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1. Taxonomy, Conservation, and the Future of Native Aquatic Snails in the Hawaiian Islands

   https://doi.org/10.3390/d13050215  

   Christensen, Carl C.; Hayes, Kenneth A.; Yeung, Norine W. (May 2021, Diversity)

   null (Ed.)

   Freshwater systems are among the most threatened habitats in the world and the biodiversity inhabiting them is disappearing quickly. The Hawaiian Archipelago has a small but highly endemic and threatened group of freshwater snails, with eight species in three families (Neritidae, Lymnaeidae, and Cochliopidae). Anthropogenically mediated habitat modifications (i.e., changes in land and water use) and invasive species (e.g., Euglandina spp., non-native sciomyzids) are among the biggest threats to freshwater snails in Hawaii. Currently, only three species are protected either federally (U.S. Endangered Species Act; Erinna newcombi) or by Hawaii State legislation (Neritona granosa, and Neripteron vespertinum). Here, we review the taxonomic and conservation status of Hawaii’s freshwater snails and describe historical and contemporary impacts to their habitats. We conclude by recommending some basic actions that are needed immediately to conserve these species. Without a full understanding of these species’ identities, distributions, habitat requirements, and threats, many will not survive the next decade, and we will have irretrievably lost more of the unique books from the evolutionary library of life on Earth. 

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2. DNA methylation signatures of duplicate gene evolution in angiosperms

   https://doi.org/10.1093/plphys/kiad220  

   Kenchanmane Raju, Sunil K.; Ledford, Marshall; Niederhuth, Chad E. (April 2023, Plant Physiology)

   Abstract Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomic approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole-genome duplicates were typically enriched for CG-only gene body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was a characteristic of more recent single-gene duplicates. Core angiosperm gene families were differentiated into those which preferentially retain paralogs and “duplication-resistant” families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence–absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication. 

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3. Do Coral Reefs Promote Morphological Diversification? Exploration of Habitat Effects on Labrid Pharyngeal Jaw Evolution in the Era of Big Data

   https://doi.org/10.1093/icb/icz103  

   Evans, Kory M; Williams, Keiffer L; Westneat, Mark W (June 2019, Integrative and Comparative Biology)

   Abstract Coral reefs are complex marine habitats that have been hypothesized to facilitate functional specialization and increased rates of functional and morphological evolution. Wrasses (Labridae: Percomorpha) in particular, have diversified extensively in these coral reef environments and have evolved adaptations to further exploit reef-specific resources. Prior studies have found that reef-dwelling wrasses exhibit higher rates of functional evolution, leading to higher functional variation than in non-reef dwelling wrasses. Here, we examine this hypothesis in the lower pharyngeal tooth plate of 134 species of reef and non-reef-associated labrid fishes using high-resolution morphological data in the form of micro-computed tomography scans and employing three-dimensional geometric morphometrics to quantify shape differences. We find that reef-dwelling wrasses do not differ from non-reef-associated wrasses in morphological disparity or rates of shape evolution. However, we find that some reef-associated species (e.g., parrotfishes and tubelips) exhibit elevated rates of pharyngeal jaw shape evolution and have colonized unique regions of morphospace. These results suggest that while coral reef association may provide the opportunity for specialization and morphological diversification, species must still be able to capitalize on the ecological opportunities to invade novel niche space, and that these novel invasions may prompt rapid rates of morphological evolution in the associated traits that allow them to capitalize on new resources. 

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4. Adaptive introgression of the beta-globin cluster in two Andean waterfowl

   https://doi.org/https://doi.org/10.1038/s41437-021-00437-6  

   Graham, Allie M; Peters, Jeffrey L; Wilson, Robert E; Muñoz-Fuentes, Violeta; Green, Andy J; Dorfsman, Daniel A; Valqui, Thomas H; Winker, Kevin; McCracken, Kevin G (April 2021, Heredity)

   null (Ed.)

   Introgression of beneficial alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the hypoxia-inducible factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb β-globin cluster including both embryonic (HBE) and adult (HBB) paralogs, though it was yet untested whether this is due to independent parallel evolution or adaptive introgression. In this study, we find that identical amino acid substitutions in the β-globin cluster that increase Hb-O2 affinity have likely resulted from historical interbreeding between high-altitude populations of two different distantly-related species. We examined the direction of introgression and discovered that the species with a deeper mtDNA divergence that colonized high altitude earlier in history (Anas flavirostris) transferred adaptive genetic variation to the species with a shallower divergence (A. georgica) that likely colonized high altitude more recently possibly following a range shift into a novel environment. As a consequence, the species that received these β-globin variants through hybridization might have adapted to hypoxic conditions in the high-altitude environment more quickly through acquiring beneficial alleles from the standing, hybrid-origin variation, leading to faster evolution. 

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5. 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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