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Synthetic Astrobiology
Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.
Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.
Temporal partitioning of hatching, maturation, and surface activity by reptiles in Florida longleaf pine-wiregrass sandhills
Temporal partitioning of life history traits among syntopic reptiles can facilitate co-occurrence, but may be influenced by environmental factors and evolutionary history. We used 24 years of continuous capture data in the Florida sandhills to evaluate the timing and duration of hatching, maturation and/or surface activity for ten reptile species, spanning multiple clutch strategies, taxonomic relationships, and habits. We hypothesised: i) species would differ in seasonal timing of hatching and maturation; ii) hatching and maturation periods would be more seasonally-synchronised in fossorial than terrestrial or semi-aquatic reptiles; iii) monthly and annual temperature anomalies would be positively related to hatching, maturation, and surface activity anomalies, and iv) groupings of reptiles by clutch strategy, taxonomic relationship, and habit, would explain more variation in the timing and duration of hatching and maturation than species alone. Seasonal timing of response variables varied widely among species. Hatching peaked for > 1 species during most calendar months. Maturation and surface activity periods ranged from aseasonal to highly-seasonal among species. Hatching began 1.5 months earlier and was more prolonged for terrestrial than fossorial species overall. Hatching peaked in early to mid-summer for terrestrial and fossorial species, and winter for the semi-aquatic Kinosternon subrubrum. Terrestrial and fossorial species did not differ in average timing, duration, or overlap of maturation periods; semi-aquatic Liodytes pygaea matured more consistently across all seasons than other species. Monthly temperature anomalies were negatively correlated with monthly maturation for Plestiodon egregius. Annual temperature and precipitation anomalies were related to annual hatching, maturation, and surface activity trends for several species. Taxonomic relationship, habit, and species explained some variation in hatching and maturation timing and duration. Our results illustrate the influence of environment and evolutionary relationships on the timing of important life history traits. Keywords: Age class, Drift fence, Community, Interspecific, Life history
Calculations of the effects of angular momentum on the early evolution of Jupiter
Early phases in the evolutionary development of a rotating cloud of gas and dust are investigated to determine whether physically reasonable initial conditions are likely to produce a planet-satellite system with the values of specific orbital angular momentum currently observed for Jupiter and its inner satellites. Spherically symmetric computations of Jupiter's evolutionary history are reviewed, and transport of angular momentum is considered along with evolutionary sequences of individual differentially rotating models with decreasing values of equatorial radius. The problem of accounting for the present specific orbital angular momenta of Jupiter and its regular satellites is examined qualitatively, and a range of possible angular-momentum distributions in an initially tidally unstable cloud is assessed. The results show that particular physically plausible angular-momentum distributions, which could either be established as initial conditions or be caused by angular-momentum transport, will lead to favorable situations for the formation of a central planet and a surrounding rotating cloud with specific angular momentum comparable to that of the regular satellites.
Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model
Abstract Motivation The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method. Novel studies suggest that ASTRAL also performs well when given multi-locus gene trees in simulation studies. Further, Legried et al. recently demonstrated that ASTRAL is statistically consistent under the gene duplication and loss model (GDL). GDL is prevalent in evolutionary histories and is the first core process in the powerful duplication-loss-coalescence evolutionary model (DLCoal) by Rasmussen and Kellis. Results In this work, we prove that ASTRAL is statistically consistent under the general DLCoal model. Therefore, our result supports the empirical evidence from the simulation-based studies. More broadly, we prove that the quartet-based inference approach is statistically consistent under DLCoal. Supplementary information Supplementary data are available at Bioinformatics online.
Tomographic separation of composite spectra. The components of Plaskett's Star
The UV photospheric lines of Plaskett's Star (HD 47129), a 14.4 day period, double lined O-type spectroscopic binary were analyzed. Archival data from IUE (17 spectra well distributed in orbital phase) were analyzed with several techniques. A cross correlation analysis, which showed that the secondary produces significant lines in the UV, indicates that the mass ratio is q = 1.18 + or - 0.12 (secondary slightly more massive). A tomography algorithm was used to produce the separate spectra of the two stars in six spectral regions. The interpolated spectral classifications of the primary and secondary, 07.3 I and 06.2 I, respectively, were estimated through a comparison of UV line ratios with those in spectral standard stars. The intensity ratio of the stars in the UV is 0.53 + or - 0.05 (primary brighter). The secondary lines appear rotationally broadened, and the projected rotational velocity V sin i for this star is estimated to be 310 + or - 20 km/s. The possible evolutionary history of this system is discussed through a comparison of the positions of the components and evolutionary tracks in the H-R diagram.
