Abstract:
:Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first-, second- and third-degree relationships between the focal individuals, as well as the traditional alternative of being unrelated. This careful exploration of the local likelihood surface is implemented in a fast, heuristic hill-climbing algorithm. Distinction between the various categories of second-degree relatives is possible when likelihoods are calculated conditional on at least one parent of each focal individual. Performance was tested on simulated data sets with realistic genotyping error rate and missingness, based on three different large pedigrees (N = 1000-2000). This included a complex pedigree with overlapping generations, occasional close inbreeding and some unknown birth years. Parentage assignment was highly accurate down to about 100 independent SNPs (error rate <0.1%) and fast (<1 min) as most pairs can be excluded from being parent-offspring based on opposite homozygosity. For full pedigree reconstruction, 40% of parents were assumed nongenotyped. Reconstruction resulted in low error rates (<0.3%), high assignment rates (>99%) in limited computation time (typically <1 h) when at least 200 independent SNPs were used. In three empirical data sets, relatedness estimated from the inferred pedigree was strongly correlated to genomic relatedness.
journal_name
Mol Ecol Resourjournal_title
Molecular ecology resourcesauthors
Huisman Jdoi
10.1111/1755-0998.12665subject
Has Abstractpub_date
2017-09-01 00:00:00pages
1009-1024issue
5eissn
1755-098Xissn
1755-0998journal_volume
17pub_type
杂志文章abstract::We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02710.x
更新日期:2009-11-01 00:00:00
abstract::Thirty-eight microsatellite loci were developed for the bird pollinated, autohexaploid, Eremophila glabra ssp. glabra. A genomic library was screened with dinucleotide and trinucleotide sequence repeats. Polymorphism ranged from one to 21 alleles per locus. Twenty-four loci exhibited null alleles, based on patterns of...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02618.x
更新日期:2009-07-01 00:00:00
abstract::Stegodyphus lineatus spiders live in groups consisting of closely related individuals. There appears to be no discrimination against related individuals as mates but females mate multiply, despite the fact that matings are shown to carry a cost. We have developed eight polymorphic dinucleotide microsatellite markers t...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02296.x
更新日期:2009-01-01 00:00:00
abstract::Chimpanzee populations are diminishing as a consequence of human activities, and as a result this species is now endangered. In the context of conservation programmes, genetic data can add vital information, for instance on the genetic diversity and structure of threatened populations. Single nucleotide polymorphisms ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.02000.x
更新日期:2008-05-01 00:00:00
abstract::Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high-quality chromosome-scale genome was a...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13291
更新日期:2020-11-05 00:00:00
abstract::The emergence of third-generation sequencing (3GS; long-reads) is bringing closer the goal of chromosome-size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of nonmodel organisms. However, long-read technologies result in higher sequenc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13176
更新日期:2020-09-01 00:00:00
abstract::Collectively called zooxanthellae, photosynthetic dinoflagellates in the family Symbiodiniaceae are typical endosymbionts that unequivocally mediate coral responses to environmental changes. Symbiodiniaceae are genetically diverse, encompassing at least nine phylogenetically distinct genera (clades A-I). The ribosomal...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.13250
更新日期:2021-01-01 00:00:00
abstract::This article documents the public availability of approximately 15 000 polymorphic SNP loci for the bighorn sheep Ovis canadensis. ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12142
更新日期:2013-09-01 00:00:00
abstract::Our understanding of Glossina fuscipes fuscipes, a major vector of sleeping sickness, has been severely constrained by a lack of genetic markers for mapping and population genetic studies. Here we present 10 newly developed microsatellite loci for this tsetse species. Heterozygosity levels in Moyo, an Ugandan populati...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02328.x
更新日期:2008-11-01 00:00:00
abstract::We tested for cross-species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one o...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02575.x
更新日期:2009-07-01 00:00:00
abstract::A variety of challenges arise when monitoring wildlife populations for disease. Sampling tissues can be invasive to hosts, and obtaining sufficient sample sizes can be expensive and time-consuming, particularly for rare species and when pathogen prevalence is low. Environmental DNA (eDNA)-based detection of pathogens ...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12461
更新日期:2016-03-01 00:00:00
abstract::We report results of cross-species amplification in Dactylis glomerata and Lolium perenne of 12 simple sequence repeats (SSRs) isolated from Lolium multiflorum×Festuca glaucescens, 42 SSRs from Festuca arundinacea and two sequence tagged sites from Oryza sativa. We compared the transferability and diversity between D....
