Postglacial Colonization of the North European Seas by Pacific Fishes and Lamprey

A critical analysis of literature data on the distribution, morphology, and phylogeography of the Arctic lamprey (Lethenteron camtschaticum) and five species of marine and anadromous fish such as navaga (Eleginus navaga), pollock (Theragra chalcogramma), rainbow smelt (Osmerus mordax dentex), Pacific herring (Clupea pallasii), and pond smelt (Hypomesus olidus) has been performed. The results show that all these species have colonized Northern European seas, distributing along the Arctic coastline of Eurasia after the glacier retreat. The reasons that the dispersal of these species in the Atlantic Ocean may be impeded (preference for a cold environment, competition, and decrease of the evolutionary potential) are discussed.     

The Historical Speciation of Mauremys Sensu Lato: Ancestral Area Reconstruction and Interspecific Gene Flow Level Assessment Provide New Insights

Mauremys sensu lato was divided into Mauremys, Chinemys, Ocadia, and Annamemys based on earlier research on morphology. Phylogenetic research on this group has been controversial because of disagreements regarding taxonomy, and the historical speciation is still poorly understood. In this study, 32 individuals of eight species that are widely distributed in Eurasia were collected. The complete mitochondrial (mt) sequences of 14 individuals of eight species were sequenced. Phylogenetic relationships, interspecific divergence times, and ancestral area reconstructions were explored using mt genome data (10,854 bp). Subsequent interspecific gene flow level assessment was performed using five unlinked polymorphic microsatellite loci. The Bayesian and maximum likelihood analyses revealed a paraphyletic relationship among four old genera (Mauremys, Annamemys, Chinemys, and Ocadia) and suggested the four old genera should be merged into the genus (Mauremys). Ancestral area reconstruction and divergence time estimation suggested Southeast Asia may be the area of origin for the common ancestral species of this genus and genetic drift may have played a decisive role in species divergence due to the isolated event of a glacial age. However, M. japonica may have been speciated due to the creation of the island of Japan. The detection of extensive gene flow suggested no vicariance occurred between Asia and Southeast Asia. Inconsistent results between gene flow assessment and phylogenetic analysis revealed the hybrid origin of M. mutica (Southeast Asian). Here ancestral area reconstruction and interspecific gene flow level assessment were first used to explore species origins and evolution of Mauremys sensu lato, which provided new insights on this genus.     

Parasitic Attachments by Overwintering Silver Lampreys, Ichthyomyzon unicuspis, and Chestnut Lampreys, Ichthyomyzon castaneus

We present evidence that at least some parasitic-phase silver lampreys, Ichthyomyzon unicuspis, and chestnut lampreys, I. castaneus, remain attached to host fish during the winter. Lake sturgeon, Acipenser fulvescens, harvested through the ice by spearfishers in the Lake Winnebago system in Wisconsin may bear silver lampreys or fresh lamprey wounds, and sturgeon with lamprey marks were significantly larger than sturgeon without them. Silver lampreys collected on paddlefish, Polyodon spathula, in the Wisconsin River in March were not significantly longer than silver lampreys collected previously in late October, but they were significantly heavier, an indication that they were feeding to at least some extent during the intervening period. Other large fish species, including northern pike, Esox lucius, and flathead catfish, Pylodictus olivaris, have been collected or observed during the winter with silver or chestnut lampreys attached. Although energy and nutrient intake by parasitic lampreys may be reduced during the winter, lampreys attached to hosts may also benefit from the hosts' mobility and ability to avoid potentially harmful situations.     

Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates

How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F₁ hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high F_ST and d_A, but not high d_XY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high F_ST, d_XY, and d_A values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.     

Post-Viking Microbiology: New Approaches,New Data,New Insights

In the 20 years since the Viking experiments, major advances have been made in the areas of microbial systematics, microbial metabolism, microbial survival capacity, and the definition of environments on earth, suggesting that life is more versatile and tenacious than was previously appreciated. Almost all niches on earth which have available energy, and which are compatible with the chemistry of carbon-carbon bonds, are known to be inhabited by bacteria. The oldest known bacteria on earth apparently evolved soon after the formation of the planet, and are heat loving, hydrogen and/or sulfur metabolizing forms. Among the two microbial domains (kingdoms) is a great deal of metabolic diversity, with members of these forms being able to grow on almost any known energy source, organic or inorganic, and to utilize an impressive array of electron acceptors for anaerobic respiration. Both hydrothermal environments and the deep subsurface environments have been shown to support large populations of bacteria, growing on energy supplied by geothermal energy, thus isolating these ecosystems from the rest of the global biogeochemical cycles. This knowledge, coupled with new insights into the history of the solar system, allow one to speculate on possible evolution and survival of life forms on Mars.     

Postglacial Colonization of the Qinling Mountains: Phylogeography of the Swelled Vent Frog (Feirana quadranus)

Background

The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling–Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia).

