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1. 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 (June 2023, Systematic Biology)

   Smith, Stacey (Ed.)

   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. 

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2. The Divergent Responses of Salinity Generalists to Hyposaline Stress Provide Insights Into the Colonisation of Freshwaters by Diatoms

   https://doi.org/10.1111/mec.17556  

   Judy, Kathryn J; Pinseel, Eveline; Downey, Kala M; Lewis, Jeffrey A; Alverson, Andrew J (November 2024, Molecular Ecology)

   Environmental transitions, such as the salinity divide separating marine and fresh waters, shape biodiversity over both shallow and deep timescales, opening up new niches and creating opportunities for accelerated speciation and adaptive radiation. Understanding the genetics of environmental adaptation is central to understanding how organisms colonise and subsequently diversify in new habitats. We used time‐resolved transcriptomics to contrast the hyposalinity stress responses of two diatoms. Skeletonema marinoi has deep marine ancestry but has recently invaded brackish waters. Cyclotella cryptica has deep freshwater ancestry and can withstand a much broader salinity range. Skeletonema marinoi is less adept at mitigating even mild salinity stress compared to Cyclotella cryptica, which has distinct mechanisms for rapid mitigation of hyposaline stress and long‐term growth in low salinity. We show that the cellular mechanisms underlying low salinity tolerance, which has allowed diversification across freshwater habitats worldwide, includes elements that are both conserved and variable across the diatom lineage. The balance between ancestral and lineage‐specific environmental responses in phytoplankton have shaped marine–freshwater transitions on evolutionary timescales and, on contemporary timescales, will affect which lineages survive and adapt to changing ocean conditions. 

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3. Gene duplication, shifting selection, and dosage balance of silicon transporter proteins in marine and freshwater diatoms

   https://doi.org/10.1093/gbe/evad212  

   Bryłka, Karolina; Pinseel, Eveline; Roberts, Wade R; Ruck, Elizabeth C; Conley, Daniel J; Alverson, Andrew J (December 2023, Genome Biology and Evolution)

   Piganeau, Gwenael (Ed.)

   Abstract Numerous factors shape the evolution of protein-coding genes, including shifts in the strength or type of selection following gene duplications or changes in the environment. Diatoms and other silicifying organisms use a family of silicon transporters (SITs) to import dissolved silicon from the environment. Freshwaters contain higher silicon levels than oceans, and marine diatoms have more efficient uptake kinetics and less silicon in their cell walls, making them better competitors for a scarce resource. We compiled SITs from 37 diatom genomes to characterize shifts in selection following gene duplications and marine–freshwater transitions. A deep gene duplication, which coincided with a whole-genome duplication, gave rise to two gene lineages. One of them (SIT1–2) is present in multiple copies in most species and is known to actively import silicon. These SITs have evolved under strong purifying selection that was relaxed in freshwater taxa. Episodic diversifying selection was detected but not associated with gene duplications or habitat shifts. In contrast, genes in the second SIT lineage (SIT3) were present in just half the species, the result of multiple losses. Despite conservation of SIT3 in some lineages for the past 90–100 million years, repeated losses, relaxed selection, and low expression highlighted the dispensability of SIT3, consistent with a model of deterioration and eventual loss due to relaxed selection on SIT3 expression. The extensive but relatively balanced history of duplications and losses, together with paralog-specific expression patterns, suggest diatoms continuously balance gene dosage and expression dynamics to optimize silicon transport across major environmental gradients. 

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4. Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes

   https://doi.org/10.1002/ece3.6172  

   Kolmann, M.A. (April 2020, Ecology and evolution)

   Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study, we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using micro-computed tomographic (μCT) scanning and geometric morphometrics, we quantified body shape, size, and vertebral counts of 31 belonid species. We then examined the pattern and tempo of body shape and size evolution using phylogenetic comparative methods. Our results show that transitions from marine to freshwater habitats have altered the adaptive landscape for needlefishes and expanded morphospace relative to marine taxa. We provide further evidence that freshwater taxa attain reduced sizes either through dwarfism (as inferred from axial skeletal reduction) or through developmental truncation (as inferred from axial skeletal loss). We propose that transitions to freshwater habitats produce morphological novelty in response to novel prey resources and changes in locomotor demands. We find that repeated invasions of different habitats have prompted predictable changes in morphology. 

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5. Rapid and repeated invasions of fresh water by the copepod Eurytemora affinis

   https://doi.org/10.1111/j.1558-5646.1999.tb05407.x  

   Lee, Carol Eunmi (October 1999, Evolution)

   Invasions of fresh water by marine organisms have been of great interest to evolutionary biologists and paleontologists because they typically constitute major evolutionary transitions. Recent (< 200 years) invasions of fresh water by brackish or marine species offer an opportunity to understand mechanisms underlying these events, but pathways of invasion from salt water have not been confirmed using genetic data. This study employed mitochondrial DNA sequences (652 base pairs from the cytochrome oxidase I (COI) gene) to reconstruct the geographic and evolutionary history of freshwater invasion by the common estuarine and saltmarsh crustacean Eurytemora affinis (Copepoda; Poppe 1880). Phylogenetic analysis of populations from North America, Europe, and Asia revealed at least eight independent invasions of fresh water from genetically distinct lineages. At least five of these freshwater invasions most likely arose independently in different river drainages, recently from saltwater sources within each river drainage. An analysis of molecular variance (AMOVA) was performed at three geographic scales (among continents, among drainages, and within drainages) to assess the hierarchical distribution of genetic variance. Results indicated that 52% of the genetic variance was explained by differences among drainages, 43% by differences among continents, but only 5% by differences within drainages, thus supporting geographic patterns of invasions inferred from the phylogeny. Physiological experiments were performed to determine whether adults and larvae from saltwater populations could tolerate freshwater conditions. Transfer to zero salinity resulted in high mortalities, but with some survival to the second generation in one population. This study provides genetic evidence and physiological support for rapid transitions from a saline life history into fresh water, with repeated invasions on a global scale. 

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