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1
Mahé, L., D. Le Pierrès, M. C. Combes e P. Lashermes. "Introgressive hybridization between the allotetraploid Coffea arabica and one of its diploid ancestors, Coffea canephora, in an exceptional sympatric zone in New Caledonia". Genome 50, n. 3 (febbraio 2007): 316–24. http://dx.doi.org/10.1139/g07-011.
Abstract (sommario):
The importance of introgressive hybridization in plant evolution has long been recognized. Nevertheless, information on gene flow between allopolyploids and their diploid relatives is very limited, even though gene flow could play a major role in polyploid establishment and evolution. Here, we investigated the processes governing hybrid formation and introgression between the allotetraploid Coffea arabica and one of its ancestral diploid progenitors, C. canephora, in a sympatric zone of New Caledonia. The occurrence of a large assortment of hybridization events between the 2 coffee species is clearly established. First-generation hybrids (F1) and post-F1 hybrids were characterized. The involvement of unreduced gametes of C. canephora is suggested, because tetraploid F1 hybrid plants were detected. Moreover, although bidirectional mating was observed, only unidirectional gene flow from C. canephora to C. arabica was noted in post-F1 hybrids. Most of the collected post-F1 hybrid plants exhibited a high level of introgression, and the frequency of introgression observed among the different analyzed loci was homogeneous, suggesting no significant counterselection against introgressions from C. canephora. Overall, the New Caledonian central mountains appear to be a highly favourable environment for introgressive hybridization and a genetic diversity center for C. arabica.
2
Dagilis, Andrius J., e Daniel R. Matute. "The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location". PLOS Biology 21, n. 7 (17 luglio 2023): e3002185. http://dx.doi.org/10.1371/journal.pbio.3002185.
Abstract (sommario):
The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature of evolution. Examples of both adaptive and deleterious introgression exist in a variety of systems. What is unclear is how the fitness of an introgressing haplotype changes as species diverge or as the size of the introgressing haplotype changes. In a simple model, we show that introgression may more easily occur into parts of the genome which have not diverged heavily from a common ancestor. The key insight is that alleles from a shared genetic background are likely to have positive epistatic interactions, increasing the fitness of a larger introgressing block. In regions of the genome where few existing substitutions are disrupted, this positive epistasis can be larger than incompatibilities with the recipient genome. Further, we show that early in the process of divergence, introgression of large haplotypes can be favored more than introgression of individual alleles. This model is consistent with observations of a positive relationship between recombination rate and introgression frequency across the genome; however, it generates several novel predictions. First, the model suggests that the relationship between recombination rate and introgression may not exist, or may be negative, in recently diverged species pairs. Furthermore, the model suggests that introgression that replaces existing derived variation will be more deleterious than introgression at sites carrying ancestral variants. These predictions are tested in an example of introgression in Drosophila melanogaster, with some support for both. Finally, the model provides a potential alternative explanation to asymmetry in the direction of introgression, with expectations of higher introgression from rapidly diverged populations into slowly evolving ones.
3
McVay, John D., Duncan Hauser, Andrew L. Hipp e Paul S. Manos. "Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America". Genome 60, n. 9 (settembre 2017): 733–42. http://dx.doi.org/10.1139/gen-2016-0206.
Abstract (sommario):
Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.
4
Lopez Fang, Lesly, David Peede, Diego Ortega-Del Vecchyo, Emily Jane McTavish e Emilia Huerta-Sanchez. "Leveraging shared ancestral variation to detect local introgression". PLOS Genetics 20, n. 1 (8 gennaio 2024): e1010155. http://dx.doi.org/10.1371/journal.pgen.1010155.
Abstract (sommario):
Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson’s D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.
5
Karimi, Nisa, Corrinne E. Grover, Joseph P. Gallagher, Jonathan F. Wendel, Cécile Ané e David A. Baum. "Reticulate Evolution Helps Explain Apparent Homoplasy in Floral Biology and Pollination in Baobabs (Adansonia; Bombacoideae; Malvaceae)". Systematic Biology 69, n. 3 (6 novembre 2019): 462–78. http://dx.doi.org/10.1093/sysbio/syz073.
Abstract (sommario):
Abstract Baobabs (Adansonia) are a cohesive group of tropical trees with a disjunct distribution in Australia, Madagascar, and continental Africa, and diverse flowers associated with two pollination modes. We used custom-targeted sequence capture in conjunction with new and existing phylogenetic comparative methods to explore the evolution of floral traits and pollination systems while allowing for reticulate evolution. Our analyses suggest that relationships in Adansonia are confounded by reticulation, with network inference methods supporting at least one reticulation event. The best supported hypothesis involves introgression between Adansonia rubrostipa and core Longitubae, both of which are hawkmoth pollinated with yellow/red flowers, but there is also some support for introgression between the African lineage and Malagasy Brevitubae, which are both mammal-pollinated with white flowers. New comparative methods for phylogenetic networks were developed that allow maximum-likelihood inference of ancestral states and were applied to study the apparent homoplasy in floral biology and pollination mode seen in Adansonia. This analysis supports a role for introgressive hybridization in morphological evolution even in a clade with highly divergent and geographically widespread species. Our new comparative methods for discrete traits on species networks are implemented in the software PhyloNetworks. [Comparative methods; Hyb-Seq; introgression; network inference; population trees; reticulate evolution; species tree inference; targeted sequence capture.]
6
Bernatchez, Louis, Hélène Glémet, Chris C. Wilson e Roy G. Danzmann. "Introgression and fixation of Arctic char (Salvelinus alpinus) mitochondrial genome in an allopatric population of brook trout (Salvelinus fontinalis)". Canadian Journal of Fisheries and Aquatic Sciences 52, n. 1 (1 gennaio 1995): 179–85. http://dx.doi.org/10.1139/f95-018.
