini sensu lato and Clonorchis sinensis.

Opisthorchiasis and clonorchiasis are prevalent in Southeast and Far-East Asia, which are caused by the group 1 carcinogenic liver flukes Opisthorchis viverrini sensu lato and Clonorchis sinensis infection. There have been comprehensive investigations of systematics and genetic variation of these liver flukes. Previous studies have shown that O. viverrini is a species complex, called "O. viverrini sensu lato". More comprehensive investigations of molecular systematics and population genetics of each of the species that make up the species complex are required. Thus, other polymorphic genetic markers need to be developed. Therefore, this study aimed to characterize the intron regions of taurocyamine kinase gene (TK) to examine the genetic variation and population genetics of O. viverrini and C. sinensis collected from different geographical isolates and from a range of animal hosts. We screened seven intron regions embedded in TK. Of these, we selected an intron 5 of domain 1 (TkD1Int5) region to investigate the genetic variation and population genetics of theses liver flukes. The high nucleotide and haplotype diversity of TkD1Int5 was detected in O. viverrine. Heterozygosity with several insertion/deletion (indel) regions were detected in TkD1Int5 of the O. viverrine samples, whereas only an indel nucleotide was detected in one C. sinensis sample. Several O. viverrine samples contained three different haplotypes within a particular heterozygous sample. There were no genetic differences between C. sinensis isolated from various animal host. Heterozygous patterns specifically detected in humans was observed in C. sinensis. Thus, TkD1Int5 is a high polymorphic genetic marker, which could be an alternative marker for further population genetic investigations of these carcinogenic liver flukes and other related species from a wide geographical distribution and variety of animal hosts.

Variants in the mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) infected with Oryctes rhinoceros nudivirus in oil palm and coconut plantations

The CRB (coconut rhinoceros beetle) haplotype was classified into CRB-S and CRB-G, based on the presence of single nucleotide polymorphisms (SNPs) in the mitochondrial cox1 gene. Mitochondrial genomes (mitogenomes) are the most widely used genetic resources for molecular evolution, phylogenetics, and population genetics in relation to insects. This study presents the mitogenome CRB-G and CRB-S which were collected in Johor, Malaysia. The mitogenome of CRB-G collected from oil palm plantations in 2020 and 2021, and wild coconut palms in 2021 was 15,315 bp, 15,475 bp, and 17,275 bp, respectively. The CRB-S was discovered in coconut and oil palms in 2021, and its mitogenome was 15,484 bp and 17,142 bp, respectively. All the mitogenomes have 37 genes with more than 99% nucleotide sequence homology, except the CRB-G haplotype collected from oil palm in 2021 with 89.24% nucleotide sequence homology. The mitogenome of Johor CRBs was variable in the natural population due to its elevated mutation rate. Substitutions and indels in cox1, cox2, nad2 and atp6 genes were able to distinguish the Johor CRBs into two haplotypes. The mitogenome data generated in the present study may provide baseline information to study the infection and relationship between the two haplotypes of Johor CRB and OrNV in the field. This study is the first report on the mitogenomes of mixed haplotypes of CRB in the field.

A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping.

The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.

Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden.

Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (-ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT-PCR-RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins.

Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana.

Nicotiana L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the Nicotiana phylogenetic relationship and hybridization, evidence from whole genome data is still lacking. In this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 Nicotiana species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species. The incongruence among gene trees showed that the formation of N. sylvestris involved incomplete lineage sorting. The nuclear-plastid discordance and nuclear introgression absence indicated that organelle capture from section Trigonophyllae was involved in forming section Petunioides. Furthermore, we analyzed the evolutionary origin of polyploid species and dated the time of hybridization events based on the analysis of PhyloNet, sequence similarity search, and phylogeny of subgenome approaches. Our results highly evidenced the hybrid origins of five polyploid sections, including sections Nicotiana, Repandae, Rusticae, Polydicliae, and Suaveolentes. Notably, we provide novel insights into the hybridization event of section Polydicliae and Suaveolentes. The section Polydicliae formed from a single hybridization event between maternal progenitor N. attenuata and paternal progenitor N. undulata; the N. sylvestris (paternal progenitor) and the N. glauca (maternal progenitor) were involved in the formation of section Suaveolentes. This study represents the first exploration of Nicotiana polyploidization events and phylogenetic relationships using the high-throughput RNA-seq approach. It will provide guidance for further studies in molecular systematics, population genetics, and ecological adaption studies in Nicotiana and other related species.

