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1.  Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas 
Science Advances  2016;2(4):e1501385.
Native American population history is reexamined using a large data set of pre-Columbian mitochondrial genomes.
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
doi:10.1126/sciadv.1501385
PMCID: PMC4820370  PMID: 27051878
Ancient DNA; Native America; colonization; Beringia
2.  The Knight and the King: two new species of giant bent-toed gecko (Cyrtodactylus, Gekkonidae, Squamata) from northern New Guinea, with comments on endemism in the North Papuan Mountains 
ZooKeys  2016;105-130.
The diverse biota of New Guinea includes many nominally widespread species that actually comprise multiple deeply divergent lineages with more localised histories of evolution. Here we investigate the systematics of the very large geckos of the Cyrtodactylus novaeguineae complex using molecular and morphological data. These data reveal two widespread and divergent lineages that can be distinguished from each other, and from type material of Cyrtodactylus novaeguineae, by aspects of size, build, coloration and male scalation. On the basis of these differences we describe two new species. Both have wide distributions that overlap extensively in the foothill forests of the North Papuan Mountains, however one is seemingly restricted to hill and lower montane forests on the ranges themselves, while the other is more widespread throughout the surrounding lowlands. The taxon endemic to the North Papuan Mountains is related to an apparently lowland form currently known only from Waigeo and Batanta Island far to the west – hinting at a history on island arcs that accreted to form the North Papuan Mountains.
doi:10.3897/zookeys.562.6052
PMCID: PMC4768470  PMID: 27006624
Arc accretion; Endemism; Indonesia; lizard; orogeny; Papua New Guinea; Papua Province; Sepik Basin
3.  Best Practices in Insect Genome Sequencing: What Works and What Doesn’t 
The last decade of decreasing DNA sequencing costs and proliferating sequencing services in core labs and companies has brought the de-novo genome sequencing and assembly of insect species within reach for many entomologists. However, sequence production alone is not enough to generate a high quality reference genome, and in many cases, poor planning can lead to extremely fragmented genome assemblies preventing high quality gene annotation and other desired analyses. Insect genomes can be problematic to assemble, due to combinations of high polymorphism, inability to breed for genome homozygocity, and small physical sizes limiting the quantity of DNA able to be isolated from a single individual. Recent advances in sequencing technology and assembly strategies are enabling a revolution for insect genome reference sequencing and assembly. Here we review historical and new genome sequencing and assembly strategies, with a particular focus on their application to arthropod genomes. We highlight both the need to design sequencing strategies for the requirements of the assembly software, and new long-read technologies that are enabling a return to traditional assembly approaches. Finally, we compare and contrast very cost effective short read draft genome strategies with the long read approaches that although entailing additional cost, bring a higher likelihood of success and the possibility of archival assembly qualities approaching that of finished genomes.
doi:10.1016/j.cois.2015.02.013
PMCID: PMC4465116  PMID: 26085980
4.  Hemichordate genomes and deuterostome origins 
Nature  2015;527(7579):459-465.
Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal ‘gill’ slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
doi:10.1038/nature16150
PMCID: PMC4729200  PMID: 26580012
5.  Does estrogen deficiency cause lacrimal gland inflammation and aqueous-deficient dry eye in mice? 
Experimental eye research  2014;127:153-160.
Researchers have proposed that estrogen deficiency will lead to a Sjögren's syndrome (SjS)-like lacrimal gland inflammation, aqueous tear deficiency and dry eye. The purpose of this study was to determine whether this proposal is correct. Lacrimal glands were obtained from adult, age-matched wild type (WT) and aromatase knockout (ArKO) mice, in which estrogen synthesis is completely eliminated. Tissues were also obtained from autoimmune MRL/Mp-lpr/lpr (MRL/lpr) mice as inflammation controls. Tear volumes in WT and ArKO mice were measured and glands were processed for molecular biological and histological evaluation. Our results demonstrate that estrogen absence does not lead to a SjS-like inflammation in lacrimal tissue or to an aqueous-deficient dry eye. There was no upregulation of genes associated with inflammatory pathways in lacrimal glands of male or female ArKO mice. Such inflammatory activity was prominent in autoimmune MRL/lpr tissues. We also found no evidence of inflammation in lacrimal gland tissue sections of estrogen-deficient mice, and tear volumes of ArKO males were actually increased as compared to those WT controls. Interestingly, our study did show that estrogen absence influences the expression of thousands of lacrimal gland genes, and that this impact is sex- and genotype-specific. Our findings demonstrate that estrogen absence is not a risk factor for the development of SjS-like lacrimal gland inflammation or for aqueous-deficient dry eye in mice.
