The evolution of cooperative and pair breeding in thornbills Acanthiza (Pardalotidae)

Most birds breed in pairs but at least 3% of passerine species are cooperative breeders, whereby more than two adults help to raise the young. The general rarity of cooperative breeding has led to the assumption that cooperative behaviour has evolved from the ancestral trait of pair breeding. However, it has been suggested that pair breeding may be the derived state in some taxa. The primary aim of this research was to test this suggestion using the genus Acanthiza , which contains examples of both cooperatively and pair breeding species. Mitochondrial DNA sequences were used to construct a phylogenetic hypothesis for the tribe containing Acanthiza , the Acanthizini. The breeding behaviour of the species sequenced was determined from records in the literature; where there were no such data the frequency of another social behaviour, flocking, was used as an indicator of breeding behaviour. The mapping of breeding systems onto the phylogeny led to the conclusion that cooperative breeding is the ancestral state in the Acanthizini, with pair breeding evolving twice in the genus Acanthiza . Models explaining the occurrence of cooperative breeding in terms of broad environmental factors or life history do not appear to be applicable to the genus Acanthiza . The pair breeding Acanthiza species cluster into two clades, suggesting some influence of phylogenetic history on the occurrence of the different breeding systems. Combining the results of this study with other data suggests the tendency to breed cooperatively could be ancestral in the superfamily Meliphagoidea.     

REMARKABLE EXAMPLES OF SPECIATION IN ASIATIC PLANTS

The nature, extent, and tempo of speciation differ from one plant group to another, and some noteworthy examples studied in Asiatic flowering plants are considered. In the Rubia cordifolia group, Himalayan plants have epigeous cotyledons, while all Japanese plants have hypogeous cotyledons; in both groups polyploidy seems to have occurred parallelly. The pollen pattern varies in some groups correlated with polyploidy, and an example is observed within a species (Anemone hepatica) or a genus (Isopyrum, etc.). Representative examples in which polyploidy plays an important role in speciation are explained in such genera as Aucuba, Helwingia, Duchesnea, Agrimonia and Suaeda. Dysoploidy and amphiploidy are also important, and establishment of new basic numbers is occasionally found in closely allied species as exemplified in Lysimachia and Chrysosplenium, or even in one species, Chionographis japonica. As a striking example of an exceedingly polymorphous species which is considered to be undergoing speciation, the variations in Paris polyphylla are reviewed. On the contrary, Phryma leptostachya is not highly differentiated, although it occurs in two widely separated regions, and must be of very old origin.     

Discordance of species trees with their most likely gene trees: the case of five taxa

Under a coalescent model for within-species evolution, gene trees may differ from species trees to such an extent that the gene tree topology most likely to evolve along the branches of a species tree can disagree with the species tree topology. Gene tree topologies that are more likely to be produced than the topology that matches that of the species tree are termed anomalous, and the region of branch-length space that gives rise to anomalous gene trees (AGTs) is the anomaly zone. We examine the occurrence of anomalous gene trees for the case of five taxa, the smallest number of taxa for which every species tree topology has a nonempty anomaly zone. Considering all sets of branch lengths that give rise to anomalous gene trees, the largest value possible for the smallest branch length in the species tree is greater in the five-taxon case (0.1934 coalescent time units) than in the previously studied case of four taxa (0.1568). The five-taxon case demonstrates the existence of three phenomena that do not occur in the four-taxon case. First, anomalous gene trees can have the same unlabeled topology as the species tree. Second, the anomaly zone does not necessarily enclose a ball centered at the origin in branch-length space, in which all branches are short. Third, as a branch length increases, it is possible for the number of AGTs to increase rather than decrease or remain constant. These results, which help to describe how the properties of anomalous gene trees increase in complexity as the number of taxa increases, will be useful in formulating strategies for evading the problem of anomalous gene trees during species tree inference from multilocus data.     