Tomographic separation of composite spectra. I - The components of Plaskett's Star
The UV photospheric lines of Plaskett's Star (HD 47129), a 14.4 day period, double lined O-type spectroscopic binary were analyzed. Archival data from IUE (17 spectra well distributed in orbital phase) were analyzed with several techniques. A cross correlation analysis, which showed that the secondary produces significant lines in the UV, indicates that the mass ratio is q = 1.18 +/- 0.12 (secondary slightly more massive). A tomography algorithm was used to produce the separate spectra of the two stars in six spectral regions. The interpolated spectral classifications of the primary and secondary, 07.3 I and 06.2 I, respectively, were estimated through a comparison of UV line ratios with those in spectral standard stars. The intensity ratio of the stars in the UV is 0.53 +/- 0.05 (primary brighter). The secondary lines appear rotationally broadened, and the projected rotational velocity V sin i for this star is estimated to be 310 +/- 20 km/s. The possible evolutionary history of this system is discussed through a comparison of the positions of the components and evolutionary tracks in the H-R diagram.
Adaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating Environments
Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypic plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.
The Evolution of Sulfide Tolerance in the Cyanobacteria
Understanding how the function of extant microorganisms has recorded both their evolutionary histories and their past interactions with the environment is a stated goal of astrobiology. We are taking a multidisciplinary approach to investigate the diversification of sulfide tolerance mechanisms in the cyanobacteria, which vary both in their degree of exposure to sulfide and in their capacity to tolerate this inhibitor of photosynthetic electron transport. Since conditions were very reducing during the first part of Earth's history and detrital sulfides have been found in Archean sediments, mechanisms conferring sulfide tolerance may have been important for the evolutionary success of the ancestors of extant cyanobacteria. Two tolerance mechanisms have been identified in this group: (1) resistance of photosystem II, the principal target of sulfide toxicity; and (2) maintenance of the ability to fix carbon despite photosystem II inhibition by utilizing sulfide as an electron donor in photosystem I - dependent, anoxygenic photosynthesis. We are presently collecting comparative data on aspects of sulfide physiology for laboratory clones isolated from a variety of habitats. These data will be analyzed within a phylogenetic framework inferred from molecular sequence data collected for these clones to test how frequently different mechanisms of tolerance have evolved and which tolerance mechanism evolved first. In addition, by analyzing these physiological data together with environmental sulfide data collected from our research sites using microelectrodes, we can also test whether the breadth of an organism's sulfide tolerance can be predicted from the magnitude of variation in environmental sulfide concentration it has experienced in its recent evolutionary past and whether greater average sulfide concentration and/or temporal variability in sulfide favors the evolution of a particular mechanism of sulfide tolerance.
Abundances of volatile-bearing phases in carbonaceous chondrites and cooling rates of meteorites based on cation ordering of orthopyroxenes
Results of preliminary calculations of volatile abundances in carbonaceous chondrites are discussed. The method (Ganguly 1982) was refined for the calculation of cooling rate on the basis of cation ordering in orthopyroxenes, and it was applied to the derivation of cooling rates of some stony meteorites. Evaluation of cooling rate is important to the analysis of condensation, accretion, and post-accretionary metamorphic histories of meteorites. The method of orthopyroxene speedometry is widely applicable to meteorites and would be very useful in the understanding of the evolutionary histories of carbonaceous chondrites, especially since the conventional metallographic and fission track methods yield widely different results in many cases. Abstracts are given which summarize the major conclusions of the volatile abundance and cooling rate calculations.
Understanding the role of morphology and environment in the dynamical evolution of isolated galaxy triplets
The environments where galaxies reside affects their evolutionary histories. Galaxy triplets (systems composed of three physically bound galaxies) are one of simplest groups of galaxies, and are therefore excellent laboratories to study evolutionary mechanisms where effects of the environment are minimal. We present a statistical study of the dynamical properties of isolated galaxy triplets as a function of their local and large-scale environments. To explore the connection of the dynamical evolution on the systems with the evolution of the galaxies composing the triplets, we consider observational properties such as morphology and star formation rate (SFR). We used the SDSS-based catalogue of Isolated Triplets (SIT), which contains 315 triplets. We classified each triplet according to galaxy morphologies and defined a parameter Q trip to quantify the total local tidal strengths in the systems. To quantify the dynamical stage of the system we used the parameters of harmonic radius R H , velocity dispersion σvr, crossing time H 0 t c , and virial mass M vir . Triplets composed of three early-type galaxies present the smallest R H , indicating that they are in general more compact than triplets with one or more late-type galaxies. Among triplets with low values of R H and H 0 t c , SIT triplets with Q trip < –2 are relaxed systems that are more dynamically evolved, while triplets with Q trip > –2 show compact configurations due to interactions within the system, such as ongoing mergers. We found that there is no dominant galaxy in triplets in terms of properties of stellar populations such as global colour and SFR. Moreover, the global SFR in isolated triplets composed of two or more early-type galaxies increases with the stellar mass ratio of the galaxies with respect to the central galaxy, therefore the system is globally ‘rejuvenated’.
