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Adaptive radiations generate biodiversity via ecological specialization, with the emergence of ecotypes representing an intermediate step toward speciation. We investigated the genomic basis of diversification in Lake Superior Lake Trout (Salvelinus namaycush), which exhibit three distinct ecomorphotypes—leans, siscowets, and humpers—each adapted to habitats at different depths. We identified 601 single nucleotide polymorphisms within multiple islands of divergence where allele frequencies were highly differentiated between ecomorphotypes. Some of the strongest signals of adaptive divergence were within, or near, genes in the Wnt signaling pathway (Wnt5a, Frizzled-1-like, Dishevelled 2-like), suggesting this highly conserved pathway associated with early morphological development likely played a key role in the emergence of ecomorphological variation. Additional candidate genes related to lipid metabolism, circadian rhythm, immune function, eye development, and other traits were also identified. Population genetic analyses revealed that the primary axis of genetic differentiation within the Lake Superior metapopulation was between ecomorphotypes, rather than between geographic locations, prior to and during the 1990s. Individual ancestry coefficients suggest that hybridization occurred primarily between leans and humpers or humpers and siscowets, but rarely between leans and siscowets. Historical samples indicate that hybridization rates likely increased between the 1960s and 1990s, providing a mechanism for the previously documented genetic homogenization among ecomorphotypes and highlighting challenges associated with conserving ecotypic diversity.
Abstract Tropical rivers in Australia and New Guinea (Sahul) provide a rare natural experiment in vertebrate evolution: unlike other continental systems, their freshwater ichthyofaunas are composed almost entirely of marine-derived lineages rather than primary freshwater fishes. This unique biogeographic setting enables replicated tests of why some marine-to-freshwater transitions give rise to extensive adaptive radiations whereas others remain species-poor, and whether these outcomes reflect ecological opportunity or temporally structured paleoenvironmental constraints. Using a densely sampled, time-calibrated phylogenomic framework spanning 2,303 teleost species, we identified a likely range of 27–34 marine-to-freshwater transitions during the Cenozoic, including a pronounced Middle Miocene peak (16–11 Ma). Although ecological opportunity in Sahul rivers enabled repeated colonization in the absence of dominant primary freshwater incumbents, younger freshwater lineages nevertheless diversify faster than older ones, contradicting the expectation that early arrivers should undergo elevated diversification when accessing vacant niche space. Although some colonizations coincide with bursts of speciation consistent with adaptive radiation, many yielded few species despite long residence times. Functional trait analyses likewise revealed no consistent relationship between colonization timing, ecological breadth, or diversification rate, although expanded functional space characterizes previously proposed Sahul adaptive radiations. Comparisons with paleoenvironmental curves indicate that colonization success correlates with sea-level minima and low-oxygen conditions, suggesting that Earth history dynamics modulated when ecological opportunity was accessible. Our results show that although ecological opportunity enabled repeated freshwater invasions into the Sahul region, diversification outcomes are governed by the interaction of paleoenvironmental dynamics and possibly lineage-specific traits, generating stark asymmetries in freshwater radiations. Significance statement Tropical rivers in Australia and New Guinea host one of the most unusual continental freshwater fish assemblages on Earth, composed almost entirely of marine-derived lineages. This system allows asking why some colonizing lineages diversify dramatically while others remain species-poor on a continental scale. Using large-scale phylogenomic and functional trait data, we show that early arrival alone does not predict diversification success. Instead, the lineages that radiate most successfully are those whose arrival coincides with windows of paleoenvironmental opportunity created by sea-level and oxygen fluctuations. These results reveal that the fates of colonizing lineages are shaped not only by ecological opportunity, but also by Earth-history dynamics that govern when, where, and how species can invade and diversify.