Patterns of replication in the neo-sex chromosomes ofDrosophila nasuta albomicans

Drosophila nasuta albomicans (with 2n = 6), contains a pair of metacentric neo-sex chromosomes. Phylogenetically these are products of centric fusion between ancestral sex (X, Y) chromosomes and an autosome (chromosome 3). The polytene chromosome complement of males with a neo-X- and neo-Y-chromosomes has revealed asynchrony in replication between the two arms of the neo-sex chromosomes. The arm which represents the ancestral X-chromosome is faster replicating than the arm which represents ancestral autosome. The latter arm of the neo-sex chromosome is synchronous with other autosomes of the complement. We conclude that one arm of the neo-X/Y is still mimicking the features of an autosome while the other arm has the features of a classical X/Y-chromosome. This X-autosome translocation differs from the other evolutionary X-autosome translocations known in certain species ofDrosophila.     

TWO SNOW SPECIES OF THE QUADRIFLAGELLATE GREEN ALGA CHLAINOMONAS (CHLOROPHYTA,VOLVOCALES): ULTRASTRUCTURE AND PHYLOGENETIC POSITION WITHIN THE CHLOROMONAS CLADE1

The quadriflagellate snow alga Chlainomonas Christen, distributed in New Zealand and North America, has several unusual structural attributes. A process assumed to be cytokinesis involves extrusion of protoplasm from the parent through a narrow canal, C. kolii (J. T. Hardy et Curl) Hoham produces a net‐like outer envelope rather than a cell wall, and the flagellar basal apparatus of Chlainomonas consists of two semi‐independent pairs of basal bodies. Structural connections between basal body pairs appear minimal, but a connecting system different from that observed in other genera exists within each pair. Phylogenetic analysis using rbcL sequences places Chlainomonas in the Chloromonas clade, other known members of which are all biflagellate. Chlainomonas is split into two robust lineages, with New Zealand collections sharing an origin with northern North American collections. Although the quadriflagellate condition is regarded as ancestral in the Chlorophyceae, we speculate—based on ultrastructural and molecular data presented here—that Chlainomonas represents a derived form that has arisen from fusion of two ancestral biflagellate cells. Other explanations (for example, that Chlainomonas represents a diploid form of a biflagellate species) are remotely possible but are presently at odds with extensive observations of field material. Improvements in techniques for experimental manipulation of these sensitive cryophiles will be required to fully characterize their structure and progress our understanding of their biology.     

Molecular and morphological phylogeny of hooded shrimps, genera Betaeus and Betaeopsis (Decapoda, Alpheidae): testing the center of origin biogeographic model and evolution of life history traits

The phylogenetic relationships of the alpheid shrimp genera Betaeus (Dana, 1852) (15 species) and Betaeopsis (Yaldwyn, 1971) (three species), collectively known as hooded shrimps, are analyzed with morphological, molecular (16S and H3) and combined "total evidence" (morphology+DNA) datasets. The tree topology resulting from morphological and combined analyses places Betaeus jucundus as sister to all the remaining species of Betaeus and Betaeopsis, rendering Betaeus paraphyletic. On the other hand, Betaeopsis is recovered as monophyletic. Betaeus australis is positioned as sister to the remaining species of Betaeus s. str. (excluding B. jucundus), which is composed of three well-supported and resolved clades. Mapping of biogeographic traits on the combined tree suggests at least two possible historic scenarios. In the first scenario, the North-East Pacific harboring the highest diversity of hooded shrimps (seven species of Betaeus), acted as the "center of origin", where species appeared, matured and eventually migrated toward peripheral regions. In the second scenario, Betaeus+Betaeopsis originated in the southern Indo-West Pacific and subsequently colonized the North-East Pacific, where a major radiation involving dispersal/vicariance events took place. The mapping of life history traits (symbiosis vs. free living and gregariousness vs. single/pair living) in the combined tree suggests (1) that different types of symbioses with dissimilar host organisms (sea urchins, abalones, other decapods, spoon worms) evolved independently more than once in the group (in B. jucundus and in various lineages of Betaeus s. str.), and (2) that gregariousness was ancestral in the Betaeus s. str. -Betaeopsis clade and later shifted toward single/pair living in several lineages.     

