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Phylogenetic Distance (phylogenetic + distance)
Selected AbstractsPhylogenetic beta diversity: linking ecological and evolutionary processes across space in timeECOLOGY LETTERS, Issue 12 2008Catherine H. Graham Abstract A key challenge in ecological research is to integrate data from different scales to evaluate the ecological and evolutionary mechanisms that influence current patterns of biological diversity. We build on recent attempts to incorporate phylogenetic information into traditional diversity analyses and on existing research on beta diversity and phylogenetic community ecology. Phylogenetic beta diversity (phylobetadiversity) measures the phylogenetic distance among communities and as such allows us to connect local processes, such as biotic interactions and environmental filtering, with more regional processes including trait evolution and speciation. When combined with traditional measures of beta diversity, environmental gradient analyses or ecological niche modelling, phylobetadiversity can provide significant and novel insights into the mechanisms underlying current patterns of biological diversity. [source] Diverse developmental mechanisms contribute to different levels of diversity in horned beetlesEVOLUTION AND DEVELOPMENT, Issue 3 2005Armin P. Moczek Summary An ongoing challenge to evolutionary developmental biology is to understand how developmental evolution on the level of populations and closely related species relates to macroevolutionary transformations and the origin of morphological novelties. Here we explore the developmental basis of beetle horns, a morphological novelty that exhibits remarkable diversity on a variety of levels. In this study, we examined two congeneric Onthophagus species in which males develop into alternative horned and hornless morphs and different sexes express marked sexual dimorphism. In addition, both species differ in the body region (head vs. thorax) that develops the horn. Using a comparative morphological approach we show that prepupal growth of horn primordia during late larval development, as well as reabsorption of horn primordia during the pupal stage, contribute to horn expression in adults. We also show that variable combinations of both mechanisms are employed during development to modify horn expression of different horns in the same individual, the same horn in different sexes, and different horns in different species. We then examine expression patterns of two transcription factors, Distal-less (Dll) and aristaless (al), in the context of prepupal horn growth in alternative male morphs and sexual dimorphisms in the same two species. Expression patterns are qualitatively consistent with the hypothesis that both transcription factors function in the context of horn development similar to their known roles in patterning a wide variety of arthropod appendages. Our results suggest that the origin of morphological novelties, such as beetle horns, rests, at least in part, on the redeployment of already existing developmental mechanisms, such as appendage patterning processes. Our results also suggest, however, that little to no phylogenetic distance is needed for the evolution of very different modifier mechanisms that allow for substantial modulation of trait expression at different time points during development in different species, sexes, or tissue regions of the same individual. We discuss the implications of our results for our understanding of the evolution of horned beetle diversity and the origin and diversification of morphological novelties. [source] Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stressFEMS MICROBIOLOGY ECOLOGY, Issue 1 2006Lau Chui Yim Abstract We report an assessment of whole-community diversity for an extremely isolated geothermal location with considerable phylogenetic and phylogeographic novelty. We further demonstrate, using multiple statistical analyses of sequence data, that the response of community diversity is not monotonic to thermal stress along a gradient of 52,83°C. A combination of domain- and division-specific PCR was used to obtain a broad spectrum of community phylotypes, which were resolved by denaturing gradient gel electrophoresis. Among 58 sequences obtained from microbial mats and streamers, some 95% suggest novel archaeal and bacterial diversity at the species level or higher. Moreover, new phylogeographic and thermally defined lineages among the Cyanobacteria, Chloroflexi, Eubacterium and Thermus are identified. Shannon,Wiener diversity estimates suggest that mats at 63°C supported highest diversity, but when alternate models were applied [Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD)] that also take into account the phylogenetic relationships between phylotypes, it is evident that greatest taxonomic diversity (AvTD) occurred in streamers at 65,70°C, whereas greatest phylogenetic distance between taxa (VarTD) occurred in streamers of 83°C. All models demonstrated that diversity is not related to thermal stress in a linear fashion. [source] Oviposition and feeding preference of Acrolepiopsis assectella Zell. (Lep., Acrolepiidae)JOURNAL OF APPLIED ENTOMOLOGY, Issue 9-10 2007J. Allison Abstract:, The leek moth, Acrolepiopsisassectella (Zell.), is a recently discovered exotic species in eastern Ontario and western Quebec. This Allium spp. (Asparagales, Alliaceae) specialist can cause up to 40% crop damage. A no-choice experiment was used to determine the relationship between oviposition behaviour and larval survival of the leek moth as the phylogenetic distance from the preferred host Allium ampeloprasum var. porrum L. increased. Results indicate that oviposition preference and larval survival of the leek moth declined as the phylogenetic distance from the preferred host increased. These results support the conclusion that the leek moth is a specialist feeder on closely related Allium spp. although the strength of this preference may decline as the motivation to oviposit increases. This may indicate that the leek moth is able to use closely related novel hosts as temporary refuges if the preferred host plant is unavailable. [source] Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversityJOURNAL OF ECOLOGY, Issue 3 2007OLIVIER J. HARDY Summary 1Analysing the phylogenetic structure of natural communities may illuminate the processes governing the assembly and coexistence of species in ecological communities. 