doi:10.1016/j.exer.2014.07.017
PMCID: PMC4175142  PMID: 25084452
lacrimal gland; mice; estrogen; male; female; sex difference; inflammation; tear volume; gene expression
6.  Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature 
Cell Reports  2015;12(5):821-836.
Summary
Acute myeloid leukemia (AML) is characterized by recurrent mutations that affect the epigenetic regulatory machinery and signaling molecules, leading to a block in hematopoietic differentiation. Constitutive signaling from mutated growth factor receptors is a major driver of leukemic growth, but how aberrant signaling affects the epigenome in AML is less understood. Furthermore, AML cells undergo extensive clonal evolution, and the mutations in signaling genes are often secondary events. To elucidate how chronic growth factor signaling alters the transcriptional network in AML, we performed a system-wide multi-omics study of primary cells from patients suffering from AML with internal tandem duplications in the FLT3 transmembrane domain (FLT3-ITD). This strategy revealed cooperation between the MAP kinase (MAPK) inducible transcription factor AP-1 and RUNX1 as a major driver of a common, FLT3-ITD-specific gene expression and chromatin signature, demonstrating a major impact of MAPK signaling pathways in shaping the epigenome of FLT3-ITD AML.
Graphical Abstract
Highlights
•FLT3-ITD signaling is associated with a common gene expression signature•FLT3-ITD-specific gene expression is associated with a common chromatin signature•FLT3-ITD AML displays chronic activation of the inducible transcription factor AP-1•AP-1 cooperates with RUNX1 to shape the epigenome of FLT3-ITD AML
Cauchy et al. identify a specific gene expression and regulatory signature associated with aberrant signaling in acute myeloid leukemia with FLT3-ITD mutations. In FLT3-ITD AML, the inducible transcription factor AP-1 is chronically activated and cooperates with RUNX1, shaping the epigenome to transactivate specific target genes.
doi:10.1016/j.celrep.2015.06.069
PMCID: PMC4726916  PMID: 26212328
7.  Enhancement of insulin-mediated rat muscle glucose uptake and microvascular perfusion by 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside 
Background
Insulin-induced microvascular recruitment is important for optimal muscle glucose uptake. 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR, an activator of AMP-activated protein kinase), can also induce microvascular recruitment, at doses that do not acutely activate glucose transport in rat muscle. Whether low doses of AICAR can augment physiologic insulin action is unknown. In the present study we used the euglycemic hyperinsulinemic clamp to assess whether insulin action is augmented by low dose AICAR.
Methods
Anesthetized rats were studied during saline infusion or euglycemic insulin (3 mU/kg/min) clamp for 2 h in the absence or presence of AICAR for the last hour (5 mg bolus followed by 3.75 mg/kg/min). Muscle glucose uptake (R’g) was determined radioisotopically with 14C-2-deoxyglucose and muscle microvascular perfusion by contrast-enhanced ultrasound with microbubbles.
Results
AICAR did not affect blood glucose, or lower leg R’g, although it significantly (p < 0.05) increased blood lactate levels and augmented muscle microvascular blood volume via a nitric oxide synthase dependent pathway. Insulin increased femoral blood flow, whole body glucose infusion rate (GIR), R’g, hindleg glucose uptake, and microvascular blood volume. Addition of AICAR during insulin infusion increased lactate production, further increased R’g in Type IIA (fast twitch oxidative) and IIB (fast twitch glycolytic) fiber containing muscles, and hindleg glucose uptake, but decreased R’g in the Type I (slow twitch oxidative) fiber muscle. AICAR also decreased GIR due to inhibition of insulin-mediated suppression of hepatic glucose output. AICAR augmented insulin-mediated microvascular perfusion.
