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1. Sufficient versus optimal climatic stability during the Late Quaternary: using environmental quality to guide phylogeographic inferences in a Neotropical montane system

   https://doi.org/10.1093/jmammal/gyz162  

   Soley-Guardia, Mariano; Carnaval, Ana Carolina; Anderson, Robert P (November 2019, Journal of Mammalogy)

   Powell, Roger (Ed.)

   Abstract Quaternary climatic oscillations affected species distributions worldwide, creating cycles of connectivity and isolation that impacted population demography and promoted lineage divergence. These effects have been well studied in temperate regions. Taxa inhabiting mesic montane habitats in tropical ecosystems show high levels of endemism and diversification in the distinct mountain ranges they inhabit; such a pattern has commonly been ascribed to past climatic oscillations, but few phylogeographic studies have tested this hypothesis. Here, we combine ecological niche models of species distributions with molecular data to study phylogeographic patterns in two rodents endemic to the highlands of Costa Rica and western Panama (Reithrodontomys creper and Nephelomys devius). In so doing, we apply a novel approach that incorporates a basic ecological principle: the expected positive relationship between environmental suitability and population abundance. Specifically, we use niche models to predict potential patterns of population connectivity and stability of different suitability levels during climatic extremes of the last glacial–interglacial cycle; we then test these predictions with population genetic analyses of a mitochondrial and a nuclear marker. The detailed predictions arising from the different levels of suitability were moderately to highly congruent with the molecular data depending on the species. Overall, results suggest that in these tropical montane ecosystems, cycles of population connectivity and isolation followed a pattern opposite to that typically described for temperate or lowland tropical ecosystems: namely, higher connectivity during the colder glacials, with isolation in montane refugia during the interglacials, including today. Nevertheless, the individualistic patterns for each species indicate a potentially wide gamut of phylogeographic histories reflecting particularities of their niches. Taken together, this study illustrates how phylogeographic inferences may benefit from niche model outputs that provide more detailed predictions of connectivity and finer characterizations of potential refugia through time. 

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2. How Veeries vary: Whole genome sequencing resolves genetic structure in a long-distance migratory bird

   https://doi.org/10.1093/ornithology/ukad061  

   Kimmitt, Abigail A; Pegan, Teresa M; Jones, Andrew W; Winker, Kevin; Winger, Benjamin M (December 2023, Ornithology)

   Abstract In high-latitude species with high dispersal ability, such as long-distance migratory birds, populations are often assumed to exhibit little genetic structure due to high gene flow or recent postglacial expansion. We sequenced over 120 low-coverage whole genomes from across the breeding range of a long-distance migratory bird, the Veery (Catharus fuscescens), revealing strong evidence for isolation by distance. Additionally, we found distinct genetic structure between boreal, western montane U.S., and southern Appalachian sampling regions. We suggest that population genetic structure in this highly migratory species is detectable with the high resolution afforded by whole-genomic data because, similar to many migratory birds, the Veery exhibits high breeding-site fidelity, which likely limits gene flow. Resolution of isolation by distance across the breeding range was sufficient to assign likely breeding origins of individuals sampled in this species’ poorly understood South American nonbreeding range, demonstrating the potential to assess migratory connectivity in this species using genomic data. As the Veery’s breeding range extends across both historically glaciated and unglaciated regions in North America, we also evaluated whether contemporary patterns of structure and genetic diversity are consistent with historical population isolation in glacial refugia. We found that patterns of genetic diversity did not support southern montane regions (southern Appalachians or western U.S. mountains) as glacial refugia. Overall, our findings suggest that isolation by distance yields subtle associations between genetic structure and geography across the breeding range of this highly vagile species even in the absence of obvious historical vicariance or contemporary barriers to dispersal. 

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3. Ice and ocean constraints on early human migrations into North America along the Pacific coast

   https://doi.org/10.1073/pnas.2208738120  

   Praetorius, Summer K.; Alder, Jay R.; Condron, Alan; Mix, Alan C.; Walczak, Maureen H.; Caissie, Beth E.; Erlandson, Jon M. (February 2023, Proceedings of the National Academy of Sciences)

   Founding populations of the first Americans likely occupied parts of Beringia during the Last Glacial Maximum (LGM). The timing, pathways, and modes of their southward transit remain unknown, but blockage of the interior route by North American ice sheets between ~26 and 14 cal kyr BP (ka) favors a coastal route during this period. Using models and paleoceanographic data from the North Pacific, we identify climatically favorable intervals when humans could have plausibly traversed the Cordilleran coastal corridor during the terminal Pleistocene. Model simulations suggest that northward coastal currents strengthened during the LGM and at times of enhanced freshwater input, making southward transit by boat more difficult. Repeated Cordilleran glacial-calving events would have further challenged coastal transit on land and at sea. Following these events, ice-free coastal areas opened and seasonal sea ice was present along the Alaskan margin until at least 15 ka. Given evidence for humans south of the ice sheets by 16 ka and possibly earlier, we posit that early people may have taken advantage of winter sea ice that connected islands and coastal refugia. Marine ice-edge habitats offer a rich food supply and traversing coastal sea ice could have mitigated the difficulty of traveling southward in watercraft or on land over glaciers. We identify 24.5 to 22 ka and 16.4 to 14.8 ka as environmentally favorable time periods for coastal migration, when climate conditions provided both winter sea ice and ice-free summer conditions that facilitated year-round marine resource diversity and multiple modes of mobility along the North Pacific coast. 

