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1
Di Pietro, Lorena, Mozhgan Boroumand, Wanda Lattanzi, Barbara Manconi, Martina Salvati, Tiziana Cabras, Alessandra Olianas, et al. "A Catalog of Coding Sequence Variations in Salivary Proteins’ Genes Occurring during Recent Human Evolution." International Journal of Molecular Sciences 24, no. 19 (October 9, 2023): 15010. http://dx.doi.org/10.3390/ijms241915010.
Анотація:
Saliva houses over 2000 proteins and peptides with poorly clarified functions, including proline-rich proteins, statherin, P-B peptides, histatins, cystatins, and amylases. Their genes are poorly conserved across related species, reflecting an evolutionary adaptation. We searched the nucleotide substitutions fixed in these salivary proteins’ gene loci in modern humans compared with ancient hominins. We mapped 3472 sequence variants/nucleotide substitutions in coding, noncoding, and 5′-3′ untranslated regions. Despite most of the detected variations being within noncoding regions, the frequency of coding variations was far higher than the general rate found throughout the genome. Among the various missense substitutions, specific substitutions detected in PRB1 and PRB2 genes were responsible for the introduction/abrogation of consensus sequences recognized by convertase enzymes that cleave the protein precursors. Overall, these changes that occurred during the recent human evolution might have generated novel functional features and/or different expression ratios among the various components of the salivary proteome. This may have influenced the homeostasis of the oral cavity environment, possibly conditioning the eating habits of modern humans. However, fixed nucleotide changes in modern humans represented only 7.3% of all the substitutions reported in this study, and no signs of evolutionary pressure or adaptative introgression from archaic hominins were found on the tested genes.
2
Mbah, David A., Chi Lawrence Tawah, and Magellan Guewo-Fokeng. "Genetic Modification of Animals: Potential benefits and concerns." Journal of the Cameroon Academy of Sciences 15, no. 3 (August 4, 2020): 163–74. http://dx.doi.org/10.4314/jcas.v15i3.2.
Анотація:
Genetic modification (GM), a process whereby gene and genotype frequencies are changed among individuals of each generation, is driven by natural and artificial forces. Natural forces include mutation, fitness and migration/introgression, while artificial forces include selection, crossbreeding and transgenesis/genetic engineering. Genetic modification, driven by natural forces, is essentially adaptive, while modification driven by artificial forces is controlled by human intervention aimed at meeting food, health and other needs. Conventional genetic modification, under sexual reproduction within species, produces both beneficial and negative effects. Modern genetic modification – interspecific exchange of genes using genetic engineering – has beneficial and negative effects as well, which are at varying degrees depending on the species involved. Control/management systems/mechanisms are developed and applied to enable societal benefits while minimizing/preventing negative effects of conventional and modern genetic modification. Targeted analysis of selected nutrients in animal products is made on a case-by-case basis to test substantial equivalence of any compositional changes resulting from genetic modification. Unique identifiers are established to track GM animals and their products in the food chain.
Modification génétique, processus par lequel les fréquences des gènes et des génotypes sont changes parmi les individus de chaque génération, est entraînée par des forces naturelles et artificielles. Les forces naturelles incluent la mutation, compétence de mère/père pour se reproduire/survivre et la migration / introgression. Les forces artificielles comprennent la sélection, le croisement et la transgénèse / génie génétique. La modification génétique entraînée par les forces naturelles est essentiellement adaptative, tandis que celle entraînée par les forces artificielles est contrôlée par une intervention humaine visant à répondre aux besoins alimentaires, sanitaires et autres. La modification génétique conventionnelle, lors de la reproduction sexuelle au sein des espèces, produit des effets à la fois bénéfiques et négatifs. Modification génétique moderne - échange interspécifique de gènes par génie génétique - a également des effets bénéfiques et négatifs mais à des degrés divers selon les espèces impliquées. Des systèmes / mécanismes de contrôle / gestion sont développés et appliqués pour permettre des avantages pour la société tout en minimisant / empêchant les effets négatifs des modifications génétiques conventionnelles et modernes. Une analyse ciblée de nutriments sélectionnés dans les produits d’origine animale est effectuée au cas par cas afin de tester l’équivalence substantielle de tout changement de composition résultant d’une modification génétique. Des identifiants uniques sont établis pour suivre les animaux GM et leurs produits dans la chaîne alimentaire.
3
Árnason, Einar, and Katrín Halldórsdóttir. "Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids." Science Advances 5, no. 3 (March 2019): eaat8788. http://dx.doi.org/10.1126/sciadv.aat8788.
Анотація:
Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.
4
Böheim, Denise, Felix Knauer, Milomir Stefanović, Richard Zink, Anna Kübber-Heiss, Annika Posautz, Christoph Beiglböck, et al. "Signals of Pig Ancestry in Wild Boar, Sus scrofa, from Eastern Austria: Current Hybridisation or Incomplete Gene Pool Differentiation and Historical Introgressions?" Diversity 15, no. 6 (June 19, 2023): 790. http://dx.doi.org/10.3390/d15060790.
