Role of epibenthic resource opportunities in the parallel evolution of lake whitefish species pairs (Coregonus sp.)

Climatic and geological changes across time are presumed to have shaped the rich biodiversity of tropical regions. However, the impact climatic drying and subsequent tropical rainforest contraction had on speciation has been controversial because of inconsistent palaeoecological and genetic data. Despite the strong interest in examining the role of climatic change on speciation in the Neotropics there has been few comparative studies, particularly, those that include non-rainforest taxa. We used bird species that inhabit humid or dry habitats that dispersed across the Panamanian Isthmus to characterize temporal and spatial patterns of speciation across this barrier. Here, we show that these two assemblages of birds exhibit temporally different speciation time patterns that supports multiple cycles of speciation. Evidence for these cycles is further corroborated by the finding that both assemblages consist of ‘young’ and ‘old’ species, despite dry habitat species pairs being geographically more distant than pairs of humid habitat species. The matrix of humid and dry habitats in the tropics not only allows for the maintenance of high species richness, but additionally this study suggests that these environments may have promoted speciation. We conclude that differentially expanding and contracting distributions of dry and humid habitats was probably an important contributor to speciation in the tropics.

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Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

10.1101/2022.01.15.476463 ◽

2022 ◽

Author(s):

Claire M&eacuterot ◽

Kristina S R Stenl&oslashkk ◽

Clare Venney ◽

Martin Laporte ◽

Michel Moser ◽

...

Keyword(s):

Transposable Elements ◽

Genetic Architecture ◽

Large Fraction ◽

Sympatric Species ◽

Secondary Contact ◽

Species Differentiation ◽

Lake Whitefish ◽

Structural Variants ◽

Species Pairs ◽

Long Read

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

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Novel syntaxin gene sequences from Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system

Journal of Cell Science ◽

10.1242/jcs.115.8.1635 ◽

2002 ◽

Vol 115 (8) ◽

pp. 1635-1642 ◽

Cited By ~ 3

Author(s):

Joel B. Dacks ◽

W. Ford Doolittle

Keyword(s):

Protein Interactions ◽

Calcium Binding ◽

Parallel Evolution ◽

Membrane System ◽

Compartment System ◽

Eukaryotic Diversity ◽

Wide Range ◽

Membrane Compartment ◽

Isoleucine Residue

SNAP receptors or SNARES are crucial components of the intracellular membrane system of eukaryotes. The syntaxin family of SNAREs have been shown to have roles in neurotransmission, vesicular transport, membrane fusion and even internal membrane compartment reconstruction. While syntaxins and SNAREs in general have been well characterized in mammalian and yeast models, little is known about their overall distribution across eukaryotic diversity or about the evolution of the syntaxin gene family. By combining bioinformatic,molecular biological and phylogenetic approaches, we demonstrate that various syntaxin homologs are not only present in `eukaryotic crown taxa' but across a wide range of eukaryotic lineages. The alignment of evolutionarily diverse syntaxin paralogs shows that an isoleucine residue critical to nSec1—syntaxin complex formation and the characteristic syntaxin glutamine residue are nearly universally conserved, implying a general functional importance for these residues. Other identified functional residues involved in botulism toxicity and calcium-binding-protein interactions are also compared. The presence of Golgi-related syntaxins in the intestinal parasite Giardia intestinalis provides further evidence for a cryptic Golgi in this `adictyosomal' taxon, and another likely case of secondary reduction in this parasite. The phylogeny of syntaxins shows a number of nested duplications, including a case of parallel evolution in the plasma membrane-associated syntaxins, and ancestral duplications in the other syntaxin paralogs. These speak to ancient events in the evolution of the syntaxin system and emphasize the universal role of the syntaxins in the eukaryotic intracellular compartment system.

