scholarly journals Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations

2020 ◽  
Vol 37 (10) ◽  
pp. 2825-2837 ◽  
Author(s):  
Paolo Franchini ◽  
Andreas F Kautt ◽  
Alexander Nater ◽  
Gloria Antonini ◽  
Riccardo Castiglia ◽  
...  
Keyword(s):  
House Mouse ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Large Scale ◽  
Chromosomal Races ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Demographic Patterns ◽  
Aeolian Archipelago

Abstract Chromosomal evolution is widely considered to be an important driver of speciation, as karyotypic reorganization can bring about the establishment of reproductive barriers between incipient species. One textbook example for genetic mechanisms of speciation are large-scale chromosomal rearrangements such as Robertsonian (Rb) fusions, a common class of structural variants that can drastically change the recombination landscape by suppressing crossing-over and influence gene expression by altering regulatory networks. Here, we explore the population structure and demographic patterns of a well-known house mouse Rb system in the Aeolian archipelago in Southern Italy using genome-wide data. By analyzing chromosomal regions characterized by different levels of recombination, we trace the evolutionary history of a set of Rb chromosomes occurring in different geographical locations and test whether chromosomal fusions have a single shared origin or occurred multiple times. Using a combination of phylogenetic and population genetic approaches, we find support for multiple, independent origins of three focal Rb chromosomes. The elucidation of the demographic patterns of the mouse populations within the Aeolian archipelago shows that an interplay between fixation of newly formed Rb chromosomes and hybridization events has contributed to shaping their current karyotypic distribution. Overall, our results illustrate that chromosome structure is much more dynamic than anticipated and emphasize the importance of large-scale chromosomal translocations in speciation.

scholarly journals A genome‐wide linkage map for the house sparrow ( Passer domesticus ) provides insights into the evolutionary history of the avian genome

2020 ◽  
Vol 20 (2) ◽  
pp. 544-559 ◽  
Author(s):  
Ingerid J. Hagen ◽  
Sigbjørn Lien ◽  
Anna M. Billing ◽  
Tore O. Elgvin ◽  
Cassandra Trier ◽  
...  
Keyword(s):  
Linkage Map ◽  
Evolutionary History ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Genome Wide ◽  
A Genome ◽  
Avian Genome ◽  
History Of

scholarly journals Extreme Genomic Makeover: Evolutionary History of Maternally-transmitted Clam Symbionts

2020 ◽  
Author(s):  
M Perez ◽  
C Breusing ◽  
B Angers ◽  
YJ Won ◽  
CR Young
Keyword(s):  
Genome Evolution ◽  
Evolutionary History ◽  
Free Living ◽  
Genome Wide ◽  
A Genome ◽  
Chemosynthetic Bacteria ◽  
History Of ◽  
Vesicomyid Clam ◽  
Do So

AbstractGiven their recent switch to a vertically-transmitted intracellular lifestyle, the chemosynthetic bacteria associated with deep-sea vesicomyid clams are an excellent model system to study the processes underlying reductive genome evolution. In this study, we provide the first estimates of the relative contributions of drift, recombination and selection in shaping the ongoing reductive genome evolution in these symbionts. To do so, we compared the genomes of endosymbionts associated with 11 vesicomyid clam species to that of closely related free-living bacteria and their respective hosts’ mitochondria. Our investigation confirmed that neutral evolutionary processes were the dominant driver of reductive genome evolution in this group and highlighted the important role of horizontal gene transfer in mitigating genome erosion. Finally, a genome-wide screen for episodic positive selection across the symbiont phylogeny revealed the pervasive role of selective processes in maintaining symbiont functional integrity.

scholarly journals The essential genome of the crenarchaeal model Sulfolobus islandicus

2018 ◽  
Author(s):  
Changyi Zhang ◽  
Alex P. R. Phillips ◽  
Rebecca L. Wipfler ◽  
Gary J. Olsen ◽  
Rachel J. Whitaker
Keyword(s):  
Cell Biology ◽  
Evolutionary History ◽  
Experimental System ◽  
Essential Genes ◽  
Future Research ◽  
Sulfolobus Islandicus ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Gene Knockouts

AbstractSulfolobus islandicus is a model experimental system in the TACK superphylum of the Archaea, a key lineage in the evolutionary history of cell biology. Here we report a genome-wide identification of the repertoire of genes essential to S. islandicus growth in culture. We confirm previous targeted gene knockouts, uncover the non-essentiality of functions assumed to be essential to the Sulfolobus cell, including the proteinaceous S-layer, and highlight key essential genes whose functions are yet to be determined. Phyletic distributions illustrate the potential transitions that have occurred during the evolution of this contemporary archaeal cell and highlight the sets of genes that may have been associated with each transition. We use this comparative context as a lens to focus future research on archaea-specific uncharacterized essential genes for which future functional data would provide valuable insights into the evolutionary history of the contemporary cell.

