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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 63,046 bioRxiv papers from 279,617 authors.

Most downloaded bioRxiv papers, all time

in category evolutionary biology

4,175 results found. For more information, click each entry to expand.

1: Population Replacement in Early Neolithic Britain
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Posted to bioRxiv 18 Feb 2018

Population Replacement in Early Neolithic Britain
9,125 downloads evolutionary biology

Selina Brace, Yoan Diekmann, Thomas J. Booth, Zuzana Faltyskova, Nadin Rohland, Swapan Mallick, Matthew Ferry, Megan Michel, Jonas Oppenheimer, Nasreen Broomandkhoshbacht, Kristin Stewardson, Susan Walsh, Manfred Kayser, Rick Schulting, Oliver E Craig, Alison Sheridan, Mike Parker Pearson, Chris Stringer, David Reich, Mark G. Thomas, Ian Barnes

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Anatolian ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain c. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, the pattern and process of the British Neolithic transition remains unclear. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 10.5-4.5 kBP, a dataset that includes 22 newly reported individuals and the first genomic data from British Mesolithic hunter-gatherers. Our analyses reveals persistent genetic affinities between Mesolithic British and Western European hunter-gatherers over a period spanning Britain's separation from continental Europe. We find overwhelming support for agriculture being introduced by incoming continental farmers, with small and geographically structured levels of additional hunter-gatherer introgression. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

2: Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA
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Posted to bioRxiv 18 Jan 2017

Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA
7,405 downloads evolutionary biology

Dejian Yuan, Xiaoyun Lei, Yuanyuan Gui, Mingrui Wang, Ye Zhang, Zuobin Zhu, Dapeng Wang, Jun Yu, Shi Huang

The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variations among racial groups to be largely a result of parallel mutations rather than recent common ancestry and admixture as commonly assumed. We derived an age of 1.86-1.92 million years for the first split in modern human populations based on autosomal diversity data. We found evidence of modern Y and mtDNA originating in East Asia and dispersing via hybridization with archaic humans. Analyses of autosomes, Y and mtDNA all suggest that Denisovan and Neanderthal were archaic Africans with Eurasian admixtures and ancestors of South Asia Negritos and Aboriginal Australians. Verifying our model, we found more ancestry of Southern Chinese from Hunan in Africans relative to other East Asian groups examined. These results suggest multiregional evolution of autosomes and replacements of archaic Y and mtDNA by modern ones originating in East Asia, thereby leading to a coherent account of modern human origins.

3: Towards a new history and geography of human genes informed by ancient DNA
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Posted to bioRxiv 21 Mar 2014

Towards a new history and geography of human genes informed by ancient DNA
7,283 downloads evolutionary biology

Joseph K. Pickrell, David Reich

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

4: A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
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Posted to bioRxiv 05 May 2015

A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years
6,810 downloads evolutionary biology

Hang Zhou, Sile Hu, Rostislav Matveev, Qianhui Yu, Jing Li, Philipp Khaitovich, Li Jin, Michael Lachmann, Mark Stoneking, Qiaomei Fu, Kun Tang

The spatiotemporal distribution of recent human adaptation is a long standing question. We developed a new coalescent-based method that collectively assigned human genome regions to modes of neutrality or to positive, negative, or balancing selection. Most importantly, the selection times were estimated for all positive selection signals, which ranged over the last half million years, penetrating the emergence of anatomically modern human (AMH). These selection time estimates were further supported by analyses of the genome sequences from three ancient AMHs and the Neanderthals. A series of brain function-related genes were found to carry signals of ancient selective sweeps, which may have defined the evolution of cognitive abilities either before Neanderthal divergence or during the emergence of AMH. Particularly, signals of brain evolution in AMH are strongly related to Alzheimer's disease pathways. In conclusion, this study reports a chronological atlas of natural selection in Human.

5: Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia
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Posted to bioRxiv 08 Mar 2018

Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia
6,654 downloads evolutionary biology

Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, J. Víctor Moreno Mayar, Uffe Gram Wilken, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Ana Prohaska, Ashot Margarayan, Peter de Barros Damgaard, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Supannee Kaewsutthi, Patcharee Lertrit, Huong Mai Nguyen, Hsiao-chun Hung, Thi Minh Tran, Huu Nghia Truong, Shaiful Shahidan, Ketut Wiradnyana, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Bérénice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham, Robert A. Foley, Marta Mirazón Lahr, Ludovic Orlando, Martin Sikora, Charles Higham, David M. Lambert, Eske Willerslev

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

6: Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago
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Posted to bioRxiv 05 Jun 2017

Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago
6,572 downloads evolutionary biology

Carina M Schlebusch, Helena Malmström, Torsten Günther, Per Sjödin, Alexandra Coutinho, Hanna Edlund, Arielle R Munters, Maryna Steyn, Himla Soodyall, Marlize Lombard, Mattias Jakobsson

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region's human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|'hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) 'hot spot' for the evolution of our species.

