Phylogenetic relationships of Palaearctic Formica species (Hymenoptera, Formicidae) based on mitochondrial cytochrome b sequences

Peer reviewe

Genomic analysis of expressed sequence tags in American black bear Ursus americanus

<p>Abstract</p> <p>Background</p> <p>Species of the bear family (<it>Ursidae</it>) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (<it>Ursus americanus</it>).</p> <p>Results</p> <p>Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (<it>PLN</it>), cysteine glycine-rich protein 3 (<it>CSRP3</it>) and Troponin I type 3 (<it>TNNI3</it>), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (<it>BPHL</it>) and <it>CSRP3</it>, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes.</p> <p>Conclusion</p> <p>We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.</p

Opportunities and barriers to translating the hibernation phenotype for neurocritical care

Targeted temperature management (TTM) is standard of care for neonatal hypoxic ischemic encephalopathy (HIE). Prevention of fever, not excluding cooling core body temperature to 33°C, is standard of care for brain injury post cardiac arrest. Although TTM is beneficial, HIE and cardiac arrest still carry significant risk of death and severe disability. Mammalian hibernation is a gold standard of neuroprotective metabolic suppression, that if better understood might make TTM more accessible, improve efficacy of TTM and identify adjunctive therapies to protect and regenerate neurons after hypoxic ischemia brain injury. Hibernating species tolerate cerebral ischemia/reperfusion better than humans and better than other models of cerebral ischemia tolerance. Such tolerance limits risk of transitions into and out of hibernation torpor and suggests that a barrier to translate hibernation torpor may be human vulnerability to these transitions. At the same time, understanding how hibernating mammals protect their brains is an opportunity to identify adjunctive therapies for TTM. Here we summarize what is known about the hemodynamics of hibernation and how the hibernating brain resists injury to identify opportunities to translate these mechanisms for neurocritical care

Population dynamics and demographic history of Eurasian collared lemmings.

BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene

Modulation of gene expression in heart and liver of hibernating black bears (Ursus americanus)

<p>Abstract</p> <p>Background</p> <p>Hibernation is an adaptive strategy to survive in highly seasonal or unpredictable environments. The molecular and genetic basis of hibernation physiology in mammals has only recently been studied using large scale genomic approaches. We analyzed gene expression in the American black bear, <it>Ursus americanus</it>, using a custom 12,800 cDNA probe microarray to detect differences in expression that occur in heart and liver during winter hibernation in comparison to summer active animals.</p> <p>Results</p> <p>We identified 245 genes in heart and 319 genes in liver that were differentially expressed between winter and summer. The expression of 24 genes was significantly elevated during hibernation in both heart and liver. These genes are mostly involved in lipid catabolism and protein biosynthesis and include RNA binding protein motif 3 (<it>Rbm3</it>), which enhances protein synthesis at mildly hypothermic temperatures. Elevated expression of protein biosynthesis genes suggests induction of translation that may be related to adaptive mechanisms reducing cardiac and muscle atrophies over extended periods of low metabolism and immobility during hibernation in bears. Coordinated reduction of transcription of genes involved in amino acid catabolism suggests redirection of amino acids from catabolic pathways to protein biosynthesis. We identify common for black bears and small mammalian hibernators transcriptional changes in the liver that include induction of genes responsible for fatty acid β oxidation and carbohydrate synthesis and depression of genes involved in lipid biosynthesis, carbohydrate catabolism, cellular respiration and detoxification pathways.</p> <p>Conclusions</p> <p>Our findings show that modulation of gene expression during winter hibernation represents molecular mechanism of adaptation to extreme environments.</p

Genetic divergence estimates within and between the phylogenetic groups in <i>Formica</i> (%): average distances within the groups (the diagonal, in bold), mean uncorrected (below the diagonal) and net (above the diagonal) distances between the groups.

<p>Genetic divergence estimates within and between the phylogenetic groups in <i>Formica</i> (%): average distances within the groups (the diagonal, in bold), mean uncorrected (below the diagonal) and net (above the diagonal) distances between the groups.</p

Maximum likelihood tree showing phylogenetic relationships among 32 mtDNA <i>Formica</i> haplotypes with the outgroup <i>Polyergus rufescens</i>.

<p>Bootstrap percentages with values over 70 are shown for major nodes. Specimens refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041697#pone-0041697-t001" target="_blank">Table 1</a>.</p

Maximum likelihood tree showing phylogenetic relationships among 32 mtDNA <i>Formica</i> haplotypes.

<p>Bootstrap percentages with values over 70 are shown for nodes. Specimens refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041697#pone-0041697-t001" target="_blank">Table 1</a>.</p

Impact of past climate warming on genomic diversity and demographic history of collared lemmings across the Eurasian Arctic

The Arctic climate was warmer than today at the last interglacial and the Holocene thermal optimum. To reveal the impact of past climate-warming events on the demographic history of an Arctic specialist, we examined both mitochondrial and nuclear genomic variation in the collared lemming ( Dicrostonyx torquatus , Pallas), a keystone species in tundra communities, across its entire distribution in northern Eurasia. The ancestral phylogenetic position of the West Beringian group and divergence time estimates support the hypothesis of continental range contraction to a single refugial area located in West Beringia during high-magnitude warming of the last interglacial, followed by westward recolonization of northern Eurasia in the last glacial period. The West Beringian group harbors the highest mitogenome diversity and its inferred demography indicates a constantly large effective population size over the Late Pleistocene to Holocene. This suggests that northward forest expansion during recent warming of the Holocene thermal optimum did not affect the gene pool of the collared lemming in West Beringia but reduced genomic diversity and effective population size in all other regions of the Eurasian Arctic. Demographic inference from genomic diversity was corroborated by species distribution modeling showing reduction in species distribution during past climate warming. These conclusions are supported by recent paleoecological evidence suggesting smaller temperature increases and moderate northward forest advances in the extreme northeast of Eurasia during the Late Pleistocene-to-Holocene warming events. This study emphasizes the importance of West Beringia as a potential refugium for cold-adapted Arctic species under ongoing climate warming