Signatures of kin selection in a natural population of the bacteria Bacillus subtilis.

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.

Introducing the New Editorial Team

Forensic GenomicsVol. 3, No. 2 EditorialFree AccessIntroducing the New Editorial TeamNicole M.M. NovroskiNicole M.M. Novroski*Address correspondence to: Nicole M.M. Novroski, PhD, Forensic Science Program, Department of Anthropology, University of Toronto, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada. E-mail Address: nicole.novroski@utoronto.ca Thank you for reading,, Nicole M.M. Novroski, PhD, Editor-in-Chief, Forensic Genomics https://orcid.org/0000-0001-9071-9278Forensic Science Program, Department of Anthropology, University of Toronto, Mississauga, Canada.Search for more papers by this authorPublished Online:12 Jun 2023https://doi.org/10.1089/forensic.2023.0008.editorialAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail It has been an exciting year as the new Editor-in-Chief at Forensic Genomics, the official journal of the International Symposium on Human Identification (ISHI). I am delighted to take this opportunity to introduce the new outstanding editorial team, share our team's current priorities, and the initiatives we are taking that will help propel Forensic Genomics forward.Forensic Genomics is a quarterly published journal in its third year. Started in 2021 by founding Editor David Mittleman, PhD (who is the chief executive officer at Othram, Inc.), the journal addresses how advances in genetic testing and genomic analysis can enable investigators to break through previously impenetrable forensic DNA barriers. The core focus of the journal is the use of DNA testing technologies, algorithms, artificial intelligence, and genealogical research methods to support human identification using inference tools and inductive reasoning.The journal provides a high-profile international forum for ground-breaking original research articles, review articles, captivating front matter, industry profiles, and commentary, and at its core is an academic publication. Our editorial team comprises leading experts who span the diversity of disciplines within the field of forensic genetics.Associate EditorsOur new associate editors are fully committed to the success of our outstanding journal.Robert A. Bever, PhD (inaugural associate editor), is a senior scientist at Bode Technology. Dr. Bever brings over 27 years of research and operational experience, has served as laboratory director for three DNA typing laboratories, has technically reviewed over 40,000 cases, and testified in over 150 cases. In addition, Dr. Bever has over 20 years experience in analyzing kinship casework to establish parentage, sib-ship, and avuncular relationships. Dr. Bever's research in forensic genetics has focused on developing methods to obtain DNA profiles from highly degraded samples, to collect and extract DNA from touched objects, mixture deconvolution using next-generation sequencing, and indentification of geographical origin of material through DNA.Claus Børsting, MSc, PhD, is a senior researcher in the Section of Forensic Genetics, Department of Forensic Medicine at the University of Copenhagen in Copenhagen, Denmark. Dr. Børsting brings over 20 years of research experience and is an active contributor to forensic literature, being first author or coauthor of 79 peer-reviewed articles, 12 book chapters, 40 peer-reviewed conference proceedings, and 52 other conference contributions. His primary fields of research include human identification using biallelic markers, human pigmentation, epigenetic studies, and the use of next-generation sequencing in forensic genetics. His current research interests center around human pigmentation and human identity using single nucleotide polymorphisms.Bruce Budowle, PhD (inaugural associate editor), is currently an adjunct faculty member with the Radford University Forensic Science Institute and maintains a visiting professor status with the Department of Forensic Medicine, University of Helsinki, Helsinki, Finland. He is an internationally recognized and acclaimed expert in forensic genomics, microbial forensics, human trafficking, bioterrorism, and counter terrorism. Dr. Budowle recently retired (2022) as the director of the Center for Human Identification in Fort Worth, Texas, where, among other things, he directed the processing of DNA cases for the US National DNA database system CODIS (which he was one of the original architects of).With over 40 years of experience, Dr. Budowle has carried out research, development, and validation of methods for forensic biological analyses. He has published more than 700 