Ecological Distinctiveness Research Articles

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

Microbiologists are challenged to explain the origins of enormous numbers of bacterial species worldwide. Contributing to this extreme diversity may be a simpler process of speciation in bacteria than in animals and plants, requiring neither sexual nor geographical isolation between nascent species. Here, we propose and test a novel hypothesis for the extreme diversity of bacterial species-that splitting of one population into multiple ecologically distinct populations (cladogenesis) may be as frequent as adaptive improvements within a single population's lineage (anagenesis). We employed a set of experimental microcosms to address the relative rates of adaptive cladogenesis and anagenesis among the descendants of a Bacillus subtilis clone, in the absence of competing species. Analysis of the evolutionary trajectories of genetic markers indicated that in at least 7 of 10 replicate microcosm communities, the original population founded one or more new, ecologically distinct populations (ecotypes) before a single anagenetic event occurred within the original population. We were able to support this inference by identifying putative ecotypes formed in these communities through differences in genetic marker association, colony morphology and microhabitat association; we then confirmed the ecological distinctness of these putative ecotypes in competition experiments. Adaptive mutations leading to new ecotypes appeared to be about as common as those improving fitness within an existing ecotype. These results suggest near parity of anagenesis and cladogenesis rates in natural populations that are depauperate of bacterial diversity.

The ecology of trunk-to-trunk leaping in <i>Saguinus fuscicollis</i>: implications for understanding locomotor diversity in Callitrichines

Several species of callitrichines (tamarins, marmosets, and callimicos) are reported to frequently leap between vertical supports when foraging and traveling in the forest understory. In the present study, we examine trunk-to-trunk leaping in a wild group of four habituated adult saddleback tamarins (Saguinus fuscicollis weddelli) in northern Bolivia. From June through July, 2011 we analyzed 200 leaps in which the tamarins moved between vertical supports. On average, takeoff height was 4.1 m (±1.3 m, range 1-7.5 m). During the airborne phase of travel the monkeys lost an average of 0.5 m (±0.5 m) at contact with the landing support, and the mean distance leapt was 1.4 m (± 0.7 m). We found no correlation between the diameter at breast height (DBH) of landing and takeoff supports, and either the distance leapt or height gained/lost during leaping. Across callitrichine taxa, it appears that ecological distinctions in diet, patterns of habitat utilization, and predator avoidance strategies have played an important role in understanding the frequency and context of trunk-to-trunk leaping behavior.

Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria

Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port. The significance of this specific fraction of the exoproteome is discussed.

Niche divergence and lineage diversification among closely related Sistrurus rattlesnakes

Comparing niche divergence among closely related taxa can yield important insights into the ecological distinctiveness of genetically similar forms, and identify the processes that are responsible for diversification in such organisms. Here, we apply newly developed techniques for analysing niche divergence to assess how ecologically distinct a group of closely related rattlesnakes (Sistrurus sp.) are and to explore the role that niche divergence may have played in their diversification. We find that all taxa even the most recently evolved subspecies (approximately 100,000 years old) are now ecologically distinct, implying a role for ecology in the diversification process. Statistical analysis based on comparisons with null models show that niche divergence between forms is more common than niche conservation. Finally, there is nonlinear relationship between phylogenetic and niche divergence in this group whereby niche divergence develops more rapidly between recently diverged subspecies than more distantly related forms. Overall, our results argue that ecology may play an important role in the diversification process in these snakes.

Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park

Past analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genus Synechococcus, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only two habitats, we studied the distribution of Synechococcus sequence variants at 1°C intervals along the effluent flow channel and at 80-μm vertical-depth intervals throughout the upper photic layer of the microbial mat. Diversity at the psaA locus, which encodes a photosynthetic reaction center protein (PsaA), was sampled by PCR amplification, cloning, and sequencing methods at 60, 63, and 65°C sites. The evolutionary simulation programs Ecotype Simulation and AdaptML were used to identify putative ecologically distinct populations (ecotypes). Ecotype Simulation predicted a higher number of putative ecotypes in cases where habitat variation was limited, while AdaptML predicted a higher number of ecologically distinct phylogenetic clades in cases where habitat variation was high. Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O₂, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O₂ concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes.

