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    Geographic and Ecological Dimensions of Host Plant-Associated Genetic Differentiation and Speciation in theᅠRhagoletis cingulataᅠ(Diptera: Tephritidae) Sibling Species Group
    (MDPI, 2019) Doellman, Meredith M.; Schuler, Hannes; Jean Saint, Gilbert; Hood, Glen R.; Egan, Scott P.; Powell, Thomas H.Q.; Glover, Mary M.; Bruzzese, Daniel J.; Smith, James J.; Yee, Wee L.; Goughnour, Robert B.; Rull, Juan; Aluja, Martin; Feder, Jeffrey L.
    Ascertaining the causes of adaptive radiation is central to understanding how new species arise and come to vary with their resources. The ecological theory posits adaptive radiation via divergent natural selection associated with novel resource use; an alternative suggests character displacement following speciation in allopatry and then secondary contact of reproductively isolated but ecologically similar species. Discriminating between hypotheses, therefore, requires the establishment of a key role for ecological diversification in initiating speciation versus a secondary role in facilitating co-existence. Here, we characterize patterns of genetic variation and postzygotic reproductive isolation for tephritid fruit flies in the Rhagoletis cingulata sibling species group to assess the significance of ecology, geography, and non-adaptive processes for their divergence. Our results support the ecological theory: no evidence for intrinsic postzygotic reproductive isolation was found between two populations of allopatric species, while nuclear-encoded microsatellites implied strong ecologically based reproductive isolation among sympatric species infesting different host plants. Analysis of mitochondrial DNA suggested, however, that cytoplasmic-related reproductive isolation may also exist between two geographically isolated populations within R cingulata. Thus, ecology associated with sympatric host shifts and cytoplasmic effects possibly associated with an endosymbiont may be the key initial drivers of the radiation of the R. cingulata group.
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    Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis
    (BioMed Central, 2016) Long, Kyle A.; Nossa, Carlos W.; Sewell, Mary A.; Putnam, Nicholas H.; Ryan, Joseph F.
    BACKGROUND: There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and sand dollars), and Holothuroidea (sea cucumbers). These animals are known for their pentaradial symmetry as adults, unique water vascular system, mutable collagenous tissues, and endoskeletons of high magnesium calcite. To our knowledge, the only echinoderm species with a genome sequence available to date is Strongylocentrotus pupuratus (Echinoidea). The availability of additional echinoderm genome sequences is crucial for understanding the biology of these animals. FINDINGS: Here we present assembled draft genomes of the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis from Illumina sequence data with coverages of 12.5x, 22.5x, and 21.4x, respectively. CONCLUSIONS: These data provide a resource for mining gene superfamilies, identifying non-coding RNAs, confirming gene losses, and designing experimental constructs. They will be important comparative resources for future genomic studies in echinoderms.
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    Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals
    (BioMed Central, 2014) Maxwell, Evan K.; Schnitzler, Christine E.; Havlak, Paul; Putnam, Nicholas H.; Nguyen, Anh-Dao; Moreland, R. Travis
    Background: The recent expansion of whole-genome sequence data available from diverse animal lineages provides an opportunity to investigate the evolutionary origins of specific classes of human disease genes. Previous studies have observed that human disease genes are of particularly ancient origin. While this suggests that many animal species have the potential to serve as feasible models for research on genes responsible for human disease, it is unclear whether this pattern has meaningful implications and whether it prevails for every class of human disease. Results: We used a comparative genomics approach encompassing a broad phylogenetic range of animals with sequenced genomes to determine the evolutionary patterns exhibited by human genes associated with different classes of disease. Our results support previous claims that most human disease genes are of ancient origin but, more importantly, we also demonstrate that several specific disease classes have a significantly large proportion of genes that emerged relatively recently within the metazoans and/or vertebrates. An independent assessment of the synonymous to non-synonymous substitution rates of human disease genes found in mammals reveals that disease classes that arose more recently also display unexpected rates of purifying selection between their mammalian and human counterparts. Conclusions: Our results reveal the heterogeneity underlying the evolutionary origins of (and selective pressures on) different classes of human disease genes. For example, some disease gene classes appear to be of uncommonly recent (i.e., vertebrate-specific) origin and, as a whole, have been evolving at a faster rate within mammals than the majority of disease classes having more ancient origins. The novel patterns that we have identified may provide new insight into cases where studies using traditional animal models were unable to produce results that translated to humans. Conversely, we note that the larger set of disease classes do have ancient origins, suggesting that many non-traditional animal models have the potential to be useful for studying many human disease genes. Taken together, these findings emphasize why model organism selection should be done on a disease-by-disease basis, with evolutionary profiles in mind.