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4. Coastal Elites: Recurrent Trans‐Arctic Migration and Vicariance in a Cosmopolitan Sea Slug Driven by Pleistocene Glacial Cycles

   https://doi.org/10.1111/zsc.12738  

   Ellingson, Ryan A; Vo, Julia; Llaban, Angela; Lugo, Lisa M; Vendetti, Jann E; Krug, Patrick J (June 2025, Zoologica Scripta)

   ABSTRACT Many coastal marine species experienced Pleistocene gene flow between the North Pacific and Atlantic. Understanding historical connectivity between ocean basins should aid in predicting how regional faunas will respond to recent warming that has intensified trans‐Arctic dispersal. Wetland fauna of the Northwestern Atlantic may have survived in estuarine refugia throughout glacial cycles, or recolonised from the southern coast, North Pacific or Northeastern Atlantic. Here, we used multilocus genetic markers and historical climate data to investigate lineage distribution and connectivity among populations of the nominally cosmopolitan sea slugAlderia modesta, sampled from mudflats on both coasts of the North Pacific and North Atlantic. Mitochondrial DNA clades from European and North American populations were deeply divergent and reciprocally monophyletic; differences at seven polymorphic nuclear loci indicated prolonged absence of trans‐Atlantic gene flow. A Pacific ancestor likely first colonised the Atlantic during the marine biotic interchange of the middle Pliocene ~3.5 Ma. Both mtDNA phylogenetics and nuclear genotype assignments support repeated trans‐Arctic colonisation of the Northwestern Atlantic from the Pacific during inter‐glacial cycles; no gene flow was evident since the last glacial maximum, however. Time‐calibrated coalescent phylogenies, Bayesian skyline plots and haplotype networks all indicated recent population expansions in the Pacific and Europe, but not Northwestern Atlantic. In both the Pacific and Northwestern Atlantic, older lineages persisted in patchy refugia north of glacial margins, while a derived clade of Pacific haplotypes indicates northward post‐LGM expansion. The biogeographical history ofAlderiacontrasts with rocky‐shore taxa that were largely extirpated by glacial advance and recolonised from refugia following the last glacial maximum. Based on molecular differences and distinctions in radular and penial stylet morphology, we resurrect the nameAlderia harvardiensisGould 1870 forAlderiafrom the Northwestern Atlantic and North Pacific;A. modestarefers exclusively to European slugs. 

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5. Exploring movement patterns and changing distributions of baleen whales in the western North Atlantic using a decade of passive acoustic data

   https://doi.org/10.1111/gcb.15191  

   Davis, Genevieve E.; Baumgartner, Mark F.; Corkeron, Peter J.; Bell, Joel; Berchok, Catherine; Bonnell, Julianne M.; Bort Thornton, Jacqueline; Brault, Solange; Buchanan, Gary A.; Cholewiak, Danielle M.; et al (January 2020, Global Change Biology)

   Six baleen whale species are found in the temperate western North Atlantic Ocean, with limited information existing on the distribution and movement patterns for most. There is mounting evidence of distributional shifts in many species, including marine mammals, likely because of climate-driven changes in ocean temperature and circulation. Previous acoustic studies examined the occurrence of minke (Balaenoptera acutorostrata) and North Atlantic right whales (NARW; Eubalaena glacialis). This study assesses the acoustic presence of humpback (Megaptera novaeangliae), sei (B. borealis), fin (B. physalus), and blue whales (B. musculus) over a decade, based on daily detections of their vocalizations. Data collected from 2004 to 2014 on 281 bottommounted recorders, totaling 35,033 days, were processed using automated detection software and screened for each species' presence. A published study on NARW acoustics revealed significant changes in occurrence patterns between the periods of 2004–2010 and 2011–2014; therefore, these same time periods were examined here. All four species were present from the Southeast United States to Greenland; humpback whales were also present in the Caribbean. All species occurred throughout all regions in the winter, suggesting that baleen whales are widely distributed during these months. Each of the species showed significant changes in acoustic occurrence after 2010. Similar to NARWs, sei whales had higher acoustic occurrence in mid-Atlantic regions after 2010. Fin, blue, and sei whales were more frequently detected in the northern latitudes of the study area after 2010. Despite this general northward shift, all four species were detected less on the Scotian Shelf area after 2010, matching documented shifts in prey availability in this region. A decade of acoustic observations have shown important distributional changes over the range of baleen whales, mirroring known climatic shifts and identifying new habitats that will require further protection from anthropogenic threats like fixed fishing gear, shipping, and noise pollution. 

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