A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well‐documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae– the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation‐by‐distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.     

A phylogenetic analysis of the adipokinetic neuropeptides of Ensifera

Abstract.  Adipokinetic neuropeptides, from the corpora cardiaca of various species of the suborder Ensifera, encompassing members of all superfamilies (except the Gryllacridoidea), were isolated by liquid chromatography, and identified structurally by comparison of retention times and mass spectrometry data with respect to information from known members of this peptide family. Ensiferan species always contain only one adipokinetic hormone (AKH) peptide, as assessed for a few species by monitoring typical AKH mass peaks from a crude corpora cardiaca extract. This AKH is an octapeptide, and is either Scg-AKH-II (pGlu-Leu-Asn-Phe-Ser-Thr-Gly-Trp amide) which occurs in all Tettigoniidea (except Schizodactyloidea) and in Gryllotalpoidea, or Grb-AKH (pGlu-Val-Asn-Phe-Ser-Thr-Gly-Trp amide) which occurs in Grylloidea (except Gryllotalpoidea) and Schizodactyloidea. Using the structural information of these neuropeptides in conjunction with morpho-anatomical characters, these data are interpreted in a phylogenetic framework. The lack of a decapeptide and the presence of the octapeptide Scg-AKH-II are ancestral in Ensifera. The ancestral Scg-AKH-II twice underwent an independent and convergent modification to Grb-AKH.     

Pollen embryogenesis: atavism or totipotency?

Summary The origins of pollen embryogenesis are still in doubt. Totipotency of plant cells has traditionally been put forward as an explanation for this phenomenon but we have found this interpretation to involve some shortcomings. The pollen grain is a highly differentiated structure which should have a very reduced capability of regenerating a whole plant, whereas in some species the induction of androgenesis appears to occur with greater facility than somatic embryogenesis. Furthermore, some microspores seem to have a tendency to morphogenesis and organogenesis; spontaneous androgenesis occurs naturally in various species and many examples also occur of pollen dimorphism. Totipotency would seem to be insufficient to explain androgenesis and we propose that its origin might be found in the phenomenon of atavism. According to studies published on ancestral precursors of pollen, these structures appear to have had high proliferation capacity. The ability to form a multicellular structure from a single haploid cell is shared by the meiocytes of ancestral algae, of the first land plants, and of present-day ferns, which are evolutionarily related to pollen. Atavism is only expressed under certain circumstances, as indeed is androgenesis, normally as a consequence of an environmental stress. Our conclusion is that there is evidence enough to suggest that androgenesis may well be the expression of archaic genes of meiocytes with morphogenic capacity which were naturally expressed in the ancestors of flowering plants.     

L-alanine production from glucose fermentation by hyperthermophilic members of the domains bacteria and Archaea: a remnant of an ancestral metabolism?

New members of the order Thermotogales were isolated from nonvolcanically heated geothermal environments, including oil fields and waters of the Great Artesian Basin of Australia, thereby extending their known habitats, previously recognized primarily as volcanic. The hyperthermophilic and thermophilic members of Thermotogales of volcanic origin, together with the recently described nonvolcanic species of this order and three new isolates described in this paper, were all found to produce L-alanine from glucose fermentation, in addition to acetate, lactate, CO2 and H2. L-alanine production from glucose is a trait in common with Pyrococcus furiosus and Thermococcus profundus. We propose that L-alanine production from sugar fermentation be regarded as an ancestral metabolic characteristic.     