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02168.x
更新日期:2009-01-01 00:00:00
abstract::Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12379
更新日期:2015-09-01 00:00:00
abstract::Biodiversity analyses based on next-generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of suc...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12472
更新日期:2016-03-01 00:00:00
abstract::Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of ha...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12235
更新日期:2014-07-01 00:00:00
abstract::Degraded DNA from suboptimal field sampling is common in molecular ecology. However, its impact on techniques that use restriction site associated next-generation DNA sequencing (RADSeq, GBS) is unknown. We experimentally examined the effects of in situDNA degradation on data generation for a modified double-digest RA...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12404
更新日期:2015-11-01 00:00:00
abstract::We isolated 18 microsatellites from Sycoscapter australis, a nonpollinating fig wasp that develops in figs of Ficus macrophylla, and assessed their variability in 20 wasps. We further optimized nine of these loci for use in three other Sycoscapter species that develop in Ficus rubiginosa figs and assessed their variab...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02284.x
更新日期:2009-05-01 00:00:00
abstract::Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02447.x
更新日期:2009-03-01 00:00:00
abstract::Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and descr...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.12023
更新日期:2013-01-01 00:00:00
abstract::Twelve polymorphic microsatellite loci were isolated for the bonefish, Albula vulpes using a polymerase chain reaction-based procedure. The number of alleles ranged from two to 23 (mean = 8.8) in 37 specimens from south Florida. Observed and expected heterozygosities ranged from 0.07 to 0.77 (mean = 0.42) and from 0.0...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01954.x
更新日期:2008-03-01 00:00:00
abstract::The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS....
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12622
更新日期:2017-07-01 00:00:00
abstract::To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the techni...
journal_title:Molecular ecology resources
pub_type: 杂志文章,评审
doi:10.1111/1755-0998.13247
更新日期:2021-01-01 00:00:00
abstract::The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the s...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12979
更新日期:2019-03-01 00:00:00
abstract::Adaptation to different ecological environments can promote speciation. Although numerous examples of such 'ecological speciation' now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of th...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2012.03121.x
更新日期:2012-05-01 00:00:00
abstract::With striking morphological diversity and adaptability, Chamaedorea palms constitute an ecologically and economically important understorey component of Neotropical forests. Nine loci developed for Chamaedorea elegans evaluated in three Veracruz populations resulted in a large number of alleles (8-18), and high expect...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01942.x
更新日期:2008-03-01 00:00:00
abstract::Asian arowana or dragonfish (Scleropages formosus) is an important fish species due to its unusual breeding biology and high economic value in the ornamental fish markets. In the present study, we aimed to (i) create the first transcriptome by Roche 454 pyrosequencing of Asian arowana brain and gonad samples; (ii) ide...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/1755-0998.12212
更新日期:2014-05-01 00:00:00
abstract::We report the development of 60 microsatellite markers on four species of the fungal complex Microbotryum, causing anther smut of the Caryophyllaceae. Microsatellites were found in four expressed sequence tag (EST) libraries, built from isolates of M. lychnis-dioicae, M. violaceum sensus stricto, M. lagerheimii and M....
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01967.x
更新日期:2008-03-01 00:00:00
abstract::We isolated and characterized 52 novel microsatellite markers from Florida largemouth bass, Micropterus salmoides floridanus, for use in conservation, management and population genetic studies. Markers were assessed in M. s. floridanus from peninsular Florida (n = 30) and averaged eight alleles per locus with observed...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1471-8286.2007.01917.x
更新日期:2008-01-01 00:00:00
abstract::Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used fo...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2009.02699.x
更新日期:2009-09-01 00:00:00
abstract::Crepidula convexa, a calyptreid gastropod with direct embryonic development, changes sex from male to female in the course of its lifetime (protandry). Under sex-allocation theory, male reproductive success should be independent from age and size (a proxy used for age). However, this may be counterbalanced by female c...
journal_title:Molecular ecology resources
pub_type: 杂志文章
doi:10.1111/j.1755-0998.2008.02479.x
更新日期:2009-05-01 00:00:00