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Journal articles on the topic 'Reticulate Evolutionary Event'

Author: Grafiati

Published: 4 June 2021

Last updated: 18 February 2022

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1

Hariyanto, Sucipto, Hasan Adro’i, Mahrus Ali, and Bambang Irawan. "DNA Barcoding: A Study of Guppy Fish (Poecilia reticulata) in East Java, Indonesia." Biosaintifika: Journal of Biology & Biology Education 11, no. 2 (2019): 272–78. http://dx.doi.org/10.15294/biosaintifika.v11i2.20222.

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Poecilia reticulata is a freshwater fish from the northeastern part of South America and spread widely to various countries in Asia and other continents. However, research about P. reticulate is limited even though it is a well-known fish species in Indonesia. The purpose of study was to identify the fish species of P. reticulata through DNA barcoding using the COI gene to determine the phylogenetic relationships among fish populations in East Java, Indonesia. In a present study, there were eight samples of P. reticulata from four different freshwater locations in East Java. Extraction, amplif

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Ma, Eric J., Nichola J. Hill, Justin Zabilansky, Kyle Yuan, and Jonathan A. Runstadler. "Reticulate evolution is favored in influenza niche switching." Proceedings of the National Academy of Sciences 113, no. 19 (2016): 5335–39. http://dx.doi.org/10.1073/pnas.1522921113.

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Reticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in t

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Yan, Chi, Qianni Hu, and Genlou Sun. "Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus." Genome 57, no. 2 (2014): 97–109. http://dx.doi.org/10.1139/gen-2014-0002.

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Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species tha

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VAN IERSEL, LEO, STEVEN KELK, and MATTHIAS MNICH. "UNIQUENESS, INTRACTABILITY AND EXACT ALGORITHMS: REFLECTIONS ON LEVEL-K PHYLOGENETIC NETWORKS." Journal of Bioinformatics and Computational Biology 07, no. 04 (2009): 597–623. http://dx.doi.org/10.1142/s0219720009004308.

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Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network determines how non-treelike the evolution can be, with level-0 networks being trees. We study the problem of constructing level-k phylogenetic networks from triplets, i.e. phylogenetic trees for three leaves (taxa). We give, for each k, a level-k network that is uniquely defined by its triplets. We demonstrate the applicability of this result by using it to pro

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Łabiszak, Bartosz, and Witold Wachowiak. "Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa." Forests 12, no. 4 (2021): 489. http://dx.doi.org/10.3390/f12040489.

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Speciation mechanisms, including the role of interspecific gene flow and introgression in the emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species may be challenged by past hybridization events, but at the same time, it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modeling framework, we tested the role of hybridization and introgression in the evolutionary hi

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SHENG, RUOGU, and SERGEY BEREG. "APPROXIMATING METRICS WITH PLANAR BOUNDARY-LABELED PHYLOGENETIC NETWORKS." Journal of Bioinformatics and Computational Biology 10, no. 06 (2012): 1250017. http://dx.doi.org/10.1142/s0219720012500175.

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Phylogenetic networks are useful for visualizing evolutionary relationships between species with reticulate events such as hybridizations and horizontal gene transfers. In this paper, we consider the problem of constructing undirected phylogenetic networks that (1) are planar graphs and (2) admit embeddings in the plane where the vertices labeling all taxa are on the boundary of the network. We develop a new algorithm for constructing phylogenetic networks satisfying these constraints. First, we show that only approximate networks can be constructed for some distance matrices with at least fiv

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Gradstein, Felix, Anna Waskowska, and Larisa Glinskikh. "The First 40 Million Years of Planktonic Foraminifera." Geosciences 11, no. 2 (2021): 85. http://dx.doi.org/10.3390/geosciences11020085.

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We provide a biochronology of Jurassic planktonic foramininfera, using first order linkage to ammonite and nannofossil stratigraphy and geochronology. This enigmatic and understudied group of microfossils occurred from middle Toarcian through Tithonian time, from ~180 to ~143 Ma; its origin is unknown. There are three genera: Globuligerina, Conoglobigerina and Petaloglobigerina. The genus Globuligerina, with a smooth to pustulose test surface texture appeared in Toarcian (late Early Jurassic) and Conoglobigerina, with a rough reticulate test surface texture in Oxfordian (early Late Jurassic) t

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Brooks, Daniel R., and Kaila E. Folinsbee. "Paleobiogeography: Documenting the Ebb and Flow of Evolutionary Diversification." Paleontological Society Papers 11 (October 2005): 15–44. http://dx.doi.org/10.1017/s1089332600001224.

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Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas. The second is the development of a powerful method for producing area cladograms from complex data, especially cases of reticulated area

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De Andrade, Felipe Silva, Isabelle Aquemi Haga, Johnny Sousa Ferreira, Shirlei Maria Recco-Pimentel, Luís Felipe Toledo, and Daniel Pacheco Bruschi. "A new cryptic species of Pithecopus (Anura, Phyllomedusidae) in north-eastern Brazil." European Journal of Taxonomy 723 (November 10, 2020): 108–34. http://dx.doi.org/10.5852/ejt.2020.723.1147.

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The genus of Neotropical frogs Pithecopus includes 11 species occurring east of the Andes from southern Venezuela to northern Argentina. Recent genetic approaches pointed out an unusual genetic diversity among populations from localities in north-eastern Brazil recognized as P. nordestinus. In fact, one of these studies confirmed the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus, resulting in two principal, highly divergent clades. Herein we formally describe this divergent clade as a new

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van Berkum, Peter, and Jeffry J. Fuhrmann. "Evidence from Internally Transcribed Spacer Sequence Analysis of Soybean Strains that Extant Bradyrhizobium spp. Are Likely the Products of Reticulate Evolutionary Events." Applied and Environmental Microbiology 75, no. 1 (2008): 78–82. http://dx.doi.org/10.1128/aem.01408-08.

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ABSTRACT The internally transcribed spacer (ITS) sequences of several members within each of 17 soybean bradyrhizobial serogroups were determined to establish whether the regions within all members of each serogroup were identical. The rationale was to provide a sequence-based alternative to serology. The objective also was to link the extensive older literature on soybean symbiosis based on serology with ITS sequence data for more recent isolates from both soybean and other legumes nodulated by rhizobia within the genus Bradyrhizobium. With the exception of serogroup 31 and 110 strains, seque

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Rose, Jeffrey P., Cassio A. P. Toledo, Emily Moriarty Lemmon, Alan R. Lemmon, and Kenneth J. Sytsma. "Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal." Systematic Biology 70, no. 1 (2020): 162–80. http://dx.doi.org/10.1093/sysbio/syaa049.

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Abstract Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordanc

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Zhang, Wei, Brian X. Leon-Ricardo, Bas van Schooten, et al. "Comparative Transcriptomics Provides Insights into Reticulate and Adaptive Evolution of a Butterfly Radiation." Genome Biology and Evolution 11, no. 10 (2019): 2963–75. http://dx.doi.org/10.1093/gbe/evz202.

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Abstract Butterfly eyes are complex organs that are composed of a diversity of proteins and they play a central role in visual signaling and ultimately, speciation, and adaptation. Here, we utilized the whole eye transcriptome to obtain a more holistic view of the evolution of the butterfly eye while accounting for speciation events that co-occur with ancient hybridization. We sequenced and assembled transcriptomes from adult female eyes of eight species representing all major clades of the Heliconius genus and an additional outgroup species, Dryas iulia. We identified 4,042 orthologous genes

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Xing, Henry, Steven W. Kembel, and Vladimir Makarenkov. "Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks." Bioinformatics 36, no. 9 (2020): 2740–49. http://dx.doi.org/10.1093/bioinformatics/btaa043.

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Abstract Motivation Phylogenetic trees and the methods for their analysis have played a key role in many evolutionary, ecological and bioinformatics studies. Alternatively, phylogenetic networks have been widely used to analyze and represent complex reticulate evolutionary processes which cannot be adequately studied using traditional phylogenetic methods. These processes include, among others, hybridization, horizontal gene transfer, and genetic recombination. Nowadays, sequence similarity and genome similarity networks have become an efficient tool for community analysis of large molecular d

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KOZŁOWSKA, ANNA, DENIS BATES, JAN ZALASIEWICZ, and SIGITAS RADZEVIČIUS. "Evolutionary significance of the retiolitine Gothograptus (Graptolithina) with four new species from the Silurian of the East European Platform (Baltica), Poland and Lithuania." Zootaxa 4568, no. 3 (2019): 435. http://dx.doi.org/10.11646/zootaxa.4568.3.2.

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Gothograptid retiolitines were distinctive in being one of the very few graptolite groups to thrive through the late Wenlock extinction event that killed off most graptoloid species, and their distinctive construction may have been a factor in this success amid environmental adversity. New and rich material from two localities in Poland and five localities in Lithuania contains Gothograptus nassa, Gothograptus obtectus and four new species. The detailed morphology and reconstruction of the tubarium shows its specific features, different from other lundgreni Biozone retiolitines. The tubarium i

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Götesson, Arvid, Jerry S. Marshall, David A. Jones, and Adrienne R. Hardham. "Characterization and Evolutionary Analysis of a Large Polygalacturonase Gene Family in the Oomycete Plant Pathogen Phytophthora cinnamomi." Molecular Plant-Microbe Interactions® 15, no. 9 (2002): 907–21. http://dx.doi.org/10.1094/mpmi.2002.15.9.907.

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Polygalacturonases (PGs) are secreted by fungal pathogens during saprophytic and parasitic growth, and their degradation of pectin in the plant cell wall is believed to play a major role in tissue invasion and maceration. In this study, PG activity was demonstrated in culture filtrates of the oo-mycete plant pathogen, Phytophthora cinnamomi. A P. cinnamomi pg gene fragment amplified using degenerate primers based on conserved regions in fungal and plant PGs was used to isolate 17 complete P. cinnamomi pg genes and pseudogenes from a genomic library and partial sequence for another two genes. G

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Rabier, Charles-Elie, Vincent Berry, Marnus Stoltz, et al. "On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo." PLOS Computational Biology 17, no. 9 (2021): e1008380. http://dx.doi.org/10.1371/journal.pcbi.1008380.

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For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hyb

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Stefanović, Saša, and Mihai Costea. "Reticulate evolution in the parasitic genus Cuscuta (Convolvulaceae): over and over againThis paper is one of a selection of papers published in the Special Issue on Systematics Research." Botany 86, no. 8 (2008): 791–808. http://dx.doi.org/10.1139/b08-033.

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The frequency and relative importance of hybridization in plants has been an area of intense debate. Although this evolutionary phenomenon has received considerable attention from plant biologists, there are no well-supported cases of reticulate evolution involving parasitic plants, to date. Recent molecular phylogenetic analyses revealed that the subgenus Grammica , the largest and most diverse group of the stem-parasitic genus Cuscuta (dodder), consists of 15 major clades. We describe here five cases of strongly supported discordance between phylogenies derived from plastid and nuclear data,

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Mitchell, David J., Regina Vega-Trejo, and Alexander Kotrschal. "Experimental translocations to low predation lead to non-parallel increases in relative brain size." Biology Letters 16, no. 1 (2020): 20190654. http://dx.doi.org/10.1098/rsbl.2019.0654.

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Predation is a near ubiquitous factor of nature and a powerful selective force on prey. Moreover, it has recently emerged as an important driver in the evolution of brain anatomy, though population comparisons show ambiguous results with considerable unexplained variation. Here, we test the reproducibility of reduced predation on evolutionary trajectories of brain evolution. We make use of an introduction experiment, whereby guppies ( Poecilia reticulata ) from a single high predation stream were introduced to four low predation streams. After 8–9 years of natural selection in the wild and two

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Bastide, Paul, Claudia Solís-Lemus, Ricardo Kriebel, K. William Sparks, and Cécile Ané. "Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations." Systematic Biology 67, no. 5 (2018): 800–820. http://dx.doi.org/10.1093/sysbio/syy033.

