scholarly journals The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus

2018 ◽  
Author(s):  
Adam Herman ◽  
Yaniv Brandvain ◽  
James Weagley ◽  
William R. Jeffery ◽  
Alex C. Keene ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary Process ◽  
Secondary Contact ◽  
Demographic Model ◽  
Astyanax Mexicanus ◽  
Surface Population ◽  
Whole Genomes ◽  
Repeated Evolution ◽  
Blind Cave ◽  
Genomic Regions

ABSTRACTUnderstanding the molecular basis of repeated evolved phenotypes can yield key insights into the evolutionary process. Quantifying the amount of gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture is more common between diverging lineages than previously thought. In this study, we resequenced and analyzed nearly 50 whole genomes of the Mexican tetra from three blind cave populations, two surface populations, and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our dataset. The two lineages likely diverged ∼257k generations ago, which, assuming 1 generation per year, is substantially younger than previous mitochondrial estimates of 5-7mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ∼161k - 191k generations ago. The favored demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified abundant gene flow between cave and surface fish, between caves, and between separate lineages of cave and surface fish. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite substantial gene flow with surface populations. After incorporating these new demographic estimates, our models support that selection may drive the evolution of cave-derived traits, as opposed to the classic hypothesis of disuse and drift. Finally, we show that a key QTL is enriched for genomic regions with very low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. In sum, our study shows that shared evolutionary history via gene flow must be considered in studies of independent, repeated trait evolution.

scholarly journals The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra,Astyanax mexicanus

2018 ◽  
Vol 27 (22) ◽  
pp. 4397-4416 ◽  
Author(s):  
Adam Herman ◽  
Yaniv Brandvain ◽  
James Weagley ◽  
William R. Jeffery ◽  
Alex C. Keene ◽  
...  
Keyword(s):  
Gene Flow ◽  
Astyanax Mexicanus ◽  
Repeated Evolution

scholarly journals DILS: Demographic Inferences with Linked Selection by using ABC

2020 ◽  
Author(s):  
Christelle Fraïsse ◽  
Iva Popovic ◽  
Clément Mazoyer ◽  
Bruno Spataro ◽  
Stéphane Delmotte ◽  
...  
Keyword(s):  
Gene Flow ◽  
Published Data ◽  
Demographic Model ◽  
Size Change ◽  
Genetic Patterns ◽  
And Migration ◽  
Approximate Bayesian ◽  
Genomic Regions ◽  
Analysis Platform ◽  
Linked Selection

ABSTRACTWe present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single-population or two-population datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, 2) the best genomic model to determine whether the effective size Ne and migration rate N.m are heterogeneously distributed along the genome (implying linked selection) and 3) loci in genomic regions most associated with barriers to gene flow. Also available via a web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations, and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.

scholarly journals Demographic histories and genome-wide patterns of divergence in incipient species of shorebirds

2019 ◽  
Author(s):  
Xuejing Wang ◽  
Kathryn H. Maher ◽  
Nan Zhang ◽  
Pingjia Que ◽  
Chenqing Zheng ◽  
...  
Keyword(s):  
Gene Flow ◽  
Evolutionary Biology ◽  
De Novo ◽  
Secondary Contact ◽  
Z Chromosome ◽  
Phenotypic Traits ◽  
Incipient Species ◽  
Genome Wide ◽  
Genomic Regions ◽  
Kentish Plover

AbstractUnderstanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealbatus) plovers, which differ in their phenotype, ecology and behaviour, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.

scholarly journals Why Do Centromeres Evolve So Fast: BIR Replication, Hypermutation, Transposition, and Molecular-Drive

2020 ◽  
Author(s):  
William Rice
Keyword(s):  
Rapid Evolution ◽  
Evolutionary Process ◽  
Epigenetic Mark ◽  
Replication Forks ◽  
Nucleotide Substitutions ◽  
Molecular Drive ◽  
Repeat Structure ◽  
Repeat Units ◽  
Initiation Of Replication ◽  
Genomic Regions

