Regulative germ cell specification in axolotl embryos: a primitive trait conserved in the mammalian lineage

How germ cells are specified in the embryos of animals has been a mystery for decades. Unlike most developmental processes, which are highly conserved, embryos specify germ cells in very different ways. Curiously, in mouse embryos germ cells are specified by extracellular signals; they are not autonomously specified by maternal germ cell determinants (germ plasm), as are the germ cells in most animal model systems. We have developed the axolotl (Ambystoma mexicanum), a salamander, as an experimental system, because classic experiments have shown that the germ cells in this species are induced by extracellular signals in the absence of germ plasm. Here, we provide evidence that the germ cells in axolotls arise from naive mesoderm in response to simple inducing agents. In addition, by analysing the sequences of axolotl germ-cell-specific genes, we provide evidence that mice and urodele amphibians share a common mechanism of germ cell development that is ancestral to tetrapods. Our results imply that germ plasm, as found in species such as frogs and teleosts, is the result of convergent evolution. We discuss the evolutionary implications of our findings.     

The cambrian evolutionary ‘explosion’ recalibrated

The sudden appearance in the fossil record of the major animal phyla apparently records a phase of unparalleled, rapid evolution at the base of the Cambrian period, 545 Myr ago. This has become known as the Cambrian evolutionary ‘explosion’, and has fuelled speculation about unique evolutionary processes operating at that time. The acceptance of the palaeontological evidence as a true reflection of the evolutionary narrative has been criticised in two ways: from a reappraisal of the phylogenetic relationships of the early fossils, and from predicitions of molecular divergence times, based on six appropriate metazoan genes. Phylogenetic analysis of the arthropods implies an earlier, Precambrian history for most clades, and hence an extensive period of cladogenesis unrecorded by fossils. A similar argument can be applied to molluscs, lophophorates and deuterostomes. Molecular evidence implies divergence between clades to at least 1000 Myr ago. The apparent paradox between the sudden appearance of recognisable metazoans and their extended evolutionary history might be explained by a sudden Cambrian increase in body size, which was accompanied by skeletisation. A new paradigm suggests that the ‘explosion’ in the record may have been decoupled from the evolutionary innovation.     

Geographic distributions and origins of human head lice (Pediculus humanus capitis) based on mitochondrial data

Human head lice (Pediculus humanus capitis) are subdivided into 3 deeply divergent mitochondrial clades (Clades A, B, and C), each having unique geographical distributions. Determining the evolutionary history and geographic distribution of these mitochondrial clades can elucidate the evolutionary history of the lice as well as their human hosts. Previous data suggest that lice belonging to mitochondrial Clade B may have originated in North America or Asia; however, geographic sampling and sample sizes have been limited. With newly collected lice, we calculate the relative frequency, geographic distribution, and genetic diversity of louse mitochondrial clades to determine the geographic origin of lice belonging to Clade B. In agreement with previous studies, genetic diversity data support a North American origin of Clade B lice. It is likely that lice belonging to this mitochondrial clade recently migrated to other geographic localities, e.g., Europe and Australia, and, if not already present, may disperse further to occupy all geographic regions.     

A Phylogenetic Analysis of the Evolution of the Stridulatory Apparatus in True Crickets (Orthoptera, Grylloidea)

The stridulatory apparatus (or stridulum) is currently assumed ancestral in crickets. Models of its subsequent evolution consider only one modality of evolutionary change: the stridulum would have been progressively lost in multiple cricket lineages. A phylogenetic test of this hypothesis is presented here. The morpho-functional types of stridulum have been optimized on the cladistic phylogenies of two monophyletic cricket clades, and parsimonious evolutionary scenarios of the evolution of the stridulum in these clades have been derived. The phylogenetic patterns thus obtained support the hypothesis that the stridulum has been lost several times convergently in crickets. They indicate, however, that the loss of the stridulum could be reversible, and that several modalities of evolutionary change exist for the stridulum. Phylogenetic analysis thus reveals an unsuspected complexity in the evolution of acoustic communication in crickets.     

Temporal germ cell development strategy during spermatogenesis within the testis of the Ground Skink, Scincella lateralis (Sauria: Scincidae)

Ground Skink (Scincella lateralis) testes were examined histologically to determine the testicular organization and germ cell development strategy employed during spermatogenesis. Testicular tissues were collected from 19 ground skinks from Aiken County, South Carolina during the months of March-June, August, and October. The testes consisted of seminiferous tubules lined with germinal epithelia in which germ cells matured in close association with Sertoli cells. As germ cells matured, they migrated away from the basal lamina of the epithelia towards the lumina of the seminiferous tubules. The testes were spermatogenically active during the months of March, April, May, June, and October (largest seminiferous tubule diameters and epithelial heights), but entered a quiescent period in August (smallest seminiferous tubule diameter and epithelial height) where only spermatogonia type A and B and early spermatocytes were present in low numbers within the seminiferous epithelium. Although the testicular organization was similar to other amniotes, a temporal germ cell development strategy was employed during spermatogenesis within Ground Skinks, similar to that of anamniotes. Thus, this skink's germ cell development strategy, which also has been recently reported in all other major reptilian clades, may represent an evolutionary intermediate in terms of testicular organization between anamniotes and birds and mammals.     

