Top 10 Biorxiv Papers Today in Evolutionary Biology


2.07 Mikeys
#1. Memory in trait macroevolution
Emma E Goldberg, Jasmine Foo
The history of a trait within a lineage may influence its future evolutionary trajectory, but macroevolutionary theory of this process is not well developed. For example, consider the simple binary trait of living in cave versus surface habitat. The longer a species has been cave-dwelling, the more may accumulated loss of vision, pigmentation, and defense restrict future adaptation if the species encounters the surface environment. However, the Markov model of discrete trait evolution that is widely adopted in phylogenetics does not allow the rate of cave-to-surface transition to decrease with longer duration as a cave-dweller. Here, we describe three models of evolution that remove this 'memory-less' constraint, using a renewal process to generalize beyond the typical Poisson process of discrete trait macroevolution. We then show how the two-state renewal process can be used for inference, and we investigate the potential of phylogenetic comparative data to reveal different influences of trait duration, or 'memory' in trait...
more | pdf
Figures
None.
Tweets
biorxivpreprint: Memory in trait macroevolution https://t.co/msz5es4fa1 #bioRxiv
biorxiv_evobio: Memory in trait macroevolution https://t.co/7LTIHb2Cvj #biorxiv_evobio
fsantini2015: Memory in trait macroevolution https://t.co/r7NHFLxZIB https://t.co/suuwhs5kFH
Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
Scoobiefoo: New paper, with Emma E. Goldberg: Memory in trait macroevolution https://t.co/vDLtdtUTbV
BESMacroecol: RT @ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
BESMacroecol: RT @Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
mtanichthys: RT @biorxivpreprint: Memory in trait macroevolution https://t.co/msz5es4fa1 #bioRxiv
juvelas: RT @ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
hsauquet_rbgsyd: RT @Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
jason_nge: RT @Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
oconned5: RT @ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
kk_matsunaga: RT @Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
javi_igea: RT @ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
JesusNPL: RT @ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
RagoVago: RT @ajhelmstetter: Preprint now out! https://t.co/ftOW9ZqJ1P https://t.co/3QuzjaotuM
luizebg: RT @Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
InostrozaMich: RT @Lepidodendron: Very interesting preprint. Is trait evolution non-markovian? Now we can test it! https://t.co/t3vaxk4mEd
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 2
Total Words: 13241
Unqiue Words: 2892

2.01 Mikeys
#2. Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets
Thomas Blankers, Emma L Berdan, Matthias Hennig, Frieder Mayer
Behavioral isolation is a potent barrier to gene flow and a source of striking diversity in the animal kingdom. However, it remains unclear if the linkage disequilibrium (LD) between sex-specific traits required for behavioral isolation results mostly from physical linkage between signal and preference loci or from directional mate preferences. Here, we test this in the field crickets Gryllus rubens and G. texensis . These closely related species diverged with gene flow and have strongly diverged songs and preference functions for the mate calling song rhythm. We map quantitative trait loci for signal and preference traits (pQTL) as well as for gene expression associated with these traits (eQTL). We find strong, positive genetic covariance between song traits and between song and preference. Our results show that this is in part explained by incomplete physical linkage: although both linked pQTL and eQTL couple male and female traits, major effect loci for different traits were never on the same chromosome. We suggest that the...
more | pdf
Figures
Tweets
JoshPenalba: "Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets [NEW RESULTS]" https://t.co/ajPEQUVJi7
EllikaFaust: Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets https://t.co/JV9P3csDYw
Github

a collection of evolutionary statistical analyses. a phylogenetically corrected generalized least squares for multivariate response variables as in Blankers et al. 2012. J. Evol. Biol, a power, sample size, and true number of loci calculator for QTL mapping studies, a bootstrapped analysis of eigenvalue matrices for studies on phenotypic integration.

