Soil composition affects the nesting behavior of blue-tailed bee-eaters (Merops philippinus) on Kinmen Island

The blue-tailed bee-eater (Merops philippinus) is a summer migrant that breeds on Kinmen Island, located off the west coast of Taiwan, about 5 km from the southern coast of mainland China. The aim of this study was to investigate why blue-tailed bee-eaters build their nests in sandy loam and sandy clay loam, but not in clay loam. Soil chemical and physical properties, and mineralogical composition were measured for the different soil types. Clay loam had a significantly lower pH, Na, and base saturation than did sandy loam or sandy clay loam. Clay loam had a significantly higher N, cation-exchange capacity (CEC), K, and free iron (Fe_d) and aluminum oxide (Al_d) contents than the other soil types. Clay loam had significantly lower sand and higher clay content, and higher bulk density and penetration resistance than the other soil types. The correlation coefficients (r ²) between penetration resistance and Fe_d, Al_d, and clay contents were 0.997, 0.848, and 0.779, respectively. Soil strength and compaction are important criteria for bee-eaters nesting-site selection. The lower pH of clay loam would enhance the exchangeable Al and acidity, further increasing the soil aggregation. Thus, it might prevent the bee-eaters from excavating nesting burrows.     

Horizontal and vertical ectoparasite transmission of three species of Malophaga, and individual variation in european bee-eaters (Merops apiaster)

Dispersal of avian ectoparasites can occur through either vertical transmission from adult birds to their offspring in the nest or through horizontal transmission between adult birds or through phoresy. In this study, we investigated the importance of the 2 main transmission modes in the colonial European bee-eater and examined whether individual differences in ectoparasite intensity exist in relation to age, sex, and morphological features of the birds. The intensity of 3 chewing lice species was investigated. Almost all adult bee-eaters (98.3%, n = 176) were infested with 1 of the 3 ectoparasite species, whereas only 10.8% (n = 167) of all chicks were infested. Meropoecus meropis was the most frequent ectoparasite species on adult bee-eaters (prevalence 94.3%), whereas Meromenopon meropis was the most common species on chicks (prevalence 9.6%). Our results suggest that chewing lice are mainly horizontally transmitted among adult bee-eaters and mainly among pair members, whereas vertical transmission between parents and nestlings is less frequent. These conclusions were supported by a relation in ectoparasite intensity of pair members and a parasite removal experiment. Ectoparasite intensity was in general low in nestlings and did not correlate with ectoparasite intensity of their parents. Host age, sex, weight, and other morphological features did not explain variation in chewing lice infestation.     

Rainbow bee-eaters (Merops ornatus) as a monitoring tool for honeybees (Apis mellifera L.; Hymenoptera: Apidae)

Abstract Regurgitated pellets were collected from underneath roosts of rainbow bee-eaters in suburban Darwin, Australia, and examined for the presence of wings of honeybees. The proportion of pellets containing wings was compared prior to and after placement or removal of honeybee hives in the vicinity of four roosts. On each occasion, the addition or removal of hives was reflected in proportions of pellets containing wings. The results suggest that examination of pellets beneath bee-eater roosts would be a useful technique for monitoring the occurrence of feral honeybees. Potential uses for this technique in eradication of unwanted bees are discussed.     

类群取样与系统发育分析精确度之探索

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.     

Challenges of phylogenetic analyses of aDNA sequences

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.     