Анотація:
In wild boar, Sus scrofa, from Europe, domestic pig-typical ancestry is traced at varying levels. We hypothesised wild boar with pig-typical gene pool characteristics, i.e., “introgression”, congregate more in peri-urban habitats, because of less shyness and better adaptation to anthropogenic stress. We used 16 microsatellites to study introgression levels of 375 wild boar from peri-urban Vienna, Austria, and rural regions in comparison to commercial slaughter pigs, Mangaliza, and Turopolje pigs. We also expected more introgression in locations of warmer climates and lower precipitation. Despite discrimination of wild boar and pigs with 99.73% and 97.87% probability, respectively, all wild boars exhibited pig-typical gene pool characteristics, mostly at a very low level. Recent hybridisation was suspected in only 0.53% of wild boar, corresponding to the current largely indoor pig breeding/rearing in the region, with no chance of natural gene exchange between pigs and wild boar. Rather, pig ancestry in wild boar stems from incomplete gene pool differentiation during domestication and/or historical introgressions, when free-ranging pig farming was common. Individual introgression levels were lower in wild boar from peri-urban habitats, possibly reflecting the largely historical absence of pig farms there. Moreover, a marginal precipitation effect, but no temperature effect on introgression was observed. The latter, however, needs to be explored further by a more comprehensive data set.
5
Arnold, Michael L., and Noland H. Martin. "Adaptation by introgression." Journal of Biology 8, no. 9 (2009): 82. http://dx.doi.org/10.1186/jbiol176.
6
Villanueva, Gloria, Elena Rosa-Martínez, Ahmet Şahin, Edgar García-Fortea, Mariola Plazas, Jaime Prohens, and Santiago Vilanova. "Evaluation of Advanced Backcrosses of Eggplant with Solanum elaeagnifolium Introgressions under Low N Conditions." Agronomy 11, no. 9 (September 3, 2021): 1770. http://dx.doi.org/10.3390/agronomy11091770.
Анотація:
Selection and breeding of eggplant (Solanum melongena) materials with good performance under low nitrogen (N) fertilization inputs is a major breeding objective to reduce environmental degradation, risks for human health, and production costs. Solanum elaeagnifolium, an eggplant wild relative, is a potential source of variation for introgression breeding in eggplant. We evaluated 24 plant, fruit, and composition traits in a set of genotyped advanced backcrosses (BC2 and BC3) of eggplant with S. elaeagnifolium introgressions under low N conditions. Significant differences were found between the two parents for most traits, and a wide phenotypic diversity was observed in the advanced backcrosses, with some individuals with a much higher yield, nitrogen use efficiency (NUE), and phenolics content than the S. melongena parent. In general, the lower the proportion of S. elaeagnifolium genome introgressed in the advanced backcrosses, the higher was the general phenotypic resemblance to S. melongena. Putative QTLs were detected for stem diameter (pd4), presence of prickles in stem (ps6), leaf (pl6) and fruit calyx (pc6), fruit width (fw7), chlorogenic acid content (cg5), total phenolic acid peaks area (ph6), chlorogenic acid peak area (ca1), and phenolic acids pattern (cp1). Our results reveal that introgression breeding of eggplant with S. elaeagnifolium has a great interest for eggplant breeding, particularly for adaptation to low N conditions. These materials can potentially contribute to the development of improved eggplant varieties for a more sustainable agriculture.
7
Gouy, Alexandre, and Laurent Excoffier. "Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens." Molecular Biology and Evolution 37, no. 5 (January 14, 2020): 1420–33. http://dx.doi.org/10.1093/molbev/msz306.
Анотація:
Abstract Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.
8
Calfee, Erin, Daniel Gates, Anne Lorant, M. Taylor Perkins, Graham Coop, and Jeffrey Ross-Ibarra. "Selective sorting of ancestral introgression in maize and teosinte along an elevational cline." PLOS Genetics 17, no. 10 (October 11, 2021): e1009810. http://dx.doi.org/10.1371/journal.pgen.1009810.
Анотація:
While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations.
9
Suarez-Gonzalez, Adriana, Christian Lexer, and Quentin C. B. Cronk. "Adaptive introgression: a plant perspective." Biology Letters 14, no. 3 (March 2018): 20170688. http://dx.doi.org/10.1098/rsbl.2017.0688.
Анотація:
Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.
10
Falk, Duane E. "Generating and maintaining diversity at the elite level in crop breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”." Genome 53, no. 11 (November 2010): 982–91. http://dx.doi.org/10.1139/g10-081.
Анотація:
Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may “pollute” the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.
11
Svedberg, Jesper, Vladimir Shchur, Solomon Reinman, Rasmus Nielsen, and Russell Corbett-Detig. "Inferring Adaptive Introgression Using Hidden Markov Models." Molecular Biology and Evolution 38, no. 5 (January 27, 2021): 2152–65. http://dx.doi.org/10.1093/molbev/msab014.
Анотація:
Abstract Adaptive introgression—the flow of adaptive genetic variation between species or populations—has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
12
Cheng, Hong, Zhuangbiao Zhang, Jiayue Wen, Johannes A. Lenstra, Rasmus Heller, Yudong Cai, Yingwei Guo, et al. "Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep." PLOS Genetics 19, no. 2 (February 23, 2023): e1010615. http://dx.doi.org/10.1371/journal.pgen.1010615.
Анотація:
The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.
13
Cabezas, Diego, Ivone de Bem Oliveira, Mia Acker, Paul Lyrene, and Patricio R. Munoz. "Evaluating Wild Germplasm Introgression into Autotetraploid Blueberry." Agronomy 11, no. 4 (March 24, 2021): 614. http://dx.doi.org/10.3390/agronomy11040614.
