Table 1.
Open in new tab

Number of Primate Genes Trees and Gene Copies Included with Different Filtering Approaches.

FilterMIN4MIN27
Gene familiesGene copiesGene familiesGene copies
Single-copy clusters5,77194,9941,82051,733
Lineage-specific duplicates (LSD)13,627297,8317,693219,441
Two-species duplicates (TSD)14,931332,7188,719248,759
Maximum inclusion27,880331,9904,849137,733
Maximuminclusion (LSD)22,360464,22411,479327,434
Maximuminclusion (TSD)21,793473,00012,046343,652
Monophyleticoutgroups9,724200,5034,805136,749
Monophyleticoutgroups (LSD)16,962387,91510,222291,374
Monophyleticoutgroups (TSD)17,104390,58410,254292,257
Subtreeextraction20,562470,46512,198347,994
Allparalogs18,484568,34211,555454,509
Oneparalogs18,484428,12911,555330,115
FilterMIN4MIN27
Gene familiesGene copiesGene familiesGene copies
Single-copy clusters5,77194,9941,82051,733
Lineage-specific duplicates (LSD)13,627297,8317,693219,441
Two-species duplicates (TSD)14,931332,7188,719248,759
Maximum inclusion27,880331,9904,849137,733
Maximuminclusion (LSD)22,360464,22411,479327,434
Maximuminclusion (TSD)21,793473,00012,046343,652
Monophyleticoutgroups9,724200,5034,805136,749
Monophyleticoutgroups (LSD)16,962387,91510,222291,374
Monophyleticoutgroups (TSD)17,104390,58410,254292,257
Subtreeextraction20,562470,46512,198347,994
Allparalogs18,484568,34211,555454,509
Oneparalogs18,484428,12911,555330,115

LSD and TSD indicate when lineage-specific and both lineage-specific and two-species specific duplicates were trimmed; the SE method trims these automatically. The MIN4 data set required a minimum of 4 taxa (out of 29 total), while the MIN27 data set required a minimum of 27 taxa.

Table 1.
Open in new tab

Number of Primate Genes Trees and Gene Copies Included with Different Filtering Approaches.

FilterMIN4MIN27
Gene familiesGene copiesGene familiesGene copies
Single-copy clusters5,77194,9941,82051,733
Lineage-specific duplicates (LSD)13,627297,8317,693219,441
Two-species duplicates (TSD)14,931332,7188,719248,759
Maximum inclusion27,880331,9904,849137,733
Maximuminclusion (LSD)22,360464,22411,479327,434
Maximuminclusion (TSD)21,793473,00012,046343,652
Monophyleticoutgroups9,724200,5034,805136,749
Monophyleticoutgroups (LSD)16,962387,91510,222291,374
Monophyleticoutgroups (TSD)17,104390,58410,254292,257
Subtreeextraction20,562470,46512,198347,994
Allparalogs18,484568,34211,555454,509
Oneparalogs18,484428,12911,555330,115
FilterMIN4MIN27
Gene familiesGene copiesGene familiesGene copies
Single-copy clusters5,77194,9941,82051,733
Lineage-specific duplicates (LSD)13,627297,8317,693219,441
Two-species duplicates (TSD)14,931332,7188,719248,759
Maximum inclusion27,880331,9904,849137,733
Maximuminclusion (LSD)22,360464,22411,479327,434
Maximuminclusion (TSD)21,793473,00012,046343,652
Monophyleticoutgroups9,724200,5034,805136,749
Monophyleticoutgroups (LSD)16,962387,91510,222291,374
Monophyleticoutgroups (TSD)17,104390,58410,254292,257
Subtreeextraction20,562470,46512,198347,994
Allparalogs18,484568,34211,555454,509
Oneparalogs18,484428,12911,555330,115

LSD and TSD indicate when lineage-specific and both lineage-specific and two-species specific duplicates were trimmed; the SE method trims these automatically. The MIN4 data set required a minimum of 4 taxa (out of 29 total), while the MIN27 data set required a minimum of 27 taxa.

Close
This Feature Is Available To Subscribers Only

Sign In or Create an Account

Close

This PDF is available to Subscribers Only

View Article Abstract & Purchase Options

For full access to this pdf, sign in to an existing account, or purchase an annual subscription.

Close