Repository: statistics
User: thomasblankers
Language: R
Stargazers: 0
Subscribers: 0
Forks: 0
Open Issues: 0
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 4
Total Words: 12801
Unqiue Words: 4023

2.009 Mikeys
#3. Evolutionary Models of Amino Acid Substitutions Based on the Tertiary Structure of their Neighborhoods
Elias Primetis, Spyridon Chavlis, Pavlos Pavlidis
Intra-protein residual vicinities depend on the involved amino acids. Energetically favorable vicinities (or interactions) have been preserved, while unfavorable vicinities have been eliminated during evolution. We describe, statistically, the interactions between amino acids using resolved protein structures. Based on the frequency of amino acid interactions, we have devised an amino acid substitution model that implements the following idea: amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors. Using known tertiary structures for α-helical membrane (HM) proteins, we build evolutionary substitution matrices. We constructed maximum likelihood phylogenies using our amino acid substitution matrices and compared them to widely-used methods. Our results suggest that amino acid substitutions are associated with the spatial neighborhoods of amino acid residuals.
more | pdf
Figures
Tweets
PavelProsselkov: "...amino acids that have similar neighbors in the protein tertiary structure can replace each other, while substitution is more difficult between amino acids that prefer different spatial neighbors" https://t.co/p9V6nxlqUa
dendritesgr: Dr Chavlis new preprint is out in collaboration with Pavlos Pavlidis lab! "Evolutionary Models of Amino Acid Substitutions Based on the Tertiary Structure of their Neighborhoods" https://t.co/G4M1RjHKQi
dendritesgr: @spiros1776 new preprint is out in collaboration with Pavlos Pavlidis lab! "Evolutionary Models of Amino Acid Substitutions Based on the Tertiary Structure of their Neighborhoods" https://t.co/G4M1RjHKQi
nidaios: New manuscript in BioRxiv. Amino acid substitution models are actually related to the 3D neighborhood of amino acids in the tertiary structure of the proteins and that amino acids with similar neighborhoods tend to replace each other during evolution. https://t.co/2gTTtHh9De
nidaios: New manuscript in @biorxivpreprint . Amino acid substitution models are actually related to the 3D neighborhood of amino acids in proteins and that amino acids with similar neighborhoods tend to replace each other during evolution. https://t.co/2gTTtHh9De
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 3
Total Words: 7343
Unqiue Words: 2161

2.0 Mikeys
#4. Patterns and mechanisms of diminishing returns from beneficial mutations
Xinzhu Wei, Jianzhi Zhang
Diminishing returns epistasis causes the benefit of the same advantageous mutation smaller in fitter genotypes, and is frequently observed in experimental evolution. However, its occurrence in other contexts, environment-dependence, and mechanistic basis are unclear. Here we address these questions using 1005 sequenced segregants generated from a yeast cross. Under each of 47 examined environments, 66-92% of tested polymorphisms exhibit diminishing returns epistasis. Surprisingly, improving environment quality also reduces the benefits of advantageous mutations even when fitness is controlled for, indicating the necessity to revise the global epistasis hypothesis. We propose that diminishing returns originates from the modular organization of life where the contribution of each functional module to fitness is determined jointly by the genotype and environment and has an upper limit, and demonstrate that our model predictions match empirical observations. These findings broaden the concept of diminishing returns epistasis, reveal...
more | pdf
Figures
Tweets
biorxivpreprint: Patterns and mechanisms of diminishing returns from beneficial mutations https://t.co/QVluLEIxQf #bioRxiv
biorxiv_evobio: Patterns and mechanisms of diminishing returns from beneficial mutations https://t.co/RkH7Yi8bCk #biorxiv_evobio
TonyBurnetti: RT @biorxiv_evobio: Patterns and mechanisms of diminishing returns from beneficial mutations https://t.co/RkH7Yi8bCk #biorxiv_evobio
Github

Data and code from Wei and Zhang, 2018

Repository: Diminishing-Returns-Epistasis
User: AprilWei001
Language: Matlab
Stargazers: 0
Subscribers: 0
Forks: 0
Open Issues: 0
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 2
Total Words: 11840
Unqiue Words: 2557

