Intraspecific Clusters Research Articles

A wide hybrid zone mediated by precipitation contributed to confused geographical structure of Scutiger boulengeri.

Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology. In this study, we generated a time-calibrated phylogeny of Scutiger boulengeri, an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang (Tibet) Plateau (QTP). Based on three mitochondrial DNA (mtDNA) genes, eight clades were assigned to three deeply divergent lineages. Analysis of nuclear DNA (nuDNA) genes revealed three distinct clusters without geographic structure, indicating significantly high rates of gene flow. Coalescent theory framework analysis (approximate Bayesian computation model DIYABC and Migrate-N) suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago (Ma). The ratio of mtDNA F ST (fixation index) to nuDNA F ST was 2.3, thus failing to show male-biased dispersal. Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China, without significant reproductive isolation but with strong introgression in S. boulengeri, suggesting high hybrid fitness. Furthermore, mtDNA genes exhibited isolation by distance (IBD) while nuDNA genes exhibited significant isolation by environment (IBE). Results suggested that mitonuclear discordance may have initially been caused by geographic isolation, followed by precipitation-mediated hybridization, producing a wide hybrid zone and geographic structure confusion of nuDNA genes in S. boulengeri. This study indicated that complicated historical processes may have led to specific genetic patterns, with a specific climate factor facilitating gene flow in the system.

Interaction between hunting strategy, habitat type and stratum drive intraguild predation and cannibalism

Intraguild predation (IGP) is a common interaction between generalist predators when they competitively exploit similar resources and prey on each other. Theoretical models predict limitations for intraguild predator coexistence unless some mechanisms, such as the utilization of alternative prey (i.e. trophic niche partitioning) and cannibalism, increase the relative intraspecific clustering and interspecific segregation. As hunting strategies determine trophic niches of predators and their own vulnerability to predation, the hunting strategies may also determine the relative importance of cannibalism, predation, and exploitative competition and consequently the intensity of IGP. The importance of hunting strategies on the potential outcome of IGP and how habitat properties modify the interaction between hunting strategies remain poorly understood. Using published data on spider prey of spider predators, we first investigated how predation of a top‐predator on a mesopredator is determined by the functional distance between both predators to understand how predation and exploitation are distributed in spider communities. Subsequently, we investigated the predation among spiders with particular hunting strategies to understand which strategies interact most frequently. We also investigated whether the interaction between hunting strategies was influenced by habitat type (forest, open (semi)natural habitat, agroecosystem) or by habitat stratum (ground versus vegetation). The hunting strategies of top‐predators and mesopredators interacted to determine the relative capture proportions of conspecifics and hetero‐specifics. This interaction was further modified by habitat type and stratum. Two mechanisms can reinforce coexistence in highly diverse spider communities. First, top‐predators preyed most frequently on functionally distinct mesopredators, which indicates the overall intensity of IGP may be relaxed by a balanced distribution between exploitative competition and predation. Second, cannibalism was common for top‐predators with a hunting strategy of frequently preying on functionally similar mesopredators. Cannibalism may lead to self‐limitation of top‐predator populations and may thereby facilitate coexistence between two predator species.

Small-scale spatial structure affects predator-prey dynamics and coexistence

Small-scale spatial variability can affect community dynamics in many ecological and biological processes, such as predator-prey dynamics and immune responses. Spatial variability includes short-range neighbour-dependent interactions and small-scale spatial structure, such as clustering where individuals aggregate together, and segregation where individuals are spaced apart from one another. Yet, a large class of mathematical models aimed at representing these processes ignores these factors by making a classical mean-field approximation, where interactions between individuals are assumed to occur in proportion to their average density. Such mean-field approximations amount to ignoring spatial structure. In this work, we consider an individual-based model of a two-species community that is composed of consumers and resources. The model describes migration, predation, competition and dispersal of offspring, and explicitly gives rise to varying degrees of spatial structure. We compare simulation results from the individual-based model with the solution of a classical mean-field approximation, and this comparison provides insight into how spatial structure can drive the system away from mean-field dynamics. Our analysis reveals that mechanisms leading to intraspecific clustering and interspecific segregation, such as short-range predation and short-range dispersal, tend to increase the size of the resource species relative to the mean-field prediction. We show that under certain parameter regimes these mechanisms lead to the extinction of consumers whereas the classical mean-field model predicts the coexistence of both species.