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    Individual and combined effects of two types of phenological shifts on predator–prey interactions
    (Ecological Society of America, 2016) Rasmussen, Nick L.; Rudolf, Volker H.W.
    Timing of phenological events varies among years with natural variation in environmental conditions and is also shifting in response to climate change. These phenological shifts likely have many effects on species interactions. Most research on the ecological consequences of phenological shifts has focused on variation in simple metrics such as phenological firsts. However, for a population, a phenological event exhibits a temporal distribution with many attributes that can vary (e.g., mean, variance, skewness), each of which likely has distinct effects on interactions. In this study, we manipulated two attributes of the phenological distribution of a prey species to determine their individual and combined effects on predatorヨprey interactions. Specifically, we studied how shifts in the mean and variation around the mean (i.e., synchrony) of hatching by tadpoles (Hyla cinerea) affected interactions with predatory dragonfly naiads (Tramea carolina). At the end of larval development, we quantified survival and growth of predator and prey. We found that both types of shifts altered demographic rates of the prey; that the effects of synchrony shifts, though rarely studied, were at least as strong as those due to mean shifts; and that the combined effects of shifts in synchrony and mean were additive rather than synergistic. By dissecting the roles of two types of shifts, this study represents a significant step toward a comprehensive understanding of the complex effects of phenological shifts on species interactions. Embracing this complexity is critical for predicting how climate change will alter community dynamics.
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    Timing and Scope of Genomic Expansion within Annelida: Evidence from Homeoboxes in the Genome of the Earthworm Eisenia fetida
    (Oxford University Press, 2015) Zwarycz, Allison S.; Nossa, Carlos W.; Putnam, Nicholas H.; Ryan, Joseph F.
    Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid lineage and better understand the diversity within the group. We sequenced and assembled the genome of the common earthworm, Eisenia fetida. As a first pass at understanding the diversity within the group, we classified 363 earthworm homeoboxes and compared them with those of the leech Helobdella robusta and the polychaete Capitella teleta. We inferred many gene expansions occurring in the lineage connecting the most recent common ancestor (MRCA) of Capitella and Eisenia to the Eisenia/Helobdella MRCA. Likewise, the lineage leading from the Eisenia/Helobdella MRCA to the leech H. robusta has experienced substantial gains and losses. However, the lineage leading from Eisenia/Helobdella MRCA to E. fetida is characterized by extraordinary levels of homeobox gain. The evolutionary dynamics observed in the homeoboxes of these lineages are very likely to be generalizable to all genes. These genome expansions and losses have likely contributed to the remarkable biology exhibited in this group. These results provide a new perspective from which to understand the diversity within these lineages, show the utility of sub-draft genome assemblies for understanding genomic evolution, and provide a critical resource from which the biology of these animals can be studied.
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    Conspecific Plasticity and Invasion: Invasive Populations of Chinese Tallow (Triadica sebifera)ᅠHave Performance Advantage over Native Populations Only in Low Soil Salinity
    (Public Library of Science, 2013) Chen, Leiyi; Tiu, Candice J.; Peng, Shaolin; Siemann, Evan
    Global climate change may increase biological invasions in part because invasive species may have greater phenotypic plasticity than native species. This may be especially important for abiotic stresses such as salt inundation related to increased hurricane activity or sea level rise. If invasive species indeed have greater plasticity, this may reflect genetic differences between populations in the native and introduced ranges. Here, we examined plasticity of functional and fitness-related traits of Chinese tallow (Triadica sebifera) populations from the introduced and native ranges that were grown along a gradient of soil salinity (control: 0 ppt; Low: 5 ppt; Medium: 10 ppt; High: 15 ppt) in a greenhouse. We used both norm reaction and plasticity index (PIv) to estimate the conspecific phenotypic plasticity variation between invasive and native populations. Overall, invasive populations had higher phenotypic plasticity of height growth rate (HGR), aboveground biomass, stem biomass and specific leaf area (SLA). The plasticity Index (PIv) of height growth rate (HGR) and SLA each were higher for plants from invasive populations. Absolute performance was always comparable or greater for plants from invasive populations versus native populations with the greatest differences at low stress levels. Our results were consistent with the ?Master-of-some? pattern for invasive plants in which the fitness of introduced populations was greater in more benign conditions. This suggests that the greater conspecific phenotypic plasticity of invasive populations compared to native populations may increase invasion success in benign conditions but would not provide a potential interspecific competitive advantage in higher salinity soils that may occur with global climate change in coastal areas.