1.998 Mikeys
#5. Phylogenomics, biogeography, and evolution in the American palm genus Brahea
Craig Barrett, Brandon Sinn, Loren King, Jesus Medina, Christine Bacon, Sean Lahmeyer, Donald Hodel
Slow rates of molecular evolution at low taxonomic levels hamper studies of relationships among species, and subsequent biogeographic and evolutionary analyses. An example is the genus Brahea, which is among the most poorly understood lineages of American palms and is characterized by a wide variety of growth forms and intermediate morphological features. We generated approximately 400 kb of genome-scale data from all three genomes for the 11 currently described species of Brahea to infer phylogenetic relationships, reconstruct ancestral growth form, estimate ancestral geographic ranges, and test for niche equivalency among closely related species with geographic overlap. Relationships receive strong support, and conform to previous subgeneric assignments, except for placement of the dwarf species B. moorei within subgenus Erythea. Our robust phylogenetic hypothesis reveals trends in growth form including an overall increase in height in the B. armata clade, and independent evolution of dwarf forms from taller ancestors in the B....
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 7
Total Words: 13353
Unqiue Words: 4474

1.998 Mikeys
#6. Population genetic structure of the bank vole Myodes glareolus within its glacial refugium in peninsular Italy
Andrea Chiocchio, Paolo Colangelo, Gaetano Aloise, Gianni Amori, Sandro Bertolino, Robeta Bisconti, Riccardo Castiglia, Daniele Canestrelli
It is now well established that Southern European peninsulas have been major glacial refugia for temperate species during Pleistocene climatic oscillations. However, substantial environmental changes occurred also within these peninsulas throughout the Pleistocene, rising questions about the role and interplay of various of micro-evolutionary processes in shaping patterns of intraspecific diversity within these areas. Here, we investigate the patterns of genetic variation in the bank vole Myodes glareolus within the Italian peninsula. By using a panel of 13 microsatellite loci, we found more intra-specific variation than expected based on previous assessments. Indeed, both Bayesian and ordination-based clustering analyses of variation recovered five main geographic/genetic clusters along the peninsula, with three clusters geographically restricted to the southern portion of the study area. This pattern supports the occurrence of multiple sub-refugia for the bank vole in peninsular Italy, likely promoted by the major...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 8
Total Words: 6486
Unqiue Words: 2268

1.998 Mikeys
#7. Untangling the Evolutionary History of European Bison (Bison bonasus)
Ayla L. van Loenen, Emilia Hofman-Kamińska, Kieren J. Mitchell, Bastien Llamas, Hervé́ Bocherens, Julien Soubrier, Holly Heiniger, Martina Pacher, Daniel Makowiecki, Giedrė Pilĭciauskienė, Dorothée Drucker, Rafał Kowalczyk, Alan Cooper
European bison ( Bison bonasus ) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 13
Total Words: 8375
Unqiue Words: 2727

0.0 Mikeys
#8. The most primitive extant ancestor of organisms and discovery of definitive evolutionary equations
Kenji Sorimachi
Organisms are classified into three domains, Prokaryota, Archaea, and Eukaryota, and their evolutionary divergence has been characterized based on morphological and molecular features using rationale based on Darwins theory of natural selection. However, universal rules that govern genome evolution have not been identified. Here, a simple, innovative approach has been developed to evaluate biological evolution initiating the origin of life: whole genomes were divided into several fragments, and then differences in normalized nucleotide content between nucleotide pairs were compared. Based on nucleotide content structures, Monosiga brevicollis mitochondria may be the most primitive extant ancestor of the species examined here. The two normalized nucleotide contents are universally expressed by a linear regression line, (X − Y)/(X + Y) = a (X − Y) + b, where X and Y are nucleotide contents and (a) and (b) are constants. The value of (G + C), (G + A), (G + T), (C + A), (C + T) and (A + T) was ~0.5. Plotting (X − Y)/(X + Y) against...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 1
Total Words: 7066
Unqiue Words: 2421

