scholarly journals The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation

Genetics ◽  
2019 ◽  
Vol 211 (3) ◽  
pp. 1089-1104 ◽  
Author(s):  
Mingzi Xu ◽  
Kerry L. Shaw
Keyword(s):  
Candidate Genes ◽  
Gene Prediction ◽  
Interspecific Variation ◽  
Genomic Region ◽  
Species Variation ◽  
Behavioral Isolation ◽  
Singing Behavior ◽  
Rapid Speciation ◽  
Species Specific ◽  
Temporal Rhythm

Differences in mating behaviors evolve early during speciation, eventually contributing to reproductive barriers between species. Knowledge of the genetic and genomic basis of these behaviors is therefore integral to a causal understanding of speciation. Acoustic behaviors are often part of the mating ritual in animal species. The temporal rhythms of mating songs are notably species-specific in many vertebrates and arthropods and often underlie assortative mating. Despite discoveries of mutations that disrupt the temporal rhythm of these songs, we know surprisingly little about genes affecting naturally occurring variation in the temporal pattern of singing behavior. In the rapidly speciating Hawaiian cricket genus Laupala, the striking species variation in song rhythms constitutes a behavioral barrier to reproduction between species. Here, we mapped the largest-effect locus underlying interspecific variation in song rhythm between two Laupala species to a narrow genomic region, wherein we find no known candidate genes affecting song temporal rhythm in Drosophila. Whole-genome sequencing, gene prediction, and functional annotation of this region reveal an exciting and promising candidate gene, the putative cyclic nucleotide-gated ion channel-like gene, for natural variation in mating behavior, suggesting that ion channels are important targets of selection on rhythmic signaling during establishment of behavioral isolation and rapid speciation.

Genes underlying species differences in CHC production between Drosophila melanogaster and D. simulans.

Genome ◽  
2020 ◽  
Author(s):  
Heather Ward ◽  
Amanda J. Moehring
Keyword(s):  
Drosophila Melanogaster ◽  
Candidate Genes ◽  
Species Differences ◽  
Chemical Compounds ◽  
Species Variation ◽  
Candidate Locus ◽  
Interspecies Hybrids ◽  
Survival And Reproduction ◽  
Specific Variation ◽  
Species Specific

Surface chemical compounds are key components of survival and reproduction in many species. Cuticular hydrocarbons (CHCs) are chemical compounds produced by all insects that are used for both desiccation resistance and chemical communication, including communication related to mating. In the species pair of Drosophila melanogaster and D. simulans, female CHCs stimulate conspecific males to mate and repel heterospecific males. While CHCs are a critical contributor to both reproductive success within a species and isolation between species, few genes underlying species variation in CHC profiles are known. Here, we use genetic mapping of the 3rd chromosome to test a suite of candidate genes for interspecies variation in CHCs. Candidate gene CG5946 was found to be involved in species differences in the production of 7,11-heptacosadiene and 7-tricosene between D. melanogaster and D. simulans. This is therefore a new candidate locus contributing to species-specific variation in the CHC profile. In the process of mapping genes for CHCs, we also identified 29 candidate genes for the reduced survival or inviability of interspecies hybrids.

scholarly journals Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingyi Wang ◽  
Hui Liu ◽  
Kadambot H. M. Siddique ◽  
Guijun Yan
Keyword(s):  
Candidate Genes ◽  
Quantitative Trait ◽  
Genomic Region ◽  
Nucleotide Polymorphisms ◽  
Near Isogenic Lines ◽  
Gene Effects ◽  
Isogenic Lines ◽  
Trait Locus ◽  
Grain Yield And Quality ◽  
Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

Investigating the species-specific association between anuran calling phenology and air temperature

2021 ◽  
Author(s):  
Samantha Wong
Keyword(s):  
Climate Change ◽  
Air Temperature ◽  
Management Strategies ◽  
Temporal Trends ◽  
Interspecific Variation ◽  
Northern Ontario ◽  
Anuran Species ◽  
Calling Behaviour ◽  
Survival And Development ◽  
Species Specific

Climate change has been associated in phenological shifts for a variety of taxa. Amphibians, specifically the order Anura (frogs and toads), are considered particularly vulnerable due to their sensitivity to anthropogenic and environmental change. Previous research has documented shifts in the timing of anuran breeding that can be attributed, in part, to climate change, with potential implications for reproduction, survival, and development. This study aims to investigate how air temperature is associated with anuran calling phenology. I will examine the temporal trends in spring and summer air temperature in a lake in northern Ontario, Canada. and quantify seasonal patterns of calling anuran species using acoustic monitoring over a four-month period. I predict that there will be interspecific variation in peak calling associated with air temperature. Additionally, I expect to find asymmetrical association between air temperature and anuran species’ calling behaviour – wherein prolonged breeding species will have a larger optimal temperature range for calling compared to explosive breeding species. The findings of this research will aid in future conservation and provide insight for management strategies of anurans in Canada in response to anticipated climate warming.

scholarly journals Across-species differences in pitch perception are consistent with differences in cochlear filtering

