Evolution Of Isolation Research Articles

A fine-grained investigation on the predictors of urban green space growth in Nanjing

ABSTRACT Existing studies have primarily examined urban green space (UGS) evolution in isolation from the urban development context, neglecting the dynamicity of the factors affecting UGS growth in different spatiotemporal conditions and urban development levels. Taking Nanjing as the study site, we constructed spatial lag models using multi-source data and investigated the patterns and predictors of UGS growth across diverse spatiotemporal conditions in high-density environments. The model results show that: (1) although good natural conditions can support UGS development, this effect is greatly weakened in fast urban expansion as other land uses show higher priority in land occupation; (2) industrial and public service lands and commercial lands show a negative effect on UGS growth in the early and late urbanization, respectively, while residential lands demonstrated sustained negative effect in all the urbanization phases; (3) the effect of the total population and population structure varies in different urban development phases; (4) at an advanced urban development level, the areas close to city centre have better opportunities to install new UGSs. These findings offer useful references to the decision makers and planners, especially for their work on the UGS layout optimization within the high-density areas.

Evolutionary history of an island endemic, the Azorean common quail.

Oceanic islands are characterized by conditions that favour diversification into endemic lineages that can be very different from their mainland counterparts. This can be the result of fast phenotypic divergence due to drift or the result of slower adaptation to local conditions. This uniqueness can obscure their evolutionary history. Here we used morphological, stable isotope, genetic and genomic data to characterize common quails (Coturnix coturnix) in the Azores archipelago and assess the divergence from neighbouring common quail populations. Historical documents suggested that these quails could have a recent origin associated with the arrival of humans in the last centuries. Our results show that Azorean quails constitute a well-differentiated lineage with small size and dark throat pigmentation that has lost the migratory ability and that diverged from mainland quail lineages more than 0.8 mya, contrary to the notion of a recent human-mediated arrival. Even though some Azorean quails carry an inversion that affects 115 Mbp of chromosome 1 and that has been associated with the loss of the migratory behaviour in other common quail populations, half of the analysed individuals do not have that inversion and still do not migrate. The long coexistence and evolution in isolation in the Azores of two chromosomal variants (with and without the inversion) is best explained by balancing selection. Thus, a unique and long evolutionary history led to the island endemic that we know today, C. c. conturbans.

Redshift and stellar mass dependence of intrinsic shapes of disc-dominated galaxies from COSMOS observations below z = 1.0

ABSTRACT The high abundance of disc galaxies without a large central bulge challenges predictions of current hydrodynamic simulations of galaxy formation. We aim to shed light on the formation of these objects by studying the redshift and mass dependence of their intrinsic 3D shape distributions in the COSMOS galaxy survey below redshift z = 1.0. This distribution is inferred from the observed distribution of 2D shapes, using a reconstruction method which we test using hydrodynamic simulations. Our tests reveal a moderate bias for the inferred average disc circularity and relative thickness, but a large bias on the dispersion of these quantities. Applying the reconstruction method on COSMOS data, we find variations of the average disc circularity and relative thickness with redshift of around ∼1 per cent and ∼10 per cent, respectively, which is comparable to the error estimates on these quantities. The average relative disc thickness shows a significant mass dependence which can be accounted for by the scaling of disc radius with galaxy mass. We conclude that our data provides no evidence for a strong dependence of the average circularity and absolute thickness of disc-dominated galaxies on redshift and mass that is significant with respect to the statistical uncertainties in our analysis. These findings are expected in the absence of disruptive merging or feedback events that would affect galaxy shapes. They hence support a scenario where present-day discs form early ( z > 1.0) and subsequently undergo a tranquil evolution in isolation. However, more data and a better understanding of systematics are needed to reaffirm our results.

From Traditional Ethnopharmacology to Modern Natural Drug Discovery: A Methodology Discussion and Specific Examples.

