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1. Museum genomics reveals the Xerces blue butterfly ( Glaucopsyche xerces ) was a distinct species driven to extinction

   https://doi.org/10.1098/rsbl.2021.0123  

   Grewe, Felix; Kronforst, Marcus R.; Pierce, Naomi E.; Moreau, Corrie S. (July 2021, Biology Letters)

   null (Ed.)

   The last Xerces blue butterfly was seen in the early 1940s, and its extinction is credited to human urban development. This butterfly has become a North American icon for insect conservation, but some have questioned whether it was truly a distinct species, or simply an isolated population of another living species. To address this question, we leveraged next-generation sequencing using a 93-year-old museum specimen. We applied a genome skimming strategy that aimed for the organellar genome and high-copy fractions of the nuclear genome by a shallow sequencing approach. From these data, we were able to recover over 200 million nucleotides, which assembled into several phylogenetically informative markers and the near-complete mitochondrial genome. From our phylogenetic analyses and haplotype network analysis we conclude that the Xerces blue butterfly was a distinct species driven to extinction. 

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2. Genome Sequence of Synechococcus sp. Strain LA31, Isolated from a Temperate Estuary

   https://doi.org/10.1128/mra.00775-21  

   Kling, Joshua D.; Webb, Eric A.; Hutchins, David A. (February 2022, Microbiology Resource Announcements)

   Stewart, Frank J. (Ed.)

   ABSTRACT Cluster 5 Synechococcus species are widely acknowledged for their broad distribution and biogeochemical importance. In particular, subcluster 5.2 strains inhabit freshwater, estuarine, and marine environments but are understudied, compared to other subclusters. Here, we present the genome for Synechococcus sp. strain LA31, a strain that was recently isolated from Narragansett Bay, Rhode Island, USA. 

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3. Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus

   https://doi.org/10.1098/rspb.2024.0337  

   Siddiqui, Raheyma; Swank, Samantha; Ozark, Allison; Joaquin, Franklin; Travis, Matthew P; McMahan, Caleb D; Bell, Michael A; Stuart, Yoel E (April 2024, Proceedings of the Royal Society B: Biological Sciences)

   Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish,Gasterosteus doryssus.This lineage appeared and, over approximately 8000 generations, evolved significant reduction of 12 of 16 traits related to armour, swimming and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extantGasterosteus aculeatus. Therefore, we infer that reproductive isolation was evolving.However, local extinction ofG. doryssuslineages shows how young, isolated, speciating populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Extinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales. 

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4. Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts

   https://doi.org/10.1128/MRA.00373-23  

   Tran, Wyatt C.; Sullivan, Brendan; Kitzmiller, Claire E.; Choudoir, Mallory; Simoes, Rachel; Dayarathne, Nipuni; DeAngelis, Kristen M. (November 2023, Microbiology Resource Announcements)

   Newton, Irene L. (Ed.)

   ABSTRACT Paenibacillussp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species. 

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5. Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov.

   https://doi.org/10.1002/yea.3905  

   Opulente, Dana A; Langdon, Quinn K; Jarzyna, Martin; Buh, Kelly V; Haase, Max_A B; Groenewald, Marizeth; Hittinger, Chris Todd (December 2023, Yeast)

   Abstract A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genusPichia. Strain yHMH446 falls within a clade that includesPichia norvegensis,Pichia pseudocactophila,Candida inconspicua, andPichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to allPichiaspecies with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results,Pichia galeolatasp. nov. is proposed to accommodate yHMH446^T(=NRRL Y‐64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions. 

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