A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide

Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation

(2019) Alexandre Lemopoulos et al.   Ecology and Evolution

Too much of a good thing? Finding the most informative genetic dataset to answer conservation questions

(2019) Elspeth A. McLennan et al.   Molecular Ecology Resources

Little Adaptive Potential in a Threatened Passerine Bird

(2019) Pierre de Villemereuil et al.   CURRENT BIOLOGY

Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations

(2019) David Wildt et al.   BIOSCIENCE

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Genotyping-by-sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias

(2018) Catherine R. M. Attard et al.   Molecular Ecology Resources

Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird

(2018) Derrick J. Thrasher et al.   Molecular Ecology Resources

Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild

(2018) Catherine E. Grueber et al.   Evolutionary Applications

The Peril of Gene-Targeted Conservation

(2018) Marty Kardos et al.   TRENDS IN ECOLOGY & EVOLUTION

Founder relationships and conservation management: empirical kinships reveal the effect on breeding programmes when founders are assumed to be unrelated

(2018) C. J. Hogg et al.   ANIMAL CONSERVATION

Effectiveness of SNPs for parentage and sibship assessment in polygamous yellowtail kingfish Seriola lalandi

(2018) H.K.A. Premachandra et al.   AQUACULTURE

Parentage assignment with genotyping‐by‐sequencing data

(2018) Andrew Whalen et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

The future of parentage analysis: from microsatellites to SNPs and beyond

(2018) Sarah P. Flanagan et al.   MOLECULAR ECOLOGY

Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data

(2018) Ryan K Waples et al.   MOLECULAR ECOLOGY

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

(2018) Stephanie J. Galla et al.   Genes

Estimating pairwise relatedness in a small sample of individuals

(2017) J Wang   HEREDITY

Contrasting Patterns of Gene Flow for Amazonian Snakes That Actively Forage and Those That Wait in Ambush

(2017) Rafael de Fraga et al.   JOURNAL OF HEREDITY

Using relatedness networks to infer contemporary dispersal: Application to the endangered mammal Galemys pyrenaicus

(2017) Lídia Escoda et al.   MOLECULAR ECOLOGY

Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population

(2017) Pirmin Nietlisbach et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Increasing generations in captivity is associated with increased vulnerability of Tasmanian devils to vehicle strike following release to the wild

(2017) Catherine E. Grueber et al.   Scientific Reports

No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding

(2017) Rebecca Gooley et al.   Scientific Reports

Evaluation of alternative management strategies for maintenance of genetic variation in wildlife populations

(2016) R. M. Giglio et al.   ANIMAL CONSERVATION

Role of genomics and transcriptomics in selection of reintroduction source populations

(2016) Xiaoping He et al.   CONSERVATION BIOLOGY

A novel holistic framework for genetic-based captive-breeding and reintroduction programs

(2016) C.R.M. Attard et al.   CONSERVATION BIOLOGY

Genomics advances the study of inbreeding depression in the wild

(2016) Marty Kardos et al.   Evolutionary Applications

Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding

(2016) U Knief et al.   HEREDITY

Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs

(2016) Jamie A. Ivy et al.   JOURNAL OF HEREDITY

Within-group relatedness is correlated with colony-level social structure and reproductive sharing in a social fish

(2016) Jennifer K. Hellmann et al.   MOLECULAR ECOLOGY

Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances

(2016) Stephanie J. Galla et al.   MOLECULAR ECOLOGY

Pedigrees or markers: Which are better in estimating relatedness and inbreeding coefficient?

(2016) Jinliang Wang   THEORETICAL POPULATION BIOLOGY

Pedigree analysis for the genetic management of group-living species

(2016) Belén Jiménez-Mena et al.   Ecology and Evolution

A pedigree gone bad: increased offspring survival after using DNA-based relatedness to minimize inbreeding in a captive population

(2015) S. C. Hammerly et al.   ANIMAL CONSERVATION

Construction of relatedness matrices using genotyping-by-sequencing data

(2015) Ken G. Dodds et al.   BMC GENOMICS

Influence of genetic provenance and birth origin on productivity of the Tasmanian devil insurance population

(2015) Carolyn J. Hogg et al.   CONSERVATION GENETICS

Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity

(2015) Helen R. Taylor et al.   CONSERVATION GENETICS

Quantifying realized inbreeding in wild and captive animal populations

(2015) U Knief et al.   HEREDITY

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

(2015) M Kardos et al.   HEREDITY

The use and abuse of genetic marker-based estimates of relatedness and inbreeding

(2015) Helen R. Taylor   Ecology and Evolution

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Combining genetic data to identify relatedness among founders in a genetically depauperate parrot, the Kakapo (Strigops habroptilus)

(2014) Laura M. Bergner et al.   CONSERVATION GENETICS

Using genomics to characterize evolutionary potential for conservation of wild populations

(2014) Katherine A. Harrisson et al.   Evolutionary Applications

Measuring Relatedness between Inbred Individuals

(2014) P. W. Hedrick et al.   JOURNAL OF HEREDITY

The impacts of inbreeding, drift and selection on genetic diversity in captive breeding populations

(2014) Janna R. Willoughby et al.   MOLECULAR ECOLOGY

Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

(2014) Camillo Bérénos et al.   MOLECULAR ECOLOGY

Relatedness in the post-genomic era: is it still useful?