peer-reviewed articles, made more than 800 presentations, and testified in well over 300 criminal cases in the areas of molecular biology, population genetics, statistics, quality assurance, and forensic biology. He has been a chair and member of the Scientific Working Group on DNA Methods, chair of the DNA Commission of the International Society for Forensic Genetics (ISFG), a member of the DNA Advisory Board, and a commissioner on the Texas Forensic Science Commission.Claire L. Glynn, PhD, is an associate professor and founding director of the coveted online graduate certificate in Forensic Genetic Genealogy Program at the University of New Haven in New Haven, Connecticut. Dr. Glynn previously worked as a forensic scientist at Eurofins Forensic Services (formerly named LGC Forensics) in Oxfordshire, England, before pursuing a doctoral degree and joining the University of New Haven in 2014. Dr. Glynn was awarded the University of New Haven's Faculty Excellence in Research and Creative Activity in 2017. She also was designated a University Research Scholar for 2017–2020.Lastly, Dr. Glynn was named one of Connecticut's “40 under 40” for the class of 2022 by Connecticut Magazine. Dr. Glynn is prominently featured in the media discussing her opinions and expertise in forensic investigative genetic genealogy (FIGG) and served as an inaugural advisory board member for ISHI.Denise Syndercombe Court, PhD (inaugural associate editor), is a professor of forensic genetics at King's College London in London, United Kingdom. Dr. Syndercombe Court is a scientist, geneticist, statistician, academic, editor, and published author of over 93 peer-reviewed scientific publications, including serving as both editor and author of the award-winning textbook “Medical Science.”Dr. Syndercombe Court is a chartered scientist and a chartered biologist, and is a member or fellow of a number of professional bodies including the Academy of Forensic Medical Sciences, Biochemical Society, British Academy of Forensic Sciences, Chartered Society of Forensic Sciences, Institute of Biological and Medical Sciences, ISFG, International Society of Blood Pattern Analysts, Royal College of Pathologists Faculty of Forensic and Legal Medicine, Royal Society of Biology, and the Royal Statistical Society.With more than 30 years of experience in scientific research, forensic evidence examination, and DNA interpretation with a sound knowledge of the civil and criminal justice process, Dr. Syndercombe Court manages an ISO17025 accredited laboratory specializing in complex kinship and specialist DNA analysis for police forces, is the UK representative on the European DNA Profiling Group and the International Society of Forensic Genetics representative on the Forensic Regulator's DNA Working Group. Her research interests are in the use of DNA in complex and limited matrices, both human and nonhuman, for intelligence purposes.We have expanded our editorial board to expedite the reviewing process and prioritize publishing high-quality articles. We are most pleased to introduce our expanded editorial board, comprising a blend of inaugural board members and new members, representing the vast disciplines of forensic genetics.Rebekah Canada, BS (inaugural board member), is consultant in product marketing, development, technical writing, and genealogy research, with a home base of Houston, Texas. She is a strong media and communication professional, who is skilled in management, technical writing, and a variety of computer-based programs. To learn more about Rebekah and her areas of expertise, please visit (Haplogroup.org) or (https://rebekahcanada.com/).Jennifer Churchill Cihlar, PhD, is an assistant professor in the Center for Human Identification and Microbiology, Immunology and Genetics Department of the School of Biomedical Sciences at the University of North Texas Health Science Center in Fort Worth, Texas. With over 30 publications and dozens of conference contributions, her efforts focus on improving the forensic community's ability to identity humans associated with crime, missing persons, and human and wildlife trafficking victims through forensic genomic research.Dr. Cihlar's current research efforts are focused on rapid DNA technologies, bioinformatic assessment of the performance, and noise in mitochondrial genome analyses to guide thresholding strategies for forensic laboratories, and a heavy focus on novel markers as well as the use of portable genetic technologies to aid law enforcement efforts in curtailing wildlife trafficking.Maria Corazon A. De Ungria, PhD, is a National Sciences Research Institute DNA Analysis Laboratory Director in the Philippine Genome