How genomics can help biodiversity conservation.

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Reference genomes for conservation.

High-quality reference genomes for non-model species can benefit conservation.

The era of reference genomes in conservation genomics.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.

Towards complete and error-free genome assemblies of all vertebrate species.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Parental and environmental factors associated with physical activity among children participating in an active video game.

PURPOSE: Parental and intervention-specific environmental supports were examined as potential reinforcers for physical activity and use of a video game, Dance Dance Revolution (DDR), among a cohort of 7- to 8-year-old children. METHODS: Sixty children were randomized to an intervention (n = 40) or a control (n = 20) group. Physical activity was measured with accelerometry and DDR logs. Parental support for their child's physical activity was assessed via a questionnaire. DDR-specific environmental supports were captured on an environmental home screen and the DDR log. RESULTS: At baseline, the absence of other video games and parent DDR participation was associated with child participation in DDR. At follow-up, DDR participation of siblings and friends was associated with child participation in DDR. CONCLUSION: The primary findings of this study suggest that parental and peer participation in DDR may play a role in children's initial and sustained participation in DDR.

A pilot of a video game (DDR) to promote physical activity and decrease sedentary screen time.

OBJECTIVE: We examined the feasibility of Dance Dance Revolution (DDR), a dance video game, in participants' homes, to increase physical activity (PA) and to decrease sedentary screen time (SST). METHODS AND PROCEDURES: Sixty children (7.5 +/- 0.5 years) were randomized in a 2:1 ratio to DDR or to wait-list control (10-week delay). DDR use was logged, PA was measured objectively by accelerometry. SST was self-reported at weeks 0 and 10. At week 28, after both groups had access to DDR, accelerometry and SST were repeated. RESULTS: Mean use of DDR was 89 +/- 82 (range 0-660 min) min per week (mpw). The DDR group showed increased vigorous PA and a reduction in light PA; the control group showed no increase in moderate and/or vigorous PA (MVPA) although they also had a reduction in light PA. Differences between the groups were not observed. The DDR group also reported a decrease in SST of -1.2 +/- 3.7 h per week (hpw) (P < 0.05), whereas the controls reported an increase of +3.0 +/- 7.7 hpw (nonsignificant). The difference in SST between the groups was significant, with less SST in the DDR group. Between weeks 10 and 28, numeric reductions in SST were reported in both groups. In the DDR group, SST at week 28 (8.8 +/- 6.0 hpw) was lower than baseline (10.5 +/- 5.5 hpw; P < 0.03). DISCUSSION: This pilot study suggests that DDR reduces SST and may facilitate slight increases in vigorous PA. Further study is needed to better characterize children and contexts in which DDR may promote a healthy lifestyle.