On the selection of phylogenetic eigenvectors for ecological analyses

Among the statistical methods available to control for phylogenetic autocorrelation in ecological data, those based on eigenfunction analysis of the phylogenetic distance matrix among the species are becoming increasingly important tools. Here, we evaluate a range of criteria to select eigenvectors extracted from a phylogenetic distance matrix (using phylogenetic eigenvector regression, PVR) that can be used to measure the level of phylogenetic signal in ecological data and to study correlated evolution. We used a principal coordinate analysis to represent the phylogenetic relationships among 209 species of Carnivora by a series of eigenvectors, which were then used to model log‐transformed body size. We first conducted a series of PVRs in which we increased the number of eigenvectors from 1 to 70, following the sequence of their associated eigenvalues. Second, we also investigated three non‐sequential approaches based on the selection of 1) eigenvectors significantly correlated with body size, 2) eigenvectors selected by a standard stepwise algorithm, and 3) the combination of eigenvectors that minimizes the residual phylogenetic autocorrelation. We mapped the mean specific component of body size to evaluate how these selection criteria affect the interpretation of non‐phylogenetic signal in Bergmann's rule. For comparison, the same patterns were analyzed using autoregressive model (ARM) and phylogenetic generalized least‐squares (PGLS). Despite the robustness of PVR to the specific approaches used to select eigenvectors, using a relatively small number of eigenvectors may be insufficient to control phylogenetic autocorrelation, leading to flawed conclusions about patterns and processes. The method that minimizes residual autocorrelation seems to be the best choice according to different criteria. Thus, our analyses show that, when the best criterion is used to control phylogenetic structure, PVR can be a valuable tool for testing hypotheses related to heritability at the species level, phylogenetic niche conservatism and correlated evolution between ecological traits.     

Competition and coexistence of the European Bee-eater Merops apiaster and the Blue-cheeked Bee-eater Merops persicus in Asia

Studies were conducted over a 10-year period on the supposedly similar European Bee-eater Merops apiaster and Blue-cheeked Bee-eater Merops persicus breeding in mixed and separate colonies in four Asiatic countries. In spring, M. persicus arrived a few days later and laid up to 2 weeks later than M. apiaster. Spatial distributions of the two species were positively associated. They were sympatric and syntopic: more than half of the local breeding ranges overlapped, and many birds bred within sight and sound of the congener. Intraspecific conflict was frequent, but in mixed colonies interspecific conflict was rare. Most M. apiaster nest burrows were dug into cliffs and most M. persicus ones into level ground, but dense mixed colonies occurred only in cliffs. Burrow architecture differed specifically. Diets were qualitatively similar at insect family level but different at the species level, partly because of local variation in availability and partly because of distinct preferences of M. apiaster for small beetles, ants and termites and of M. persicus for large dragonflies and cicadas. Merops persicus was less specialized than M. apiaster and had an airborne insect prey spectrum nearly twice as broad. Diets were more alike where the two birds foraged together than where they foraged separately. There was a high incidence of egg and nestling loss by predation and starvation.
We speculate that each species may prove to breed more successfully in mixed than in monospecific colonies. We propose that the two bee-eaters do not compete for nest sites but may compete for food and coexist unaggressively by trading off food competition against improved breeding success in mixed colonies.     

Cladistic and phylogenetic analyses of the genus Cicer in Turkey

Fifteen taxa of the genus Cicer L. growing naturally in Turkey and out-groups were classified by phylogenetic and cladistic analysis. Taxa of the genus Cicer and the out-group taxa belonging to the closest genera Phaseolus L., Vicia L., Lathyrus L. and Ononis L., which are placed in Phaseoleae, Vicieae and Ononideae tribes, respectively, were used in molecular studies in order to derive their phylogenetic relationships. Morphological, palynological and seed characters were used on the basis of 143 traits. The micromorphological characters of seed and pollen grains were revealed by SEM. Lathyrus L. and Vicia L. species were used as out-groups for numerical analysis. Ten specimens were used for the measurements of metric characters related to the morphological structures of the taxa used for statistical analysis via PAUP and NTSYS-pc packages. Phylogenetic relationships between species and populations of the same species growing in different locations and their variations were determined using molecular methods performed on regions of the Inter Simple Sequence Repeat (ISSR). DNA was isolated from the collected samples, using modified CTAB protocols. ISSR was used for phylogenetic fingerprinting. The data were analyzed with NTSYS-pc package. Standardized data were used to generate a dendrogram that revealed the phylogenetic relationships of the taxa. Geographic distribution of the Cicer taxa appears to be closely related to the Anatolian Diagonal. As a result of this study, four new endemic taxa were added and evaluated for the first time.     

Mutational and phylogenetic analyses of the mycobacterial mbt gene cluster

The mycobactin siderophore system is present in many Mycobacterium species, including M. tuberculosis and other clinically relevant mycobacteria. This siderophore system is believed to be utilized by both pathogenic and nonpathogenic mycobacteria for iron acquisition in both in vivo and ex vivo iron-limiting environments, respectively. Several M. tuberculosis genes located in a so-called mbt gene cluster have been predicted to be required for the biosynthesis of the core scaffold of mycobactin based on sequence analysis. A systematic and controlled mutational analysis probing the hypothesized essential nature of each of these genes for mycobactin production has been lacking. The degree of conservation of mbt gene cluster orthologs remains to be investigated as well. In this study, we sought to conclusively establish whether each of nine mbt genes was required for mycobactin production and to examine the conservation of gene clusters orthologous to the M. tuberculosis mbt gene cluster in other bacteria. We report a systematic mutational analysis of the mbt gene cluster ortholog found in Mycobacterium smegmatis. This mutational analysis demonstrates that eight of the nine mbt genes investigated are essential for mycobactin production. Our genome mining and phylogenetic analyses reveal the presence of orthologous mbt gene clusters in several bacterial species. These gene clusters display significant organizational differences originating from an intricate evolutionary path that might have included horizontal gene transfers. Altogether, the findings reported herein advance our understanding of the genetic requirements for the biosynthesis of an important mycobacterial secondary metabolite with relevance to virulence.     

Diet of sympatrically breeding Southern Carmine Bee-eater Merops nubicoides and White-fronted Bee-eater Merops bullockoides

The Southern Carmine Bee-eater Merops nubicoides and White-fronted Bee-eater Merops bullockoides are insectivore, cavity-nesting bird species, both of which occur in the Zambezi Region, north-eastern Namibia. I examined there the diet composition of these species by an analysis of prey remnants. The Southern Carmine Bee-eater chick's diet consisted of exclusively insects, represented by seven orders. The most numerous were orthopterans and beetles (40.9% and 26.1%, respectively; n = 582 prey items). Hymenopterans (18.7%) and bugs (12.9%) supplemented the diet, whereas dragonflies (Odonata) and moths (Lepidoptera) were preyed only occasionally. In the diet of the White-fronted Bee-eater, nesting at the same site, beetles were the most important prey (81.2% of all 101 prey items identified), with scarabaeids comprising more than half of the beetle diet. In comparison with the White-fronted Bee-eater, a lower proportion of beetles, but much larger proportion of orthopterans were recorded in the diet of the Southern Carmine Bee-eater. In both bee-eater species, hymenopterans appear to be less important than was expected. The essential difference in the proportion of main prey groups recorded in Southern Carmine and White-fronted Bee-eaters breeding at the same site may represent a shift in food niche due to both temporal segregation in breeding, and differences in food preferences (feeding sites).     

Evaluating strategies of phylogenetic analyses by the coherence of their results

I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more it reflects the historical signal common to the analysed data. Under this hypothesis, the capacity of an analytical strategy to extract historical signal should correlate positively with the coherence of the obtained results. I apply this approach to a series of analyses on empirical data, basing the coherence measure on the Robinson–Foulds distances between the obtained trees. At first approximation, the analytical strategies most suitable for the data produce the most coherent results. However, risks of false positives and false negatives are identified, which are difficult to rule out.     

Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist for achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach is increasingly preferred over parsimony, but this shift also alters the way we think about samples of trees. Here we revisit stratigraphic congruence as a comparator between Bayesian and parsimony samples, but in a new visual context: treespace. Such spaces represent an ordination of unique topologies that can also be extended to create a ‘landscape’ where altitude represents some comparative measure (here congruence with stratigraphy). By co-opting existing visualization tools and applying them to a meta-analysis of 128 cladistic data sets we show that there is no consistent favouring of either Bayesian or parsimony according to stratigraphic congruence metrics, and further that empirical treespace visualizations suggest a complex variety of topological landscapes. We conclude by arguing that treespaces should become a standard exploratory tool in phylogenetic analysis.     

Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently.     

Clann: investigating phylogenetic information through supertree analyses

SUMMARY: Clann has been developed in order to provide methods of investigating phylogenetic information through the application of supertrees. AVAILABILITY: Clann has been precompiled for Linux, Apple Macintosh and Windows operating systems and is available from http://bioinf.may.ie/software/clann. Source code is available on request from the authors. SUPPLEMENTARY INFORMATION: Clann has been written in the C programming language. Source code is available on request.     

The performance of morphological characters in broad-scale phylogenetic analyses

In view of their propositional content (i.e. they can be right or wrong), character statements (i.e. statements that predicate characters of organisms) are treated as low-level hypotheses. The thesis of the present study is that such character statements, as do more complex scientific theories, come with variable scope. The scope of a hypothesis, or theory, is the domain of discourse over which the hypothesis, or theory, ranges. A character statement is initially introduced within the context of a certain domain of discourse that is defined by the scale of the initial phylogenetic analysis. The doctrine of 'total evidence' requires the inclusion of previously introduced characters in subsequent studies. As a consequence, the initial scope of character statements is widened to the extent that the scale of subsequent analyses is broadened. Scope expansion for character statements may result in incomplete characters, in the subdivision of characters, or in ambiguity of reference (indeterminacy of the extension of anatomical terms). Character statements with a wide scope are desirable because they refer to characters with the potential to resolve deep nodes in phylogenetic analyses. Care must be taken to preserve referential unambiguity of anatomical terms if the originally restricted scope of a character statement is expanded to match a broad-scale phylogenetic analysis.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 297–308.     

Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae

Phylogenetic schemes based on changing DNA sequence have made a major impact on our understanding of evolutionary relationships and significantly built on knowledge gained by morphological and anatomical studies. Here we present another approach to phylogeny, using fluorescent in situ hybridisation. The phylogenetic scheme presented is likely to be robust since it is derived from the chromosomal distribution of ten repetitive sequences with different functions and evolutionary constraints [GRS, HRS60, NTRS, the Arabidopsis-type telomere repeat (TTTAGGG)_n, 18S-5.8S-26S ribosomal DNA (rDNA), 5S rDNA, and four classes of geminiviral-related DNA (GRD)]. The basic karyotypes of all the plant species investigated Nicotiana tomentosiformis, N. kawakamii, N. tomentosa, N. otophora, N. setchellii, N. glutinosa (all section Tomentosae), and N. tabacum (tobacco, section Genuinae) are similar (x=12) but the distribution of genic and non-genic repeats is quite variable, making the karyotypes distinct. We found sequence dispersal, and locus gain, amplification and loss, all within the regular framework of the basic genomic structure. We predict that the GRD classes of sequence integrated into an ancestral genome only once in the evolution of section Tomentosae and thereafter spread by vertical transmission and speciation into four species. Since GRD is similar to a transgenic construct that was inserted into the N. tabacum genome, its fate over evolutionary time is interesting in the context of the debate on genetically modified organisms and the escape of genes into the wild. Nicotiana tabacum is thought to be an allotetraploid between presumed progenitors of N. sylvestris (maternal, S-genome donor) and a member of section Tomentosae (T-genome donor). Of section Tomentosae, N. tomentosiformis has the most similar genome to the T genome of tobacco and is therefore the most likely paternal genome donor. It is known for N. tabacum that gene conversion has converted most 18S-5.8S-26S rDNA units of N. sylvestris origin into units of an N. tomentosiformis type. Clearly if such a phenomenon were widespread across the genome, genomic in situ hybridisation (GISH) to distinguish the S and T genomes would probably not work since conversion would tend to homogenise the genomes. The fact that GISH does work suggests a limited role for gene conversion in the evolution of N. tabacum. Received: 8 November 1999; in revised form: 23 February 2000 / Accepted: 1 March 2000