Combining genetic structure and ecological niche modeling to establish units of conservation: A case study of an imperiled salamander

Identification of conservation units below the species level has been difficult for researchers and conservation planners. Methods reliant solely on genetics to identify conservation units are widely used but have limited scope. Additionally, methods used to assess ecological distinctness are typically difficult to interpret, and hence not broadly applicable. Here, we attempt to reconcile these problems by defining conservation units utilizing both genetic and ecological methods. This study suggests a framework to evaluate discreteness and significance among populations for assessment of distinct population segments (DPSs). Specifically, we highlight a methodology that incorporates genetic analyses and niche-based distribution modeling to identify conservation units. As a case study, we sought to determine whether populations of an imperiled salamander ( Notophthalmus perstriatus), appearing to exist in two regions separated by 125 km, exhibited genetic and ecological distinctness such that the regions demarcate separate conservation units. Using mtDNA ( cyt-b), we found that haplotypes were shared between localities within each region but none were shared between regions. Niche-based distribution modeling revealed significant differences in the ecological setting between the two regions. In combination, the absence of evidence for recent genetic exchange and model-based support for differing ecological conditions utilized by newts between regions provides evidence that eastern and western populations are both distinct and significant. This study formalizes a method to assess DPS distinctness and significance providing general utility for this methodology as a conservation tool for many species.

Environmental Patterns Are Imposed on the Population Structure of Escherichia coli after Fecal Deposition

The intestinal microbe Escherichia coli is subject to fecal deposition in secondary habitats, where it persists transiently, allowing for the opportunity to colonize new hosts. Selection in the secondary habitat can be postulated, but its impact on the genomic diversity of E. coli is unknown. Environmental selective pressure on extrahost E. coli can be revealed by landscape genetic analysis, which examines the influences of dispersal processes, landscape features, and the environment on the spatiotemporal distribution of genes in natural populations. We conducted multilocus sequence analysis of 353 E. coli isolates from soil and fecal samples obtained in a recreational meadow to examine the ecological processes controlling their distributions. Soil isolates, as a group, were not genetically distinct from fecal isolates, with only 0.8% of genetic variation and no fixed mutations attributed to the isolate source. Analysis of the landscape genetic structure of E. coli populations showed a patchy spatial structure consistent with patterns of fecal deposition. Controlling for the spatial pattern made it possible to detect environmental gradients of pH, moisture, and organic matter corresponding to the genetic structure of E. coli in soil. Ecological distinctions among E. coli subpopulations (i.e., E. coli reference collection [ECOR] groups) contributed to variation in subpopulation distributions. Therefore, while fecal deposition is the major predictor of E. coli distributions on the field scale, selection imposed by the soil environment has a significant impact on E. coli population structure and potentially amplifies the occasional introduction of stress-tolerant strains to new host individuals by transmission through water or food.

Skipper impoverishment on large West Mediterranean islands (Lepidoptera Hesperioidea): deterministic, historical and stochastic factors

Biogeographical analyses are applied to skipper (Hesperioidea) presence/absence data from the Western Mediterranean mainland and the three largest islands (Sardinia, Corsica and Sicily) in order to identify potential conservation issues. The analyses performed on species, both collectively and individually, indicate that regional species richness and occurrence in the Mediterranean zone are largely predicted by latitude and area but that islands have impoverished faunas. Several species, predicted to be present on these islands from logistic regression of their continental distributions, are actually absent. The number of species predicted to be present from logistic regression analyses for each island, closely matched the number of species predicted to occur in regional-focused multiple regression analysis. This suggests that missing species have been identified. When compared with species that occur in Sicily and Corsica, the missing species are shown to differ for ecological traits, mainly those linked to altitudinal tolerance. No ecological distinctions were disclosed for Sardinian skippers suggesting a mainly stochastic colonisation. These results, and those from an analogous study carried out on Papilionoidea, point to Hesperioidea having (i) overall more impoverished faunas on islands and (ii) being subject to stochastic or historical colonisation events more than Papilionoidea. Species not predicted to occur on islands based on their mainland distributions and ecological traits, are foci for conservation attention. However, as many species becoming extinct on the islands may be irreplaceable, all species, in particular the Sardinian ones, deserve to be conserved.

