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1. Understanding “Alexandrian” extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders

   https://doi.org/10.21203/rs.3.rs-769753/v1  

   Pyron, R.A. ( September 2021 , Conservation genetics)

   Species that went extinct prior to the genomic era are typically out-of-reach for modern phylogenetic studies. We refer to these as “Alexandrian” extinctions, after the lost library of the ancient world. This is particularly limiting for conservation studies, as genetic data for such taxa may be key to understand extinction threats and risks, the causes of declines, and inform management of related, extant populations. Fortunately, continual advances in biochemistry and DNA sequencing offer increasing ability to recover DNA from historical museum specimens, including fluid-preserved natural history collections. Here, we report on success in recovering nuclear and mitochondrial data from the apparently-extinct subspecies Desmognathus fuscus carri Neill, 1951, a plethodontid salamander from spring runs in central Florida. The two specimens are 50 years old and were likely preserved in unbuffered formalin, but application of a recently derived extraction procedure yielded usable DNA and partially successful Anchored Hybrid Enrichment sequencing. These data suggest that the populations of D. f. carri from peninsular Florida are conspecific with the D. auriculatus A lineage as suggested by previous authors, but likely represented an ecogeographically distinct genetic segment that has now been lost. Genetic data from this Alexandrian extinction thus confirm the geographic extent of populationmore »declines and extirpations as well as their ecological context, suggesting a possibly disproportionate loss from sandy-bottom clearwater streams compared to blackwater swamps. Success of these methods bodes well for large-scale application to fluid-preserved natural history specimens from relevant historical populations, but the possibility of significant DNA damage and related sequencing errors in additional hurdle to overcome.« less
2. Two distinct population clusters of northern sand lance ( Ammodytes dubius ) on the northwest Atlantic shelf revealed by whole genome sequencing

   https://doi.org/10.1093/icesjms/fsac217  

   Jones, Lucas F. ; Lou, R. Nicolas ; Murray, Christopher S. ; Robert, Dominique ; Bourne, Christina M. ; Bouchard, Caroline ; Kučka, Marek ; Chan, Y. Frank ; Carlon, David B. ; Wiley, David N. ; et al ( December 2022 , ICES Journal of Marine Science)

   Northern sand lance (Ammodytes dubius) are essential forage fish in most offshore, temperate-to-polar waters on the Northwest Atlantic shelf (NWA), but their population structure and genetic separation from the American sand lance (A. americanus) remain unresolved. We assembled a reference genome for A. dubius (first in the Ammodytidae) and then used low-coverage whole genome sequencing on 262 specimens collected across the species distribution (Mid-Atlantic Bight to Greenland) to quantify genetic differentiation between geographic regions based on single nucleotide polymorphisms. We found strong separation between A. dubius from locations north and south of the Scotian Shelf, largely due to massive genetic differentiation spanning most of chromosomes 21 and 24. Genetic distance increased with geographic distance in the smaller southern cluster but not in the larger northern cluster, where genetic homogeneity appeared across large geographic distances (>103 km). The two genetic clusters coincide with a clear break in winter sea surface temperature, suggesting that differential offspring survival, rather than limited transport, causes a break in realized connectivity. Nuclear and mitochondrial DNA both clearly delineated A. dubius from A. americanus, thereby confirming a species boundary through spatial niche partitioning into inshore (A. americanus) and offshore (A. dubius) sand lance species on the NWA.
3. Geographic Distribution and Seasonality of Brown Dog Tick Lineages in the United States

   https://doi.org/10.1093/jme/tjac172  

   Grant, Amber N. ; Lineberry, Megan W. ; Sundstrom, Kellee D. ; Allen, Kelly E. ; Little, Susan E. ; Hamer, ed., Sarah ( November 2022 , Journal of Medical Entomology)

   Two lineages of brown dog ticks (Rhipicephalus sanguineus sensu lato (s.l.), Latreille [Acari: Ixodidae]) have been described in North America: temperate and tropical. To characterize the distribution of these lineages across this region and evaluate seasonal activity, a 12S rRNA mitochondrial gene fragment was sequenced from R. sanguineus s.l. collected from hundreds of dogs and cats from different locations across 25 of the 50 states from 2018 to 2021. Infestations with temperate lineage predominated (78.5%) and were identified on pets from 20 states, with most (83.5%) from areas with annual mean daily average temperature <20°C. Tropical lineage submissions were less common (19.3%), submitted from 15 states, and most (80.0%) tropical lineage ticks were from areas with an annual mean daily average temperature >20°C. Although travel history was not obtained for all dogs, when tropical lineage infestations were found in colder regions, follow up conversations with veterinarians suggested some of these infestations may have resulted from recent travel of dogs. A limited number (2.2%) of dogs from Arizona and Texas were co-infested with both lineages. Both temperate and tropical lineage ticks were collected from pets in every month of the year. Temperate lineage infestations were primarily collected March through Augustmore »while tropical lineage infestations were more often collected June through November. These data confirm at least two lineages of R. sanguineus s.l. are present in the United States, each predominating in distinct, overlapping geographies, and suggest that peak activity of each lineage occurs at different times of the year.

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4. A precarious future for distinctive peripheral populations of meadow voles (Microtus pennsylvanicus)

   https://doi.org/10.1093/jmammal/gyz196  

   Jackson, Donavan J. ; Cook, Joseph A. ; Light, ed., Jessica ( December 2019 , Journal of Mammalogy)

   Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and numerous isolated populations. Because some subspecies are of high conservation concern, we examined geographic variation across the range of the species to test existing infraspecific taxonomy in terms of local and regional diversification. We sequenced mitochondrial DNA (mtDNA) from 20 subspecies of M. pennsylvanicus and contextualized infraspecific variation through comparison of pairwise genetic distances derived from an extended data set of 63 species of Microtus. We found strong support for at least three divergent clades within M. pennsylvanicus, with observed intraspecific clade divergence exceeding that between several pairwise comparisons of sister species within Microtus. Six nuclear genes were then sequenced to test the validity of mtDNA structure and to further evaluate the possibility of cryptic, species-level diversity using Bayes factor species delimitation (BFD) analyses. BFD consistently and decisively supported multiple species based on the multilocus approach. We propose that taxonomic revision of the meadow vole is required, with the eastern clade now identified as M. pennsylvanicus (Ord 1815),more »the western clade as M. drummondii (Audubon and Bachman 1853), and the coastal Florida clade as M. dukecampbelli (Woods, Post, and Kilpatrick 1982). We suggest that such an arrangement would more closely reflect evolutionary history and provide critical context for further examination of distinctive southern peripheral populations that harbor novel evolutionary legacies and adaptive potential.

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5. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias )

   https://doi.org/10.1093/sysbio/syaa085  

   Sarver, Brice A ; Herrera, Nathanael D ; Sneddon, David ; Hunter, Samuel S ; Settles, Matthew L ; Kronenberg, Zev ; Demboski, John R ; Good, Jeffrey M ; Sullivan, Jack ( January 2021 , Systematic Biology)

   Kubatko, Laura (Ed.)

   Abstract Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (Tamias canipes, Tamias cinereicollis, Tamias dorsalis, T. quadrivittatus, Tamias rufus, and Tamias umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population-genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite ofmore »rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group. [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.]« less