The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.com/dib-lab/khmer/.

Caribbean coral reefs have deteriorated substantially over the past 30 years, which is broadly attributable to the effects of global climate change. In the same time, Indo-Pacific reefs maintain higher coral cover and typically recover rapidly after disturbances. This difference in reef resilience is largely due to much higher coral recruitment rates in the Pacific. We hypothesized that the lack of Caribbean recruitment might be explained by diminishing quality of settlement cues and/or impaired sensitivity of Caribbean coral larvae to those cues, relative to the Pacific. To evaluate this hypothesis, we assembled a collection of bulk samples of reef encrusting communities, mostly consisting of crustose coralline algae (CCA), from various reefs around the world and tested them as settlement cues for several coral species originating from different ocean provinces. Cue samples were meta-barcoded to evaluate their taxonomic diversity. We observed no systematic differences either in cue potency or in strength of larval responses depending on the ocean province, and no preference of coral larvae towards cues from the same ocean. Instead, we detected significant differences in cue preferences among coral species, even for corals originating from the same reef. We conclude that the region-wide disruption of the settlement process is unlikely to be the major cause of Caribbean reef loss. However, due to their high sensitivity to the effects of climate change, shifts in the composition of CCA-associated communities, combined with pronounced differences in cue preferences among coral species, could substantially influence future coral community structure.

Caribbean coral reefs have deteriorated substantially over the past 30 years, which is broadly attributable to the effects of global climate change. In the same time, Indo-Pacific reefs maintain higher coral cover and typically recover rapidly after disturbances. This difference in reef resilience is largely due to much higher coral recruitment rates in the Pacific. We hypothesized that the lack of Caribbean coral recruitment might be explained by diminishing quality of settlement cues and/or impaired sensitivity of Caribbean coral larvae to those cues, relative to the Pacific. To evaluate this hypothesis, we assembled a collection of bulk samples of reef encrusting communities, mostly consisting of crustose coralline algae (CCA), from various reefs around the world and tested them as settlement cues for several coral species originating from different ocean provinces. Cue samples were meta-barcoded to evaluate their taxonomic diversity. We observed no systematic differences either in cue potency or in strength of larval responses depending on the ocean province, and no preference of coral larvae towards cues from the same ocean. Instead, we detected significant differences in cue preferences among coral species, even for corals originating from the same reef. We conclude that the region-wide disruption of the settlement process is unlikely to be the major cause of Caribbean reef loss. However, due to their high sensitivity to the effects of climate change, shifts in the composition of CCA-associated communities, combined with pronounced differences in cue preferences among coral species, could substantially influence future coral community structure.

Genomic methods are powerful tools for studying evolutionary responses to selection, but the application of these tools in non-model systems threatened by climate change has been limited by the availability of genomic resources in those systems. High-throughput DNA sequencing has enabled development of genome and transcriptome assemblies in non-model systems including reef-building corals, but the fragmented nature of early draft assemblies often obscures the relative positions of genes and genetic markers, and limits the functional interpretation of genomic studies in these systems. To address this limitation and improve genomic resources for the study of adaptation to ocean warming in corals, we've developed a genetic linkage map for the mountainous star coral, Orbicella faveolata. We analyzed genetic linkage among multilocus SNP genotypes to infer the relative positions of markers, transcripts, and genomic scaffolds in an integrated genomic map. To illustrate the utility of this resource, we tested for genetic associations with bleaching responses and fluorescence phenotypes, and estimated genomewide patterns of population differentiation. Mapping the significant markers identified from these analyses in the integrated genomic resource identified hundreds of genes linked to significant markers, highlighting the utility of this resource for genomic studies of corals. The functional interpretations drawn from genomic studies are often limited by the availability of genomic resources linking genes to genetic markers. The resource developed in this study provides a framework for comparing genetic studies of O. faveolata across genotyping methods or references, and illustrates an approach for integrating genomic resources that may be broadly useful in other non-model systems.

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