Ethnopharmacology, through the description of the beneficial effects of plants, has provided an early framework for the therapeutic use of natural compounds. Natural products, either in their native form or after crude extraction of their active ingredients, have long been used by different populations and explored as invaluable sources for drug design. The transition from traditional ethnopharmacology to drug discovery has followed a straightforward path, assisted by the evolution of isolation and characterization methods, the increase in computational power, and the development of specific chemoinformatic methods. The deriving extensive exploitation of the natural product chemical space has led to the discovery of novel compounds with pharmaceutical properties, although this was not followed by an analogous increase in novel drugs. In this work, we discuss the evolution of ideas and methods, from traditional ethnopharmacology to in silico drug discovery, applied to natural products. We point out that, in the past, the starting point was the plant itself, identified by sustained ethnopharmacological research, with the active compound deriving after extensive analysis and testing. In contrast, in recent years, the active substance has been pinpointed by computational methods (in silico docking and molecular dynamics, network pharmacology), followed by the identification of the plant(s) containing the active ingredient, identified by existing or putative ethnopharmacological information. We further stress the potential pitfalls of recent in silico methods and discuss the absolute need for in vitro and in vivo validation as an absolute requirement. Finally, we present our contribution to natural products’ drug discovery by discussing specific examples, applying the whole continuum of this rapidly evolving field. In detail, we report the isolation of novel antiviral compounds, based on natural products active against influenza and SARS-CoV-2 and novel substances active on a specific GPCR, OXER1.

Efflux pump activity potentiates the evolution of antibiotic resistance across S. aureus isolates

The rise of antibiotic resistance in many bacterial pathogens has been driven by the spread of a few successful strains, suggesting that some bacteria are genetically pre-disposed to evolving resistance. Here, we test this hypothesis by challenging a diverse set of 222 isolates of Staphylococcus aureus with the antibiotic ciprofloxacin in a large-scale evolution experiment. We find that a single efflux pump, norA, causes widespread variation in evolvability across isolates. Elevated norA expression potentiates evolution by increasing the fitness benefit provided by DNA topoisomerase mutations under ciprofloxacin treatment. Amplification of norA provides a further mechanism of rapid evolution in isolates from the CC398 lineage. Crucially, chemical inhibition of NorA effectively prevents the evolution of resistance in all isolates. Our study shows that pre-existing genetic diversity plays a key role in shaping resistance evolution, and it may be possible to predict which strains are likely to evolve resistance and to optimize inhibitor use to prevent this outcome.

Global radiation in a rare biosphere soil diatom

Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms.

Eco‐evolution on the edge during climate change

We urgently need to predict species responses to climate change to minimize future biodiversity loss and ensure we do not waste limited resources on ineffective conservation strategies. Currently, most predictions of species responses to climate change ignore the potential for evolution. However, evolution can alter species ecological responses, and different aspects of evolution and ecology can interact to produce complex eco‐evolutionary dynamics under climate change. Here we review how evolution could alter ecological responses to climate change on species warm and cool range margins, where evolution could be especially important. We discuss different aspects of evolution in isolation, and then synthesize results to consider how multiple evolutionary processes might interact and affect conservation strategies. On species cool range margins, the evolution of dispersal could increase range expansion rates and allow species to adapt to novel conditions in their new range. However, low genetic variation and genetic drift in small range‐front populations could also slow or halt range expansions. Together, these eco‐evolutionary effects could cause a three‐step, stop‐and‐go expansion pattern for many species. On warm range margins, isolation among populations could maintain high genetic variation that facilitates evolution to novel climates and allows species to persist longer than expected without evolution. This ‘evolutionary extinction debt’ could then prevent other species from shifting their ranges. However, as climate change increases isolation among populations, increasing dispersal mortality could select for decreased dispersal and cause rapid range contractions. Some of these eco‐evolutionary dynamics could explain why many species are not responding to climate change as predicted. We conclude by suggesting that resurveying historical studies that measured trait frequencies, the strength of selection, or heritabilities could be an efficient way to increase our eco‐evolutionary knowledge in climate change biology.