2Unifying previous works, we present a statistical framework to quantify the phylogenetic structure of communities in terms of average divergence time between pairs of individuals or species, sampled from different sites. This framework allows an additive partitioning of the phylogenetic signal into alpha (within-site) and beta (among-site) components, and is closely linked to Simpson diversity. It unifies the treatment of intraspecific (genetic) and interspecific diversity, leading to the definition of differentiation coefficients among community samples (e.g. IST, PST) analogous to classical population genetics coefficients expressing differentiation among populations (e.g. FST, NST). 3Two coefficients which express community differentiation among sites from species identity (IST) or species phylogeny (PST) require abundance data (number of individuals per species per site), and estimators that are unbiased with respect to sample size are given. Another coefficient (,ST) expresses the gain of the mean phylogenetic distance between species found in different sites compared with species found within sites, and requires only incidence data (presence/absence of each species in each site). 4We present tests based on phylogenetic tree randomizations to detect community phylogenetic clustering (PST > IST or ,ST > 0) or phylogenetic overdispersion (PST < IST or ,ST < 0). In addition, we propose a novel approach to detect phylogenetic clustering or overdispersion in different clades or at different evolutionary time depths using partial randomizations. 5IST, PST or ,ST can also be used as distances between community samples and regressed on ecological or geographical distances, allowing us to investigate the factors responsible for the phylogenetic signal and the critical scales at which it appears. 6We illustrate the approach on forest tree communities in Equatorial Guinea, where a phylogenetic clustering signal was probably due to phylogenetically conserved adaptations to the elevation gradient and was mostly contributed to by ancient clade subdivisions. 7The approach presented should find applications for comparing quantitatively phylogenetic patterns of different communities, of similar communities in different regions or continents, or of populations (within species) vs. communities (among species). [source] Morphological characterization of the testicular cells and seminiferous epithelium cycle in six species of Neotropical batsJOURNAL OF MORPHOLOGY, Issue 8 2009Mateus R. Beguelini Abstract We know little about the process of spermatogenesis in bats, a great and diverse clade of mammals that presents different reproductive strategies. In the present study, spermatogenesis in six species of Neotropical bats was investigated by light microscopy. On the basis of chromatin condensation, nuclear morphology, relative position to the basal membrane and formation of the flagellum, three types of spermatogonia were recognized: dark type A (Ad), pale type A (Ap), and type B; the development of spermatids was divided into seven steps. With the exception of Myotis nigricans, the seminiferous epithelium cycle of the other five species studied was similar to those of other mammals, showing gradual stages by the tubular morphology method. Asynchrony was observed in the seminiferous epithelium cycle of M. nigricans, shown by overlapping stages and undefined cycles. The frequencies found in the three phases of the cycle were variable with the greatest frequency occurring in the postmeiotic phase (>50%) and the least in the meiotic phase (<10%). The similarities observed in the five species of Phyllostomidae appeared to be related to their phylogenetic relationship and shorter divergence times, whereas the differences in M. nigricans appeared to be related to its greater phylogenetic distance because the Vespertilionidae family diverged earlier. J. Morphol., 2009. © 2009 Wiley-Liss, Inc. [source] PROPOSAL OF ECTOCARPUS SILICULOSUS (ECTOCARPALES, PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS,JOURNAL OF PHYCOLOGY, Issue 6 2004Akira F. Peters The emergence of model organisms that permit the application of a powerful combination of genomic and genetic approaches has been a major factor underlying the advances that have been made in the past decade in dissecting the molecular basis of a wide range of biological processes. However, the phylogenetic distance separating marine macroalgae from these model organisms, which are mostly from the animal, fungi, and higher plant lineages, limits the latters' applicability to problems specific to macroalgal biology. There is therefore a pressing need to develop similar models for the macroalgae. Here we describe a survey of potential model brown algae in which particular attention was paid to characteristics associated with a strong potential for genomic and genetic analysis, such as a small nuclear genome size, sexuality, and a short life cycle. Flow cytometry of nuclei isolated from zoids showed that species from the Ectocarpales possess smaller haploid genomes (127,290 Mbp) than current models among the Laminariales (580,720 Mbp) and Fucales (1095,1271 Mbp). Species