scholarly journals The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

2018 ◽  
Vol 35 (4) ◽  
pp. 792-806 ◽  
Author(s):  
Susanne P Pfeifer ◽  
Stefan Laurent ◽  
Vitor C Sousa ◽  
Catherine R Linnen ◽  
Matthieu Foll ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Evolutionary History ◽  
Deer Mice ◽  
The Face ◽  
History Of

scholarly journals The evolutionary history of Nebraska deer mice: local adaptation in the face of strong gene flow

2017 ◽  
Author(s):  
Susanne P. Pfeifer ◽  
Stefan Laurent ◽  
Vitor C. Sousa ◽  
Catherine R. Linnen ◽  
Matthieu Foll ◽  
...  
Keyword(s):  
Gene Flow ◽  
Theoretical Perspective ◽  
Deer Mice ◽  
Nebraska Sand Hills ◽  
Lack Of Information ◽  
Cryptic Coloration ◽  
Local Soil ◽  
Sand Hills ◽  
The Face ◽  
History Of

ABSTRACTThe interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from eleven sites along a transect spanning the Sand Hills at 660,000 SNPs across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.

A History of Niue

2021 ◽  
Author(s):  
◽  
David McDowell
Keyword(s):  
Local Adaptation ◽  
The South ◽  
The Face ◽  
History Of ◽  
Coral Rock ◽  
In The Beginning ◽  
Supernatural Agency

<p>"In the beginning, this island now called Niue was nothing but coral rock (he punga)... There came a god, an aitu, from the south, a god sailed to and fro on the face of the waters. He looked down here and saw far below on the ocean the white punga rock. He let down his hook and hauled the punga up to the surface, and lo! there stood and island!" - John Lupo. The genesis of Niue remains conjectural. The Polynesian calls in a supernatural agency, an aitu from the south, to explain the emergence of the multiplication of corals and algae from the waters of the mid-Pacific to form an island two-hundred feet high, but the story of the god and his line and hook is a local adaptation of a very ancient and widespread fable, as are in varying degrees other Polynesian versions of the birth of the island, Cook advanced two further possibilities in 1777 when he speculated: "Has this Island been raised by an earthquake? Or has the sea receded from it?"</p>

scholarly journals The evolutionary history of bears is characterized by gene flow across species

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Vikas Kumar ◽  
Fritjof Lammers ◽  
Tobias Bidon ◽  
Markus Pfenninger ◽  
Lydia Kolter ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
History Of

scholarly journals Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

2018 ◽  
Author(s):  
Gang Li ◽  
Henrique V. Figueiro ◽  
Eduardo Eizirik ◽  
William J. Murphy
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Selective Sweeps ◽  
A Genome ◽  
Chromosome Recombination ◽  
History Of ◽  
Lineage Divergence ◽  
Recurrent Patterns ◽  
Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

scholarly journals Evolution of Larval Segment Position across 12DrosophilaSpecies

2019 ◽  
Author(s):  
Gizem Kalay ◽  
Joel Atallah ◽  
Noemie C. Sierra ◽  
Austin M. Tang ◽  
Amanda E. Crofton ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Local Control ◽  
Abdominal Segment ◽  
Evolutionary History ◽  
Phenotypic Change ◽  
Rates Of Change ◽  
First Instar ◽  
The Face ◽  
History Of ◽  
Developmental Traits

AbstractMany developmental traits that are critical to the survival of the organism are also robust. These robust traits are resistant to phenotypic change in the face of variation. This presents a challenge to evolution. In this paper, we asked whether and how a well-established robust trait,Drosophilasegment patterning, changed over the evolutionary history of the genus. We compared segment position scaled to body length at the first-instar larval stage among 12Drosophilaspecies. We found that relative segment position has changed many times across the phylogeny. Changes were frequent, but primarily small in magnitude. Phylogenetic analysis demonstrated that rates of change in segment position are variable along theDrosophilaphylogenetic tree, and that these changes can occur in short evolutionary timescales. Correlation between position shifts of segments decreased as the distance between two segments increased, suggesting local control of segment position. The posterior-most abdominal segment showed the highest magnitude of change on average, had the highest rate of evolution between species, and appeared to be evolving more independently as compared to the rest of the segments. This segment was exceptionally elongated in the cactophilic species in our dataset, raising questions as to whether this change may be adaptive.

scholarly journals The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

2021 ◽  
Author(s):  
Stéphane Peyrégne ◽  
Janet Kelso ◽  
Benjamin Marco Peter ◽  
Svante Pääbo
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Modern Human ◽  
Modern Humans ◽  
Ancestral Gene ◽  
Cytoskeletal Structure ◽  
Spindle Apparatus ◽  
History Of ◽  
Segregation Of Chromosomes

Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.

A History of Niue

2021 ◽  
Author(s):  
◽  
David McDowell
Keyword(s):  
Local Adaptation ◽  
The South ◽  
The Face ◽  
History Of ◽  
Coral Rock ◽  
In The Beginning ◽  
Supernatural Agency

<p>"In the beginning, this island now called Niue was nothing but coral rock (he punga)... There came a god, an aitu, from the south, a god sailed to and fro on the face of the waters. He looked down here and saw far below on the ocean the white punga rock. He let down his hook and hauled the punga up to the surface, and lo! there stood and island!" - John Lupo. The genesis of Niue remains conjectural. The Polynesian calls in a supernatural agency, an aitu from the south, to explain the emergence of the multiplication of corals and algae from the waters of the mid-Pacific to form an island two-hundred feet high, but the story of the god and his line and hook is a local adaptation of a very ancient and widespread fable, as are in varying degrees other Polynesian versions of the birth of the island, Cook advanced two further possibilities in 1777 when he speculated: "Has this Island been raised by an earthquake? Or has the sea receded from it?"</p>

scholarly journals Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae

mBio ◽  
2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Pierre Gladieux ◽  
Bradford Condon ◽  
Sebastien Ravel ◽  
Darren Soanes ◽  
Joao Leodato Nunes Maciel ◽  
...  
Keyword(s):  
Gene Flow ◽  
South America ◽  
Magnaporthe Oryzae ◽  
Rice Blast ◽  
Evolutionary History ◽  
Blast Disease ◽  
Whole Genome ◽  
Disease Emergence ◽  
Wheat Blast ◽  
History Of

ABSTRACT Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae. These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen. IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

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