7: Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations
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Posted to bioRxiv 12 May 2016

Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations
5,538 downloads evolutionary biology

Yann X.C. Bourgeois, Khaled M Hazzouri, Ben H. Warren

1. Characterizing species history and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species. 2. The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a burst of analytical tools that can confuse users. 3. Such confusion can limit the amount of information effectively retrieved from complex genomic datasets. In addition, the lack of a unified analytical pipeline impairs the diffusion of the most recent analytical tools into fields like conservation biology. 4. To address this need, we describe possible analytical protocols and link these with more than 70 methods dealing with genome-scale datasets. We summarise the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

8: Reduced signal for polygenic adaptation of height in UK Biobank
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Posted to bioRxiv 25 Jun 2018

Reduced signal for polygenic adaptation of height in UK Biobank
4,920 downloads evolutionary biology

Jeremy J. Berg, Arbel Harpak, Nicholas A Sinnott-Armstrong, Anja Moltke Joergensen, Hakhamanesh Mostafavi, Yair Field, Evan A Boyle, Xinjun Zhang, Fernando Racimo, Jonathan K Pritchard, Graham Coop

Several recent papers have reported strong signals of selection on European polygenic height scores. These analyses used height effect estimates from the GIANT consortium and replication studies. Here, we describe a new analysis based on the the UK Biobank (UKB), a large, independent dataset. We find that the signals of selection using UKB effect-size estimates for height are strongly attenuated or absent. We also provide evidence that previous analyses were confounded by population stratification Therefore, the conclusion of strong polygenic adaptation now lacks support. Moreover, these discrepancies highlight (1) that methods for correcting for population stratification in GWAS may not always be sufficient for polygenic trait analyses, and (2) that claims of differences in polygenic scores between populations should be treated with caution until these issues are better understood.

9: Genetic landscapes reveal how human genetic diversity aligns with geography
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Posted to bioRxiv 13 Dec 2017

Genetic landscapes reveal how human genetic diversity aligns with geography
4,818 downloads evolutionary biology

Benjamin M Peter, Desislava Petkova, John Novembre

Summarizing spatial patterns in human genetic diversity to understand population history has been a persistent goal for human geneticists. Here, we use a recently developed spatially explicit method to estimate "effective migration" surfaces to visualize how human genetic diversity is geographically structured (the EEMS method). The resulting surfaces are "rugged", which indicates the relationship between genetic and geographic distance is heterogenous and distorted as a rule. Most prominently, topographic and marine features regularly align with increased genetic differentiation (e.g. the Sahara desert, Mediterranean Sea or Himalaya at large scales; the Adriatic, inter-island straits in near Oceania at smaller scales). We also see traces of historical migrations and boundaries of language families. These results provide visualizations of human genetic diversity that reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, there have regularly been factors that subtly distort the underlying relationship across space observed today. The fine-scale population structure depicted here is relevant to understanding complex processes of human population history and may provide insights for geographic patterning in rare variants and heritable disease risk.

10: Extreme positive allometry of animal adhesive pads and the size limits of adhesion-based climbing.
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Posted to bioRxiv 07 Dec 2015

Extreme positive allometry of animal adhesive pads and the size limits of adhesion-based climbing.
4,410 downloads evolutionary biology

David Labonte

Organismal functions are size-dependent whenever body surfaces supply body volumes. Larger organisms can develop strongly folded internal surfaces for enhanced diffusion, but in many cases areas cannot be folded so that their enlargement is constrained by anatomy, presenting a problem for larger animals. Here, we study the allometry of adhesive pad area in 225 climbing animal species, covering more than seven orders of magnitude in weight. Across all taxa, adhesive pad area showed extreme positive allometry and scaled with weight, implying a 200-fold increase of relative pad area from mites to geckos. However, allometric scaling coefficients for pad area systematically decreased with taxonomic level, and were close to isometry when evolutionary history was accounted for, indicating that the substantial anatomical changes required to achieve increases in relative pad area are limited by phylogenetic constraints. Using a comparative phylogenetic approach, we found that the departure from isometry is almost exclusively caused by large differences in size-corrected pad area between arthropods and vertebrates. To mitigate the expected decrease of weight-specific adhesion within closely related taxa where pad area scaled close to isometry, data for several taxa suggest that the pads' adhesive strength increased for larger animals. The combination of adjustments in relative pad area for distantly related taxa and changes in adhesive strength for closely related groups helps explain how climbing with adhesive pads has evolved in animals varying over seven orders of magnitude in body weight. Our results illustrate the size limits of adhesion-based climbing, with profound implications for large-scale bio-inspired adhesives.

