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Phylogenetic Pattern (phylogenetic + pattern)
Selected AbstractsTHE PHYLOGENETIC PATTERN OF SPECIATION AND WING PATTERN CHANGE IN NEOTROPICAL ITHOMIA BUTTERFLIES (LEPIDOPTERA: NYMPHALIDAE)EVOLUTION, Issue 7 2006Chris D. Jiggins Abstract Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification. [source] Phylogenetic patterns of enamel microstructure in dinosaur teethJOURNAL OF MORPHOLOGY, Issue 2 2005Sunny H. Hwang Abstract The tooth enamel microstructure of all the dinosaur taxa that are adequately represented in the American Museum of Natural History collections were analyzed using scanning electron microscopy. This study aims to determine whether or not better sampling within a major nonmammalian amniote (hereafter referred to descriptively as "reptile") clade will unearth phylogenetic patterns in enamel microstructure in addition to those dictated by tooth function. While interest in reptile enamel microstructure has increased in the past few years, intensive sampling focused on just one monophyletic reptile clade was not previously implemented. This study reveals that phylogenetic constraints play a larger role in shaping enamel microstructure in reptiles than previously thought. Within many monophyletic dinosaur clades the combination of enamel types and enamel features within a tooth,the schmelzmuster,is the same in all the taxa due to their common ancestry, and their schmelzmusters are diagnostic of their respective clades. While distantly related taxa with similar teeth and diets have similar schmelzmusters due to functional constraints, phylogenetic constraints keep those schmelzmusters distinct from one another. An interesting finding of this analysis is that the enamel complexity of a taxon does not necessarily coincide with the position of the taxon on a phylogenetic tree; more derived taxa do not necessarily have more derived enamel and more primitive taxa do not necessarily have more primitive enamel. J. Morphol. © 2005 Wiley-Liss, Inc. [source] Phylogenetic patterns of diversification in a clade of Neotropical frogs (Anura: Aromobatidae: Mannophryne)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2009JESÚS MANZANILLA We used partial sequences of mitochondrial 16S and cytochrome oxidase I genes to perform a phylogenetic study of collared frogs (Anura: Aromobatidae: Mannophryne), a genus endemic to Venezuela and the islands of Trinidad and Tobago. We analysed 1.2 kb from 13 of the 15 described species of Mannophryne. Maximum parsimony, maximum likelihood and Bayesian analyses support the monophyly of Mannophryne. Mannophryne consists of three deeply differentiated clades that split from each other in a relatively short period of time. The diversification of Mannophryne occurred well before the glacial-interglacial periods of the Quaternary. Our data support the taxonomic validity of M. olmonae, a species endemic to Tobago Island. Mannophryne olmonae is more closely related to the continental species Mannophryne riveroi than to the Trinidad island endemic Mannophryne trinitatis. As in most tropical clades of frogs, molecular evidence indicates that species richness in Mannophryne is largely underestimated and, consequently, current priorities for conservation are inadequate. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 185,199. [source] SOCIALITY IN THERIDIID SPIDERS: REPEATED ORIGINS OF AN EVOLUTIONARY DEAD ENDEVOLUTION, Issue 11 2006Ingi Agnarsson Abstract Evolutionary ,dead ends' result from traits that are selectively advantageous in the short term but ultimately result in lowered diversification rates of lineages. In spiders, 23 species scattered across eight families share a social system in which individuals live in colonies and cooperate in nest maintenance, prey capture, and brood care. Most of these species are inbred and have highly female-biased sex ratios. Here we show that in Theridiidae this social system originated eight to nine times independently among 11 to 12 species for a remarkable 18 to 19 origins across spiders. In Theridiidae, the origins cluster significantly in one clade marked by a possible preadaptation: extended maternal care. In most derivations, sociality is limited to isolated species: social species are sister to social species only thrice. To examine whether sociality in spiders represents an evolutionary dead end, we develop a test that compares the observed phylogenetic isolation of social species to the simulated evolution of social and non-social clades under equal diversification rates, and find that sociality in Theridiidae is significantly isolated. Because social clades are not in general smaller than their nonsocial sister clades, the spindly phylogenetic pattern,many tiny replicate social clades,may be explained by extinction