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1. Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard ( Phrynosoma cornutum ) throughout the Southwestern and Central United States

   https://doi.org/10.1093/gbe/evab260  

   Finger, Nicholas; Farleigh, Keaka; Bracken, Jason T; Leaché, Adam D; François, Olivier; Yang, Ziheng; Flouri, Tomas; Charran, Tristan; Jezkova, Tereza; Williams, Dean A; et al (January 2022, Genome Biology and Evolution)

   Baldauf, Sandra (Ed.)

   Abstract The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept. 

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2. Population genomics of seal lice provides insights into the postglacial history of northern European seals

   https://doi.org/10.1111/mec.17523  

   Sromek, Ludmila; Johnson, Kevin_P; Kunnasranta, Mervi; Ylinen, Eeva; Virrueta_Herrera, Stephany; Andrievskaya, Elena; Alexeev, Vyacheslav; Rusinek, Olga; Rosing‐Asvid, Aqqalu; Nyman, Tommi (October 2024, Molecular Ecology)

   Abstract Genetic analyses of host‐specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population‐genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent‐based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome‐based reconstructions of long‐term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts. 

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3. Regional geographies and public health lessons of the COVID-19 pandemic in the Arctic

   https://doi.org/10.3389/fpubh.2023.1324105  

   Tiwari, Sweta; Petrov, Andrey N; Golosov, Nikolay; Devlin, Michele; Welford, Mark; DeGroote, John; Degai, Tatiana; Ksenofontov, Stanislav (January 2024, Frontiers in Public Health)

   ObjectivesThis study examines the COVID-19 pandemic’s spatiotemporal dynamics in 52 sub-regions in eight Arctic states. This study further investigates the potential impact of early vaccination coverage on subsequent COVID-19 outcomes within these regions, potentially revealing public health insights of global significance. MethodsWe assessed the outcomes of the COVID-19 pandemic in Arctic sub-regions using three key epidemiological variables: confirmed cases, confirmed deaths, and case fatality ratio (CFR), along with vaccination rates to evaluate the effectiveness of the early vaccination campaign on the later dynamics of COVID-19 outcomes in these regions. ResultsFrom February 2020 to February 2023, the Arctic experienced five distinct waves of COVID-19 infections and fatalities. However, most Arctic regions consistently maintained Case Fatality Ratios (CFRs) below their respective national levels throughout these waves. Further, the regression analysis indicated that the impact of initial vaccination coverage on subsequent cumulative mortality rates and Case Fatality Ratio (CFR) was inverse and statistically significant. A common trend was the delayed onset of the pandemic in the Arctic due to its remoteness. A few regions, including Greenland, Iceland, the Faroe Islands, Northern Canada, Finland, and Norway, experienced isolated spikes in cases at the beginning of the pandemic with minimal or no fatalities. In contrast, Alaska, Northern Sweden, and Russia had generally high death rates, with surges in cases and fatalities. ConclusionAnalyzing COVID-19 data from 52 Arctic subregions shows significant spatial and temporal variations in the pandemic’s severity. Greenland, Iceland, the Faroe Islands, Northern Canada, Finland, and Norway exemplify successful pandemic management models characterized by low cases and deaths. These outcomes can be attributed to successful vaccination campaigns, and proactive public health initiatives along the delayed onset of the pandemic, which reduced the impact of COVID-19, given structural and population vulnerabilities. Thus, the Arctic experience of COVID-19 informs preparedness for future pandemic-like public health emergencies in remote regions and marginalized communities worldwide that share similar contexts. 

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4. Shortening migration by 4500 km does not affect nesting phenology or increase nest success for black brant (Branta bernicla nigricans) breeding in Arctic and subarctic Alaska

   https://doi.org/10.1186/s40462-025-00530-z  

   Matsuoka, Toshio D; Patil, Vijay P; Hupp, Jerry W; Leach, Alan G; Reed, John A; Sedinger, James S; Ward, David H (December 2025, Movement Ecology)

   Abstract BackgroundSince the 1980s, Pacific Black Brant (Branta bernicla nigricans, hereafter brant) have shifted their winter distribution northward from Mexico to Alaska (approximately 4500 km) with changes in climate. Alongside this shift, the primary breeding population of brant has declined. To understand the population-level implications of the changing migration strategy of brant, it is important to connect movement and demographic data. Our objectives were to calculate migratory connectivity, a measure of spatial and temporal overlap during the non-breeding period, for Arctic and subarctic breeding populations of brant, and to determine if variation in migration strategies affected nesting phenology and nest survival. MethodsWe derived a migratory network using light-level geolocator migration tracks from an Arctic site (Colville River Delta) and a subarctic site (Tutakoke River) in Alaska. Using this network, we quantified the migratory connectivity of the two populations during the winter. We also compared nest success rates among brant that used different combinations of winter sites and breeding sites. ResultsThe two breeding populations were well mixed during the winter, as indicated by a migratory connectivity score close to 0 (− 0.06) at the primary wintering sites of Izembek Lagoon, Alaska (n = 11 brant) and Baja California, Mexico (n = 48). However, Arctic birds were more likely to migrate the shorter distance to Izembek (transition probability = 0.24) compared to subarctic birds (transition probability = 0.09). Nest survival for both breeding populations was relatively high (0.88–0.92), and we did not detect an effect of wintering site on nest success the following year. ConclusionsNest survival of brant did not differ among brant that used wintering sites despite a 4500 km difference in migration distances. Our results also suggested that the growing Arctic breeding population is unlikely to compensate for declines in the larger breeding population of brant in the subarctic. However, this study took place in 2011–2014 and wintering at Izembek Lagoon may have greater implications for reproductive success under future climate conditions. 

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5. Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus

   https://doi.org/10.1038/s42003-021-01795-x  

   Vallejo-Marín, Mario; Friedman, Jannice; Twyford, Alex D.; Lepais, Olivier; Ickert-Bond, Stefanie M.; Streisfeld, Matthew A.; Yant, Levi; van Kleunen, Mark; Rotter, Michael C.; Puzey, Joshua R. (December 2021, Communications Biology)

   null (Ed.)

   Abstract Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments. 

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