Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.218289v1?rss=1

Authors: OKeefe, F. R.

Abstract:

The study of modularity in geometric morphometric landmark data has focused attention on an underlying question, that of whole-shape modularity, or the pattern and strength of covariation among all landmarks. Measuring whole-shape modularity allows measurement of the dimensionality of the shape, but current methods used to measure this dimensionality are limited in application. This paper proposes a metric for measuring the effective dimensionality, De, of geometric morphometric landmark data based on the Shannon entropy of the eigenvalue vector of the covariance matrix of GPA landmark data. A permutation test to establish null rank deficiency is developed to allow standardization for comparing dimensionality metrics between data sets, and a bootstrap test is employed for measures of dispersion. These novel methods are applied to a data set of 14 landmarks taken from 119 dire wolf jaws from Rancho La Brea. Comparison with the current test based on eigenvalue dispersion demonstrates that the new metric is more sensitive to detecting population differences in whole-shape modularity. The effective dimensionality metric is extended, in the dense semilandmark case, to a measure of latent dimensionality, Dl. Latent dimensionality should be comparable among landmark spaces, whether they are homologous or not.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.24.220111v1?rss=1

Authors: Waters, C. D., Clemento, A., Aykanat, T., Garza, J. C., Naish, K. A., Narum, S., Primmer, C. R.

Abstract:

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait - Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46x10-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.215707v1?rss=1

Authors: Watanabe, J., Field, D. J., Matsuoka, H.

Abstract:

Despite longstanding interest in convergent evolution, factors that result in deviations from fully convergent phenotypes remain poorly understood. In birds, the evolution of flightless wing-propelled diving has emerged as a classic example of convergence, having arisen in disparate lineages including penguins (Sphenisciformes) and auks (Pan-Alcidae, Charadriiformes). Nevertheless, little is known about the functional anatomy of the wings of flightless auks because all such taxa are extinct, and their morphology is almost exclusively represented by skeletal remains. Here, in order to re-evaluate the extent of evolutionary convergence among flightless wing-propelled divers, wing muscles and ligaments were reconstructed in two extinct flightless auks, representing independent transitions to flightlessness: Pinguinus impennis (a crown-group alcid), and Mancalla (a stem-group alcid). Extensive anatomical data were gathered from dissections of 12 species of extant charadriiforms and 4 aequornithine waterbirds including a penguin. It was found that the wings of both flightless auk taxa were characterized by an increased mechanical advantage of wing elevator/retractor muscles, and decreased mobility of distal wing joints, both of which are likely advantageous for wing-propelled diving and parallel similar functional specializations in penguins. However, the conformations of individual muscles and ligaments underlying these specializations differ markedly between penguins and flightless auks, instead resembling those in each respective groups close relatives. Thus, the wings of these flightless wing-propelled divers can be described as convergent as overall functional units, but are incompletely convergent at lower levels of anatomical organization--a result of retaining differing conditions from each groups respective volant ancestors. Detailed investigations such as this one may indicate that, even in the face of similar functional demands, courses of phenotypic evolution are dictated to an important degree by ancestral starting points.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.214924v1?rss=1

Authors: Serrato-Capuchina, A., Schwochert, T. D., Zhang, S., Roy, B., Peede, D., Koppelman, C., Matute, D. R.

Abstract:

Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminate how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs of Drosophila are as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.23.218339v1?rss=1

Authors: Hawash, M. B. F., Sanz-Remon, J., Grenier, J.-C., Kohn, J., Yotova, V., Johnson, Z., Lanford, R. E., Brinkworth, J. F., Barreiro, L. B.

Abstract:

Despite their close genetic relatedness, apes and African and Asian monkeys (AAMs), strongly differ in their susceptibility to severe bacterial and viral infections that are important causes of human disease. Such differences between humans and other primates are thought to be a result, at least in part, of inter-species differences in immune response to infection. However, due to the lack of comparative functional data across species, it remains unclear in what ways the immune systems of humans and other primates differ. Here, we report the whole genome transcriptomic responses of ape species (human, common chimpanzee) and AAMs (rhesus macaque and olive baboon) to bacterial and viral stimulation. We find stark differences in the responsiveness of these groups, with apes mounting a markedly stronger early transcriptional response to both viral and bacterial stimulation, altering the transcription of [~]40% more genes than AAMs. Additionally, we find that genes involved in the regulation of inflammatory and interferon responses show the most divergent early transcriptional responses across primates and that this divergence is attenuated over time. Finally, we find that relative to AAMs, apes engage a much less specific immune response to different classes of pathogens during the early hours of infection, upregulating genes typical of anti-viral and anti-bacterial responses regardless of the nature of the stimulus. Overall, these findings suggest apes exhibit increased sensitivity to bacterial and viral immune stimulation, activating a broader array of defense molecules that may be beneficial for early pathogen killing at the potential cost of increased energy expenditure and tissue damage.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.212225v1?rss=1

Authors: Dicks, K. L., Pemberton, J. M., Ballingall, K. T., Johnston, S. E.