Center at the University of the Philippines (UP) in Quezon City, Philippines. With a PhD in microbiology from The University of New South Wales, Dr. De Ungria returned to the Philippines, where she was immediately appointed as head of the DNA Analysis Laboratory of the UP Natural Sciences Research Institute. Since then, she has actively focused on two major areas of study: the validation of molecular procedures for forensic applications and the expansion of Philippine population databases to better understand the genetic diversity of different Philippine groups.For her efforts, Dr. De Ungria has been awarded many prestigious scientific awards such as the outstanding young scientist awarded by the National Academy of Science and Technology, and the outstanding women in the nation service (TOWNS). In 2009, Dr. De Ungria won the outstanding woman researcher in the life sciences award, organized by the Third World Organization of Women Scientists and Elsevier in Kuala Lumpur, Malaysia. In 2016, UP promoted Dr. De Ungria to the rank of university researcher V, the highest research position available, once again recognizing her academic achievements as well as her efforts in putting science at the service of society.Christopher E. Mason, PhD (inaugural board member), is a professor of physiology and biophysics at Weill Cornell Medicine in New York, New York. The Mason laboratory is working on a 10-phase 500-year plan for the survival of the human species on Earth, in space, and on other planets, where Dr. Mason is the author of over 50 peer-reviewed articles and the newly released “The Next 500 Years, Engineering Life to Reach New Worlds.” Dr. Mason's team develops and deploys new biochemical and computational methods in functional genomics to elucidate the genetic basis of human disease and human physiology.Dr. Mason focuses on novel techniques using massively parallel sequencing and the development of algorithms for tumor evolution, genome evolution, DNA and RNA modifications, and genome/epigenome engineering. Dr. Mason actively collaborates with NIST and the FDA to build international standards to ensure clinical-quality genome measurements and editing.Irene Newsham, PhD (inaugural board member), joined the department of chemistry and biochemistry at Norwich University in Northfield, Vermont, in 2022, in the role of faculty lecturer in chemistry. Before her move to Vermont, Dr. Newsham was associate professor and associate program director for the Molecular Genetic Technology program in the School of Health Professions at UT MD Anderson Cancer Center. Dr. Newsham has authored over 55 peer-reviewed publications and recently earned her certificate in genealogy research from Boston University's Center for Professional Education.Fabio Oldoni, PhD, is an assistant professor and director of the Master's in Forensic Science Program at Arcadia University in Glenside, Pennsylvania. Dr. Oldoni has developed national and international research collaborations, which allow for his current research team to be exposed to state-of-the-art research in the field of forensic molecular biology and genetics. Dr. Oldoni has peer-reviewed several forensic science journal articles since 2018 and serves as a member of the International Society of Forensic Genetics (ISFG), American Academy of Forensic Sciences (AAFS), and Council of Forensic Science Educators.Dr. Oldoni also serves as the contact person for International Scientific Relations of the Italian-speaking working group from ISFG. Dr. Oldoni's research interests include the development, validation, and optimization of biomarker assays, massively parallel sequencing, CE fragment analysis, DNA mixture deconvolution, ancestry prediction, kinship analysis, touch DNA, and probabilistic genotyping.Nathan E. Scudder, LLM LP, PhD (inaugural board member), is an adjunct associate professor at the University of Technology Sydney in Canberra, Australia, researching the policy and legal implications of new DNA technologies, including national security policy, law enforcement, forensic science, and genomic privacy. With over 17 publications and 24 years experience working for the Australian Government, Dr. Scudder has managed forensic operations teams, worked as a lawyer, positioned the agency to leverage policy opportunities, and helped shape and guide government legislation. Dr. Scudder is an inaugural member of the Forensic Genomics journal and the International Society of Forensic Genetics (ISFG) Forensics Database Advisory Board.Jodie M. Ward, PhD (inaugural board member), is the director of the Australian Facility for Taphonomic Experimental Research (AFTER) and an associate professor in the School