Does evolution in isolation from mammalian predators have behavioural and chemosensory consequences for New Zealand lizards?

Does evolution in isolation from mammalian predators have behavioural and chemosensory consequences for New Zealand lizards?

Evolution in a Community Context: Trait Responses to Multiple Species Interactions

AbstractSpecies that coexist in diverse natural communities interact in complex ways that alter each other’s abundances and affect selection on each other’s traits. Consequently, predicting trait evolution in natural communities may require understanding ecological and evolutionary dynamics involving a number of species. In August 2016, the American Society of Naturalists sponsored a symposium to explore evolution in a community context, focusing on microevolutionary processes. Here we provide an introduction to our perspectives on this topic by defining the context and describing some examples of when and how microevolutionary responses to multiple species may differ from evolution in isolation or in two-species communities. We find that indirect ecological and evolutionary effects can result in nonadditive selection and evolution that cannot be predicted from pairwise interactions. Genetic correlations of ecological traits in one species can alter trait evolution and adaptation as well as the abundances...

Formation of S0 galaxies through mergers

(Abridged version) We explore whether a scenario that combines an origin by mergers at $z\sim$1.8-1.5 with a subsequent passive evolution of the resulting S0 remnants since $z \sim$0.8-1 is compatible with observational data of S0s in the Tully-Fisher relation (TFR). We studied a set of major and minor merger experiments from the GalMer database that generate massive S0 remnants. We analysed the location of these remnants in the photometric and stellar TFRs assuming that they correspond to $z\sim0.8$ galaxies. We then estimated their evolution in these planes over the last 7 Gyr. The results were compared with data of real S0s and spirals at different redshifts. We also tested how the use of Vcirc or Vrot,max affects the results. We found that just after $\sim$1-2 Gyr of coalescence, major mergers generate S0 remnants that are outliers of the local photometric and stellar TFRs at $z\sim0.8$. After $\sim$4-7 Gyr of passive evolution in isolation, the S0 remnants move towards the local TFR, although the initial scatter among them persists. This scatter is sensitive to the indicator used for the rotation velocity: Vcirc values yield a lower scatter than when Vrot,max values are considered instead. In the planes involving Vrot,max, a clear segregation of the S0 remnants in terms of the spin-orbit coupling of the model is observed, in which the remnants of retrograde encounters overlap with local S0s hosting counter-rotating discs. The location of the S0 remnants at $z\sim 0$ agrees well with the observed distribution of local S0 galaxies in the $\sigma_0$-$M_K$, Vcirc-$\sigma_0$ and Vrot,max-$\sigma_0$ planes. Thus, massive S0 galaxies may have been formed through major mergers that occurred at high redshift and have later evolved towards the local TFR through passive evolution in relative isolation, a mechanism that would also contribute to the scatter observed in this relation.

Scientific Drilling at Lake Tanganyika, Africa: A Transformative Record for Understanding Evolution in Isolation and the Biological History of the African Continent, University of Basel, 6–8 June 2016

Abstract. We report on the outcomes of a workshop held to discuss evolutionary biology, paleobiology and paleoecology questions that could be addressed by a scientific drilling project at Lake Tanganyika, the largest, deepest and oldest of the African Rift Valley lakes. Lake Tanganyika is of special significance to evolutionary biologists as it harbors one of the most spectacular endemic faunas of any lake on earth, with hundreds of unique species of fish, molluscs, crustaceans and other organisms that have evolved over the lake's long history. Most of these groups of organisms are known from fossils in short cores from the lake, raising the possibility that both body fossil and ancient DNA records might be recovered from long drill cores. The lake's sedimentary record could also provide a record of African terrestrial ecosystem history since the late Miocene. This 3-day workshop brought together biological and geological specialists on the lake and its surroundings to prioritize paleobiological, ecological and microbiological objectives that could ultimately be incorporated into an overall drilling plan for Lake Tanganyika and to consider how biological objectives can effectively be integrated into the paleoclimate and tectonics objectives of a Lake Tanganyika drilling project already considered in prior workshops.