Long-distance migrating species of birds travel in larger groups

How individuals migrate over long distances is an enduring mystery of animal migration. Strong selection pressure for travelling in groups has been suggested in long-distance migrating species. Travelling in groups can reduce the energetic demands of long migration, increase navigational accuracy and favour group foraging at migratory halts. Nevertheless, this hypothesis has received scant attention. I examined evolutionary transitions in migration distance in all North American breeding species of birds. I documented 72 evolutionary shifts in migration distance in the pool of 409 species. In contrasting clades, long-distance migration, as opposed to short-distance migration, was associated with a larger travelling group size. No other transitions occurred alongside in other traits such as group size in the non-breeding season or body mass. The results suggest that larger group sizes have been beneficial in the evolution of long-distance migration in a large clade of birds.     

Neoendemism in Madagascan scaly tree ferns results from recent, coincident diversification bursts

More than 80% of Madagascar's 12,000 plant species are endemic with the degree of endemism reaching as much as 95% in the scaly tree ferns, an important species rich component of Madagascar's evergreen rainforests. Predominantly African or Asian ancestry and divergence times usually postdating the separation of Madagascar from the Gondwanan landmasses have been demonstrated for several Madagascan animal and angiosperm groups. However, evolutionary studies of rainforest-specific lineages are scarce and the ecological context of radiation events has rarely been investigated. Here, we examine the evolution of Madagascan tree ferns as a rainforest-specific model family, integrate results from bioclimatic niche analysis with a dated phylogenetic framework, and propose an evolutionary scenario casting new light on our knowledge of the evolution of large island endemic clades. We show that Madagascar's extant tree fern diversity springs from three distinct ancestors independently colonizing Madagascar in the Miocene and that these three monophyletic clades diversified in three coincident radiation bursts during the Pliocene, reaching exceptionally high diversification rates and most likely responding to a common climatic trigger. Recent diversification bursts may thus have played a major role in the evolution of the extant Madagascan rainforest biome, which hence contains a significant number of young, neoendemic taxa.     

Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity

Parmelioid lichens comprise about 1500 species and have a worldwide distribution. Numerous species are widely distributed and well known, including important bioindicators for atmospheric pollution. The phylogeny and classification of parmelioid lichens has been a matter of debate for several decades. Previous studies using molecular data have helped to establish hypotheses of the phylogeny of certain clades within this group. In this study, we infer the phylogeny of major clades of parmelioid lichens using DNA sequence data from two nuclear loci and one mitochondrial locus from 145 specimens (117 species) that represent the morphological and chemical diversity in these taxa. Parmelioid lichens are not monophyletic; however, a core group is strongly supported as monophyletic, excluding Arctoparmelia and Melanelia s. str., and including Parmeliopsis and Parmelaria. Within this group, seven well-supported clades are found, but the relationships among them remain unresolved. Stochastic mapping on a MC/MCMC tree sampling was employed to infer the evolution of two morphological and two chemical traits believed to be important for the evolutionary success of these lichens, and have also been used as major characters for classification. The results suggest that these characters have been gained and lost multiple times during the diversification of parmelioid lichens.     

Morphological and phylogenetic analyses of <Emphasis Type="Italic">Uromyces appendiculatus</Emphasis> and <Emphasis Type="Italic">U. vignae</Emphasis> on legumes in Japan

Uromyces appendiculatus, inclusive of three varieties, is distinguished from U. vignae primarily by the position of urediniospore germ pores and putative host specificity. However, opinions concerning these morphological and physiological features as taxonomic characters have varied greatly, and distinction of these species has often been confused. To clarify the taxonomy of these two species, morphological features of urediniospores and teliospores of 225 rust fungus specimens on species of Phaseolus, Vigna, Apios, Lablab, and Dunbaria were examined by light microscopy and scanning electron microscopy. Forty-five specimens were subjected to molecular phylogenetic analyses. As a result, the position of germ pores in urediniospores and the teliospore-wall thickness were considered as good characters to separate three morphological groups. In molecular analyses, the specimens fell into two and three clades based on the nucleotide sequence at D1/D2 domain of LSU rDNA and ITS regions, respectively. One of the D1/D2 clades corresponded to one morphological group whereas another D1/D2 clade included two other morphological groups. In contrast, each of the three ITS clades corresponded to a separate morphological group. Neither morphological groups nor molecular clades were host limited. It is suggested that the three morphological groups that corresponded to three distinct ITS clades constitute distinct species.Contribution no. 186 from the Laboratory of Plant Parasitic Mycology, Institute of Agriculture and Forestry, University of Tsukuba, Japan     

Post-Eocene climate change, niche conservatism, and the latitudinal diversity gradient of New World birds

