variation in domestic and wild yak

Variation information of wild and domestic yak: tar zxvf variation.tar.gz. The information is stored in GFF format (https://genome.ucsc.edu/FAQ/FAQformat.html#format3). There are three files: snp.gff: Single-nucleotide polymorphism information of six yak. indel.gff: Insertion and deletion information of six yak. sv.gff: structural variants of six yak

Custom perl scripts used in this article

Custom perl scripts used in this articl

Three-chamber Test for Odor Preference.

<p><b>A</b>) Schematic illustration of a classic 3-chamber design. The positions of odor vials are indicated. Shaded areas in each arm of the chamber indicate the odor zone for behavior analysis (<b>i</b>). Tracking traces of four animals in a control experiment with mineral oil vials in both chambers are shown (<b>ii</b>). <b>B</b>) Scatter plots of time spent in two zones in a control session with mineral oil. Each test session was 10 minutes. Twelve animals were examined. Pair wised <i>t</i>-test <i>p</i> value is indicated. <b>C</b>) Odor preference test for female urine (FU, <b>i</b>) and 2-MBA (<b>ii</b>). The upper panels show the tracking trace of one animal in the behavior chamber. Bar graphs indicate time spent in each zone. The number of animals (n) and <i>p</i> values of pairwise <i>t</i>-test are shown. <b>D</b>) Box plot of the ratio between test odor and MO. Dashed line indicates no difference between two zones. One-way ANOVA <i>p</i> values are indicated.</p

Behavior Assay Using PROBES.

<p><b>A</b>) Schematic illustration of odor delivery sequence in dis-habituation and cross habituation assays. S1, S2, S3 indicate odor stimulus or air control. <b>B</b>) Event log from software package. (<b>i</b>) List of event types and corresponding device locations used in the log sheet. (<b>ii</b>) An example event log listing time, type, location and magnitude. Five pairs of events are labelled with different colors. The “on” and “off” events of each pair are indicated. Time elapsed between “off” and “on” indicates the duration of an event. <b>C</b>) Raster plots showing odor port investigation of two female animals (<b>i</b> and <b>ii</b>) in response to male urine registered by PROBES and with video recording. Enlarged views of activities during the last trial of mineral oil delivery and the first trial of male urine delivery are shown to illustrate the differences in investigation measurement between PROBES and video recording. TTL square pulses are marked to indicate odor delivery. Shaded columns indicate odor delivery of mineral oil (grey) and mouse urine (blue). Arrows 1–5 mark the five event pairs in <b>B</b>. <b>D</b>) Bar plots of the duration of odor investigation shown in <b>C</b>. The total time of odor port investigation in each trial was plotted. <b>E</b>) Comparison table for these two methods.</p

Odor Delivery Controlled by the Olfactometer.

<p><b>A</b>) Sample traces of PID measurement of AA at various concentrations. <b>B</b>) Dose response curve of four different odors at seven concentrations. <b>C&D</b>) PID measurements of repeated odor applications over multiple sessions using single odor vials (<b>C</b>) and syringe top filters (<b>D</b>). Flow speed and application duration are as indicated. <b>E</b>) Normalized PID measurement values as a function of time after odor delivery. Odor concentration: 2.5×10⁻³ s.v. <b>F</b>) Sample PID traces of odor mixture delivery using olfactometer. The black bars indicate the delivery of HXH. The red bars indicate the delivery of HXO.</p

Reinforced Two-Choice Assay and Go/No Go Assay using PROBES.

<p><b>A</b>) The learning curve in a two-choice assay to discriminate AA and HPH (1∶100 concentration, v/v) in 9 animals. Individual animals’ training curves are shown in grey lines. Error bars, S.E.M. <b>B</b>) Success rate (<i>SR</i>) in two-choice testing with decreasing odor concentration using the same set of animals as <b>A</b>. Chance level of discrimination is 50%, indicated by a dashed line. <b>C</b>) Training curve in a Go/No Go training using AA as reward odor (CS+, 1∶100, v/v) and MO (CS−). Individual animals training curves are shown in grey. <b>D</b>) Success rate in Go/No Go test with increasing odor concentration. The average <i>SR</i> from eight animals are indicated in black. The psychometric performances of three individual animals are plotted in grey. The results are fit with a Weibull psychometric function. Threshold values (T) calculated from the fitting are indicated in the figure.</p

Behavior Box Design.

<p><b>A</b>) Single port design with one pair IR LED emitter and detector that can be used to trigger odor delivery. <b>B</b>) A triple port design that combines the odor port in <b>A</b> with two water ports. A water spout is included in each water port. <b>C</b>) A single port design that combines water and odor delivery. Two sets of paired IR LED emitter and detector are implemented to detect nose poking and licking activity.</p

alignments_for_phylogeny

This fasta format file contains an alignment with a length of 9175 base pair. The alignment is constructed by concatenating the four-fold degenerate sites of the 206 high-confidence single-copy genes among 11 species, wich including Anolis carolinensis, Chamaeleo chamaeleon, Chalcides ocellatus, Phrynocephalus erythrurus, Phrynocephalus putjatia, Pogona vitticeps, Rana chensinensis, Rana kukunoris, Sphenodon punctatus, Xenopus tropicalis and Danio rerio

PROBES based habituation/Dis-habituation Analysis of Innate Odor Preference.

<p><b>A&B</b>) Bar plots of odor port investigation by a single animal (upper panel) and the average of <i>NPI</i> value for FU (<b>A</b>, 10 animals) or 2-MBA (<b>B</b>, 11 animals). Dashed lines indicate 100% of average <i>NPI</i> to mineral oil. Calculation of attraction and aversion indexes is indicated. <b>C&D</b>) Comparison of attraction(<b>C</b>) and aversion (<b>D</b>) indexes obtained by PROBES assay and 3-chamber assays. The <i>p</i> values of the tests are indicated. <b>E</b>) Comparison table of PROBES and 3-chamber methods for innate preference assays.</p

The Design of PROBES.

<p><b>A</b>) Schematic illustration of the system. A single PROBES software interface gives commands and integrates readout from the olfactometers and behaviors boxes. Four separate olfactometers and behavioral boxes are independently controlled, and each olfactometer controls eight odor channels. Odor from each olfactometer is delivered to the corresponding behavior box. Readout is indicated by purple lines, commands are indicated by dark blue lines and air flow paths are indicated by green lines. <b>B</b>) Photograph of PROBES setup with four olfactometers. Each box contains two independent olfactometers. <b>C</b>) Detailed layout of a box containing two separate olfactometers. <b>D</b>) A typical behavior box with the triple port configuration for reinforced two-choice assays. Odors are delivered through the middle nose cone while the water reward ports are controlled by two water valves.</p