Evolutionary relationships among the Scarabaeini (Coleoptera: Scarabaeidae) based on combined molecular and morphological data

The Scarabaeini is an old world tribe of ball-rolling dung beetles that have origins dating back to at least the mid-upper Miocene (19-8 million years ago). The tribe has received little to no attention in morphological or molecular phylogenetics. We obtained sequence data from the mitochondrial cytochrome oxidase subunit I (1,197 bp) and 16S ribosomal RNA (461 bp) genes for 25 species of the Scarabaeini in an attempt to further resolve broad phylogenetic relationships within this tribe. Sequence data from both markers along with 216 morphological and 3 biological characters were analysed separately and combined. Independent analyses showed poorly resolved trees with many of the intermediate and basal nodes collapsed by low bootstrap values. Many sites in both genes exhibited strong A+T nucleotide bias and high interlineage divergences. The combined analysis revealed a number of well supported relationships such as the monophyly of the nocturnal species Scarabaeus satyrus, S. [Neateuchus] proboscideus, and S. zambesianus. Furthermore, the total evidence tree suggested to elevate S. (Pachysoma) to the status of an independent genus, Pachysoma, as a sister taxon to a clade containing Pachylomerus femoralis and Scarabaeus sensu lato. Within the latter, the following subgenera were maintained by the combination of data sets: S. (Scarabaeolus), S. (Sceliages), and S. (Kheper). Both, feeding specialisation and food relocation behaviour, were inferred to be polyphyletic in the Scarabaeini. Total evidence analysis found no support for common ancestry of Scarabaeini and Eucraniini.     

Evolutionary relationships of Metazoa within the eukaryotes based on molecular data from Porifera

Recent molecular data provide strong support for the view that all metazoan phyla, including Porifera, are of monophyletic origin. The relationship of Metazoa, including the Porifera, to Plantae, Fungi and unicellular eukaryotes has only rarely been studied by using cDNAs coding for proteins. Sequence data from rDNA suggested a relationship of Porifera to unicellular eukaryotes (choanoflagellates). However, ultrastructural studies of choanocytes did not support these findings. In the present study, we compared amino acid sequences that are found in a variety of metazoans (including sponges) with those of Plantae, Fungi and unicellular eukaryotes, to obtain an answer to this question. We used the four sequences from 70 kDa heat-shock proteins, the serine-threonine kinase domain found in protein kinases, beta-tubulin and calmodulin. The latter two sequences were deduced from cDNAs, isolated from the sponge Geodia cydonium for the phylogenetic analyses presented. These revealed that the sponge molecules were grouped into the same branch as the Metazoa, which is statistically (significantly) separated from those branches that comprise the sequences from Fungi, Plantae and unicellular eukaryotes. From our molecular data it seems evident that the unicellular eukaryotes existed at an earlier stage of evolution, and the Plantae and especially the Fungi and the Metazoa only appeared later.     

Evaluating residence patterns among prehistoric populations: clues from dental enamel composition

We determined enamel composition (Ca, P, Mg, Cu, Mn, Se, Zn, Al, Sr, Pb) for the mandibular canines of 94 individuals from 4 prehistoric Arikara cemetery populations, collecting the compositional data using scanning electron microscopy energy dispersive x-ray analysis. We examined each of the four samples independently and then pooled them for a group comparison using correspondence analysis. The results indicate significant intrapopulational dispersal, particularly when viewed by age and sex subgroups. When all sites are included for correspondence analysis, a distinctive pattern of adult male dispersal compared to the more tightly clustered adult female and subadult subsample is apparent. We hypothesize that the observed pattern of dispersal indicates local geographic and possible dietary differences among the groups. Furthermore, we hypothesize that the observed differences between males, and females and subadults for each site are the result of a residence pattern of out-migration for males.     