Phylogenetic Conservatism in Plant Phenology
Phenological events defined points in the life cycle of a plant or animal have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism the tendency for closely related species to share similar ecological and biological attributes in phenological traits across flowering plants. We aggregated published and unpublished data on timing of first flower and first leaf, encompassing 4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the set of included species, first, using the software program Phylomatic, and second, from DNA data. We then quantified phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to flower and leaf at similar times. By contrasting mean flowering times within and across sites, however, we illustrate that it is not the time of year that is conserved, but rather the phenological responses to a common set of abiotic cues. Our findings suggest that species cannot be treated as statistically independent when modelling phenological responses.Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories.
Investigating the Geological History of Asteroid 101955 Bennu Through Remote Sensing and Returned Sample Analyses
The NASA New Frontiers Mission OSRIS-REx will return surface regolith samples from near-Earth asteroid 101955 Bennu in September 2023. This target is classified as a B-type asteroid and is spectrally similar to CI and CM chondrite meteorites [1]. The returned samples are thus expected to contain primitive ancient Solar System materials that formed in planetary, nebular, interstellar, and circumstellar environments. Laboratory studies of primitive astromaterials have yielded detailed constraints on the origins, properties, and evolutionary histories of a wide range of Solar System bodies. Yet, the parent bodies of meteorites and cosmic dust are generally unknown, genetic and evolutionary relationships among asteroids and comets are unsettled, and links between laboratory and remote observations remain tenuous. The OSIRIS-REx mission will offer the opportunity to coordinate detailed laboratory analyses of asteroidal materials with known and well characterized geological context from which the samples originated. A primary goal of the OSIRIS-REx mission will be to provide detailed constraints on the origin and geological and dynamical history of Bennu through coordinated analytical studies of the returned samples. These microanalytical studies will be placed in geological context through an extensive orbital remote sensing campaign that will characterize the global geological features and chemical diversity of Bennu. The first views of the asteroid surface and of the returned samples will undoubtedly bring remarkable surprises. However, a wealth of laboratory studies of meteorites and spacecraft encounters with primitive bodies provides a useful framework to formulate priority scientific questions and effective analytical approaches well before the samples are returned. Here we summarize our approach to unraveling the geological history of Bennu through returned sample analyses.
A transient heating event in the history of a highlands troctolite from Apollo 12 soil 12033
A 2-mm particle, consisting of a troctolite clast attached to a small amount of glassy soil breccia, was found in a thin section of grains from Apollo 12 sample 12033,66. A description is given of the evolutionary history of the troctolite, taking into account the unique texture. It appears that the particle was broken from its parent rock and projected to Oceanus Procellarum from a source area in the highlands. Before, during, or after the flight, the troctolite was welded to a soil breccia by a minor amount of melting along the contact. It is argued that two separate heating events may be involved. The hypothesis is considered that the partial remelting and quenching of the troctolite took place very rapidly. Attention is given to melting experiments which test and confirm this hypothesis.
The dark side of galaxy stellar populations – II. The dependence of star-formation histories on halo mass and on the scatter of the main sequence
Nearby galaxies are the end result of their cosmological evolution, which is predicted to be influenced by the growth of their host dark matter haloes. This co-evolution potentially leaves signatures in present-day observed galaxy properties, which might be essential to further understand how the growth and properties of galaxies are connected to those of their host haloes. In this work, we study the evolutionary histories of nearby galaxies both in terms of their host haloes and the scatter of the star-forming main sequence by investigating their time-resolved stellar populations using absorption optical spectra drawn from the Sloan Digital Sky Survey. We find that galaxy star-formation histories depend on the masses of their host haloes, and hence they shape the evolution of the star-forming main sequence over cosmic time. Additionally, we also find that the scatter around the z = 0 star-forming main sequence is not (entirely) stochastic, as galaxies with currently different star-formation rates have experienced, on average, different star-formation histories. Furthermore, our findings suggest that dark matter haloes might play a key role in modulating the evolution of star formation in galaxies, and thus of the main sequence, and further demonstrate that galaxies at different evolutionary stages contribute to the observed scatter of this relation.
Plastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection
Comparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as a powerful model for studying evolutionary processes in monocots. We analyzed 287 plastomes across the native circum-Mediterranean range of the three annual Brachypodium species ( B. distachyon, B. stacei, B. hybridum ), focusing on their structural variation, selection patterns and phylogenomic relationships. Our analyses confirmed the differentiation of the S and D plastomes, inherited respectively from the diploid progenitor species B. stacei and B. distachyon . We identified novel structural rearrangements and indels, and unique repeat motifs, along with widespread heteroplasmy, particularly in ancestral B. hybridum -D plastotypes. SNP diversity varied among plastotypes, reflecting population dynamics and evolutionary histories, with B. hybridum -D plastotypes showing the highest normalized diversity and B. hybridum -S the lowest. Positive selection was detected in 29 plastid genes by Tajima’s neutrality test, and in nine genes by site and branch-site evolutionary models, including matK, ndhF, rbcL, and rpoC2. Phylogenomic analyses revealed well-supported clades corresponding to the S and D plastome lineages, with frequent chloroplast capture events and long-distance dispersals shaping their evolutionary trajectories.
Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa
The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.