Анотація:
Wild germplasm can be classified as the raw material essential for crop improvement. Introgression of wild germplasm is normally used in breeding to increase crop quality or resilience to evolving biotic and abiotic threats. Here, we explore the potential of introgressing Vaccinium elliottii into commercial blueberry germplasm. Vaccinium elliottii is a wild diploid blueberry species endemic to the southeastern United States that possesses highly desirable and economically important traits for blueberry breeding such as: short bloom to ripe period, adaptation to upland sandy soils, disease resistance, firmness, and pleasant flavor. To examine the potential of hybridization, we evaluated populations of interspecific hybrids across multiple stages of breeding (i.e., F1, F2, and backcrosses) in two crop seasons. We used our extensive pedigree data to generate breeding values for pre-breeding blueberry hybrid populations. Hybrid performance was evaluated considering fitness (i.e., plant vigor and plant height) in addition to evaluating six fruit-quality and marketable-related traits (i.e., size, firmness, acidity, soluble solids, weight, and yield). Overall, F2 and backcrosses rapidly achieved market thresholds, presenting values not significantly different from commercial blueberry germplasm. Our results confirmed the potential of exploiting the high genetic variability contained in V. elliottii for interspecific hybridization. Additionally, we developed germplasm resources that can be further evaluated and utilized in the breeding process, advancing selections for fruit quality and environmental adaptation.
14
Gonzalez-Segovia, Eric, Sergio Pérez-Limon, G. Carolina Cíntora-Martínez, Alejandro Guerrero-Zavala, Garrett M. Janzen, Matthew B. Hufford, Jeffrey Ross-Ibarra, and Ruairidh J. H. Sawers. "Characterization of introgression from the teosinte Zea mays ssp. mexicana to Mexican highland maize." PeerJ 7 (May 3, 2019): e6815. http://dx.doi.org/10.7717/peerj.6815.
Анотація:
Background The spread of maize cultivation to the highlands of central Mexico was accompanied by substantial introgression from the endemic wild teosinte Zea mays ssp. mexicana, prompting the hypothesis that the transfer of beneficial variation facilitated local adaptation. Methods We used whole-genome sequence data to map regions of Zea mays ssp. mexicana introgression in three Mexican highland maize individuals. We generated a genetic linkage map and performed Quantitative Trait Locus mapping in an F2 population derived from a cross between lowland and highland maize individuals. Results Introgression regions ranged in size from several hundred base pairs to Megabase-scale events. Gene density within introgression regions was comparable to the genome as a whole, and over 1,000 annotated genes were located within introgression events. Quantitative Trait Locus mapping identified a small number of loci linked to traits characteristic of Mexican highland maize. Discussion Although there was no strong evidence to associate quantitative trait loci with regions of introgression, we nonetheless identified many Mexican highland alleles of introgressed origin that carry potentially functional sequence variants. The impact of introgression on stress tolerance and yield in the highland environment remains to be fully characterized.
15
Small, Scott T., Frédéric Labbé, Neil F. Lobo, Lizette L. Koekemoer, Chadwick H. Sikaala, Daniel E. Neafsey, Matthew W. Hahn, Michael C. Fontaine, and Nora J. Besansky. "Radiation with reticulation marks the origin of a major malaria vector." Proceedings of the National Academy of Sciences 117, no. 50 (December 1, 2020): 31583–90. http://dx.doi.org/10.1073/pnas.2018142117.
Анотація:
Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus, an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes.
16
Wang, Ming-Shan, Sheng Wang, Yan Li, Yadvendradev Jhala, Mukesh Thakur, Newton O. Otecko, Jing-Fang Si, et al. "Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids." Molecular Biology and Evolution 37, no. 9 (May 11, 2020): 2616–29. http://dx.doi.org/10.1093/molbev/msaa113.
Анотація:
Abstract Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.
17
Le Corre, Valérie, Mathieu Siol, Yves Vigouroux, Maud I. Tenaillon, and Christophe Délye. "Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe." Proceedings of the National Academy of Sciences 117, no. 41 (September 28, 2020): 25618–27. http://dx.doi.org/10.1073/pnas.2006633117.
Анотація:
Global trade has considerably accelerated biological invasions. The annual tropical teosintes, the closest wild relatives of maize, were recently reported as new agricultural weeds in two European countries, Spain and France. Their prompt settlement under climatic conditions differing drastically from that of their native range indicates rapid genetic evolution. We performed a phenotypic comparison of French and Mexican teosintes under European conditions and showed that only the former could complete their life cycle during maize cropping season. To test the hypothesis that crop-to-wild introgression triggered such rapid adaptation, we used single nucleotide polymorphisms to characterize patterns of genetic variation in French, Spanish, and Mexican teosintes as well as in maize germplasm. We showed that both Spanish and French teosintes originated fromZea maysssp.mexicanarace “Chalco,” a weedy teosinte from the Mexican highlands. However, introduced teosintes differed markedly from their Mexican source by elevated levels of genetic introgression from the high latitude Dent maize grown in Europe. We identified a clear signature of divergent selection in a region of chromosome 8 introgressed from maize and encompassingZCN8, a major flowering time gene associated with adaptation to high latitudes. Moreover, herbicide assays and sequencing revealed that French teosintes have acquired herbicide resistance via the introgression of a mutant herbicide-target gene (ACC1) present in herbicide-resistant maize cultivars. Altogether, our results demonstrate that adaptive crop-to-wild introgression has triggered both rapid adaptation to a new climatic niche and acquisition of herbicide resistance, thereby fostering the establishment of an emerging noxious weed.
18
Hsieh, PingHsun, Mitchell R. Vollger, Vy Dang, David Porubsky, Carl Baker, Stuart Cantsilieris, Kendra Hoekzema, et al. "Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes." Science 366, no. 6463 (October 17, 2019): eaax2083. http://dx.doi.org/10.1126/science.aax2083.
Анотація:
Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.
19
Signore, Anthony V., Ying-Zhong Yang, Quan-Yu Yang, Ga Qin, Hideaki Moriyama, Ri-Li Ge, and Jay F. Storz. "Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression." Molecular Biology and Evolution 36, no. 10 (July 30, 2019): 2227–37. http://dx.doi.org/10.1093/molbev/msz097.