Bioinformatics Analysis of Bacterial Annexins – Putative Ancestral Relatives of Eukaryotic Annexins

Annexins are Ca²⁺-binding, membrane-interacting proteins, widespread among eukaryotes, consisting usually of four structurally similar repeated domains. It is accepted that vertebrate annexins derive from a double genome duplication event. It has been postulated that a single domain annexin, if found, might represent a molecule related to the hypothetical ancestral annexin. The recent discovery of a single-domain annexin in a bacterium, Cytophaga hutchinsonii, apparently confirmed this hypothesis. Here, we present a more complex picture. Using remote sequence similarity detection tools, a survey of bacterial genomes was performed in search of annexin-like proteins. In total, we identified about thirty annexin homologues, including single-domain and multi-domain annexins, in seventeen bacterial species. The thorough search yielded, besides the known annexin homologue from C. hutchinsonii, homologues from the Bacteroidetes/Chlorobi phylum, from Gemmatimonadetes, from beta- and delta-Proteobacteria, and from Actinobacteria. The sequences of bacterial annexins exhibited remote but statistically significant similarity to sequence profiles built of the eukaryotic ones. Some bacterial annexins are equipped with additional, different domains, for example those characteristic for toxins. The variation in bacterial annexin sequences, much wider than that observed in eukaryotes, and different domain architectures suggest that annexins found in bacteria may actually descend from an ancestral bacterial annexin, from which eukaryotic annexins also originate. The hypothesis of an ancient origin of bacterial annexins has to be reconciled with the fact that remarkably few bacterial strains possess annexin genes compared to the thousands of known bacterial genomes and with the patchy, anomalous phylogenetic distribution of bacterial annexins. Thus, a massive annexin gene loss in several bacterial lineages or very divergent evolution would appear a likely explanation. Alternative evolutionary scenarios, involving horizontal gene transfer between bacteria and protozoan eukaryotes, in either direction, appear much less likely. Altogether, current evidence does not allow unequivocal judgement as to the origin of bacterial annexins.     

Genetic differentiation,polyploidization and hybridization in northern EuropeanDactylorhiza (Orchidaceae): Evidence from allozyme markers

Taxa endemic to North-western Europe are rare, but the orchid genusDactylorhiza contains several species restricted to this area. Evidence from morphological and cytological studies have indicated that some species may have arisen recently and may be of hybrid origin. In the present report, I use allozymes to characterize the genomes in various species ofDactylorhiza and evaluate the possibilities for rapid evolutionary change in the genus. Allotetraploid species have evolved repeatedly from two principal diploid ancestral lineages. These lineages include extant diploid and autotetraploid species, from which allotetraploid derivatives may still arise. It is suggested that allotetraploidization dominates over introgression as speciation mechanism in the genus. The more common and widespread allotetraploid species could be characterized by their allozyme characters over considerable distances, indicating that each of them may have a unique origin and that they have spread from their ancestral populations to the present distribution areas. However, it is also possible that some allotetraploid species contain local populations that have been independently derived from the ancestral lineages.     

Evolution of ant-cultivar specialization and cultivar switching in Apterostigma fungus-growing ants

Almost all of the more than 200 species of fungus-growing ants (Formicidae: Attini) cultivate litter-decomposing fungi in the family Lepiotaceae (Basidiomycota: Agaricales). The single exception to this rule is a subgroup of ant species within the lower attine genus Apterostigma, which cultivate pterulaceous fungi distantly related to the Lepiotaceae. Comparison of cultivar and ant phylogenies suggests that a switch from lepiotaceous to pterulaceous fungiculture occurred only once in the history of the fungus-growing ants. This unique switch occurred after the origin of the genus Apterostigma, such that the basal Apterostigma lineages retained the ancestral attine condition of lepiotaceous fungiculture, and none of the Apterostigma lineages in the monophyletic group of pterulaceous fungiculturists are known to have reverted back to lepiotaceous fungiculture. The origin of pterulaceous fungiculture in attine ants may have involved a unique transition from the ancestral cultivation of litter-decomposing lepiotaceous fungi to the cultivation of wood-decomposing pterulaceous fungi. Phylogenetic analyses further indicate that distantly related Apterostigma ant species sometimes cultivate the same cultivar lineage, indicating evolutionarily frequent, and possibly ongoing, exchanges of fungal cultivars between Apterostigma ant species. The pterulaceous cultivars form two sister clades, and different Apterostigma ant lineages are invariably associated with, and thus specialized on, only one of the two cultivar clades. However, within clades Apterostigma ant species are able to switch between fungi. This pattern of broad specialization by attine ants on defined cultivar clades, coupled with flexible switching between fungi within cultivar clades, is also found in other attine lineages and appears to be a general phenomenon of fungicultural evolution in all fungus-growing ants.     

