Top 10 Biorxiv Papers Today in Evolutionary Biology


2.071 Mikeys
#1. A definition of song using human music universals observed in primate calls
David Schruth, Christopher N. Templeton, Darryl J. Holman
Musical behavior is likely as old as our species with song originating as early as 60 million years ago in the primate order. Early singing likely evolved into the music of modern humans via multiple selective events, but efforts to disentangle these influences have been stifled by challenges to precisely define this behavior in a broadly applicable way. Detailed here is a method to quantify the elaborateness of acoustic displays using published spectrograms (n=832 calls) culled from the literature on primate vocalizations. Each spectrogram was scored by five trained analysts via visual assessments along six musically relevant acoustic parameters: tone, interval, transposition, repetition, rhythm, and syllabic variation. Principal Components Analysis (PCA) was used to reduce this multivariate assessment into a simplified measure of musical elaborateness. The resulting “acoustic reappearance diversity” index simultaneously captures syllabic variation and spectral/temporal redundancy in a single continuous variable. The potential...
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biorxivpreprint: A definition of song using human music universals observed in primate calls https://t.co/eBYEwuoncA #bioRxiv
biorxiv_evobio: A definition of song using human music universals observed in primate calls https://t.co/UmhVRYLgpO #biorxiv_evobio
Lab_Machine: RT @biorxivpreprint: A definition of song using human music universals observed in primate calls https://t.co/eBYEwuoncA #bioRxiv
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2.045 Mikeys
#2. AEGIS: An In Silico Tool to Model Genome Evolution in Age-Structured Populations
William John Bradshaw, Arian Sajina, Dario Riccardo Valenzano
AEGIS (Ageing of Evolving Genomes In Silico) is a versatile population-genetics numerical-simulation tool that enables the evolution of life history trajectories under sexual and asexual reproduction and a wide variety of evolutionary constraints. By encoding age-specific survival and reproduction probabilities as discrete genomic elements, AEGIS allows these probabilities to evolve freely and independently over time. Simulation of population evolution with AEGIS demonstrates that ageing-like phenotypes evolve in stable environments under a wide range of conditions, that life history trajectories depend heavily on mutation rates, and that sexual populations are better able to accumulate high levels of beneficial mutations affecting early-life survival and reproduction. AEGIS is free and open-source, and aims to become a standard reference tool in the study of life-history evolution and the evolutionary biology of ageing.
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biorxivpreprint: AEGIS: An In Silico Tool to Model Genome Evolution in Age-Structured Populations https://t.co/M4bRAm0tdJ #bioRxiv
biorxiv_evobio: AEGIS: An In Silico Tool to Model Genome Evolution in Age-Structured Populations https://t.co/Ek7013VNEO #biorxiv_evobio
darissambaya: RT @biorxivpreprint: AEGIS: An In Silico Tool to Model Genome Evolution in Age-Structured Populations https://t.co/M4bRAm0tdJ #bioRxiv
Github
Repository: aegis
User: valenzano-lab
Language: Python
Stargazers: 0
Subscribers: 2
Forks: 0
Open Issues: 0
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Authors: 3
Total Words: 7216
Unqiue Words: 2201

