scholarly journals Fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish

2018 ◽  
Author(s):  
Alice F. Shanfelter ◽  
Sophie L. Archambeault ◽  
Michael A. White
Keyword(s):  
Gasterosteus Aculeatus ◽  
Demographic History ◽  
Strong Association ◽  
Threespine Stickleback ◽  
Open Chromatin ◽  
Fine Scale ◽  
Recombination Rates ◽  
Transcription Start Sites ◽  
Marine Population ◽  
Recombination Hotspots

AbstractMeiotic recombination is a highly conserved process that has profound effects on genome evolution. Recombination rates can vary drastically at a fine-scale across genomes and often localize to small recombination “hotspots” with highly elevated rates surrounded by regions with little recombination. Hotspot targeting to specific genomic locations is variable across species. In some mammals, hotspots have divergent landscapes between closely related species which is directed by the binding of the rapidly evolving protein, PRDM9. In many species outside of mammals, hotspots are generally conserved and tend to localize to regions with open chromatin such as transcription start sites. It remains unclear if the location of recombination hotspots diverge in taxa outside of mammals. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using an LD-based approach, we found recombination rates varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had divergent landscapes between stickleback populations, where only ~15% were shared, though part of this divergence could be due to demographic history. Additionally, we did not detect a strong association of PRDM9 with recombination hotspots in threespine stickleback fish. Our results suggest fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish and argue for additional molecular characterization to verify the extent of the divergence.

scholarly journals Stable recombination hotspots in birds

2015 ◽  
Author(s):  
Sonal Singhal ◽  
Ellen Leffler ◽  
Keerthi Sannareddy ◽  
Isaac Turner ◽  
Oliver Venn ◽  
...  
Keyword(s):  
Critical Role ◽  
Cpg Islands ◽  
Natural Populations ◽  
Bird Species ◽  
Indirect Evidence ◽  
Fine Scale ◽  
Recombination Rates ◽  
Transcription Start Sites ◽  
Recombination Hotspots ◽  
Meiotic Recombination Hotspots

Although the DNA-binding protein PRDM9 plays a critical role in the specification of meiotic recombination hotspots in mice and apes, it appears to be absent from many vertebrate species, including birds. To learn about the determinants of fine-scale recombination rates and their evolution in natural populations lacking PRDM9, we inferred fine-scale recombination maps from population resequencing data for two bird species, the zebra finchTaeniopygia guttata, and the long-tailed finch,Poephila acuticauda, whose divergence is on par with that between human and chimpanzee. We find that both bird species have hotspots, and these are enriched near CpG islands and transcription start sites. In sharp contrast to what is seen in mice and apes, the hotspots are largely shared between the two species, with indirect evidence of conservation extending across bird species tens of millions of years diverged. These observations link the evolution of hotspots to their genetic architecture, suggesting that in the absence of PRDM9 binding specificity, accessibility of the genome to the cellular recombination machinery, particularly around functional genomic elements, both enables increased recombination and constrains its evolution.

scholarly journals Diversity and sexual dimorphism in the head lateral line system in North Sea populations of threespine sticklebacks, Gasterosteus aculeatus (Teleostei: Gasterosteidae)

Zoomorphology ◽  
2020 ◽  
Author(s):  
Harald Ahnelt ◽  
David Ramler ◽  
Maria Ø. Madsen ◽  
Lasse F. Jensen ◽  
Sonja Windhager
Keyword(s):  
Sexual Dimorphism ◽  
North Sea ◽  
Lateral Line ◽  
Gasterosteus Aculeatus ◽  
Sensory System ◽  
Threespine Stickleback ◽  
Lateral Line System ◽  
Line System ◽  
Marine Population ◽  
Threespine Sticklebacks

AbstractThe mechanosensory lateral line of fishes is a flow sensing system and supports a number of behaviors, e.g. prey detection, schooling or position holding in water currents. Differences in the neuromast pattern of this sensory system reflect adaptation to divergent ecological constraints. The threespine stickleback, Gasterosteus aculeatus, is known for its ecological plasticity resulting in three major ecotypes, a marine type, a migrating anadromous type and a resident freshwater type. We provide the first comparative study of the pattern of the head lateral line system of North Sea populations representing these three ecotypes including a brackish spawning population. We found no distinct difference in the pattern of the head lateral line system between the three ecotypes but significant differences in neuromast numbers. The anadromous and the brackish populations had distinctly less neuromasts than their freshwater and marine conspecifics. This difference in neuromast number between marine and anadromous threespine stickleback points to differences in swimming behavior. We also found sexual dimorphism in neuromast number with males having more neuromasts than females in the anadromous, brackish and the freshwater populations. But no such dimorphism occurred in the marine population. Our results suggest that the head lateral line of the three ecotypes is under divergent hydrodynamic constraints. Additionally, sexual dimorphism points to divergent niche partitioning of males and females in the anadromous and freshwater but not in the marine populations. Our findings imply careful sampling as an important prerequisite to discern especially between anadromous and marine threespine sticklebacks.

