Posted on Authorea 29 Jun 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.162495929.94655412/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 70,USA 47907, 5 4 Mexico USA 3 77843, TX Station, College brough, 2 1 DeWoody neouinr esetv ncneprr eei odi hetndseist inform to species threatened Mathur in Samarth load genetic contemporary efforts conservation on future perspective rescue evolutionary genetically from genetic An stems enlighten mutations. flow deleterious gene can assisted of species when proportion most lowest given the the genomics a benefit have population should of that a populations populations demography inbred apply that donor small, We historical mutations diverse that and selection. deleterious suggest phylogeography data purifying as Our ineffective depression the and efforts. inbreeding how inbreeding, suffer showcase drift, to to to (Cyrtonyx likely due framework more Quail mutations, homogenized are deleterious Montezuma are fewer genetic populations purging relatively of that carrying isolated escape but Despite pairs small, bottlenecks, bottlenecks. how donor-recipient demographically during stronger demonstrate mutations with both potential deleterious we populations on lose of smaller in to based sequences pronounced demographic tend analyses, is that populations genome purging Our all and whole that nature time. indicate in as over populations, dynamic well mutations montezumae) evolutionarily deleterious is as a load of simulations with a genetic distribution explicit associated that as the distribution show is serve empirical influences we fitness the principle, greatly Here, driving evolutionary processes history in in crucial. evolutionary of is reduction can, understanding mutations A better translocations deleterious a populations. thus, such of and recipient that mutations enter deleterious argued of to diverse load have mutations genetically higher from studies deleterious individuals new simulation translocating for by recent populations conduit However, “recipient” fragile populations. in reduced “donor” be can erosion genomic theory, In Abstract 2021 29, June 4 3 2 1 DeWoody Mathur efforts Samarth conservation future inform in to load species genetic threatened contemporary on perspective evolutionary An eateto oetyadNtrlRsucs udeUiest,75W tt t,Ws aaet,IN Lafayette, West St., State W. 715 University, Purdue Resources, Natural USA and 78121 Forestry TX, of Vernia, Department La Department, Wildlife and Parks Potos´ı 78600, Luis Texas San Hidalgo, de Kim- Salinas 73, Potos´ı, John Iturbide Luis 534 San Campus University, Postgraduados, de A&M Colegio Texas USA 47907, Management, IN Fisheries Lafayette, and West St., Wildlife, State Rangeland, W. of 915 Department University, Purdue Sciences, Biological of Department ea ak n idieDepartment Wildlife Potosi and Luis Parks San Texas Campus Postgraduados de Colegio University A&M Texas University Purdue 1,5 1 1+* 1 on .Tomeˇcek M. John. , onTomeˇcek John , 2 usTarango-Ar´ambula Luis , 2 usA Tarango-Ar´ambula A. Luis , 1 3 oetPerez Robert , 3 oetM Perez M. Robert , 4 n Andrew and , 4 .Andrew J. , Posted on Authorea 29 Jun 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.162495929.94655412/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. pce a lob eedn nacetadrcn vltoayhsoy(eaz ta. 07 Grossen, 2017; al., Lohmueller, et Kim, (Benazzo Brown, Robinson, history 2020; evolutionary Lohmueller, recent & Wayne, and Kyriazis, ancient 2020; Croll, on endangered & of dependent Keller, probability Guillaume, be extinction subsequent also and contemporary depression allelic may inbreeding shape species of of 2019). risk selection effects that al., shows and fitness et evidence Recent demography (Bell the Un- populations like of wild 2020). processes understanding Frankham, in evolutionary limited & pools Lacy, how our gene Sunnucks, by and deleterious Ralls, hindered (mutations) 1991; of 2017; variants masking Charlesworth, are al., the efforts & et and allelic conservation (Barrett Frankham heterozygosity providing fortunately, 2015; depression increased by (Frankham, via inbreeding fitness alleles 2015) reducing increases Tallmon, recessive rescue by & aims Genetic & Funk, and rescue”) Fitzpatrick, (Bijlsma populations. adaptation (“genetic Whiteley, most isolated erosion translocations for for small, genetic via paramount necessary flow in to is gene variants fitness due fitness Assisted mean time 2018). and increase over al., diversity to et fit genetic (Ralls of po- less efforts preservation isolated and conservation The modern produces diverse, 2005). which less Frankham, 2003), smaller, 2012; (Fahrig, Loeschcke, become habitat often natural that subdivide pulations and reduce activities Anthropogenic Ring Quail; Introduction Montezuma mutations; Deleterious variation; flow Functional Species gene Demography; assisted mutations. history; deleterious when Evolutionary of most proportion the lowest the benefit have should that Keywords: rescue populations populations genetic to inbred donor enlighten framework diverse small, can genomics genetically species homogenized that population from given are suggest stems a a purging data of apply demography We escape Our historical selection. that efforts. and purifying phylogeography mutations ineffective the deleterious how and are as showcase inbreeding, populations depression drift, isolated inbreeding small, to bottlenecks. how suffer due stronger demonstrate to with we populations likely Montezuma mutations, smaller deleterious of more in fewer pairs pronounced relatively is donor-recipient carrying purging potential Despite genetic of demographical- that greatly but sequences both history