Evolutionary and biogeographical patterns within Iberian populations of the genus Squalius inferred from molecular data

Origins and biogeography of the chub, genus Squalius (formerly within the genus Leuciscus), in the Iberian Peninsula were inferred from comparison between patterns of geographic distribution and phylogenetic relationships among populations belonging to 14 European Squalius species. The phylogeny recovered was based on the complete sequence of the mitochondrial cytochrome b gene. Squalius species were grouped into three major clades. The basal clade included species distributed across the ancient Paratethys Sea. The second clade included species from Central and East Europe and the northern areas of the Mediterranean basin towards Minor Asia. The third clade included species from the Mediterranean Peninsulas (Iberian, Italy, and Balkans). The Iberian Squalius species do not constitutes a monophyletic group. Our data indicate that the Iberian Peninsula was colonized at least twice by two different monophyletic lineages, a meridional group and a Central Europe group. The amount of species diversity found in the Iberian Peninsula and the phylogenetic relationships among these species, together with their geographic distribution, suggest that the Central Europe lineage colonized the Iberian Peninsula at a latter time. Our data indicate that the northeastern Iberian lineage is phylogenetically close to Greek populations of Squalius cephalus, while the second lineage formed a monophyletic group including Squalius pyrenaicus, Squalius carolitertii, Squalius aradensis, and Squalius torgalensis. The speciation process that generated these species and the geographic structure of their populations, principally in S. pyrenaicus, can be attributed to paleogeographical events like the ancient endorrheism and the development of hydrographic basins.     

Estimation of relatedness among non-pedigreed Yakutian cryo-bank bulls using molecular data: implications for conservation and breed management

Background

Yakutian cattle, the last remaining native cattle breed in Siberia, are well adapted to the extreme sub-arctic conditions. Nowadays only ca. 1200 purebred animals are left in Yakutia. The semen of six Yakutian bulls was stored in a cryo-bank without any pedigree documentation because of the traditional free herding style of the population.

Methods

To clarify the genetic relatedness between these bulls and to provide recommendations to use their semen in future conservation and breed management programs, we have analysed 30 autosomal microsatellites and mitochondrial DNA sequences in 60 individuals including the six for which semen has been stored. Four relatedness estimators were calculated. In addition, we assessed the value of the cryo-bank bulls for the preservation of genetic variation of the contemporary Yakutian cattle by calculating allelic and gene diversity estimates and mean molecular coancestries.

Results

On the basis of microsatellite variability, including the Yakutian cryo-bank bulls increases the allelic variation in the contemporary population by 3% and in the male subpopulation by 13%. In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population. Although 30 loci are insufficient to resolve definitely their relatedness categories, the data suggest four pairs of cryo-bank bulls as possible half-sibs.

Conclusions

Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck. We propose a breeding scheme based on the rotation of breeding females and the division of cryo-bank bulls into three groups. Thus, if molecular data (e.g. autosomal microsatellite genotypes) for the contemporary population are available and based on relatively small-scale laboratory analyses, it is possible to avoid serious mistakes in their use for breeding applications. The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.     

Evolutionary relationships among eight species of South American phyllotine rodents (Rodentia: Muridae) based on allozymic data

Rodents of the tribe Phyllotini represents one of the main radiations of South American Sigmodontini. Phylogenetic relationships among species of this highly diversified group are poorly known. In this paper we analyse evolutionary relationships among eight phyllotine species belonging to the genera Calomys , Graomys , Phyllotis and Eligmodontia , on the basis of allozymic polymorphisms. Most of the differences among species were in allele frequencies and not of allele class. Neighbour-joining and maximum likelihood methods place P. xanthopygus in the same group as E. typus and G. griseoflavus , in agreement with results obtained by several authors on the basis of morphological characters. Parsimony analysis of 0–9 coded data suggest that the genus Calomys is paraphyletic, but with a low bootstrap support. In the tree based on genetic distance data, the genus also appears as paraphyletic. The maximum likelihood method yields a tree where Calomys is monophyletic, but this phylogeny is supported by only two out of 78 alleles analysed. Calomys hummelincki and C. venustus occupy a basal position among Calomys species. Calomys musculinus and C. lepidus are the most closely related species of the genus, with C. laucha as sister to them. These relationships are strongly supported by bootstrap percentages.     

Evolutionary and morphometric implications of morphological variation among flowers within an inflorescence: a case-study using European orchids

