Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

The processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F3 hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long-standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential

Nitrogen Oxide Concentrations in Natural Waters on Early Earth

A key challenge in origins-of-life studies is estimating the abundances of species relevant to the chemical pathways proposed to have contributed to the emergence of life on early Earth. Dissolved nitrogen oxide anions (NO$_{X}^{-}$), in particular nitrate (NO$_{3}^{-}$) and nitrite (NO$_{2}^{-}$), have been invoked in diverse origins-of-life chemistry, from the oligomerization of RNA to the emergence of protometabolism. Recent work has calculated the supply of NO$_{X}^{-}$ from the prebiotic atmosphere to the ocean, and reported steady-state [NO$_{X}^{-}$] to be high across all plausible parameter space. These findings rest on the assumption that NO$_{X}^{-}$ is stable in natural waters unless processed at a hydrothermal vent. Here, we show that NO$_{X}^{-}$ is unstable in the reducing environment of early Earth. Sinks due to UV photolysis and reactions with reduced iron (Fe$^{2+}$) suppress [NO$_{X}^{-}$] by several orders of magnitude relative to past predictions. For pH$=6.5-8$ and $T=0-50^\circ$C, we find that it is most probable that NO$_{X}^{-}$]$<1~\mu$M in the prebiotic ocean. On the other hand, prebiotic ponds with favorable drainage characteristics may have sustained [NO$_{X}^{-}$]$\geq 1~\mu$M. As on modern Earth, most NO$_{X}^{-}$ on prebiotic Earth should have been present as NO$_{3}^{-}$, due to its much greater stability. These findings inform the kind of prebiotic chemistries that would have been possible on early Earth. We discuss the implications for proposed prebiotic chemistries, and highlight the need for further studies of NO$_{X}^{-}$ kinetics to reduce the considerable uncertainties in predicting [NO$_{X}^{-}$] on early Earth.Comment: In review for publication at Geochemistry, Geophysics, and Geosystems (G-cubed). Comments, questions, and criticism solicited; please contact corresponding author at [email protected]. SI at: https://web-cert.mit.edu/sukrit/Public/nox_si.pdf. GitHub at: https://github.com/sukritranjan/no

Using mathematical modelling to investigate the adaptive divergence of whitefish in Fennoscandia

Modern speciation theory has greatly benefited from a variety of simple mathematical models focusing on the conditions and patterns of speciation and diversification in the presence of gene flow. Unfortunately the application of general theoretical concepts and tools to specific ecological systems remains a challenge. Here we apply modeling tools to better understand adaptive divergence of whitefish during the postglacial period in lakes of northern Fennoscandia. These lakes harbor up to three different morphs associated with the three major lake habitats: littoral, pelagic, and profundal. Using large-scale individual-based simulations, we aim to identify factors required for in situ emergence of the pelagic and profundal morphs in lakes initially colonized by the littoral morph. The importance of some of the factors we identify and study - sufficiently large levels of initial genetic variation, size- and habitat-specific mating, sufficiently large carrying capacity of the new niche - is already well recognized. In addition, our model also points to two other factors that have been largely disregarded in theoretical studies: fitness-dependent dispersal and strong predation in the ancestral niche coupled with the lack of it in the new niche(s). We use our theoretical results to speculate about the process of diversification of whitefish in Fennoscandia and to identify potentially profitable directions for future empirical research.Peer reviewe

Evolution of a stream ecosystem in recently deglaciated terrain

Climate change and associated glacial recession create new stream habitat that leads to the assembly of new riverine communities through primary succession. However, there are still very few studies of the patterns and processes of community assembly during primary succession for stream ecosystems. We illustrate the rapidity with which biotic communities can colonize and establish in recently formed streams by examining Stonefly Creek in Glacier Bay, Alaska (USA), which began to emerge from a remnant glacial ice mass between 1976 and 1979. By 2002, 57 macroinvertebrate and 27 microcrustacea species had become established. Within 10 years of the stream's formation, pink salmon and Dolly Varden charr colonized, followed by other fish species, including juvenile red and silver salmon, Coast Range sculpin, and sticklebacks. Stable-isotope analyses indicate that marine-derived nitrogen from the decay of salmon carcasses was substantially assimilated within the aquatic food web by 2004. The findings from Stonefly Creek are compared with those from a long-term study of a similarly formed but older stream (12 km to the northeast) to examine possible similarities in macroinvertebrate community and biological trait composition between streams at similar stages of development. Macroinvertebrate community assembly appears to have been initially strongly deterministic owing to low water temperature associated with remnant ice masses. In contrast, microcrustacean community assembly appears to have been more stochastic. However, as stream age and water temperature increased, macroinvertebrate colonization was also more stochastic, and taxonomic similarity between Stonefly Creek and a stream at the same stage of development was,<50%. However the most abundant taxa were similar, and functional diversity of the two communities was almost identical. Tolerance is suggested as the major mechanism of community assembly. The rapidity with which salmonids and invertebrate communities have become established across an entire watershed has implications for the conservation of biodiversity in freshwater habitats

Superprocesses as models for information dissemination in the Future Internet

Future Internet will be composed by a tremendous number of potentially interconnected people and devices, offering a variety of services, applications and communication opportunities. In particular, short-range wireless communications, which are available on almost all portable devices, will enable the formation of the largest cloud of interconnected, smart computing devices mankind has ever dreamed about: the Proximate Internet. In this paper, we consider superprocesses, more specifically super Brownian motion, as a suitable mathematical model to analyse a basic problem of information dissemination arising in the context of Proximate Internet. The proposed model provides a promising analytical framework to both study theoretical properties related to the information dissemination process and to devise efficient and reliable simulation schemes for very large systems

Rendition in the "War on Terror"

The CIA’s rendition, detention and interrogation (RDI) programme was a central component of the first phase of the ‘war on terror’, from 2001-2008. Through constructing a global network of secret prisons, wherein hundreds of terror suspects were tortured, the US and its allies embarked upon a concerted campaign of state terrorism in pursuit of their wider political goals. This chapter provides an account of the employment of state terror through the CIA’s RDI programme. We outline the main features of the programme, and the involvement of a range of other states, many of which were Western democracies. We also show that the attempt to secure valuable intelligence through coercion, torture and terror proved to be a clear failure, resulting in the detention and torture of dozens of individuals who posed no threat and the use of barbaric methods which did nothing but produce poor intelligence and dehumanise all those involved

Reconstructing Prehistoric Civilizations in a New Theory of Civilizations

A new mathematical theory of the oscillations of civilizations is successfully applied to Mayan, pre-historic Egyptian, sub-Saharan African (Great Zimbabwe) and prehistoric Chinese civilizations