of Mathematical and Physical Sciences at University of Technology Sydney in Sydney, Australia. In addition, she is the program lead of the National DNA Program for Unidentified and Missing Persons at the Australian Federal Police. This unique joint appointment facilitates her valuable contribution to the research, development, and application of forensic human identification techniques for missing persons investigations in Australia.Dr. Ward is an internationally recognized forensic expert who passionately uses interdisciplinary forensic approaches to identify unidentified human remains, link them to known missing persons, and provide answers to their families. Previously, she held operational forensic roles with the NSW Forensic and Analytical Science Service and NSW Police Force, and academic forensic roles with the Canberra Institute of Technology and University of Canberra.For her efforts, Dr. Ward has been awarded the Churchill Fellowship to investigate world-leading DNA identification techniques for missing persons and disaster victims, was invited to the International Commission on Missing Persons Expert Panel of Scientific Advisors, Missing Persons Advocacy Network Board and Forensic Genomics Editorial Board, and was recognized as one of the 2017 Superstars of STEM (Science & Technology Australia), 2018 100 Women of Influence (Australian Financial Review), 2021 Emerging Leaders in the Public and University Sector (Women's Agenda), and 2023 NSW Woman of Excellence (NSW Government).Frank Wendt, PhD, is an assistant professor in the Forensic Science Program, Department of Anthropology and Division of Biostatistics, Dalla Lana School of Public Health at the University of Toronto in Toronto, Ontario, Canada. He is the principal investigator of the Forensic and Complex Trait Genetics Laboratory at UTM and specializes in the development and application of statistical genetics methods for understanding the cause and consequence of pleiotropy across the human phenome.Dr. Wendt serves as a mentor, CANSSI Ontario STAGE (Strategic Training for Advanced Genetic Epidemiology), which is a formal and comprehensive training program in genetic epidemiology and statistical genetics, the first of its kind in Canada and one of few in the world. With over 74 peer-reviewed articles and dozens of contributions to conferences, Dr. Wendt has a diversity of research interests including genetic epidemiology, biological psychiatry, forensic genomics, psychiatry, ancestry diversity, genome-wide association studies, polygenicity, and pleiotropy.Our goal at Forensic Genomics is to maintain a diverse team of editorial members that provide expertise in a diversity of forensic genetics research areas and geographical regions. Understanding the importance of the article review process, we thank those individuals in our community who have served on the editorial board as well as our ad-hoc reviewers for providing timely and constructive comments. Since joining Forensic Genomics in 2022, I have appointed new editorial board members, and will continue looking for qualified editorial board members to expand upon our growing network of experts.I firmly believe that a strong editorial board will help propel the journal forward in a new direction. And, as our submission numbers continue to increase, we will also recruit new reviewers. Furthermore, we are exploring options to expand our marketing to reach new laboratories and research groups as well as to recruit new authors and reviewers.In closing, I am thrilled to have such a privileged opportunity to work with excellent emerging and leading scholars from the global forensic genetics' community. I thank Sheryl Nale, Sophie Reisz, and the team at Mary Ann Liebert, Inc., publishers, for their generous and timely support during the transition period. I also express my gratitude to Ms. Runa Daniel, who has been a vital contributor to the success of Forensic Genomics through her friendship and collegiality. I understand that the role of editor-in-chief is a significant responsibility. Beyond making the editorial decision, I will strive to approach my work as a facilitator, and I welcome each one of your contributions! I look forward to working closely with our editorial team, reviewers, authors, and the Mary Ann Liebert, Inc., publishers, team!FiguresReferencesRelatedDetails Volume 3Issue 2Jun 2023 InformationCopyright 2023, Mary Ann Liebert, Inc., publishersTo cite this article:Nicole M.M. Novroski.Introducing the New Editorial Team.Forensic Genomics.Jun 2023.31-34.http://doi.org/10.1089/forensic.2023.0008.editorialPublished in Volume: 3 Issue 2: June 12, 2023Online Ahead of Print:June 2, 2023PDF download