Анотація:
Abstract A key question in evolutionary biology concerns the relative importance of different sources of adaptive genetic variation, such as de novo mutations, standing variation, and introgressive hybridization. A corollary question concerns how allelic variants derived from these different sources may influence the molecular basis of phenotypic adaptation. Here, we use a protein-engineering approach to examine the phenotypic effect of putatively adaptive hemoglobin (Hb) mutations in the high-altitude Tibetan wolf that were selectively introgressed into the Tibetan mastiff, a high-altitude dog breed that is renowned for its hypoxia tolerance. Experiments revealed that the introgressed coding variants confer an increased Hb–O2 affinity in conjunction with an enhanced Bohr effect. We also document that affinity-enhancing mutations in the β-globin gene of Tibetan wolf were originally derived via interparalog gene conversion from a tandemly linked β-globin pseudogene. Thus, affinity-enhancing mutations were introduced into the β-globin gene of Tibetan wolf via one form of intragenomic lateral transfer (ectopic gene conversion) and were subsequently introduced into the Tibetan mastiff genome via a second form of lateral transfer (introgression). Site-directed mutagenesis experiments revealed that the increased Hb–O2 affinity requires a specific two-site combination of amino acid replacements, suggesting that the molecular underpinnings of Hb adaptation in Tibetan mastiff (involving mutations that arose in a nonexpressed gene and which originally fixed in Tibetan wolf) may be qualitatively distinct from functionally similar changes in protein function that could have evolved via sequential fixation of de novo mutations during the breed’s relatively short duration of residency at high altitude.
20
Hill, Geoffrey E. "Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression." Integrative and Comparative Biology 59, no. 4 (April 27, 2019): 912–24. http://dx.doi.org/10.1093/icb/icz019.
Анотація:
Abstract The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
21
Zhang, Xinjun, Kelsey E. Witt, Mayra M. Bañuelos, Amy Ko, Kai Yuan, Shuhua Xu, Rasmus Nielsen, and Emilia Huerta-Sanchez. "The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans." Proceedings of the National Academy of Sciences 118, no. 22 (May 28, 2021): e2020803118. http://dx.doi.org/10.1073/pnas.2020803118.
Анотація:
Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000–59,500) y ago, and selection started around 9,000 (2,500–42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.
22
Boratyński, Z., J. Melo-Ferreira, P. C. Alves, S. Berto, E. Koskela, O. T. Pentikäinen, P. Tarroso, M. Ylilauri, and T. Mappes. "Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?" Heredity 113, no. 4 (April 2, 2014): 277–86. http://dx.doi.org/10.1038/hdy.2014.28.
23
Grun, Paul, and M. D. Orzolek. "451 PB 294 BREEDING SAVORY PEPPER” FOR ADAPTATION IN NORTHEAST U.S." HortScience 29, no. 5 (May 1994): 496a—496. http://dx.doi.org/10.21273/hortsci.29.5.496a.
Анотація:
Savory Peppers™ (Sp™) is the low heat form of Capsicum chinense from northern South America where it is widely used as a condiment. We are adapting it to northeastern conditions through introgression of genes from adapted C. annum, selection within SP™, and use of improved culture methods. Introgression is progressing in spite of species isolation barriers expressed as failure of F1 seeds to germinate, and F1 and later generation male sterilities. Selection has been carried out on plants of two landraces, producing ten improved strains which were tested at three stations last summer: 1) west PA on sandy soil with long growing season: 2) central PA on clay loam with short growing season, and 3) eastern PA on clay loam with long growing season. Strains of both landraces yielded well in region 1), and poorly in region 2), and one landrace yielded well in region 3), while those of the other yielded poorly as a result of early wilt. Roles of soil and temperatures in producing these results will be discussed.
24
Runemark, Anna, Fabrice Eroukhmanoff, Angela Nava-Bolaños, Jo S. Hermansen, and Joana I. Meier. "Hybridization, sex-specific genomic architecture and local adaptation." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1757 (August 27, 2018): 20170419. http://dx.doi.org/10.1098/rstb.2017.0419.
Анотація:
While gene flow can reduce the potential for local adaptation, hybridization may conversely provide genetic variation that increases the potential for local adaptation. Hybridization may also affect adaptation through altering sexual dimorphism and sexual conflict, but this remains largely unstudied. Here, we discuss how hybridization may affect sexual dimorphism and conflict due to differential effects of hybridization on males and females, and then how this, in turn, may affect local adaptation. First, in species with heterochromatic sexes, the lower viability of the heterogametic sex in hybrids could shift the balance in sexual conflict. Second, sex-specific inheritance of the mitochondrial genome in hybrids may lead to cytonuclear mismatches, for example, in the form of ‘mother's curse’, with potential consequences for sex ratio and sex-specific expression. Third, sex-biased introgression and recombination may lead to sex-specific consequences of hybridization. Fourth, transgressive segregation of sexually antagonistic alleles could increase sexual dimorphism in hybrid populations. Sexual dimorphism can reduce sexual conflict and enhance intersexual niche partitioning, increasing the fitness of hybrids. Adaptive introgression of alleles reducing sexual conflict or enhancing intersexual niche partitioning may facilitate local adaptation, and could favour the colonization of novel habitats. We review these consequences of hybridization on sex differences and local adaptation, and discuss how their prevalence and importance could be tested empirically. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences'.