of the Ectocarpales may complete their life histories in as little as 6 weeks in laboratory culture and are amenable to genetic analyses. Based on this study, we propose Ectocarpus siliculosus (Dillwyn) Lyngbye as an optimal choice for a general model organism for the molecular genetics of the brown algae. [source] Microsatellite markers for the polygamous termite Nasutitermes corniger (Isoptera: Termitidae)MOLECULAR ECOLOGY RESOURCES, Issue 2 2007LYNN ATKINSON Abstract We developed eight highly variable microsatellite markers for the termite Nasutitermes corniger. Allele number per locus ranged from nine to 34, and expected heterozygosity from 0.45 to 0.94, in samples from seven sites in the former canal zone of Panama. The utility of these markers was assessed for five congeners varying in phylogenetic distance to N. corniger. The markers will be useful for fine-scale examination of population and colony genetic structure in N. corniger and other closely related species. [source] Begging call matching between a specialist brood parasite and its host: a comparative approach to detect coevolutionBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009MICHAEL G. ANDERSON Studies of avian brood parasite systems have typically investigated the mimicry of host eggs by specialist parasites. Yet, several examples of similarity between host and parasite chick appearance or begging calls suggest that the escalation of host,parasite arms races may also lead to visual or vocal mimicry at the nestling stage. Despite this, there have been no large-scale comparative studies of begging calls to test whether the similarity of host and parasite is greater than predicted by chance or phylogenetic distance within a geographically distinct species assemblage. Using a survey of the begging calls of all native forest passerines in New Zealand, we show that the begging call of the host-specialist shining cuckoo (Chrysococcyx lucidus) is most similar to that of its grey warbler (Gerygone igata) host compared to any of the other species, and that this is unlikely to have occurred by chance. Randomization tests revealed that the incorporation of the shining cuckoo's begging calls into our species-set consistently reduced the phylogenetic signal within cluster trees based on begging call similarity. By contrast, the removal of the grey warbler calls did not reduce the phylogenetic signal in the begging call similarity trees. These two results support a scenario in which coevolution of begging calls has not taken place: the begging call of the host retains its phylogenetic signal, whereas that of the parasite has changed to match that of its host. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 208,216. [source] Host specificity of ambrosia and bark beetles (Col., Curculionidae: Scolytinae and Platypodinae) in a New Guinea rainforestECOLOGICAL ENTOMOLOGY, Issue 6 2007JIRI HULCR Abstract 1.,Bark and ambrosia beetles are crucial for woody biomass decomposition in tropical forests worldwide. Despite that, quantitative data on their host specificity are scarce. 2.,Bark and ambrosia beetles (Scolytinae and Platypodinae) were reared from 13 species of tropical trees representing 11 families from all major lineages of dicotyledonous plants. Standardised samples of beetle-infested twigs, branches, trunks, and roots were taken from three individuals of each tree species growing in a lowland tropical rainforest in Papua New Guinea. 3.,A total of 81 742 beetles from 74 species were reared, 67 of them identified. Local species richness of bark and ambrosia beetles was estimated at 80,92 species. 4.,Ambrosia beetles were broad generalists as 95% of species did not show any preference for a particular host species or clade. Similarity of ambrosia beetle communities from different tree species was not correlated with phylogenetic distances between tree species. Similarity of ambrosia beetle communities from individual conspecific trees was not higher than that from heterospecific trees and different parts of the trees hosted similar ambrosia beetle communities, as only a few species preferred particular tree parts. 5.,In contrast, phloeophagous bark beetles showed strict specificity to host plant genus or family. However, this guild was poor in species (12 species) and restricted to only three plant families (Moraceae, Myristicaceae, Sapindaceae). 6.,Local diversity of both bark and ambrosia beetles is not driven by the local diversity of trees in tropical forests, since ambrosia beetles display no host specificity and bark beetles are species poor and restricted to a few plant families. [source] ENVIRONMENTAL NICHE EQUIVALENCY VERSUS CONSERVATISM: QUANTITATIVE APPROACHES TO NICHE EVOLUTIONEVOLUTION, Issue 11 2008Dan L. Warren Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology. [source] Beetle horns are regulated by the Hox gene, Sex combs reduced, in a species- and sex-specific mannerEVOLUTION AND DEVELOPMENT, Issue 4 2010Bethany R. Wasik SUMMARY Discovering the mechanisms that underlie the origin of novel features represents a major frontier in developmental and evolutionary biology. Here we begin to characterize the role of the Hox gene Sex combs reduced (Scr) during the development and evolution of a morphologically novel trait: beetle horns. Beetle horns develop as epidermal outgrowths from the prothorax and/or head, and size and location vary dramatically across species and between sexes. Using both comparative gene expression and larval RNA interference in two species of the horned beetle genus Onthophagus, we show that Scr functions in patterning adult labial mouthpart identity and suppressing wing development in the prothorax. At the same time, however, our results illustrate that Scr has acquired, within its ancestral domain of expression, additional new