Genomics reveals the origins of ancient specimens

Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We deduced geographical origins of several ancient specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old, poorly documented specimens that serve as irreplaceable embodiments of species concepts. The ability to figure out where they were collected will resolve many on-going disputes. More broadly, we show the utility of genomics applied to ancient museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

[1]  E. Spamer Know thyself: Responsible science and the lectotype of Homo sapiens Linnaeus, 1758 , 1999 .

[2]  Nick V Grishin,et al.  Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense , 2015, Cell reports.

[3]  Juan Carlos Fernández,et al.  Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms , 2014, Ann. Oper. Res..

[4]  N. Grishin,et al.  Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae) , 2019, Proceedings of the Royal Society B.

[5]  Arnaud Martin,et al.  Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems. , 2014, Developmental biology.

[6]  R. I. Hill,et al.  Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand , 2012, Proceedings of the National Academy of Sciences.

[7]  T. Nauss,et al.  Middle Stone Age foragers resided in high elevations of the glaciated Bale Mountains, Ethiopia , 2019, Science.

[8]  K. Holsinger,et al.  Genetics in geographically structured populations: defining, estimating and interpreting FST , 2009, Nature Reviews Genetics.

[9]  A. Warren,et al.  A New Name for Alpine Populations of Hesperia colorado (Scudder) (Hesperiidae, Hesperiinae) in Colorado , 2016 .

[10]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[11]  Conservation and flexibility in the gene regulatory landscape of heliconiine butterfly wings , 2019, EvoDevo.

[12]  O. Mathieu‐costello Muscle adaptation to altitude: tissue capillarity and capacity for aerobic metabolism. , 2001, High altitude medicine & biology.

[13]  N. Grishin,et al.  Gypsy moth genome provides insights into flight capability and virus–host interactions , 2019, Proceedings of the National Academy of Sciences.

[14]  M. Tyers,et al.  Structural basis for the recruitment of glycogen synthase by glycogenin , 2014, Proceedings of the National Academy of Sciences.

[15]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

[16]  P. Opler,et al.  Case 3709 – Conservation of the usage of names of western North American Hesperia comma-group subspecies (Lepidoptera, Hesperiidae) through designation of neotypes for Pamphila colorado Scudder, 1874, Pamphila manitoba Scudder, 1874, Pamphila cabelus Edwards, 1881, Pamphila harpalus Edwards, 1881, P , 2018, The Bulletin of Zoological Nomenclature.

[17]  N. Grishin,et al.  Genomes of skipper butterflies reveal extensive convergence of wing patterns , 2019, Proceedings of the National Academy of Sciences.

[18]  N. Grishin,et al.  When COI barcodes deceive: complete genomes reveal introgression in hairstreaks , 2017, Proceedings of the Royal Society B: Biological Sciences.

[19]  Simon H. Martin,et al.  Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci , 2014, bioRxiv.

[20]  James Mallet,et al.  Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution , 2016, G3: Genes, Genomes, Genetics.

[21]  N. Patel,et al.  Macroevolutionary shifts of WntA function potentiate butterfly wing-pattern diversity , 2017, Proceedings of the National Academy of Sciences.

[22]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[23]  J. Calhoun An Updated Itinerary of Theodore L. Mead in Colorado in 1871, with Type Locality Clarifications and a Lectotype Designation for Melitaea eurytion Mead (Nymphalidae) , 2015 .

[24]  J. Littleton,et al.  Shank Modulates Postsynaptic Wnt Signaling to Regulate Synaptic Development , 2016, The Journal of Neuroscience.

[25]  Joseph K. Pickrell,et al.  Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data , 2012, PLoS genetics.

[26]  P. Smouse,et al.  genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .

[27]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .