scholarly journals Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

2018 ◽  
Author(s):  
Ethan Linck ◽  
Kevin Epperly ◽  
Paul van Els ◽  
Garth M. Spellman ◽  
Robert W. Bryson ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Reticulate Evolution ◽  
Extensive Study ◽  
Biased Sampling ◽  
Evolutionary Patterns ◽  
Multispecies Coalescent ◽  
Genome Wide ◽  
Evolutionary Distinctiveness ◽  
The Face ◽  
Mexico Border

Incomplete 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 / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of a widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or sibling) lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

scholarly journals Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex

2019 ◽  
Author(s):  
Ethan Linck ◽  
Kevin Epperly ◽  
Paul Van Els ◽  
Garth M Spellman ◽  
Robert W Bryson ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Reticulate Evolution ◽  
Extensive Study ◽  
Biased Sampling ◽  
Evolutionary Patterns ◽  
Multispecies Coalescent ◽  
Genome Wide ◽  
Evolutionary Distinctiveness ◽  
The Face ◽  
Mexico Border

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 cryptic (or “sibling”) lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group’s range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E.difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

scholarly journals Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

2021 ◽  
Vol 12 ◽  
Author(s):  
Nur Shuhadah Mohd Saad ◽  
Anita A. Severn-Ellis ◽  
Aneeta Pradhan ◽  
David Edwards ◽  
Jacqueline Batley
Keyword(s):  
Climate Change ◽  
Reverse Genetics ◽  
Agronomic Traits ◽  
Crop Evolution ◽  
Breeding Cycle ◽  
World Population ◽  
Genome Wide ◽  
The Face ◽  
Selection Of ◽  
The Way

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

scholarly journals Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Stephen J. Mondo ◽  
Diego Javier Jiménez ◽  
Ronald E. Hector ◽  
Anna Lipzen ◽  
Mi Yan ◽  
...  
Keyword(s):  
Wheat Straw ◽  
Purifying Selection ◽  
Reticulate Evolution ◽  
Phylogenomic Analysis ◽  
Lignocellulolytic Enzymes ◽  
Genome Expansion ◽  
Lack Of Information ◽  
Genome Wide ◽  
A Genome ◽  
Furanic Compounds

Abstract Background Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). Results The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. Conclusions We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and “eco-enzymology” of lignocellulolytic Coniochaeta species.

scholarly journals Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution

2019 ◽  
Vol 5 (6) ◽  
pp. eaau3648 ◽  
Author(s):  
Jason Hill ◽  
Pasi Rastas ◽  
Emily A. Hornett ◽  
Ramprasad Neethiraj ◽  
Nathan Clark ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Evolution ◽  
Chromosome Structure ◽  
Holocentric Chromosomes ◽  
Chromosome Counts ◽  
Pieris Napi ◽  
Haploid Chromosome Number ◽  
Genome Wide ◽  
The Face ◽  
Chromosome Level

Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.

scholarly journals The BPP program for species tree estimation and species delimitation

2015 ◽  
Vol 61 (5) ◽  
pp. 854-865 ◽  
Author(s):  
Ziheng Yang
Keyword(s):  
Species Delimitation ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Species Tree ◽  
Joint Analysis ◽  
Coalescent Model ◽  
Species Phylogeny ◽  
Multispecies Coalescent ◽  
Tree Estimation ◽  
Nuclear Loci

Abstract This paper provides an overview and a tutorial of the BPP program, which is a Bayesian MCMC program for analyzing multi-locus genomic sequence data under the multispecies coalescent model. An example dataset of five nuclear loci from the East Asian brown frogs is used to illustrate four different analyses, including estimation of species divergence times and population size parameters under the multispecies coalescent model on a fixed species phylogeny (A00), species tree estimation when the assignment and species delimitation are fixed (A01), species delimitation using a fixed guide tree (A10), and joint species delimitation and species-tree estimation or unguided species delimitation (A11). For the joint analysis (A11), two new priors are introduced, which assign uniform probabilities for the different numbers of delimited species, which may be useful when assignment, species delimitation, and species phylogeny are all inferred in one joint analysis. The paper ends with a discussion of the assumptions, the strengths and weaknesses of the BPP analysis.

scholarly journals Predicting the Landscape of Recombination Using Deep Learning

2020 ◽  
Vol 37 (6) ◽  
pp. 1790-1808 ◽  
Author(s):  
Jeffrey R Adrion ◽  
Jared G Galloway ◽  
Andrew D Kern
Keyword(s):  
Deep Learning ◽  
Evolutionary History ◽  
Model Misspecification ◽  
Natural Populations ◽  
High Accuracy ◽  
Demographic Model ◽  
Recombination Rates ◽  
Genome Wide ◽  
A Genome ◽  
The Face

Abstract Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERNN), a deep learning method for estimating a genome-wide recombination map that is accurate even with small numbers of pooled or individually sequenced genomes. Rather than use summaries of linkage disequilibrium as its input, ReLERNN takes columns from a genotype alignment, which are then modeled as a sequence across the genome using a recurrent neural network. We demonstrate that ReLERNN improves accuracy and reduces bias relative to existing methods and maintains high accuracy in the face of demographic model misspecification, missing genotype calls, and genome inaccessibility. We apply ReLERNN to natural populations of African Drosophila melanogaster and show that genome-wide recombination landscapes, although largely correlated among populations, exhibit important population-specific differences. Lastly, we connect the inferred patterns of recombination with the frequencies of major inversions segregating in natural Drosophila populations.

Neurotic Fantasy: The Third Temple As a Metaphor in the Contemporary Israeli Art of Nira Pereg and Yael Bartana

2019 ◽  
Vol 6 (3-4) ◽  
pp. 238-251
Author(s):  
Sigal Barkai
Keyword(s):  
Extensive Study ◽  
Israeli Society ◽  
The Political ◽  
Historical Discourse ◽  
Religious Rituals ◽  
Jewish Art ◽  
Political Reality ◽  
The Face ◽  
Temple Mount ◽  
The Temple

In the political reality of Israel, some symbols lie at the heart of the political, religious, national, and historical discourse that characterize the peoples and cultures living on the Israeli-Palestinian soil. Among these, the Temple Mount in Jerusalem is one of the most complex and conflictual symbols. The multiple religious claims to the Temple Mount—Jewish, Christian, and Muslim—are the subject of extensive study, but this article focuses on their reflection in contemporary Israeli art. In traditional Jewish art, the visual representations of the Temple or of Jews praying nearby expressed the longing of the Jews for generations to return to the Mount. In contrast, Yael Bartana and Nira Pereg view the multiple socio-political currents and religious rituals surrounding the Temple Mount as a reflection of the internal public debate regarding the face of the Israeli society today. This article discusses the contribution of their visual art to a conscious and aware discourse about the Israeli society and the underground currents that shape its contemporary identity. The analysis of their work tracks a “politics of aesthetics”—interpretation of the images within a socio-political context—and draws upon Israeli sociology, art history, and visual culture. In-depth personal interviews with the artists also inform the analysis.

scholarly journals The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

2019 ◽  
Vol 286 (1911) ◽  
pp. 20191311 ◽  
Author(s):  
Vlad Dincă ◽  
Kyung Min Lee ◽  
Roger Vila ◽  
Marko Mutanen
Keyword(s):  
Species Delimitation ◽  
Dna Analysis ◽  
Restriction Site ◽  
Significant Proportion ◽  
Ongoing Debate ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Mtdna Lineages ◽  
Eastern Kazakhstan

The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise F ST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.

scholarly journals Population Genomic Evidence Reveals Subtle Patterns of Differentiation in the Trophically Polymorphic Cuatro Ciénegas Cichlid, Herichthys minckleyi

2019 ◽  
Vol 110 (3) ◽  
pp. 361-369 ◽  
Author(s):  
Katherine L Bell ◽  
Chris C Nice ◽  
Darrin Hulsey
Keyword(s):  
Gene Flow ◽  
Biological Diversity ◽  
Molecular Genetic ◽  
Molecular Ecology ◽  
Cichlid Fish ◽  
Genome Wide ◽  
A Genome ◽  
The Face ◽  
Or Gene ◽  
Herichthys Minckleyi

Abstract In recent decades, an increased understanding of molecular ecology has led to a reinterpretation of the role of gene flow during the evolution of reproductive isolation and biological novelty. For example, even in the face of ongoing gene flow strong selection may maintain divergent polymorphisms, or gene flow may introduce novel biological diversity via hybridization and introgression from a divergent species. Herein, we elucidate the evolutionary history and genomic basis of a trophically polymorphic trait in a species of cichlid fish, Herichthys minckleyi. We explored genetic variation at 3 hierarchical levels; between H. minckleyi (n = 69) and a closely related species Herichthys cyanoguttatus (n = 10), between H. minckleyi individuals from 2 geographic locations, and finally between individuals with alternate morphotypes at both a genome-wide and locus-specific scale. We found limited support for the hypothesis that the H. minckleyi polymorphism is the result of ongoing hybridization between the 2 species. Within H. minckleyi we found evidence of geographic genetic structure, and using traditional population genetic analyses found that individuals of alternate morphotypes within a pool appear to be panmictic. However, when we used a locus-specific approach to examine the relationship between multi-locus genotype, tooth size, and geographic sampling, we found the first evidence for molecular genetic differences between the H. minckleyi morphotypes.

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