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Genome Diversity of Adaptation and Speciation
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Genome Diversity of Adaptation and Speciation

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 35263

Special Issue Editors

Dr. Taras K Oleksyk

E-Mail Website
Guest Editor
Oakland University, Rochester, MI, USA
Interests: evolution, comparative genomics, environmental toxicology, genetic epidemiology, adaptation, speciation and disease, admixture, population genetics, candidate disease genes, genome assembly and analysis; selection scans
Dr. Aleksey Komissarov

E-Mail Website
Guest Editor
ITMO University, St. Petersburg, Russia
Interests: comparative genomics, genome graphs for working with human and animal genomic data, non-coding, satellite DNA, SINE repeats, repetitive DNA, reproductive isolation, incipient speciation, eukaryotic genomes, prokaryotic genomes
Dr. Fabia U. Battistuzzi

E-Mail Website
Guest Editor
Department of Biological Sciences, Oakland University, 118 Library Dr., Rochester, MI 48309, USA
Interests: microbial evolution; early life evolution; phylogenetic tools; tempo and mode of evolution; speciation patterns; timing of the origin of species; genomic innovations; adaptations; speciation events

Special Issue Information

Dear Colleagues,

Uncovering the underlying mechanisms of adaptation and speciation is perhaps the most significant quest of evolutionary science ever since the introduction of the concept in the “Origin of Species.” Darwin recognized that for evolution to take place, individuals in populations had to be different from each other, and that these differences become the substrate of the divergence into different species. However, the science of his time was extremely limited in the type of diversity that could be documented. As we entered the genomics era, the situation has changed drastically: every time genome data is released for a new species, or a new sequencing technology or analytic tool is introduced, the scope of opportunities expands for exploring inter- and intra-specific variation. These new opportunities allow us to document and study the process of adaptation and speciation in a whole new way.

The process of speciation is a key aspect of understanding biodiversity. Explaining how species evolve is an essential step to reconstructing past and current biodiversity, and predict its future. The availability of the genome data provides a unique window into speciation mechanisms with virtually infinite amounts of information. At the same time, recent computational developments are supplying an unprecedented power to simulations, analytic and reconstruction algorithms. Given these new opportunities, past evolutionary events that left important clues about the history of species can now be documented, interpreted, and explained. At the same time, these developments are raising new and challenging questions that require improved understanding of the underlying molecular mechanisms, evolutionary concepts, and factors to be addressed.  

Whether at the level of the Tree of Life or within specific clades, the quest that evolutionary biologists now face is how to interpret the information embedded within genomes to explain biodiversity. This quest can be tackled with many different approaches that are rooted in the optimization and development of computational and analytical tools to interpret data. With a new arsenal of genomic data, bioinformatic and analytical tools, we are given an opportunity to answer pressing questions (i) on the predictions of evolutionary theory in the face of the environmental change, (ii) how mechanisms of adaptation and long-term survival are linked to the concepts of species diversity, genetic load, and extinction, and (iii) how evolutionary models can be refined to better represent the complexities of genome changes.  All these questions have strong implications for conservation biology, ecosystem balance, and the genomics changes associated with the birth and death of species.

We invite you to contribute to this Special Issue, which will showcase original contributions to the advancement in the genomic diversity of adaptation and speciation. 

Dr. Taras K Oleksyk
Dr. Aleksey Komissarov
Prof. Dr. Fabia U. Battistuzzi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Mutation
  • Selection
  • Drift
  • Gene flow
  • Extinction
  • Molecular clocks
  • Conservation
  • Sequencing
  • Synteny
  • Phylogeny
  • Tree of Life

Published Papers (9 papers)

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Editorial

Jump to: Research

4 pages, 206 KiB  
Editorial
Genomics of Adaptation and Speciation
by Walter W. Wolfsberger, Fabia U. Battistuzzi and Taras K. Oleksyk
Genes 2022, 13(7), 1187; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13071187 - 01 Jul 2022
Cited by 1 | Viewed by 1641
Abstract
The availability of genome data provides a unique window into speciation mechanisms with virtually infinite amounts of information, providing a pathway for a better understanding of major evolutionary questions [...] Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)