Characterization of the complete mitochondrial genome of Culex vishnui (Diptera: Culicidae), one of the major vectors of Japanese encephalitis virus.

Culex mosquitoes (Diptera: Culicidae) can transmit a variety of arthropod-borne viruses (arboviruses), causing human and animal diseases. Cx. vishnui, Cx. pseudovishnui, and Cx. tritaeniorhynchus are three representative species in Culex vishnui subgroup, which are widely distributed in southeast Asia, and they have been proved as the main vectors transmitting Japanese encephalitis virus (JEV) that could cause human infectious mosquito-borne disease across Asia. However, the epidemiology, biology, and even molecular information of those mosquitos remain poorly understood, and only the mitochondrial genome (mitogenome) of Cx. tritaeniorhynchus has been reported in these species. In the present study, we sequenced and annotated the complete mitogenome sequence of Cx. vishnui which was 15,587bp in length, comprising 37 genes. Comparisons of nucleotide and amino acid sequences between Cx. vishnui and Cx. tritaeniorhynchus revealed that most genes within Culex vishnui subgroup were conserved, except atp8, nad1, atp6, and nad6, with differences of 0.4 (rrnS) - 15.1% (tRNAs) and 0 (nad4L) - 9.4% (atp8), respectively, interestingly suggesting the genes nad4L and rrnS were the most conserved but atp8 gene was the least. The results based on nucleotide diversity also supported a relatively uniform distribution of the intraspecific differences in Cx. vishnui and Cx. tritaeniorhynchus with only one highly pronounced peak of divergence centered at the control region. Phylogenetic analyses using concatenated amino acid sequences of 13 protein-coding genes supported the previous taxonomic classification of the family Culicidae and the monophyly of tribes Aedini, Culicini, Mansoniini, and Sabethini. The present study revealed detailed information on the subgroup Culex vishnui, reanalyzed the relationships within the family Culicidae, provided better markers to identify and distinguish Culex species, and offered more markers for studying the molecular epidemiology, population genetics, and molecular phylogenetics of Cx. vishnui.

India-EMBO Lecture Course: understanding malaria from molecular epidemiology, population genetics, and evolutionary perspectives

India-EMBO Lecture Course: understanding malaria from molecular epidemiology, population genetics, and evolutionary perspectives

Population genetics and phylogeography of alfalfa mosaic virus in China and a comparison with other regional epidemics based on the cp gene.

Alfalfa mosaic virus (AMV) is the most pervasive epidemic virus affecting alfalfa production. However, detailed investigations on the molecular population genetics and evolutionary dynamics of AMV are scarce. This study aimed to report on a large-scale long-term survey of genetic variability in AMV populations from China and perform a comparative analysis of AMV population genetics in the three most thoroughly studied countries to date: China, Iran, and Spain. The study was based on the analysis of the coat protein gene (cp) using two analytical approaches: an analysis of molecular variance (AMOVA) and a Bayesian Markov Chain Monte Carlo approach that investigates the association between geographical origin and phylogeny. Both analytical approaches found significant genetic differentiation within localities, but not among localities nor among provinces. This observation might result from inappropriate agronomical practices involving extensive exchange of plant materials followed by rapid viral diversification within localities. In the Chinese population, both methods found that genetic diversification in AMV was strongly associated with different bioclimatic zones. Rates of molecular evolution were similar in the three countries. The estimated epidemic exponential population size and growth rate suggest that the epidemics grew faster and with higher incidence in Iran, followed by Spain and China. Estimates of the time to the most recent common ancestors suggest that AMV was first seen in Spain by the beginning of the twentieth century and later on in eastern and central Eurasia. After ruling out the existence of recombination breakpoints within the cp gene, a codon-based selection analysis per population was performed and identified many codons under significant negative selection and a few under significant positive selection; the latter varied among countries, suggesting regional differences in selective pressures.

