Using Haplotype Information for Conservation Genomics

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

Download Full-text

High throughput crop genome genotyping by a combination of pool next generation sequencing and haplotype-based data processing

10.21203/rs.3.rs-415602/v1 ◽

2021 ◽

Author(s):

Michael Schneider ◽

Asis Shrestha ◽

Agim Ballvora ◽

Jens Leon

Keyword(s):

Next Generation Sequencing ◽

Allele Frequency ◽

Frequency Estimation ◽

Whole Genome ◽

Next Generation ◽

Conservation Genomics ◽

High Coverage ◽

Allele Frequency Estimation ◽

Low Coverage ◽

Generation Sequencing

Abstract BackgroundThe identification of environmentally specific alleles and the observation of evolutional processes is a goal of conservation genomics. By generational changes of allele frequencies in populations, questions regarding effective population size, gene flow, drift, and selection can be addressed. The observation of such effects often is a trade-off of costs and resolution, when a decent sample of genotypes should be genotyped for many loci. Pool genotyping approaches can derive a high resolution and precision in allele frequency estimation, when high coverage sequencing is utilized. Still, pool high coverage pool sequencing of big genomes comes along with high costs.ResultsHere we present a reliable method to estimate a barley population’s allele frequency at low coverage sequencing. Three hundred genotypes were sampled from a barley backcross population to estimate the entire population’s allele frequency. The allele frequency estimation accuracy and yield were compared for three next generation sequencing methods. To reveal accurate allele frequency estimates on a low coverage sequencing level, a haplotyping approach was performed. Low coverage allele frequency of positional connected single polymorphisms were aggregated to a single haplotype allele frequency, resulting in two to 271 times higher depth and increased precision. We compared different haplotyping tactics, showing that gene and chip marker-based haplotypes perform on par or better than simple contig haplotype windows. The comparison of multiple pool samples and the referencing against an individual sequencing approach revealed whole genome pool resequencing having the highest correlation to individual genotyping (up to 0.97), while transcriptomics and genotyping by sequencing indicated higher error rates and lower correlations.ConclusionUsing the proposed method allows to identify the allele frequency of populations with high accuracy at low cost. This is particularly interesting for conservation genomics in species with big genomes, like barley or wheat. Whole genome low coverage resequencing at 10x coverage can deliver a highly accurate estimation of the allele frequency, when a loci-based haplotyping approach is applied. Using annotated haplotypes allows to capitalize from biological background and statistical robustness.

Download Full-text

Desert Tortoises in the Genomic Age: Population Genetics and the Landscape

10.1101/195743 ◽

2017 ◽

Cited By ~ 3

Author(s):

H. Bradley Shaffer ◽

Evan McCartney-Melstad ◽

Peter L. Ralph ◽

Gideon Bradburd ◽

Erik Lundgren ◽

...

Keyword(s):

Gene Flow ◽

Genetic Resistance ◽

Habitat Modeling ◽

Desert Tortoise ◽

Conservation Genomics ◽

California Department ◽

Resistance Distance ◽

Tissue Samples ◽

Continuous Space ◽

Landscape Genomics

The California Department of Fish and Wildlife (CDFW) provided research funds to study the conservation genomics and landscape genomics of the Mojave desert tortoise, Gopherus agassizii, in response to the Desert Renewable Energy Conservation Plan (DRECP). To do this, we consolidated tissue samples of the desert tortoise from across the species range within California and southern Nevada, generated a DNA dataset consisting of full genomes of 270 tortoises, and analyzed the way in which the environment of the desert tortoise has determined modern patterns of relatedness and genetic diversity across the landscape. Here we present the implications of these results for the conservation and landscape genomics of the desert tortoise. Our work strongly indicates that several well-defined genetic groups exist within the species, including a primary north-south genetic discontinuity at the Ivanpah Valley and another separating western from eastern Mojave samples. We also use existing desert tortoise habitat modeling data with a novel extension of genetic "resistance distance" using geographic maps of continuous space to predict the relative impacts of five proposed development alternatives within the DRECP and rank them with respect to their likely impacts on desert tortoise gene flow and connectivity in the Mojave. Finally, we analyzed the impacts of each of the 214 distinct proposed development area "chunks", derived from the proposed development polygons, and ranked each chunk in terms of its range-wide impacts on desert tortoise gene flow.

Download Full-text

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

10.1101/2021.04.09.439138 ◽

2021 ◽

Author(s):

Thomas K. F. Wong ◽

Teng Li ◽

Louis Ranjard ◽

Steven Wu ◽

Jeet Sukumaran ◽

...

Keyword(s):

Dna Sequences ◽

Dna Barcode ◽

Real Data ◽

Reference Sequence ◽

Nucleotide Polymorphisms ◽

Data Set ◽

Single Nucleotide ◽

Short Read ◽

Pooled Samples ◽

Haplotype Information

AbstractA current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian model of inference to estimates the phylogeny of the haplotypes and their relative frequencies, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and frequencies of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.

Download Full-text

The California environmental DNA “CALeDNA” program

10.1101/503383 ◽

2019 ◽

Cited By ~ 4

Author(s):

Rachel S Meyer ◽

Emily E Curd ◽

Teia Schweizer ◽

Zack Gold ◽

Dannise Ruiz Ramos ◽

...

Keyword(s):

Environmental Dna ◽

Conservation Genomics ◽

The Public ◽

Biodiversity Inventories ◽

Research And Education ◽

Science Framework ◽

Community Complexity ◽

Community Science ◽

Threaten Species ◽

The University

AbstractGlobal change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program, a community science initiative monitoring California’s biodiversity through environmental DNA (eDNA)—DNA shed from organisms through fur, mucus, spores, pollen, etc. Community scientists collect soil and sediment samples, then researchers analyze the eDNA in the samples and share results with the public. The results are catalogues of thousands of organisms per sample, ranging from microbes to mammals. The CALeDNA website presents biodiversity inventories in a platform designed for the public and researchers alike, as well as user-friendly analysis tools and educational modules. Here, we present CALeDNA as a scalable community science framework that can harmonize with future biodiversity research and education initiatives.

Download Full-text