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Abstract The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species’ traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to network

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Charlesworth, Deborah, Yexin Zhang, Roberta Bergero, Chay Graham, Jim Gardner, and Lengxob Yong. "Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species." Molecular Biology and Evolution 37, no. 12 (2020): 3550–62. http://dx.doi.org/10.1093/molbev/msaa187.

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Abstract Genetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, s

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Boulila, Moncef. "Molecular Evolutionary Characteristics of the 2019 Novel Coronavirus (SARS-CoV-2) Contracted by Tunisian Citizens: Comparison and Relationship to Other Human and Animal Coronaviruses Based on Spike Glycoprotein-Coding Gene Sequences Analysis." International Journal of Coronaviruses 2, no. 4 (2021): 9–44. http://dx.doi.org/10.14302/issn.2692-1537.ijcv-21-3756.

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In contributing to the initiative to address the COVID-19 pandemic and in order to enhance the knowledge on driving forces shaping the evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (isolated from Tunisian patients), a comparison in relation to other coronaviruses infecting humans (SARS-CoV-1, MERS-CoV, HCoV/229E, HCoV/NL63, HCoV/OC43, and HCoV/HKU1) as well as animals (SARS-CoVs in tiger, bats, civet, pangolin, bovine, and MERS-CoV in dromedary/camel), was conducted. In-depth analysis was carried out involving 115 sequences of spike glycoprotein-coding gene extracte

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Brochmann, C. "Polyploid evolution in arctic-alpine Draba (Brassicaceae)." Sommerfeltia 4, s4 (1992): 1–44. http://dx.doi.org/10.2478/som-1992-0003.

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Abstract The mainly arctic-alpine genus Draba is well known for its complex morphological and chromosomal vanation. This paper reviews a larger study of Nordic Draba, aimed to provide insights into evolutionary processes that confound taxonomic relationships in the genus. The populations analyzed were referred to 16 currently recognized species of the sections Draba (petals white), Chrysodraba (petals yellow), andDrabella (petals yellow), and investigated using enzyme electrophoresis, restriction site analysis of cpDNA and rDNA, and analysis of chromosome numbers, artificial and natural hybrid

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Abreu, Narjara Lopes de, Ruy José Válka Alves, Sérgio Ricardo Sodré Cardoso, et al. "The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)." PeerJ 6 (June 15, 2018): e4916. http://dx.doi.org/10.7717/peerj.4916.

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BackgroundCurrent evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found inPolystachyaHook. (Orchidaceae), a genus that stands out due to sever

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Andriessen, Melissa, Madeleen Struwig, and Stefan J. Siebert. "Pollen morphology of Prototulbaghia Vosa: A comparative palynological study of the Southern African Alliaceae." Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie 32, no. 1 (2013). http://dx.doi.org/10.4102/satnt.v32i1.389.

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The Southern African Alliaceae Borkh. is represented by four genera (Allium L., Nothoscordum Kunth, Tulbaghia L. and Prototulbaghia Vosa) and 28 species. The pollen morphology of the endangered monotypic genus Prototulbaghia has not been described before. A comparative study of the pollen morphology of Prototulbaghia siebertii Vosa, Nothoscordum borbonicum Kunth, Tulbaghia simmleri P.Beauv. and T. violaceae Harv. is presented in this article. Scanning electron microscopy, as well as light microscopy, were used to examine the pollen. The pollen morphology of the species can be described as perp

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Gross, Elizabeth, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long, and Yukihiro Murakami. "Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes." Journal of Mathematical Biology 83, no. 3 (2021). http://dx.doi.org/10.1007/s00285-021-01653-8.

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AbstractPhylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model-based methods for reconstructing phylogenetic networks. For these methods to be consistent, the network parameter needs to be identifiable from data generated under the model. Here, we show that the semi-directed network parameter of a triangle-free,

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Debray, Kevin, Marie-Christine Le Paslier, Aurélie Bérard, et al. "Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa." Systematic Biology, July 30, 2021. http://dx.doi.org/10.1093/sysbio/syab064.