Some Effects of Potassium Deficiency on Seedling Development

Seedlings with leaf-like photosynthetic cotyledons such as Cucumissativus, Sinapis alba and Trifolium pratense have higher growthrates and a greater requirement for an external supply of potassiumthan hypogeal species (Pisum sativum, Vicia faba) or epigealspecies with very fleshy cotyledons (Phaseolus vulgaris, Lupinusalbus, Lupinus angustifolius). The initial stages of seedlingdevelopment in the latter two groups involve mainly transferof reserves from cotyledons to axis and a relatively small increasein total seedling dry weight takes place during the first 2to 3 weeks. Potassium may be drawn either from the supply already presentin the cotyledons or from an external source. Species with expandingphotosynthetic cotyledons utilize the reserve potassium duringcotyledon development and it is not transported to the epicotyl.Thus, in these species an external supply of potassium is essentialfor full development of the photosynthetic system and the roots.In species whose cotyledons are not major photosynthetic organsthe reserve potassium is transported from the cotyledons tothe developing axis. In these species culture in a nutrientsolution deficient in potassium or in distilled water increasesroot dry weight but reduces plumule weight (although to a lesserextent than in species with leaf-like cotyledons). In general,the response of seedlings to culture in a nutrient solutiondeficient in potassium was very similar to culture in distilledwater only. Thus, although all the species studied had similar levels ofpotassium in the seed (µg potassium/mg dry weight) itssite of utilization differs. It appears that seedlings withleaf-like cotyledons are more susceptible during early seedlinggrowth to deficiencies in external factors, such as potassium,than are species with fleshy cotyledons.     

Comparative anatomical analysis of the cotyledonary region in three Mediterranean Basin Quercus (Fagaceae)

Anatomical changes at the cotyledonary node from the embryo to the seedling stage in Quercus coccifera, Q. ilex, and Q. humilis were investigated by light and scanning electron microscopy techniques. Mature embryos of Q. humilis possess 2-3 pairs of leaf primordia and a pair of cotyledonary buds, whereas in Q. coccifera and Q. ilex there are two incipient primordia, and cotyledonary buds are not observed until 1 wk after germination. In all three species the cotyledonary buds multiply, forming bud clusters, and a vascular connection is well established within 5-6 wk after germination. As development proceeds, the cotyledonary region becomes woody, but buds, which are exogenous in origin, never become embedded in the periderm. In comparison with Q. suber, another native Mediterranean Basin oak, the cotyledonary node is short and axillary buds are not present below the insertion of cotyledons. In addition, starch accumulation in the cotyledonary region is not observed from histological analysis in the three oaks. Therefore, in Q. coccifera, Q. ilex, and Q. humilis seedlings the cotyledonary node can be considered to be an important regenerative structure enabling them to resprout after the elimination of the shoot above the cotyledons, despite the absence of a lignotuberous structure.     

The origin and evolution of protein superfamilies.

