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Among the surveyed ardeid birds, the major phylogenetic controversies have been related to the classifications of the A. ibis, A. modesta, A. intermedia and I. flavicollis and to the genus relationships within Ardeinae [ 39– 45].
Considering those five main plant genera, a close genus-to-genus relationship exists between them and some primarily frugivorous bat genera.
Within-genus relationships for genera with many representatives were inferred by the inclusion of as many gene sequences as possible.
To infer within-genus relationships, ortholog families shared by all members of a genus were aligned at the protein level and the gaps were copied into the nucleotide sequence to generate nucleotide (nt) alignments.
Ribosomal DNA (rDNA) sequences are most useful for resolving ("genus" level) relationships near the tips of the dinoflagellate tree [12], [17] [21].
Deeper sampling within both families is needed to resolve family and genus level relationships.
Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships.
As ≥40% similarity indicates a genus-level relationship [ 35], we can conclude that JG068 is a novel member of the Autographivirinae subfamily and the ϕKMV-like phages genus.
While nuclear, mtDNA sequence data and AFLP data do not support monophyly for this genus, the relationships among Stenella species and other members of the subfamily do differ significantly between the data types.
Only whole genome sequence could help resolve the mystery of the strain Bairam-Ali and clarify its phylogenetic position in the Leptospira genus and relationships with the pathogenic Leptospira species.
We used Cyt B to determine the divergence time between the Northern and Southern lineage and the population clusters of túngara frogs, because this gene has been proven useful for intraspecific and genus level relationships in several amphibian species [ 2, 75- 77].
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