25
Zhang, Zheng-Ren, Wei-Ying Li, Yi-Yi Dong, Jing-Xin Liu, Qin-Ying Lan, Xue Yang, Pei-Yao Xin, and Jie Gao. "Geographic Cline and Genetic Introgression Effects on Seed Morphology Variation and Germination Fitness in Two Closely Related Pine Species in Southeast Asia." Forests 13, no. 3 (February 23, 2022): 374. http://dx.doi.org/10.3390/f13030374.
Анотація:
There is still limited information on how genetic introgression impacts morphological variation and population fitness in long-lived conifer species. Two closely related pine species, Pinus kesiya Royle ex Gordon and Pinus yunnanensis Franch. are widely distributed over Southeast Asia and Yunnan province of China, with a large spatial scale of asymmetric genetic introgression and hybridization, and form a hybrid lineage, P. kesiya var. langbianensis, where their ranges overlap in southeast Yunnan. We compared seed trait variation and germination performance between hybrids and parental species and characterized environmental gradients to investigate the genetic and ecological evolutionary consequences of genetic introgression. We found that seed width (SW) differed significantly among the three pines, and all the seed traits were significantly negatively correlated with latitude and associated with the mean temperatures of the driest and wettest quarters. A higher germination fitness of hybrids was detected at a low temperature, indicating that they had better adaptability to temperature stress than their parental species during the germination process. Our results suggest that environmental factors shape seed phenotypic variation in the pine species and that genetic introgression significantly affects seed germination fitness. Therefore, assisting gene flow in natural forest populations might facilitate their adaptation to climate change.
26
Rossi, Matteo, Alexander E. Hausmann, Pepe Alcami, Markus Moest, Rodaria Roussou, Steven M. Van Belleghem, Daniel Shane Wright, et al. "Adaptive introgression of a visual preference gene." Science 383, no. 6689 (March 22, 2024): 1368–73. http://dx.doi.org/10.1126/science.adj9201.
Анотація:
Visual preferences are important drivers of mate choice and sexual selection, but little is known of how they evolve at the genetic level. In this study, we took advantage of the diversity of bright warning patterns displayed by Heliconius butterflies, which are also used during mate choice. Combining behavioral, population genomic, and expression analyses, we show that two Heliconius species have evolved the same preferences for red patterns by exchanging genetic material through hybridization. Neural expression of regucalcin1 correlates with visual preference across populations, and disruption of regucalcin1 with CRISPR-Cas9 impairs courtship toward conspecific females, providing a direct link between gene and behavior. Our results support a role for hybridization during behavioral evolution and show how visually guided behaviors contributing to adaptation and speciation are encoded within the genome.
27
Hardigan, Michael A., F. Parker E. Laimbeer, Linsey Newton, Emily Crisovan, John P. Hamilton, Brieanne Vaillancourt, Krystle Wiegert-Rininger, et al. "Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato." Proceedings of the National Academy of Sciences 114, no. 46 (October 30, 2017): E9999—E10008. http://dx.doi.org/10.1073/pnas.1714380114.
Анотація:
Cultivated potatoes (Solanum tuberosum L.), domesticated from wild Solanum species native to the Andes of southern Peru, possess a diverse gene pool representing more than 100 tuber-bearing relatives (Solanum section Petota). A diversity panel of wild species, landraces, and cultivars was sequenced to assess genetic variation within tuber-bearing Solanum and the impact of domestication on genome diversity and identify key loci selected for cultivation in North and South America. Sequence diversity of diploid and tetraploid S. tuberosum exceeded any crop resequencing study to date, in part due to expanded wild introgressions following polyploidy that captured alleles outside of their geographic origin. We identified 2,622 genes as under selection, with only 14–16% shared by North American and Andean cultivars, showing that a limited gene set drove early improvement of cultivated potato, while adaptation of upland (S. tuberosum group Andigena) and lowland (S. tuberosum groups Chilotanum and Tuberosum) populations targeted distinct loci. Signatures of selection were uncovered in genes controlling carbohydrate metabolism, glycoalkaloid biosynthesis, the shikimate pathway, the cell cycle, and circadian rhythm. Reduced sexual fertility that accompanied the shift to asexual reproduction in cultivars was reflected by signatures of selection in genes regulating pollen development/gametogenesis. Exploration of haplotype diversity at potato’s maturity locus (StCDF1) revealed introgression of truncated alleles from wild species, particularly S. microdontum in long-day–adapted cultivars. This study uncovers a historic role of wild Solanum species in the diversification of long-day–adapted tetraploid potatoes, showing that extant natural populations represent an essential source of untapped adaptive potential.
28
Huerta-Sánchez, Emilia, Xin Jin, Asan, Zhuoma Bianba, Benjamin M. Peter, Nicolas Vinckenbosch, Yu Liang, et al. "Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA." Nature 512, no. 7513 (July 2, 2014): 194–97. http://dx.doi.org/10.1038/nature13408.
29
Wu, Dong-Dong, Xiang-Dong Ding, Sheng Wang, Jan M. Wójcik, Yi Zhang, Małgorzata Tokarska, Yan Li, et al. "Pervasive introgression facilitated domestication and adaptation in the Bos species complex." Nature Ecology & Evolution 2, no. 7 (May 21, 2018): 1139–45. http://dx.doi.org/10.1038/s41559-018-0562-y.
30
Barley, Anthony J., Adrián Nieto-Montes de Oca, Norma L. Manríquez-Morán, and Robert C. Thomson. "The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization." Science 377, no. 6607 (August 12, 2022): 773–77. http://dx.doi.org/10.1126/science.abn1593.