The organization of proteins into superfamilies based primarily on their sequences is introduced: examples are given of the methods used to cluster the related sequences and to elucidate the evolutionary history of the corresponding genes within each superfamily. Within the framework of this organization, the amount of sequence information currently and potentially available in all living forms can be discussed. The 116 superfamilies already sampled reflect possibly 10% of the total number. There are related proteins from many species in all of these superfamilies, suggesting that the origin of a new superfamily is rare indeed. The proteins so far sequenced are so rigorously conserved by the evolutionary process that we would expect to recognize as related descendants of any protein found in the ancestral vertebrate. The evolutionary history of the thyrotropin-gonadotropin beta chain superfamily is discussed in detail as an example. Some proteins are so constrained in structure that related forms can be recognized in prokaryotes and eukaryotes. Evolution in these superfamilies can be traced back close to the origin of life itself. From the evolutionary tree of the c-type cytochromes the identity of the prokaryote types involved in the symbiotic origin of mitochondria and chloroplasts begins to emerge.     

A second uniquely human mutation affecting sialic acid biology

Siglecs are immunoglobulin superfamily member lectins that selectively recognize different types and linkages of sialic acids, which are major components of cell surface and secreted glycoconjugates. We report here a human Siglec-like molecule (Siglec-L1) that lacks a conserved arginine residue known to be essential for optimal sialic acid recognition by previously known Siglecs. Loss of the arginine from an ancestral molecule was caused by a single nucleotide substitution that occurred after the common ancestor of humans with the great apes but before the origin of modern humans. The chimpanzee Siglec-L1 ortholog remains fully functional and preferentially recognizes N-glycolylneuraminic acid, which is a common sialic acid in great apes and other mammals. Reintroducing the ancestral arginine into the human molecule regenerates the same properties. Thus, the single base pair mutation that replaced the arginine on human Siglec-L1 is likely to be evolutionarily related to the previously reported loss of N-glycolylneuraminic acid expression in the human lineage. Siglec-L1 and its chimpanzee Siglec ortholog also have a different expression pattern from previously reported Siglecs because they are found on the lumenal edge of epithelial cell surfaces. Notably, the human genome contains several Siglec-like pseudogenes that have independent mutations that would have replaced the arginine residue required for optimal sialic acid recognition. Thus, additional changes in the biology of sialic acids may have taken place during human evolution.     

The few virus-like genes of Cotesia congregata bracovirus

The origin of the symbiotic association between parasitoid wasps and bracoviruses is still unknown. From phylogenetic analyses, bracovirus-associated wasp species constitute a monophyletic group, the microgastroid complex. Thus all wasp-bracovirus associations could have originated from the integration of an ancestral virus in the genome of the ancestor of the microgastroids. In an effort to identify a set of virus genes that would give clues on the nature of the ancestral virus, we have recently performed the complete sequencing of the genome of CcBV, the bracovirus of the wasp Cotesia congregata. We describe here the putative proteins encoded by CcBV genome having significant similarities with sequences from known viruses and mobile elements. The analysis of CcBV gene content does not lend support to the hypothesis that bracoviruses originated from a baculovirus. Moreover, no consistent homology was found between CcBV genes and any set of genes constituting the core genome of a known free-living virus. We discuss the significance of the scarce homology found between proteins from CcBV and other viruses or mobile elements.     

The evolution of ecomorphological traits within the Abrothrichini (Rodentia: Sigmodontinae): a Bayesian phylogenetics approach

The generally accepted hypothesis regarding the origin of fossorial mammals proposes adaptive convergence from open environments towards the use of subterranean environments. We evaluated this hypothesis for South American mole-mice using conventional and Bayesian frameworks, with independent evidence. By using a molecular approach based on Cytochrome b and IRBP sequences, we evaluated phylogenetic relationships, time of origin, the ancestral trait of fossoriality, and ancestral distributions of species belonging to the Andean Clade (Rodentia: Sigmodontinae). Our results indicate that the Andean Clade is highly sustained; with one clade grouping all fossorial forms and another grouping all cursorial species. We hypothesized that fossoriality originated in the Miocene/Pliocene transition, in the Temperate Forests of southern South America. We conclude that the origin of fossorial ecomorphological traits did not necessarily occur under a general model of open environments, the origin of these traits depends on the ecological-historical relationship of the taxon with the environment.