0.0 Mikeys
#9. Cultural Selection Shapes Network Structure
Marco Smolla, Erol Akcay
Cultural evolution relies on the social transmission of cultural traits across a population, along the ties of an underlying social network that emerges from non-random interactions among individuals. Research indicates that the structure of those interaction networks affects information spread, and thus a population's ability for cumulative culture. However, how network structure itself is driven by population-culture co-evolution remains largely unclear. We use a simple but realistic model of complex dynamic social networks to investigate how populations negotiate the trade-off between acquiring new skills and getting better at existing skills, and how this trade-off, in turn, shapes the social structure of the population. Our results reveal unexpected eco-evolutionary feedback from culture onto social network structure and vice versa. We show that selecting for generalists (favouring a broad repertoire of skills) results in sparsely connected networks with highly diverse skill sets, whereas selecting for specialists (favouring...
more | pdf
Figures
Tweets
razibkhan: Cultural Selection Shapes Network Structure https://t.co/yIkk6v32eK #genetics
akcayerol: Very happy to post our new preprint w/ @smollamarco on @biorxivpreprint: Cultural selection shapes Network Structure https://t.co/D70bsDh1D7
WarrenCntrPenn: .@akcayerol and @smollamarco use a simple but realistic model of complex dynamic social networks to investigate how populations negotiate the trade-off between acquiring new skills and getting better at existing skills in their recent preprint. https://t.co/XIWDVA5JaL @PennSAS https://t.co/ZdQLv4ztgD
mapiasal: Cultural Selection Shapes Network Structure | bioRxiv https://t.co/9xPlAFAZSt
cedric_p: On the evolutionary feedback between cultural selection and network structure: https://t.co/LmRG5guya2
a_baronca: Cultural Selection Shapes Network Structure https://t.co/RYZrsiQWov
jplotkin: RT @biorxivpreprint: Cultural Selection Shapes Network Structure https://t.co/raHJnGRsoC #bioRxiv
EvolutionistXX: RT @razibkhan: Cultural Selection Shapes Network Structure https://t.co/yIkk6v32eK #genetics
acerbialberto: RT @a_baronca: Cultural Selection Shapes Network Structure https://t.co/RYZrsiQWov
smollamarco: RT @cedric_p: On the evolutionary feedback between cultural selection and network structure: https://t.co/LmRG5guya2
omnidelic: RT @mapiasal: Cultural Selection Shapes Network Structure | bioRxiv https://t.co/9xPlAFAZSt
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 2
Total Words: 9061
Unqiue Words: 2576

0.0 Mikeys
#10. Diversification rates and phylogenies: what are we estimating, and how good are the estimates?
Pascal O Title, Daniel Rabosky
Species-specific diversification rates, or "tip rates", can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent modeling approaches. However, there is significant confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics. We compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of...
more | pdf
Figures
Tweets
razibkhan: Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/JaLnZBpjDV #genetics #evolution
dan_rabosky: "Diversification rates and phylogenies: what are we estimating, and how good are the estimates?" Nice work by @pascal_title! https://t.co/jKtbgBhfh2
fsantini2015: new preprint by @pascal_title & @dan_rabosky Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/NnkJGFrCn9 https://t.co/ZIl8waiVxp
PromPreprint: Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/vwEstRDxLu
valentina_peona: Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/gb9bDrB2Rq
iamcuriousblue: RT @razibkhan: Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/JaLnZBpjDV #gene…
juvelas: RT @razibkhan: Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/JaLnZBpjDV #gene…
antropoteuthis: RT @valentina_peona: Diversification rates and phylogenies: what are we estimating, and how good are the estimates? https://t.co/gb9bDrB2Rq
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 2
Total Words: 30419
Unqiue Words: 3301

About

Assert is a website where the best academic papers on arXiv (computer science, math, physics), bioRxiv (biology), BITSS (reproducibility), EarthArXiv (earth science), engrXiv (engineering), LawArXiv (law), PsyArXiv (psychology), SocArXiv (social science), and SportRxiv (sport research) bubble to the top each day.

Papers are scored (in real-time) based on how verifiable they are (as determined by their Github repos) and how interesting they are (based on Twitter).

To see top papers, follow us on twitter @assertpub_ (arXiv), @assert_pub (bioRxiv), and @assertpub_dev (everything else).

To see beautiful figures extracted from papers, follow us on Instagram.

Tracking 56,475 papers.

Search
Sort results based on if they are interesting or reproducible.
Interesting
Reproducible
Feedback
Online
Stats
Tracking 56,475 papers.