11: The infinitesimal model
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Posted to bioRxiv 15 Feb 2016

The infinitesimal model
4,345 downloads evolutionary biology

N H Barton, A M Etheridge, A Véber

Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. We first review the long history of the infinitesimal model in quantitative genetics. Then we provide a definition of the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, ... We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. In each case, by conditioning on the pedigree relating individuals in the population, we incorporate arbitrary selection and population structure. We suppose that we can observe the pedigree up to the present generation, together with all the ancestral traits, and we show, in particular, that the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order M^{-1/2}. Simulations suggest that in particular cases the convergence may be as fast as 1/M.

12: The hidden elasticity of avian and mammalian genomes
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Posted to bioRxiv 16 Oct 2016

The hidden elasticity of avian and mammalian genomes
4,256 downloads evolutionary biology

Aurélie Kapusta, Alexander Suh, Cédric Feschotte

Genome size in mammals and birds shows remarkably little interspecific variation compared to other taxa. Yet, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been co-variation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size homeostasis. To test this model, we develop a computational pipeline to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 million years (My) in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extent across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified 'accordion' model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.

13: Adaptive evolution within the gut microbiome of individual people
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Posted to bioRxiv 24 Oct 2017

Adaptive evolution within the gut microbiome of individual people
4,115 downloads evolutionary biology

Shijie Zhao, Tami D. Lieberman, Mathilde Poyet, Sean M. Gibbons, Mathieu Groussin, Ramnik J. Xavier, Eric J. Alm

Individual bacterial lineages stably persist for years in the human gut microbiome. However, it is unknown if these lineages adapt during colonization of healthy people. Here, we assess evolution within individual microbiomes by sequencing the genomes of 602 Bacteroides fragilis isolates cultured from 12 healthy subjects. We find that B. fragilis within-subject populations contain significant de novo nucleotide and mobile element diversity, which preserve years of within-person evolutionary history. This evolutionary history contains signatures of within-person adaptation to both subject-specific and common selective forces, including parallel mutations in seventeen genes. These seventeen genes are involved in cell-envelope biosynthesis and polysaccharide utilization, as well as yet under-characterized pathways. Notably, one of these genes has been shown to be critical for B. fragilis colonization in mice, indicating that key genes have not already been optimized for survival in vivo. This lack of optimization, given historical signatures of purifying selection in these genes, suggests that varying selective forces with discordant solutions act upon B. fragilis in vivo. Remarkably, in one subject, two B. fragilis sublineages coexisted at a stable relative frequency over a 1.5-year period despite rapid adaptive dynamics within one of the sublineages. This stable coexistence suggests that competing selective forces can lead to B. fragilis niche-differentiation even within a single person. We conclude that B. fragilis adapts rapidly within the microbiomes of individual healthy people, providing a new route for the discovery of key genes in the microbiome and implications for microbiome stability and manipulation.

14: A zombie LIF gene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage
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Posted to bioRxiv 12 Sep 2017

A zombie LIF gene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage
4,097 downloads evolutionary biology

Juan Manuel Vazquez, Michael Sulak, Sravanthi Chigurupati, Vincent Lynch

Among the evolutionary and developmental constraints on the evolution of very large body sizes is an increased risk of developing cancer because large bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms with fewer cells. This expectation predicts a positive correlation between body size and cancer risk, however, there is no correlation between body size and cancer risk across species; this lack of correlation is often referred to as "Peto's Paradox". Here we show that elephants and their extinct relatives (Proboscideans) resolved Peto's Paradox at least in part through re-functionalizing a leukemia inhibitory factor pseudogene (LIF6) with pro-apoptotic functions. The re-functionalized LIF gene is transcriptionally up-regulated by TP53 in response to DNA damage, and translocates to the mitochondria where it induces apoptosis. Phylogenetic analyses of living and extinct Proboscidean LIF6 genes indicates its TP53 response element evolved coincident with the evolution of large body sizes in the Proboscidean stem-lineage. These results suggest that re-functionalizing of a pro-apoptotic LIF pseudogene may have played a role in the evolution of large body sizes in Proboscideans.

15: Independent evolution of ab- and adaxial stomatal density enables adaptation
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Posted to bioRxiv 15 Dec 2015

Independent evolution of ab- and adaxial stomatal density enables adaptation
4,043 downloads evolutionary biology

Christopher David Muir

Are organisms free to reach their adaptive optima or constrained by hard-wired developmental programs? Recent evidence suggests that the arrangement of stomata on abaxial (lower) and adaxial (upper) leaf surfaces may be an important adaptation in plants, but stomatal traits on each surface likely share developmental pathways that could hamper evolution. We reviewed the quantitative genetics of stomatal density to look for loci that (1) affected ab- or adaxial density independently or (2) pleiotropically affected stomatal density on both surfaces. We also used phylogenetic comparative methods to test for independent versus correlated evolution of stomatal traits (density, size, and pore index) on each surface from 14 amphistomatous wild tomato taxa (Solanum; Solanaceae). Naturally occurring and laboratory-induced genetic variation alters stomatal density on one surface without affecting the other, indicating that development does not strongly constrain the spectrum of available mutations. Among wild tomato taxa, traits most closely related to function (stomatal pore index and density) evolved independently on each surface, whereas stomatal size was constrained by correlated evolution. Genetics and phylogenetics demonstrate mostly independent evolution of stomatal function on each leaf surface, facilitating largely unfettered access to fitness optima.