bottlenecks, on genome during demographic based whole that analyses, as and Our ( well nature Quail time. as over in simulations mutations dynamic explicit deleterious better evolutionarily ly a of is crucial. thus, distribution A load is and the mutations populations. genetic mutations deleterious influences recipient deleterious that of enter of show distribution to load empirical we the mutations higher Here, driving deleterious a translo- processes with new evolutionary such associated for of that is understanding conduit fitness argued a evolutionary have as in from studies serve individuals reduction simulation principle, translocating recent in by However, populations can, “recipient” cations populations. fragile “donor” in reduced diverse be genetically can erosion genomic theory, In Abstract 0000-0002-7315-5631 DeWoody: Andrew J. Tarango-Ar´ambula: 0000-0002-7662-1319 A. Luis Tomeˇcek: 0000-0002-7494-283X M. John 0000-0002-6446-5718 Mathur: Samarth IDs: ORCID author: *Corresponding USA Title: 43210, Running OH Columbus, Ave, 12th W 318 + urn drs:Dprmn fEouin clg,adOgnsa ilg,TeOi tt University, State Ohio The Biology, Organismal and Ecology, Evolution, of Department address: Current ytnxmontezumae Cyrtonyx vltoayhsoyo eei load genetic of history Evolutionary aat ahrEmi:[email protected] E-mail: Mathur Samarth ouain,idct htalppltostn ols eeeiu mutations deleterious lose to tend populations all that indicate populations, ) 2 Posted on Authorea 29 Jun 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.162495929.94655412/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. utrhretdwnsiiilycletdb adle l 21) hra ye lo ise eetaken were tissues blood lysed whereas (2019), donated from al. biosystems taken et Kapa were Randel from samples Arizona by kit construction collected 6000. 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Data may be preliminary. aeoie ssnnmu ie,nurl fte a opeitdeeto rti rnlto rfunction. or translation were protein Variants on 0.1]. effect [0.05, predicted no history [?] had demographic score recent they < Reconstructing categories: SIFT if score two with neutral) SIFT (i.e., mutations into with synonymous missense variants mutations (i.e. as were missense the functional categorized mutations were rank classified deleterious mutations and We weakly Deleterious acids 0.05, amino deleterious”. deleteriousness. “Weakly of scores their and properties SIFT physical on “Deleterious” GRCg6a). the (assembly based classify genome and further variants two reference homology To chicken non-synonymous) the the sequence score). in between from prediction changes determined generated acid low concordant as amino are or 2003) were possible (Ng, data all scores classes Tolerant) of for from VEP lack impact Intolerant structure by (Sorting to the protein SIFT due used to where we (either consequences mutations, warnings annotations non-synonymous predicted without retained on were classification based only and impact v4.3 “High”) We subjective methods SNPEff a and and provide “Moderate”, function. 2016) approaches “Low”, Both al., and (“Modifier”, et sites. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162495929.94655412/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. omr ul nesadtetmoa n pta itiuino eoi ainsascae ihload, with associated variants genomic of distribution spatial and temporal the understand species fully ring a more resembles To due history demographic fitness and individual phylogeography of Quail of consequences Montezuma loss suffer The to 2013). likely homogenized. al., more are et are mutations populations deleterious inbred more to smaller For mutations, as to deleterious depression selection. lead of inbreeding overpowers processes proportion drift these F lower when between Both a only relationship more persist positive beneficial. are significant can or populations a mutations neutral diverse deleterious are weakly more purging that that larger, at mutations that efficient genic more or more are Load populations populations carry diverse small to more than likely larger, mutations that mean deleterious and could heterozygosity strongly This genome-wide S13A). between (Fig. relationship mutations negative significant a found We Fig. 2C). 2021; (Fig. DeWoody, quail & 2018). 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Fg 1)adaelkl ors nfeunya iia ae Fg C.Ti en neta deleterious ancestral purifying means weak This only 4C). facing thus (Fig. neutral rates nearly similar likely at more populations frequency two 4C). are in the (Fig. bottlenecks translocations/reintroductions rise in selection natural by frequencies to survive mediated similar likely that at be are are mutations segregate can and populations mutations and strongly S18) as deleterious adaptation against Shared bottleneck (Fig. selection local 2020). post Purifying of al., immediately environments. et sign deleterious effective new (Grossen a the most colonize is of is founders populations mutations Most two and purging deleterious the inset). higher, between genetic 4B shared is means are inbreeding thus, (Fig. bottleneck This smaller smaller, and post-bottleneck the 4B) the the density S18). after Fig. but in mutation pre-bottleneck; immediately kya) reduction in (Fig. arose a alleles drop (15-25 (i.e. is a Arizona ancestral deleterious bottleneck are by there in of purge mutations seen populations, arose time effectively as both mutations the more kya) In deleterious around (10-15 to 4A). more arose continued 100kya, Fig. to that population last 10,308; originated mutations Texas models (N= the populations deleterious Texas Within linear West Quail of in Montezuma created S17). proportion than in then as (Fig. mutations population. 