Research

Jump to: Editorial

17 pages, 3879 KiB  
Article
Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology
by Azamat Totikov, Andrey Tomarovsky, Dmitry Prokopov, Aliya Yakupova, Tatiana Bulyonkova, Lorena Derezanin, Dmitry Rasskazov, Walter W. Wolfsberger, Klaus-Peter Koepfli, Taras K. Oleksyk and Sergei Kliver
Genes 2021, 12(9), 1336; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091336 - 28 Aug 2021
Cited by 10 | Viewed by 4171
Abstract
Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, [...] Read more.
Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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29 pages, 3958 KiB  
Article
Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles
by Sofiia Kolchanova, Alexey Komissarov, Sergei Kliver, Anyi Mazo-Vargas, Yashira Afanador, Jafet Velez-Valentín, Ricardo Valentín de la Rosa, Stephanie Castro-Marquez, Israel Rivera-Colon, Audrey J. Majeske, Walter W. Wolfsberger, Taylor Hains, André Corvelo, Juan-Carlos Martinez-Cruzado, Travis C. Glenn, Orlando Robinson, Klaus-Peter Koepfli and Taras K. Oleksyk
Genes 2021, 12(4), 608; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12040608 - 20 Apr 2021
Cited by 3 | Viewed by 7280
Abstract
Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, [...] Read more.
Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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13 pages, 3695 KiB  
Article
Hybridogenesis in the Water Frogs from Western Russian Territory: Intrapopulation Variation in Genome Elimination
by Ikuo Miura, Vladimir Vershinin, Svetlana Vershinina, Andrei Lebedinskii, Alexander Trofimov, Ivan Sitnikov and Michihiko Ito
Genes 2021, 12(2), 244; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020244 - 08 Feb 2021
Cited by 5 | Viewed by 2257
Abstract
Hybridogenesis in an interspecific hybrid frog is a coupling mechanism in the gametogenic cell line that eliminates the genome of one parental species with endoduplication of the remaining genome of the other parental species. It has been intensively investigated in the edible frog [...] Read more.
Hybridogenesis in an interspecific hybrid frog is a coupling mechanism in the gametogenic cell line that eliminates the genome of one parental species with endoduplication of the remaining genome of the other parental species. It has been intensively investigated in the edible frog Pelophylax kl. esculentus (RL), a natural hybrid between the marsh frog P. ridibundus (RR) and the pool frog P. lessonae (LL). However, the genetic mechanisms involved remain unclear. Here, we investigated the water frogs in the western Russian territory. In three of the four populations, we genetically identified 16 RL frogs living sympatrically with the parental LL species, or with both parental species. In addition, two populations contained genome introgression with another species, P. bedriagae (BB) (a close relative of RR). In the gonads of 13 RL frogs, the L genome was eliminated, producing gametes of R (or R combined with the B genome). In sharp contrast, one RL male eliminated the L or R genome, producing both R and L sperm. We detected a variation in genome elimination within a population. Based on the genetic backgrounds of RL frogs, we hypothesize that the introgression of the B genome resulted in the change in choosing a genome to be eliminated. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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16 pages, 2420 KiB  
Article
Chromosomal Polymorphism and Speciation: The Case of the Genus Mazama (Cetartiodactyla; Cervidae)
by David Javier Galindo, Gabriela Siqueira Martins, Miluse Vozdova, Halina Cernohorska, Svatava Kubickova, Agda Maria Bernegossi, Dita Kadlcikova, Jiri Rubes and José Maurício Barbanti Duarte
Genes 2021, 12(2), 165; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020165 - 26 Jan 2021
Cited by 15 | Viewed by 2911
Abstract
Chromosomal polymorphism plays a major role in speciation processes in mammals with high rates of karyotypic evolution, as observed in the family Cervidae. One remarkable example is the genus Mazama that comprises wide inter- and intra-specific chromosomal variability. To evaluate the impact of [...] Read more.
Chromosomal polymorphism plays a major role in speciation processes in mammals with high rates of karyotypic evolution, as observed in the family Cervidae. One remarkable example is the genus Mazama that comprises wide inter- and intra-specific chromosomal variability. To evaluate the impact of chromosomal polymorphisms as reproductive barriers within the genus Mazama, inter-specific hybrids between Mazama gouazoubira and Mazama nemorivaga (MGO × MNE) and intra-specific hybrids between cytotypes of Mazama americana (MAM) differing by a tandem (TF) or centric fusion (Robertsonian translocations—RT) were evaluated. MGO × MNE hybrid fertility was evaluated by the seminal quality and testicular histology. MAM hybrids estimation of the meiotic segregation products was performed by sperm-FISH analysis. MGO × MNE hybrids analyses showed different degrees of fertility reduction, from severe subfertility to complete sterility. Regarding MAM, RT, and TF carriers showed a mean value for alternate segregation rate of 97.74%, and 67.23%, and adjacent segregation rate of 1.80%, and 29.07%, respectively. Our results suggested an efficient post-zygotic barrier represented by severe fertility reduction for MGO × MNE and MAM with heterozygous TF. Nevertheless, RT did not show a severe effect on the reproductive fitness in MAM. Our data support the validity of MGO and MNE as different species and reveals cryptic species within MAM. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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28 pages, 3643 KiB  