Анотація:
Hybridization between diverging lineages is associated with the generation and loss of species diversity, introgression, adaptation, and changes in reproductive mode, but it is unknown when and why it results in these divergent outcomes. We estimate a comprehensive evolutionary network for the largest group of unisexual vertebrates and use it to understand the evolutionary outcomes of hybridization. Our results show that rates of introgression between species decrease with time since divergence and suggest that species must attain a threshold of evolutionary divergence before hybridization results in transitions to unisexuality. Rates of hybridization also predict genome-wide patterns of genetic diversity in whiptail lizards. These results distinguish among models for hybridization that have not previously been tested and suggest that the evolutionary outcomes can be predictable.
31
Sertse, Demissew, Frank M. You, Valentyna Klymiuk, Jemanesh K. Haile, Amidou N’Diaye, Curtis J. Pozniak, Sylvie Cloutier, and Sateesh Kagale. "Historical Selection, Adaptation Signatures, and Ambiguity of Introgressions in Wheat." International Journal of Molecular Sciences 24, no. 9 (May 7, 2023): 8390. http://dx.doi.org/10.3390/ijms24098390.
Анотація:
Wheat was one of the crops domesticated in the Fertile Crescent region approximately 10,000 years ago. Despite undergoing recent polyploidization, hull-to-free-thresh transition events, and domestication bottlenecks, wheat is now grown in over 130 countries and accounts for a quarter of the world’s cereal production. The main reason for its widespread success is its broad genetic diversity that allows it to thrive in different environments. To trace historical selection and hybridization signatures, genome scans were performed on two datasets: approximately 113K SNPs from 921 predominantly bread wheat accessions and approximately 110K SNPs from about 400 wheat accessions representing all ploidy levels. To identify environmental factors associated with the loci, a genome–environment association (GEA) was also performed. The genome scans on both datasets identified a highly differentiated region on chromosome 4A where accessions in the first dataset were dichotomized into a group (n = 691), comprising nearly all cultivars, wild emmer, and most landraces, and a second group (n = 230), dominated by landraces and spelt accessions. The grouping of cultivars is likely linked to their potential ancestor, bread wheat cv. Norin-10. The 4A region harbored important genes involved in adaptations to environmental conditions. The GEA detected loci associated with latitude and temperature. The genetic signatures detected in this study provide insight into the historical selection and hybridization events in the wheat genome that shaped its current genetic structure and facilitated its success in a wide spectrum of environmental conditions. The genome scans and GEA approaches applied in this study can help in screening the germplasm housed in gene banks for breeding, and for conservation purposes.
32
Nikolov, I. S., B. C. Stoeckle, G. Markov, and R. Kuehn. "Substantial hybridisation between wild boars (Sus scrofa scrofa) and East Balkan pigs (Sus scrofa f. domestica) in natural environment as a result of semi-wild rearing in Bulgaria." Czech Journal of Animal Science 62, No. 1 (January 14, 2017): 1–8. http://dx.doi.org/10.17221/49/2015-cjas.
Анотація:
The East Balkan pig (EBP) is a traditional domestic pig breed in Bulgaria managed in semi-wild conditions and well-adapted to the continental climate and rearing on pastures. From the genetical and historical point of view it is important to preserve this ancient breed. However, over the last several years, a dramatic decline of EBP herds has been observed. Moreover, introgression between EBP and wild boar in Bulgaria (WBB) is very likely to have occurred. In this study we used a set of 10 microsatellites and the polymerase chain reaction–restriction fragment length polymorphism method on melanocortin-1 receptor (MC1R) polymorphisms to study the degree of hybridisation between WBB, EBP, and a commercial pig breed (CPB). MC1R results identified WBB-EBP hybrids and the analysis of the microsatellite data with a Bayesian assignment approach and the Discriminant Analysis of Principal Components revealed a low genetic differentiation between WBB and EBP and a high amount of introgression of WBB into EBP. A mentionable introgression of CPB into EBP was also revealed. It is apparent that the traditional rearing system of EBP, which is hundreds of years old, has led to a permanent hybridisation between WBB and EBP. In our opinion, the preservation of the semi-wild rearing system is a prerequisite for the conservation of this old, indigenous pig breed and its genetic composition, as the semi-wild rearing system allows the continuous introgression with WBB. Moreover, the introgression of commercial breeds into EBP or WBB should be prevented. Due to the bidirectional gene flow these hybridisation events would have negative consequences (i.e. loss of viability and adaptation) for the wild boars as well as for the indigenous pig breed.
33
Jones, Matthew R., L. Scott Mills, Paulo Célio Alves, Colin M. Callahan, Joel M. Alves, Diana J. R. Lafferty, Francis M. Jiggins, Jeffrey D. Jensen, José Melo-Ferreira, and Jeffrey M. Good. "Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares." Science 360, no. 6395 (June 21, 2018): 1355–58. http://dx.doi.org/10.1126/science.aar5273.
Анотація:
Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow cover. We show that cis-regulatory variation controlling seasonal expression of the Agouti gene underlies this adaptive winter camouflage polymorphism. Genetic variation at Agouti clustered by winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent interspecific gene flow. Brown winter coats in snowshoe hares likely originated from an introgressed black-tailed jackrabbit allele that has swept to high frequency in mild winter environments. These discoveries show that introgression of genetic variants that underlie key ecological traits can seed past and ongoing adaptation to rapidly changing environments.
34
Zaman, M. W. "Introgression in Brassica napus for adaptation to the growing conditions in Bangladesh." Theoretical and Applied Genetics 77, no. 5 (May 1989): 721–28. http://dx.doi.org/10.1007/bf00261250.
35
Prohens, J., P. Gramazio, M. Plazas, A. Fita, E. García Fortea, G. Mangino, A. Arrones, et al. "Biotechnological tools for introgression breeding for adaptation of crops to climate change." Journal of Biotechnology 305 (November 2019): S19. http://dx.doi.org/10.1016/j.jbiotec.2019.05.077.
