Little Brown Bat (Myotis lucifugus)

[docmanny]

• Name: Myotis lucifugus
• Common name: Little Brown Bat

Description: The Little Brown Bat, Myotis lucifugus, was one of the first non-human mammals sequenced by the NIH Mammalian Genome Project. The Ensembl accession ID is Myoluc2.0 (GCA_000147115.1).

Note: Maybe you don't know a lot of the things below - but, that's OK! The criteria are that (a) the choice is reasonable, and (b) the rationale is clear. What we want is a "reasonable estimate" (or, "best guess") - if you were to use a number in a paper, what would you use and how would you justify it to your collaborators? For instance, for "generation time", best would be to cite a paper that actually measures or estimates generation time. But most species don't have this; next best would be to give a number used in the literature, and provide a citation that used it (and hopefully the publication gives a justification also). Lacking this, you might provide a number from a related species (and a citation for this).

Here is the checklist of things that we need to add a species to the catalogue. Each thing should be provided, with a justification (maybe short) and a citation.

Demographic information:

• [] generation time in years
• [] "default" population size

Chromosome structure:

Note: The assembly should be chromosome-level, i.e., not composed of thousands of scaffolds.

• [] ensembl assembly ID or, if the assembly is not in Ensembl, a list of chromosomes with name and length (in bp)

Note: species in Ensembl can be found in one of these lists: vertebrates, "metazoa", plants, fungi, protists, or bacteria.

Recombination rates:

• [] genetic map of recombination rates (as a hapmap or csv file)
• [] genome-wide mean recombination rate (which will be used as the default)

Mutation rate:

• [] genome-wide mean mutation rate

Demographic model:

• [] as a list of population sizes, growth rates, migration rates, etcetera. (optional)
• [] citation

Other information:

These are things we don't currently use, but will want to use in the future:

• [] sex determination system, and which chromosomes are the sex chromosome(s)
• [] ploidy

[docmanny]

There are many studies that have generated PopGen data for Myotis lucifugus, including (in no particular order):

• Wilder, A.P., Kunz, T.H. and Sorenson, M.D. (2015), Population genetic structure of a common host predicts the spread of white‐nose syndrome, an emerging infectious disease in bats. Mol Ecol, 24: 5495-5506. https://doi.org/10.1111/mec.13396
• Donaldson ME, Davy CM, Willis CKR, McBurney S, Park A, Kyle CJ. Profiling the immunome of little brown myotis provides a yardstick for measuring the genetic response to white-nose syndrome. Evol Appl. 2017;10(10):1076-1090. Published 2017 Sep 3. doi:10.1111/eva.12514
• Miller-Butterworth CM, Vonhof MJ, Rosenstern J, Turner GG, Russell AL. Genetic structure of little brown bats (Myotis lucifugus) corresponds with spread of white-nose syndrome among hibernacula. J Hered. 2014 May-Jun;105(3):354-64. doi: 10.1093/jhered/esu012. Epub 2014 Mar 3. PMID: 24591103.
• Michael D. Dixon, Population genetic structure and natal philopatry in the widespread North American bat Myotis lucifugus, Journal of Mammalogy, Volume 92, Issue 6, 14 December 2011, Pages 1343–1351, https://doi.org/10.1644/10-MAMM-A-426.1
• Vonhof MJ, Russell AL, Miller-Butterworth CM (2015) Range-Wide Genetic Analysis of Little Brown Bat (Myotis lucifugus) Populations: Estimating the Risk of Spread of White-Nose Syndrome. PLoS ONE 10(7): e0128713. https://doi.org/10.1371/journal.pone.0128713
• Thomas M Lilley, Ian W Wilson, Kenneth A Field, DeeAnn M Reeder, Megan E Vodzak, Gregory G Turner, Allen Kurta, Anna S Blomberg, Samantha Hoff, Carl J Herzog, Brent J Sewall, Steve Paterson, Genome-Wide Changes in Genetic Diversity in a Population of Myotis lucifugus Affected by White-Nose Syndrome, G3 Genes|Genomes|Genetics, Volume 10, Issue 6, 1 June 2020, Pages 2007–2020, https://doi.org/10.1534/g3.119.400966
• Christina M. Davy, Michael E. Donaldson, Yessica Rico, Cori L. Lausen, Kathleen Dogantzis, Kyle Ritchie, Craig K.R. Willis, Douglas W. Burles, Thomas S. Jung, Scott McBurney, Allysia Park, Donald F. McAlpine, Karen J. Vanderwolf, and Christopher J. Kyle. Prelude to a panzootic: Gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome. FACETS. 2(2): 690-714. https://doi.org/10.1139/facets-2017-0022

