Introduction
Rapid evolutionary change can alter ecological processes which in turn
change the course of evolutionary processes (Turcotte et al. 2013;
Matthews et al. 2016). This process is described as eco-evolutionary
dynamics, which provides a framework for understanding the interplay
between evolution and ecological interactions (Rudman et al. 2018; Post
et al. 2009). The emergence of studies that focus on eco-evolutionary
dynamics has provided more insight on the processes of community
assembly, ecological speciation, and adaptive radiations (Rudman et al.
2018). A better understanding of these eco-evolutionary dynamics can be
applied to host-microbiota interactions, in which the co-evolutionary
processes of the microbiome can impact host performance and fitness
(Gould et al. 2018; Macke et al. 2017; Walters et al. 2020). The
microbial community may also play a large role in the physiology,
ecology, and evolution of the host (Baldo et al. 2017; Trevelline and
Kohl 2020).
Several studies have now examined gut microbiome diversification in an
adaptive radiation of hosts, including fishes (Baldo et al. 2017; Baldo
et al. 2019; Loo et al. 2019; Macke et al. 2017; Rennison et al. 2019).
Phylosymbiosis, in which the host microbiome recapitulates host
phylogeny, is frequently the primary hypothesis in these studies (Brooks
et al. 2016; Lim and Bordenstein, 2020). However, these studies rarely
examine outgroups to the focal radiation in order to compare rates of
microbiome divergence. Furthermore, phylosymbiosis (comparable to
phylogenetic conservatism; Losos, 2008) is actually the antithesis to
the theory of adaptive radiation, which predicts that the microbiome
within an adaptive radiation should diverge far more quickly than
outgroup taxa due to rapid ecological divergence and specialization
(Stroud and Losos 2016, Schluter 2000, Martin and Richards 2019,
Gillespie et al. 2020, Rundell and Price 2009). Thus, we predicted
greater microbiome divergence within a recent adaptive radiation of
trophic specialists than in outgroup generalist taxa with far older
divergence times (5 Mya), in contrast to the predictions of
phylosymbiosis.
An adaptive radiation of Cyprinodon pupfishes provides an
excellent opportunity to test the relative roles of rapid trophic
divergence and phylosymbiosis in shaping the gut microbiome. Pupfishes
are found in saline lakes or coastal areas throughout the Caribbean and
Atlantic (most are allopatric) and within isolated desert pools and
streams (Martin et al. 2016, 2020; Echelle and Echelle 2020). However,
there are only two sympatric adaptive radiations of trophic specialists
across this range (Martin and Wainwright 2011). One radiation is endemic
to San Salvador Island, Bahamas, containing a generalist algivorous and
detritivorous species, Cyprinodon variegatus , and two trophic
specialist species, a molluscivore C. brontotheroides and a
scale-eater C. desquamator (Martin and Wainwright, 2011; Martin
and Wainwright, 2013; Richards and Martin, 2017). Scale-eating and
molluscivore niches are uniquely derived within this sympatric radiation
on San Salvador Island relative to generalist outgroup populations
spread across the Caribbean and desert interior of North America (Martin
and Feinstein 2014; Richards and Martin 2016). These two specialist
species diverged from a generalist common ancestor within the past 10
kya, drawing adaptive alleles from ancient standing genetic variation
across the Caribbean (Richards et al. 2020; McGirr and Martin 2020),
whereas the most divergent generalist population in our study, the
checkered pupfish Cualac tessellatus , has persisted for up to 5
Mya in El Potosà desert spring system in Mexico (Echelle et al. 2005).
Thus, this radiation provides an excellent opportunity to compare
microbiome divergence within a sympatric adaptive radiation of trophic
specialists to closely related and ancient outgroup generalist taxa
which have not substantially shifted their dietary niches.
We compared gut length, overall microbiome diversity, and enrichment of
specific microbial taxa among three sympatric Cyprinodon pupfish
species from two different isolated lake populations on San Salvador
Island, Bahamas to three generalist species: closely related C.
laciniatus from Lake Cunningham, New Providence Island, Bahamas; more
distantly related C. variegatus from Fort Fisher, North Carolina;
and the most closely related extant genus Cualac tessellatus from
San Luis PotosÃ, Mexico. We raised all these species in a common
laboratory environment for at least one generation and fed them an
identical commercial pellet diet for one month before sampling gut
microbiomes. We addressed the following questions: 1) Do microbial gut
communities vary by diet or phylogenetic distance among these species?
2) Is there a microbiome signal associated with lepidophagy
(scale-eating) or molluscivory?