Methodology/Principal Findings

We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang–Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling–Micang–Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang–Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline.

Conclusions/Significance

The Qinling–Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang–Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.     

Postglacial expansion and genome subdivision in the European grasshopper Chorthippus parallelus

A noncoding nuclear DNA marker sequence (Cpnl-1) was used to investigate subdivision in the grasshopper Chorthippus parallelus and deduce postglacial expansion patterns across its species range in Europe. Investigation of the spatial distribution of 71 Cpnl-1 haplotypes and estimation of levels of genetic differentiation (K_ST values) between populations and geographic regions provided evidence for subdivision of C. parallelus into at least five major geographic regions and indicated that the French form of C. parallelus originated after range expansion from a Balkan refugium, Further evidence for subdivision of C. parallelus between Italy and northern Europe suggests that the Alps may have formed a significant barrier to gene flow in this grasshopper.     

Gene Flow in European Beech (Fagus sylvatica L.)

Three relatively isolated stands were used to study gene flow in European beech (Fagus sylvatica L.) in Northern Germany. Nine allozyme loci (Got-B, Idh-A, Lap-A, Mdh-B, Mdh-C, Mnr-A, 6-pgdh-A, Pgi-B and Pgm-A) were utilized for multilocus-genotyping adult trees and seeds. Expected heterozygosity (He) ranged from 0.325 to 0.351 for the three stands. F(ST) revealed that there was small differentiation among stands (mean F(ST) = 0.013). The indirect estimates of gene flow (Nm) based on the mean F(ST) were high and the average Nm was 19.14. External gene flow by pollen ranged from 0.7 to 1.2% inferred from new alleles in seed samples. Moreover, paternity analysis was used to assess effective pollen dispersal by inferring paternity of offspring. The weighted mean distances of pollen dispersal for these three stands were 36.8 and 37.1 m based on simple exclusion procedure and most-likely method, respectively. Two of the trees in one stand had rare allozyme alleles (Lap-A1 and Idh-A4, respectively), which were used to directly measure pollen movement away from those trees. The frequency of the rare Lap and Idh alleles in seeds declines as the distance from the source tree increases. The weighted mean distance of pollen dispersal with rare allele Lap-A1 or Idh-A4 was 26.3 m.     

Speciation through cytonuclear incompatibility: Insights from yeast and implications for higher eukaryotes

Several features of the yeast mitochondrial genome, including high mutation rate, dynamic genomic structure, small effective population size, and dispensability for cellular viability, make it a promising candidate for generating hybrid incompatibility and driving speciation. Cytonuclear incompatibility, a specific type of Dobzhansky‐Muller genetic incompatibility caused by improper interactions between mitochondrial and nuclear genomes, has previously been observed in a variety of organisms, yet its role in speciation remains obscure. Recent studies in Saccharomyces yeast species provide a new insight, with experimental evidence that cytonuclear incompatibility and DNA sequence divergence are both causes of the reproductive isolation of different yeast species. Interestingly, these two mechanisms seem to be perfectly complementary to each other in terms of their effects and evolutionary trajectories. Direct molecular analyses of the incompatible genes in yeasts have started to shed light on the evolutionary forces driving speciation. Editor's suggested further reading in BioEssays The cytoplasmic structure hypothesis for ribosome assembly, vertical inheritance, and phylogeny Abstract Mitochondrial bioenergetics as a major motive force of speciation Abstract     

Maximum Likelihood Implementation of an Isolation-with-Migration Model with Three Species for Testing Speciation with Gene Flow

We implement an isolation with migration model for three species, with migration occurring between two closely related species while an out-group species is used to provide further information concerning gene trees and model parameters. The model is implemented in the likelihood framework for analyzing multilocus genomic sequence alignments, with one sequence sampled from each of the three species. The prior distribution of gene tree topology and branch lengths at every locus is calculated using a Markov chain characterization of the genealogical process of coalescent and migration, which integrates over the histories of migration events analytically. The likelihood function is calculated by integrating over branch lengths in the gene trees (coalescent times) numerically. We analyze the model to study the gene tree-species tree mismatch probability and the time to the most recent common ancestor at a locus. The model is used to construct a likelihood ratio test (LRT) of speciation with gene flow. We conduct computer simulations to evaluate the LRT and found that the test is in general conservative, with the false positive rate well below the significance level. For the test to have substantial power, hundreds of loci are needed. Application of the test to a human-chimpanzee-gorilla genomic data set suggests gene flow around the time of speciation of the human and the chimpanzee.     

Postglacial vegetation on Umnak Island,Aleutian Islands,Alaska

Pollen analyses of a peat section, 9,945 ± 320 radiocarbon years of age from Umnak Island in the eastern Aleutians, point to a tripartite sequence of postglacial plant communities beginning with a sedge-grass tundra, followed by an interval of willow dominance (8,500 – 3,500 years ago), and ending with a grass-sedge tundra.