swsc: A sitewise UCE partitioner

swsc reduces the combinatorially explosive search space for effective ultraconserved element (UCE) partitioning schemes through use of a candidate window plus extension procedure. It is a development on the best UCE partitioning procedure described by Tagliacollo, V. A., & Lanfear, R. (2018) (https://doi.org/10.1093/molbev/msy069)

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations

Additional file 2: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Supplementary Materials detailing permits, genome assembly, MAKER annotation, Demographic history reconstruction- Propithecus and Microcebus, VCF Filtration. (DOCX 31 kb

Additional file 9: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Results of read mapping of published lemur reference genomes. Accession numbers, coverage, standard deviation, variants and origin of tissue are listed below. (DOCX 46 kb

Additional file 3: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Comparison of scaffolds and contigs across different assembly programs. The top row shows the largest 1000 and 10,000 scaffolds across each program (from left to right) and the bottom row displays the longest 5000 and 50,000 contigs. ALLP in the figure caption represents the ALLPATHS assembly. (JPG 3784 kb

Additional file 11: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

PSMC estimates of effective population size following Pleistocene bottleneck. (DOCX 35 kb

Additional file 14: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Historical range calculations based on varying levels of forest buffer. Forest area is given in square kilometers. (DOCX 39 kb

Additional file 8: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Statistics from mitochondrial genomes from the five Prolemur simus and one Hapalemur griseus. Coverage statistics as well as the GenBank Accession numbers are listed. (DOCX 61 kb

Additional file 5: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

GenomeScope Profile of the KIAN8.4 high coverage genome. (TIFF 2484 kb