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The evolutionary history of Nothofagus (Nothofagaceae)

Australian Systematic Botany ◽

10.1071/sb9930111 ◽

1993 ◽

Vol 6 (2) ◽

pp. 111 ◽

Cited By ~ 63

Author(s):

RS Hill ◽

GJ Jordan

Keyword(s):

Parallel Evolution ◽

Cladistic Analysis ◽

Long Distance ◽

Interesting Insight ◽

Extant Species ◽

Singular Event ◽

History Of ◽

Morphological Differences ◽

The Relationship

A cladistic analysis of Nothofagus is presented. Comparison of potential outgroups (Fagus and Betulaceae) suggests that Fagus is most satisfactory, but clear morphological differences between it and Nothofagus support the placement of the latter in the monogeneric family Nothofagaceae. The cladistic analysis supports the four subgenera and four extant pollen groups proposed in the most recent revisions and is consistent with the extensive fossil record, although not especially supported by it. The evolution of the deciduous or evergreen habit. so long considered a singular event of importance in Nothofagus, probably occurred several times, and is an example of parallel evolution. Resolution within subgenera is not high in most cases, but subgenus Lophozonia offers a particularly interesting insight into the relationship among extant species and the role of rare long distance dispersal across significant ocean barriers in Nothofagus biogeography. More data are required to refine the phylogeny.

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Unusual Steroid Constituents from the Tropical Starfish Leiaster sp

Natural Product Communications ◽

10.1177/1934578x1601100914 ◽

2016 ◽

Vol 11 (9) ◽

pp. 1934578X1601100

Author(s):

Timofey V. Malyarenko ◽

Alla A. Kicha ◽

Natalia V. Ivanchina ◽

Anatoly I. Kalinovsky ◽

Pavel S. Dmitrenok ◽

...

Keyword(s):

Bile Acid ◽

Sodium Salt ◽

Parallel Evolution ◽

Steroid Glycoside ◽

First Report ◽

Acid Sodium Salt ◽

Steroid Glycosides ◽

First Time ◽

Primary Bile Acid

Two polar steroid compounds, taurochenodeoxycholic acid sodium salt (1) and a rare cyclic steroid glycoside luzonicoside A (2), were isolated from the tropical starfish Leiaster sp. and identified by extensive NMR and ESIMS techniques. The isolation of primary bile acid 1 is the first report from a representative of the class Asteroidea and on the whole in invertebrates. Its presence confirms the hypothesis about the digestive role of some polar steroids in starfish and possibly demonstrates the parallel evolution of fat emulsifying agents in vertebrates and some starfish. Compound 2 was also obtained from starfish belonging to this genus for the first time. This finding indicates that cyclic steroid glycosides are more widely distributed in starfish than the two species of the genus Echinaster from which they were isolated earlier.

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Parallel adaptation of rabbit populations to myxoma virus

Science ◽

10.1126/science.aau7285 ◽

2019 ◽

Vol 363 (6433) ◽

pp. 1319-1326 ◽

Cited By ~ 38

Author(s):

Joel M. Alves ◽

Miguel Carneiro ◽

Jade Y. Cheng ◽

Ana Lemos de Matos ◽

Masmudur M. Rahman ◽

...

Keyword(s):

Genetic Basis ◽

Parallel Evolution ◽

Rapid Evolution ◽

Antiviral Effect ◽

Myxoma Virus ◽

European Rabbit ◽

The United Kingdom ◽

Before And After ◽

Evolution Of Resistance

In the 1950s the myxoma virus was released into European rabbit populations in Australia and Europe, decimating populations and resulting in the rapid evolution of resistance. We investigated the genetic basis of resistance by comparing the exomes of rabbits collected before and after the pandemic. We found a strong pattern of parallel evolution, with selection on standing genetic variation favoring the same alleles in Australia, France, and the United Kingdom. Many of these changes occurred in immunity-related genes, supporting a polygenic basis of resistance. We experimentally validated the role of several genes in viral replication and showed that selection acting on an interferon protein has increased the protein’s antiviral effect.

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