Brain Transcriptional Profiles of Male Alternative Reproductive Tactics in Bluegill Sunfish

Brain Transcriptional Profiles of Male Alternative Reproductive Tactics in Bluegill Sunfish

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Bluegill sunfish are one of the classic systems for studying male alternative reproductive tactics (ARTs) in teleost fishes. In this species, there are two distinct life histories: parental and cuckolder, encompassing three reproductive tactics, parental, satellite, and sneaker. The parental tactic is fixed, whereas individuals who enter the cuckolder life history transition from the sneaker to the satellite tactic as they grow. For this study, we used RNAseq to characterize the brain transcriptome of the three male tactics during spawning to identify gene categories associated with each tactic and identify potential candidate genes influencing their different spawning behaviors. We found that sneaker males had higher levels of gene differentiation compared to the other two tactics, suggesting that life history does not exclusively drive differential gene expression. Sneaker males had high expression in ionotropic glutamate receptor genes, specifically AMPA receptors, which may be important for increased working spatial memory while attempting to cuckold nests in bluegill colonies. We also found significant expression differences in several candidate genes involved in ARTs that were previously identified in other species and suggest a previously undescribed role for cytosolic 5-nucleotidase II (nt5c2) in influencing parental male behavior during spawning.

Incomplete domestication of South American grain amaranth (Amaranthus caudatus) from its wild relatives

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Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria

Protein homeostasis imposes a barrier on functional integration of horizontally transferred genes in bacteria

Shimon Bershtein, Adrian Serohijos, Sanchari Bhattacharyya, Michael Manhart, Jeong-Mo Choi, Wangmen Mu, Jingwen Zhou, Eugene Shakhnovich

Allele-specific expression reveals interactions between genetic variation and environment

Allele-specific expression reveals interactions between genetic variation and environment

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Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

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A resurrection experiment finds evidence of both reduced genetic diversity and adaptive evolution in the agricultural weed Ipomoea purpurea

A resurrection experiment finds evidence of both reduced genetic diversity and adaptive evolution in the agricultural weed Ipomoea purpurea
Adam Kuester, Shu-Mei Chang, Regina Baucom
doi: http://dx.doi.org/10.1101/024950

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their ability to persist and thrive in agricultural fields. Here, we use a resurrection ecology approach and compare the neutral and adaptive genetic variation of temporally sampled seed progenies of Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart, suggesting that populations of this species sampled from agricultural fields experience genetic bottleneck and/or founder events through time. We further found that populations of this species exhibit modest increases in herbicide resistance over time and evidence that this increase was due to adaptation and not genetic drift. Our results show that even in light of reduced genetic variation, populations of this noxious weed are capable of adapting to strong selection imparted by herbicide application. We likely uncovered only modest increases in resistance between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that non-resistant migrants germinate from the seed bank.

Neighbourhoods of phylogenetic trees: exact and asymptotic counts

Neighbourhoods of phylogenetic trees: exact and asymptotic counts

Jamie V. De Jong, Jeanette C McLeod, Mike Steel
(Submitted on 15 Aug 2015)

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the neighbourhoods of trees under tree rearrangement operations. The diameter and size of the immediate neighbourhood of a tree has been well-studied, however little is known about the number of trees at distance two, three or (more generally) k from a given tree. In this paper we provide a number of exact and asymptotic results concerning these quantities, and identify some key aspects of tree shape that play a role in determining these quantities. We obtain several new results for two of the main tree rearrangement operations – Nearest Neighbour Interchange and Subtree Prune and Regraft — as well as for the Robinson-Foulds metric on trees.