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1. Geographical patterns of intraspecific genetic diversity reflect the adaptive potential of the coral Pocillopora damicornis species complex

   https://doi.org/10.1371/journal.pone.0316380  

   Carr, M; Kratochwill, C; Daly-Engel, T; Crombie, T; van_Woesik, R (January 2025, PLOS ONE)

   Tavakoli-Kolour, Parviz (Ed.)

   Marine heatwaves are increasing in intensity and frequency however, responses and survival of reef corals vary geographically. Geographical differences in thermal tolerance may be in part a consequence of intraspecific diversity, where high-diversity localities are more likely to support heat-tolerant alleles that promote survival through thermal stress. Here, we assessed geographical patterns of intraspecific genetic diversity in the ubiquitous coralPocillopora damicornisspecies complex using 428 sequences of the Internal Transcribed Spacer 2 (ITS2) region across 44 sites in the Pacific and Indian Oceans. We focused on detecting genetic diversity hotspots, wherein some individuals are likely to possess gene variants that tolerate marine heatwaves. A deep-learning, multi-layer neural-network model showed that geographical location played a major role in intraspecific diversity, with mean sea-surface temperature and oceanic regions being the most influential predictor variables differentiating diversity. The highest estimate of intraspecific variation was recorded in French Polynesia and Southeast Asia. The corals on these reefs are more likely than corals elsewhere to harbor alleles with adaptive potential to survive climate change, so managers should prioritize high-diversity regions when forming conservation goals. 

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2. Evidence for ephemeral ring species formation during the diversification history of western fence lizards ( Sceloporus occidentalis )

   https://doi.org/10.1111/mec.15836  

   Bouzid, Nassima M.; Archie, James W.; Anderson, Roger A.; Grummer, Jared A.; Leaché, Adam D. (March 2021, Molecular Ecology)

   Abstract Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence withinSceloporus occidentalis(western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation–expansion model of divergence during Quaternary glacial–interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring‐like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an “ephemeral ring species” and contrastS. occidentaliswith the classic North American ring species,Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post‐Quaternary‐glaciation expansion, the ephemeral nature of divergence inS. occidentalishas produced centres of high genetic diversity for different reasons in the south (long‐term stability) vs. the north (secondary contact). 

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3. Genome‐wide diversity and habitat underlie fine‐scale phenotypic differentiation in the rainbow darter ( Etheostoma caeruleum )

   https://doi.org/10.1111/eva.13135  

   Oliveira, Daniel R.; Reid, Brendan N.; Fitzpatrick, Sarah W. (October 2020, Evolutionary Applications)

   Abstract Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal‐limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold‐water species at‐risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine‐scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site‐specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake‐stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response. 

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4. Has past climate change affected cold‐specialized species differentially through space and time?

   https://doi.org/10.1111/syen.12341  

   Schoville, Sean D.; Bougie, Tierney C.; Dudko, Roman Y.; Medeiros, Matthew J. (December 2018, Systematic Entomology)

   Abstract Quaternary climate change has been strongly linked to distributional shifts and recent species diversification. Montane species, in particular, have experienced enhanced isolation and rapid genetic divergence during glacial fluctuations, and these processes have resulted in a disproportionate number of neo‐endemic species forming in high‐elevation habitats. In temperate montane environments, a general model of alpine population history is well supported, where cold‐specialized species track favourable climate conditions downslope during glacial episodes and upslope during warmer interglacial periods, which leads to a climate‐driven population or species diversification pump. However, it remains unclear how geography mediates distributional changes and whether certain episodes of glacial history have differentially impacted rates of diversification. We address these questions by examining phylogenomic data in a North American clade of flightless, cold‐specialized insects, the ice crawlers (Insecta: Grylloblattodea: Grylloblattidae:Grylloblatta). These low‐vagility organisms have the potential to reveal highly localized refugia and patterns of spatial recolonization, as well as a longer history of in situ diversification. Using continuous phylogeographic analysis of species groups, we show that all species tend to retreat to nearby low‐elevation habitats across western North America during episodes of glaciation, but species at high latitude exhibit larger distributional shifts. Lineage diversification was examined over the course of the Neogene and Quaternary periods, with statistical analysis supporting a direct association between climate variation and diversification rate. Major increases in lineage diversification appear to be correlated with warm and dry periods, rather than with extreme glacial events. Finally, we identify substantial cryptic diversity among ice crawlers, leading to high endemism across their range. This diversity provides new insights into highly localized glacial refugia for cold‐specialized species across western North America. 

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5. Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA

   https://doi.org/10.1007/s10329-021-00912-y  

   Phukuntsi, Metlholo A.; Du Plessis, Morne; Dalton, Desiré L.; Jansen, Raymond; Sauther, Michelle L.; Cuozzo, Frank P.; Kotze, Antoinette (July 2021, Primates)

   The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of populations of G. moholi using two mitochondrial gene regions, the cytochrome C oxidase subunit I gene (COI) and the displacement loop of the control region (D-loop). Samples from five localities in northern South Africa were obtained from archived collections. The two mitochondrial DNA gene regions were amplified and sequenced to provide population summary statistics, differentiation [proportion of the total genetic variation in a population relative to the total genetic variance of all the populations (FST), differentiation within populations among regions (ΦST)], genetic distance and structure. There was discernible genetic structure among the individuals, with two COI and six D-loop haplotypes belonging to two genetically different groups. There was population differentiation among regions (FST = 0.670; ΦST = 0.783; P < 0.01). However, there were low levels of differentiation among populations, as haplotypes were shared between distant populations. Adjacent populations were as divergent from each other as from distant populations. The results suggest that genetic introgression, most likely due to past migrations or recent unintentional translocations that include the animal trade, may have led to connectivity among populations. 

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