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Asher D Cutter

Joanna D Bundus, Donglin Wang, Asher D Cutter
Hybrid male sterility often evolves before female sterility or inviability of hybrids, implying that the accumulation of divergence between separated lineages should lead hybrid male sterility to have a more polygenic basis. However, experimental evidence is mixed. Here, we use the nematodes Caenorhabditis remanei and C. latens to characterize the underlying genetic basis of asymmetric hybrid male sterility and hybrid inviability. We demonstrate that hybrid male sterility is consistent with a simple genetic basis, involving a single X-autosome incompatibility...
April 7, 2018: Heredity
Da Yin, Erich M Schwarz, Cristel G Thomas, Rebecca L Felde, Ian F Korf, Asher D Cutter, Caitlin M Schartner, Edward J Ralston, Barbara J Meyer, Eric S Haag
To reveal impacts of sexual mode on genome content, we compared chromosome-scale assemblies of the outcrossing nematode Caenorhabditis nigoni to its self-fertile sibling species, C. briggsae C. nigoni 's genome resembles that of outcrossing relatives but encodes 31% more protein-coding genes than C. briggsae C. nigoni genes lacking C. briggsae orthologs were disproportionately small and male-biased in expression. These include the male secreted short ( mss ) gene family, which encodes sperm surface glycoproteins conserved only in outcrossing species...
January 5, 2018: Science
Céline Ferrari, Romain Salle, Nicolas Callemeyn-Torre, Richard Jovelin, Asher D Cutter, Christian Braendle
BACKGROUND: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar external morphology despite deep genomic divergence. METHODS: To characterize the dynamics and specificity of colonization and exploitation of ephemeral resource patches, we conducted manipulative field experiments and the largest sampling effort to date for Caenorhabditis outside of Europe...
December 19, 2017: BMC Ecology
Asher D Cutter
Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to "rules" of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial interfertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis...
November 13, 2017: Molecular Ecology
Anne Vielle, Nicolas Callemeyn-Torre, Clotilde Gimond, Nausicaa Poullet, Jeremy C Gray, Asher D Cutter, Christian Braendle
Sperm cells provide essential, if usually diminutive, ingredients to successful sexual reproduction. Despite this conserved function, sperm competition and coevolution with female traits can drive spectacular morphological change in these cells. Here, we characterize four repeated instances of convergent evolution of sperm gigantism in Caenorhabditis nematodes using phylogenetic comparative methods on 26 species. Species at the extreme end of the 50-fold range of sperm-cell volumes across the genus have sperm capable of comprising up to 5% of egg-cell volume, representing severe attenuation of the magnitude of anisogamy...
November 2016: Evolution; International Journal of Organic Evolution
Asher D Cutter, Jeremy C Gray
The richness of biodiversity in the tropics compared to high-latitude parts of the world forms one of the most globally conspicuous patterns in biology, and yet few hypotheses aim to explain this phenomenon in terms of explicit microevolutionary mechanisms of speciation and extinction. We link population genetic processes of selection and adaptation to speciation and extinction by way of their interaction with environmental factors to drive global scale macroecological patterns. High-latitude regions are both cradle and grave with respect to species diversification...
October 2016: Evolution; International Journal of Organic Evolution
Richard Jovelin, Asher D Cutter
Nested genes represent an intriguing form of non-random genomic organization in which the boundaries of one gene are fully contained within another, longer host gene. The C. elegans genome contains over 10,000 nested genes, 92% of which are ncRNAs, which occur inside 16% of the protein coding gene complement. Host genes are longer than non-host coding genes, owing to their longer and more numerous introns. Indel alleles are available for nearly all of these host genes that simultaneously alter the nested gene, raising the possibility of nested gene disruption contributing to phenotypes that might be attributed to the host gene...
April 2016: Worm
Richard Jovelin, Aldis Krizus, Bakhtiyar Taghizada, Jeremy C Gray, Patrick C Phillips, Julie M Claycomb, Asher D Cutter
MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes...
July 2016: RNA
Asher D Cutter
Recent research has filled many gaps about Caenorhabditis natural history, simultaneously exposing how much remains to be discovered. This awareness now provides means of connecting ecological and evolutionary theory with diverse biological patterns within and among species in terms of adaptation, sexual selection, breeding systems, speciation, and other phenomena. Moreover, the heralded laboratory tractability of C. elegans, and Caenorhabditis species generally, provides a powerful case study for experimental hypothesis testing about evolutionary and ecological processes to levels of detail unparalleled by most study systems...
September 2015: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
Janna L Fierst, John H Willis, Cristel G Thomas, Wei Wang, Rose M Reynolds, Timothy E Ahearne, Asher D Cutter, Patrick C Phillips
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system...
June 2015: PLoS Genetics
Joanna D Bundus, Ravin Alaei, Asher D Cutter
Deciphering the genetic and developmental causes of the disproportionate rarity, inviability, and sterility of hybrid males, Haldane's rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and prezygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here, we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito-nuclear incompatibility as a genetic cause...