16: Niche construction in evolutionary theory: the construction of an academic niche?
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Posted to bioRxiv 19 Feb 2017

Niche construction in evolutionary theory: the construction of an academic niche?
3,973 downloads evolutionary biology

Manan Gupta, N G Prasad, Sutirth Dey, Amitabh Joshi, T. N. C. Vidya

In recent years, fairly far-reaching claims have been repeatedly made about how niche construction, the modification by organisms of their environment, and that of other organisms, represents a vastly neglected phenomenon in ecological and evolutionary thought. The proponents of this view claim that the niche construction perspective greatly expands the scope of standard evolutionary theory and that niche construction deserves to be treated as a significant evolutionary process in its own right, almost at par with natural selection. Claims have also been advanced about how niche construction theory represents a substantial extension to, and re-orientation of, standard evolutionary theory, which is criticized as being narrowly gene-centric and ignoring the rich complexity and reciprocity of organism-environment interactions. We examine these claims in some detail and show that they do not stand up to scrutiny. We suggest that the manner in which niche construction theory is sought to be pushed in the literature is better viewed as an exercise in academic niche construction whereby, through incessant repetition of largely untenable claims, and the deployment of rhetorically appealing but logically dubious analogies, a receptive climate for a certain sub-discipline is sought to be manufactured within the scientific community. We see this as an unfortunate, but perhaps inevitable, nascent post-truth tendency within science.

17: The Genetic Cost of Neanderthal Introgression
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Posted to bioRxiv 30 Oct 2015

The Genetic Cost of Neanderthal Introgression
3,883 downloads evolutionary biology

Kelley Harris, Rasmus Nielsen

Approximately 2-4\% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.

18: Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)
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Posted to bioRxiv 28 Jan 2016

Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)
3,806 downloads evolutionary biology

Stephen E. Harris, Jason Munshi-South

Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations, and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP dataset under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes, and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in NYC are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggest selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.

19: Trees, Population Structure, F-statistics!
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Posted to bioRxiv 09 Oct 2015

Trees, Population Structure, F-statistics!
3,765 downloads evolutionary biology

Benjamin M Peter

Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose are F-statistics, that measure shared genetic drift between sets of two, three and four populations, and can be used to test simple and complex hypotheses about admixture between populations. Here, we put these statistics in context of phylogenetic and population genetic theory. We show how measures of genetic drift can be interpreted as branch lengths, paths through an admixture graph or in terms of the internal branches in coalescent trees. We show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing us to generalize applications for arbitrary phylogenetic trees. Furthermore, we derive novel expressions for the F-statistics, which enables us to explore the behavior of F-statistic under population structure models. In particular, we show that population substructure may complicate inference.

20: Unravelling the diversity behind Ophiocordyceps unilateralis complex: Three new species of Zombie-Ant fungus from Brazilian Amazon
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Posted to bioRxiv 03 Apr 2014

Unravelling the diversity behind Ophiocordyceps unilateralis complex: Three new species of Zombie-Ant fungus from Brazilian Amazon
3,760 downloads evolutionary biology

João P. M. Araújo, Harry C Evans, David M Geiser, William P Mackay, David P. Hughes

In tropical forests, one of the most common relationships between parasites and insects is that between the fungus Ophiocordyceps (Ophiocordycipitaceae, Hypocreales, Ascomycota) and ants, especially within the tribe Camponotini. These fungi have the ability to penetrate the exoskeleton of the ant and to manipulate the behavior of the host, making it leave the nest and ascend understorey shrubs, to die biting onto the vegetation: hence, the term zombie-ant fungi to describe this behavioral changes on the host. It is posited that this behavioral change aids spore dispersal and thus increases the chances of infection. Despite their undoubted importance for ecosystem functioning, these fungal pathogens are still poorly documented, especially regarding their diversity, ecology and evolutionary relationships. Here, we describe three new and host-specific species of the genus Ophiocordyceps on Camponotus ants from the central Amazonian region of Brazil which can readily be separated using classic taxonomic criteria, in particular ascospore morphology. In addition, we also employed molecular techniques to show for the first time the phylogenetic relationships between these taxa and closely related species within the Ophiocordyceps unilateralis complex, as well as with other members of the family Ophiocordycipitaceae.

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