More Like this

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. 

   more » « less
2. Biogeography of Therorhodion in Northeast Asia and Western North America Emphasising Their Past and Future Expansion

   https://doi.org/10.1111/jbi.70024  

   Polezhaeva, Maria A; Iunusova, Diana R; Shuvaev, Denis N; Marchuk, Elena A; Ickert‐Bond, Stefanie M (October 2025, Journal of Biogeography)

   ABSTRACT AimTo assess the origin, biogeographic history of threeTherorhodionspecies in the Pacific region; to reveal the differentiation withinT. camtschaticumacross its range from Beringia to Japan; and to discuss the role of Beringia as a refugium in the past and the future. LocationNortheast Asia and Western North America. MethodsWe analysed 122 original specimens of three species (T. redowskianum,T. glandulosumandT. camtschaticum) from Russia, China, the United States and 43 GenBank accessions from Japan, using seven nuclear loci. We use different approaches to infer genetic structure, divergence time estimations, ancestral area reconstructions and species distribution modelling to better understand the history of the mountain flora in the Pacific region. ResultsThree genetic clusters with an origin in northeast Asia corresponding to the three species were distinguished. The divergence time betweenT. redowskianumand the other two species was estimated at 19.2 Mya and betweenT. glandulosumandT. camtschaticumwas estimated at 2.13 Mya. WithinT. glandulosumandT. camtschaticum, no Western or Eastern Beringian clades were recovered. At the same time, two subclusters were inferred withinT. camtschaticum, one including populations from Kamchatka, the Aleutian Isl., the Kuril Isl. and partly Japan, and a second one including other populations from Japan, Sakhalin and Khabarovsk, which were identified with a divergence time estimation at 228 Ka BP. Species distribution modelling revealed that the global distribution area during the LGM remained relatively stable for all three taxa, although we observed some local geographical contractions. In contrast, global range contractions for the three species were predicted for the LIG and future climatic changes in 2061–2080. Main ConclusionsWe show thatTherorhodionoriginated in northeast Asia and diverged during the cooling of the late Miocene, with further diversification and dispersal across the Bering land bridge during the late Pliocene‐Pleistocene. Although previous studies found no obvious signs of hybridisation between species in their range overlaps, we revealed traces of some genetic contribution ofT. glandulosuminT. camtschaticumpopulations in Khabarovsk Krai. This study highlights the significance of the including samples from entire range of a species and using different types of markers for adequate biogeographic inferences. It also supports the role of Beringia as a refugium for arctic flora not only in the past, but also into the future. 

   more » « less
3. The Late Quaternary climate impact on the genome of the woodland strawberry (Fragaria vesca), a perennial herb

   https://doi.org/10.1038/s42003-026-09539-5  

   Toivainen, Tuomas; Salonen, J Sakari; Kirshner, Jonathan; Lembinen, Sergei; De_Kort, Hanne; Lyyski, Annina; Edger, Patrick P; Hilmarsson, Hrannar Smári; Hallsson, Jón Hallsteinn; Sargent, Daniel J; et al (December 2026, Communications Biology)

   Abstract Genomes record past climatic impact on species’ range shifts, admixture, refugial isolation, and adaptative evolution. However, these processes are poorly understood in perennial herbaceous species forming a dominant group of temperate flora. We present a demographic history of the perennial herb woodland strawberry (Fragaria vescaL.) reconstructed from 200 genomes spanning most of its European range. Temporal population structure reveals a strong division into western and eastern genetic clusters along a longitudinal climatic gradient, with eastern core populations showing greater resilience during glaciations. Divergence patterns indicate that postglacial recolonization of western and eastern Europe occurred from distinct refugia in multiple waves. The current largest, admixed populations from the Mediterranean to northern Europe form a continuous chain maintained by east–west gene flow through Central Europe, with historical migration patterns indicating comparable connections during earlier interglacials. Our reconstruction of woodland strawberry’s climatic history with high temporal resolution reveals how the late Pleistocene core-periphery dynamics shaped its survival and genome evolution under climate change. The data points to populations that are essential for maintaining the long term genetic diversity of the species and opens new avenues to understand climatic adaptation of temperate flora. 

   more » « less
4. 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. 

   more » « less
5. 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. 

   more » « less