scholarly journals Effect of Heterogeneity in Recombination Rate on Variation in Realised Relationship

2018 ◽  
Author(s):  
Ian M.S. White ◽  
William G. Hill
Keyword(s):  
Recombination Rate ◽  
Genetic Information ◽  
Fine Scale ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Identical By Descent ◽  
Small Influence ◽  
Scale Levels ◽  
Pedigree Relationship ◽  
Actual Relationship

ABSTRACTIndividuals of specified pedigree relationship vary in the proportion of the genome they share identical by descent, i.e. in their realised or actual relationship. Basing predictions of the variance in realised relationship solely on the proportion of the map length shared implicitly assumes that both recombination rate and genetic information are uniformly distributed along the genome, ignoring the possible existence of recombination hotspots, and failing to distinguish between coding and non-coding sequences. In this paper we quantify the effects of heterogeneity in recombination rate at broad and fine scale levels on the variation in realised relationship. A chromosome with variable recombination rate usually shows more variance in realised relationship than does one having the same map length with constant recombination rate, especially if recombination rates are higher towards chromosome ends. Reductions in variance can also be found, and the overall pattern of change is quite complex. In general, local (fine-scale) variation in recombination rate, e.g. hotspots, has a small influence on the variance in realised relationship. Differences in rates across longer regions and between chromosome ends can increase or decrease the variance in realised relationship, depending on the genomic architecture.

scholarly journals Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish

2019 ◽  
Vol 11 (6) ◽  
pp. 1552-1572 ◽  
Author(s):  
Alice F Shanfelter ◽  
Sophie L Archambeault ◽  
Michael A White
Keyword(s):  
Threespine Stickleback ◽  
Fine Scale ◽  
Marine Population

scholarly journals Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

2019 ◽  
Vol 5 (10) ◽  
pp. eaaw9206 ◽  
Author(s):  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Binding Sites ◽  
Demographic History ◽  
Dna Binding Protein ◽  
Polycomb Group ◽  
Human Populations ◽  
Polycomb Group Proteins ◽  
Fine Scale ◽  
Population Differences ◽  
Recombination Rates ◽  
History Of

Fine-scale rates of meiotic recombination vary by orders of magnitude across the genome and differ between species and even populations. Studying cross-population differences has been stymied by the confounding effects of demographic history. To address this problem, we developed a demography-aware method to infer fine-scale recombination rates and applied it to 26 diverse human populations, inferring population-specific recombination maps. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding further evidence that Polycomb group proteins and the trimethylation of H3K27 elevate recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.

scholarly journals Fine-scale crossover rate variation on the C. elegans X chromosome

2016 ◽  
Author(s):  
Max R. Bernstein ◽  
Matthew V. Rockman
Keyword(s):  
X Chromosome ◽  
Nucleosome Occupancy ◽  
Gc Content ◽  
Genotypic Diversity ◽  
Rate Variation ◽  
Open Chromatin ◽  
Fine Scale ◽  
Recombination Rates ◽  
Crossover Rate ◽  
Scale Variation

AbstractMeiotic recombination creates genotypic diversity within species. Recombination rates vary substantially across taxa and the distribution of crossovers can differ significantly among populations and between sexes. Crossover locations within species have been found to vary by chromosome and by position within chromosomes, where most crossover events occur in small regions known as recombination hotspots. However, several species appear to lack hotspots despite significant crossover heterogeneity. The nematode Caenorhabditis elegans was previously found to have the least fine-scale variation in crossover distribution among organisms studied to date. It is unclear whether this pattern extends to the X chromosome given its unique compaction through the pachytene stage of meiotic prophase in hermaphrodites. We generated 798 recombinant nested near-isogenic lines (NILs) with crossovers in a 1.41 Mb region on the left arm of the X chromosome to determine if its recombination landscape is similar to that of the autosomes. We find that the fine-scale variation in crossover rate is lower than that of other model species and is inconsistent with hotspots. The relationship of genomic features to crossover rate is dependent on scale, with GC content, histone modifications, and nucleosome occupancy being negatively associated with crossovers. We also find that the abundances of 4-6 base pair DNA motifs significantly explain crossover density. These results are consistent with recombination occurring at unevenly distributed sites of open chromatin.