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    Daptomycin Resistance in Enterococci Is Associated with Distinct Alterations of Cell Membrane Phospholipid Content
    (Public Library of Science, 2012) Mishra, Nagendra N.; Bayer, Arnold S.; Tran, Truc T.; Shamoo, Yousif; Mileykovskaya, Eugenia; Dowhan, William; Guan, Ziqiang; Arias, Cesar A.
    Background: The lipopeptide antibiotic, daptomycin (DAP) interacts with the bacterial cell membrane (CM). Development of DAP resistance during therapy in a clinical strain of Enterococcus faecalis was associated with mutations in genes encoding enzymes involved in cell envelope homeostasis and phospholipid metabolism. Here we characterized changes in CM phospholipid profiles associated with development of DAP resistance in clinical enterococcal strains. Methodology: Using two clinical strain-pairs of DAP-susceptible and DAP-resistant E. faecalis (S613 vs. R712) and E. faecium (S447 vs. R446) recovered before and after DAP therapy, we compared four distinct CM profiles: phospholipid content, fatty acid composition, membrane fluidity and capacity to be permeabilized and/or depolarized by DAP. Additionally, we characterized the cell envelope of the E. faecium strain-pair by transmission electron microscopy and determined the relative cell surface charge of both strain-pairs. Principal Findings: Both E. faecalis and E. faecium mainly contained four major CM PLs: phosphatidylglycerol (PG), cardiolipin, lysyl-phosphatidylglycerol (L-PG) and glycerolphospho-diglycodiacylglycerol (GP-DGDAG). In addition, E. faecalis CMs (but not E. faecium) also contained: i) phosphatidic acid; and ii) two other unknown species of amino-containing PLs. Development of DAP resistance in both enterococcal species was associated with a significant decrease in CM fluidity and PG content, with a concomitant increase in GP-DGDAG. The strain-pairs did not differ in their outer CM translocation (flipping) of amino-containing PLs. Fatty acid content did not change in the E. faecalis strain-pair, whereas a significant decrease in unsaturated fatty acids was observed in the DAP-resistant E. faecium isolate R446 (vs S447). Resistance to DAP in E. faecium was associated with distinct structural alterations of the cell envelope and cell wall thickening, as well as a decreased ability of DAP to depolarize and permeabilize the CM. Conclusion: Distinct alterations in PL content and fatty acid composition are associated with development of enterococcal DAP resistance.
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    Ontogenetic functional diversity: Size structure of a keystone predator drives functioning of a complex ecosystem
    (Wiley, 2013) Rudolf, Volker H.W.; Rasmussen, Nick L.
    A central challenge in community ecology is to understand the connection between biodiversity and the functioning of ecosystems. While traditional approaches have largely focused on species-level diversity, increasing evidence indicates that there exists substantial ecological diversity among individuals within species. By far, the largest source of this intraspecific diversity stems from variation among individuals in ontogenetic stage and size. Although such ontogenetic shifts are ubiquitous in natural communities, whether and how they scale up to influence the structure and functioning of complex ecosystems is largely unknown. Here we take an experimental approach to examine the consequences of ontogenetic niche shifts for the structure of communities and ecosystem processes. In particular we experimentally manipulated the stage structure in a keystone predator, larvae of the dragonfly Anax junius, in complex experimental pond communities to test whether changes in the population stage or size structure of a keystone species scale up to alter community structure and ecosystem processes, and how functional differences scale with relative differences in size among stages. We found that the functional role of A. junius was stage-specific. Altering what stages were present in a pond led to concurrent changes in community structure, primary producer biomass (periphyton and phytoplankton), and ultimately altered ecosystem processes (respiration and net primary productivity), indicating a strong, but stage-specific, trophic cascade. Interestingly, the stage-specific effects did not simply scale with size or biomass of the predator, but instead indicated clear ontogenetic niche shifts in ecological interactions. Thus, functional differences among stages within a keystone species scaled up to alter the functioning of entire ecosystems. Therefore, our results indicate that the classical approach of assuming an average functional role of a species can be misleading because functional roles are dynamic and will change with shifts in the stage structure of the species. In general this emphasizes the importance of accounting for functional diversity below the species level to predict how natural and anthropogenic changes alter the functioning of natural ecosystems.
