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1. Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes

   https://doi.org/10.1093/icb/icac085  

   de Brito, Victor; Betancur-R, Ricardo; Burns, Michael D.; Buser, Thaddaeus J.; Conway, Kevin W.; Fontenelle, João Pedro; Kolmann, Matthew A.; McCraney, W. Tyler; Thacker, Christine E.; Bloom, Devin D. (June 2022, Integrative And Comparative Biology)

   Abstract Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species. 

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2. Have Niche, Will Travel. New Means of Linking Diet and Ecomorphology Reveals Niche Conservatism in Freshwater Cottoid Fishes

   https://doi.org/10.1093/iob/obz023  

   Buser, T J; Finnegan, D L; Summers, A P; Kolmann, M A (January 2019, Integrative Organismal Biology)

   Synopsis Evolutionary transitions between habitats have been catalysts for some of the most stunning examples of adaptive diversification, with novel niches and new resources providing ecological opportunity for such radiations. In aquatic animals, transitions from saltwater to freshwater habitats are rare, but occur often enough that in the Neotropics for example, marine-derived fishes contribute noticeably to regional ichthyofaunal diversity. Here, we investigate how morphology has evolved in a group of temperate fishes that contain a marine to freshwater transition: the sculpins (Percomorpha; Cottoidea). We devised a novel method for classifying dietary niche and relating functional aspects of prey to their predators. Coupled with functional measurements of the jaw apparatus in cottoids, we explored whether freshwater sculpins have fundamentally changed their niche after invading freshwater (niche lability) or if they retain a niche similar to their marine cousins (niche conservatism). Freshwater sculpins exhibit both phylogeographical and ecological signals of phylogenetic niche conservatism, meaning that regardless of habitat, sculpins fill similar niche roles in either saltwater or freshwater. Rather than competition guiding niche conservatism in freshwater cottoids, we argue that strong intrinsic constraints on morphological and ecological evolution are at play, contra to other studies of diversification in marine-derived freshwater fishes. However, several intertidal and subtidal sculpins as well as several pelagic freshwater species from Lake Baikal show remarkable departures from the typical sculpin bauplan. Our method of prey categorization provides an explicit, quantitative means of classifying dietary niche for macroevolutionary studies, rather than relying on somewhat arbitrary means used in previous literature. 

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3. Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology

   https://doi.org/10.1371/journal.pone.0258889  

   McCord, Charlene L.; Nash, Chloe M.; Cooper, W. James; Westneat, Mark W. (October 2021, PLOS ONE)

   Aguirre, Windsor E. (Ed.)

   The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes. 

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4. Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance

   https://doi.org/10.1093/sysbio/syad038  

   Roberts, Wade R.; Ruck, Elizabeth C.; Downey, Kala M.; Pinseel, Eveline; Alverson, Andrew J.; Smith, ed., Stacey (June 2023, Systematic Biology)

   Abstract Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms. [hemiplasy; homoplasy; phylogenomics; salinity, Thalassiosirales.] 

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5. Linking Phylogeny and Morphology to Resource Assimilation Within Aquatic Assemblages

   https://doi.org/10.1002/ece3.70641  

   Lodato, Matthew_B; van_Ee, Brian_C; Atkinson, Carla_L (November 2024, Ecology and Evolution)

   ABSTRACT Niche partitioning promotes species coexistence. Yet, it remains unclear how phylogeny and morphology influence the trophic niches of closely related aquatic species with shared feeding modes. Freshwater mussels (Family: Unionidae) are a group of filter‐feeding bivalves that are ideal for investigating mechanisms of niche partitioning. Particle size selection and patterns of ingestion are controlled by gill latero‐frontal cirri density (CD) and the number of cilia per cirrus (CC). We investigated trophic assimilation and niche area using stable isotope signatures (𝛿¹³C and 𝛿¹⁵N) and gill morphology with scanning‐electron microscopy for a diverse mussel assemblage from the Sipsey River, Alabama, USA. We predicted that (1) trophic niches and gill morphology would differ within and among species across sites; (2) co‐occurring species would partition food resources; (3) greater phylogenetic distances among species would result in increased trophic dissimilarity; (4) more CC and higher CD would result in a narrower trophic niche area, or more constrained range of food items assimilated. We found that (1) species identity and site influenced gill morphology and stable isotope signatures but that the trophic niche area of a species was only affected by species identity; (2) the average proportion of niche area overlap between co‐occurring species was low across sites (0.04 to 0.18); (3) trophic dissimilarity among species increased with phylogenetic distance; (4) CD but not the number of CC negatively related to trophic niche area. Our results indicate that gill morphology and evolutionary history are likely key factors governing the trophic niches of mussels. In addition, intraspecific variation in gill morphology across sites may either reflect a phenotypic response to differences in local resource availability or suggest that other mechanisms shape particle selection. Examining the interplay among the trophic niche, phylogeny, and morphology among functionally similar species further informs our understanding of the mechanisms facilitating their coexistence. 

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