rapid enough that a nonsocial sister group does not have time to diversify while the social lineage remains extant. In this case, this repeated origin and extinction of sociality suggests a conflict between the short-term benefits and long-term costs of inbred sociality. Although benefits of group living may initially outweigh costs of inbreeding (hence the replicate origins), in the long run the subdivision of the populations in relatively small and highly inbred colony lineages may result in higher extinction, thus an evolutionary dead end. [source] Searching for phylogenetic pattern in biological invasionsGLOBAL ECOLOGY, Issue 1 2008erban Proche Abstract It has been suggested that alien species with close indigenous relatives in the introduced range may have reduced chances of successful establishment and invasion (Darwin's naturalization hypothesis). Studies trying to test this have in fact been addressing four different hypotheses, and the same data can support some while rejecting others. In this paper, we argue that the phylogenetic pattern will change depending on the spatial and phylogenetic scales considered. Expectations and observations from invasion biology and the study of natural communities are that at the spatial scale relevant to competitive interactions, closely related species will be spatially separated, whereas at the regional scale, species in the same genera or families will tend to co-occur more often than by chance. We also argue that patterns in the relatedness of indigenous and naturalized plants are dependent on the continental/island setting, spatial occupancy levels, and on the group of organisms under scrutiny. Understanding how these factors create a phylogenetic pattern in invasions will help us predict which groups are more likely to invade where, and should contribute to general ecological theory. [source] Morphological evolution of the lizard skull: A geometric morphometrics surveyJOURNAL OF MORPHOLOGY, Issue 1 2005C. Tristan Stayton Abstract Patterns of diversity among lizard skulls were studied from a morphological, phylogenetic, and functional perspective. A sample of 1,030 lizard skulls from 441 species in 17 families was used to create a lizard skull morphospace. This morphospace was combined with a phylogeny of lizard families to summarize general trends in the evolution of the lizard skull. A basal morphological split between the Iguania and Scleroglossa was observed. Iguanians are characterized by a short, high skull, with large areas of attachment for the external adductor musculature, relative to their sister group. The families of the Iguania appear to possess more intrafamilial morphological diversity than families of the Scleroglossa, but rarefaction of the data reveals this to be an artifact caused by the greater number of species represented in Iguanian families. Iguanian families also appear more dissimilar to one another than families of the Scleroglossa. Permutation tests indicate that this pattern is real and not due to the smaller number of families in the Iguanidae. Parallel and convergent evolution is observed among lizards with similar diets: ant and termite specialists, carnivores, and herbivores. However, these patterns are superimposed over the more general phylogenetic pattern of lizard skull diversity. This study has three central conclusions. Different clades of lizards show different patterns of disparity and divergence in patterns of morphospace occupation. Phylogeny imposes a primary signal upon which a secondary ecological signal is imprinted. Evolutionary patterns in skull metrics, taken with functional landmarks, allow testing of trends and the development of new hypotheses concerning both shape and biomechanics. J. Morphol. 263:47,59, 2005. © 2004 Wiley-Liss, Inc. [source] Phylogenetic autocorrelation and heritability of geographic range size, shape and position of fiddler crabs, genus Uca (Crustacea, Decapoda)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2010J. C. Nabout Abstract The aim of this study was to evaluate the levels of phylogenetic heritability of the geographical range size, shape and position for 88 species of fiddler crabs of the world, using phylogenetic comparative methods and simulation procedures to evaluate their fit to the neutral model of Brownian motion. The geographical range maps were compiled from literature, and range size was based on the entire length of coastline occupied by each species, and the position of each range was calculated as its latitudinal and longitudinal midpoint. The range shape of each species was based in fractal dimension (box-counting technique). The evolutionary patterns in the geographical range metrics were explored by phylogenetic correlograms using Moran's I autocorrelation coefficients, autoregressive method (ARM) and phylogenetic eigenvector regression (PVR). The correlograms were compared with those obtained by simulations of Brownian motion processes across phylogenies. The distribution of geographical range size of fiddler crabs is right-skewed and weak phylogenetic autocorrelation was observed. On the other hand, there was a strong phylogenetic pattern in the position of the range (mainly along longitudinal axis). Indeed, the ARM and PVR evidenced, respectively, that ca. 86% and 91% of the longitudinal midpoint could be explained by phylogenetic relationships among the species. The strong longitudinal phylogenetic pattern may be due to vicariant allopatric speciation and geographically structured cladogenesis in the group. The traits analysed (geographical range size and position) did not follow a Brownian motion process, thus suggesting that both adaptive ecological and evolutionary processes must be invoked to explain their dynamics, not following a simple neutral inheritance in the fiddler-crab evolution. Resumen El objetivo de este trabajo fue estimar los niveles de herencia filogenética existentes en la posición geográfica, forma y el tamaño de rango geográfico en 88 especies de cangrejo violinista del mundo, mediante simulaciones y métodos comparativos filogenéticos para así evaluar su ajuste al modelo neutro de evolución browniana. Los mapas de rango geográfico se obtuvieron de la literatura. La forma de rango geográfico fue estimada en la dimensión fractal. Los patrones evolutivos en el tamaño y forma del rango geográfico y la posición geográfica fueron explorados mediante correlogramas filogenéticos utilizando el índice I de Moran, coeficientes autorregresivos (ARM) y regressión por autovetores filogenéticos (PVR). Estos correlogramas fueron comparados con aquellos obtenidos mediante la simulación de procesos de evolución browniana en las filogenias. El tamaño y forma de rango geográfico del cangrejo violinista mostró una distribución apuntada hacia la derecha aunque no se encontró autocorrelación filogenética. Por otra parte, se observó un marcado patrón filogenético para la posición geográfica del rango (principalmente a lo largo del eje longitudinal). De hecho, el ARM y PVR evidenció respectivamente que cerca del 86% y 91% de la localización del punto medio longitudinal del rango se puede explicar mediante las relaciones filogenéticas existentes entre las especies. El fuerte patrón filogenético en la longitud podría ser debido a especiación alopátrica y a una cladogénesis estructurada geográficamente para el grupo, tal y como se propuso en las hipótesis. Los rasgos analizados (rango geográfico y posición geográfica) no siguieron un proceso de evolución browniana, sugiriendo pues que tanto los procesos evolutivos como la adaptación ecológica deberían ser tenidos en cuenta para explicar sus dinámicas, ya que el transcurso de la evolución del cangrejo violinista no se explica mediante un simple modelo de herencia neutra. [source] Broad versus narrow auditory tuning and corresponding bat-evasive flight behaviour in praying mantidsJOURNAL OF ZOOLOGY, Issue 1 2001Jeffrey D. Triblehorn Abstract Most praying mantids possess a single tympanal ear located in the ventral midline between the metathoracic legs. The auditory system is generally most sensitive to ultrasound in the 25,50 kHz range. Flying males exhibit a short-latency, stereotyped, multi-component response to ultrasound that allows them to escape from attacking bats. This study describes a small subset of species that differs in three major respects from the majority of mantis species: (1) their auditory tuning is 1.5,2 times broader; (2) they are sensitive to frequencies above 60 kHz (up to 130 kHz in some species) with thresholds as low or lower than at 25,50 kHz; (3) the behavioural response of the broadly tuned (BT) species includes 10,50 times more flight cessations and can be far less stereotyped, i.e. more ,evitable', than that of narrowly tuned (NT) species. However, BT species do not differ from NT species in overall sensitivity. Two species from one subfamily, the Amelinae (family Mantidae), stand out because they are among the least sensitive of any hearing mantids so far tested. Although the two amelines differ from one another in tuning curve shape, they are both more broadly tuned than most mantids. The occurrence of BT species does not follow any obvious phylogenetic pattern; they are patchily distributed among the mantis families, and both BT and NT species can be found in the same subfamily or tribe. We suggest that BT species are responding to a shared ecological pressure. Based on their tuning, the nature of their behavioural response, and their geographic distribution, we hypothesize that high duty cycle (HDC) bats (Rhinolophidae and Hipposideridae) pose a special