Abstract (sommario):
Although mitochondrial introgression between taxa has been increasingly documented, interspecific replacement of mtDNA is rare, particularly when the donor species is absent. We document evidence for a population of brook trout (Salvelinus fontinalis) in which all individuals possess the mitochondrial genome of Arctic char (S. alpinus) despite the present-day absence of the latter species in the watershed where the population is located. The mitochondrial genotype of 48 brook trout from Lake Alain (Québec) was characterized by RFLP analysis performed over the entire mtDNA molecule and/or a 2.5-kb PCR-amplified segment of the ND-5/6 region. Although the fish examined were morphologically indistinguishable from typical brook trout and homozygous for the diagnostic alleles characteristic of brook trout, the mtDNA of all individuals was identical to the Québec Arctic char haplotype. Together, these results indicate that the mtDNA haplotype observed in Lake Alain brook trout has resulted from ancient introgression with Arctic char rather than ancestral polymorphism or convergent evolution. They also demonstrate that introgressive hybridization between those two species can have significant and long-term effects on their genetic composition.
7
Wu, Meng Yue, Giovanni Forcina, Gabriel Weijie Low, Keren R. Sadanandan, Chyi Yin Gwee, Hein van Grouw, Shaoyuan Wu, Scott V. Edwards, Maude W. Baldwin e Frank E. Rheindt. "Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene". PLOS Genetics 19, n. 1 (19 gennaio 2023): e1010551. http://dx.doi.org/10.1371/journal.pgen.1010551.
Abstract (sommario):
Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20–50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.
8
Calfee, Erin, Daniel Gates, Anne Lorant, M. Taylor Perkins, Graham Coop e Jeffrey Ross-Ibarra. "Selective sorting of ancestral introgression in maize and teosinte along an elevational cline". PLOS Genetics 17, n. 10 (11 ottobre 2021): e1009810. http://dx.doi.org/10.1371/journal.pgen.1009810.
Abstract (sommario):
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
Luo, Min-Xin, Yi-Ting Tseng, Jui-Tse Chang, Chien-Ti Chao e Pei-Chun Liao. "Different Roles of Introgression on the Demographic Change in Two Snakebark Maples, Acer caudatifolium and A. morrisonense, with Contrasted Postglacial Expansion Routes". Plants 11, n. 5 (26 febbraio 2022): 644. http://dx.doi.org/10.3390/plants11050644.
Abstract (sommario):
Hybridization frequently occurs in plant species. With repeated backcross, the introgression may influence evolutionary trajectories through the entry of foreign genes. However, the genetic admixture via hybridization events is often confused with the ancestral polymorphism, especially in closely related species that have experienced similar evolutionary events. In Taiwan, two independent-originated endemic snakebark maples have contrasted postglacial range expansion routes: northward and upward expansion in Acer caudatifolium and downward expansion in A. morrisonense. The range expansion causes the current parapatric distribution, increasing the possibility of introgression. This study elucidates how their genetic variation reflects introgression and historical demography. With 17 EST-SSR markers among the intensely sampled 657 individuals, we confirmed that the genetic admixture between species mainly was attributed to recent introgression instead of common ancestral polymorphism. The secondary contact scenario inferred by approximate Bayesian computation suggested that A. morrisonense received more genetic variations from A. caudatifolium. Introgression occurred in colonized Taiwan around the early Last Glacial Period. Furthermore, the demography of A. caudatifolium was more severely affected by introgression than A. morrisonense, especially in the wavefront populations with high altitude range expansion, implying an altitude-related adaptive introgression. In contrast, A. morrisonense exhibited ubiquitous introgression independent of postglacial expansion, suggesting that introgression in A. morrisonense was neutral. In terms of different genetic consequences, introgression had different demographic impacts on species with different altitude expansion directions even under the same climate-change conditions within an island.
10
Matus, I., A. Corey, T. Filichkin, P. M. Hayes, M. I. Vales, J. Kling, O. Riera-Lizarazu, K. Sato, W. Powell e R. Waugh. "Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background". Genome 46, n. 6 (1 dicembre 2003): 1010–23. http://dx.doi.org/10.1139/g03-080.
Abstract (sommario):
The ancestor of barley (Hordeum vulgare subsp. spontaneum) may be a source of novel alleles for crop improvement. We developed a set of recombinant chromosome substitution lines (RCSLs) using an accession of H. vulgare subsp. spontaneum (Caesarea 26-24, from Israel) as the donor and Hordeum vulgare subsp. vulgare 'Harrington' (the North American malting quality standard) as the recurrent parent via two backcrosses to the recurrent parent, followed by six generations of selfing. Here we report (i) the genomic architecture of the RCSLs, as inferred by simple sequence repeat (SSR) markers, and (ii) the effects of H. vulgare subsp. spontaneum genome segment introgressions in terms of three classes of phenotypes: inflorescence yield components, malting quality traits, and domestication traits. Significant differences among the RCSLs were detected for all phenotypes measured. The phenotypic effects of the introgressions were assessed using association analysis, and these were referenced to quantitative trait loci (QTL) reported in the literature. Hordeum vulgare subsp. spontaneum, despite its overall inferior phenotype, contributed some favorable alleles for agronomic and malting quality traits. In most cases, the introgression of the ancestral genome resulted in a loss of desirable phenotypes in the cultivated parent. Although disappointing from a plant breeding perspective, this finding may prove to be a useful tool for gene discovery.Key words: Hordeum vulgare subsp. vulgare, Hordeum vulgare subsp spontaneum, association analysis, QTLs, genetic resources.
11
Poroshina, A. A., D. Y. Sherbakov e T. E. Peretolchina. "Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers". Vavilov Journal of Genetics and Breeding 24, n. 4 (2 luglio 2020): 420–26. http://dx.doi.org/10.18699/vj20.634.
Abstract (sommario):
In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that g nerated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual “patterns” of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.
12
Zhang, Xinjun, Kelsey E. Witt, Mayra M. Bañuelos, Amy Ko, Kai Yuan, Shuhua Xu, Rasmus Nielsen e Emilia Huerta-Sanchez. "The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans". Proceedings of the National Academy of Sciences 118, n. 22 (28 maggio 2021): e2020803118. http://dx.doi.org/10.1073/pnas.2020803118.
Abstract (sommario):
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.
13
Peris, David, Armando Arias, Sandi Orlić, Carmela Belloch, Laura Pérez-Través, Amparo Querol e Eladio Barrio. "Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species". Molecular Phylogenetics and Evolution 108 (marzo 2017): 49–60. http://dx.doi.org/10.1016/j.ympev.2017.02.008.
14
MIMS, MERYL C., C. DARRIN HULSEY, BENJAMIN M. FITZPATRICK e J. TODD STREELMAN. "Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids". Molecular Ecology 19, n. 5 (marzo 2010): 940–51. http://dx.doi.org/10.1111/j.1365-294x.2010.04529.x.