Origin of Non-axisymmetric Features of Virgo Cluster Early-type Dwarf Galaxies. I. Bar Formation and Recurrent Buckling

Abstract A fraction of early-type dwarf galaxies in the Virgo cluster have a disk component and even possess disk features such as bar, lens, and spiral arms. In this study, we construct 15 galaxy models that resemble VCC856, which is considered to be an infalling progenitor of disk dwarf galaxies, within observational error ranges, and use N-body simulations to study their long-term dynamical evolution in isolation as well as the formation of bar in them. We find that dwarf disk galaxies readily form bars unless they have an excessively concentrated halo or a hot disk. This suggests that infalling dwarf disk galaxies are intrinsically unstable to bar formation, even without any external perturbation, accounting for a population of barred dwarf galaxies in the outskirts of the Virgo cluster. The bars form earlier and stronger in galaxies with a lower fraction of counter-streaming motions, lower halo concentration, lower velocity anisotropy, and thinner disk. Similarly to normal disk galaxies, dwarf disk galaxies also undergo recurrent buckling instabilities. The first buckling instability tends to shorten the bar and to thicken the disk, and drives a dynamical transition in the bar pattern speed as well as mass inflow rate. In nine models, the bars regrow after the mild first buckling instability due to the efficient transfer of disk angular momentum to the halo, and are subject to recurrent buckling instabilities to turn into X-shaped bulges.

Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease

BackgroundHuman parechoviruses (HPeVs) (family Picornaviridae), are common pathogens in young children. Despite their high prevalence, research on their genetic identity, diversity and evolution have remained scarce. ObjectivesComplete coding regions of three previously reported HPeV-4 isolates from Finnish children with sepsis-like disease were sequenced in order to elucidate the phylogenetic relationships and potential recombination events during the evolution of these isolates. Study designThe isolated viruses were sequenced and aligned with all HPeV complete genome sequences available in GenBank. Phylogenetic trees were constructed and similarity plot and bootscanning methods were used for recombination analysis. ResultsThe three HPeV-4 isolates had 99.8% nucleotide sequence similarity. The phylogenetic analysis indicated that capsid-encoding sequences of these HPeV-4 isolates were closely related to other HPeV-4 strains (80.7-94.7% nucleotide similarity), whereas their non-structural region genes 2A to 3C clustered together with several HPeV-1 and HPeV-3 strains, in addition to the HPeV-4 strain K251176-02 (isolated 2002 in the Netherlands), but not with other HPeV-4 strains. However, in 3D-encoding sequence the Finnish HPeV-4 isolates did not cluster with the strain HPeV-4/K251176-02, but instead, formed a distinct group together with several HPeV-1 and HPeV-3 strains. Similarity plot and Bootscan analyses further confirmed intertypic recombination events in the evolution of the Finnish HPeV-4 isolates. ConclusionIntertypic recombination event(s) have occurred during the evolution of HPeV-4 isolates from children with sepsis-like disease. However, due to the low number of parechovirus complete genomes available, the precise recombination partners could not be detected. The results suggest frequent intratypic recombination among parechoviruses.

Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus.