Conclusions
AICAR, at levels that have no direct effect on muscle glucose uptake, augments insulin-mediated microvascular blood flow and glucose uptake in white fiber type muscles. Agents targeted to endothelial AMPK activation are promising insulin sensitizers, however, the decrease in GIR and the propensity to increase blood lactate cautions against AICAR as an acute insulin sensitizer.
doi:10.1186/s12933-015-0251-y
PMCID: PMC4509722  PMID: 26194188
Muscle; Insulin; Glucose; Microcirculation; Microbubbles
8.  Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions 
Nature Communications  2015;6:7344.
Lucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.
Lucilia cuprina is a parasitic blowfly of major economic importance worldwide that feeds on the tissues of animals such as sheep. Here, the authors sequence the genome of L. cuprina and provide insights into the fly's molecular biology, interactions with the host animal and insecticide resistance.
doi:10.1038/ncomms8344
PMCID: PMC4491171  PMID: 26108605
9.  A Re-Appraisal of the Early Andean Human Remains from Lauricocha in Peru 
PLoS ONE  2015;10(6):e0127141.
The discovery of human remains from the Lauricocha cave in the Central Andean highlands in the 1960’s provided the first direct evidence for human presence in the high altitude Andes. The skeletons found at this site were ascribed to the Early to Middle Holocene and represented the oldest known population of Western South America, and thus were used in several studies addressing the early population history of the continent. However, later excavations at Lauricocha led to doubts regarding the antiquity of the site. Here, we provide new dating, craniometric, and genetic evidence for this iconic site. We obtained new radiocarbon dates, generated complete mitochondrial genomes and nuclear SNP data from five individuals, and re-analyzed the human remains of Lauricocha to revise the initial morphological and craniometric analysis conducted in the 1960’s. We show that Lauricocha was indeed occupied in the Early to Middle Holocene but the temporal spread of dates we obtained from the human remains show that they do not qualify as a single contemporaneous population. However, the genetic results from five of the individuals fall within the spectrum of genetic diversity observed in pre-Columbian and modern Native Central American populations.
doi:10.1371/journal.pone.0127141
PMCID: PMC4464891  PMID: 26061688
10.  The genomes of two key bumblebee species with primitive eusocial organization 
Sadd, Ben M | Barribeau, Seth M | Bloch, Guy | de Graaf, Dirk C | Dearden, Peter | Elsik, Christine G | Gadau, Jürgen | Grimmelikhuijzen, Cornelis JP | Hasselmann, Martin | Lozier, Jeffrey D | Robertson, Hugh M | Smagghe, Guy | Stolle, Eckart | Van Vaerenbergh, Matthias | Waterhouse, Robert M | Bornberg-Bauer, Erich | Klasberg, Steffen | Bennett, Anna K | Câmara, Francisco | Guigó, Roderic | Hoff, Katharina | Mariotti, Marco | Munoz-Torres, Monica | Murphy, Terence | Santesmasses, Didac | Amdam, Gro V | Beckers, Matthew | Beye, Martin | Biewer, Matthias | Bitondi, Márcia MG | Blaxter, Mark L | Bourke, Andrew FG | Brown, Mark JF | Buechel, Severine D | Cameron, Rossanah | Cappelle, Kaat | Carolan, James C | Christiaens, Olivier | Ciborowski, Kate L | Clarke, David F | Colgan, Thomas J | Collins, David H | Cridge, Andrew G | Dalmay, Tamas | Dreier, Stephanie | du Plessis, Louis | Duncan, Elizabeth | Erler, Silvio | Evans, Jay | Falcon, Tiago | Flores, Kevin | Freitas, Flávia CP | Fuchikawa, Taro | Gempe, Tanja | Hartfelder, Klaus | Hauser, Frank | Helbing, Sophie | Humann, Fernanda C | Irvine, Frano | Jermiin, Lars S | Johnson, Claire E | Johnson, Reed M | Jones, Andrew K | Kadowaki, Tatsuhiko | Kidner, Jonathan H | Koch, Vasco | Köhler, Arian | Kraus, F Bernhard | Lattorff, H Michael G | Leask, Megan | Lockett, Gabrielle A | Mallon, Eamonn B | Antonio, David S Marco | Marxer, Monika | Meeus, Ivan | Moritz, Robin FA | Nair, Ajay | Näpflin, Kathrin | Nissen, Inga | Niu, Jinzhi | Nunes, Francis MF | Oakeshott, John G | Osborne, Amy | Otte, Marianne | Pinheiro, Daniel G | Rossié, Nina | Rueppell, Olav | Santos, Carolina G | Schmid-Hempel, Regula | Schmitt, Björn D | Schulte, Christina | Simões, Zilá LP | Soares, Michelle PM | Swevers, Luc | Winnebeck, Eva C | Wolschin, Florian | Yu, Na | Zdobnov, Evgeny M | Aqrawi, Peshtewani K | Blankenburg, Kerstin P | Coyle, Marcus | Francisco, Liezl | Hernandez, Alvaro G | Holder, Michael | Hudson, Matthew E | Jackson, LaRonda | Jayaseelan, Joy | Joshi, Vandita | Kovar, Christie | Lee, Sandra L | Mata, Robert | Mathew, Tittu | Newsham, Irene F | Ngo, Robin | Okwuonu, Geoffrey | Pham, Christopher | Pu, Ling-Ling | Saada, Nehad | Santibanez, Jireh | Simmons, DeNard | Thornton, Rebecca | Venkat, Aarti | Walden, Kimberly KO | Wu, Yuan-Qing | Debyser, Griet | Devreese, Bart | Asher, Claire | Blommaert, Julie | Chipman, Ariel D | Chittka, Lars | Fouks, Bertrand | Liu, Jisheng | O’Neill, Meaghan P | Sumner, Seirian | Puiu, Daniela | Qu, Jiaxin | Salzberg, Steven L | Scherer, Steven E | Muzny, Donna M | Richards, Stephen | Robinson, Gene E | Gibbs, Richard A | Schmid-Hempel, Paul | Worley, Kim C
Genome Biology  2015;16(1):76.
Background
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.
Results
We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.
Conclusions
These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0623-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-015-0623-3
PMCID: PMC4414376  PMID: 25908251
11.  Parallel Histories of Horizontal Gene Transfer Facilitated Extreme Reduction of Endosymbiont Genomes in Sap-Feeding Insects 
Molecular Biology and Evolution  2014;31(4):857-871.
Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host’s role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids.
doi:10.1093/molbev/msu004
PMCID: PMC3969561  PMID: 24398322
amino acid biosynthesis; endosymbionts; lateral gene transfer; Pachypsylla venusta; psyllids
12.  AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome 
Insect molecular biology  2010;19(0 2):5-12.
AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com.
doi:10.1111/j.1365-2583.2009.00930.x
PMCID: PMC4372297  PMID: 20482635
13.  A full-length cDNA resource for the pea aphid, Acyrthosiphon pisum 
Insect molecular biology  2010;19(0 2):23-31.
Large collections of full-length cDNAs are important resources for genome annotation and functional genomics. We report the creation of a collection of 50,599 full-length cDNA clones from the pea aphid, Acyrthosiphon pisum. Sequencing from 5’ and 3’ ends of the clones generated 97,828 high-quality expressed sequence tags (ESTs), representing approximately 9,000 genes. These sequences were imported to AphidBase and are shown to play crucial roles in both automatic gene prediction and manual annotation. Our detailed analyses demonstrated that the full-length cDNAs can further improve gene models and can even identify novel genes that are not included in the current version of the official gene set. This full-length cDNA collection can be utilized for a wide variety of functional studies, serving as a community resource for the study of the functional genomics of the pea aphid.