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    Hemichordate genomes and deuterostome origins
    (Macmillan Publishers Limited, 2015) Simakov, Oleg; Kawashima, Takeshi; Marlétaz, Ferdinand; Jenkins, Jerry; Koyanagi, Ryo; Mitros, Therese; Hisata, Kanako; Bredeson, Jessen; Shoguchi, Eiichi; Gyoja, Fuki; Yue, Jia-Xing; Chen, Yi-Chih; Freeman, Robert M.; Sasaki, Akane; Hikosaka-Katayama, Tomoe; Sato, Atsuko; Fujie, Manabu; Baughman, Kenneth W.; Levine, Judith; Gonzalez, Paul; Cameron, Christopher; Fritzenwanker, Jens H.; Pani, Ariel M.; Goto, Hiroki; Kanda, Miyuki; Arakaki, Nana; Yamasaki, Shinichi; Qu, Jiaxin; Cree, Andrew; Ding, Yan; Dinh, Huyen H.; Dugan, Shannon; Holder, Michael; Jhangiani, Shalini N.; Kovar, Christie L.; Lee, Sandra L.; Lewis, Lora R.; Morton, Donna; Nazareth, Lynne V.; Okwuonu, Geoffrey; Santibanez, Jireh; Chen, Rui; Richards, Stephen; Muzny, Donna M.; Gillis, Andrew; Peshkin, Leonid; Wu, Michael; Humphreys, Tom; Su, Yi-Hsien; Putnam, Nicholas H.; Schmutz, Jeremy; Fujiyama, Asao; Yu, Jr-Kai; Tagawa, Kunifumi; Worley, Kim C.; Gibbs, Richard A.; Kirschner, Marc W.; Lowe, Christopher J.; Satoh, Noriyuki; Rokhsar, Daniel S.; Gerhart, John
    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 sequen
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    Phenological synchronization drives demographic rates of populations
    (Ecological Society of America, 2015) Rasmussen, Nick L.; Rudolf, Volker H.W.
    Phenology is increasingly recognized as an important factor structuring communities because it determines when and at what life stage organisms interact. Previous work indicates that changes in first or mean timing of a phenological event can affect populations and communities, but little is known about the consequences of changes in the distribution (e.g., synchrony) of a phenological event. We conducted an experiment using an anuran study system to determine how synchrony of reproduction and egg hatching affects offspring performance, whether the effects are density dependent, and how hatching synchrony influences the synchrony of a subsequent phenological event (metamorphosis). Changes in hatching synchrony altered survival, development rates, and body size at metamorphosis, which can affect post-metamorphosis performance. The degree of synchrony at hatching also affected the degree of synchrony at metamorphosis, indicating that timing of one stage can carry over to affect that of later ones. Importantly, these effects were all density dependent, likely because decreasing hatching synchrony switched intraspecific interactions from scramble to contest competition. This study demonstrates that phenological synchrony has important consequences for ecological interactions and population dynamics, emphasizing the need to develop a comprehensive understanding of how shifts in phenological distributions affect communities.
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    The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution
    (American Association for the Advancement of Science, 2013) Ryan, Joseph F.; Pang, Kevin; Schnitzler, Christine E.; Nguyen, Anh-Dao; Moreland, R. Travis; Simmons, David K.; Koch, Bernard J.; Francis, Warren R.; Havlak, Paul; NISC Comparative Sequencing Program; Smith, Stephen A.; Putnam, Nicholas H.; Haddock, Steven H.D.; Dunn, Casey W.; Wolfsberg, Tyra G.; Mullikin, James C.; Martindale, Mark Q.; Baxevanis, Andreas D.
    An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.
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    Intraspecific priority effects and disease interact to alter population growth
    (Ecological Society of America, 2014) Dibble, Christopher J.; Hall, Spencer R.; Rudolf, Volker H.W.