36
Ray, Dylan D., Lex Flagel, and Daniel R. Schrider. "IntroUNET: Identifying introgressed alleles via semantic segmentation." PLOS Genetics 20, no. 2 (February 20, 2024): e1010657. http://dx.doi.org/10.1371/journal.pgen.1010657.
Анотація:
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient—ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual’s alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled “ghost” population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method’s success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
37
Lazic, Desanka, Andrew L. Hipp, John E. Carlson, and Oliver Gailing. "Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks." Forests 12, no. 6 (May 27, 2021): 690. http://dx.doi.org/10.3390/f12060690.
Анотація:
Adaptive divergence is widely accepted as a contributor to speciation and the maintenance of species integrity. However, the mechanisms leading to reproductive isolation, the genes involved in adaptive divergence, and the traits that shape the adaptation of wild species to changes in climate are still largely unknown. In studying the role of ecological interactions and environment-driven selection, trees have emerged as potential model organisms because of their longevity and large genetic diversity, especially in natural habitats. Due to recurrent gene flow among species with different ecological preferences, oaks arose as early as the 1970s as a model for understanding how speciation can occur in the face of interspecific gene flow, and what we mean by “species” when geographically and genomically heterogeneous introgression seems to undermine species’ genetic coherence. In this review, we provide an overview of recent research into the genomic underpinnings of adaptive divergence and maintenance of species integrity in oaks in the face of gene flow. We review genomic and analytical tools instrumental to better understanding mechanisms leading to reproductive isolation and environment-driven adaptive introgression in oaks. We review evidence that oak species are genomically coherent entities, focusing on sympatric populations with ongoing gene flow, and discuss evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation. As the evolution of drought- and freezing-tolerance have been key to the parallel diversification of oaks, we investigate the question of whether the same or a similar set of genes are involved in adaptive divergence for drought and stress tolerance across different taxa and sections. Finally, we propose potential future research directions on the role of hybridization and adaptive introgression in adaptation to climate change.
38
Findley, Anthony S., Xinjun Zhang, Carly Boye, Yen Lung Lin, Cynthia A. Kalita, Luis Barreiro, Kirk E. Lohmueller, Roger Pique-Regi, and Francesca Luca. "A signature of Neanderthal introgression on molecular mechanisms of environmental responses." PLOS Genetics 17, no. 9 (September 27, 2021): e1009493. http://dx.doi.org/10.1371/journal.pgen.1009493.
Анотація:
Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.
39
Leducq, Jean-Baptiste, Mathieu Henault, Guillaume Charron, Lou Nielly-Thibault, Yves Terrat, Heather L. Fiumera, B. Jesse Shapiro, and Christian R. Landry. "Mitochondrial Recombination and Introgression during Speciation by Hybridization." Molecular Biology and Evolution 34, no. 8 (April 21, 2017): 1947–59. http://dx.doi.org/10.1093/molbev/msx139.
Анотація:
Abstract Genome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation.
40
Vinarao, Ricky, Christopher Proud, Peter Snell, Shu Fukai, and Jaquie Mitchell. "QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems." Plants 10, no. 10 (October 3, 2021): 2099. http://dx.doi.org/10.3390/plants10102099.
Анотація:
Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3–17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7–15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4’s effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.
41
Byerly, Amy R., Clara Jenck, Alexander R. B. Goetz, David B. Weissman, David A. Gray, Charles L. Ross, Luana S. Maroja, and Erica L. Larson. "Geographic variation in phenotypic divergence between two hybridizing field cricket species." Journal of Orthoptera Research 32, no. 2 (September 25, 2023): 189–200. http://dx.doi.org/10.3897/jor.32.90713.
Анотація:
Patterns of morphological divergence across species’ ranges can provide insight into local adaptation and speciation. In this study, we compared phenotypic divergence among 4,221 crickets from 337 populations of two closely related species of field cricket, Gryllus firmus and G. pennsylvanicus, and their hybrids. We found that these species differ across their geographic range in key morphological traits, such as body size and ovipositor length, and we directly compared phenotype with genotype for a subset of crickets to demonstrate nuclear genetic introgression, phenotypic intermediacy of hybrids, and essentially unidirectional mitochondrial introgression. We discuss how these morphological traits relate to life history differences between the two species. Our comparisons across geographic areas support prior research suggesting that cryptic variation within G. firmus may represent different species. Our study highlights how variable morphology can be across wide-ranging species and the importance of studying reproductive barriers in more than one or two transects of a hybrid zone.
42
Zhang, Yubo, Dequn Teng, Wei Lu, Min Liu, Hua Zeng, Lei Cao, Laura Southcott, et al. "A widely diverged locus involved in locomotor adaptation in Heliconius butterflies." Science Advances 7, no. 32 (August 2021): eabh2340. http://dx.doi.org/10.1126/sciadv.abh2340.
Анотація:
Heliconius butterflies have undergone adaptive radiation and therefore serve as an excellent system for exploring the continuum of speciation and adaptive evolution. However, there is a long-lasting paradox between their convergent mimetic wing patterns and rapid divergence in speciation. Here, we characterize a locus that consistently displays high divergence among Heliconius butterflies and acts as an introgression hotspot. We further show that this locus contains multiple genes related to locomotion and conserved in Lepidoptera. In light of these findings, we consider that locomotion traits may be under selection, and if these are heritable traits that are selected for, then they might act as species barriers.
