Evolutionary Genetic Research Research Articles

Dobzhansky and the Brazilians from his letters and reminiscences

Theodosius Dobzhansky (1900-1975) had an important role in the origin and development of evolutionary genetics in Brazil. Not only in 1943, when he had been here for the first time, about six months, but also in other moments, for more extended periods, he was responsible for the formation of the first generation of Drosophila geneticists with an emphasis on evolution, who later originated groups of research in evolutionary genetics in their respective states/countries. His relationship with three members of the 1943 group deserves special attention. Dobzhansky's relationship with André Dreyfus (1897-1952), at the time the head of the Department of General Biology at the University of São Paulo, was always respectful and friendly; with Crodowaldo Pavan (1919-2009), Dobzhansky was highly affectionate, although he was worried about the future of his most beloved disciple; Dobzhansky's relationship with Antonio Brito da Cunha (1925-2019) was one of admiration for his general culture and sophistication, however, it was less intense than with Pavan. Moreover, several members of his research team, from 1943 to 1956 deserved comments in his reminiscences (not always positive) for the Oral History of Columbia University, for more than 40 pages.

Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.

Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.

Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies

AbstractThe application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.

Paracelsus’ 16 th Century Philosophy Applied to Current Evolutionary Genetics

Paracelsus contributed greatly to medical philosophy in the early sixteenth century, yet his reputation was so tainted by his hypocrisy that he left few followers and is often forgotten. Many aspects of his teachings, however, can be applied to current theories governing evolutionary genetic research. His claim, “Where diseases arise, one can also find the roots of health” hints at the intimate relationships between health and  disease that are the foundations of fascinating research. In many devastating medical cases, it has been  found that expression of one genetic disease can confer resistance for another. Sickle­cell anemia sufferers have an increased resistance to malaria, cystic fibrosis is associated with decreased susceptibility to  influenza, tuberculosis and cholera, and even the human immunodeficiency virus (HIV­1) is theorized to  have stemmed from a selection for resistance to the Bubonic Plague. These examples demonstrate the ambiguities in distinguishing between health and disease. While scientists today would likely scoff at Paracelsus’ dated medical rants, when they discover a disease favoured by natural selection, one of the first questions is how it could have conferred a benefit ancestrally. Applying Paracelsus’ theories to a discipline as contrary to evolutionary genetics demonstrates both the robustness of his claims, and the potential impact philosophy can have on medical, scientific and sociological questions surrounding challenging  epidemics

Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates

Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii–Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.

Group membership, geography and shared ancestry: Genetic variation in the Basotho of Lesotho.

The investigation of the evolution of cultural and genetic traits and how they interact represents a vibrant area of research in evolutionary genetics, whose dynamics are particularly relevant for our species. One of the key assumptions of the "gene-culture coevolution" framework is the coinheritance of cultural and genetic traits. A corollary of the model is that culturally defined groups with a unique (or a limited number of) common origin(s) whose membership is inherited only through the male or female line are expected to show a relatively low intragroup variation for genetic markers similarly transmitted. Across human societies this is expected to be the case for cultural toponymies and family names within patrilineal and matrilineal groups considered in association with the nonrecombining region of the Y chromosome (NRY) and the mitochondrial DNA (mtDNA) portion of the genome, respectively. This study aims at exploring the degree of correlation between culture and genetics by investigating the genetic variation of culturally and geographically defined groups. We analyzed the genetic variation at NRY and mtDNA in 181 individuals from the Basotho, a Southern African patrilineal population from Lesotho, in combination with information about group membership and geographic origin. Our results show that (a) the genetic distance between individuals belonging to the same culturally defined group is lower than the population as a whole when NRY markers are considered; (b) cultural traits have a bigger impact than geography for the within-group variation of Y chromosome, but not mtDNA; and (c) within-group genetic variation is compatible with a more homogeneous origin for less common groups. Our results provided additional evidence for the relevance of the dual inheritance model (culture and genetics) in understanding the patterns of human genetic variation, as implied by gene-culture coevolution theory.

Toward conservation of genetic and phenotypic diversity in Japanese sticklebacks.

Stickleback fishes have been established as a leading model system for studying the genetic mechanisms that underlie naturally occurring phenotypic diversification. Because of the tremendous diversification achieved by stickleback species in various environments, different geographical populations have unique phenotypes and genotypes, which provide us with unique opportunities for evolutionary genetic research. Among sticklebacks, Japanese species have several unique characteristics that have not been found in other populations. The sympatric marine threespine stickleback species Gasterosteus aculeatus and G. nipponicus (Japan Sea stickleback) are a good system for speciation research. Gasterosteus nipponicus also has several unique characteristics, such as neo-sex chromosomes and courtship behaviors, that differ from those of G. aculeatus. Several freshwater populations derived from G. aculeatus (Hariyo threespine stickleback) inhabit spring-fed ponds and streams in central Honshu and exhibit year-round reproduction, which has never been observed in other stickleback populations. Four species of ninespine stickleback, including Pungitius tymensis and the freshwater, brackish water and Omono types of the P. pungitius-P. sinensis complex, are also excellent model systems for speciation research. Anthropogenic alteration of environments, however, has exposed several Japanese stickleback populations to the risk of extinction and has actually led to extinction of several populations and species. Pungitius kaibarae, which is endemic to East Asia, used to inhabit Kyoto and Hyogo prefectures, but is now extinct. Causes of extinction include depletion of spring water, landfill of habitats, and construction of river-mouth weirs. Here, we review the importance of Japanese sticklebacks as genetic resources, the status of several endangered stickleback populations and species, and the factors putting these populations at risk.

Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces

Saccharomyces interspecies hybrids are critical biocatalysts in the fermented beverage industry, including in the production of lager beers, Belgian ales, ciders, and cold-fermented wines. Current methods for making synthetic interspecies hybrids are cumbersome and/or require genome modifications. We have developed a simple, robust, and efficient method for generating allotetraploid strains of prototrophic Saccharomyces without sporulation or nuclear genome manipulation. S. cerevisiae×S. eubayanus, S. cerevisiae×S. kudriavzevii, and S. cerevisiae×S. uvarum designer hybrid strains were created as synthetic lager, Belgian, and cider strains, respectively. The ploidy and hybrid nature of the strains were confirmed using flow cytometry and PCR-RFLP analysis, respectively. This method provides an efficient means for producing novel synthetic hybrids for beverage and biofuel production, as well as for constructing tetraploids to be used for basic research in evolutionary genetics and genome stability.

Profile of Brian Charlesworth

National Academy of Sciences foreign associate Brian Charlesworth has been at the forefront of evolutionary genetics research for the last four decades. Using theoretical ideas to design experiments and experimental data as a stimulant for the development of theory, Charlesworth investigates fundamental life processes. His work has contributed to improved understanding of molecular evolution and variation, the evolution of genetic and sexual systems, and the evolutionary genetics of life history traits. In 2010, Charlesworth retired from his faculty position as professor at the University of Edinburgh’s Institute of Evolutionary Biology but actively continues to inspire students and conduct research. Profile photograph of Brian Charlesworth. Image courtesy of Xulio Maside. Until age 8, Charlesworth lived near the English seaside in Hove, East Sussex. There, he explored marine life in rockpools, studied snails collected from a bombsite, admired a giant tortoise that lived in a garden behind his apartment, and went on walks with his parents in the Sussex countryside. His family later moved to London, but Charlesworth’s interest in nature remained. At age 11, he entered the private Haberdashers’ Aske’s Boys’ School, which he attended on a local government scholarship. “It had well-equipped labs and some very good teachers,” Charlesworth says. He read extensively, visited London museums, and attended public lectures at University College London. His early role models were physics and biology teacher Theodore Savory and biology teacher Barry Goater. He says, “The notion of discovering how the natural world works, purely from observation and reasoning, thrilled me from an early age and continues to do so.” In 1966, Charlesworth earned a BA in natural sciences with honors at the University of Cambridge. During his final year at the university, he studied genetics and soon became interested in evolution and the application of mathematics to evolutionary genetics. “I met …

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing.

Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.

The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus.

How organisms adapt to the range of environments they encounter is a fundamental question in biology. Elucidating the genetic basis of adaptation is a difficult task, especially when the targets of selection are not known. Emerging sequencing technologies and assembly algorithms facilitate the genomic dissection of adaptation and population differentiation in a vast array of organisms. Here we describe the attributes of Kryptolebias marmoratus, one of two known self-fertilizing hermaphroditic vertebrates that make this fish an attractive genetic system and a model for understanding the genomics of adaptation. Long periods of selfing have resulted in populations composed of many distinct naturally homozygous strains with a variety of identifiable, and apparently heritable, phenotypes. There also is strong population genetic structure across a diverse range of mangrove habitats, making this a tractable system in which to study differentiation both within and among populations. The ability to rear K. marmoratus in the laboratory contributes further to its value as a model for understanding the genetic drivers for adaptation. To date, microsatellite markers distinguish wild isogenic strains but the naturally high homozygosity improves the quality of de novo assembly of the genome and facilitates the identification of genetic variants associated with phenotypes. Gene annotation can be accomplished with RNA-sequencing data in combination with de novo genome assembly. By combining genomic information with extensive laboratory-based phenotyping, it becomes possible to map genetic variants underlying differences in behavioral, life-history, and other potentially adaptive traits. Emerging genomic technologies provide the required resources for establishing K. marmoratus as a new model organism for behavioral genetics and evolutionary genetics research.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.)

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.Electronic supplementary materialThe online version of this article (doi:10.1007/s10709-011-9554-4) contains supplementary material, which is available to authorized users.