Aim The aim of this study was to test a variant of the evolutionary time hypothesis for the bird latitudinal diversity gradient derived from the effects of niche conservatism in the face of global climate change over evolutionary time. Location The Western Hemisphere. Methods We used digitized range maps of breeding birds to estimate the species richness at two grain sizes, 756 and 12,100 km². We then used molecular phylogenies resolved to family to quantify the root distance (RD) of each species as a measure of its level of evolutionary development. Birds were classified as ‘basal’ or ‘derived’ based on the RD of their family, and richness patterns were contrasted for the most basal and most derived 30% of species. We also generated temperature estimates for the Palaeogene across the Western Hemisphere to examine how spatial covariation between past and present climates might make it difficult to distinguish between ecological and evolutionary hypotheses for the current richness gradient. Results The warm, wet tropics support many species from basal bird clades, whereas the northern temperate zone and cool or dry tropics are dominated by species from more recent, evolutionarily derived clades. Furthermore, crucial to evaluating how niche conservatism among birds may drive the hemispherical richness gradient, the spatial structure of the richness gradient for basal groups is statistically indistinguishable from the overall gradient, whereas the richness gradient for derived groups is much shallower than the overall gradient. Finally, modern temperatures and the pattern of climate cooling since the Eocene are indistinguishable as predictors of bird species richness. Main conclusions Differences in the richness gradients of basal vs. derived clades suggest that the hemispherical gradient has been strongly influenced by the differential extirpation of species in older, warm‐adapted clades from parts of the world that have become cooler in the present. We propose that niche conservatism and global‐scale climate change over evolutionary time provide a parsimonious explanation for the contemporary bird latitudinal diversity gradient in the New World, although dispersal limitation of some highly derived clades probably plays a secondary role.     

Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: I. Ancient clade splitting revealed by mitochondrial haplotype markers

The codling moth (Cydia pomonella L., Tortricidae, Lepidoptera) is an important pest of pome fruit with global distribution. It has adapted successfully to different habitats by forming various ecotypes and populations, often termed strains, which differ among each other in several morphological, developmental, and physiological features. Many strains of Cydia pomonella have developed resistance against a broad range of chemically different pesticides. Obviously, pesticide-resistant strains must have a genetic basis inherent to the gene pool of codling moth populations, and this deserves our particular attention. The primary intention of the present study was to contribute novel information regarding the evolutionary phylogeny and phylogeography of codling moth populations in Central Europe. In addition, we aimed at testing the hypothesis that differential biological traits and response patterns towards pesticides in codling moth populations may be reflected at a mitochondrial DNA level. In particular, we wanted to test if pesticide resistance in codling moths is associated repeatedly and independently with more than one mitochondrial haplotype. To this end, we analyzed mitochondrial DNA and constructed phylogenetic trees based on three mitochondrial genes: cytochrome oxidase I (COI), the A+T-rich region of the control region (CR), and the nicotinamide adenine dinucleotide dehydrogenase subunit 5 (ND5). The results indicate that Central European populations of Cydia pomonella are clearly divided in two ancient clades. As shown by means of a molecular clock approach, the splitting of the two clades can be dated to a time period between the lower and middle Pleistocene, about 1.29-0.20 million years ago. It is assumed that the cyclic changes of warm and cold periods during Pleistocene may have lead to the geographic separation of codling moth populations due to glaciation, giving rise to the formation of the two separate refugial clades, as already shown for many other European animal species. Due to their inclination towards developing novel detoxification gene variants, codling moth individuals from both clades independently and multifariously may have developed pesticide resistance, and this process may be ongoing. During their more recent evolutionary history, natural events such as the gradual disappearance of climate-specific geographic barriers, as well as human-aided dispersal in recent historic times, may have allowed codling moth haplotypes from the original clades to interbreed and completely merge again, creating a globally successful insect species with a gene pool capable of responding to novel selective challenges by rapid adaptation.     

Inferring the evolutionary history of vibrios by means of multilocus sequence analysis

We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br).     

Endogenous viral elements in animal genomes

Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs) derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.     

Diet and Diversification in the Evolution of Coral Reef Fishes

The disparity in species richness among evolutionary lineages is one of the oldest and most intriguing issues in evolutionary biology. Although geographical factors have been traditionally thought to promote speciation, recent studies have underscored the importance of ecological interactions as one of the main drivers of diversification. Here, we test if differences in species richness of closely related lineages match predictions based on the concept of density-dependent diversification. As radiation progresses, ecological niche-space would become increasingly saturated, resulting in fewer opportunities for speciation. To assess this hypothesis, we tested whether reef fish niche shifts toward usage of low-quality food resources (i.e. relatively low energy/protein per unit mass), such as algae, detritus, sponges and corals are accompanied by rapid net diversification. Using available molecular information, we reconstructed phylogenies of four major reef fish clades (Acanthuroidei, Chaetodontidae, Labridae and Pomacentridae) to estimate the timing of radiations of their subclades. We found that the evolution of species-rich clades was associated with a switch to low quality food in three of the four clades analyzed, which is consistent with a density-dependent model of diversification. We suggest that ecological opportunity may play an important role in understanding the diversification of reef-fish lineages.