Morphological variation of the Common Lizard (Zootoca vivipara Jacquin, 1787) in the Central Balkans

The variation in some of the morphometric, meristic and qualitative characters of the Common Lizard (Zootoca vivipara) in five population samples from mountains of the Central Balkans was analyzed using univariate and multivariate statistics. The morphological differentiation was greater in males than in females and is more expressed in the morphometric than in the pholidosis and qualitative characters. The largest differences in morphometric traits appeared between the populations from the Sara and Stara Planina mountains. The 'median' pileus pattern generally prevailed, with the appearance of other states in a certain proportion in some of the populations. Further analyses of the possible morphological and ecological distinctions of the population from Mt Tara are proposed. .

Molecules, ecology, morphology, and songs in concert: how many species is Arremon torquatus (Aves: Emberizidae)?

The acceptance of the generalized or unified concept of species (i.e. that species are segments of population lineages) implies that an important task for systematists is to focus on identifying lineages and on testing hypotheses about the acquisition of properties such as phenotypic diagnosability, reciprocal monophyly, or mechanisms of reproductive isolation. However, delimiting species objectively remains one of the most challenging problems faced by biologists. In the present study, we begin to tackle the thorny issue of species delimitation in a complicated group of Neotropical passerine birds (the Arremon torquatus complex, Emberizidae) in which sets of characters vary substantially across space, but do not obviously vary in a concerted fashion. To earlier discussions of species limits in the group, we add a historical perspective offered by a recent molecular phylogeny, present quantitative analyses of morphological and vocal variation, and incorporate ecological niche models as a new tool that aids species delimitation by highlighting cases of ecological distinctiveness and cases where populations appear to be in independent evolutionary trajectories, despite being connected by environments unlikely to represent barriers to gene flow. We demonstrate that at least one pair of taxa (and likely another) currently treated as conspecific are, in fact, distinct lineages that merit species status under essentially any species criterion. However, other pairwise comparisons are not as straightforward owing to nonconcordant patterns of variation in different traits and to the impossibility of distinguishing which characters are causes and which are consequences of reproductive (and evolutionary) isolation. After considering several alternatives, we propose a provisional classification of the complex recognizing eight tentative species-level taxa. Although this classification is likely to change as more detailed work is conducted, it provides a better foundation for studying the biology of these birds and helps to better describe their diversity, which is obscured when all taxa are subsumed into a single species name. The present study highlights several outstanding challenges, both practical and conceptual, for future studies.

Demonstration of a satellite-based index to monitor habitat at continental-scales

An important initial step in the conservation and sustainable management of the Earth's biodiversity is to implement systems to both identify and subsequently monitor components of biological diversity, along with developing a better understanding of the processes that significantly threaten their conservation or sustainable use. Key factors in both species diversity and richness are related to environmental heterogeneity which is driven by temporal and spatial variation in the biological, physical, and chemical features of the environment. These environmental characteristics are manifest through the condition and change in vegetation productivity (considered as an integrated response of vegetation to climate and soil conditions). Earth observation is uniquely capable of synoptically covering large areas of the planet in a repeatable, and cost effective manner, and is a well-established technology for detecting terrestrial vegetation productivity. A recently developed dynamic habitat index (DHI), based on satellite observations of the fraction of radiation absorbed by the canopy (fPAR), has been shown to effectively cluster remotely sensed observations into a range of habitat regimes which in turn have been related to breeding bird surveys in the Canadian Province of Ontario and across the conterminous United States. With evidence that the index is well correlated with species diversity, we consider, in this subsequent paper, whether such an index is a suitable candidate as a continental index to characterize and subsequently monitor habitat conditions. To do so, we first utilise available fPAR data available from 2000 to 2005 over North America, and apply the index. Using information on continental terrestrial ecozones and their ecological distinctiveness, we then compare and contrast the index and utilize trajectory analysis to assess what changes have occurred in the index over the 6-year time period and possible implications for continental biodiversity. The potential application of the index is the discussed.

The presence of generalist plant pathogens might not explain the long-term coexistence of plant species

Pathogens have been shown to contribute to the possibility of coexistence of competing plant species by creating ecological distinction between the coexisting species. This coexistence promoting mechanism resembles intra-specific density dependence as found in Lotka–Volterra models. However, plant species adapt in their level of resistance against pathogen infection and this adaptation has been shown to be traded-off by a reduction in growth rate. A model is developed to show that taking into account the possible adaptation of plant species to increase their resistance against pathogen infection by generalist pathogens has consequences for the coexistence of the plant species. The results show that in systems where plants adapt to the pathogen infection, coexistence becomes impossible. The implication of this finding is that plant pathogens might contribute less to the coexistence of plant species than is commonly thought.

