Top 8 Biorxiv Papers Today in Evolutionary Biology


2.014 Mikeys
#1. Approximating the coalescent under facultative sex
Matthew Hartfield
Genome studies of facultative sexual species are providing insight into the evolutionary consequences of mixed reproductive modes. However, it is unclear if the evolutionary history of facultative sexuals' genomes can be captured by standard population genetic models; in particular, whether they can be approximated by Wright-Fisher dynamics while assuming a rescaled effective population size Ne. Here, I determine when the gene genealogies of diploid facultative sexuals, which can either reproduce by sex or parthenogenesis, can be approximated by the standard coalescent, and further derive coalescent-based estimates of Ne. When sex is frequent (occurring at a frequency much greater than 1/N, for N the actual population size), the underlying genealogy can be approximated by the standard coalescent and Ne is approximately equal to N. When sex is very rare (at frequency much lower than 1/N), Ne can be defined for two alleles, which is independent of N and is instead influence by the frequencies of sex and mitotic gene conversion....
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biorxivpreprint: Approximating the coalescent under facultative sex https://t.co/J5SGnIjxDF #bioRxiv
biorxiv_evobio: Approximating the coalescent under facultative sex https://t.co/jzvWg250lu #biorxiv_evobio
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Supplemental material for manuscript "Approximating the coalescent under facultative sex". Simulation code and Mathematica file.

Repository: FacSexNe
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2.009 Mikeys
#2. Chromosome painting does not support a sex chromosome turnover in Lacerta agilis Linnaeus, 1758
Artem Lisachov, Massimo Giovannotti, Jorge C. Pereira, Daria Andreyushkova, Svetlana Romanenko, Malcolm A. Ferguson-Smith, Pavel Borodin, Vladimir Trifonov
Reptiles show a remarkable diversity of sex determination mechanisms and sex chromosome systems, derived from different autosomal pairs. The origin of the ZW sex chromosomes of Lacerta agilis, a widespread Eurasian lizard species, is a matter of discussion: is it a small macrochromosome from the 11-18 group, common to all lacertids, or this species has unique ZW pair derived from the large chromosome 5. Using independent molecular cytogenetic methods, we investigated the karyotype of L. agilis exigua from Siberia, Russia, to identify the sex chromosomes. FISH with the flow-sorted chromosome painting probe, derived from L. strigata and specific to chromosomes 13, 14, and Z, confirmed that the Z chromosome of L. agilis is a small macrochromosome, the same as in L. strigata. FISH with the telomeric probe showed an extensive accumulation of the telomeric repeat on the W chromosome in agreement with previous studies, excluding the possibility that the lineages of L. agilis studied in different works could have different sex chromosome...
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biorxivpreprint: Chromosome painting does not support a sex chromosome turnover in Lacerta agilis Linnaeus, 1758 https://t.co/L3iNBG3wYq #bioRxiv
biorxiv_evobio: Chromosome painting does not support a sex chromosome turnover in Lacerta agilis Linnaeus, 1758 https://t.co/5CRf8SiO9p #biorxiv_evobio
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Total Words: 4972
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1.999 Mikeys
#3. Recombination, variance in genetic relatedness, and selection against introgressed DNA
Carl Veller, Nathaniel B. Edelman, Pavitra Muralidhar, Martin A. Nowak
The genomic proportion that two relatives share identically by descent - their genetic relatedness - can vary depending on the patterns of recombination and segregation in their pedigree. Here, we calculate the precise connection between genome-wide genetic shuffling and variance in genetic relatedness. For the relationships of grandparent-grandoffspring and siblings, the variance in genetic relatedness is a simple decreasing function of r̄ , the average proportion of locus pairs that recombine in gametogenesis. These formulations explain several recent observations about variance in genetic relatedness. They further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling F2-based tests for various kinds of selection, such as Dobzhansky-Muller incompatibilities and hybrid vigor. Our calculations also allow us to characterize how recombination affects the rate at which selection eliminates deleterious introgressed DNA after hybridization - by modulating the variance of introgressed ancestry...
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EvolPaper: RT @biorxiv_evobio: Recombination, variance in genetic relatedness, and selection against introgressed DNA https://t.co/2b5i176oSg #biorxi…
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1.999 Mikeys
#4. Rates of molecular evolution predict intraspecies genetic diversity
Jiaqi Wu, Takahiro Yonezawa, Hirohisa Kishino
Because the evolution of modern humans from early mammals has been a continuous process, human genetic diversity at the molecular level should reflect mammalian genetic diversity. To test this prediction, we contrasted the proportion of segregating sites, q, in human data from the 1000 Genome Project with phylogenetic trees of genes in 96 mammalian genomes ranging from human to platypus. The evolvability of a gene in the human population was found to be positively correlated with the long-term molecular evolutionary rate (r = 0.592). Further analysis of human singleton and de novo mutations suggested that natural selection begins shaping intraspecies genetic diversity soon after a mutation's initial appearance. By introducing the rate of molecular evolution as a predictor of q, species-specific selection on genes can be detected as deviations from predicted values. We analyzed the average deviations of 10,173 disease-related gene sets and detected 33 gene sets likely to be under human species-specific selection. Among them, nine...