scholarly journals A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids

2011 ◽  
Vol 21 (8) ◽  
pp. 1294-1305 ◽  
Author(s):  
Bridgett M. vonHoldt ◽  
John P. Pollinger ◽  
Dent A. Earl ◽  
James C. Knowles ◽  
Adam R. Boyko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Wide Perspective

scholarly journals Genetic legacy of state centralization in the Kuba Kingdom of the Democratic Republic of the Congo

2018 ◽  
Vol 116 (2) ◽  
pp. 593-598 ◽  
Author(s):  
Lucy van Dorp ◽  
Sara Lowes ◽  
Jonathan L. Weigel ◽  
Naser Ansari-Pour ◽  
Saioa López ◽  
...  
Keyword(s):  
Large Scale ◽  
Democratic Republic ◽  
Central Province ◽  
Genome Wide ◽  
Genetic Patterns ◽  
Genetic Impact ◽  
Genome Wide Data ◽  
Republic Of The Congo ◽  
History Of ◽  
State Centralization

Few phenomena have had as profound or long-lasting consequences in human history as the emergence of large-scale centralized states in the place of smaller scale and more local societies. This study examines a fundamental, and yet unexplored, consequence of state formation: its genetic legacy. We studied the genetic impact of state centralization during the formation of the eminent precolonial Kuba Kingdom of the Democratic Republic of the Congo (DRC) in the 17th century. We analyzed genome-wide data from over 690 individuals sampled from 27 different ethnic groups from the Kasai Central Province of the DRC. By comparing genetic patterns in the present-day Kuba, whose ancestors were part of the Kuba Kingdom, with those in neighboring non-Kuba groups, we show that the Kuba today are more genetically diverse and more similar to other groups in the region than expected, consistent with the historical unification of distinct subgroups during state centralization. We also found evidence of genetic mixing dating to the time of the Kingdom at its most prominent. Using this unique dataset, we characterize the genetic history of the Kasai Central Province and describe the historic late wave of migrations into the region that contributed to a Bantu-like ancestry component found across large parts of Africa today. Taken together, we show the power of genetics to evidence events of sociopolitical importance and highlight how DNA can be used to better understand the behaviors of both people and institutions in the past.

scholarly journals Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation

2005 ◽  
Vol preprint (2007) ◽  
pp. e137
Author(s):  
Joti Giordano ◽  
Yongchao Ge ◽  
Yevgeniy Gelfand ◽  
Gyorgy Abrusan ◽  
Gary Benson ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genome Wide ◽  
History Of

Phenotypic Screen and Transcriptomics Approach Complement Each Other in Functional Genomics of Defensive Stink Gland Physiology

2021 ◽  
Author(s):  
Sabrina Lehmann ◽  
Bibi Atika ◽  
Daniela Grossmann ◽  
Christian Schmitt-Engel ◽  
Nadi Strohlein ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Large Scale ◽  
Reverse Genetics ◽  
Expression Profiles ◽  
Forward Genetics ◽  
Large Set ◽  
Knock Down ◽  
Genome Wide ◽  
Phenotypic Screen ◽  
A Genome

Abstract Background Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before. Results Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum. This gene set is the result of a large-scale systematic phenotypic screen using a reverse genetics strategy based on RNA interference applied in a genome-wide forward genetics manner. In this first-pass screen, 130 genes were identified, of which 69 genes could be confirmed to cause knock-down gland phenotypes, which vary from necrotic tissue and irregular reservoir size to irregular color or separation of the secreted gland compounds. The knock-down of 13 genes caused specifically a strong reduction of para-benzoquinones, suggesting a specific function in the synthesis of these toxic compounds. Only 14 of the 69 confirmed gland genes are differentially overexpressed in stink gland tissue and thus could have been detected in a transcriptome-based analysis. Moreover, of the 29 previously transcriptomics-identified genes causing a gland phenotype, only one gene was recognized by this phenotypic screen despite the fact that 13 of them were covered by the screen. Conclusion Our results indicate the importance of combining diverse and independent methodologies to identify genes necessary for the function of a certain biological tissue, as the different approaches do not deliver redundant results but rather complement each other. The presented phenotypic screen together with a transcriptomics approach are now providing a set of close to hundred genes important for odoriferous defensive stink gland physiology in beetles.

scholarly journals A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

2019 ◽  
Vol 7 (6) ◽  
pp. 161 ◽  
Author(s):  
Ming-Hsin Tsai ◽  
Yen-Yi Liu ◽  
Von-Wun Soo ◽  
Chih-Chieh Chen
Keyword(s):  
Microbial Diversity ◽  
Large Scale ◽  
Gene Selection ◽  
Marker Gene ◽  
Genome Comparison ◽  
Marker Genes ◽  
Species Classification ◽  
Genome Wide ◽  
A Genome ◽  
Comparison Approach

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

scholarly journals A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

2019 ◽  
Vol 11 (8) ◽  
pp. 2078-2098 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Jingjing Jin ◽  
Rajani Sarojam ◽  
Srinivasan Ramachandran
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Family Members ◽  
Terpene Synthase ◽  
Limited Information ◽  
Terpene Synthases ◽  
Genome Wide ◽  
A Genome ◽  
Family Expansion ◽  
Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

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