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Molecular biology and evolution [journal]
- SMBE Editors and Council. [Journal Article]
- Mol Biol Evol 2014 Aug; 31(8):i3.
- Associate editors. [Journal Article]
- Mol Biol Evol 2014 Aug; 31(8):i2.
- Cover. [Journal Article]
- Mol Biol Evol 2014 Aug; 31(8):i1.
- Blame It on the Chimps: Researchers Resolve Evolutionary Origins of Human Herpes Viruses. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jul 18.
- Maximum likelihood inference of population size contractions from microsatellite data. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jul 11.
Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In the present work, we develop a maximum likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MsVar) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared to alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that violations of a single step mutation assumption induce very high bias towards false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the Migraine software package.
- Modular Evolution of DNA Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jul 12.
Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to cis-regulatory modules. Transcription factor proteins that bind these cis-regulatory modules may also evolve to produce novelty. Coding changes are considered to be rarer, however, because transcription factors are multifunctional and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. Here, we demonstrate that orthologous transcription factors can also evolve a changed preference for a secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. Using Protein Binding Microarray, Surface Plasmon Resonance, and in vivo reporter assays, we demonstrate an important difference in DNA binding preference between Tbrain protein orthologs in two species of echinoderms, the sea star, Patiria miniata, and the sea urchin, Strongylocentrotus purpuratus. While both orthologs recognize the same primary motif, only the sea star Tbr also has a secondary binding motif. Our in vivo assays demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs. We hypothesize that this divergence provides modularity that allows orthologous transcription factors to evolve novel roles in gene regulatory networks through modification of binding to secondary sites.
- selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jul 10.
Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated genomic datasets grow larger, spanning thousands of samples and millions of markers, there is a need for a fast and efficient implementation of these scans for general use. Here we present selscan, an efficient multi-threaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity (XPEHH). selscan accepts phased genotypes in multiple formats, including TPED, and performs extremely well on both simulated and real data and over an order of magnitude faster than existing available implementations. It calculates iHS on chromosome 22 (22, 147 loci) across 204 CEU haplotypes in 353s on one thread (33s on 16 threads) and calculates XPEHH for the same data relative to 210 YRI haplotypes in 578s on one thread (52s on 16 threads). Source code and binaries (Windows, OSX and Linux) are available at https://github.com/szpiech/selscan.
- The Loss of Adipokine Genes in the Chicken Genome and Implications for Insulin Metabolism. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jul 10.
Gene loss is one of the main drivers in the evolution of genomes and species. The demonstration that a gene has been lost by pseudogenisation is truly complete when one finds the pseudogene in the orthologous genomic region with respect to active genes in other species. In some cases, the identification of such orthologous loci is not possible because of chromosomal rearrangements or if the gene of interest has not yet been sequenced. This question is particularly important in the case of birds because the genomes of avian species possess only about 15,000 predicted genes, in comparison with 20,000 in mammals. Yet, gene loss raises the question of which functions are affected by the changes in gene counts. We describe a systematic approach that makes it possible to demonstrate gene loss in the chicken genome even if a pseudogene has not been found. By using phylogenetic and synteny analysis in vertebrates, genome-wide comparisons between the chicken genome and ESTs, RNAseq data analysis, statistical analysis of the chicken genome, and Radiation Hybrid mapping, we show that resistin, TNFα and PAI-1 (SERPINE1), three genes encoding adipokines inhibiting insulin sensitivity, have been lost in chicken as well as zebra finch genomes. Moreover, omentin, a gene encoding an adipokine that enhances insulin sensitivity, has also been lost in the chicken genome. Overall, only one adipokine inhibiting insulin sensitivity, and five adipokines enhancing insulin sensitivity, are still present in the chicken genome. These genetic differences between mammals and chicken, given the functions of the genes in mammals, would have dramatic consequences on chicken endocrinology, leading to novel equilibriums especially in the regulation of energy metabolism, insulin sensitivity, as well as appetite and reproduction.
- Large-scale genetic survey provides insights into the captive management and reintroduction of giant pandas. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jul 10.
The captive genetic management of threatened species strives to preserve genetic diversity and avoid inbreeding to ensure populations remain available, healthy and viable for future reintroduction. Determining and responding to the genetic status of captive populations is therefore paramount to these programs. Here, we genotyped 19 microsatellite loci for 240 captive giant pandas (Ailuropoda melanoleuca) (~64% of the captive population) from four breeding centers, Wolong (WL), Chengdu (CD), Louguantai (LGT) and Beijing (BJ), and analyzed 655 base pairs of mitochondrial DNA control region sequence for 220 of these animals. High levels of genetic diversity and low levels of inbreeding were estimated in the breeding centers, indicating that the captive population is genetically healthy and deliberate further genetic input from wild animals is unnecessary. However, the LGT population faces a higher risk of inbreeding, and significant genetic structure was detected among breeding centers, with LGT-CD and WL-BJ clustering separately. Based on these findings, we highlight that: (i) the LGT population should be managed as an independent captive population to resemble the genetic distinctness of their Qinling Mountain origins; (ii) exchange between CD and WL should be encouraged because of similar wild founder sources; (iii) the selection of captive individuals for reintroduction should consider their geographic origin, genetic background and genetic contribution to wild populations; and (iv) combining our molecular genetic data with existing pedigree data will better guide giant panda breeding and further reduce inbreeding into the future.