15
Rinker, David C., Corinne N. Simonti, Evonne McArthur, Douglas Shaw, Emily Hodges e John A. Capra. "Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations". Nature Ecology & Evolution 4, n. 10 (27 luglio 2020): 1332–41. http://dx.doi.org/10.1038/s41559-020-1261-z.
16
Grant, Peter R., e B. Rosemary Grant. "Hybridization increases population variation during adaptive radiation". Proceedings of the National Academy of Sciences 116, n. 46 (28 ottobre 2019): 23216–24. http://dx.doi.org/10.1073/pnas.1913534116.
Abstract (sommario):
Adaptive radiations are prominent components of the world’s biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin’s finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis. Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.
17
Smith, Joel, e Marcus R. Kronforst. "Do Heliconius butterfly species exchange mimicry alleles?" Biology Letters 9, n. 4 (23 agosto 2013): 20130503. http://dx.doi.org/10.1098/rsbl.2013.0503.
Abstract (sommario):
Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.
18
Boehm, Jeffrey, e Xiwen Cai. "Enrichment and Diversification of the Wheat Genome via Alien Introgression". Plants 13, n. 3 (23 gennaio 2024): 339. http://dx.doi.org/10.3390/plants13030339.
Abstract (sommario):
Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome’s polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.
19
Meleshko, Olena, Michael D. Martin, Thorfinn Sand Korneliussen, Christian Schröck, Paul Lamkowski, Jeremy Schmutz, Adam Healey et al. "Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus". Molecular Biology and Evolution 38, n. 7 (3 marzo 2021): 2750–66. http://dx.doi.org/10.1093/molbev/msab063.
Abstract (sommario):
Abstract The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.
20
Lowery, Robert K., Gabriel Uribe, Eric B. Jimenez, Mark A. Weiss, Kristian J. Herrera, Maria Regueiro e Rene J. Herrera. "Neanderthal and Denisova genetic affinities with contemporary humans: Introgression versus common ancestral polymorphisms". Gene 530, n. 1 (novembre 2013): 83–94. http://dx.doi.org/10.1016/j.gene.2013.06.005.
21
Li, Yao, Chao Tan, Wenxu Zhang, Lu Wang, Zhi Yang, Yanming Fang, Yong Yang e Lingfeng Mao. "Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China". Forests 15, n. 3 (14 marzo 2024): 537. http://dx.doi.org/10.3390/f15030537.
Abstract (sommario):
Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale genetic variation patterns of six sympatric oaks (Quercus, Fagaceae) in the hot-dry valley ESOFs of the Jinsha River, southwestern China. Three cp genomes were assembled for each species. Nine cp genome haplotypes and 16 nrDNA haplotypes were identified based on single-nucleotide variants and indels. Our results demonstrated that discordance existed between the cpDNA and nrDNA phylogenies of the sclerophyllous oaks in section Ilex. The nrDNA phylogeny was consistent with species boundaries, while the cpDNA phylogeny was decoupled from taxonomy. Interspecific sharing of closely related cp genome haplotypes was detected between Quercus cocciferoides and the other two sclerophyllous oaks, Q. longispica and Q. franchetii. Specifically, Q. cocciferoides and Q. longispica sampled in a mixed stand exhibited two haplotypes that differed by a 9 bp indel. The local distribution of the two highly similar haplotypes suggested that they may have arisen from ancient introgression. Given that the two species have diverged for a long time, it is possible that the ancestral cp genome of one species was captured by another species through asymmetric introgression in early times, and an indel event occurred subsequently. Phylogenetic analyses using more previously published cp genome sequences indicated that Q. cocciferoides and Q. franchetii shared multiple cpDNA lineages of Ilex oaks, which may be caused by shared ancestral polymorphism and/or ancient introgression. Our study showed that at least three highly variable regions (ψycf1, ndhF-rpl32, and trnKUUU-rps16 or rpl32-trnLUAG) can distinguish the nine haplotypes identified by whole-cp genome sequences. These markers are useful for the evolutionary studies of the maternal lineages of oaks in hot-dry valley ESOFs.
22
Vanderpool, Dan, Bui Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R. Alan Harris, Muthuswamy Raveendran et al. "Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression". PLOS Biology 18, n. 12 (3 dicembre 2020): e3000954. http://dx.doi.org/10.1371/journal.pbio.3000954.
Abstract (sommario):
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.
23
Giuffra, E., J. M. H. Kijas, V. Amarger, Ö. Carlborg, J.-T. Jeon e L. Andersson. "The Origin of the Domestic Pig: Independent Domestication and Subsequent Introgression". Genetics 154, n. 4 (1 aprile 2000): 1785–91. http://dx.doi.org/10.1093/genetics/154.4.1785.
Abstract (sommario):
Abstract The domestic pig originates from the Eurasian wild boar (Sus scrofa). We have sequenced mitochondrial DNA and nuclear genes from wild and domestic pigs from Asia and Europe. Clear evidence was obtained for domestication to have occurred independently from wild boar subspecies in Europe and Asia. The time since divergence of the ancestral forms was estimated at ~500,000 years, well before domestication ~9,000 years ago. Historical records indicate that Asian pigs were introduced into Europe during the 18th and early 19th centuries. We found molecular evidence for this introgression and the data indicated a hybrid origin of some major “European” pig breeds. The study is an advance in pig genetics and has important implications for the maintenance and utilization of genetic diversity in this livestock species.
24
Tosi, Anthony J., e Hirohisa Hirai. "X Chromosome Introgression and Recombination in the cephus Group of Cercopithecus Monkeys". Cytogenetic and Genome Research 153, n. 1 (2017): 29–35. http://dx.doi.org/10.1159/000480656.
Abstract (sommario):
A representative of Cercopithecus erythrotis was surveyed at a 9.3-kb region of the X chromosome. The data were compared against homologous sequences of closely related Cercopithecus monkeys including C. cephus, a species recently shown to have 2 polymorphic X-chromosomal lineages. Direct sequence comparisons and subsequent phylogenetic analyses revealed that synapomorphies in the first 4.3 kb cluster C. erythrotis with one C. cephus lineage, while synapomorphies in the latter 5.0 kb join it with the second C. cephus lineage. This pattern very likely reflects an ancestral episode of introgression from C. cephus into C. erythrotis followed by a recombination event. Similar groups of synapomorphies occur at different phylogenetic depths within the C. erythrotis/C. cephus/C. ascanius radiation and reveal new details in the evolutionary history of this 3-species clade.
