About me

I am a bioinformatics scientist at Arcadia Biosciences.

Complimenting my technical ability to analyze genomic and other biological data, I have deep understanding and experience applying evolutionary theory spanning molecular, individual, and ecological levels.

Earlier, I founded End2End Genomics to develop and adapt modern genomic tools to the study of non-model systems.

As a postdoc in Dmitri Petrov's lab at Stanford, I studied contemporary evolution in wild populations. For example, how do yearly fluctuations in available food affect natural selection on behavior2. Or, when populations evolve in response to seasonality: is it always the same genes?3

I also founded the Stanford Program for Conservation Genomics with Dmitri and Liz Hadly to apply genomic tools for practical conservation research and management.

As a gruaduate sudent in Andrew McAdam's lab at MSU, I studied the quantitative genetics of behavior in wild red squirrels and natural selection on behavior on an annual scale.

News

10/07/19

I joined the R&D team at Arcadia Biosciences to apply genomic tools to their hemp breeding program.

07/17/19

Chromosome-level Lion genome assembly! bioRxiv.

07/09/19

A preprint for our study of 65 tiger genomes is up! Demography, selection, population genomics, and runs of homozygosity. bioRxiv.

05/24/19

Reconsidering the management paradigm of fragmented populations. bioRxiv. Play with the model here!

04/10/19

Our multiplex PCR manuscript is published!

03/31/19

Sarah just posted a preprint on maternal nest defense behavior in red squirrels.

07/30/18

We just published a preprint on bioArxiv showing that our multiplex PCR approach to non-invasive genotyping works really well!

09/28/2017

Here is our new preprint showing that high quality mammalian genomes can be completed for about $2500 using 10x Genomics Linked-reads. We assembled 3 African wild dog genomes.


10/17/16

I have been awarded a NIH SBIR grant to research technique for bringing genomic tools to wildlife research and management. Genomic tools have the potential for immediate impact on wildlife management, but also a powerfull long term impact if data can be generated consistently in large scale. I will investigate the utility of 10x Genomics linked-reads for genome assembly, and then methods of genotyping individuals in the wild.


6/20/16

We have finished 2 wild dog genome assemblies, working on Sam, sister of Natt now.


6/1/16

We now have over 80 samples from wild and captive Sumatran, Malyan, Siberian and Bengal Tigers, still seeking South East China samples...


11/11/15

Wild dog blood samples have arrived after a very long import process... Next step extract DNA!


3/27/15

Along with Painted Dog Conservation, we are starting a project to sequence and assemble the African wild dog genome!


December 22, 2014

The International Rhino Foundation has awarded me, Dmitri and Raoul du Toit a grant to genotype 800 black rhinos! See below for details.


November 25, 2014

My photo of a juvenile red squirrel is on the cover of this month's JEB!


September 05, 2014

Our paper "Selection on female behaviour fluctuates with offspring environment" has been accepted by the Journal of Evolutionary biology! Now published!


September 04, 2014

Our paper "Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements" is published! PLoS ONE.


January 21, 2014

Our paper using Moleculo Illumina long reads for de novo assembly is on bioRxiv!

Current Projects


Non-invasive Genotyping

I founded the Stanford Program for Conservation Genomics (with Dmitri Petrov and Elizabeth Hadly) in order to enable the use of genomics in conservation management and research.

The most immediate and useful application of genomics lies in monitoring individuals through non-invasive sampling. We needed a way to cheaply and easily genotype individuals from a variety of poor quality samples including hair, scat, saliva, parts (like at a market), pelts, and more.

In collaboration with Meghana Natesh and Uma Ramakrishnan from NCBS in Bangalor, India, we have developed a surpisingly straightforward method to genotype thousands of SNPs from extremely low quality samples.

I designed thousands of primers targeting known polymorphic loci in the Tiger genome. These primers are used to amplify short (40-90bp) segments of the tiger genome and the amplified product is sequenced on an illumina sequencer.

We have published a manuscript detailing the method and our results, including its use in a completely different system of Carribien Queen Conch, by Nathan Truelove and Steve Palumbi.

If you would like to use this technique in your sytem contact me, I'm happy to help

Tiger worldwide genetic diversity

In collaboration with Dr. Uma Ramakrishnan we have started a large scale study of captive and wild genetic diversity in Tigers.

African wild dog genomics

The first stage of this project has been completed (read the publication here). We assembled 3 wild dog genomes using 10x Genomics Linked-reads. Our manuscript shows that these genomes are high quality, and the total cost per genome was less than $2800. This approach is no longer the only way to assemble a mammalian size genome for low cost, but I think it might still be the easiest.

The next step is to resequence, or otherwise genotype, as many indiviuals as possible. Samples will principally come from Painted Dog Conservation, an amazing organization run by Peter Blinston in Zimbabwe.

Along with whole genome sequencing, we will develop a set of multiplex PCR primers to allow low cost genoptying of non-invasive samples (hair, saliva, scat). This will allow widespread non-invasive monitoring of wild dogs across Africa.

