Each panel is one measure, titled with its column name in the snapshot
history. Each color is one membership rule; the dashed line is snapshots
rebuilt from studbook dates.
Which way each panel moves
-
fe, fg and neGD (founder equivalents, founder genome equivalents
and gene diversity): higher means more of the founders' diversity is
still in the colony. fe falls when the founders' contributions grow more
unequal; fg and neGD also fall when founder alleles are lost by chance.
neGD is a share between 0 and 1, not a number of animals.
-
nFounders, nMaleFounders and nFemaleFounders: the known founders
(animals with no recorded parents) among the analyzed animals and their
ancestors. They rise when such an animal joins, an import for example;
in a series of living animals they also fall when a founder and all its
descendants have left.
-
neSexRatio and neVariance (the sex-ratio and variance effective
sizes, counted over the living breeders): higher means less diversity is
lost each generation. neSexRatio falls when breeding relies on few
animals of one sex; neVariance falls when a few breeders produce most of
the offspring. Read each as an index, not a head count.
-
meanIndivMeanKin and medianIndivMeanKin: the colony's average and
median of each animal's mean kinship. A rise means the animals are, on
average, more closely related to the rest of the colony.
-
meanGu and medianGu (genome uniqueness): neither direction is
better. They fall when a rare founder allele is lost, and also when
breeding spreads it into more animals, so a fall alone is not a loss; fg
and neGD show loss.
-
The skewness and kurtosis panels: the shape of the spread across
animals, not a measure of health. Positive skewness means a few animals
with unusually high values stretch the upper tail.
-
fgSE and meanGuSE: how precise fg and meanGu are, not how healthy
the colony is. They shrink when more gene-drop iterations are run.
When a change is real
-
The grey band around fg and meanGu spans one standard error on each side
of each point. A change smaller than the bands can come from the random
sampling alone.
-
fe, the founder counts, the effective sizes and the mean-kinship panels
have no band because they are calculated without random sampling: a
change in them is a change in the records. The other genome-uniqueness
panels have no band but come from the same sampling as meanGu.
-
A point drawn with a different shape was taken with different settings
(the number of gene-drop iterations, the rare-allele threshold or the
package version) than the point before it, and the caption names the
change; a jump there may come from the settings, not the colony.
What a past trend can answer
-
How fast founder diversity is being lost: the slope of fg and neGD
across the years.
-
Whether an import or a change in breeding shows: an unrelated import
with no recorded parents lowers mean kinship and raises the founder
counts as soon as it is in the population, and raises fe and fg once it
has offspring there. A change in breeding practice shows as a change of
slope from that year on, for example a fall in neSexRatio when fewer
sires are used.
-
A baseline: rebuilt years let today's snapshot of the living animals be
read against the colony's past instead of alone.