doi:10.1111/j.1365-2583.2009.00946.x
PMCID: PMC4370113  PMID: 20482637
full-length cDNA; aphid; functional genomics; EST analysis
14.  The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 
Chipman, Ariel D. | Ferrier, David E. K. | Brena, Carlo | Qu, Jiaxin | Hughes, Daniel S. T. | Schröder, Reinhard | Torres-Oliva, Montserrat | Znassi, Nadia | Jiang, Huaiyang | Almeida, Francisca C. | Alonso, Claudio R. | Apostolou, Zivkos | Aqrawi, Peshtewani | Arthur, Wallace | Barna, Jennifer C. J. | Blankenburg, Kerstin P. | Brites, Daniela | Capella-Gutiérrez, Salvador | Coyle, Marcus | Dearden, Peter K. | Du Pasquier, Louis | Duncan, Elizabeth J. | Ebert, Dieter | Eibner, Cornelius | Erikson, Galina | Evans, Peter D. | Extavour, Cassandra G. | Francisco, Liezl | Gabaldón, Toni | Gillis, William J. | Goodwin-Horn, Elizabeth A. | Green, Jack E. | Griffiths-Jones, Sam | Grimmelikhuijzen, Cornelis J. P. | Gubbala, Sai | Guigó, Roderic | Han, Yi | Hauser, Frank | Havlak, Paul | Hayden, Luke | Helbing, Sophie | Holder, Michael | Hui, Jerome H. L. | Hunn, Julia P. | Hunnekuhl, Vera S. | Jackson, LaRonda | Javaid, Mehwish | Jhangiani, Shalini N. | Jiggins, Francis M. | Jones, Tamsin E. | Kaiser, Tobias S. | Kalra, Divya | Kenny, Nathan J. | Korchina, Viktoriya | Kovar, Christie L. | Kraus, F. Bernhard | Lapraz, François | Lee, Sandra L. | Lv, Jie | Mandapat, Christigale | Manning, Gerard | Mariotti, Marco | Mata, Robert | Mathew, Tittu | Neumann, Tobias | Newsham, Irene | Ngo, Dinh N. | Ninova, Maria | Okwuonu, Geoffrey | Ongeri, Fiona | Palmer, William J. | Patil, Shobha | Patraquim, Pedro | Pham, Christopher | Pu, Ling-Ling | Putman, Nicholas H. | Rabouille, Catherine | Ramos, Olivia Mendivil | Rhodes, Adelaide C. | Robertson, Helen E. | Robertson, Hugh M. | Ronshaugen, Matthew | Rozas, Julio | Saada, Nehad | Sánchez-Gracia, Alejandro | Scherer, Steven E. | Schurko, Andrew M. | Siggens, Kenneth W. | Simmons, DeNard | Stief, Anna | Stolle, Eckart | Telford, Maximilian J. | Tessmar-Raible, Kristin | Thornton, Rebecca | van der Zee, Maurijn | von Haeseler, Arndt | Williams, James M. | Willis, Judith H. | Wu, Yuanqing | Zou, Xiaoyan | Lawson, Daniel | Muzny, Donna M. | Worley, Kim C. | Gibbs, Richard A. | Akam, Michael | Richards, Stephen
PLoS Biology  2014;12(11):e1002005.
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Author Summary
Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
doi:10.1371/journal.pbio.1002005
PMCID: PMC4244043  PMID: 25423365
15.  Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of Drosophila pseudoobscura 
G3: Genes|Genomes|Genetics  2014;4(12):2433-2449.
There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standard models. Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.
doi:10.1534/g3.114.014860
PMCID: PMC4267939  PMID: 25326424
codon bias; stabilizing selection; chromosomal inversions; recombination
16.  Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans 
Nature communications  2013;4:1764.
Haplogroup (hg) H dominates present-day Western European mitochondrial (mt) DNA variability (>40%), yet was less common (~19%) amongst Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete hg H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of hg H were largely established by the Mid-Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated hg H genomes allow us to reconstruct the recent evolutionary history of hg H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
doi:10.1038/ncomms2656
PMCID: PMC3978205  PMID: 23612305
17.  Microvascular Contributions to Insulin Resistance 
Diabetes  2013;62(2):343-345.
doi:10.2337/db12-1193
PMCID: PMC3554389  PMID: 23349541
18.  Transcription, Translation, and Function of Lubricin, a Boundary Lubricant, at the Ocular Surface 
JAMA ophthalmology  2013;131(6):10.1001/jamaophthalmol.2013.2385.