Variation of territory size and defense behavior in breeding pairs of the endemic Lake Tanganyika cichlid fish Variabilichromis moorii

Lake Tanganyika harbors the ecologically, morphologically, and behaviorally most diverse species flock of cichlid fishes. It is comprised by substrate breeding and mouthbrooding species, most of which live in littoral habitats. Species communities are characterized by complex behavioral and trophic interactions, resulting in a dense pattern of partially overlapping territories, depending on the degree of ecological distinctness. We studied territorial behavior of breeding pairs in a substrate breeding species, with respect to territory size and defense behavior. The study species Variabilichromis moorii belongs to the tribe Lamprologini, the most species rich tribe of cichlids in Lake Tanganyika. Our study shows that breeding pairs of V. moorii can have highly complex territories, in which both parents hold separate sub-territories which are shifted slightly according to the movements of the fry, but the outer borders are conjointly defended. The size of the total defended territory varied from <1 to almost 4 m2, averaging at about 2 m2. Depending on presence of competitors or fry-predators evoking agonistic interactions, the territory size varied quite substantially over the day. Attack rates and size of the defended area decreased with water depth. Agonistic behavior was observed toward heterospecifics as well as conspecifics, with heterospecific attacks mostly concerning territorial neighbors and potential fry-predators in about equal frequencies.

Reproductive isolation and ecological niche partition among larvae of the morphologically cryptic sister species Chironomus riparius and C. piger.

BackgroundOne of the central issues in ecology is the question what allows sympatric occurrence of closely related species in the same general area? The non-biting midges Chironomus riparius and C. piger, interbreeding in the laboratory, have been shown to coexist frequently despite of their close relatedness, similar ecology and high morphological similarity.Methodology/Principal FindingsIn order to investigate factors shaping niche partitioning of these cryptic sister species, we explored the actual degree of reproductive isolation in the field. Congruent results from nuclear microsatellite and mitochondrial haplotype analyses indicated complete absence of interspecific gene-flow. Autocorrelation analysis showed a non-random spatial distribution of the two species. Though not dispersal limited at the scale of the study area, the sister species occurred less often than expected at the same site, indicating past or present competition. Correlation and multiple regression analyses suggested the repartition of the available habitat along water chemistry gradients (nitrite, conductivity, CaCO3), ultimately governed by differences in summer precipitation regime.ConclusionsWe show that these morphologically cryptic sister species partition their niches due to a certain degree of ecological distinctness and total reproductive isolation in the field. The coexistence of these species provides a suitable model system for the investigation of factors shaping the distribution of closely related, cryptic species.

When Land Was Cheap, and Labor Dear: James Madison's ‘Address to the Albemarle Agricultural Society’ and the Problem of Southern Agricultural Reform

AbstractJames Madison's 1818 Address to the Albemarle Agricultural Society offers new insight into the diverse historiography of agricultural reform in the American South. Madison described a planet with limited resources, accused Virginia farmers of wasting what little they had, and offered suggestions for ways to intensify cultivation. Many scholars have analyzed the southern agricultural reform crusade, but differ widely on whether it was successful, and the reasons why. Madison tried to balance high farming with southern independence. Southern farming could not imitate modern agriculture from England and the Northeastern states because of the region's ecological distinctiveness. Madison was reluctant to risk tested adaptations by importing to crops, animals, and fertilizers. Southern farmers reflected his ecological conservatism, and the movement for reform stalled.

Molecular Identification of Adoxophyes orana complex (Lepidoptera: Tortricidae) in Korea and Japan

Species identification in the Adoxophyes orana complex has historically posed a problem, due to marked morphological similarities among the members. Although pheromonal studies have often been suggested as a better indicator for ecological distinctions among species than morphological similarities, no molecular proof has yet been provided in this regard. Here, we have sequenced the COI barcoding region (~ 660 bp) as well as another COI region (~ 940 bp) and 18S rDNA (~ (~ 1820 bp) for species in Korea and Japan. We determined that the specimens recently collected in Korea were A. orana, which is identical to the Japanese A. orana fasciata; the Korean A. honmai is identical to the Japanese A. honmai; the Korean Adoxophyes sp., which has previously been identified as A. orana in Korea, is not actually A. orana but a third, possibly new, species; and the Japanese A. dubia is identical to A. honmai in Japan and A. honmai in Korea. p-distances among the species and their phylogenetic trees are also provided herein.