Evidence for a stochastic geometry of biodiversity: the effects of species abundance, richness and intraspecific clustering

Summary Most ecological theories that aim to explain coexistence in megadiverse communities employ a set of three rules to describe the stochastic geometry of biodiversity: (i) individuals exhibit intraspecific clustering; (ii) species abundances vary according to a log‐normal distribution and (iii) the spatial arrangement between species is independent. The first two rules have received strong empirical support, but the third remains largely unexplored. To address this deficiency, we evaluated the independent species arrangement rule in a species‐rich shrubland and its potential drivers, that is, the levels of species richness and intraspecific clustering exhibited by a given species at different scales, and the relative abundance of such species in the community. We found that interspecific associations were rare and that independence was positively related to species richness and intraspecific clustering, but negatively related to relative species abundances. Synthesis. Our results agree with the independent species arrangement rule and they provide empirical support for the stochastic geometry of biodiversity. In the context of species‐rich plant communities, the likelihood of two species encountering is very small. However, our study demonstrated a novel feature of this context, where both intraspecific clustering (due limitations on dispersal) and relative species abundances play fundamental roles in determining the probability of two species encountering and interacting, especially at very fine spatial scales.

Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae).

It is difficult to interpret mitochondrial diversity in terms of taxonomy even in cases in which a concordance exists between mitochondrial, ecological and morphological markers. Here we demonstrate this difficulty through a study of Israeli Hyponephele butterflies. We show that samples commonly identified as Hyponephele lycaon are represented on Mount Hermon in Israel by two sympatric groups of individuals distinct both in mitochondrial DNA-barcodes (uncorrected p-distance = 3.5%) and hindwing underside pattern. These two groups were collected in different biotopes. They also tended to be different in length of brachia in male genitalia, although the latter character is variable. We reject the hypothesis that the discovered COI haplogroups are selectively neutral intraspecific characters. We hypothesize that they represent: either (1) two different biological species, or (2) a consequence of a strong positive selection acting at intraspecific level and resulting in two intraspecific clusters adapted to low and to high elevations. If we accept the first hypothesis, then provisionally these two haplogroups can be attributed to transpalearctic Hyponephele lycaon sensu stricto and to Hyponephele lycaonoides, previously known from Iran and East Turkey.

Spatial distribution of Tephrocactus aoracanthus (Lem.) Lem. in relation to shrubs in the hyperarid regions of west‐central Argentina

AbstractThe spatial intraspecific and interspecific distribution of Tephrocactus aoracanthus (Lem.) Lem. was studied using univariate and bivariate point pattern analysis, at landscape scale in four different physiographic units and at microscale in terms of the shrubs found in those units. The influence of shrubs on photosynthetically active radiation and on soil temperature under their canopies was analysed. Results show a high environmental variability in light and temperature under shrubs that generally has no influence on the distribution of T. aoracanthus. Apparently, this cactus has great ability to adapt to different conditions of both photosynthetically active radiation and temperature. However, intraspecific distribution was highly clustered in all physiographic units, independently of bushes. Possibly, the mode of seed dispersal and the rooting of cladodes at small scale are the main processes that determine the strong intraspecific clustering of T. aoracanthus.