    Intraspecific variation may shape colonization of new habitat patches through a variety of mechanisms. In particular, trait variation among colonizing individuals can produce intraspecific priority effects (IPEs), where early arrivers of a single species affect the establishment or growth of later conspecifics. While we have some evidence for the importance of IPEs, we lack a general understanding of factors affecting their presence or magnitude across a landscape. Specifically, IPEs should depend strongly on success of colonizers in the new habitat patch. This success hinges on interactions between colonizer traits and local selective pressures, but such context dependence remains unexplored experimentally. We addressed this gap by looking for the dynamical signature of IPEs in environments with and without a selective (parasite) pressure. We tested whether IPEs affected the population dynamics of a zooplankton host species (Daphnia dentifera) collected from two populations showing a tradeoff between growth rate and resistance to a fungal parasite (Metschnikowia bicuspidata). Differences in arrival order significantly altered population growth during a period of rapid resource depletion, driving large (up to 65%) differences in population abundance. Furthermore, the presence of IPEs was context dependent, as parasites reduced the impact of early arrivers on later arrivers. Such context-dependent IPEs, mediated by colonizer traits, colonization order, and selective pressures, may play an unanticipated role in the ecological and evolutionary dynamics of natural metapopulations. This mechanism highlights the overall importance of intraspecific variation for understanding ecological patterns.
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    Balancing anti-herbivore benefits and anti-pollinator costs of defensive mutualists
    (Ecological Society of America, 2014) Ohm, Johanna R.; Miller, Tom E.X.
    Quantifying costs and benefits of ostensibly mutualistic interactions is an important step toward understanding their evolutionary trajectories. In food-for-protection interactions between ants and extrafloral nectar (EFN)-bearing plants, tending by aggressive ants may deter herbivores, but it may also deter pollinators. The fitness costs of pollinator deterrence are not straightforward for long-lived iteroparous plants, because reproductive vital rates often contribute weakly to fitness relative to growth and survival (vital rates that may be enhanced by ant defense). We used field manipulations of ant and pollinator activity and demographic modeling to examine how pollination costs of ant defense translate to plant fitness, given the benefits of ant defense elsewhere in the plant life cycle. We contrasted the net fitness effects of alternative ant partner species. Our work focused on the tree cholla cactus, Opuntia imbricata, an EFN-bearing plant associated with two ant species (Crematogaster opuntiae and Liometopum apiculatum) that differ in quality of defense against insect herbivores. We found that ant defense imposed pollination costs, despite evidence for ant-repellent floral volatiles and temporal partitioning of ant and pollinator activity. The two partner species similarly reduced pollinator visitation and seed mass, and one (C. opuntiae) additionally reduced seed number. We used the experimental data and other long-term demographic data to parameterize an integral projection model that integrated costs and benefits of ant defense over the complete plant life cycle. Model results indicated that the pollination costs of L. apiculatum were balanced by beneficial effects on growth, leading to a net fitness effect that was neutral to positive. By contrast, pollination costs outweighed benefits for C. opuntiae, the weaker defender, rendering this species a reproductive parasite. Thus, we infer that pollination costs destabilize mutualism with one partner species, but are offset by strong defensive benefits provided by the other, leading to contrasting selective pressures imposed by alternative associations. Accounting for ontogenetic turnover in ant partner identity indicated that most plants avoid the parasitic effects of C. opuntiae by associating nonrandomly with L. apiculatum at reproductive life stages. Our results highlight the value of a demographic approach to quantifying the costs and benefits of mutualism.
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    Climate warming increases biological control agent impact on a non-target species
    (Wiley, 2015) Lu, Xinmin; Siemann, Evan; He, Minyan; Wei, Hui; Shao, Xu; Ding, Jianqing
    Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming affects impacts of a multivoltine introduced biocontrol beetle on the non-target native plant Alternanthera sessilis in China. In field surveys across a latitudinal gradient covering their full distributions, we found beetle damage on A. sessilis increased with rising temperature and plant life history changed from perennial to annual. Experiments showed that elevated temperature changed plant life history and increased insect overwintering, damage and impacts on seedling recruitment. These results suggest that warming can shift phenologies, increase non-target effect magnitude and increase non-target effect occurrence by beetle range expansion to additional areas where A. sessilis occurs. This study highlights the importance of understanding how climate change affects species interactions for future biological control of invasive species and conservation of native species.
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    The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
    (Public Library of Science, 2014) Chipman, Ariel D.; Ferrier, David E.K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S.T.; Schrӧder, 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
    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.
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    Computational approaches to species phylogeny inference and gene tree reconciliation
    (Elsevier, 2013) Nakhleh, Luay
    An intricate relationship exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating evolutionary processes and parameters. In a 1997 paper, Maddison discussed this relationship, reviewed the signatures left by three major evolutionary processes on the gene trees, and surveyed parsimony and likelihood criteria for utilizing these signatures to computationally elucidate this relationship. Here, we review progress that has been made on developing computational methods for analyses under these two criteria, and survey remaining challenges.