functions including the regulation of prepupal growth and pupal remodeling of pronotal horn primordia. Furthermore, comparative analyses of our results across both Onthophagus species, which differ in location of horn development (thoracic horns vs. thoracic and head horns) as well as patterns of sexual dimorphism (traditional vs. reversed sexual dimorphism), reveal surprising differences in exactly when, where, and to what degree Scr regulates horn formation in different sexes. These observations suggest that the interactions between Scr and its targets in the regulation of horn development can diversify quickly over remarkably short phylogenetic distances. More generally, our results suggest that the Hox complex can play an integral role in the development and evolution of novel complex traits while maintaining traditional patterning responsibilities. [source] GEOMETRIC MORPHOMETRICS OF THE SKULL ROOF OF STEREOSPONDYLS (AMPHIBIA: TEMNOSPONDYLI)PALAEONTOLOGY, Issue 2 2006C. TRISTAN STAYTON Abstract:, Geometric morphometric analysis using relative warps is applied to the skull roof of 62 species of stereospondyls and their closest outgroups (i.e. basal archegosauriforms) from among temnospondyl amphibians. Twenty-one landmarks and five taxonomic groups are used for comparisons. Their skull evolution is quantified in a morphospace defined by two relative warps axes. The majority of groups show poor concordance between morphological and phylogenetic distances. The only exception is represented by Yates and Warren's study of stereospondyl relationships, in which concordance is high. Only basal archegosauriforms and rhinesuchids show significant overlap in morphospace, although this might be due to low sample sizes. Regression of estimated mean disparity against taxon sample size shows that species within both the trematosauroid and the rhytidostean groups are more widely dispersed in morphospace than species belonging to any of the remaining stereospondyl groups. Stereospondyl skull evolution was characterized by divergence between major clades and convergence within those clades. Changes in patterns of morphospace occupation through time agree with the hypothesis of an ,explosive' radiation in the early Early Triassic, after the extinction of basal archegosauriforms at the end of the Permian. [source] Genetic Variation and Differentiation Within a Natural Community of Five Oak Species (Quercus spp.)PLANT BIOLOGY, Issue 1 2007A. L. Curtu Abstract: Chloroplast DNA and two categories of nuclear markers - isozymes and microsatellites - were used to examine a very rich natural community of oaks (Quercus spp.) situated in west-central Romania. The community consists of five oak species: Q. robur, Q. petraea, Q. pubescens, and Q. frainetto - that are closely related -, and Q. cerris. A total of five chloroplast haplotypes was identified. Q. cerris was fixed for a single haplotype. The other four species shared the two most common haplotypes. One haplotype was confined to Q. robur and a very rare one was restricted to Q. petraea. Both types of nuclear markers revealed a larger genetic variation for Q. pubescens and Q. petraea than for Q. frainetto and Q. robur, although the differences between species are in most cases not significant. At the nuclear level, Q. cerris could be clearly separated from the other four oak species confirming the taxonomic classification. Regardless of the estimate used, the levels of polymorphism revealed by microsatellites were much higher than those based on isozymes. For the four closely related species the overall genetic differentiation was significant at both categories of nuclear markers. Several loci, such as Acp-C for isozymes, and ssrQpZAG36 and ssrQrZAG96 for microsatellites were very useful to discriminate among species. However, the level of differentiation varied markedly between pairs of species. The genetic affinities among the species may reflect different phylogenetic distances and/or different rates of recurrent gene flow at this site. [source] A Hierarchical View of Convergent Evolution in Microbial Eukaryotes,THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2008BRIAN S. LEANDER ABSTRACT. Distinguishing convergent evolution from other causes of similarity in organisms is necessary for reconstructing phylogenetic relationships, inferring patterns of character evolution, and investigating the forces of natural selection. In contrast to animals and land plants, the pervasiveness and adaptive significance of convergent evolution in microbes has yet to be systematically explored or articulated. Convergent evolution in microbial eukaryotes, for instance, often involves very distantly related lineages with relatively limited repertoires of morphological features. These large phylogenetic distances weaken the role of ancestral developmental programs on the subsequent evolution of morphological characters, making convergent evolution between very distantly related lineages fundamentally different from convergent evolution between closely related lineages. This suggests that examples of convergence at different levels in the phylogenetic hierarchy offer different clues about the causes and processes of macroevolutionary diversification. Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence,"parallel", "proximate" and "ultimate",that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. Microbial eukaryotes living in planktonic environments, interstitial environments, and the intestinal environments of metazoan hosts provide compelling examples of ultimate convergence. After describing selected examples in microbial eukaryotes, I suggest some future directions needed to more fully understand the hierarchical structure of convergent evolution and the overall history of life. [source] | ||||||||||||||||||||||