danger to BT mantids in addition to the threat that all flying mantids face from the more common and widely distributed low duty cycle (LDC) bats. [source] The enigmatic invasive Spartina densiflora: A history of hybridizations in a polyploidy contextMOLECULAR ECOLOGY, Issue 19 2008P. M. FORTUNE Abstract The aim of this study was to explore the origin of the invasive Spartina densiflora by analysing samples from the native region (South America) and from a recently colonized area (California). A combination of various molecular data (chloroplast and nuclear sequences, molecular fingerprint) and ploidy level estimations was used to answer the question whether the reticulate phylogenetic pattern previously detected in S. densiflora was restricted to California, or alternatively, whether a more ancient hybrid origin preceded formation of this species in its native area. We found that this species is heptaploid in both its native and introduced range. Identification of nuclear homeologous sequences indicate that this species has a reticulate origin in its native range, involving a lineage related to the hexaploid clade formed by S. alterniflora, S. foliosa, and S. maritima, and another lineage related to the sub-Antarctic endemic S. arundinacea that provided the chloroplast genome. The samples from California displayed similar multilocus patterns to the samples from Chile, supporting the hypothesis that this species originated on the southeast American coast (Argentina), from where it eventually spread to the west coast of South America (Chile) first and to the Northern Hemisphere (California) later. [source] Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizationsMOLECULAR ECOLOGY, Issue 4 2005JENNIFER L. TRUSTY Abstract A molecular phylogenetic study of Bystropogon L'Hèr. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution. [source] An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssiMOLECULAR MICROBIOLOGY, Issue 6 2003Georges N. Cohen Summary The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome. [source] A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?BIOLOGICAL REVIEWS, Issue 1 2002HAROLD N. BRYANT ABSTRACT The proposal to implement a phylogenetic nomenclatural system (governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy, in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs. [source] A new dimension in combining data?ACTA ZOOLOGICA, Issue 1 2010The use of morphology, phylogenomic data in metazoan systematics Abstract Giribet, G. 2010. A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. ,Acta Zoologica (Stockholm) 91: 11,19 Animal phylogenies have been traditionally inferred by using the character state information derived from the observation of a diverse array of morphological and anatomical features, but the incorporation of molecular data into the toolkit of phylogenetic characters has shifted drastically the way researchers infer phylogenies. A main reason for this is the ease at which molecular data can be obtained, compared to, e.g., traditional histological and microscopical techniques. Researchers now routinely use genomic data for reconstructing relationships among animal phyla (using whole genomes or Expressed Sequence Tags) but the amount of morphological data available to study the same phylogenetic patterns has not grown accordingly. Given the disparity between the amounts of molecular and morphological data, some authors have questioned entire morphological programs. In this review I discuss issues related to the combinability of genomic and morphological data, the informativeness of each set of characters, and conclude with a discussion of how morphology could be made scalable by utilizing new techniques that allow for non-intrusive examination of large amounts of preserved museum specimens. Morphology should therefore remains a strong field in evolutionary and comparative biology, as it continues to provide information for inferring phylogenetic patterns, is an important complement for the patterns derived from the molecular data, and it is the common nexus that allows studying fossil taxa with large data sets of molecular data. [source] WHY DOES A TRAIT EVOLVE MULTIPLE TIMES WITHIN A CLADE?EVOLUTION, Issue 1 2006REPEATED EVOLUTION OF SNAKELINE BODY FORM IN SQUAMATE REPTILES Abstract Why does a trait evolve repeatedly within a clade? When examining the evolution of a trait, evolutionary biologists typically focus on the selective advantages it may confer and the genetic and developmental mechanisms that allow it to vary. Although these factors may be necessary to explain why a trait evolves in a particular instance, they may not be sufficient to explain phylogenetic patterns of repeated evolution or conservatism. Instead, other factors may also be important, such as biogeography and