scholarly journals Positive selection and comparative molecular evolution of reproductive proteins from New Zealand tree weta (Orthoptera, Hemideina)

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0188147 ◽  
Author(s):  
Victoria G. Twort ◽  
Alice B. Dennis ◽  
Duckchul Park ◽  
Kathryn F. Lomas ◽  
Richard D. Newcomb ◽  
...  
Keyword(s):  
New Zealand ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Reproductive Proteins ◽  
Tree Weta

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

scholarly journals Molecular Evolution of Cytochrome c Oxidase Subunit IV: Evidence for Positive Selection in Simian Primates

1997 ◽  
Vol 44 (5) ◽  
pp. 477-491 ◽  
Author(s):  
Wei Wu ◽  
Morris Goodman ◽  
Margaret I. Lomax ◽  
Lawrence I. Grossman
Keyword(s):  
Molecular Evolution ◽  
Cytochrome C ◽  
Positive Selection ◽  
Cytochrome C Oxidase ◽  
Oxidase Subunit

scholarly journals Molecular Evolution of GYPC: Evidence for Recent Structural Innovation and Positive Selection in Humans

2009 ◽  
Vol 26 (12) ◽  
pp. 2679-2687 ◽  
Author(s):  
Jason A. Wilder ◽  
Elizabeth K. Hewett ◽  
Meredith E. Gansner
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Structural Innovation

Persisting in a glaciated landscape: Pleistocene microrefugia evidenced by the tree wētā Hemideina maori in central South Island, New Zealand

2020 ◽  
Vol 47 (11) ◽  
pp. 2518-2531
Author(s):  
Keith J. King ◽  
Debbie M. Lewis ◽  
Jonathan M. Waters ◽  
Graham P. Wallis
Keyword(s):  
New Zealand ◽  
Tree Weta ◽  
Central South

A phylogenetic analysis of New Zealand giant and tree weta (Orthoptera : Anostostomatidae : Deinacrida and Hemideina) using morphological and genetic characters

2001 ◽  
Vol 15 (1) ◽  
pp. 1 ◽  
Author(s):  
Mary Morgan-Richards ◽  
George W. Gibbs
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Sound Production ◽  
Morphological Characters ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Life Styles ◽  
Multiple Origins ◽  
Tree Weta ◽  
Genetic Characters

A phylogenetic analysis of New Zealand weta from the sub-family Deinacridinae is presented. Eighteen species were studied using 27 genetic characters (allozyme and cytogenetic) and 25 morphological characters. The combined data set produced a phylogenetic hypothesis with twelve well-supported nodes. Despite the great diversity of habitats and life styles exhibited by the eleven Deinacrida White species a well-supported bipartition separates them from the seven Hemideina Walker species. Six of the Hemideina species formed a monophyletic clade, with respect to H. broughi (Buller). Evolution of stridulatory ridges used for sound production in both defence and intraspecific communication appears to have occurred at least twice. Adaptation to the recent New Zealand alpine environment has also had multiple origins. Biogeographic interpretations from the phylogenetic hypothesis are discussed.

scholarly journals Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion

2015 ◽  
Vol 11 (7) ◽  
pp. 20150349 ◽  
Author(s):  
Alexander Van Nynatten ◽  
Devin Bloom ◽  
Belinda S. W. Chang ◽  
Nathan R. Lovejoy
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Visual Pigment ◽  
Large Scale ◽  
Marine Species ◽  
South American ◽  
Sequence Analyses ◽  
Freshwater Habitats ◽  
Varying Environments ◽  
Visual Pigment Evolution

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.

scholarly journals Rapid molecular evolution across amniotes of the IIS/TOR network

2015 ◽  
Vol 112 (22) ◽  
pp. 7055-7060 ◽  
Author(s):  
Suzanne E. McGaugh ◽  
Anne M. Bronikowski ◽  
Chih-Horng Kuo ◽  
Dawn M. Reding ◽  
Elizabeth A. Addis ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Insulin Receptor ◽  
Metabolic Diseases ◽  
Vital Role ◽  
Evolutionary Rates ◽  
Evolutionary Analysis ◽  
Binding Surface ◽  
Tor Network ◽  
Positively Selected Sites

The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.

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