BACKGROUND AND AIMS: This study explores the previously largely ignored morphological variation that occurs among flowers within a single inflorescence. METHODS: Variation in four metric parameters (labellum length and width, spur length and width) that together strongly influence pollination frequency is documented within the simple racemose inflorescences of eight individuals that represent a primary hybrid and six species of European orchids. KEY RESULTS: Regression of each parameter against the location of each flower on the inflorescence, and calculation of correlation coefficients for each pair of parameters within each inflorescence, demonstrate significant decoupling of labellum and spur development, despite the fact that they are different portions of the same floral organ. Spur length and diameter are constant across inflorescences of Dactylorhiza other than the vestigial-spurred D. viridis, whereas in other genera spur length declines in parallel with labellum dimensions. These differences are likely to reflect selection pressures or developmental constraints. Strong negative deviations from the regression line for one or more parameters are evident in occasional flowers, occurring most frequently in the lowermost and uppermost one or two flowers, and so reflecting transitions in meristematic behaviour. Thus, population-level morphometric studies are best conducted on flowers taken from approximately the mid-point of the inflorescence. Moreover, in the two relatively large inflorescences where lower flowers were removed for measurement before the upper flowers had opened, labellum size increased significantly in the flowers immediately above the excisions, suggesting that excision liberated resources that were diverted into the opening buds. Repeat measurement of all flowers from one selected inflorescence demonstrated typical measurement errors of only +/- 30-80 micro m, irrespective of the size of the structure studied. If flowers are not mounted and measured immediately following excision, modest negative deviations of 30-50 micro m result from post-mounting shrinkage; this occurs less rapidly in the spur than in the thinner labellum, which should therefore be measured first. Variation in all four parameters among all the flowers of a single inflorescence is between 42 % and 107 % of that observed between a similar number of flowers sampled from a consistent location on different (but conspecific and coexisting) inflorescences. CONCLUSIONS: This result demonstrates the strong influence of epigenesis on flower morphology and further emphasizes the importance of (a) sampling from a consistent location within the inflorescences under comparison, (b) interpreting morphometric ordinations hierarchically, building from individuals to infraspecific taxa and species via populations, and (c) considering in any microevolutionary study the potentially profound effects of the cline in flower size within each inflorescence.     

Phylogenetic relationships among Neoechinorhynchus species (Acanthocephala: Neoechinorhynchidae) from North-East Asia based on molecular data

Phylogenetic and statistical analyses of DNA sequences of two genes, cytochrome oxidase subunit 1 (cox 1) of the mitochondrial DNA and 18S subunit of the nuclear ribosomal RNA (18S rRNA), was used to characterize Neoechinorhynchus species from fishes collected in different localities of North-East Asia. It has been found that four species can be clearly recognized using molecular markers—Neoechinorhynchus tumidus, Neoechinorhynchus beringianus, Neoechinorhynchus simansularis and Neoechinorhynchus salmonis. 18S sequences ascribed to Neoechinorhynchus crassus specimens from North-East Asia were identical to those of N. tumidus, but differed substantially from North American N. crassus. We renamed North-East Asian N. crassus specimens to N. sp., although the possibility that they represent a subspecies of N. tumidus cannot be excluded, taking into account a relatively small distance between cox 1 sequences of North-East Asian specimens of N. crassus and N. tumidus. Maximum likelihood, maximum parsimony and Bayesian inference analyses were performed for phylogeny reconstruction. All the phylogenetic trees showed that North-East Asian species of Neoechinorhynchus analyzed in this study represent independent clades, with the only exception of N. tumidus and N. sp. for 18S data. Phylogenetic analysis has shown that the majority of species sampled (N. tumidus + N. sp., N. simansularis and N. beringianus) are probably very closely related, while N. salmonis occupies separate position in the trees, possibly indicating a North American origin of this species.     

General response patterns of fish populations to stress: an evaluation using an individual-based simulation model

General response patterns of fish populations tostress, originally proposed by Colby for fisheriesrehabilitation and later adapted by Munkittrick forcontaminants, were evaluated using an individual-basedsimulation model. General response patterns relatechanges in population-level variables to the type ofstress. The model follows the daily growth,mortality, and spawning of individual yellow perch andwalleye through their lifetime, and was corroboratedusing Oneida Lake data. Two versions of the model wereused: population (yellow perch only) and community(dynamic predation on yellow perch by walleye). Eightstresses were imposed on the population and communityversions of the model and 100-year simulations wereperformed. Response patterns were defined by changesin predicted yellow perch mean population abundance,mean age of adults, and mean adult growth (representedby mean length at age-7). Proposed response patternswere similar to those predicted using the populationversion of the model. Simulations using the communityversion of the model distorted the response patterns,either causing amplification, dampening, or reversalof many of the patterns. Predicted response patternsbecame unique when additional variables were included.Our model results suggest that caution is appropriatein interpreting general response patterns based onmean age, or when the population of interest plays amajor role in a relatively simple food web. The responsepattern approach may be better at identifying the lifestage impacted rather than the mechanism of the stress.     

