Category Archives: genomics

Procrustes Analyses in R

Procrustes transformations (i.e. a form of multidimensional scaling that allows the comparison of two data sets) have been used extensively in recent literature to assess the similarity of geographical and genetic distributions of species, following the lead of Wang et … Continue reading

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Posted in genomics, howto, population genetics, R, software | Tagged , , , | Leave a comment

Adaptive divergence in the monkey flower

Theory suggests adaptive divergence can proceed in the face of gene flow when adaptive alleles occur in areas of the genome, such as chromosomal inversions, that are protected from recombination, which can break up beneficial allele pairings. In their recent Evolution paper, … Continue reading

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The brave new world of environmental genomics

A new special issue of Heredity reflects on the recent advances in environmental genomics (see other posts about eDNA here and here) and highlights the ways NGS can aid in characterizing complex biological systems. The cryptic, as well as the rare but active … Continue reading

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The gopher tortoise gut microbiome

A few weeks ago I wrote about a study on socially structured gut microbiomes in wild baboons. Well, now I’m here to tell you about a new study that examined the population structure of tortoise gut microbiomes.

Posted in community ecology, genomics, natural history, next generation sequencing, population genetics, Uncategorized | Tagged , , | Leave a comment

Gorillas (genomes) in the mist

Mountain gorillas are an endangered great ape subspecies that number around 800 individuals, inhabiting mountain ranges in central Africa. They have been the subject of numerous field studies, but few genetic analyses have been carried out. Xue et al. (2015) sequenced … Continue reading

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Don’t trust your data: reviewing Bioinformatics Data Skills

There is little debate on the importance of bioinformatics for the present and future of science. As molecular ecologists, we are likely more aware of this than most disciplines due to the data explosion that has accompanied the wide application of … Continue reading

Posted in bioinformatics, book review, genomics, software | Tagged | 1 Comment

A transcriptomic approach for reduced representation in population genomics

                    Many population genomics studies use methods that provide a reduced representation of the genome, for example RADseq or UCEs. Targeting a subset of the genome reduces the cost of sequencing … Continue reading

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F-statistics Manhattan Plots in R

Characterizing differentiation across individual genomes sampled from different populations can be very informative of the demographic processes that resulted in the differentiation in the first place. Manhattan plots have grown to be very popular representations of genome-wide differentiation statistics in … Continue reading

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Killer genetic differentiation

Like most of you out there, I sometimes get bogged down in literature, and the pressure to keep up with new methods can lead to a towering “to-read” folder. I feel forced to read many of these papers no matter … Continue reading

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Haploid-diploidy, a (brief?) history

Haploid-diploid life cycles are not only good exercise for the brain, but they’re also fantastic study systems to investigate a myriad of questions. Yet, the majority of molecular studies have focused on the diploid-dominated life cycles of animal and plant … Continue reading

Posted in DNA barcoding, domestication, evolution, genomics, haploid-diploid, natural history, population genetics, selection, speciation | Tagged , , , , , | Leave a comment