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    Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above-belowground herbivore interactions
    (Macmillan Publishers Limited, 2014) Huang, Wei; Siemann, Evan; Xiao, Li; Yang, Xuefang; Ding, Jianqing
    Conspecific and heterospecific aboveground and belowground herbivores often occur together in nature and their interactions may determine community structure. Here we show how aboveground adults and belowground larvae of the tallow tree specialist beetle Bikasha collaris and multiple heterospecific aboveground species interact to determine herbivore performance. Conspecific aboveground adults facilitate belowground larvae, but other aboveground damage inhibits larvae or has no effect. Belowground larvae increase conspecific adult feeding, but decrease heterospecific aboveground insect feeding and abundance. Chemical analyses and experiments with plant populations varying in phenolics show that all these positive and negative effects on insects are closely related to root and shoot tannin concentrations. Our results show that specific plant herbivore responses allow herbivore facilitation and inhibition to co-occur, likely shaping diverse aboveground and belowground communities. Considering species-specific responses of plants is critical for teasing apart inter- and intraspecific interactions in aboveground and belowground compartments.
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    Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication
    (BioMed Central, 2014) Nossa, Carlos W.; Havlak, Paul; Yue, Jia-Xing; Lv, Jie; Vincent, Kimberly Y.; Brockmann, H.Jane; Putnam, Nicholas H.
    Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” As arthropods, they belong to the Ecdysozoa, an ancient super-phylum whose sequenced genomes (including insects and nematodes) have thus far shown more divergence from the ancestral pattern of eumetazoan genome organization than cnidarians, deuterostomes and lophotrochozoans. However, much of ecdysozoan diversity remains unrepresented in comparative genomic analyses. Here we apply a new strategy of combined de novo assembly and genetic mapping to examine the chromosome-scale genome organization of the Atlantic horseshoe crab, Limulus polyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per sample. The map includes 84,307 sequence markers grouped into 1,876 distinct genetic intervals and 5,775 candidate conserved protein coding genes. Comparison with other metazoan genomes shows that the L. polyphemus genome preserves ancestral bilaterian linkage groups, and that a common ancestor of modern horseshoe crabs underwent one or more ancient whole genome duplications 300 million years ago, followed by extensive chromosome fusion. These results provide a counter-example to the often noted correlation between whole genome duplication and evolutionary radiations. The new, low-cost genetic mapping method for obtaining a chromosome-scale view of non-model organism genomes that we demonstrate here does not require laboratory culture, and is potentially applicable to a broad range of other species.
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    An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
    (Public Library of Science, 2014) Liu, Kevin J.; Dai, Jingxuan; Truong, Kathy; Song, Ying; Kohn, Michael H.; Nakhleh, Luay
    One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM?a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.
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    Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance
    (American Society for Microbiology, 2013) Miller, Corwin A.; Kong, Jiayi; Tran, Truc T.; Arias, Cesar A.; Saxer, Gerda; Shamoo, Yousif
    With increasing numbers of hospital-acquired antibiotic resistant infections each year and staggering health care costs, there is a clear need for new antimicrobial agents, as well as novel strategies to extend their clinical efficacy. While genomic studies have provided a wealth of information about the alleles associated with adaptation to antibiotics, they do not provide essential information about the relative importance of genomic changes, their order of appearance, or potential epistatic relationships between adaptive changes. Here we used quantitative experimental evolution of a single polymorphic population in continuous culture with whole-genome sequencing and allelic frequency measurements to study daptomycin (DAP) resistance in the vancomycin-resistant clinical pathogen Enterococcus faecalis S613. Importantly, we sustained both planktonic and nonplanktonic (i.e., biofilm) populations in coculture as the concentration of antibiotic was raised, facilitating the development of more ecological complexity than is typically observed in laboratory evolution. Quantitative experimental evolution revealed a clear order and hierarchy of genetic changes leading to resistance, the signaling and metabolic pathways responsible, and the relative importance of these mutations to the evolution of DAP resistance. Despite the relative simplicity of this ex vivo approach compared to the ecological complexity of the human body, we showed that experimental evolution allows for rapid identification of clinically relevant adaptive molecular pathways and new targets for drug design in pathogens.