Importance
Lubricin may be an important barrier to the development of corneal and conjunctival epitheliopathies that may occur in dry eye disease and contact lens wear.
Objective
To test the hypotheses that lubricin (ie, proteoglycan 4 [PRG4]), a boundary lubricant, is produced by ocular surface epithelia and acts to protect the cornea and conjunctiva against significant shear forces generated during an eyelid blink and that lubricin deficiency increases shear stress on the ocular surface and promotes corneal damage.
Design, Setting, and Participants
Human, porcine, and mouse tissues and cells were processed for molecular biological, immunohistochemical, and tribological studies, and wild-type and PRG4 knockout mice were evaluated for corneal damage.
Results
Our findings demonstrate that lubricin is transcribed and translated by corneal and conjunctival epithelial cells. Lubricin messenger RNA is also present in lacrimal and meibomian glands, as well as in a number of other tissues. Absence of lubricin in PRG4 knockout mice is associated with a significant increase in corneal fluorescein staining. Our studies also show that lubricin functions as an effective friction-lowering boundary lubricant at the human cornea-eyelid interface. This effect is specific and cannot be duplicated by the use of hyaluronate or bovine serum albumin solutions.
Conclusions and Relevance
Our results show that lubricin is transcribed, translated, and expressed by ocular surface epithelia. Moreover, our findings demonstrate that lubricin presence significantly reduces friction between the cornea and conjunctiva and that lubricin deficiency may play a role in promoting corneal damage.
doi:10.1001/jamaophthalmol.2013.2385
PMCID: PMC3887468  PMID: 23599181
19.  Influence of Aromatase Absence on the Gene Expression and Histology of the Mouse Meibomian Gland 
Purpose.
We hypothesize that aromatase, an enzyme that controls estrogen biosynthesis, plays a major role in the sex-related differences of the meibomian gland. To begin to test this hypothesis, we examined the influence of aromatase absence, which completely eliminates estrogen production, on glandular gene expression and histology in male and female mice.
Methods.
Meibomian glands were obtained from adult, age-matched wild-type (WT) and aromatase knockout (ArKO) mice. Tissues were processed for histology or the isolation of total RNA, which was analyzed for differentially expressed mRNAs by using microarrays.
Results.
Our results show that aromatase significantly influences the expression of more than a thousand genes in the meibomian gland. The nature of this effect is primarily sex-dependent. In addition, the influence of aromatase on sex-related differences in gene expression is predominantly genotype-specific. However, many of the sex-related variations in biological process, molecular function, and cellular component ontologies, as well as in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, are remarkably similar between WT and ArKO mice. The loss of aromatase activity has no obvious effect on the histology of meibomian glands in male or female mice.
Conclusions.
Our findings demonstrate that aromatase has a significant impact on gene expression in the meibomian gland. The nature of this influence is sex-dependent and genotype-specific; however, many of the sex-related variations in gene ontologies and KEGG pathways are similar between WT and ArKO mice. Consequently, it appears that aromatase, and by extension estrogen, do not play a major role in the sex-related differences of the mouse meibomian gland.
Aromatase exerts a significant sex- and genotype-specific effect on meibomian gland gene expression. However, this enzyme, and by extension estrogen, do not play a major role in the sex-related differences in this tissue.