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Kerry MM Walker ◽  
Ray Gonzalez ◽  
Joe Z Kang ◽  
Josh H McDermott ◽  
Andrew J King
Keyword(s):  
Fundamental Frequency ◽  
Species Differences ◽  
Pitch Perception ◽  
Species Variation ◽  
Opposite Pattern ◽  
Auditory Periphery ◽  
Cochlear Tuning ◽  
Animal Vocalizations ◽  
Species Specific ◽  
Relative Salience

Pitch perception is critical for recognizing speech, music and animal vocalizations, but its neurobiological basis remains unsettled, in part because of divergent results across species. We investigated whether species-specific differences exist in the cues used to perceive pitch and whether these can be accounted for by differences in the auditory periphery. Ferrets accurately generalized pitch discriminations to untrained stimuli whenever temporal envelope cues were robust in the probe sounds, but not when resolved harmonics were the main available cue. By contrast, human listeners exhibited the opposite pattern of results on an analogous task, consistent with previous studies. Simulated cochlear responses in the two species suggest that differences in the relative salience of the two pitch cues can be attributed to differences in cochlear filter bandwidths. The results support the view that cross-species variation in pitch perception reflects the constraints of estimating a sound’s fundamental frequency given species-specific cochlear tuning.

Distribution of a Secale cereale DNA repeat sequence among 25 Hordeum species

Genome ◽  
1989 ◽  
Vol 32 (3) ◽  
pp. 383-388 ◽  
Author(s):  
P. K. Gupta ◽  
G. Fedak ◽  
S. J. Molnar ◽  
Roger Wheatcroft
Keyword(s):  
Dna Sequences ◽  
Secale Cereale ◽  
Dna Hybridization ◽  
Interspecific Variation ◽  
Repeat Sequence ◽  
Species Variation ◽  
Repeated Dna ◽  
Repeat Units ◽  
Dna Repeat ◽  
Hordeum Species

DNA of 61 accessions representing 25 Hordeum species was tested for homology to a highly repeated 120-bp sequence from Secale cereale (rye). Homology to the probe (pSC119) was detected in dot blots of all species except H. vulgare (cultivated barley) and its related species, H. agriocrithon and H. spontaneum. Hybridization patterns of Southern blots of restriction fragments demonstrated both intraspecific and interspecific variation in the organization of complex units of DNA having homology to the probe. For eight species, digestion of the DNA with BamHI gave ladder patterns characteristic of tandem arrays of 120-bp repeat units. For EcoRI, HindIII, and SacI digests, the hybridization patterns appeared to be highly conserved in the section Hordeum, except those for H. bulbosum, which were unique. A further set of patterns for these three enzymes was common among the remaining species of the genus. Thus, DNA hybridization with pSC119 generally gave patterns consistent with the current taxonomy of Hordeum species, except that H. bulbosum and H. vulgare were not shown to be closely related.Key words: Hordeum, repeated DNA sequences, pSC119, species variation.

scholarly journals Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Pasan C. Fernando ◽  
Paula M. Mabee ◽  
Erliang Zeng
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Gene Networks ◽  
Prediction Accuracy ◽  
Gene Prediction ◽  
Anatomical Entity ◽  
Anatomy Ontology ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Entity Relationships

Abstract Background Identification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, such as gene knockout, are high in resource and time consumption. Protein–protein interaction (PPI) networks are frequently used to predict disease genes for humans and gene candidates for molecular functions, but they are rarely used to predict genes for anatomical entities. Moreover, PPI networks suffer from network quality issues, which can be a limitation for their usage in predicting candidate genes. Therefore, we developed an integrative framework to improve the candidate gene prediction accuracy for anatomical entities by combining existing experimental knowledge about gene-anatomical entity relationships with PPI networks using anatomy ontology annotations. We hypothesized that this integration improves the quality of the PPI networks by reducing the number of false positive and false negative interactions and is better optimized to predict candidate genes for anatomical entities. We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes. These anatomy-based gene networks were semantic networks, as they were constructed based on the anatomy ontology annotations that were obtained from the experimental data in the literature. We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database and compared the performance of their network-based candidate gene predictions. Results According to evaluations of candidate gene prediction performance tested under four different semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated networks, which were semantically improved PPI networks, showed better performances by having higher area under the curve values for receiver operating characteristic and precision-recall curves than PPI networks for both zebrafish and mouse. Conclusion Integration of existing experimental knowledge about gene-anatomical entity relationships with PPI networks via anatomy ontology improved the candidate gene prediction accuracy and optimized them for predicting candidate genes for anatomical entities.

scholarly journals Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Peter D. Olson ◽  
Alan Tracey ◽  
Andrew Baillie ◽  
Katherine James ◽  
Stephen R. Doyle ◽  
...  
Keyword(s):  
Complete Genome ◽  
Gene Prediction ◽  
Low Complexity ◽  
Complex Species ◽  
Complete Representation ◽  
Spliced Leader ◽  
Long Read ◽  
Reference Quality ◽  
Species Specific ◽  
Genome Representation

Abstract Background Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution. Results Long-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader trans-splicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes. Conclusions Despite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation.

scholarly journals Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H. A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Interspecific Variation ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome ◽  
Ecological Niches ◽  
Content Type ◽  
Evolutionary Trajectories ◽  
Species Specific

ABSTRACT The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes. IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

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