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freddelsuc: RT @biorxiv_evobio: Rates of molecular evolution predict intraspecies genetic diversity https://t.co/oZ8jkYjTcu #biorxiv_evobio
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1.997 Mikeys
#5. Divergence in hormone signalling links local adaptation and hybrid failure
Melanie Joy Wilkinson, Federico Roda, Gregory Matthew Walter, Rick Nipper, Jessica Walsh, Scott Allen, Diana Marcela Bernal, Henry North, Christine Beveridge, Daniel Ortiz-Barrientos
Natural selection is a major driver for the origins of adaptations and new species. Whether or not the processes driving adaptation and speciation share a molecular basis remains largely unknown. Here, we show that divergence in hormone signalling contributed to the evolution of complex adaptations and intrinsic reproductive isolation in the Australian wildflower Senecio lautus. We provide evidence that differences in the auxin pathway, a hormone required for plant growth and development, has led to the repeated evolution of erect and prostrate forms along the Australian coast. Using multiple hybrid and natural populations, we show that adjacent erect and prostrate populations repeatedly diverged in auxin-related genes and auxin-dependent phenotypes, such as gravitropism. Analysis of a multi-year field selection experiment revealed that variation in fitness of an F10 hybrid population explained variation in gravitropism of their offspring. Genotyping of F11 hybrid individuals with extreme values of gravitropism revealed that...
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dlrhj: RT @biorxiv_evobio: Divergence in hormone signalling links local adaptation and hybrid failure https://t.co/CagfZBbt1y #biorxiv_evobio
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1.996 Mikeys
#6. Counting the paternal founders of Austroasiatic speakers associated with the language dispersal in South Asia
Prajjval Pratap Singh, Shani Vishwakarma, Gazi Nurun Nahar Sultana, Arno Pilvar, Monika Karmin, Siiri Rootsi, Richard Villems, Mait Metspalu, Doron Behar, Toomas Kivisild, George van Driem, Gyaneshwer Chaubey
The phylogenetic analysis of Y chromosomal haplogroup O2a-M95 was crucial to determine the nested structure of South Asian branches within the larger tree, predominantly present in East and Southeast Asia. However, it had previously been unclear how many founders brought the haplogroup O2a-M95 to South Asia. On the basis of the updated Y chromosomal tree for haplogroup O2a-M95, we analysed 1,437 male samples from South Asia for various downstream markers, carefully selected from the extant phylogenetic tree. With this increased resolution, we were able to identify at least three founders downstream to haplogroup O2a-M95 who are likely to have been associated with the dispersal of Austroasiatic languages to South Asia. The fourth founder was exclusively present amongst Tibeto-Burman speakers of Manipur and Bangladesh. In sum, our new results suggest the arrival of Austroasiatic languages in South Asia during last five thousand years.
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1.931 Mikeys
#7. Inferring phylogenetic trees from mutational distance of transposable elements.
Juanjo Bermudez
There are many methods for establishing a phylogeny available to researchers. Some of these are based on the mutational distance between ortholog sequences of DNA, and, from these, some are based on the analysis (presence/absence) of transposable elements in specific loci of ortholog sequences. We present a new approach: a method for inferring a phylogeny based on the mutational distance of transposable elements distributed along any segment of DNA. Our method doesn't require previously having ortholog segments of DNA from every organism. The method can be fully automated, not requiring any previous or posterior data analysis nor data preparation.
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1.91 Mikeys
#8. Proximate causes of infertility and embryo mortality in captive zebra finches
Yifan Pei, Wolfgang Forstmeier, Daiping Wang, Katrin Martin, Joanna Rutkowska, Bart Kempenaers
Some species show high rates of reproductive failure, which is puzzling because natural selection works against such failure in every generation. Hatching failure is common in both captive and wild zebra finches (Taeniopygia guttata), yet little is known about its proximate causes. Here we analyze data on reproductive performance (fate of >23,000 eggs) based on up to 14 years of breeding of four captive zebra finch populations. We find that virtually all aspects of reproductive performance are negatively affected by inbreeding (mean r = -0.117), by an early-starting, age-related decline (mean r = -0.132), and by poor early-life nutrition (mean r = -0.058). However, these effects together explain only about 3% of the variance in infertility, offspring mortality, fecundity and fitness. In contrast, individual repeatability of different fitness components varied between 15% and 50%. As expected, we found relatively low heritability in fitness components (median: 7% of phenotypic, and 29% of individually repeatable variation). Yet,...
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