4.2 | Conservation unit designations in the light of
complex demographic histories
Given current rates of extirpation and extinction, it is imperative to
have strong, scientifically supported management frameworks,
particularly given tight resources for conservation (Jackiw, Mandil, &
Hager, 2015). Recent work shows that admixture between lineages is
common (Coates et al., 2018; vonHoldt et al., 2017), and that new
sequencing technologies are allowing us to uncover the complex
demographic histories of threatened taxa (Supple & Shapiro, 2018;
vonHoldt et al., 2017). Both for caribou and more broadly, now is the
time to decide what this means for management and conservation unit
designations.
Recent discussion has highlighted that ‘hybrid’ level gene flow is not
always negative, particularly in inbred populations or those needing to
adapt to rapid change where admixture could be an important source of
variation (Supple & Shapiro, 2018, vonHoldt et al., 2017). For example,
we find the barrenground caribou to be very admixed and also to have the
lowest individual inbreeding co-efficients, and similarly eastern
migratory caribou from Ontario/Manitoba have lower inbreeding
co-efficients than the non-admixed individuals from Quebec/Labrador
(Table S1). Some argue that gene flow could even be facilitated to aid
populations under threat from climate change (i.e. genetic rescue;
Hamilton & Miller, 2015), which would be easiest between intra-specific
populations (Hedrick & Fredrickson, 2010). Good conservation unit
designations with an understanding of natural patterns of admixture is
key to assess the potential to use such a strategy (Coates et al.,
2018). Most discussions have focussed on policy for inter-species
hybridisation (but see Coates et al., 2018; Supple & Shapiro, 2018),
but a clear framework for conservation unit designation of admixed
intra-specific lineages is needed.
Conservation unit designations depend on the goal of conservation, and
whether the focus is on the preservation of phenotypes (or ‘pure’
genomes), or evolutionary and ecological processes to maintain
resilience of an ecosystem (Fitzpatrick et al., 2015; vonHoldt et al..
2017; Waples & Lindley, 2018). The latter is likely more useful when
attempting to designate units for non-discreet entities, such as we see
in caribou. With this in mind, some authors have suggested a flexible
approach with each case considered on a context specific basis (Jakiw et
al., 2015), whereas others promote the need for a structured and uniform
framework to decide on management decisions (Coates et al., 2018). For
caribou, it seems appropriate for a structured approach in the naming of
subspecies. Coates et al., (2018) suggest that subspecies show local
adaptation with or without gene flow. Coupling this idea with our
phylogenomic and population genomic results and results from previous
studies, Canadian caribou appear to fit into three subspecies; those in
the NAL, those in the BEL, and Peary caribou which sit phylogenetically
in the BEL but show strong population genomic differences and clear
local adaptation of phenotype (Banfield, 1961; COSEWIC, 2011).
The most relevant application of our findings is in the delineation of
conservation units in a species with complex and admixed evolutionary
histories. We recommend that previously defined Designatable Units based
on subspecies and subspecific ecotypes be reconsidered: specifically,
because the boreal caribou from the Northwest Territories sit within a
different lineage to the other caribou within the boreal DU and appear
to have evolved in parallel, they could be split into separate DUs.
Further fine scale work will be needed to refine the boundary of the BEL
boreal vs the NAL boreal DU. Similarly, given the apparent parallel
evolution of the eastern migratory ecotype and the different levels of
admixture of Ontario/Manitoba vs Quebec/Labrador populations with the
BEL lineage, should be divided into separate DUs. Consideration of
whether this will help maximise the resilience of the ecosystem is
needed, but this would match the evolutionary processes which have led
to the evolution of the groups. Confusingly, Grant’s caribou and
barrenground caribou are currently separate subspecies but one DU.
Barrenground caribou are very admixed which contrasts with the Grant’s
caribou we sampled and so perhaps they warrant listing as separate DUs.
Further sampling is needed to resolve the mountain caribou, especially
the central mountain population which has been shown to have
mitochondrial DNA from both the BEL and NAL lineages (McDevitt et al.,
2009). Additionally, genomic data from the southern mountain, and all
other DUs not included in this study, is needed to further resolve the
complex evolutionary histories and patterns of introgression more
broadly. These divisions have significant implications for the status
listing of each DU as threat status is assessed based on criteria such
as abundance, and priority for management is given to DUs at greatest
risk of extinction (COSEWIC, 2015). Given recent rapid declines in both
range and population sizes, efficient conservation strategies are needed
for caribou.
Our guidelines add to the current discussion about management of admixed
populations and those with complex demographic histories (Coates et al.,
2018; Fitzpatrick et al., 2015; Hamilton & Miller, 2015; Jackiw et al.,
2015; Supple & Shapiro, 2018; vonHoldt et al., 2017). Namely, that
subspecies designations are useful and could follow a structured
framework (Coates et al., 2018), but that conservation units below the
subspecies level likely require a case by case consideration especially
given different regulations in different countries (Coates et al., 2018,
vonHoldt et al., 2017). Many taxa are facing an increasing threat from
climate change and habitat destruction (Hoffman et al., 2017; Ikeda et
al., 2017) and genomic data and appropriate conservation unit
designations will help with prioritisation given limited resources.
Further, genomic data are essential for decisions of genetic rescue
strategies. A key next step to achieve these goals, including for
caribou, is to investigate adaptive genomic variation to incorporate
with demographic history information (Funk, McKay, Hohenloe, &
Allendorf, 2012; Funk, Forester, Converse, Darst, & Moreys, 2019).