A genetic assessment of parentage in the blackspot sergeant damselfish, Abudefduf sordidus (Pisces: Pomacentridae)

Microsatellite markers were used to investigate the reproductive behavior of the damselfish Abudefduf sordidus at Johnston Atoll, Central Pacific Ocean. Genetic results indicated that ten males maintained guardianship over their nest territories for up to nine nest cycles during a 3.5 month period. Genotypes of 1025 offspring sampled from 68 nests (composed of 129 clutches) were consistent with 95% of the offspring being sired by the guardian male. Offspring lacking paternal alleles at two or more loci were found in 19 clutches, indicating that reproductive parasitism and subsequent alloparental care occurred. Reconstructed maternal genotypes allowed the identification of a minimum of 74 different females that spawned with these ten territorial males. Males were polygynous, mating with multiple females within and between cycles. Genetic data from nests, which consisted of up to four clutches during a reproductive cycle, indicated that each clutch usually had only one maternal contributor and that different clutches each had different dams. Females displayed sequential polyandry spawning with one male within a cycle but switched males in subsequent spawning cycles. These results highlight new findings regarding male parasitic spawning, polygyny, and sequential polyandry in a marine fish with exclusive male paternal care.Published versio

Genetic identity determines risk of post-settlement mortality of a marine fish

Author Posting. © Ecological Society of America, 2007. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecology 88 (2007): 1263–1277, doi:10.1890/06-0066.Longitudinal sampling of four cohorts of Neopomacentrus filamentosus, a common tropical damselfish from Dampier Archipelago, Western Australia, revealed the evolution of size structure after settlement. Light traps collected premetamorphic individuals from the water column (“settlers”) to establish a baseline for each cohort. Subsequently, divers collected benthic juveniles (“recruits”) at 1–3-month intervals to determine the relative impacts of post-settlement mortality during the first three months. Growth trajectories for individual fish were back-calculated from otolith records and compared with nonlinear mixed-effects models. Size-selective mortality was detected in all cohorts with the loss of smaller, slower growing individuals. Three months after settlement, recruits showed significantly faster growth as juveniles, faster growth as larvae, and larger sizes as hatchlings. The timing and intensity of post-settlement selection differed among cohorts and was correlated with density at settlement. The cohort with the greatest initial abundance experienced the strongest selective mortality, with most of this mortality occurring between one and two months after settlement when juveniles began foraging at higher positions in the water column. Significant genetic structure was found between settlers and three-month-old recruits in this cohort as a result of natural selection that changed the frequency of mtDNA haplotypes measured at the control region. The extent of this genetic difference was enlarged or reduced by artificially manipulating the intensity of size-based selection, thus establishing a link between phenotype and haplotype. Sequence variation in the control region of the mitochondrial genome has been linked to mitochondrial efficiency and weight gain in other studies, which provides a plausible explanation for the patterns observed here.The project was funded by the Australian Institute of Marine Science, the Australian European Award Program, le Ministe` re franc¸ ais des Affaires Etrange` res, ARC-DEET, Boston University, and the National Science Foundation (Biological Oceanography, OCE 0349177)

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function

Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad “aquascape” scale, and few if any have applied the newest nanopore technology. Results We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5–1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers. Conclusions Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space

Accuracy and Completeness of Long Read Metagenomic Assemblies

Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library using a VolTRAX V2 and sequenced using a MinION mk1b. We basecalled with Guppy v5.0.7 using the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10× read depth. Polishing assemblies using Medaka had a predictable improvement in quality. We found Flye to be the most robust across taxa and was the most effective assembler for recovering plasmids. Based on Flye’s consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies

Data from: Runaway coevolution: adaptation to heritable and nonheritable environments

Populations evolve in response to the external environment, whether abiotic (e.g., climate) or biotic (e.g., other conspecifics). We investigated how adaptation to biotic, heritable environments differs from adaptation to abiotic, non-heritable environments. We found that, for the same selection coefficients, the coadaptive process between genes and heritable environments is much faster than genetic adaptation to an abiotic non-heritable environment. The increased rate of adaptation results from of the positive association generated by reciprocal selection between the heritable environment and the genes responding to it. These associations result in a runaway process of adaptive coevolution, even when the genes creating the heritable environment and genes responding to the heritable environment are unlinked. Although tightening the degree of linkage accelerates the coadaptive process, the acceleration caused by a comparable amount of inbreeding is greater, because inbreeding has a cumulative effect on reducing functional recombination over generations. Our results suggest that that adaptation to local abiotic environmental variation may result in the rapid diversification of populations and subsequent reproductive isolation not directly but rather via its effects on heritable environments and the genes responding to them

Runaway indirect genetic effects code and data

MATLAB code used to numerically iterate the full recursions in the main paper. Raw data for each figure in the main paper

Consumer resource interactions and the evolution of migration

Theoretical studies have demonstrated that selection will favor increased migration when fitnesses vary both temporally and spatially, but it is far from clear how pervasive those theoretical conditions are in nature. While consumer-resource interactions are omnipresent in nature and can generate spatial and temporal variation, it is unknown even in theory whether these dynamics favor the evolution of migration. We develop a mathematical model to address whether and how migration evolves when variability in fitness is determined at least in part by consumer-resource coevolutionary interactions. Our analyses show that such interactions can drive the evolution of migration in the resource, consumer, or both species and thus supplies a general explanation for the pervasiveness of migration. Over short time scales, we show the direction of change in migration rate is determined primarily by the state of local adaptation of the species involved: rates increase when a species is locally maladapted and decrease when locally adapted. Our results reveal that long-term evolutionary trends in migration rates can differ dramatically depending on the strength or weakness of interspecific interactions and suggest an explanation for the evolutionary divergence of migration rates among interacting species

Genome Sequence of Erysipelothrix sp. Strain Poltava, Isolated from Acute Septic Erysipelas of Swine in Ukraine.

The complete genome of Erysipelothrix sp. strain Poltava, isolated from fatal acute septic erysipelas of swine in Ukraine, was assembled using Nanopore sequences. One circular chromosome of 1,794,858 bp (N50, 1,794,858 bp) encodes 16 putative antibiotic resistance genes and secreted virulence factors, highlighting the risk of cross-species livestock and human infection

Appendix C. Difference in size and genetic structure between settlers and recruits based on size at hatching for both natural and augmented selection regimes.

Difference in size and genetic structure between settlers and recruits based on size at hatching for both natural and augmented selection regimes

Appendix B. Results of nonlinear mixed effects (NLME) model analyses of growth back-calculated from otoliths of four cohorts of Neopomacentrus filamentosus.

Results of nonlinear mixed effects (NLME) model analyses of growth back-calculated from otoliths of four cohorts of Neopomacentrus filamentosus