2.043 Mikeys
#3. The rapid regenerative response of a model sea anemone species Exaiptasia pallida is characterised by tissue plasticity and highly coordinated cell communication
Chloe A van der Burg, Ana Pavasovic, Edward K Gilding, Elise S Pelzer, Joachim M Surm, Terence P Walsh, Peter J Prentis
Regeneration of a limb or tissue can be achieved through multiple different pathways and mechanisms. The sea anemone Exaiptasia pallida has been observed to have excellent regenerative proficiency but this has not yet been described transcriptionally. In this study we examined the genetic expression changes during a regenerative timecourse and report key genes involved in regeneration and wound healing. We found that the major response was an early (within the first 8 hours) upregulation of genes involved in cellular movement and cell communication, which likely contribute to a high level of tissue plasticity resulting in the rapid regeneration response observed in this species. Fifty-nine genes differentially expressed during regeneration were identified as having no orthologues in other species, indicating that regeneration in E. pallida may rely on the activation of species-specific novel genes. We examined the immune response during regeneration and find the immune system is only transcriptionally active in the first eight...
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biorxivpreprint: The rapid regenerative response of a model sea anemone species Exaiptasia pallida is characterised by tissue plasticity and highly coordinated cell communication https://t.co/n5hX1eTNc5 #bioRxiv
biorxiv_evobio: The rapid regenerative response of a model sea anemone species Exaiptasia pallida is characterised by tissue plasticity and highly ... https://t.co/yIx2ydmzCf #biorxiv_evobio
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Authors: 7
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2.029 Mikeys
#4. The genetic interaction between HIV and the antibody repertoire
Nicolas Strauli, Emily K Fryer, Olivia Pham, Mohamed Abdel-Mohsen, Shelley N Facente, Christopher Pilcher, Pleuni Pennings, Satish Pillai, Ryan D. Hernandez
The interaction between human immunodeficiency virus (HIV) and the antibody repertoire (AbR) during chronic infection can provide important information for HIV vaccine research, yet has not been well-characterized on a systems level. We deeply sequenced the HIV population and the AbR of ten HIV-infected, antiretroviral (ART)-naïve individuals, each with 10-20 longitudinal samples spanning 4-14 years. Our unbiased sequencing approach identified partitions of AbRs showing evidence of interaction with autologous HIV populations. We show that these HIV-associated partitions are enriched for the V gene segments of known HIV broadly neutralizing antibodies (bnAbs), indicating that the HIV-responding component of the AbR can be identified via time-series genetic data. Despite this evidence for larger-scale AbR/HIV interactions at the sub-population level, we found little to no evidence for coevolution. This suggests that coevolution is either rare, or hard to detect, which has important vaccine design implications.
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biorxivpreprint: The genetic interaction between HIV and the antibody repertoire https://t.co/CIcD0erjkS #bioRxiv
biorxiv_evobio: The genetic interaction between HIV and the antibody repertoire https://t.co/5uiXTPgMOn #biorxiv_evobio
dmrmay: RT @biorxivpreprint: The genetic interaction between HIV and the antibody repertoire https://t.co/CIcD0erjkS #bioRxiv
Github

Software associated with the manuscript: "The genetic interaction between HIV and the antibody repertoire".

Repository: abr_hiv_evo
User: nbstrauli
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Subscribers: 1
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Sample Sizes : [10, 100]
Authors: 9
Total Words: 16299
Unqiue Words: 5215

2.023 Mikeys
#5. Parental care shapes evolution of aposematism and provides lifelong protection against predators
Carita Lindstedt, Giuseppe Boncoraglio, Sheena Cotter, James Gilbert, Rebecca Kilner
Social interactions within species can modulate the response to selection and determine the extent of evolutionary change. Yet relatively little work has determined whether the social environment can influence the evolution of traits that are selected by interactions with other species - a major source of natural selection. Here we show that the amount of parental care received as an offspring can influence the expression, and potential evolution, of warning displays deployed against predators in adulthood. In theory, warning displays by prey are selected by predators for uniformity and to reliably advertise the extent to which individuals are chemically defended. However, the correlated evolution of intensity of the visual display and strength of the chemical defense is only possible if there is a genetic correlation between them. Adult burying beetles Nicrophorus vespilloides bear bright orange elytral markings which advertise their chemical defenses. We experimentally manipulated the level of maternal care that individuals...
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biorxivpreprint: Parental care shapes evolution of aposematism and provides lifelong protection against predators https://t.co/UCtU23oP8A #bioRxiv
biorxiv_evobio: Parental care shapes evolution of aposematism and provides lifelong protection against predators https://t.co/C7PDFx9mLt #biorxiv_evobio
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2.023 Mikeys
#6. Robust and window-insensitive mixture model approaches for localizing balancing selection
Xiaoheng Cheng, Michael DeGiorgio
Long-term balancing selection typically leaves narrow footprints of increased genetic diversity, and therefore most detection approaches only achieve optimal performances when sufficiently small genomic regions (i.e., windows) are examined. Such methods are sensitive to window sizes and suffer substantial losses in power when windows are large. This issue creates a tradeoff between noise and power in empirical applications. Here, we employ mixture models to construct a set of five composite likelihood ratio test statistics, which we collectively term B statistics. These statistics are agnostic to window sizes and can operate on diverse forms of input data. Through simulations, we show that they exhibit comparable power to the best-performing current methods, and retain substantially high power regardless of window sizes. Moreover, these methods display considerable robustness to high mutation rates and uneven recombination landscapes, as well as an array of other common confounding scenarios. Further, we applied these statistics...
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biorxivpreprint: Robust and window-insensitive mixture model approaches for localizing balancing selection https://t.co/OKeoCYNnf6 #bioRxiv
biorxiv_evobio: Robust and window-insensitive mixture model approaches for localizing balancing selection https://t.co/QIWa65NIkp #biorxiv_evobio
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2.012 Mikeys
#7. A conservative approach for species delimitation based on multi-locus DNA sequences: a case study of the genus Giraffa (Mammalia, Cetartiodactyla)
Alexandre HASSANIN, Alice Petzold
Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described. In this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genus Giraffa. Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizes G. camelopardalis sensu strico,...
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biorxivpreprint: A conservative approach for species delimitation based on multi-locus DNA sequences: a case study of the genus Giraffa (Mammalia, Cetartiodactyla) https://t.co/Oh7g7Ugn8N #bioRxiv
biorxiv_evobio: A conservative approach for species delimitation based on multi-locus DNA sequences: a case study of the genus Giraffa (Mammalia, ... https://t.co/HLpAyHuYo2 #biorxiv_evobio
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2.008 Mikeys
#8. Insulin-like growth factor 1 is related to the expression of plumage traits in a passerine species
Katharina Mahr, Orsolya Vincze, Zsófia Tóth, Herbert Hoi, Ádám Z. Z Lendvai
Avian plumage colors and ornaments are ideal models to study the endocrine mechanisms linking sexually selected traits and individual parameters of quality and condition. The insulin-like growth factor 1 (IGF-1), an evolutionarily highly conserved peptide hormone, represents a link between body condition and the individual capacity to grow elaborated ornamental features, due to its regulatory role in cell proliferation and differentiation and its high sensitivity to the nutritional state of individuals. We investigated whether IGF-1 levels during molting affect the expression of multiple ornaments in a sexually dichromatic passerine species, the bearded reedling (Panurus biarmicus). We collected blood samples of males and females shortly before the molting completed and measured the size and colors of ornamental traits. Our results indicate that in males, structural plumage colors, the size of the melanin based ornament (beard) and tail length are independent traits. IGF-1 levels predict the length of the tail and the expression...
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biorxivpreprint: Insulin-like growth factor 1 is related to the expression of plumage traits in a passerine species https://t.co/qMSo0YzYqK #bioRxiv
biorxiv_evobio: Insulin-like growth factor 1 is related to the expression of plumage traits in a passerine species https://t.co/ZFvgObvf7f #biorxiv_evobio
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Authors: 5
Total Words: 8495
Unqiue Words: 2779