ABSTRACT Lake charr (Salvelinus namaycush) head and body variation were compared among lakes across the species range in North America, to determine if variation was organized more strongly among morphs or lakes. For 3445 lake charr, head‐shape variation was > 17 times greater among morphs than lakes and body‐shape variation was > 16 times greater among morphs than lakes. Body depth, head depth, caudal peduncle length and depth, pectoral and pelvic fins lengths, and preorbital length varied more among morphs than lakes. Four morphs were delineated based on cluster analysis of combined head and body shape. The fat–fat (short head + fat body) morph had a shorter preorbital head length, deeper head and body, shorter and deeper caudal peduncle, and longer paired fins than the lean–lean (long head + slender body) morph, which had a longer preorbital length, shallower head and body, longer and narrower caudal peduncle, and shorter paired fins. The fat–lean (short head + slender body) morph was similar to the fat–fat morph in preorbital length, body depth, caudal peduncle length, and paired fin lengths, but not in head depth or caudal peduncle depth. The lean–fat (long head + fat body) morph was similar to the fat–fat morph in body depth, head depth at the eye, caudal peduncle length, and paired fin lengths, but was similar to the lean–lean morph in maximum head depth and preorbital length. The most extreme fat–fat morphs were from widely separated Great Bear Lake and Lake Superior, whereas the most extreme lean–lean morphs were from Skilak Lake (Alaska), Lake Superior, and Great Bear Lake. The lean–lean morph, present in every lake, was the common morph. A fat–fat morph was present in multiple lakes, but differed greatly in ecological function among lakes, which was more consistent with a hypothesis that multiple lake charr morphs differentiated in multiple lakes across the species' range, rather than were derived from a single already‐specialized morph that colonized multiple lakes from common glacial refugia.
The skipjack herring Alosa chrysochloris inhabits Gulf of Mexico drainages, primarily the Mississippi River Basin, and estuarine environments in the Gulf of Mexico. The trophic ecology of the skipjack herring is poorly understood, therefore we quantified the length, mouth gape and gut contents of juvenile skipjack herring from the Mississippi River (fish n = 6), Illinois River (fish n = 181) and Ohio River (fish n = 255) and tested for changes in diets and predator-prey size ratios during ontogeny. We identified statistically significant changes in prey type consumption during ontogeny. Aquatic insects dominated the diets of skipjack herring <40 mm standard length (SL), with zooplankton and terrestrial insects also contributing to diets. The diets of skipjack herring >40 mm SL were primarily composed of fishes. The most prevalent fish species consumed by skipjack herring were invasive bigheaded carps Hypophthalmichthys spp. and preliminary evidence indicated that inter-annual variation in the consumption of bigheaded carps was driven by variation in juvenile bigheaded carp abundance. Additional research is needed to determine if the enhancement of native skipjack herring populations could be used as a tool to limit bigheaded carp population sizes. Skipjack herring SL and mouth gape were both significantly positively correlated with maximum, median and minimum sizes of prey consumed. There were allometric changes in the mouth gape of juvenile skipjack herring, with the ratio of mouth gape to SL increasing until ~80 mm SL, then gradually declining. Maximum mouth gape to SL ratios corresponded to substantial increases in the consumption of fishes, indicating that mouth gape allometry may facilitate the ontogenetic transition to piscivory in the skipjack herring. This study improves our understanding of skipjack herring ecology and provides data that can be incorporated into future ecological and evolutionary research, such as the development of food web models.
Connectivity is a multifaceted concept that has important implications for the management and conservation of marine and freshwater fishes. We developed a conceptual framework that encompasses multiple, interrelated categories of connectedness, including landscape (e.g., structural, functional) connectivity and ecological (e.g., trophic, genetic, demographic) connectivity, that together shape the flow of organisms, energy and information across ecosystems. We also synthesised six key methods that can be used to study connectivity of fishes: (1) telemetry, including satellite, acoustic, radio and passive integrated transponders (PIT), (2) mark-recapture, (3) environmental tracers, including stable isotopes and otolith-microchemistry, (4) genetics, (5) community structure analysis and (6) emerging technologies and tools (e.g., remote sensing and artificial intelligence). For each method, we describe the categories of connectivity it can assess and provide real-world examples where they have been effectively used. We also identify limitations of each method. This article highlights the diverse and evolving toolbox of methods used to assess fish connectivity, underscoring the need for continued collaboration, innovation and integration of new approaches to refine our understanding and address remaining challenges in this critical area of aquatic ecology and fisheries management.