25
Anseeuw, Dieter, Bruno Nevado, Paul Busselen, Jos Snoeks e Erik Verheyen. "Extensive Introgression among Ancestral mtDNA Lineages: Phylogenetic Relationships of the Utaka within the Lake Malawi Cichlid Flock". International Journal of Evolutionary Biology 2012 (10 maggio 2012): 1–9. http://dx.doi.org/10.1155/2012/865603.
Abstract (sommario):
We present a comprehensive phylogenetic analysis of the Utaka, an informal taxonomic group of cichlid species from Lake Malawi. We analyse both nuclear and mtDNA data from five Utaka species representing two (Copadichromis and Mchenga) of the three genera within Utaka. Within three of the five analysed species we find two very divergent mtDNA lineages. These lineages are widespread and occur sympatrically in conspecific individuals in different areas throughout the lake. In a broader taxonomic context including representatives of the main groups within the Lake Malawi cichlid fauna, we find that one of these lineages clusters within the non-Mbuna mtDNA clade, while the other forms a separate clade stemming from the base of the Malawian cichlid radiation. This second mtDNA lineage was only found in Utaka individuals, mostly within Copadichromis sp. “virginalis kajose” specimens. The nuclear genes analysed, on the other hand, did not show traces of divergence within each species. We suggest that the discrepancy between the mtDNA and the nuclear DNA signatures is best explained by a past hybridisation event by which the mtDNA of another species introgressed into the ancestral Copadichromis sp. “virginalis kajose” gene pool.
26
Makhov, Ilia A., Yelizaveta Y. U. Gorodilova e Vladimir A. Lukhtanov. "Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia?" Biological Journal of the Linnean Society 134, n. 2 (3 luglio 2021): 342–65. http://dx.doi.org/10.1093/biolinnean/blab089.
Abstract (sommario):
Abstract The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypotheses that might explain the mitochondrial pattern observed: cryptic speciation, ancestral polymorphism, interspecific mitochondrial introgression, secondary admixture of allopatrically evolved populations and an effect of intracellular Wolbachia endosymbionts. We demonstrate that in A. deversata and Th. chlorosaria the mitochondrial differences are not correlated with differences in nuclear genes, morphology, ecology and Wolbachia infection status, thus not supporting the hypothesis of cryptic species and an effect of Wolbachia. Mitochondrial introgression can lead to a situation in which one species has both its own mitochondrial lineage and the lineage obtained from another species. We found this situation in the species pair Alcis repandata and Alcis extinctaria. We conclude that the mitochondrial heterogeneity in A. deversata and Th. chlorosaria is most likely to be attributable to the secondary admixture of allopatrically evolved populations.
27
Tusso, Sergio, Bart P. S. Nieuwenhuis, Fritz J. Sedlazeck, John W. Davey, Daniel C. Jeffares e Jochen B. W. Wolf. "Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast". Molecular Biology and Evolution 36, n. 9 (20 maggio 2019): 1975–89. http://dx.doi.org/10.1093/molbev/msz126.
Abstract (sommario):
Abstract Mutation and recombination are key evolutionary processes governing phenotypic variation and reproductive isolation. We here demonstrate that biodiversity within all globally known strains of Schizosaccharomyces pombe arose through admixture between two divergent ancestral lineages. Initial hybridization was inferred to have occurred ∼20–60 sexual outcrossing generations ago consistent with recent, human-induced migration at the onset of intensified transcontinental trade. Species-wide heritable phenotypic variation was explained near-exclusively by strain-specific arrangements of alternating ancestry components with evidence for transgressive segregation. Reproductive compatibility between strains was likewise predicted by the degree of shared ancestry. To assess the genetic determinants of ancestry block distribution across the genome, we characterized the type, frequency, and position of structural genomic variation using nanopore and single-molecule real-time sequencing. Despite being associated with double-strand break initiation points, over 800 segregating structural variants exerted overall little influence on the introgression landscape or on reproductive compatibility between strains. In contrast, we found strong ancestry disequilibrium consistent with negative epistatic selection shaping genomic ancestry combinations during the course of hybridization. This study provides a detailed, experimentally tractable example that genomes of natural populations are mosaics reflecting different evolutionary histories. Exploiting genome-wide heterogeneity in the history of ancestral recombination and lineage-specific mutations sheds new light on the population history of S. pombe and highlights the importance of hybridization as a creative force in generating biodiversity.
28
Denton, Robert D., Ariadna E. Morales e H. Lisle Gibbs. "Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species". Evolution 72, n. 8 (25 luglio 2018): 1689–700. http://dx.doi.org/10.1111/evo.13528.
29
Morris, Jake, Joseph J. Hanly, Simon H. Martin, Steven M. Van Belleghem, Camilo Salazar, Chris D. Jiggins e Kanchon K. Dasmahapatra. "Deep Convergence, Shared Ancestry, and Evolutionary Novelty in the Genetic Architecture of Heliconius Mimicry". Genetics 216, n. 3 (3 settembre 2020): 765–80. http://dx.doi.org/10.1534/genetics.120.303611.
Abstract (sommario):
Convergent evolution can occur through different genetic mechanisms in different species. It is now clear that convergence at the genetic level is also widespread, and can be caused by either (i) parallel genetic evolution, where independently evolved convergent mutations arise in different populations or species, or (ii) collateral evolution in which shared ancestry results from either ancestral polymorphism or introgression among taxa. The adaptive radiation of Heliconius butterflies shows color pattern variation within species, as well as mimetic convergence between species. Using comparisons from across multiple hybrid zones, we use signals of shared ancestry to identify and refine multiple putative regulatory elements in Heliconius melpomene and its comimics, Heliconius elevatus and Heliconius besckei, around three known major color patterning genes: optix, WntA, and cortex. While we find that convergence between H. melpomene and H. elevatus is caused by a complex history of collateral evolution via introgression in the Amazon, convergence between these species in the Guianas appears to have evolved independently. Thus, we find adaptive convergent genetic evolution to be a key driver of regulatory changes that lead to rapid phenotypic changes. Furthermore, we uncover evidence of parallel genetic evolution at some loci around optix and WntA in H. melpomene and its distant comimic Heliconius erato. Ultimately, we show that all three of convergence, conservation, and novelty underlie the modular architecture of Heliconius color pattern mimicry.