scholarly journals Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

2019 ◽  
Author(s):  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Binding Sites ◽  
Demographic History ◽  
Dna Binding Protein ◽  
Polycomb Group ◽  
Human Populations ◽  
Polycomb Group Proteins ◽  
Fine Scale ◽  
Recombination Rates ◽  
Confounding Effect ◽  
History Of

AbstractFine-scale rates of meiotic recombination vary by several orders of magnitude across the genome, and are known to differ between species and even between populations. Studying the differences in recombination maps across populations has been stymied by the confounding effect of differences in demographic history. To address this problem, we developed a method that infers fine-scale recombination rates while taking demography into account and applied our method to infer population-specific recombination maps for each of 26 diverse human populations. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding an unexpected role for Polycomb-group proteins and the tri-methylation of H3K27 in elevating recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA-binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.

STIMULUS-SPECIFIC AND RESPONSE-SPECIFIC HABITUATION IN COURTING STICKLEBACK: DEVELOPMENTAL AND FUNCTIONAL CONSIDERATIONS

Behaviour ◽  
2000 ◽  
Vol 137 (7-8) ◽  
pp. 933-945 ◽  
Author(s):  
Jennifer Jenkins ◽  
William Rowland
Keyword(s):  
New York ◽  
Gasterosteus Aculeatus ◽  
Gravid Female ◽  
Threespine Stickleback ◽  
The Other ◽  
Male Mating ◽  
Specific Nature ◽  
Marine Population ◽  
Direct Attack ◽  
Over Time

AbstractMale threespine stickleback, Gasterosteus aculeatus, from a marine population on Long Island, New York were presented simultaneously with two dummies, one simulating a normally distended ('thinner') gravid female and the other a highly distended ('fatter') one. Males initially courted the dummies much as they do real females, but showed stimulus-specific and response-specific habituation to the dummies. Males initially courted the fatter dummy slightly more than the thinner one but showed clear signs of habituation toward the thinner dummy after about 4 min while courtship to the fatter one continued throughout the 1 hr presentation period. Thus, within 12 min males were directing a much greater proportion of courtship to the fatter dummy, and this difference increased over time. Males also attacked both dummies and, in contrast to their courtship response, divided biting equally between the two dummies. Moreover, bite rates to the thinner and the fatter dummy doubled within the first 12 min and then fluctuated around that level for the remainder of the trial. The stimulusspecific and response-specific nature of habituation may be adaptive for male mating success because it leads the male to focus courtship on the preferred female and to direct attack against the fish presenting a greater threat to the nest but a lower potential reproductive payoff.

scholarly journals Evolutionary implications of recombination differences across diverging populations of Anopheles

2021 ◽  
Author(s):  
Joel T. Nelson ◽  
Omar E. Cornejo ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Rate Variation ◽  
Anopheles Coluzzii ◽  
Fine Scale ◽  
Recombination Rates ◽  
Population Genetic Differentiation ◽  
Recombination Hotspots

AbstractRecombination is one of the main evolutionary mechanisms responsible for changing the genomic architecture of populations; and in essence, it is the main mechanism by which novel combinations of alleles, haplotypes, are formed. A clear picture that has emerged across study systems is that recombination is highly variable, even among closely related species. However, it is only until very recently that we have started to understand how recombination variation between populations of the same species impact genetic diversity and divergence. Here, we used whole-genome sequence data to build fine-scale recombination maps for nine populations within two species of Anopheles, Anopheles gambiae and Anopheles coluzzii. The genome-wide recombination averages were on the same order of magnitude for all populations except one. Yet, we identified significant differences in fine-scale recombination rates among all population comparisons. We report that effective population sizes, and presence of a chromosomal inversion has major contribution to recombination rate variation along the genome and across populations. We identified over 400 highly variable recombination hotspots across all populations, where only 9.6% are shared between two or more populations. Additionally, our results are consistent with recombination hotspots contributing to both genetic diversity and absolute divergence (dxy) between populations and species of Anopheles. However, we also show that recombination has a small impact on population genetic differentiation as estimated with FST. The minimal impact that recombination has on genetic differentiation across populations represents the first empirical evidence against recent theoretical work suggesting that variation in recombination along the genome can mask or impair our ability to detect signatures of selection. Our findings add new understanding to how recombination rates vary within species, and how this major evolutionary mechanism can maintain and contribute to genetic variation and divergence within a prominent malaria vector.

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