doi:10.1167/iovs.12-10992
PMCID: PMC3565996  PMID: 23233261
20.  Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species 
Bradnam, Keith R | Fass, Joseph N | Alexandrov, Anton | Baranay, Paul | Bechner, Michael | Birol, Inanç | Boisvert, Sébastien | Chapman, Jarrod A | Chapuis, Guillaume | Chikhi, Rayan | Chitsaz, Hamidreza | Chou, Wen-Chi | Corbeil, Jacques | Del Fabbro, Cristian | Docking, T Roderick | Durbin, Richard | Earl, Dent | Emrich, Scott | Fedotov, Pavel | Fonseca, Nuno A | Ganapathy, Ganeshkumar | Gibbs, Richard A | Gnerre, Sante | Godzaridis, Élénie | Goldstein, Steve | Haimel, Matthias | Hall, Giles | Haussler, David | Hiatt, Joseph B | Ho, Isaac Y | Howard, Jason | Hunt, Martin | Jackman, Shaun D | Jaffe, David B | Jarvis, Erich D | Jiang, Huaiyang | Kazakov, Sergey | Kersey, Paul J | Kitzman, Jacob O | Knight, James R | Koren, Sergey | Lam, Tak-Wah | Lavenier, Dominique | Laviolette, François | Li, Yingrui | Li, Zhenyu | Liu, Binghang | Liu, Yue | Luo, Ruibang | MacCallum, Iain | MacManes, Matthew D | Maillet, Nicolas | Melnikov, Sergey | Naquin, Delphine | Ning, Zemin | Otto, Thomas D | Paten, Benedict | Paulo, Octávio S | Phillippy, Adam M | Pina-Martins, Francisco | Place, Michael | Przybylski, Dariusz | Qin, Xiang | Qu, Carson | Ribeiro, Filipe J | Richards, Stephen | Rokhsar, Daniel S | Ruby, J Graham | Scalabrin, Simone | Schatz, Michael C | Schwartz, David C | Sergushichev, Alexey | Sharpe, Ted | Shaw, Timothy I | Shendure, Jay | Shi, Yujian | Simpson, Jared T | Song, Henry | Tsarev, Fedor | Vezzi, Francesco | Vicedomini, Riccardo | Vieira, Bruno M | Wang, Jun | Worley, Kim C | Yin, Shuangye | Yiu, Siu-Ming | Yuan, Jianying | Zhang, Guojie | Zhang, Hao | Zhou, Shiguo | Korf, Ian F
GigaScience  2013;2:10.
Background
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.
Results
In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.
Conclusions
Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
doi:10.1186/2047-217X-2-10
PMCID: PMC3844414  PMID: 23870653
Genome assembly; N50; Scaffolds; Assessment; Heterozygosity; COMPASS
21.  The Drosophila melanogaster Genetic Reference Panel 
Nature  2012;482(7384):173-178.
A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.
doi:10.1038/nature10811
PMCID: PMC3683990  PMID: 22318601
22.  Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor 
BMC Genomics  2013;14:187.
Background
MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits. The gall midge Mayetiola destructor, commonly known as the Hessian fly, is a destructive pest of wheat and model organism for studying gall midge biology and insect – host plant interactions.
Results
In this study, we systematically analyzed miRNAs from the Hessian fly. Deep-sequencing a Hessian fly larval transcriptome led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects, and 184 novel miRNAs that have not been reported from other species. A genome-wide search through a draft Hessian fly genome sequence identified a total of 611 putative miRNA-encoding genes based on sequence similarity and the existence of a stem-loop structure for miRNA precursors. Analysis of the 611 putative genes revealed a striking feature: the dramatic expansion of several miRNA gene families. The largest family contained 91 genes that encoded 20 different miRNAs. Microarray analyses revealed the expression of miRNA genes was strictly regulated during Hessian fly larval development and abundance of many miRNA genes were affected by host genotypes.
Conclusion
The identification of a large number of miRNAs for the first time from a gall midge provides a foundation for further studies of miRNA functions in gall midge biology and behavior. The dramatic expansion of identical or similar miRNAs provides a unique system to study functional relations among miRNA iso-genes as well as changes in sequence specificity due to small changes in miRNAs and in their mRNA targets. These results may also facilitate the identification of miRNA genes for potential pest control through transgenic approaches.
doi:10.1186/1471-2164-14-187
PMCID: PMC3608969  PMID: 23496979
23.  Fine-Scale Mapping of the Nasonia Genome to Chromosomes Using a High-Density Genotyping Microarray 
G3: Genes|Genomes|Genetics  2013;3(2):205-215.