The order in which genes are organized within a genome is generally not conserved between distantly related species. However, within virus orders and families, strong conservation of gene order is observed. The factors that constrain or promote gene-order diversity are largely unknown, although the regulation of gene expression is one important constraint for viruses. Here we investigate why gene order is conserved for a positive-strand RNA virus encoding a single polyprotein in the context of its authentic multicellular host. Initially, we identified the most plausible trajectory by which alternative gene orders could evolve. Subsequently, we studied the accessibility of key steps along this evolutionary trajectory by constructing two virus intermediates: (1) duplication of a gene followed by (2) loss of the ancestral gene. We identified five barriers to the evolution of alternative gene orders. First, the number of viable positions for reordering is limited. Second, the within-host fitness of viruses with gene duplications is low compared to the wild-type virus. Third, after duplication, the ancestral gene copy is always maintained and never the duplicated one. Fourth, viruses with an alternative gene order have even lower fitness than viruses with gene duplications. Fifth, after more than half a year of evolution in isolation, viruses with an alternative gene order are still vastly inferior to the wild-type virus. Our results show that all steps along plausible evolutionary trajectories to alternative gene orders are highly unlikely. Hence, the inaccessibility of these trajectories probably contributes to the conservation of gene order in present-day viruses.

The CALIFA survey across the Hubble sequence

This paper characterizes the radial structure of stellar population properties of galaxies in the nearby universe, based on 300 galaxies from the CALIFA survey. The sample covers a wide range of Hubble types, and galaxy stellar mass. We apply the spectral synthesis techniques to recover the stellar mass surface density, stellar extinction, light and mass-weighted ages, and mass-weighted metallicity, for each spatial resolution element in our target galaxies. To study mean trends with overall galaxy properties, the individual radial profiles are stacked in seven bins of galaxy morphology. We confirm that more massive galaxies are more compact, older, more metal rich, and less reddened by dust. Additionally, we find that these trends are preserved spatially with the radial distance to the nucleus. Deviations from these relations appear correlated with Hubble type: earlier types are more compact, older, and more metal rich for a given mass, which evidences that quenching is related to morphology, but not driven by mass. Negative gradients of ages are consistent with an inside-out growth of galaxies, with the largest ages gradients in Sb-Sbc galaxies. Further, the mean stellar ages of disks and bulges are correlated, with disks covering a wider range of ages, and late type spirals hosting younger disks. The gradients in stellar mass surface density depend mostly on stellar mass, in the sense that more massive galaxies are more centrally concentrated. There is a secondary correlation in the sense that at the same mass early type galaxies have steeper gradients. We find mildly negative metallicity gradients, shallower than predicted from models of galaxy evolution in isolation. The largest gradients occur in Sb galaxies. Overall we conclude that quenching processes act in manners that are independent of mass, while metallicity and galaxy structure are influenced by mass-dependent processes.

Spontaneous behavior of basal Copionodontinae cave catfishes from Brazil (Teleostei, Siluriformes, Trichomycteridae)

Cave animals are particularly interesting due to their behavioral specializations, resultant from evolution in isolation. We present data from a spontaneous behavior study (spatial distribution and preference for microhabitats) of two troglobitic catfish from Brazil: Glaphyropoma spinosum and a new species of Copionodon. We compared the data with those obtained of a sympatric epigean species, Copionodon pecten. These Trichomycteridae species belong to a basal and apparently monophyletic subfamily – Copiono dontinae, endemic to Chapada Diamantina, central Bahia state, eastern Brazil. We observed the fishes in natural and laboratory conditions through ad libitum and focal animal methods. Each spatial behavioral category (hidden, bottom, midwater, surface and wall swimming and stationary in the bottom) was timed individually, with a sample of 12 specimens per species. Unlike most troglobitic fishes, cave copionodon tines tested herein did not extend exploratory behavior to midwater, with benthonic and thigmotacticrelated exploratory behavior. This behavior is possibly related to its feeding behavior specializations, strong territorialism and photophobic behavior. The epigean Copionodon species is also benthonic. The spatial behavior of the cave Copionodontinae could be interpreted as a retained and plesiomorphic characterstate in relation to other trichomycterid catfishes.

Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection.