(2014) Doug Speed et al.   NATURE REVIEWS GENETICS

High-throughput sequencing reveals inbreeding depression in a natural population

(2014) J. I. Hoffman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Variation in actual relationship among descendants of inbred individuals

(2013) W. G. HILL et al.   Genetics Research

Kinship-Based Management Strategies for Captive Breeding Programs When Pedigrees Are Unknown or Uncertain

(2013) A. S. Putnam et al.   JOURNAL OF HEREDITY

Estimating relatedness and inbreeding using molecular markers and pedigrees: the effect of demographic history

(2013) S. P. Robinson et al.   MOLECULAR ECOLOGY

A comparison of pedigree- and DNA-based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie-chicken

(2013) Susan C. Hammerly et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update

(2012) R. Peakall et al.   BIOINFORMATICS

Extending Pedigree Analysis for Uncertain Parentage and Diverse Breeding Systems

(2012) Robert C. Lacy   JOURNAL OF HEREDITY

A Comparison of Strategies for Selecting Breeding Pairs to Maximize Genetic Diversity Retention in Managed Populations

(2012) Jamie A. Ivy et al.   JOURNAL OF HEREDITY

Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation

(2012) WOLFGANG FORSTMEIER et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Characterisation of microsatellite loci in the critically endangered orange-fronted kākāriki (Cyanoramphus malherbi) isolated using genomic next generation sequencing

(2012) B. Jane Andrews et al.   Conservation Genetics Resources

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Using microsatellite diversity in wild Anegada iguanas (Cyclura pinguis) to establish relatedness in a captive breeding group of this critically endangered species

(2011) Adele A. Mitchell et al.   CONSERVATION GENETICS

Quantification of Inbreeding Due to Distant Ancestors and Its Detection Using Dense Single Nucleotide Polymorphism Data

(2011) Matthew C. Keller et al.   GENETICS

Variation in actual relationship as a consequence of Mendelian sampling and linkage

(2011) W.G. HILL et al.   Genetics Research

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Conservation genetic management of a critically endangered New Zealand endemic bird: minimizing inbreeding in the Black Stilt Himantopus novaezelandiae

(2011) ERIN N. HAGEN et al.   IBIS

Decision analysis for conservation breeding: Maximizing production for reintroduction of whooping cranes

(2011) Des H.V. Smith et al.   JOURNAL OF WILDLIFE MANAGEMENT

Dye shift: a neglected source of genotyping error in molecular ecology

(2011) JOLENE T. SUTTON et al.   Molecular Ecology Resources

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

(2011) Jarrod A. Chapman et al.   PLoS One

A Comparison of Approaches to Estimate the Inbreeding Coefficient and Pairwise Relatedness Using Genomic and Pedigree Data in a Sheep Population

(2011) Meng-Hua Li et al.   PLoS One

PMx: software package for demographic and genetic analysis and management of pedigreed populations

(2011) Robert C. Lacy et al.   Methods in Ecology and Evolution

Status of the California Condor (Gymnogyps californianus) and Efforts to Achieve Its Recovery

(2010) Jeffrey R. Walters et al.   AUK

Genetic analyses reveal hybridization but no hybrid swarm in one of the world’s rarest birds

(2010) TAMMY E. STEEVES et al.   MOLECULAR ECOLOGY

On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs

(2010) ANNA W. SANTURE et al.   MOLECULAR ECOLOGY

coancestry: a program for simulating, estimating and analysing relatedness and inbreeding coefficients

(2010) JINLIANG WANG   Molecular Ecology Resources

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Methods and Prospects for Using Molecular Data in Captive Breeding Programs: An Empirical Example Using Parma Wallabies (Macropus parma)

(2009) Jamie A. Ivy et al.   JOURNAL OF HEREDITY

Molecular genetic analysis of a captive-breeding program: the vulnerable endemic Jamaican yellow boa

(2008) Athanasia C. Tzika et al.   CONSERVATION GENETICS

Development of polymorphic microsatellite markers for the New Zealand black stilt (Himantopus novaezelandiae) and cross-amplification in the pied stilt (Himantopus himantopus leucocephalus)

(2008) TAMMY E. STEEVES et al.   Molecular Ecology Resources

Wild pedigrees: the way forward

(2008) J.M Pemberton   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic adaptation to captivity in species conservation programs

(2007) RICHARD FRANKHAM   MOLECULAR ECOLOGY