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1. Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change

   Jacob M. Daane, JM; Auvinet, J; Stoebenau, A; Yergeau, D; Harris, MP; Detrich, HW (October 2020, PLOS genetics)

   null (Ed.)

   In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglo- bin, the oxygen-transport system of virtually all vertebrates. Here, we integrate paleoclimate records with an extensive phylogenomic dataset of notothenioid fishes to understand the evolution of trait loss associated with climate change. In contrast to buoyancy adaptations in this clade, we find relaxed selection on the genetic regions controlling erythropoiesis evolved only after sustained cooling in the SO. This pattern is seen not only within icefishes but also occurred independently in other high-latitude notothenioids. We show that one spe- cies of the red-blooded dragonfish clade evolved a spherocytic anemia that phenocopies human patients with this disease via orthologous mutations. The genomic imprint of SO cli- mate change is biased toward erythrocyte-associated conserved noncoding elements (CNEs) rather than to coding regions, which are largely preserved through pleiotropy. The drift in CNEs is specifically enriched near genes that are preferentially expressed late in erythropoiesis. Furthermore, we find that the hematopoietic marrow of icefish species retained proerythroblasts, which indicates that early erythroid development remains intact. Our results provide a framework for understanding the interactions between development and the genome in shaping the response of species to climate change. 

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2. Bone microstructure and bone mineral density are not systemically different in Antarctic icefishes and related Antarctic notothenioids

   https://doi.org/10.1111/joa.13537  

   Ashique, Amir M.; Atake, Oghenevwogaga J.; Ovens, Katie; Guo, Ruiyi; Pratt, Isaac V.; Detrich, III, H. William; Cooper, David M. L.; Desvignes, Thomas; Postlethwait, John H.; Eames, B. Frank (August 2021, Journal of Anatomy)

   Abstract Ancestors of the Antarctic icefishes (family Channichthyidae) were benthic and had no swim bladder, making it energetically expensive to rise from the ocean floor. To exploit the water column, benthopelagic icefishes were hypothesized to have evolved a skeleton with “reduced bone,” which gross anatomical data supported. Here, we tested the hypothesis that changes to icefish bones also occurred below the level of gross anatomy. Histology and micro‐CT imaging of representative craniofacial bones (i.e., ceratohyal, frontal, dentary, and articular) of extant Antarctic fish species specifically evaluated two features that might cause the appearance of “reduced bone”: bone microstructure (e.g., bone volume fraction and structure linear density) and bone mineral density (BMD, or mass of mineral per volume of bone). Measures of bone microstructure were not consistently different in bones from the icefishesChaenocephalus aceratusandChampsocephalus gunnari, compared to the related benthic notothenioidsNotothenia coriicepsandGobionotothen gibberifrons. Some quantitative measures, such as bone volume fraction and structure linear density, were significantly increased in some icefish bones compared to homologous bones of non‐icefish. However, such differences were rare, and no microstructural measures were consistently different in icefishes across all bones and species analyzed. Furthermore, BMD was similar among homologous bones of icefish and non‐icefish Antarctic notothenioids. In summary, “reduced bone” in icefishes was not due to systemic changes in bone microstructure or BMD, raising the prospect that “reduced bone” in icefish occurs only at the gross anatomic level (i.e., smaller or fewer bones). Given that icefishes exhibit delayed skeletal development compared to non‐icefish Antarctic fishes, combining these phenotypic data with genomic data might clarify genetic changes driving skeletal heterochrony. 

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3. Herbarium specimens reveal a constrained seasonal climate niche despite diverged annual climates across a wildflower clade

   https://doi.org/10.1073/pnas.2503670122  

   Bontrager, Megan; Worthy, Samantha J; Cacho, N Ivalú; Leventhal, Laura; Maloof, Julin N; Gremer, Jennifer R; Schmitt, Johanna; Strauss, Sharon Y (July 2025, Proceedings of the National Academy of Sciences)