Of these papers, only Davy et al (2017) gives estimates of Ne. Using the Fst estimates in the other papers to calculate Theta and Ne and a variety of commonly-used mutation rate estimates, we get Ne's in the 10^6 - 10^9 range...

The individual used for the MyoLuc2 genome is from Framingham, MA according to the Biosample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02953645/.

We are settling on the Davy et al (2017) population size of 1682.9 (794.0–261 726.6) based on their sequences from Eastern Canada, as it is the only reasonable Ne estimate close to Massachusetts.

[docmanny]

For Generation time, these are some of the citations we found:

• Frick, W.F., Reynolds, D.S. and Kunz, T.H. (2010), Influence of climate and reproductive timing on demography of little brown myotis Myotis lucifugus. Journal of Animal Ecology, 79: 128-136. https://doi.org/10.1111/j.1365-2656.2009.01615.x
• Humphrey SR Cope JB .1976. Population ecology of the little brown bat, Myotis lucifugus, in Indiana and north-central Kentucky. Special Publications. Am Soc Mammal. 4:1–81.

Everyone seems to cite Humphrey and Cope (1976) as saying 2 years for generational time; the closest we find in that publication is a table that says that females are reproductively mature at 1 y/o and live a max lifespan of 2 years. The Frick et al (2010) paper also mentions 2 years through their analysis.

[docmanny]

(Note for posterity, all comments here are alongside @lauterbur )

[docmanny]

Mutation Rate:

• Ray, D. A., Feschotte, C., Pagan, H. J., Smith, J. D., Pritham, E. J., Arensburger, P., Atkinson, P. W., & Craig, N. L. (2008). Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome research, 18(5), 717–728. https://doi.org/10.1101/gr.071886.107

Ray et al (2008) calculated a neutral mutation rate of 2.366 × 10^−9 per site per year by aligning 4 introns from genes in a variety of species, then use the phylogeny and a site model of TIM+G (Γ = 1.2597) to arrive at that estimate.

[docmanny]

Ensemble link to MyoLuc2: https://uswest.ensembl.org/Myotis_lucifugus/Info/Annotation

[docmanny]

Citation for MyoLuc2:

• Lindblad-Toh, K., Garber, M., Zuk, O. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476–482 (2011). https://doi.org/10.1038/nature10530

[docmanny]

Recombination rate:

There are no published Recomb Rates or maps for M. lucifugus as far and as wide as we have seen. A recombination rate could be calculated if we had locus SNP data for a contiguous scaffold of M. lucifugus, however, that data does not yet exist. However, this data does exist for M. myotis. We can settle on some default mammalian recombination rate once we find such a citation.

[docmanny]

Bats' closest relatives are horses and cows. Recombination rates for these species work out to be ~10^-8 according to Dumont and Payseur (2008). As such, we will use a default of 10^-8 for the recombination rate as the default for now.

• Dumont, B.L. and Payseur, B.A. (2008), EVOLUTION OF THE GENOMIC RATE OF RECOMBINATION IN MAMMALS. Evolution, 62: 276-294. https://doi.org/10.1111/j.1558-5646.2007.00278.x

[petrelharp]

These people estimated a mutation-to-recombination rate ratio for a horseshoe bat: https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-294X.2006.02879.x

[lauterbur]

I think they just use mtDNA though.