Phylogeography of the Calonectris shearwaters using molecular and morphometric data

We investigated phylogenetic relationships and the biogeographic history of the Calonectris species complex, using both molecular and biometric data from one population of the Cape Verde shearwater Calonectris edwardsii (Cape Verde Islands), one from the streaked shearwater C. leucomelas (western Pacific Ocean) and 26 from Cory's shearwater populations distributed across the Atlantic (C. d. borealis) and the Mediterranean (C. d. diomedea). The streaked shearwater appeared as the most basal and distant clades, whereas the genetic divergences among the three main clades within the Palearctic were similar. Clock calibrations match the first speciation event within Calonectris to the Panama Isthmus formation, suggesting a vicariant scenario for the divergence of the Pacific and the Palearctic clades. The separation between the Atlantic and Mediterranean clades would have occurred in allopatry by range contraction followed by local adaptation during the major biogeographic events of the Pleistocene. The endemic form from Cape Verde probably evolved as a result of ecological divergence from the Mediterranean subspecies. Finally, one Mediterranean population (Almeria) was unexpectedly grouped into the Atlantic subspecies clade, both by genetic and by morphometric analyses, pointing out the Almeria-Oran oceanographic front (AOOF) as the actual divide between the two Cory's shearwater subspecies. Our results highlight the importance of oceanographic boundaries as potentially effective barriers shaping population and species phylogeographical structure in pelagic seabirds.     

Systematics of Alloteuthis (Cephalopoda:Loliginidae) based on molecular and morphometric data

Alloteuthis is a group of small, slender loliginid squids of minor fisheries importance. There are three nominal Alloteuthis species—A. media (Linnaeus), A. subulata (Lamarck) and A. africana Adam. Two of these species (A. media and A. subulata) have largely overlapping ranges in the Mediterranean and northeastern Atlantic, while A. africana is found along the west coast of Africa. Despite the low level of species diversity, Alloteuthis taxonomy and systematics are confused, and assignment of specimens to species can be difficult. To clarify Alloteuthis systematics, we gathered morphometric data and DNA sequence data from two mitochondrial loci and a nuclear locus from Alloteuthis specimens collected from several localities. Analyses of the morphometric data suggest that head width is the main variable allowing separation of A. africana from the other two species, and central club sucker size separates A. media from A. subulata. One easily diagnosable character often used to distinguish Alloteuthis species—relative fin length—appears to be of little taxonomic value. Only three specimens assignable to A. subulata both morphologically and genetically were found, all from the Adriatic; possible reasons for this apparent rarity are discussed. Gene tree parsimony and coalescent-based methods were used to estimate species relationships from the molecular data, and both supported a sister-species relationship between A. media and A. subulata. Analyses of molecular variation (AMOVA's) revealed significant genetic differentiation between Atlantic and Mediterranean A. media. This study highlights the importance of 1) sampling multiple individuals, locations and loci for species-level phylogenetic studies, 2) using morphometric analyses to reveal taxonomically meaningful morphological characters and 3) accounting for the stochastic nature of the coalescent process when estimating species phylogenies for closely related taxa.     

Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1alpha, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.     

Evolutionary relationships among rice species with AA genome based on SINE insertion analysis

Previous studies based on morphological and molecular markers indicated that there are two cultivated and five wild rice species within the Oryza genus with the AA genome. In the cultivated rice species, Oryza sativa, a retroposon named p-SINE1 has been identified. Some of the p-SINE1 members characterized previously showed interspecific insertion polymorphisms in the species with the AA genome. In this study, we identified new p-SINE1 members showing interspecific insertion polymorphisms from representative strains of four wild rice species with the AA genome: O. barthii, O. glumaepatula, O. longistaminata, and O. meridionalis. Some of these members were present only in strains of one species, whereas the others were present in strains of two or more species. The p-SINE1 insertion patterns in the strains of the Asian and African cultivated rice species O. sativa and O. glaberrima were very similar to those of the Asian and African wild rice species O. rufipogon and O. barthii, respectively. This is consistent with the previous hypothesis that O. sativa and O. glaberrima are derived from specific wild rice species. Phylogenetic analysis based on the p-SINE1 insertion patterns showed that the strains of each of the five wild rice species formed a cluster. The strains of O. longistaminata appear to be distantly related to those of O. meridionalis. The strains of these two species appear to be distantly related to those of three other species, O. rufipogon, O. barthii and O. glumaepatula. The latter three species are closely related to one another with O. barthii and O. glumaepatula being most closely related. A phylogenetic tree including a hypothetical ancestor with all loci empty for p-SINE1 insertion showed that the strains of O. longistaminata are related most closely to the hypothetical ancestor. This indicates that O. longistaminata and O. meridionalis diverged early on, whereas the other species diverged relatively recently, and suggests that the Oryza genus with AA genome might have originated in Africa, rather than in Asia.     