30
Henriques, Romina, Sophie von der Heyden e Conrad A. Matthee. "When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensisandM. paradoxus)". PeerJ 4 (28 marzo 2016): e1827. http://dx.doi.org/10.7717/peerj.1827.
Abstract (sommario):
In the marine environment, an increasing number of studies have documented introgression and hybridization using genetic markers. Hybridization appears to occur preferentially between sister-species, with the probability of introgression decreasing with an increase in evolutionary divergence. Exceptions to this pattern were reported for the Cape hakes (Merluccius capensisandM. paradoxus), two distantly related Merluciidae species that diverged 3–4.2 million years ago. Yet, it is expected that contemporary hybridization between such divergent species would result in reduced hybrid fitness. We analysed 1,137 hake individuals using nine microsatellite markers and control region mtDNA data to assess the validity of the described hybridization event. To distinguish between interbreeding, ancestral polymorphism and homplasy we sequenced the flanking region of the most divergent microsatellite marker. Simulation and empirical analyses showed that hybrid identification significantly varied with the number of markers, model and approach used. Phylogenetic analyses based on the sequences of the flanking region of Mmerhk-3b, combined with the absence of mito-nuclear discordance, suggest that previously reported hybridization betweenM. paradoxusandM. capensiscannot be substantiated. Our findings highlight the need to conducta priorisimulation studies to establish the suitability of a particular set of microsatellite loci for detecting multiple hybridization events. In our example, the identification of hybrids was severely influenced by the number of loci and their variability, as well as the different models employed. More importantly, we provide quantifiable evidence showing that homoplasy mimics the effects of heterospecific crossings which can lead to the incorrect identification of hybridization.
31
Gillespie, Lynn J., Laurie L. Consaul e Susan G. Aiken. "Hybridization and the origin of the arctic grass Poa hartzii (Poaceae): evidence from morphology and chloroplast DNA restriction site data". Canadian Journal of Botany 75, n. 11 (1 novembre 1997): 1978–97. http://dx.doi.org/10.1139/b97-910.
Abstract (sommario):
The hypothesized hybrid origin of Poa hartzii Gand. (Poaceae) was investigated by analysis of morphological and molecular data. This endemic nearctic caespitose grass has been considered to be a hybrid between two of the three sympatric arctic species, Poa glauca M. Vahl, Poa arctica R. Br., and Poa abbreviata R. Br. Field observations and morphological studies indicate that Poa hartzii is a morphologically distinct apomictic species that reproduces and disperses by seed. Restriction enzyme analysis of polymerase chain reaction amplified chloroplast DNA revealed the presence in Poa hartzii of two very different haplotypes. One haplotype is identical to the dominant type found in Poa glauca, while the second is identical to the haplotype of Poa secunda J. Presl., located south of the arctic region. These results are consistent with an hypothesis of ancient hybrid origin involving Poa glauca and Poa secunda, but not Poa arclica nor Poa abbreviata. They are also consistent with an hypothesis of cytoplasmic transfer via hybridization and introgression from Poa glauca to an ancestral Poa hartzii in the Poa secunda complex. Direction of transfer is suggested by the widespread occurrence of the Poa secunda haplotype in Poa hartzii and by closer morphological similarity with Poa secunda than Poa glauca. The origin of Poa hartzii provides an excellent example of reticulate evolution and the importance of hybridization in the speciation of arctic grasses. Key words: Poa hartzii, arctic Poa, chloroplast DNA, restriction enzyme analysis, hybridization, introgression.
32
Brockhouse, C., J. A. B. Bass e N. A. Straus. "Chromocentre polymorphism in polytene chromosomes of Simulium costatum (Diptera: Simuliidae)". Genome 32, n. 4 (1 agosto 1989): 510–15. http://dx.doi.org/10.1139/g89-476.
Abstract (sommario):
The polytene chromosomes of the black fly species Simulium (Nevermannia) costatum are joined at the centromeres in a strongly heterochromatic chromocentre. Examination of the larval salivary gland chromosomes revealed two populations with a unique polymorphism for attachment to the chromocentre involving all centromeres. All three homologous pairs of chromosomes are polymorphic for centromeres that do not join to the chromocentre. Samples from one of these populations were large enough for thorough study. In this population, the attachment polymorphism is in Hardy-Weinberg equilibrium for two of the centromeres and was in the same frequency for 2 successive years of sampling. The polymorphism could be either primary, retained from an ancestral nonchromocentric state, or secondary, evolving independently or introduced via hybrid introgression. The evolution of chromocentres is discussed in the context of species in the Simulium vernum group.Key words: black fly, polytene chromosome, chromocentre, polymorphism, evolution.
33
Almeida-Silva, Diego, Leonardo Matheus Servino, Matheus Pontes-Nogueira e Ricardo J. Sawaya. "Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae)". PeerJ 12 (16 aprile 2024): e17232. http://dx.doi.org/10.7717/peerj.17232.
Abstract (sommario):
The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a “south-north” or a “north-south” direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines’ ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years.
34
Sharpe, A. G., e D. J. Lydiate. "Mapping the mosaic of ancestral genotypes in a cultivar of oilseed rape (Brassica napus) selected via pedigree breeding". Genome 46, n. 3 (1 giugno 2003): 461–68. http://dx.doi.org/10.1139/g03-031.
Abstract (sommario):
Recent oilseed rape breeding has produced low glucosinolate cultivars that yield proteinaceous meal suitable for animal feed. The low glucosinolate character was introduced into modern cultivars from Brassica napus 'Bronowski', a cultivar that is agronomically inferior in most other respects. Residual segments of 'Bronowski' genotype in modern cultivars probably cause reduced yield, poorer winter hardiness, and lower oil content. The quantity and distribution of the 'Bronowski' genotype in the modern oilseed rape cultivar Brassica napus 'Tapidor' was investigated using a segregating population derived from a cross between 'Tapidor' and its high glucosinolate progenitor. This population was analyzed with 65 informative Brassica RFLP probes and a genetic linkage map, based on the segregation at 77 polymorphic loci, was constructed. The mapping identified 15 residual segments of donor genotype in 'Tapidor', which together occupy approximately 29% of the B. napus genome. Mapping the loci that control variation for the accumulation of total seed glucosinolates in the segregating population has identified three loci that together explain >90% of the variation for this character. All of these loci are in donor segments of the 'Tapidor' genome. This result shows the extent to which conventional breeding programmes have difficulty in eliminating residual segments of donor genotype from elite material.Key words: genetic drag, glucosinolates, marker-assisted selection, RFLP, trait introgression.