Genotyping indivdiaul wild dogs will allow us to identify sires, and confirm dams, for all the offspring in the packs that PDC monitor. We will also be able to help Peter and his team to better understand wild dog movement and migration.

Black rhino population genomics

In collaboration with Raoul du Toit, Director of the Lowveld Rhino Trust in Zimbabwe, we are using genomic tools to measure the reproductive success of over 800 rhinos in managed herds. Previous attempts with microsatellite loci were inconclusive due to low genetic diversity. We will then assess whether management actions (such as dehorning, or relocation) affect reproductive success.

Using the high-density genotypes we will also characterize genetic diversity, structure, and inbreeding within managed rhino herds. Finally, we will test for evidence of a prehistoric biogeographic barrier separating Kwazulu-Natal origin and Zambezi origin populations.

Red squirrel de novo genome assembly

We are working on a 10X Genomics based reference genome for the North American red squirrel. Andreas Chavez is developing a trascriptome and we are generating a linkage map to improve theassembly.

Red squirrel behavior

I'm still working on questions related to my PhD dissertation!

Past Projects


D. melanogaster seasonality

Does seasonal selection on D. melanogaster phenotypes result in repeatable evolution of allele frequencies across space and time?

Update: The answer is yes! See our preprint here.

Publications


Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data. Ellie E. Armstrong, Ryan W. Taylor, Danny E Miller, Christopher Kaelin, Gregory Barsh, Elizabeth A Hadly, Dmitri Petrov. bioRxiv 705483.

Sarah E. Westrick, Ryan W. Taylor, Stan Boutin, Jeffrey E. Lane, Andrew G. McAdam, Ben Dantzer. Fitness Benefits of a Motivated Mom. 2019. bioRxiv.  PDF

Meghana Natesh*, Ryan Taylor*, Nathan Truelove, Elizabeth Hadly, Stephen Palumbi, Uma Ramakrishnan*, Dmitri Petrov*. Empowering conservation practice with efficient and economical genotyping from poor quality samples using mPCRseq. 2018. Methods in Ecology and Evolution.  PDF

* Authors contributed equally.

Ellie E Armstrong, Ryan W Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza-Chikerema, John Stuelpnagel, Claudio Sillero-Zubiri, Dmitri Petrov. Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads. 2018. GigaScience.  PDF

Heather Machado, Alan O Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel Fabian, Thomas Flatt, Josefa Gonzalez, Talia Karasov, Iryna Kozeretska, Brian Lazzaro, Thomas Merritt, John Pool, Katherine O'Brien, Subhash Rajpurohit, Paula Roy, Stephen Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov. Broad geographic sampling reveals predictable and pervasive seasonal adaptation in Drosophila. 2018. bioRxiv.  PDF

Eve B Cooper, Ryan W Taylor, Amanda D Kelley, April Robin Martinig, Stan Boutin, Murray M Humphries, Ben Dantzer, Jeffrey E Lane, Andrew G McAdam. Personality is correlated with natal dispersal in North American red squirrels (Tamiasciurus hudsonicus). 2017. Behaviour 154, 939—961.  PDF

Taylor, R. W., Humphries, M. M., Boutin, S., Gorrell, J. C., Coltman, D. W., and McAdam, A. G. Selection on female behaviour fluctuates with offspring environment. 2014. Journal of Evolutionary Biology, 27(11), 2308—2321. Source code on GitHub.  PDF

Rajiv C McCoy, Ryan W Taylor, Timothy A Blauwkamp, Joanna L Kelley, Michael Kertesz, Dmitry Pushkarev, Dmitri A Petrov, Anna-Sophie Fiston-Lavier. 2014. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements. PLoS ONE 9: e106689. Originally posted on bioRxiv.

Taylor, R. W., Humphries, M. M., Boutin, S., Gorrell, J. C., Coltman, D. W., and McAdam, A. G. Disassortative mate-choice on behavior in red squirrels. In Preparation.

Shonfield, J., Taylor, R. W., Boutin, S., Humphries, M. M., McAdam, A. G. 2012. Territorial defence behaviour in red squirrels is influenced by local density. Behaviour 149: 369—390.  PDF

Taylor, R. W., Boon, A. K., Dantzer, B., Réale, D., Humphries, M. M., Boutin, S., Gorrell, J. C., Coltman, D. W., and McAdam, A. G. 2012. Low heritabilities, but genetic and maternal correlations between red squirrel behaviours. Journal of Evolutionary Biology, 25(4), 614—624.  PDF      Supporting Information

McFarlane, S. E., Lane, J. E., Taylor, R. W., Gorrell, J. C., Coltman, D. W., Humphries, M. M., Boutin, S., et al. (2011). The heritability of multiple male mating in a promiscuous mammal. Biology Letters, 7(3), 368—371.  PDF

Wildlife Photography