Characterization and phylogenetic implication of complete mitochondrial genome of the Cataglyphis aenescens (Hymenoptera: Formicidae): Genomic comparisons in Formicinae

AbstractAnts are the most widely distributed social insects in terrestrial ecosystems with the largest number of species and quantities; their ecological function is very significant and they have certain medicinal value. Because mitochondria have their own DNA (mtDNA) and genetic system, so the complete mitochondrial genome has been used more and more in molecular phylogeny, population genetics, molecular diagnosis, and evolution of insects. In this study, the mitochondrial genome of Cataglyphis aenescens (Nylander, 1849) (Hymenoptera: Formicidae) was sequenced and annotated. The results showed that the total length of the mitochondrial genome of C. aenescens (Nylander, 1849) was 17,197 bp; it contained 37 genes, including 13 protein coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs) and a non‐coding region. All PCGs of C. aenescens were initiated with ATN codons and terminated with the TAA codon. The overall nucleotide composition of C. aenescens was AT‐biased (81.74%). Cataglyphis and Formica clustered together. C. aenescens is closely related to Formica sinae, Formica. fusca and Formica selysi. This work enhances the genetic data of Formicidae and contributes to our understanding of their phylogenic relationship, evolution, and utilization.

Molecular evolution and population genetics of glutamate decarboxylase acid resistance pathway in lactic acid bacteria.

Glutamate decarboxylase (GAD) pathway (GDP) is a major acid resistance mechanism enabling microorganisms' survival in low pH environments. We aimed to study the molecular evolution and population genetics of GDP in Lactic Acid Bacteria (LAB) to understand evolutionary processes shaping adaptation to acidic environments comparing species where the GDP genes are organized in an operon structure (Levilactobacillus brevis) versus lack of an operon structure (Lactiplantibacillus plantarum). Within species molecular population genetic analyses of GDP genes in L. brevis and L. plantarum sampled from diverse fermented food and other environments showed abundant synonymous and non-synonymous nucleotide diversity, mostly driven by low frequency changes, distributed throughout the coding regions for all genes in both species. GAD genes showed higher level of replacement polymorphism compared to transporter genes (gadC and YjeM) for both species, and GAD genes that are outside of an operon structure showed even higher level of replacement polymorphism. Population genetic tests suggest negative selection against replacement changes in all genes. Molecular structure and amino acid characteristics analyses showed that in none of the GDP genes replacement changes alter 3D structure or charge distribution supporting negative selection against non-conservative amino acid changes. Phylogenetic and between species divergence analyses suggested adaptive protein evolution on GDP genes comparing phylogenetically distant species, but conservative evolution comparing closely related species. GDP genes within an operon structure showed slower molecular evolution and higher conservation. All GAD and transporter genes showed high codon usage bias in examined LAB species suggesting high expression and utilization of acid resistance genes. Substantial discordances between species, GAD, and transporter gene tree topologies were observed suggesting molecular evolution of GDP genes do not follow speciation events. Distribution of operon structure on the species tree suggested multiple independent gain or loss of operon structure in LABs. In conclusion, GDP genes in LABs exhibit a dynamic molecular evolutionary history shaped by gene loss, gene transfer, negative and positive selection to maintain its active role in acid resistance mechanism, and enable organisms to thrive in acidic environments.

New distribution record and DNA barcoding of Sapria himalayana Griff. (Rafflesiaceae), a rare and endangered holoparasitic plant from Mizoram, India

Sapria himalayana Griff. is a rare and endangered holoparasitic plant that prefers a specific host (Tetrastigma sp.). It is one of the lesser-known and poorly understood plants facing threats of extinction owing to human interference in the evergreen forests of Mizoram. The flower is the only visible part of this endophyte and blooms from November to December. The plant was encountered for the first time in the evergreen forest near Rullam village in the Serchhip District of Mizoram, India. In the present study, DNA barcoding was used to identify the plants, and the internal transcribed spacer 2 (ITS2) region of S. himalayana was amplified and sequenced. The ITS2 sequence could accurately identify up to the species level for this endangered species. The absence of the ribulose-biphosphate carboxylase gene (rbcL) region in the genome supports its holoparasitic nature. Hence, DNA barcoding can help in taxonomic and biodiversity research and aid in selecting taxa for various molecular ecology and population genetics studies. The phylogenetic tree was analyzed using the maximum-likelihood method, and our findings showed that species from different families were clearly discriminated in a phylogenetic tree. To the best of our knowledge, this is the first report of DNA barcoding using ITS2 region of S. himalayana from Mizoram, India.