35
Wirth, Anna, Jürgen Duda e Ottmar Distl. "Impact of Inbreeding and Ancestral Inbreeding on Longevity Traits in German Brown Cows". Animals 13, n. 17 (30 agosto 2023): 2765. http://dx.doi.org/10.3390/ani13172765.
Abstract (sommario):
A recent study on the population structure of the German Brown population found increasing levels of classical and ancestral inbreeding coefficients. Thus, the aim of this study was to determine the effects of inbreeding depression and purging on longevity traits using classical and ancestral inbreeding coefficients according to Kalinowski (2002) (Fa_Kal, FNew), Ballou (1997) (Fa_Bal), and Baumung (2015) (Ahc). For this purpose, uncensored data of 480,440 cows born between 1990 and 2001 were available. We analyzed 17 longevity traits, including herd life, length of productive life, number of calvings, lifetime and effective lifetime production for milk, fat, and protein yield, the survival to the 2nd, 4th, 6th, 8th, and 10th lactation number, and the culling frequencies due to infertility, or udder and foot and leg problems. Inbreeding depression was significant and negative for all traits but for culling due to udder and to foot and leg problems. When expressed in percentages of genetic standard deviations, inbreeding depression per 1% increase in inbreeding was −3.61 to −10.98%, −2.42 to −2.99%, −2.21 to −4.58%, and 5.13% for lifetime production traits, lifetime traits, survival rates, and culling due to infertility, respectively. Heterosis and recombination effects due to US Brown Swiss genes were positive and counteracted inbreeding depression. The effects of FNew were not significantly different from zero, while Fa_Kal had negative effects on lifetime and lifetime production traits. Similarly, the interaction of F with Fa_Bal was significantly negative. Thus, purging effects could not be shown for longevity traits in German Brown. A possible explanation may be seen in the breed history of the German Brown, that through the introgression of US Brown Swiss bulls ancestral inbreeding increased and longevity decreased. Our results show, that reducing a further increase in inbreeding in mating plans is advisable to prevent a further decline in longevity due to inbreeding depression, as purging effects were very unlikely in this population.
36
Osborne, Owen G., Adam Ciezarek, Trevor Wilson, Darren Crayn, Ian Hutton, William J. Baker, Colin G. N. Turnbull e Vincent Savolainen. "Speciation in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation". Molecular Biology and Evolution 36, n. 12 (18 luglio 2019): 2682–97. http://dx.doi.org/10.1093/molbev/msz166.
Abstract (sommario):
Abstract Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.
37
Gilles, André, Rémi Chappaz, Laurent Cavalli, Mathias Lörtscher e Eric Faure. "Genetic differentiation and introgression between putative subspecies of Leuciscus soufia (Teleostei: Cyprinidae) of the region of the Mediterranean Alps". Canadian Journal of Fisheries and Aquatic Sciences 55, n. 10 (1 ottobre 1998): 2341–54. http://dx.doi.org/10.1139/f98-103.
Abstract (sommario):
Because of interspecific hybridization, there is considerable controversy over the taxonomic status of many members within the family Cyprinidae. In this study, morphological and genetic characters of Leuciscus soufia, a cyprinid fish of southern France and northern Italy, were examined to verify the existence of three subspecies. Leuciscus soufia agassizi differs from Leuciscus soufia multicellus in morphology, in heterozygosity at two diagnostic allozyme loci, and by distinct mitochondrial lineages. Leuciscus s. soufia is morphologically similar to L. s. agassizi but exhibits decreased enzymatic polymorphism. However, two specimens of L. s. soufia from the Var River were found to have mitochondria of the subspecies multicellus, while four Bevera River specimens of L. s. multicellus possessed the mitochondria of the subspecies agassizi. These data argue in favour of introgressive hybridization between L. s. soufia and L. s. multicellus, rejecting the hypothesis that an ancestral population was fragmented, generating three "subspecies" that retained the original polymorphism. We propose that L. s. soufia and L. s. agassizi be regrouped within the soufia subspecies. A calibrated molecular clock dates the separation of the remaining subspecies back to the Messinian (5 million years ago). Sea level fluctuations likely mediated their secondary contact and subsequent introgressive hybridization.
38
Thanou, Evanthia, Panagiotis Kornilios, Petros Lymberakis e Adam D. Leaché. "Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake". Current Zoology 66, n. 1 (19 aprile 2019): 99–111. http://dx.doi.org/10.1093/cz/zoz018.
Abstract (sommario):
Abstract Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes, because each genome carries different inheritance properties and evolutionary characteristics. Furthermore, mitonuclear discordance may arise from ecological adaptation, historic isolation, population size changes, and sex-biased dispersal. Closely related taxa are expected to experience gene flow; however, this may not be true for insular populations or populations isolated in refugia. The four-lined snake Elaphe quatuorlineata has a fragmented distribution, separating populations of the Italian and Balkan Peninsulas, whereas several insular Aegean populations of significantly smaller body size (Cyclades island group and Skyros Island, Greece) are currently considered distinct subspecies. We constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences, aiming to detect convergence and discrepancies between biparentally and maternally inherited genomes. Population structuring, phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple sub-refugia. Where biogeographical barriers did not restrict subsequent dispersal, extensive genetic exchange occurred between mainland Balkan populations. This process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral (East Greece) and insular populations (North Cyclades and Skyros). The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 Mya. Considering their distinct morphology, insular E. quatuorlineata populations should be the future focus of an extensive sampling, especially since the mitonuclear discordance observed in this species could be related to ecological adaptations, such as the island-dwarfism phenomenon.