Strangles, the most frequently diagnosed infectious disease of horses worldwide, is caused by Streptococcus equi. Despite its prevalence, the global diversity and mechanisms underlying the evolution of S. equi as a host-restricted pathogen remain poorly understood. Here, we define the global population structure of this important pathogen and reveal a population replacement in the late 19th or early 20th Century. Our data reveal a dynamic genome that continues to mutate and decay, but also to amplify and acquire genes despite the organism having lost its natural competence and become host-restricted. The lifestyle of S. equi within the horse is defined by short-term acute disease, strangles, followed by long-term infection. Population analysis reveals evidence of convergent evolution in isolates from post-acute disease samples as a result of niche adaptation to persistent infection within a host. Mutations that lead to metabolic streamlining and the loss of virulence determinants are more frequently found in persistent isolates, suggesting that the pathogenic potential of S. equi reduces as a consequence of long-term residency within the horse post-acute disease. An example of this is the deletion of the equibactin siderophore locus that is associated with iron acquisition, which occurs exclusively in persistent isolates, and renders S. equi significantly less able to cause acute disease in the natural host. We identify several loci that may similarly be required for the full virulence of S. equi, directing future research toward the development of new vaccines against this host-restricted pathogen.

An island called India: phylogenetic patterns across multiple taxonomic groups reveal endemic radiations

Island systems from around the world have provided fascinating opportunities for studies pertaining to various evolutionary processes. One recurring feature of isolated islands is the presence of endemic radiations. In this regard, the Indian subcontinent is an interesting entity given it has been an island during much of its history following separation from Madagascar and currently is isolated from much of Eurasia by the Himalayas in the north and the Indian Ocean in the south. Not surprisingly, recent molecular studies on a number of endemic taxa from India have reported endemic radiations. These studies suggest that the uniqueness of Indian biota is not just due to its diverse origin, but also due to evolution in isolation. The isolation of India has generated some peculiarities typically seen on oceanic islands. However, these patterns might be confined to, groups with low dispersal ability.

Evolution in isolation: the Gyraulus species flock from Miocene Lake Steinheim revisited

The Miocene Steinheim Basin in SW Germany is an ancient (long-lived) palaeo-lake that has existed over some hundreds of thousands of years. It is an iconic fossil site, because the historically oldest phylogenetic tree of extinct organisms was based on specimens described from this locality. Today the basin contains 30–40 m thickness of lake sediments with planorbid snails of the genus Gyraulus occurring in rock-forming quantities. The shells are morphologically highly disparate with forms ranging from the tiny, planispiral founder species Gyraulus kleini, to fragile corkscrew-like uncoiled forms and to large trochiform morphs with thick shells. In total, this presumably monophyletic species flock contains 17 species distributed in time and space, all of which are endemic, except for the founder species. Up to nine of them occur in a single sedimentary level and are inferred to have lived together. Such an extreme rate of endemism makes fossil Lake Steinheim special among extant and fossil lakes. This review article summarises and discusses the species concept(s), indications for endemism, speciation processes, the phylogenetic concept(s) and factors controlling evolution. It also provides directions for future research.

Giant Low Surface Brightness Galaxies: Evolution in Isolation

Giant Low Surface Brightness (GLSB) galaxies are amongst the most massive spiral galaxies that we know of in our Universe. Although they fall in the class of late type spiral galaxies, their properties are far more extreme. They have very faint stellar disks that are extremely rich in neutral hydrogen gas but low in star formation and hence low in surface brightness. They often have bright bulges that are similar to those found in early type galaxies. The bulges can host low luminosity Active Galactic Nuclei (AGN) that have relatively low mass black holes. GLSB galaxies are usually isolated systems and are rarely found to be interacting with other galaxies. In fact many GLSB galaxies are found under dense regions close to the edges of voids. These galaxies have very massive dark matter halos that also contribute to their stability and lack of evolution. In this paper we briefly review the properties of this unique class of galaxies and conclude that both their isolation and their massive dark matter halos have led to the low star formation rates and the slower rate of evolution in these galaxies.