Centromeres are among the fastest evolving genomic regions in a diverse array of organisms. The evolutionary process driving this rapid evolution has not been unambiguously established. Here I integrate diverse information to motivate a model in which centromeres evolve rapidly because of their intrinsic molecular phenotype: they tightly bind centromeric proteins throughout the cell cycle. DNA-bound proteins have been shown to cause stalling and collapse of DNA replication forks in many genomic regions, including centromeres. Collapsed replication forks generate one-sided double strand breaks (DSBs) that are repaired by the Break-Induced Repair (BIR) pathway. Here I show why this repair is expected to generate tandem repeat structure and three key features at centromeres: i) increased nucleotide substitution mutation rates, ii) out-of- register re-initiation of replication that leads to indels spanning one or more repeat units, and iii) elevated rates of large and small transpositions within centromeres and between genomic regions. These phenotypes lead to: i) a rapid rate of nucleotide substitutions within a clade of centromeric sequences, ii) continual turnover of monomers within centromeres that fosters molecular-drift and molecular-drive, and iii) recurrent quantum leaps in centromere sequence due to the formation of mosaic monomers and new sequences transposed into non-homologous centromeres. These features are plausibly the major reason centromeres evolve so rapidly. I also speculate on how the DNA sequence of centromeres might perpetually coevolve with the protein sequence of histone CENH3 –the major epigenetic mark of centromeres.

Evidence for rapid phenotypic and behavioural shifts in a recently established cavefish population

2019 ◽  
Author(s):  
Suzanne E McGaugh ◽  
Sam Weaver ◽  
Erin N Gilbertson ◽  
Brianna Garrett ◽  
Melissa L Rudeen ◽  
...  
Keyword(s):  
Extreme Environments ◽  
Time Frame ◽  
South Texas ◽  
Astyanax Mexicanus ◽  
North East ◽  
Surface Population ◽  
Cave Population ◽  
Cave Environment ◽  
Central Texas ◽  
Recent Origin

Abstract Cave colonization offers a natural laboratory to study an extreme environmental shift, and diverse cave species from around the world often have converged on robust morphological, physiological and behavioural traits. The Mexican tetra (Astyanax mexicanus) has repeatedly colonized caves in the Sierra de El Abra and Sierra de Guatemala regions of north-east Mexico ~0.20–1 Mya, indicating an ability to adapt to the cave environment. The time frame for the evolution of these traits in any cave animal, however, is poorly understood. Astyanax mexicanus from the Río Grande in South Texas were brought to Central Texas beginning in the early 1900s and colonized underground environments. Here, we investigate whether phenotypic and behavioural differences have occurred rapidly between a surface population and a geographically proximate cave population, probably of recent origin. Fish from the cave and surface populations differ significantly in morphological traits, including coloration, lateral line expansion and dorsal fin placement. Striking behavioural shifts in aggression, feeding and wall-following have also occurred. Together, our results suggest that morphological and behavioural changes accompanying cave colonization can be established rapidly, and this system offers an exciting and unique opportunity for isolating the genetic and environmental contributions to colonization of extreme environments.

Asymmetric acoustic signal recognition led to asymmetric gene flow between two parapatric frogs

2020 ◽  
Author(s):  
Yu-Wei Hsiao ◽  
Hui-Yun Tseng ◽  
Hung Ngoc Nguyen ◽  
Si-Min Lin
Keyword(s):  
Gene Flow ◽  
Contact Region ◽  
Character Displacement ◽  
Secondary Contact ◽  
Genetic Introgression ◽  
Genetic Integrity ◽  
Signal Recognition ◽  
Reproductive Character Displacement ◽  
Reproductive Character ◽  
Behavioural Experiments

Abstract Correct discrimination between courtship signals could help to maintain genetic integrity between closely related species. However, asymmetric usage of signals might cause asymmetric gene flow across the contact zone. Buergeria choui and B. otai are sibling-species with a parapatric distribution pattern in Taiwan, having two narrow contact zones on the east and west sides of the island. Combining behavioural experiments with genome-wide RAD-seq analyses, we test whether the ability of signal recognition influences genetic introgression across their species boundary. The playback experiments show that all B. choui populations respond strongest to their own ‘cricket’ trills, while the western population of B. otai have evolved a strong level of reproductive character displacement by showing the inclusive usage of the unique ‘chicken’ signals. In contrast, the eastern B. otai population uses both ‘chicken’ and ‘cricket’ trills, and has a stronger preference for the latter. The weak reproductive character displacement in the eastern population has led to asymmetry genetic introgression from B. choui toward B. otai. Our results support the prediction that a more specialized signal-user, compared to its sibling, generalized signal-user, might have a higher probability of maintaining their genetic integrity in the secondary contact region.

scholarly journals Secondary contact followed by gene flow between divergent mitochondrial lineages of a widespread Neotropical songbird (Zonotrichia capensis)

2014 ◽  
Vol 111 (4) ◽  
pp. 863-868 ◽  
Author(s):  
Leonardo Campagna ◽  
Cecilia Kopuchian ◽  
Pablo L. Tubaro ◽  
Stephen C. Lougheed
Keyword(s):  
Gene Flow ◽  
Secondary Contact ◽  
Zonotrichia Capensis
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