Some classic examples in animals include assortative mating by body size in stickleback species pairs [ 11] and by body shape in Gambusia mosquitofish [ 12].
Although the extent of alternative splicing of kinesin pre-mRNAs in plants is not known, there are examples in animals where alternative splicing of some kinesins results in generation of isoforms with different domains and with distinct functions [ 95, 96].
There is now an increasing number of examples in animals of ROS-based signaling, including protein tyrosine phosphatase 1B (PTP-1B) [ 56], thioredoxin [ 57], SERCA2 [ 58] and Ras [ 59].
Despite these examples of combinatorial signalling, there are no good examples in animal communication studies of individuals acoustically modifying individual calls in patterned ways to produce structurally altered vocalisations with novel meanings.
However, we know from several examples in animal models (such as CED9 alleles in Caenorhabditis elegans and their effect on programmed cell death) and Mendelian genetics (such as loss- and gain-of-function PCSK9 alleles and their effect on LDL-cholesterol) that the same gene can carry alleles that have dramatic phenotypic consequences, but in opposite directions.
For example, in animals, delivering miRNAs into cells can cause their transcriptomes to resemble the transcriptome of the tissue where the miRNA is preferentially expressed [33].
For example, in animals that are sensitized to ova albumin and infected with M. pneumoniae, airway remodeling can be observed suggesting that M. pneumoniae mediated inflammatory responses are capable of causing long-term lung damage [10].
This type of analysis is particularly relevant to EST studies as the probability of obtaining a full complement of taxa for a particular ortholog is reduced as the number of taxa in the analysis increases (see [53] for an example in animals).
For example, in animals and yeast, SUMO modifications affect cell cycle progression, DNA replication and repair, protein activity and stability, chromatin structural maintenance, subcellular localization and transcriptional regulation, as well as oxidative stress responses [ 4, 5, 10, 14– 17].
For example, in animals, many phylogenies continue to be estimated based on mitochondrial (mtDNA) data alone [e.g. [ 9- 12]], or a combined (concatenated) analysis of nuclear (nucDNA) and mtDNA data [e.g. [ 13- 18]].
For example, in animal models opioid agonists reduce isolation distress whereas opioid antagonists increase isolation distress.