Abstract:

Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant SNP haplotype. The panel of 13 SNPs was genotyped in 5951 sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of a recombinant SNP haplotype.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.20.208835v1?rss=1

Authors: Loiseau, C., Brites, D., Reinhard, M., Zuercher, K., Borrell, S., Ballif, M., Fenner, L., Cox, H., Rutaihwa, L. K., Wilkinson, R. J., Yotebieng, M., Carter, E. J., Abimiku, A., Marcy, O., Gotuzzo, E., Avihingsanon, A., Zetola, N., Doulla, B., Boettger, E. C., Egger, M., Gagneux, S.

Abstract:

We analysed 312 drug-resistant genomes of Mycobacterium tuberculosis (Mtb) collected from HIV coinfected and HIV negative TB patients from nine countries with a high tuberculosis burden. We found that rifampicin-resistant Mtb strains isolated from HIV coinfected patients carried disproportionally more resistance-conferring mutations in rpoB that are associated with a low fitness in the absence of the drug, suggesting these low fitness rpoB variants can thrive in the context of reduced host immunity.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.213363v1?rss=1

Authors: Spadavecchia, G., Chiocchio, A., Bisconti, R., Canestrelli, D.

Abstract:

The Tyrrhenian tree frog, Hyla sarda, is an amphibian endemic to the Tyrrhenian islands (Western Mediterranean). Previous investigations of its Pleistocene evolutionary history suggested that it colonised the northern portion of its current range, through a spatial diffusion process from the Sardinia island, during the last glaciation. However, southern and northern portions of the species range experienced markedly different climatic conditions during the Late Pleistocene, suggesting the possibility of an unusual two-step process of demographic expansion. Here, we use Bayesian phylogeographic approaches to locate the ancestral area in Sardinia and to characterise better the demographic component of this expansion event. These analyses located the ancestral area for H. sarda populations along the central-eastern coast of the Sardinia island, within an area previously shown to host suitable bioclimatic conditions for H. sarda populations throughout the Late Pleistocene. Historical demographic reconstructions clearly showed that a two-step process of demographic growth fits well the data, with northern populations expanding later than Sardinia populations. The harsher climatic conditions occurred in northern islands during the glacial epoch, as compared to Sardinia, likely delayed tree frog colonisation of northern territories, and the associated demographic growth.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.22.212605v1?rss=1

Authors: Zipple, M. N., Altmann, J., Campos, F. A., Cords, M., Fedigan, L. M., Lawler, R. R., Lonsdorf, E. V., Perry, S., Pusey, A. E., Stoinski, T. S., Strier, K., Alberts, S. C.

Abstract:

Primate offspring often depend on their mothers well beyond the age of weaning, and offspring that experience maternal death in early life can suffer substantial reductions in fitness across the lifespan. Here we leverage data from eight wild primate populations (seven species) to examine two underappreciated pathways linking early maternal death and offspring fitness that are distinct from direct effects of orphaning on offspring survival. First, we show that, for five of the seven species, offspring face reduced survival during the years immediately preceding maternal death, while the mother is still alive. Second, we identify an intergenerational effect of early maternal loss in three species (muriquis, baboons, and blue monkeys), such that early maternal death experienced in one generation leads to reduced offspring survival in the next. Our results have important implications for the evolution of slow life histories in primates, as they suggest that maternal condition and survival are more important for offspring fitness than previously realized.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.07.21.214528v1?rss=1

Authors: Nguyen, A. H., Bachtrog, D.

Abstract:

Sex-specific differences in lifespan are prevalent across the tree of life and influenced by heteromorphic sex chromosomes. In species with XY sex chromosomes, females often outlive males. Males and females can differ in their overall repeat content due to the repetitive Y chromosome, and repeats on the Y might lower survival of the heterogametic sex (toxic Y effect). Here, we take advantage of the well-assembled young Y chromosome of Drosophila miranda to study the sex-specific dynamics of chromatin structure and repeat expression during aging in male and female flies. Male D. miranda have about twice as much repetitive DNA compared to females, and live shorter than females. Heterochromatin is crucial for silencing of repetitive elements, yet old D. miranda flies lose H3K9me3 modifications in their pericentromere, with heterochromatin loss being more severe during aging in males than females. Satellite DNA becomes de-repressed more rapidly in old vs. young male flies relative to females. In contrast to what is observed in D. melanogaster, we find that transposable elements (TEs) are expressed at higher levels in male D. miranda throughout their life. We show that epigenetic silencing via heterochromatin formation is ineffective on the large TE- rich neo-Y chromosome, resulting in up-regulation of Y-linked TEs already in young males. This is consistent with an interaction between the age of the Y chromosome and the genomic effects of aging. Our data support growing evidence that "toxic Y chromosomes" can diminish male fitness and a reduction in heterochromatin can contribute to sex-specific aging.

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