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Casein haplotypes were inferred within each of the four loci using BEAGLE.
Hence, the contamination inferred within these zones along profiles 1 and 3 might be the result of percolating leachate from the topsoil.
Internal interfaces could also be imaged if the attenuation was higher than that inferred within volcanic plains on Mars, but not as high as measured in a strongly fractured volcanic tuff on Earth.
Furthermore, lower-level relationships inferred within Suloidea exhibit varying degrees of congruence and conflict between molecular and morphological datasets.
When one of the parental sequences implicated in an event could not be inferred within the sequence alignment, it was denoted as "unknown parental".
Note however, that two reversals to state "2" are inferred within the Fregata + Suloidea clade in the MPTs: one on the lineage leading to Plotopteridae, and one on the lineage leading to non-'microcormorant' Phalacrocorax.
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To investigate the diversity change, we inferred within- and between-host mean diversities for the 1980s and the 2000s, respectively, using the nucleotide diversity, π, implemented in MEGA4 under the K80+G model again.
To infer within-population dynamics of CMS, we searched for polymorphisms in CMS or restorers in either of the populations.
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.
Only duplication nodes with d S < 2 (to avoid saturation as found in Vanneste et al. 2013), and d S ≥ 0.01 (to avoid incorrectly inferring within-species allelic variants or isoforms as paralogs) were analyzed.
First, strain pairs collected from the nasopharynx and lungs of individual hosts with pulmonary infection (rather than from healthy and sick hosts, respectively) should be used to infer within-host evolution.
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