Corrigendum

CorrigendaCorrigendumPublished Online:01 Jul 2011https://doi.org/10.1152/ajpgi.zh3-5961-corr.2011Original articleMoreSectionsPDF (31 KB)Download PDF ToolsExport citationAdd to favoritesGet permissionsTrack citations ShareShare onFacebookTwitterLinkedInEmailWeChat Volume 296, April 2009Volume 59, April 2009Ma X, Mao Y-K, Wang B, Huizinga JD, Bienenstock J, and Kunze W. Lactobacillus reuteri ingestion prevents hyperexcitability of colonic DRG neurons induced by noxious stimuli. Am J Physiol Gastrointest Liver Physiol 296: , 2009.We have become aware of the fact that our laboratory has wrongly identified a bacterium that we have referred to in a number of publications as Lactobacillus reuteri. Indeed, we can now verify that this bacterium, used in all of our published experiments, is Lactobacillus rhamnosus, which we identified by bar coding and DNA fingerprinting. We have asked an independent laboratory, the Bacteria Collection Laboratory for Microbiology, University of Ghent, Belgium, to identify the bacterium, and they have confirmed it to be an L. rhamnosus, using DNA fingerprinting via the AFLP technique. Furthermore, they were unable to assign it to any of the seven intraspecific clusters they have previously reported among 118 strains of this species from around the world (1). Future experiments by our group will refer to this bacterium as L. rhamnosus (JB-1).We sincerely apologize to all our colleagues for any difficulties arising from this error.REFERENCE1. Vancanneyt M , Huys G , Lefebvre K , Vankerckhoven V , Goossens H , Swings J. Intraspecific genotypic characterization of Lactobacillus rhamnosus strains intended for probiotic use and isolates of human origin. Appl Environ Microbiol 72: 5376–5383, 2006.Crossref | PubMed | ISI | Google Scholar Download PDF Previous Back to Top FiguresReferencesRelatedInformationRelated ArticlesLactobacillus reuteri ingestion prevents hyperexcitability of colonic DRG neurons induced by noxious stimuli 01 Apr 2009American Journal of Physiology-Gastrointestinal and Liver PhysiologyCited BySmall Molecules Dorsomorphin and LDN-193189 Inhibit Myostatin/GDF8 Signaling and Promote Functional Myoblast DifferentiationJournal of Biological Chemistry, Vol. 290, No. 6 More from this issue > Video Abstract Volume 301Issue 1July 2011Pages G195-G195 Copyright & PermissionsCopyright © 2011 the American Physiological Societyhttps://doi.org/10.1152/ajpgi.zh3-5961-corr.2011PubMed21508334History Published online 1 July 2011 Published in print 1 July 2011 Metrics

Corrigendum

CorrigendumCorrigendumPublished Online:01 Jun 2011https://doi.org/10.1152/ajpregu.zh6-7624-corr.2011Original articleMoreSectionsPDF (84 KB)Download PDF ToolsExport citationAdd to favoritesGet permissionsTrack citations ShareShare onFacebookTwitterLinkedInEmailWeChat Volume 64, October 2008van der Kleij H, O'Mahony C, Shanahan F, O'Mahony L, Bienenstock J. Protective effects of Lactobacillus reuteri and Bifidobacterium infantis in murine models for colitis do not involve the vagus nerve. Am J Physiol Regul Integr Comp Physiol 295: , 2008. First published July 30, 2008; doi:10.1152/ajpregu.90434.2008 (http://ajpregu.physiology.org/content/295/4/R1131.full).We have become aware of the fact that our laboratory has wrongly identified a bacterium, which we have referred to in a number of publications as Lactobacillus reuteri. Indeed, we can now verify that this bacterium, used in all of our published experiments, is Lactobacillus rhamnosus that we identified by bar coding and DNA fingerprinting. We have asked an independent laboratory, the Bacteria Collection Laboratory for Microbiology, University of Ghent, Belgium to identify the bacterium, and they have confirmed it to be an L. rhamnosus, using DNA fingerprinting via the AFLP technique. Furthermore, they were unable to assign it to any of the seven intraspecific clusters they have previously reported among 118 strains of this species from around the world (Vancanneyt et al., Appl Environ Microbiol 78: 5376–5383, 2006). Future experiments by our group will refer to this bacterium as L. rhamnosus (JB-1).We sincerely apologize to all our colleagues for any difficulties arising from this error.This article has no references to display. Download PDF Previous Back to Top FiguresReferencesRelatedInformationRelated ArticlesProtective effects of Lactobacillus reuteri and Bifidobacterium infantis in murine models for colitis do not involve the vagus nerve 01 Oct 2008American Journal of Physiology-Regulatory, Integrative and Comparative Physiology More from this issue > Volume 300Issue 6June 2011Pages R1596-R1596 Copyright & PermissionsCopyright © 2011 the American Physiological Societyhttps://doi.org/10.1152/ajpregu.zh6-7624-corr.2011History Published online 1 June 2011 Published in print 1 June 2011 Metrics