Morphological Characteristics and Comparative Chloroplast Genome Analyses between Red and White Flower Phenotypes of Pyracantha fortuneana (Maxim.) Li (Rosaceae), with Implications for Taxonomy and Phylogeny.

Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding.

Characterization of the complete mitochondrial genome of the fluke of turdus, Plagiorchis elegans, and phylogenetic implications

Plagiorchis elegans (Trematoda: Digenea) is mainly parasitic in the intestines of vertebrate animals, including humans, causing irreversible pathological damage and herd-spherical influences. However, little information is available about its molecular epidemiology, population genetics, and phylogeny. In the present study, we sequenced, assembled, and annotated the complete mitochondrial (mt) genome of P. elegans. Combining with the available mitochondrial data of subclass Digenea, phylogenetic analysis was performed based on Bayesian inference (BI). These results showed that the complete length of P. elegans is 13,862 bp, including 12 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding region (NCR). There was an obvious A + T content from 61.0% to 71.3% and the values of the Ka/Ks ratio ranged from 0.119 (cox1) to 1.053 (nad6). In the BI analysis, different from previous studies, phylogenetic analysis showed genus Glypthelmins was paraphyletic rather than monophyletic and had a closer relationship with Plagiorchis and Orientocreadium. Additionally, the BI tree also presented that the genus Echinostoma was monophyletic. Our results provided molecular data in the family Plagiorchiidae proposing new insight within Xiphidiata and Echinostomata.

Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus.

The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89–104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.

Analysis of complete mitochondrial genome sequence of Pontania dolichura (Hymenoptera: Tenthredinidae) (Thomson, 1871)

Pontania dolichura is a leaf-eating pest that mainly damages willow trees and is widely distributed in northern regions. In this study, we sequenced the entire mitochondrial genome of P. dolichura (GenBank accession number: MZ726800). The circular gene was 16,104 bp in length and comprised 38 column elements, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region. Most of the PCGs of P. dolichura have typical ATN (Met) start codons and typical TAN stop codons. The A + T contents of the genome, PCGs, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) were 80.32%, 78.66%, 81.94%, and 82.59%, respectively. Phylogenetic analysis supported the close genetic relationship between P. dolichura and Mesoneura rufonota indicating that the two species share more recent common ancestor gene. These data will be useful for further molecular identification and population genetics studies.

Identification of new polymorphic positions in rDNA sequences of the "intermediate" Fasciola forms.

Fascioliasis is a foodborne zoonotic disease generally caused by the parasitic flukes Fasciola gigantica and Fasciola hepatica in class Trematoda. An "intermediate" Fasciola forms between F. gigantica and F. hepatica has been shown to exist. However, the relationships among F. gigantica, F. hepatica, and "intermediate" Fasciola forms remain unclear. In this study, we found five new polymorphic positions in 18S and 28S rDNAs sequences of "intermediate" Fasciola forms. According to the high-throughput sequencing results, all known 16 polymorphic positions of "intermediate" Fasciola forms show a clear and consistent tendency for F. gigantica or F. hepatica, and the percentages of the most frequently occurring bases were different in specimens. In the three ITS sequence fragments, hybrid-type base combinations of the polymorphic positions were detected, and the percentages of the most frequent base combinations were different in specimens too. In addition, interestingly, the newly detected ITS-802 position was not a traditional polymorphic position in "intermediate" Fasciola forms, and the bases in ITS-802 position are not same as the allele bases of F. gigantica or F. hepatica. Our results will be helpful to investigations into the molecular taxonomy, population genetics, and ecology of F. gigantica, F. hepatica, and "intermediate" Fasciola forms.