43
Wang, Xiuge, Zhihua Ju, Qiang Jiang, Jifeng Zhong, Chengkun Liu, Jinpeng Wang, Jesse L. Hoff, et al. "Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle." Genomics 113, no. 3 (May 2021): 1491–503. http://dx.doi.org/10.1016/j.ygeno.2021.03.023.
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Silva, Diogo Nuno, Vítor Várzea, Octávio Salgueiro Paulo, and Dora Batista. "Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust." Molecular Plant Pathology 19, no. 7 (February 22, 2018): 1742–53. http://dx.doi.org/10.1111/mpp.12657.
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Ai, Huashui, Xiaodong Fang, Bin Yang, Zhiyong Huang, Hao Chen, Likai Mao, Feng Zhang, et al. "Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing." Nature Genetics 47, no. 3 (January 26, 2015): 217–25. http://dx.doi.org/10.1038/ng.3199.
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Muirhead, Christina A., and Daven C. Presgraves. "Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species." American Naturalist 187, no. 2 (February 2016): 249–61. http://dx.doi.org/10.1086/684583.
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Schneider, A., P. Ruffa, G. Tumino, M. Fontana, P. Boccacci, and S. Raimondi. "Genetic relationships and introgression events between wild and cultivated grapevines (Vitis vinifera L.): focus on Italian Lambruscos." Scientific Reports 14, no. 1 (May 29, 2024). http://dx.doi.org/10.1038/s41598-024-62774-w.
Анотація:
AbstractResearch efforts on genomic structure and ecology of wild populations of Vitis vinifera L. offer insights on grape domestication processes and on the assortment evolution of the cultivated forms. Attention is also paid to the origin of traditional, long-cultivated varieties, often producing renowned and valuable wines. The genetic relationships between 283 Vitis vinifera cultivated varieties (subsp. sativa) and 65 individuals from 9 populations of the sylvestris subspecies mainly from northern Italy were explored by means of molecular markers (27 nuclear and 4 chloroplastic microsatellites). Several episodes of contamination of the wild germplasm by the pollen of specific grape cultivars were detected, implying concern for maintaining the purity of the wild form. At the same time, events of introgression from the wild subspecies resulted playing a crucial role in the emergence of several cultivated varieties with a clear admixed genome ancestry sativa-sylvestris. These included Lambruscos originated from the flat areas crossed by the Po and Adige rivers in northern Italy, while other cultivars still called Lambrusco but typical of hilly areas did not show the same admixed genome. Historical and ecological evidences suggesting an adaptative recent post-domestication process in the origin of several Italian Lambruscos are discussed.
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Morales-Cruz, Abraham, Jonas A. Aguirre-Liguori, Yongfeng Zhou, Andrea Minio, Summaira Riaz, Andrew M. Walker, Dario Cantu, and Brandon S. Gaut. "Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation." Genome Biology 22, no. 1 (September 3, 2021). http://dx.doi.org/10.1186/s13059-021-02467-z.
Анотація:
Abstract Background Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. Results By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce’s disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. Conclusions Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
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Storz, Jay F., and Anthony V. Signore. "Introgressive Hybridization and Hypoxia Adaptation in High-Altitude Vertebrates." Frontiers in Genetics 12 (June 22, 2021). http://dx.doi.org/10.3389/fgene.2021.696484.
Анотація:
In natural populations of animals, a growing body of evidence suggests that introgressive hybridization may often serve as an important source of adaptive genetic variation. Population genomic studies of high-altitude vertebrates have provided strong evidence of positive selection on introgressed allelic variants, typically involving a long-term highland species as the donor and a more recently arrived colonizing species as the recipient. In high-altitude humans and canids from the Tibetan Plateau, case studies of adaptive introgression involving the HIF transcription factor, EPAS1, have provided insights into complex histories of ancient introgression, including examples of admixture from now-extinct source populations. In Tibetan canids and Andean waterfowl, directed mutagenesis experiments involving introgressed hemoglobin variants successfully identified causative amino acid mutations and characterized their phenotypic effects, thereby providing insights into the functional properties of selectively introgressed alleles. We review case studies of adaptive introgression in high-altitude vertebrates and we highlight findings that may be of general significance for understanding mechanisms of environmental adaptation involving different sources of genetic variation.
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Horta, Pedro, Helena Raposeira, Adrián Baños, Carlos Ibáñez, Orly Razgour, Hugo Rebelo, and Javier Juste. "Counteracting forces of introgressive hybridization and interspecific competition shape the morphological traits of cryptic Iberian Eptesicus bats." Scientific Reports 12, no. 1 (July 8, 2022). http://dx.doi.org/10.1038/s41598-022-15412-2.
Анотація:
AbstractCryptic species that coexist in sympatry are likely to simultaneously experience strong competition and hybridization. The first phenomenon would lead to character displacement, whereas the second can potentially promote morphological similarity through adaptive introgression. The main goal of this work was to investigate the effect of introgressive hybridization on the morphology of cryptic Iberian Eptesicus bats when facing counteracting evolutionary forces from interspecific competition. We found substantial overlap both in dentition and in wing morphology traits, though mainly in individuals in sympatry. The presence of hybrids contributes to a fifth of this overlap, with hybrids showing traits with intermediate morphometry. Thus, introgressive hybridization may contribute to species adaptation to trophic and ecological space responding directly to the macro-habitats characteristics of the sympatric zone and to local prey availability. On the other hand, fur shade tended to be browner and brighter in hybrids than parental species. Colour differences could result from partitioning of resources as an adaptation to environmental factors such as roost and microhabitats. We argue that a balance between adaptive introgression and niche partitioning shapes species interactions with the environment through affecting morphological traits under selection.