competitive interactions. In squamate reptiles (lizards and snakes) a dramatic transition in body form has occurred repeatedly, from a fully limbed, lizardlike body form to a limbreduced, elongate, snakelike body form. We analyze this trait in a phylogenetic and biogeographic context to address why this transition occurred so frequently. We included 261 species for which morphometric data and molecular phylogenetic information were available. Among the included species, snakelike body form has evolved about 25 times. Most lineages of snakelike squamates belong to one of two ecomorphs, either short-tailed burrowers or long-tailed surface dwellers. The repeated origins of snakelike squamates appear to be associated with the in situ evolution of these two ecomorphs on different continental regions (including multiple origins of the burrowing morph within most continents), with very little dispersal of most limb-reduced lineages between continental regions. Overall, the number of repeated origins of snakelike morphology seems to depend on large-scale biogeographic patterns and community ecology, in addition to more traditional explanations (e.g., selection, development). [source] Targeted genomic detection of biosynthetic pathways: anaerobic production of hopanoid biomarkers by a common sedimentary microbeGEOBIOLOGY, Issue 1 2005W. W. FISCHER ABSTRACT The lipid biomarker principle requires that preservable molecules (molecular fossils) carry specific taxonomic, metabolic, or environmental information. Historically, an empirical approach was used to link specific taxa with the compounds they produce. The lipids extracted from numerous, but randomly cultured species provided the basis for the interpretation of biomarkers in both modern environments and in the geological record. Now, with the rapid sequencing of hundreds of microbial genomes, a more focused genomic approach can be taken to test phylogenetic patterns and hypotheses about the origins of biomarkers. Candidate organisms can be selected for study on the basis of genes that encode proteins fundamental to the synthesis of biomarker compounds. Hopanoids, a class of pentacyclic triterpenoid lipid biomarkers, provide an illustrative example. For many years, interpretations of biomarker data were made with the assumption that hopanoids are produced only by aerobic organisms. However, the recent discovery of 13C-depleted hopanoids in environments undergoing anaerobic methane oxidation and in enrichment cultures of anammox planctomycetes indicates that some hopanoids are produced anaerobically. To further examine the potential distribution of hopanoid biosynthesis by anaerobes, we searched publicly available genomic databases for the presence of squalene-hopene cyclase genes in known obligate or facultative anaerobes. Here we present evidence that Geobacter sulfurreducens, Geobacter metallireducens, and Magnetospirillum magnetotacticum, all bacteria common in anoxic environments, have the appropriate genes for hopanoid biosynthesis. We further show that these data accurately predict that G. sulfurreducens does produce a variety of complex hopanoids under strictly anaerobic conditions in pure culture. [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] Phylogenetic patterns of enamel microstructure in dinosaur teethJOURNAL OF MORPHOLOGY, Issue 2 2005Sunny H. Hwang Abstract The tooth enamel microstructure of all the dinosaur taxa that are adequately represented in the American Museum of Natural History collections were analyzed using scanning electron microscopy. This study aims to determine whether or not better sampling within a major nonmammalian amniote (hereafter referred to descriptively as "reptile") clade will unearth phylogenetic patterns in enamel microstructure in addition to those dictated by tooth function. While interest in reptile enamel microstructure has increased in the past few years, intensive sampling focused on just one monophyletic reptile clade was not previously implemented. This study reveals that phylogenetic constraints play a larger role in shaping enamel microstructure in reptiles than previously thought. Within many monophyletic dinosaur clades the combination of enamel types and enamel features within a tooth,the schmelzmuster,is the same in all the taxa due to their common ancestry, and their schmelzmusters are diagnostic of their respective clades. While distantly related taxa with similar teeth and diets have similar schmelzmusters due to functional constraints, phylogenetic constraints keep those schmelzmusters distinct from one another. An interesting finding of this analysis is that the enamel complexity of a taxon does not necessarily coincide with the position of the taxon on a phylogenetic tree; more derived taxa do not necessarily have more derived enamel and more primitive taxa do not necessarily have more primitive enamel. J. Morphol. © 2005 Wiley-Liss, Inc. [source] Identification and gene expression profiling of the Pum1 and Pum2 members of the Pumilio family in the chickenMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 1 2008Jee Young Lee Abstract Members of the Pumilio (Pum) family of RNA-binding proteins act as translational repressors and are required for germ cell development and asymmetric division. We identified the chicken Pum1 and Pum2 genes and analyzed their expression patterns in various tissues. Comparative sequence analysis of the Pum1 and Pum2 proteins from the drosophila, chicken, mouse, and human revealed a high degree of evolutionary conservation in terms of the levels of homology of the peptide sequences and the structure of Pumilio homology domain (PUM-HD), C-terminal RNA-binding domain, with similar spacing between the adjacent Pum eight tandem repeats. In addition, phylogenetic patterns of pumilio family showed that Pum 1 and 2 of chicken are more closely related to those of mouse and human than other species and Pum1 is more conserved than Pum2. Using real-time RT-PCR, the expression levels of the Pum1 and Pum2 genes were found to be highest in hatched female gonads, and high-level expression of Pum2 was detected in 12-day and hatched gonads among the various chicken embryonic tissues tested. In adult tissues, the expression levels of Pum1 and Pum2 were expressed at higher levels in the testis and muscle than in any other tissue. The characteristics of the tissue-specific expression of Pum genes suggest that Pum1 and Pum2 have effects crucially in particular stage during development of chicken gonads depending on sexual maturation. Mol. Reprod. Dev. 75: 184,190, 2008. © 2007 Wiley-Liss, Inc. [source] The tail end of hummingbird evolution: parallel flight system development in living and ancient birdsBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2009ROBERT BLEIWEISS Evolutionary innovations are central to debates about biological uniformitarianism because their very novelty implies a distinct evolutionary dynamic. Traditional scenarios for innovations in the development of avian powered flight exemplify the kinds of distinctions considered to occur at different times during the history of innovations. Thus, the progressive change of the wing stroke mechanism early in its evolution is considered to have imposed strong functional and historical constraints on tail shape diversity, whereas attainment of the modern flight stroke mechanism is considered to have liberated the tail to radiate into a wide variety of other functions and forms. Detailed analyses of living hummingbirds revealed that these highly aerial birds actually expressed many parallel functional constraints and historically progressive patterns observed earlier in avian history: (1) more basal lineages had relatively weak wing muscles (patagial muscles and tendons, TPB), convex to square tails, and more linear flight employed in nonterritorial foraging; (2) more derived lineages had a stronger TPB, forked tails, accentuated growth of tail fork, and more manoeuvrable and agile flight employed in territorial foraging; and (3) the most derived lineage had the strongest TPB, greatly reduced tails, and mainly bee-like flight. These associations make functional sense because convex tails increase stability and efficiency in linear flight, concave tails augment lift for turning flight in territorial defence, and tails become aerodynamically disadvantageous if the wings provide sufficient lift. Derived hummingbird lineages also demonstrated the same expansion of tail shape and taxonomic diversity associated with perfection of the modern wing stroke mechanism earlier in avian history. Thus, living hummingbirds are a microcosm of overall avian flight evolution. Other living avian (,aerial courser') and extinct reptilian (Pterosaur) clades with extraordinary flight abilities provide evidence for similar patterns, suggesting a broadly defined uniformitarianism (early constraint followed by later radiation) at the limits of the flight performance envelope throughout vertebrate history. Correlated evolution of TPB and tail form suggests that natural selection on an integrated flight system was the principal mechanism fostering the avian patterns, although strengthening of wing muscles in derived lineages may have facilitated expansion of caudal morphological diversity through a balance between natural and sexual selection on males. These findings suggest that wing muscles, locomotor integration, and phylogenetic patterns are essential for understanding function and adaptation of tails in living as well as ancient birds. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 467,493. [source] | ||||||||||||||||||||||