Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. [PDF]
PLoS Genetics, 2016 Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material.
Claudia Solís-Lemus, Cécile Ané
doaj +8 more sources
TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting. [PDF]
PLoS Genetics, 2023 Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny.
Iker Rivas-González +3 more
doaj +4 more sources
Incomplete lineage sorting is common in extant gibbon genera. [PDF]
PLoS ONE, 2013 We sequenced reduced representation libraries by means of Illumina technology to generate over 1.5 Mb of orthologous sequence from a representative of each of the four extant gibbon genera (Nomascus, Hylobates, Symphalangus, and Hoolock).
Jeffrey D Wall +6 more
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Parsimonious inference of hybridization in the presence of incomplete lineage sorting. [PDF]
Syst Biol, 2013 Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and
Yu Y, Barnett RM, Nakhleh L.
europepmc +7 more sources
Coalescent simulations reveal hybridization and incomplete lineage sorting in Mediterranean Linaria. [PDF]
PLoS ONE, 2012 We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnL(UAG), trnS-trnG).
José Luis Blanco-Pastor +2 more
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Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data. [PDF]
PLoS Computational Biology, 2016 Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species.
Andrej Kuritzin +3 more
doaj +4 more sources
Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression [PDF]
eLife, 2020 The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences – a phenomenon known as hemiplasy ...
Mark S Hibbins +2 more
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Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization [PDF]
BMC Evolutionary Biology, 2012 Background Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification.
Thomé Maria Tereza C +3 more
doaj +7 more sources
Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships [PDF]
PeerJ, 2020 Recent and continued progress in the scale and sophistication of phylogenetic research has yielded substantial advances in knowledge of the tree of life; however, segments of that tree remain unresolved and continue to produce contradicting or unstable ...
Matthew A. Campbell +3 more
doaj +5 more sources
Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species [PDF]
PeerJ, 2021 Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis.
José Cerca +6 more
doaj +3 more sources