Distinctiveness, Use, and Value of Midwestern Oak Savannas and Woodlands as Avian Habitats

AbstractOak savannas and woodlands historically covered millions of hectares in the midwestern United States but are rare today. We evaluated the ecological distinctiveness and conservation value of savannas and woodlands by examining bird distributions across a fire-maintained woody-vegetation gradient in northwest Indiana encompassing five habitats—open habitats with low canopy cover, savannas, woodlands, scrublands, and forests—during migration, breeding, and overwintering. Savannas and woodlands were significantly different in overall bird species composition from open and forest habitats but were often intermediate between open and forest in guild densities. Few bird species were consistently and highly concentrated in savannas or woodlands, and the Red-headed Woodpecker (Melanerpes erythrocephalus) was the only species significantly more abundant in savannas and woodlands than in open, scrub, and forest habitats. Fire frequency over a 15-year interval was a significant predictor of bird community composition and was positively related to species diversity, spring transient migrant density, and density of the most threatened species. Each habitat type had characteristics potentially important for avian conservation. Scrub had the highest density of transient migrants, which suggests it plays an important role as migration stopover habitat. More species were significantly concentrated in open or forest habitats than in the other habitats. Lack of species concentration and intermediate community composition suggested that birds experienced savannas and woodlands more as ecotones than as habitats distinct from forests or grasslands. However, this intermediate character can benefit conservation, as evidenced by savannas and woodlands having the highest density of the most threatened species along this woody-vegetation gradient.Características Únicas, Uso y Valor de las Sabanas y Bosques Abiertos de Roble del Oeste Central como Hábitats para las Aves

Genomics, environmental genomics and the issue of microbial species

A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.

Dental Divergence Supports Species Status of the Extinct Sea Mink (Carnivora: Mustelidae:Neovison macrodon)

The sea mink (Neovison macrodon (Prentiss, 1903): Mustelinae) was an unusual late-Cenozoic example of an organism that had rapidly evolved toward a marine niche. Except for the otters, it was probably the most aquatic member of the Musteloidea. Its status as a separate species has not been resolved. A larger relative of the American mink (N. vison), it inhabited the shores of New England and possibly the Canadian Maritime Provinces until it was hunted to extinction in the 19th century. Skeletal and skin specimens were not collected by zoologists, but the former are known from Native American archaeological sites. The hypothesis that the sea mink showed dental divergence from N. vison, an indication of systematic and ecological distinctness, was tested on 111 dentally mature mink specimens originally collected from the Turner Farm archaeological site (Penobscot Bay, Maine). These teeth, dating from about 5,000 to 250 years ago, were compared with 158 other specimens measured for this study and published data from 78 individuals, representing 4 subspecies of N. vison and 22 additional musteloid genera. Thirteen dental measurements were taken on all species and studied using regressions, principal component analysis, and significance testing. Based on comparisons with American mink, it appears likely that the archaeological specimens included primarily N. macrodon but also N. vison. Although pairs of species within the Lutrinae and genus Mustela showed divergence comparable to that of N. vison and N. macrodon, the dental proportions of male and female N. vison and of the several N. vison subspecies were nearly identical. These analyses suggest that N. macrodon was sufficiently distinct from N. vison to support its recognition as a separate species.

DISTINCTIVENESS, USE, AND VALUE OF MIDWESTERN OAK SAVANNAS AND WOODLANDS AS AVIAN HABITATS

Abstract Oak savannas and woodlands historically covered millions of hectares in the midwestern United States but are rare today. We evaluated the ecological distinctiveness and conservation value of savannas and woodlands by examining bird distributions across a fire-maintained woody-vegetation gradient in northwest Indiana encompassing five habitats—open habitats with low canopy cover, savannas, woodlands, scrublands, and forests—during migration, breeding, and overwintering. Savannas and woodlands were significantly different in overall bird species composition from open and forest habitats but were often intermediate between open and forest in guild densities. Few bird species were consistently and highly concentrated in savannas or woodlands, and the Red-headed Woodpecker (Melanerpes erythrocephalus) was the only species significantly more abundant in savannas and woodlands than in open, scrub, and forest habitats. Fire frequency over a 15-year interval was a significant predictor of bird community c...