1Dept. of Biological Sciences. Texas Tech University, Lubbock, TX 79402

Sarah F. Mangum1 , Roy N. Platt II1 , and David A. Ray1

Introduction▪ Spermophilus (Ictidomys) tridecemlineatus▪ Transposable elements (TEs)▪ LINE (L1) “Extinction”

Materials and methods▪ Preliminary bioinformatic analysis▪ Bench work▪ Bioinformatic analysis

Results and Discussion▪ Numbers/passed quality control▪ Preliminary findings

13-lined ground squirrel Ranges over central North America

Recent findings about very low L1 activity

• Class I • Mobilization via an RNA intermediate

Pol III transcription

Reverse transcription and insertion

L1 elements

T0 T 1 T2

T0 T3 T100

Number of mutations = 0Avg. genetic distance = 0

Number of mutations = 14Avg. genetic distance = 2.3

Number of mutations = 53Avg. genetic distance = 8.9

Young Old Oldest

Platt et al. 2012

S. tridecemlineatus

250 most similar (most recently active) L1 ORF2 fragments from human, mouse, rat, and 13-lined ground squirrel.

19-26 MYA

Platt et al. 2012

Spermophilus tridecemlineatus

Based on the presence of L1 in Primates, Mouse, Rat, and many other species it has generally been assumed that L1 is present and active in all mammals.

Identified L1 extinction events Megabats (Cantrell et al. 2008) Sigmodontine rodents (Grahn et al. 2005) Spider monkey (Boissinot et al. 2004) Tasmanian devil (Gallus et al. 2015)

35 mya

12 myaWhat happened to L1s in neighboring taxa?

Look at taxa diverged prior and after extinction event occurred.

Herron et al 2004

Used well-annotated L1s from other mammals Degenerate primer for region of ORF2 <500bp This allows for amplification of 100s of 1000s of

different LINE L1 elementsCantrell et al. 2000

Identify ORF2 fragment Develop primers Isolate DNA from liver tissue PCR Sanger sequencing to verify

diversity of amplicons Illumina paired end

sequencing

Spermophilus tridecemlineatus

Spermophilus parvidens

Spermophilus mexicanus

Cynomys ludovicianus

Spermophilus spilosoma

Marmota flavivientris

Spermophilus variegatus

Ammospermophilus harrissi

Tamias dorsalis

Glaucomys volans

Tamiasciurus hudsonicus

Sciurus niger

300bp reads from each end of amplified L1 ORF2 fragment

Overlap of ~100bp allows whole fragment to be sequenced

Read 1 (≤300bp)Read 2 (≤300bp)

This methodology allows for generation of huge data sets

Preliminary analyses

Raw CollapsedStri 64,344 42,697Spar 62,546 43,202Smex 388,986 181,563Clud 71,824 49,717Sspi 14,317 7,603Sric 120,142 75,874Mfla 41,203 29,631Svar 64,659 38,644Ahar 30,836 24,161Tdor 1,202 36,347Gvol 5,330 156Thud 45,135 970Snig 16,808 359Total Paired Reads 927,332 530,924Total Base Pairs <600,000,000 320,000,000

Ammospermophilus harrisii

Cynomys ludovicianus

Spermophilus parvidens

Most similar L1 fragments from each taxon

Use most similar in order to obtain the most recent active L1 elements

Long branches L1s highly diverged over

all taxa

L1 elements in sciurids have had very little recent activity.

Hypothesis based on preliminary data:

Suggests a group-wise shutdown of these LINE elements

Single extinction event ~25 mya (affecting all in-group taxa)

Use all available data

Did extinction event occur in neighboring taxa at the same time?

How wide-spread is the extinction?

Natural Science Research Laboratory(Museum of Texas Tech University)

Dr. Roy N. Platt, IIDr. David RayDr. Robert BradleyLaura Blanco-BerdugoKevin Sullivan Wesli Kay Stubbs

Texas Tech University Research and Testing

Texas Tech University High Performance Computer Center