39
Lee, Yerim, Thomas Thieme e Hyojoong Kim. "Complex evolution in Aphis gossypii group (Hemiptera: Aphididae), evidence of primary host shift and hybridization between sympatric species". PLOS ONE 16, n. 2 (4 febbraio 2021): e0245604. http://dx.doi.org/10.1371/journal.pone.0245604.
Abstract (sommario):
Aphids provide a good model system to understand the ecological speciation concept, since the majority of the species are host-specific, and they spend their entire lifecycle on certain groups of host plants. Aphid species that apparently have wide host plant ranges have often turned out to be complexes of host-specialized biotypes. Here we investigated the various host-associated populations of the two recently diverged species, Aphis gossypii and A. rhamnicola, having multiple primary hosts, to understand the complex evolution with host-associated speciation. Using mitochondrial DNA marker and nine microsatellite loci, we reconstructed the haplotype network, and analyzed the genetic structure and relationships. Approximate Bayesian computation was also used to infer the ancestral primary host and host-associated divergence, which resulted in Rhamnus being the most ancestral host for A. gossypii and A. rhamnicola. As a result, Aphis gossypii and A. rhamnicola do not randomly use their primary and secondary host plants; rather, certain biotypes use only some secondary and specific primary hosts. Some biotypes are possibly in a diverging state through specialization to specific primary hosts. Our results also indicate that a new heteroecious race can commonly be derived from the heteroecious ancestor, showing strong evidence of ecological specialization through a primary host shift in both A. gossypii and A. rhamnicola. Interestingly, A. gossypii and A. rhamnicola shared COI haplotypes with each other, thus there is a possibility of introgression by hybridization between them by cross-sharing same primary hosts. Our results contribute to a new perspective in the study of aphid evolution by identifying complex evolutionary trends in the gossypii sensu lato complex.
40
Capy, P., A. Koga, J. R. David e D. L. Hartl. "Sequence analysis of active mariner elements in natural populations of Drosophila simulans." Genetics 130, n. 3 (1 marzo 1992): 499–506. http://dx.doi.org/10.1093/genetics/130.3.499.
Abstract (sommario):
Abstract Active and inactive mariner elements from natural and laboratory populations of Drosophila simulans were isolated and sequenced in order to assess their nucleotide variability and to compare them with previously isolated mariner elements from the sibling species Drosophila mauritiana and Drosophila sechellia. The active elements of D. simulans are very similar among themselves (average 99.7% nucleotide identity), suggesting that the level of mariner expression in different natural populations is largely determined by position effects, dosage effects and perhaps other factors. Furthermore, the D. simulans elements exhibit nucleotide identities of 98% or greater when compared with mariner elements from the sibling species. Parsimony analysis of mariner elements places active elements from the three species into separate groups and suggests that D. simulans is the species from which mariner elements in D. mauritiana and D. sechellia are most likely derived. This result strongly suggests that the ancestral form of mariner among these species was an active element. The two inactive mariner elements sequenced from D. simulans are very similar to the inactive peach element from D. mauritiana. The similarity may result from introgression between D. simulans and D. mauritiana or from selective constraints imposed by regulatory effects of inactive elements.
41
Byrne, M., e B. Hines. "Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae)". Australian Journal of Botany 52, n. 4 (2004): 459. http://dx.doi.org/10.1071/bt03117.
Abstract (sommario):
Comparative phylogeography can reveal significant historical events that have had common influences on species with similar distributions. Phylogeographic analyses of eucalypts should provide insight into the influence of historical processes, since eucalypts are a dominant component of the Australian flora. However, use of chloroplast DNA in eucalypts is complicated by sharing of haplotypes among species, which has been attributed to hybridisation and introgression, although these patterns could also be accounted for by incomplete lineage sorting of ancestral polymorphism. Phylogeographic patterns in the cp genome of E. loxophleba Benth., a widespread species throughout southern Western Australia, were investigated by using RFLP analysis. The chloroplast diversity was structured into two geographically distinct lineages and nested clade analysis inferred historical fragmentation as the major influence on the phylogeographic pattern. The divergence between the lineages and their geographic distributions were similar to geographically discrete divergent lineages that have been identified in two other unrelated species from different families in southern Western Australia. Congruence of phylogeographic patterns in the three species provides evidence to support the hypothesis of significant influence of climatic instability during the Pleistocene caused by cyclic contraction and expansion of the mesic and arid zones.
42
Whiting, James R., Josephine R. Paris, Mijke J. van der Zee, Paul J. Parsons, Detlef Weigel e Bonnie A. Fraser. "Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies". PLOS Genetics 17, n. 5 (24 maggio 2021): e1009566. http://dx.doi.org/10.1371/journal.pgen.1009566.
Abstract (sommario):
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
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Vidya, T. N. C., Raman Sukumar e Don J. Melnick. "Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants". Proceedings of the Royal Society B: Biological Sciences 276, n. 1658 (18 novembre 2008): 893–902. http://dx.doi.org/10.1098/rspb.2008.1494.
Abstract (sommario):
Recent phylogeographic studies of the endangered Asian elephant ( Elephas maximus ) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understanding the species's evolution. Previous explanations for the divergent clades include introgression of mtDNA haplotypes between ancestral species, allopatric divergence of the clades between Sri Lanka or the Sunda region and the mainland, historical trade of elephants, and retention of divergent lineages due to large population sizes. However, these studies lacked data from India and Myanmar, which host approximately 70 per cent of all extant Asian elephants. In this paper, we analyse mtDNA sequence data from 534 Asian elephants across the species's range to explain the current distribution of the two divergent clades. Based on phylogenetic reconstructions, estimates of times of origin of clades, probable ancestral areas of origin inferred from dispersal–vicariance analyses and the available fossil record, we believe both clades originated from Elephas hysudricus . This probably occurred allopatrically in different glacial refugia, the α clade in the Myanmar region and the β clade possibly in southern India–Sri Lanka, 1.6–2.1 Myr ago. Results from nested clade and dispersal–vicariance analyses indicate a subsequent isolation and independent diversification of the β clade in both Sri Lanka and the Sunda region, followed by northward expansion of the clade. We also find more recent population expansions in both clades based on mismatch distributions. We therefore suggest a contraction–expansion scenario during severe climatic oscillations of the Quaternary, with range expansions from different refugia during warmer interglacials leading to the varying geographical overlaps of the two mtDNA clades. We also demonstrate that trade in Asian elephants has not substantially altered the species's mtDNA population genetic structure.
