Trachylepis affinis locality points in Cameroon

List of coordinate points for sites in Cameroon where T. affinis has been found during the period of 2001 to 2005

Trachylepis affinis thermal performance values

Range of thermal physiological metrics for each individual collected in the ecotone (n=7) and forest sites (n=29) from June 2015 to April 2016. These values were extracted from the "double exponential" model fit to the raw maximum running speed data (Appendix 1, Table A1)

Trachylepis affinis raw maximum running speed data

Maximum running speed values (in m/s) measured at seven different body temperatures for individuals collected from ecotone (n=7) and forest sites (n=29) from June 2015 to April 2016

Trachylepis affinis forest and ecotone thermal tolerance

Critical thermal minimum and maximum values measured for all individuals collected in the ecotone (n=7) and forest sites (n=29) from June 2015 to April 2016

Specimen isolation data.

<p>Specimen isolation data.</p

Grouping Scan analysis.

<p>Sequence fragments of 250 bases incrementing by 100 bases with 100 bootstrap replicates, were used to compare and analyse (a) <i>P.t.troglodytes/P.t.ellioti</i> recombinant FJ98098.1 (b) <i>P.t.ellioti/P.t.troglodytes</i> recombinant FJ98099.1 (c) <i>P.t.schweinfurthii</i> isolate A498266; (d) <i>P.t.troglodytes</i> AM117396 (e) <i>P.t.troglodytes</i> recombinant AB046525 (f) study recombinant <i>Gorilla gorilla</i> HBV sequence (ECO50003); to sequence groups from <i>Gorilla gorilla</i> (red), <i>Pan troglodytes ellioti</i> (blue), <i>Pan troglodytes troglodytes</i> (green), <i>Pan troglodytes verus</i> (yellow), <i>Pan troglodytes schweinfurthii</i> (purple) and human genotype HBV/C (light blue) with respect to A498266. Values >0.5 indicate clustering within the indicated group.</p

Tree Order Scan of HBV sequences.

<p><b>Figure 2(a)</b>. TreeOrder Scan of HBV sequences, indicating positions of individual sequences (y axis) in Phylogenetic trees generated from sequential 250-base sequence fragments, incrementing by 50 bases. Changes in sequence order as a result of changes in phylogeny at the 70% bootstrap level are shown. Sequences are colour coded by genotype and host species, as indicated by the labels in left and right margin: genotype A, purple; B, light blue; C, wine; D, emerald; E, royal blue; F, orange; G, pale green; H, navy; Gorilla, blue (Gor); Chimpanzee, green (Pan); and Woolly monkey (WM-out-group on line 1), red. For comparison the Tree Order Scan has been aligned with scale genome of HBV (top panel). Recombinant sequences are highlighted as by dashed lines; black gorilla/<i>P.t.e</i> ECO50003LIP3, green FJ798099 <i>P.t.e/P.t.t</i>, pink FJ798098 <i>P.t.e/P.t.t</i>, orange AB046525 <i>P.t.t</i> and purple AF498266 <i>P.t.s </i><b>2(b).</b> Tree Order Scan of HBV sequences, indicating positions of individual sequences (y axis) in phylogenetic trees generated from sequential 250-base sequence fragments, incrementing by 50 bases. Changes in sequence order as a result of changes in phylogeny at the 70% bootstrap level are shown. Sequences are colour coded by host species and sub-species of chimpanzee, as indicated by the labels in left and right margin: <i>Gorilla gorilla</i>, blue (Gor); <i>Pan troglodytes troglodytes</i>, yellow (<i>Ptt</i>); <i>Pan troglodytes ellioti</i>, green (<i>Pte</i>); <i>Pan troglodytes verus</i>, purple (<i>Ptv</i>); <i>Pan troglodytes schweinfurthii</i>, violet (<i>Pts</i>); and <i>Hylobates pileatus</i> (<i>Hyl</i>) (out-group-line 1-GII), red. For comparison the Tree Order Scan has been aligned with scale genome of HBV (top panel). Recombinant sequences are highlighted as by dashed lines; black gorilla/<i>P.t.e</i> ECO50003LIP3, green FJ798099 <i>P.t.e/P.t.t</i>, brown FJ798098 <i>P.t.e/P.t.t</i>, orange AB046525 <i>P.t.t</i> and blue AF498266 <i>P.t.s.</i></p

Sequence Capture Gene Trees

Maximum likelihood (ML) trees for each sequence capture gene used for species tree analyses. ML analyses were run with RAxML

Sequence Capture Loci

Sequence capture loci (a.k.a. anchored phylogenomics data). The data are in Nexus format (partitioned)

Pathogen-Host Associations and Predicted Range Shifts of Human Monkeypox in Response to Climate Change in Central Africa

<div><p>Climate change is predicted to result in changes in the geographic ranges and local prevalence of infectious diseases, either through direct effects on the pathogen, or indirectly through range shifts in vector and reservoir species. To better understand the occurrence of monkeypox virus (MPXV), an emerging Orthopoxvirus in humans, under contemporary and future climate conditions, we used ecological niche modeling techniques in conjunction with climate and remote-sensing variables. We first created spatially explicit probability distributions of its candidate reservoir species in Africa's Congo Basin. Reservoir species distributions were subsequently used to model current and projected future distributions of human monkeypox (MPX). Results indicate that forest clearing and climate are significant driving factors of the transmission of MPX from wildlife to humans under current climate conditions. Models under contemporary climate conditions performed well, as indicated by high values for the area under the receiver operator curve (AUC), and tests on spatially randomly and non-randomly omitted test data. Future projections were made on IPCC 4^th Assessment climate change scenarios for 2050 and 2080, ranging from more conservative to more aggressive, and representing the potential variation within which range shifts can be expected to occur. Future projections showed range shifts into regions where MPX has not been recorded previously. Increased suitability for MPX was predicted in eastern Democratic Republic of Congo. Models developed here are useful for identifying areas where environmental conditions may become more suitable for human MPX; targeting candidate reservoir species for future screening efforts; and prioritizing regions for future MPX surveillance efforts.</p></div