August 2015: Evolution; International Journal of Organic Evolution
Asher D Cutter
Everyone appreciates the happy fiction that species conform to the simple theoretical convenience of a single panmictic population. In speciation genetics, a further standard simplification is that it is only those genetic differences that are fixed between diverging populations that need concern us in order to understand the accumulation of intrinsic barriers to reproduction. To a first approximation, of course, both of these assumptions are appropriate and theory based on them provides compelling insights into diverse evolutionary phenomena (Orr & Turelli )...
April 2015: Molecular Ecology
Cristel G Thomas, Wei Wang, Richard Jovelin, Rajarshi Ghosh, Tatiana Lomasko, Quang Trinh, Leonid Kruglyak, Lincoln D Stein, Asher D Cutter
The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C...
May 2015: Genome Research
Shikui Tu, Monica Z Wu, Jie Wang, Asher D Cutter, Zhiping Weng, Julie M Claycomb
As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution...
January 2015: Nucleic Acids Research
Richard Jovelin, Asher D Cutter
Micro-RNA (miRNA) genes encode abundant small regulatory RNAs that play key roles during development and in homeostasis by fine tuning and buffering gene expression. This layer of regulatory control over transcriptional networks is preserved by selection across deep evolutionary time, yet selection pressures on individual miRNA genes in contemporary populations remain poorly characterized in any organism. Here, we quantify nucleotide variability for 129 miRNAs in the genome of the nematode Caenorhabditis remanei to understand the microevolution of this important class of regulatory genes...
2014: Genome Biology and Evolution
Alivia Dey, Qi Jin, Yen-Chu Chen, Asher D Cutter
Determining the causes and evolution of reproductive barriers to gene flow between populations, speciation, is the key to understanding the origin of diversity in nature. Many species manifest hybrid breakdown when they intercross, characterized by increasingly exacerbated problems in later generations of hybrids. Recently, Caenorhabditis nematodes have emerged as a genetic model for studying speciation, and here we investigate the nature and causes of hybrid breakdown between Caenorhabditis remanei and C. latens...
November 2014: Evolution & Development
Janice J Ting, Gavin C Woodruff, Gemma Leung, Na-Ra Shin, Asher D Cutter, Eric S Haag
Conflict between the sexes over reproductive interests can drive rapid evolution of reproductive traits and promote speciation. Here we show that inter-species mating between Caenorhabditis nematodes sterilizes maternal individuals. The principal effectors of male-induced harm are sperm cells, which induce sterility and shorten lifespan by displacing conspecific sperm, invading the ovary, and sometimes breaching the gonad to infiltrate other tissues. This sperm-mediated harm is pervasive across species, but idiosyncrasies in its magnitude implicate both independent histories of sexually antagonistic coevolution within species and differences in reproductive mode (self-fertilizing hermaphrodites versus females) in determining its severity...
July 2014: PLoS Biology
Zhen-Xia Chen, David Sturgill, Jiaxin Qu, Huaiyang Jiang, Soo Park, Nathan Boley, Ana Maria Suzuki, Anthony R Fletcher, David C Plachetzki, Peter C FitzGerald, Carlo G Artieri, Joel Atallah, Olga Barmina, James B Brown, Kerstin P Blankenburg, Emily Clough, Abhijit Dasgupta, Sai Gubbala, Yi Han, Joy C Jayaseelan, Divya Kalra, Yoo-Ah Kim, Christie L Kovar, Sandra L Lee, Mingmei Li, James D Malley, John H Malone, Tittu Mathew, Nicolas R Mattiuzzo, Mala Munidasa, Donna M Muzny, Fiona Ongeri, Lora Perales, Teresa M Przytycka, Ling-Ling Pu, Garrett Robinson, Rebecca L Thornton, Nehad Saada, Steven E Scherer, Harold E Smith, Charles Vinson, Crystal B Warner, Kim C Worley, Yuan-Qing Wu, Xiaoyan Zou, Peter Cherbas, Manolis Kellis, Michael B Eisen, Fabio Piano, Karin Kionte, David H Fitch, Paul W Sternberg, Asher D Cutter, Michael O Duff, Roger A Hoskins, Brenton R Graveley, Richard A Gibbs, Peter J Bickel, Artyom Kopp, Piero Carninci, Susan E Celniker, Brian Oliver, Stephen Richards
Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species...
July 2014: Genome Research
Marie-Anne Félix, Christian Braendle, Asher D Cutter
The rapid pace of species discovery outstrips the rate of species description in many taxa. This problem is especially acute for Caenorhabditis nematodes, where the naming of distinct species would greatly improve their visibility and usage for biological research, given the thousands of scientists studying Caenorhabditis. Species description and naming has been hampered in Caenorhabditis, in part due to the presence of morphologically cryptic species despite complete biological reproductive isolation and often enormous molecular divergence...
2014: PloS One
Richard Jovelin, Jennifer S Comstock, Asher D Cutter, Patrick C Phillips
The discovery that genetic pathways can be manipulated to extend lifespan has revolutionized our understanding of aging, yet their function within natural populations remains poorly characterized. In particular, evolutionary theories of aging predict tradeoffs in resource investment toward somatic maintenance vs. reproductive output that should impose strong natural selection on genetic components that influence this balance. To explore such selective pressure at the molecular level, we examine population genetic variation in the insulin-like signaling pathway of the nematode Caenorhabditis remanei...
June 2014: G3: Genes—Genomes—Genetics
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