Potential constraints on evolution: sexual dimorphism and the problem of protandry in the butterfly Bicyclus anynana

The earlier mean adult emergence between males and females, protandry, has been well studied mathematically and in comparative studies. However, quantitative and evolutionary genetic research on protandry is scarce. The butterfly, Bicyclus anynana exhibits protandry and here we selected for each of the different combinations of male and female development time in this species, thus including direct selection on protandry (i.e., FAST, fast males and fast females; SLOW, slow males and slow females; FMSF, fast males and slow females; and SMFF, slow males and fast females). After eight generations of selection there was no significant response for increased or decreased protandry, whereas selection for increased or decreased development time in both sexes (FAST or SLOW) was successful. Continued selection (> 30 generations) for decreased or increased protandry showed a significant difference between the FMSFC and SMFFC lines (subscript c for continued selection), which was of the same magnitude as the nonsignificant difference observed between the FMSF and SMFF lines at generation eight. This indicated that the initial selection was successful, but that the difference between the lines did not increase with continued selection. Our results also indicate that the genetic covariance across sexes for development time is near unity. Interestingly, lines selected for decreased protandry (SMFF) had lower egg-to-adult survival, and broods from these lines had lower rates of egg hatching. This suggests that interactions with fertility might constrain certain directions of change in patterns of protandry. Moreover, selection yielded a change in the ratio of male to female development time for slow lines, suggesting that some amount of sex-specific genetic variance for development time is still present in this population. The FMSFC line showed the largest effect of selection on protandry, mainly through an effect on female developmental time. Lastly, our results show that temperature has an effect on the amount of protandry in the selected lines. These results are discussed in relation to the ecology of this species and the evolution of protandry.

Modelling epistatic effects of embryo and endosperm QTL on seed quality traits

Coordinated expression of embryo and endosperm tissues is required for proper seed development. The coordination among these two tissues is controlled by the interaction between multiple genes expressed in the embryo and endosperm genomes. In this article, we present a statistical model for testing whether quantitative trait loci (QTL) active in different genomes, diploid embryo and triploid endosperm, epistatically affect a trait expressed on the endosperm tissue. The maximum likelihood approach, implemented with the EM algorithm, was derived to provide the maximum likelihood estimates of the locations of embryo- and endosperm-specific QTL and their main effects and epistatic effects. This model was used in a real example for rice in which two QTL, one from the embryo genome and the other from the endosperm genome, exert a significant interaction effect on gel consistency on the endosperm. Our model has successfully detected Waxy, a candidate gene in the embryo genome known to regulate one of the major steps of amylose biosynthesis in the endosperm. This model will have great implications for agricultural and evolutionary genetic research.

Statistical model for characterizing epistatic control of triploid endosperm triggered by maternal and offspring QTLs

To study the effects of maternal and endosperm quantitative trait locus (QTL) interaction on endosperm development, we derive a two-stage hierarchical statistical model within the maximum-likelihood context, implemented with an expectation-maximization algorithm. A model incorporating both maternal and offspring marker information can improve the accuracy and precision of genetic mapping. Extensive simulations under different sampling strategies, heritability levels and gene action modes were performed to investigate the statistical properties of the model. The QTL location and parameters are better estimated when two QTLs are located at different intervals than when they are located at the same interval. Also, the additive effect of the offspring QTLs is better estimated than the additive effect of the maternal QTLs. The implications of our model for agricultural and evolutionary genetic research are discussed.

The Fallacy of Biological Determinism

The SciencesVolume 16, Issue 2 p. 6-10 The Fallacy of Biological Determinism R.C. Lewontin, R.C. Lewontin R. C. Lewontin, Alexander Agassiz Professor of Zoology at Harvard University, is a population geneticist engaged in both theoretical and experimental research in evolutionary genetics. In 1970, Dr. Lewontin resigned from the National Academy of Sciences in protest against its conducting classified research for military purposes. This article is based on a New York Academy of Sciences public lecture.Search for more papers by this author R.C. Lewontin, R.C. Lewontin R. C. Lewontin, Alexander Agassiz Professor of Zoology at Harvard University, is a population geneticist engaged in both theoretical and experimental research in evolutionary genetics. In 1970, Dr. Lewontin resigned from the National Academy of Sciences in protest against its conducting classified research for military purposes. This article is based on a New York Academy of Sciences public lecture.Search for more papers by this author First published: March‐April 1976 https://doi.org/10.1002/j.2326-1951.1976.tb01213.xCitations: 11 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume16, Issue2March‐April 1976Pages 6-10 RelatedInformation

Evolutionary genetics research reports—list of titles, 1973–1974

Evolutionary genetics research reports—list of titles, 1973–1974

Evolutionary genetics research reports—list of titles, 1968–1973

Evolutionary genetics research reports—list of titles, 1968–1973

Evolutionary genetics research reports

Evolutionary genetics research reports