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Abstract Reticulation, caused by hybridization and allopolyploidization, is considered an important and frequent phenomenon in the evolution of numerous plant lineages. Although both processes represent important driving forces of evolution, they are mostly ignored in phylogenetic studies involving a large number of species. Indeed only a scattering of methods exists to recover a comprehensive reticulated evolutionary history for a broad taxon sampling. Among these methods, comparisons of topologies obtained from plastid markers with those from a few nuclear sequences are favored, even though

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Liu, Qing, Lei Lin, Xiangying Zhou, Paul M. Peterson, and Jun Wen. "Unraveling the evolutionary dynamics of ancient and recent polyploidization events in Avena (Poaceae)." Scientific Reports 7, no. 1 (2017). http://dx.doi.org/10.1038/srep41944.

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Abstract Understanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Aven

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Nauheimer, Lars, Lujing Cui, Charles Clarke, Darren M. Crayn, Greg Bourke, and Katharina Nargar. "Genome skimming provides well resolved plastid and nuclear phylogenies, showing patterns of deep reticulate evolution in the tropical carnivorous plant genus Nepenthes (Caryophyllales)." Australian Systematic Botany, 2019. http://dx.doi.org/10.1071/sb18057.

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Nepenthes is a genus of carnivorous plants consisting of ~160 species that are distributed in the paleotropics. Molecular systematics has so far not been able to resolve evolutionary relationships of most species because of the limited genetic divergence in previous studies. In the present study, we used a genome-skimming approach to infer phylogenetic relationships on the basis of 81 plastid genes and the highly repetitive rRNA (external transcribed spacer (ETS)–26S) for 39 accessions representing 34 species from eight sections. Maximum-likelihood analysis and Bayesian inference were performe

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Barrón, Maite G., Christophe Paupy, Nil Rahola, et al. "A new species in the major malaria vector complex sheds light on reticulated species evolution." Scientific Reports 9, no. 1 (2019). http://dx.doi.org/10.1038/s41598-019-49065-5.

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Abstract Complexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studied Anopheles fontenillei sp.n., a new species in the Anopheles gambiae complex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, with Anopheles gambiae and Anopheles coluzzii, of genes directly involved in v

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Zinner, Dietmar, Linn F. Groeneveld, Christina Keller, and Christian Roos. "Mitochondrial phylogeography of baboons (Papiospp.) – Indication for introgressive hybridization?" BMC Evolutionary Biology 9, no. 1 (2009). http://dx.doi.org/10.1186/1471-2148-9-83.

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Abstract Background Baboons of the genus Papio are distributed over wide ranges of Africa and even colonized parts of the Arabian Peninsula. Traditionally, five phenotypically distinct species are recognized, but recent molecular studies were not able to resolve their phylogenetic relationships. Moreover, these studies revealed para- and polyphyletic (hereafter paraphyletic) mitochondrial clades for baboons from eastern Africa, and it was hypothesized that introgressive hybridization might have contributed substantially to their evolutionary history. To further elucidate the phylogenetic relat

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Guo, Xinyi, Terezie Mandáková, Karolína Trachtová, Barış Özüdoğru, Jianquan Liu, and Martin A. Lysak. "Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe." Molecular Biology and Evolution, December 17, 2020. http://dx.doi.org/10.1093/molbev/msaa327.

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Abstract Pervasive hybridization and whole genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. While frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in

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Linck, Ethan, Kevin Epperly, Paul Van Els, et al. "Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex." Systematic Biology, April 23, 2019. http://dx.doi.org/10.1093/sysbio/syz027.

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AbstractIncomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely

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Giraud, Delphine, Oscar Lima, Mathieu Rousseau-Gueutin, Armel Salmon, and Malika Aïnouche. "Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)." Frontiers in Genetics 12 (March 25, 2021). http://dx.doi.org/10.3389/fgene.2021.589160.

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Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploidSpartinaspecies (Poaceae, Chloridoideae) that successively diverged in the last 6–10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century

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