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Boissinot, Stéphane, e Pierre Boursot. "Discordant Phylogeographic Patterns Between the Y Chromosome and Mitochondrial DNA in the House Mouse: Selection on the Y Chromosome?" Genetics 146, n. 3 (1 luglio 1997): 1019–34. http://dx.doi.org/10.1093/genetics/146.3.1019.
Abstract (sommario):
We have compared patterns of geographic variation and molecular divergence of mitochondrial DNA (mtDNA) and Y chromosome over the range of the different subspecies of Mus musculus. MtDNA was typed for 305 nucleotides in the control region, the Y chromosome for 834 base pairs (bp) in Zfy introns and 242 bp in Sry, a Zfy2 18-bp deletion, and two microsatellites. Apparent discrepancies exist between the distributions of the lineages of mtDNA and of the two major Y-chromosome lineages thus defined: some subspecies share the same mtDNA lineage but have different Y-chromosome lineages or vice versa. One microsatellite reveals a geographically clustered variation inside the distribution of each Y-chromosome lineage, showing that new Y-chromosome variants can rapidly spread locally. The two major Y-chromosome lineages have a divergence time only about one fourth of that between mtDNA lineages. Although this recent coalescence of the Y chromosomes between subspecies could partly be due to a lower ancestral polymorphism of the Y chromosome, it suggests that secondary introgression after the radiation of the subspecies might have occurred. There is evidence that the differentiation of the Y-chromosome lineages contributes to partial reproductive isolation between subspecies, and patterns of molecular evolution suggest that selection has played a role in the rapid spread across subspecies.
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Sohn, Soo-In, Senthil Kumar Thamilarasan, Subramani Pandian, Young-Ju Oh, Tae-Hun Ryu, Gang-Seob Lee e Eun-Kyoung Shin. "Interspecific Hybridization of Transgenic Brassica napus and Brassica rapa—An Overview". Genes 13, n. 8 (13 agosto 2022): 1442. http://dx.doi.org/10.3390/genes13081442.
Abstract (sommario):
In nature, interspecific hybridization occurs frequently and can contribute to the production of new species or the introgression of beneficial adaptive features between species. It has great potential in agricultural systems to boost the process of targeted crop improvement. In the advent of genetically modified (GM) crops, it has a disadvantage that it involves the transgene escaping to unintended plants, which could result in non-specific weedy crops. Several crop species in the Brassica genus have close kinship: canola (Brassica napus) is an ancestral hybrid of B. rapa and B. oleracea and mustard species such as B. juncea, B. carinata, and B. nigra share common genomes. Hence, intraspecific hybridization among the Brassica species is most common, especially between B. napus and B. rapa. In general, interspecific hybrids cause numerous genetic and phenotypic changes in the parental lines. Consequently, their fitness and reproductive ability are also highly varied. In this review, we discuss the interspecific hybridization and reciprocal hybridization studies of B. napus and B. rapa and their potential in the controlled environment. Further, we address the fate of transgenes (herbicide resistance) and their ability to transfer to their progenies or generations. This could help us to understand the environmental influence of interspecific hybrids and how to effectively manage their transgene escape in the future.
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Jensen, Axel, Frances Swift, Dorien de Vries, Robin Beck, Lukas F. K. Kuderna, Sascha Knauf, Idrissa S. Chuma et al. "Complex evolutionary history with extensive ancestral gene flow in an African primate radiation". Molecular Biology and Evolution, 21 novembre 2023. http://dx.doi.org/10.1093/molbev/msad247.
Abstract (sommario):
Abstract Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world’s largest primate radiations, we show that rampant gene flow characterizes their evolutionary history, and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by co-introgression of co-adapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role and outcomes of ancestral hybridization in a large mammalian radiation.
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Thawornwattana, Yuttapong, Fernando A. Seixas, Ziheng Yang e James Mallet. "Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies". Systematic Biology, 16 febbraio 2022. http://dx.doi.org/10.1093/sysbio/syac009.
Abstract (sommario):
Abstract Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the erato-sara clade of Heliconius butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of Heliconius telesiphe, a likely hybrid speciation origin for Heliconius hecalesia, and gene flow between the sister species Heliconius erato and Heliconius himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the MSC makes it possible to extract rich historical information of species divergence and gene flow from genomic data. [3s; bpp; gene flow; Heliconius; hybrid speciation; introgression; inversion; multispecies coalescent]
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Chen, Ze-Hui, Ya-Xi Xu, Xing-Long Xie, Dong-Feng Wang, Diana Aguilar-Gómez, Guang-Jian Liu, Xin Li et al. "Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep". Communications Biology 4, n. 1 (18 novembre 2021). http://dx.doi.org/10.1038/s42003-021-02817-4.
Abstract (sommario):
AbstractThe domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000–5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Churakov, G., A. Kuritzin, K. Chukharev, F. Zhang, F. Wünnemann, V. Ulyantsev e J. Schmitz. "A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees". Systematic Biology, 23 gennaio 2023. http://dx.doi.org/10.1093/sysbio/syac082.
Abstract (sommario):
Abstract Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for estimating the significance of retrophylogenomic data is limited by the number of possible tree topologies it can assess in one step. To improve on this, we have extended the analysis to simultaneously compare 4-lineages, enabling us to evaluate ten distinct presence/absence insertion patterns for 26 possible tree topologies plus 129 trees with different incidences of hybridization or introgression. The new tool provides statistics for cases involving multiple ancestral hybridizations/introgressions, ancestral incomplete lineage sorting, bifurcation, and polytomy. The test is embedded in a user-friendly web R-application (http : // retrogenomics.uni-muenster.de:3838/hammlet/) and is available for use by the scientific community.
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Suvorov, Anton, Celine Scornavacca, M. Stanley Fujimoto, Paul Bodily, Mark Clement, Keith A. Crandall, Michael F. Whiting, Daniel R. Schrider e Seth M. Bybee. "Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies". Systematic Biology, 29 luglio 2021. http://dx.doi.org/10.1093/sysbio/syab063.
Abstract (sommario):
Abstract Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here, we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, nonmodel insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically “intermediate” species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression. [Gene flow; Odonata; phylogenomics; reticulate evolution.]