DNA barcoding on subsets of three families in Aves

Background and aims. Previous studies carried out with DNA barcoding, based on regional groups, have shown that a standard mitochondrial gene could be used to identify birds. In the present study, we present an additional DNA barcoding survey of birds, using taxonomic groups instead of regional groups to verify the effectiveness of DNA barcoding on distinguishing species and to test whether the intraspecific clusters of species are associated with geographical discontinuities.Materials and methods. Taxonomic groups of three avian families—Phasianidae, Accipitridae, and Strigidae—were included in the study. The cytochrome c oxidase I (COI) sequences of 49 individuals were determined. Together with 122 sequences from previous studies, a total of 171 sequences from 66 bird species were analyzed.Results and conclusion. Results showed that all 66 species investigated had unique COI sequences and no sequences were shared between the species. Our results were congruent with previous studies suggesting that the COI barcode permits distinguishing most of the closely related species. Furthermore, by using geographically distinct clusters, diagnostic characters, and threshold levels, deep genetic splits (>1.5%) were observed in three species, and we therefore suggest treating them as evolutionary significant units.

Identification and clustering of dairy propionibacteria by RAPD-PCR and CGE-REA methods.

A total of 67 classical propionic acid bacteria (PAB) strains, 10 of which were from type culture collections and 57 from milk, typical Italian cheeses, acid whey and feed flour of different regions, were analysed by Randomly Amplified Polymorphic DNA (RAPD-PCR) and by Conventional Gel Electrophoresis Restriction Endonuclease Analysis (CGE-REA). The genotypic traits achieved using RAPD-PCR with three primers (OPL-01, OPL-02 and OPL-05) and SmaI CGE-REA patterns were compared by numerical analysis and allowed a clear distinction of four clusters corresponding to the currently described species of classical propionibacteria according to type and reference strains positions. No discrepancies exist in species recognition between the two methods; 36 isolates were identified as Propionibacterium freudenreichii, 15 as P. jensenii, four as P. acidipropionici and two as P. thoenii. Many differences, however, were observed in intraspecific clustering. Numerical comparison of RAPD-PCR profiles appeared to be a suitable method for highlighting the presence of particular phenotypic characters, while intraspecific differentiation obtained by CGE-REA analysis allowed association of strains at high similarity levels on the basis of their geographical origin.

Nesting site selection by wasps in the Guianese rain forest

In the edge of the rain forests in French Guiana, the large leaves of young Astrocaryum sciophilum, a palm tree with long thin spines (up to 9 cm) along their central vein, shelter significantly more mason as well as social wasps' nests, than leaves of other plants. Other such plants include older conspecific individuals with spines, but compound leaves, and young Bactris simplifrons, a palm tree with similar leaves but devoid of spines. The choice of these leaves is due to the association of two factors: (1) these large leaves with a concave underside offer good protection against inclement weather, and (2) the spines on which the wasps' nests are anchored serve as "acquired pedicels", offering protection against ant predation. As a consequence, the wasps' nests are found under these leaves in both inter- and intraspecific clusters.

Intra and interspecific association of large pelagic fishes inferred from catch data of surface longline

This paper analyses the distribution of longline catches of swordfish, Xiphias gladius, and six species of pelagic elasmobranchs, during a fishing voyage in the tropical eastern Atlantic. Seven scales of sampling units, ranging from about 0.72 to 7.2 km were used. Observed frequencies of appearance of each species in the basic sampling unit, were compared with theoretical frequencies obtained from the Poisson and negative binomial distributions. For the study of the interspecific relationships, contingency tables were used and the degree of association was estimated using the χ2test and the coefficient v of Kendall. The catch distribution of the swordfish and the devil ray (Mobula sp.) can be explained by both randomness and a slight trend to association. For the pelagic sharks, a clear trend towards intraspecific clustering was found. Catches of two species of the genus Carcharhinus showed the most positive trends to interspecific association, especially in short ranges, probably due to attraction to previously hooked fish. The possible causes of these distributions are discussed.