Nasonia, a genus of four closely related parasitoid insect species, is a model system for genetic research. Their haplodiploid genetics (haploid males and diploid females) and interfertile species are advantageous for the genetic analysis of complex traits and the genetic basis of species differences. A fine-scale genomic map is an important tool for advancing genetic studies in this system. We developed and used a hybrid genotyping microarray to generate a high-resolution genetic map that covers 79% of the sequenced genome of Nasonia vitripennis. The microarray is based on differential hybridization of species-specific oligos between N. vitripennis and Nasonia giraulti at more than 20,000 markers spanning the Nasonia genome. The map places 729 scaffolds onto the five linkage groups of Nasonia, including locating many smaller scaffolds that would be difficult to map by other means. The microarray was used to characterize 26 segmental introgression lines containing chromosomal regions from one species in the genetic background of another. These segmental introgression lines have been used for rapid screening and mapping of quantitative trait loci involved in species differences. Finally, the microarray is extended to bulk-segregant analysis and genotyping of other Nasonia species combinations. These resources should further expand the usefulness of Nasonia for studies of the genetic basis and architecture of complex traits and speciation.
doi:10.1534/g3.112.004739
PMCID: PMC3564981  PMID: 23390597
24.  Butterfly genome reveals promiscuous exchange of mimicry adaptations among species 
Dasmahapatra, Kanchon K | Walters, James R. | Briscoe, Adriana D. | Davey, John W. | Whibley, Annabel | Nadeau, Nicola J. | Zimin, Aleksey V. | Hughes, Daniel S. T. | Ferguson, Laura C. | Martin, Simon H. | Salazar, Camilo | Lewis, James J. | Adler, Sebastian | Ahn, Seung-Joon | Baker, Dean A. | Baxter, Simon W. | Chamberlain, Nicola L. | Chauhan, Ritika | Counterman, Brian A. | Dalmay, Tamas | Gilbert, Lawrence E. | Gordon, Karl | Heckel, David G. | Hines, Heather M. | Hoff, Katharina J. | Holland, Peter W.H. | Jacquin-Joly, Emmanuelle | Jiggins, Francis M. | Jones, Robert T. | Kapan, Durrell D. | Kersey, Paul | Lamas, Gerardo | Lawson, Daniel | Mapleson, Daniel | Maroja, Luana S. | Martin, Arnaud | Moxon, Simon | Palmer, William J. | Papa, Riccardo | Papanicolaou, Alexie | Pauchet, Yannick | Ray, David A. | Rosser, Neil | Salzberg, Steven L. | Supple, Megan A. | Surridge, Alison | Tenger-Trolander, Ayse | Vogel, Heiko | Wilkinson, Paul A. | Wilson, Derek | Yorke, James A. | Yuan, Furong | Balmuth, Alexi L. | Eland, Cathlene | Gharbi, Karim | Thomson, Marian | Gibbs, Richard A. | Han, Yi | Jayaseelan, Joy C. | Kovar, Christie | Mathew, Tittu | Muzny, Donna M. | Ongeri, Fiona | Pu, Ling-Ling | Qu, Jiaxin | Thornton, Rebecca L. | Worley, Kim C. | Wu, Yuan-Qing | Linares, Mauricio | Blaxter, Mark L. | Constant, Richard H. ffrench | Joron, Mathieu | Kronforst, Marcus R. | Mullen, Sean P. | Reed, Robert D. | Scherer, Steven E. | Richards, Stephen | Mallet, James | McMillan, W. Owen | Jiggins, Chris D.
Nature  2012;487(7405):94-98.
The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation.
doi:10.1038/nature11041
PMCID: PMC3398145  PMID: 22722851
25.  Molecular phylogeny of microhylid frogs (Anura: Microhylidae) with emphasis on relationships among New World genera 
Background
Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis).
Results
One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved.
Conclusion
Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.
doi:10.1186/1471-2148-12-241
PMCID: PMC3561245  PMID: 23228209
Microhylidae; Phylogeny; Systematics; Subfamilies; New World genera

Results 1-25 (46)