Supplementary materials for: Phylogenomics, lineage diversification rates, and the evolution of diadromy in clupeiformes (anchovies, herrings, sardines, and relatives)

Migration independently evolved numerous times in animals, with a myriad
of ecological and evolutionary implications. In fishes, perhaps the most
extreme form of migration is diadromy, the migration between marine and
freshwater environments. Key and longstanding questions are: how many
times has diadromy evolved in fishes, how frequently do diadromous clades
give rise to non-diadromous species, and does diadromy influence lineage
diversification rates? Many diadromous fishes have large geographic ranges
with constituent populations that use isolated freshwater habitats. This
may limit gene flow among some populations, increasing the likelihood of
speciation in diadromous lineages relative to non-diadromous lineages.
Alternatively, diadromy may reduce lineage diversification rates if
migration is associated with enhanced dispersal capacity that facilitates
gene flow within and between populations. Clupeiformes (herrings,
sardines, shads and anchovies) is a model clade for testing hypotheses
about the evolution of diadromy because it includes an exceptionally high
proportion of diadromous species and several independent evolutionary
origins of diadromy. However, relationships among major clupeiform
lineages remain unresolved and existing phylogenies sparsely sampled
diadromous species, limiting the resolution of phylogenetically-informed
statistical analyses. We assembled a phylogenomic dataset and used
multi-species coalescent and concatenation-based approaches to generate
the most comprehensive, highly-resolved clupeiform phylogeny to date,
clarifying associations among several major clades and identifying
recalcitrant relationships needing further examination. We determined that
variation in rates of sequence evolution (heterotachy) and
base-composition (non-stationarity) had little impact on our results.
Using this phylogeny, we characterized evolutionary patterns of diadromy
and tested for differences in lineage diversification rates between
diadromous, marine, and freshwater lineages. We identified thirteen
transitions to diadromy, all during the Cenozoic Era (10 origins of
anadromy, two origins of catadromy, and one origin of amphidromy), and
seven losses of diadromy. Two diadromous lineages rapidly generated
non-diadromous species, demonstrating that diadromy is not an evolutionary
dead-end. We discovered considerably faster transition rates out of
diadromy than to diadromy. The largest lineage diversification rate
increase in Clupeiformes was associated with a transition to diadromy, but
we uncovered little statistical support for categorically faster lineage
diversification rates in diadromous versus non-diadromous fishes. We
propose that diadromy may increase the potential for accelerated lineage
diversification, particularly in species that migrate long distances.
However, this potential may only be realized in certain biogeographic
contexts, such as when diadromy allows access to ecosystems in which there
is limited competition from incumbent species.