1.998 Mikeys
#9. Into-India or out-of-India? Historical biogeography of freshwater gastropod genus Pila (Ampullariidae)
Maitreya Sil, Aravind N. A., K. Praveen Karanth
The biota of the Indian subcontinent has assembled during various points of the history of its continental drift: some when it was still a part of Gondwanaland and subsequently dispersed out-of-India and some dispersed into-India after it collided with Asia. However, the relative contribution of these connection to the current biotic assembly of the subcontinent is still under-explored. We aimed to understand the relative importance of these various routes of biotic assembly in India through studying the historical biogeography of tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny of Ampullariidae including all the described Pila species from India and published sequences of Ampullariids from all over the world from two mitochondrial and two nuclear markers. Thereafter molecular dating and ancestral area reconstruction analyses were carried out in order to ascertain the time frame and route of colonization of India. The results suggest that Pila dispersed into India as well as other parts of...
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Total Words: 9935
Unqiue Words: 2864

1.994 Mikeys
#10. The first functional characterization of ancient interleukin-15-like (IL-15L) reveals shared and distinct functions of the IL-2, -15 and -15L family cytokines
Takuya Yamaguchi, Axel Karger, Markus Keller, Eakapol Wangkahart, Tiehui Wang, Christopher J. Secombes, Azusa Kimoto, Mitsuru Furihata, Keiichiro Hashimoto, Uwe Fischer, Johannes M. Dijkstra
The ancient cytokine interleukin 15-like (IL-15L) was lost in humans and mice but not throughout mammals. This is the first study to describe IL-15L functions, namely in the fish rainbow trout. Fish have only one [alpha]-chain receptor gene IL-15Rα , whereas in mammalian evolution this gene duplicated and evolved into IL-15Rα plus IL-2Rα . Trout IL-2, IL-15 and IL-15L all could bind IL-15Rα and were able to induce phosphorylation of transcription factor STAT5. Reminiscent of the mammalian situation, trout IL-15 was more dependent on "in trans " presentation by IL-15Rα than IL-2. However, whereas trout IL-15 could also function as a free cytokine as known for mammalian IL-15, trout IL-15L function showed a total dependency on in trans presentation by IL-15Rα. Trout lymphocytes from the mucosal tissues gill and intestine were sensitive to IL-15, but refractory to IL-2 and IL-15L, which is reminiscent of sensitivities to IL-15 in mammals. Distinguishing engagement of the IL-2Rα/IL-15Rα receptor chain may explain why IL-2 and IL-15...
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