Article
Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir
by Amanda R. De La Torre, Benjamin Wilhite, Daniela Puiu, John Bradley St. Clair, Marc W. Crepeau, Steven L. Salzberg, Charles H. Langley, Brian Allen and David B. Neale
Genes 2021, 12(1), 110; https://doi.org/10.3390/genes12010110 - 18 Jan 2021
Cited by 15 | Viewed by 5100
Abstract
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among [...] Read more.
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species’ predictions under climate change. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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25 pages, 9725 KiB  
Article
Karyotype Evolution in 10 Pinniped Species: Variability of Heterochromatin versus High Conservatism of Euchromatin as Revealed by Comparative Molecular Cytogenetics
by Violetta R. Beklemisheva, Polina L. Perelman, Natalya A. Lemskaya, Anastasia A. Proskuryakova, Natalya A. Serdyukova, Vladimir N. Burkanov, Maksim B. Gorshunov, Oliver Ryder, Mary Thompson, Gina Lento, Stephen J. O’Brien and Alexander S. Graphodatsky
Genes 2020, 11(12), 1485; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121485 - 10 Dec 2020
Cited by 6 | Viewed by 3087
Abstract
Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, [...] Read more.
Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, Erignathus barbatus), and Otariidae (Eumetopias jubatus, Callorhinus ursinus, Phocarctos hookeri, and Arctocephalus forsteri). Structural and functional chromosomal features were assessed with telomere repeat and ribosomal-DNA probes and by CBG (C-bands revealed by barium hydroxide treatment followed by Giemsa staining) and CDAG (Chromomycin A3-DAPI after G-banding) methods. We demonstrated diversity of heterochromatin among pinniped karyotypes in terms of localization, size, and nucleotide composition. For the first time, an intrachromosomal rearrangement common for Otariidae and Odobenidae was revealed. We postulate that the order of evolutionarily conserved segments in the analyzed pinnipeds is the same as the order proposed for the ancestral Carnivora karyotype (2n = 38). The evolution of conserved genomes of pinnipeds has been accompanied by few fusion events (less than one rearrangement per 10 million years) and by novel intrachromosomal changes including the emergence of new centromeres and pericentric inversion/centromere repositioning. The observed interspecific diversity of pinniped karyotypes driven by constitutive heterochromatin variation likely has played an important role in karyotype evolution of pinnipeds, thereby contributing to the differences of pinnipeds’ chromosome sets. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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17 pages, 2225 KiB  
Article
Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia
by Sarita Mahtani-Williams, William Fulton, Amelie Desvars-Larrive, Sara Lado, Jean Pierre Elbers, Bálint Halpern, Dávid Herczeg, Gergely Babocsay, Boris Lauš, Zoltán Tamás Nagy, Daniel Jablonski, Oleg Kukushkin, Pablo Orozco-terWengel, Judit Vörös and Pamela Anna Burger
Genes 2020, 11(10), 1218; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101218 - 17 Oct 2020
Cited by 5 | Viewed by 5815
Abstract
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We [...] Read more.
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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14 pages, 2152 KiB  
Article
Multiple Isolated Transcription Factors Act as Switches and Contribute to Species Uniqueness
by Xin-Wei Zhao and Hirohisa Kishino
Genes 2020, 11(10), 1148; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101148 - 29 Sep 2020
Cited by 3 | Viewed by 1700
Abstract
Mammals have variable numbers (1300–2000) of transcription factors (TFs), but the reasons for this large variation are unclear. To investigate general TF patterns, we de novo identified 156,906 TFs from 96 mammalian species. We identified more than 500 human isolated TFs that are [...] Read more.
Mammals have variable numbers (1300–2000) of transcription factors (TFs), but the reasons for this large variation are unclear. To investigate general TF patterns, we de novo identified 156,906 TFs from 96 mammalian species. We identified more than 500 human isolated TFs that are rarely reported in human TF-to-TF networks. Mutations in the genes of these TFs were less lethal than those of connected TFs. Consequently, these isolated TFs are more tolerant of changes and have become unique during speciation. They may also serve as a source of variation for TF evolution. Reconciliation of TF-family phylogenetic trees with a mammalian species tree revealed an average of 37.8% TF gains and 15.0% TF losses over 177 million years, which implies that isolated TFs are pervasive in mammals. Compared with non-TF interacting genes, TF-interacting genes have unique TF profiles and have higher expression levels in mice than in humans. Different expression levels of the same TF-interacting gene contribute to species-specific phenotypes. Formation and loss of isolated TFs enabling unique TF profiles may provide variable switches that adjust divergent expression profiles of target genes to generate species-specific phenotypes, thereby making species unique. Full article
(This article belongs to the Special Issue Genome Diversity of Adaptation and Speciation)
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