PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers (Q36692219)

15 August 2017

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers (English)

1 reference

15 August 2017

Linnéa Smeds

3

0 references

Hans Ellegren

series ordinal

4

object named as

Hans Ellegren

1 reference

15 August 2017

2

Reto Burri

1 reference

PMCID

4793928

Krystyna Nadachowska-Brzyska

15 August 2017

series ordinal

1

object named as

Krystyna Nadachowska-Brzyska

1 reference

15 August 2017

21 January 2016

1 reference

15 August 2017

1 reference

15 August 2017

25

1 reference

15 August 2017

5

1 reference

15 August 2017

1058-1072

1 reference

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Evolution of Darwin's finches and their beaks revealed by genome sequencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Gibbon genome and the fast karyotype evolution of small apes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Detecting past changes of effective population size

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Genome sequencing highlights the dynamic early history of dogs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Characterizing bias in population genetic inferences from low-coverage sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Genome sequencing and population genomics in non-model organisms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The tiger genome and comparative analysis with lion and snow leopard genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Inferring the demographic history of European Ficedula flycatcher populations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Population genomics based on low coverage sequencing: how low should we go?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Analyses of pig genomes provide insight into porcine demography and evolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The genomic landscape of species divergence in Ficedula flycatchers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Deep evolutionary lineages in a Western Mediterranean snake (Vipera latastei/monticola group) and high genetic structuring in Southern Iberian populations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Increased divergence but reduced variation on the Z chromosome relative to autosomes in Ficedula flycatchers: differential introgression or the faster-Z effect?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Consequences of range contractions and range shifts on molecular diversity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Inference of human population history from individual whole-genome sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Genetic structure and diversity in Ramonda myconi (Gesneriaceae): effects of historical climate change on a preglacial relict species

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Skyline-plot methods for estimating demographic history from nucleotide sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

A framework for variation discovery and genotyping using next-generation DNA sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Approximate Bayesian Computation (ABC) in practice.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Speciation in Ficedula flycatchers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Ecology and genetics of speciation in Ficedula flycatchers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The Sequence Alignment/Map format and SAMtools

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Fast and accurate short read alignment with Burrows-Wheeler transform

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Bayesian inference of population size history from multiple loci

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Sex chromosome-linked species recognition and evolution of reproductive isolation in flycatchers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Molecular biogeography of Europe: Pleistocene cycles and postglacial trends

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

A northern glacial refugium for bank voles (Clethrionomys glareolus)

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Bayesian coalescent inference of past population dynamics from molecular sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Genetic consequences of climatic oscillations in the Quaternary

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The incomplete natural history of mitochondria

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The study of structured populations--new hope for a difficult and divided science

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Approximate Bayesian computation in population genetics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Adjustment to climate change is constrained by arrival date in a long-distance migrant bird

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Speciation, hybrid zones and phylogeography - or seeing genes in space and time

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

An integrated framework for the inference of viral population history from reconstructed genealogies.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

The genetic legacy of the Quaternary ice ages

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Comparative phylogeography and postglacial colonization routes in Europe

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Inferring human population size and separation history from multiple genome sequences

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Glacial survival of boreal trees in northern Scandinavia

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Phylogeography and genetic structure of the red-legged partridge (Alectoris rufa): more evidence for refugia within the Iberian glacial refugium

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Phylogeography of Southern Water Vole (Arvicola sapidus): evidence for refugia within the Iberian glacial refugium?

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Molecular phylogeography of the nose-horned viper (Vipera ammodytes, Linnaeus (1758)): evidence for high genetic diversity and multiple refugia in the Balkan peninsula.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Testing the genetics underlying the co-evolution of mate choice and ornament in the wild.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Approximating the coalescent with recombination

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Cryptic evolution in a wild bird population.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Adaptive plasticity in mate preference linked to differences in reproductive effort.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Lifetime Reproductive Success and Heritability in Nature.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4793928

Approximate Bayesian Computation in Evolution and Ecology

5 September 2018

1 reference

Single‐Generation Estimates of Individual Fitness as Proxies for Long‐Term Genetic Contribution

21 January 2018

1 reference

Revealing the demographic histories of species using DNA sequences

21 January 2018

1 reference

Effective population size/adult population size ratios in wildlife: a review

21 January 2018

1 reference

Post-glacial re-colonization of European biota

21 January 2018

1 reference

Lifetime Reproductive Success and Heritability in Nature

21 January 2018

1 reference

A new bird species? The taxonomic status of ‘the Atlas Flycatcher’ assessed from DNA sequence analysis

21 January 2018

1 reference

Hybridization and adaptive mate choice in flycatchers

21 January 2018

1 reference

Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca)

21 January 2018

1 reference

Female pied flycatchers choose territory quality and not male characteristics

21 January 2018

1 reference

Acceleration of senescence in the collared flycatcher Ficedula albicollis by reproductive costs

21 January 2018

1 reference

The costs of reproduction in the collared flycatcher Ficedula albicollis

21 January 2018

1 reference

Trade-offs between life-history traits and a secondary sexual character in male collared flycatchers

21 January 2018

1 reference

Large variance in reproductive success and the Ne/N ratio

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26797914

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

HALDANE'S RULE AND SEX BIASSED GENE FLOW BETWEEN TWO HYBRIDIZING FLYCATCHER SPECIES (FICEDULA ALBICOLLIS AND F. HYPOLEUCA, AVES: MUSCICAPIDAE)

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26797914

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1111/MEC.13540

1 reference

15 August 2017

1 reference

15 August 2017

1 reference

PMCID

4793928