   Quantifying species’ niches across a clade reveals how environmental tolerances evolve, and offers insights into present and future distributions. We use herbarium specimens to explore climate niche evolution across 14 annual species of theStreptanthus(s.l.) clade (Brassicaceae), which originated in deserts and diversified into cooler, moister areas. To understand how climate niches evolved, we used historical climate records to estimate each species’ 1) classic annual climate niche, averaged over specimen collection sites; 2) growing season niche, from estimated specimen germination date to collection date, averaged across specimens (specimen-specific niche); and 3) standardized seasonal niche based on average growing seasons of all species (clade-seasonal niche). In addition to estimating how phenological variation maps onto climate niche evolution, we explored how spatial refugia shape the climate experienced by species by 1) analyzing how field soil texture changes relative to the climate space that species occupy and 2) comparing soil water holding capacity from each specimen locality to that of surrounding areas. Specimen-specific niches exhibited less clade-wide variation in climatic water deficit (CWD) than did annual or clade-seasonal niches, and specimen-specific temperature niches showed no phylogenetic signal, in contrast to annual and clade-seasonal temperature niches. Species occupying cooler regions tracked hotter and drier climates by growing later into the summer, and by inhabiting refugia on drought-prone soils. These results underscore how phenological shifts, spatial refugia, and germination timing shape “lived” climate. Despite occupying a large range of annual climates, we found these species are constrained in the conditions under which they thrive. 

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4. Hidden limbs in the “limbless skink” Brachymeles lukbani : Developmental observations

   https://doi.org/10.1111/joa.13447  

   Smith‐Paredes, Daniel; Griffith, Oliver; Fabbri, Matteo; Yohe, Laurel; Blackburn, Daniel G.; Siler, Cameron D.; Bhullar, Bhart‐Anjan S.; Wagner, Günter P. (April 2021, Journal of Anatomy)

   Abstract Reduced limbs and limblessness have evolved independently in many lizard clades. Scincidae exhibit a wide range of limb‐reduced morphologies, but only some species have been used to study the embryology of limb reduction (e.g., digit reduction inChalcidesand limb reduction inScelotes). The genusBrachymeles, a Southeast Asian clade of skinks, includes species with a range of limb morphologies, from pentadactyl to functionally and structurally limbless species. Adults of the small, snake‐like speciesBrachymeles lukbanishow no sign of external limbs in the adult except for small depressions where they might be expected to occur. Here, we show that embryos ofB. lukbaniin early stages of development, on the other hand, show a truncated but well‐developed limb with a stylopod and a zeugopod, but no signs of an autopod. As development proceeds, the limb's small size persists even while the embryo elongates. These observations are made based on external morphology. We used florescent whole‐mount immunofluorescence to visualize the morphology of skeletal elements and muscles within the embryonic limb ofB. lukabni. Early stages have a humerus and separated ulna and radius cartilages; associated with these structures are dorsal and ventral muscle masses as those found in the embryos of other limbed species. While the limb remains small, the pectoral girdle grows in proportion to the rest of the body, with well‐developed skeletal elements and their associated muscles. In later stages of development, we find the small limb is still present under the skin, but there are few indications of its presence, save for the morphology of the scale covering it. By use of CT scanning, we find that the adult morphology consists of a well‐developed pectoral girdle, small humerus, extremely reduced ulna and radius, and well‐developed limb musculature connected to the pectoral girdle. These muscles form in association with a developing limb during embryonic stages, a hint that “limbless” lizards that possess these muscles may have or have had at least transient developing limbs, as we find inB. lukbani. Overall, this newly observed pattern of ontogenetic reduction leads to an externally limbless adult in which a limb rudiment is hidden and covered under the trunk skin, a situation calledcryptomelia. The results of this work add to our growing understanding of clade‐specific patterns of limb reduction and the convergent evolution of limbless phenotypes through different developmental processes. 

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5. Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

   https://doi.org/10.1093/molbev/msad029  

   Rivera-Colón, Angel G; Rayamajhi, Niraj; Minhas, Bushra Fazal; Madrigal, Giovanni; Bilyk, Kevin T; Yoon, Veronica; Hüne, Mathias; Gregory, Susan; Cheng, C H; Catchen, Julian M (March 2023, Molecular Biology and Evolution)

   Kelley, Joanna (Ed.)

   Abstract White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group. 

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