Genetic relationships among Pseudomonas stutzeri strains based on molecular typing methods

Detailed characterization of the genetic variability among strains belonging to Pseudomonas stutzeri was achieved using different rapid molecular typing methods based on polymerase chain reaction (PCR), Southern blot and Western blot. Consensus motifs complementary to fragments of repetitive elements dispersed throughout the genomes of bacteria were used as primers & allowed differentiation at subspecies levels. Further & simple differentiation was also achieved based on the direct amplification of spacer regions between 16S & 23S rRNA, combined with single-strand conformation polymorphism (SSCP) analysis of the generated fragments. These methods are fast, sensitive, reliable for determining relationships & have demonstrated a great genetic diversity among the strains of Ps. stutzeri studied in agreement with the heterogeneous phenotypic traits of the species.     

Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data

Trees inferred from DNA sequence data provide only limited insight into the phylogeny of seed plants because the living lineages (cycads, Ginkgo, conifers, gnetophytes, and angiosperms) represent fewer than half of the major lineages that have been detected in the fossil record. Nevertheless, phylogenetic trees of living seed plants inferred from sequence data can provide a test of relationships inferred in analyses that include fossils. So far, however, significant uncertainty persists because nucleotide data support several conflicting hypotheses. It is likely that improved sampling of gymnosperm diversity in nucleotide data sets will help alleviate some of the analytical issues encountered in the estimation of seed plant phylogeny, providing a more definitive test of morphological trees. Still, rigorous morphological analyses will be required to answer certain fundamental questions, such as the identity of the angiosperm sister group and the rooting of crown seed plants. Moreover, it will be important to identify approaches for incorporating insights from data that may be accurate but less likely than sequence data to generate results supported by high bootstrap values. How best to weigh evidence and distinguish among hypotheses when some types of data give high support values and others do not remains an important problem.     

Evolutionary relationships of cartilaginous fishes: an immunological study

An investigation of the phylogenetic relationships of a number of cartilaginous fish based on the use of the immunological properties of the iron-binding serum protein, transferrin. is presented. Data on immunological distance and the rate of amino acid substitution are used to produce a dendrogram. The tree confirms the close relationships of the holocephalan species examined which are a sister group of other neoselachians. The tree also indicates that the squaloids and galeoids are separate groups and that Heterodontus belongs with the galeoids. It is also clear that the divergence between the squaloids, galeoids (including Heterodontus ) and the Holocephali is an ancient one and that the rajids probably diverged from this basal stock rather than any more recent squaloid/squatinoid/galeoid grouping.     

Phylogenetic relationships of Iberian Aphodiini (Coleoptera: Scarabaeidae) based on morphological and molecular data

A phylogeny of Iberian Aphodiini dung beetles was reconstructed based on morphological and molecular data. The data set included a total of 84 variable characters from wing venation, mouthparts, genitalia, and external morphology, as well as mitochondrial partial cytochrome c oxidase I (COI), complete tRNA-Leu (UUR), and partial cytochrome c oxidase II (COII) gene nucleotide sequences (1210 positions). Phylogenetic trees based on molecular data were relatively more resolved than those based on morphological characters. The Bayesian analysis of combined molecular and morphological data provided resolution not achieved by each data set separately. Ammoecius and Aphodius are the first lineages that branch off from the tree, followed by Acrossus, Nimbus, and Heptaulacus. The remaining studied taxa are recovered in a more derived clade that lacks internal resolution. Reconstructed trees based on molecular data showed relatively short internal nodes that were weakly supported. Such pattern may reflect a rapid radiation at the origin of the tribe Aphodiini, but also saturation of mutational changes. Several tests were conducted to discern between both competing hypotheses, as well as to assess the effect of incomplete taxon sampling.