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Texas load, a from al., ancestral flow indicating gene purge et gene Bottlenecks historic populations, (Martins to two with adapted relative the Texas populations locally between to terminal Geographic are Arizona flow stable from populations gene S16). but two of 3D, Price, 2013), the 3A, rate Scordato, Bar-Yam, (Alcaide, if unequal & (Fig. rare exist Aguiar, lineage are Mexico can de western isolation from flow the Martins, reproductive individuals samples to with 2014; Quail contemporary formation similar Irwin, Montezuma Our species more & all ring are (S16). for barrier that but suitable populations landscape two estimated conditions ancestral the major (Fig. also between the K=2 populations analyses as admixed from Texas acted admixture are derived modern likely Our were Plateau formed likely Mexican ultimately lineages. most Central and East two the population the of the Arizona habitat in contemporary between hospitable Oriental the population less form ancestral Madre the to diverse Sierra West 3C); relatively since the larger, the and in The evolved from Occidental ratio have 1978). 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Data may be preliminary. vlae spr fa seseto vrl eei iest yuiggnmcrsqecn approaches. be resequencing can genomic populations using source by various diversity in genetic load overall genetic of where assessment point an a of the at part 2019; now about as al., is concerns et evaluated genetics Valk on der conservation et van based think 2020; (Ralls We challenged al., regime” populations et recently “diversity-based (Kyriazis source this been populations 2020). 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R shg,epcal hncoupled when especially high, is Load Load P P r also are Since . Posted on Authorea 29 Jun 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162495929.94655412/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. uea .A,Crer,M . at,C,Ppi,R,dlAgl . eyMosie . erso M. DePristo, . Practices . Best Toolkit . Analysis A., Genome The Levy-Moonshine, G., Calls: Variant Angel, High-Confidence del to R., Pipeline. Data Poplin, FastQ C., From Hartl, (2018). O., A. M. species Carneiro, ring ancestry A., individual a G. for Auwera, in algorithm divergence ADMIXTURE the Genomic to (2014). Enhancements (2011). E. K. estimation. D. Lange, & Irwin, H., & D. Alexander, D., T. Price, C., S. complex. E. Scordato, Where M., Populations Alcaide, in Individuals of Fitness The Load: doi:10.1146/annurev-ecolsys-110411-160257 Abundant. Mutation (2012). Are C. Alleles M. Deleterious Whitlock, & F., A. Agrawal, interests. References financial competing and no effort declare writing authors the The led JAD and manuscript. SM Interest the analyses. Competing reviewed bioinformatic collected and and and input work lab provided field wet conducted authors all RMP htt- all and LATA performed research. at SM the samples. designed accessed and key conceived JAD publicly and JMT, be Archi- SM, Read ac- can Short SRA analysis contributions NCBI’s and for Authors’ in SAMN18007393-18007458 developed available accessions scripts are study BioSample The ps://github.com/samarth8392/MQU current PRJNA703039, SRR13748610-13748675. the accession cessions during BioProject generated ve datasets sequence publication The a represents by article supported This Foundation. was accessibility Welder Foundation. Data SM Bessie Potos´ı, Wildlife Caesar Department. and Luis Welder Rob Wildlife San the the and Initiative, of Campus Texas from Parks #### Postgraduados in Texas Fellowship University; Quail de and Research State of Colegio Institute, research Graduate Ross Decline Agriculture, Research This the Sul University-Kingsville. and Wildlife Reversing from A&M Food Service, Kleberg Texas Harveson Extension for from Louis AgriLife Institute Hernandez and A&M Fidel National Texas Texas Luna Dr. for by Ryan and Miller funded Stewart Drs. Mike was Kristyn thank and as We also Moore well Joyce We Alberto wings. as hunter-harvested Schmidt, support; support. work the Ryan field work Weaver, for Mexican James field their Fish Montoya, for and Montoya B. Felipe Game Juan Angel of Olmos, Mac´ıas Duarte, Department Erasmo Olmos, Arizona Genaro the thank at also Heffelfinger J. thank our We of conservation holistic think the also for We Acknowledgements beneficial rescue. are genetic herein for prioritize conducted help individuals) biodiversity. potential to those (or deteriorating used adaptive genetic like populations be assessments source proactive can future evolutionary load best encourage maximizing genetic that the We and as at- by diversity overall such alleles). in both (e.g., decisions of deleterious conservation load maximize evaluations translocations rare that genetic can argue like of that the and efforts monitoring introduction populations of donor minimizing rescue weight evaluating simultaneously relative of for while the context success small, critical increases remains potential provide inbreeding and findings the recent isolated Our that becomes populations. conclude population risk We a that once ineffective. show However, is results selection large. Our purifying novo was via mutations pools. de population deleterious gene historic ancestral of Arizona the purging and genetic when Texas to lead extant can between bottlenecks demographic differentiation genetic the produced eeeiu uain ess n d oteidvda eei odbcueprfigselection purifying because load genetic individual the to add and persist mutations deleterious aue 511 Nature, urn rtcl nBonomtc,43 Bioinformatics, in Protocols Current M iifrais 12 Bioinformatics, BMC 70) 38.doi:10.1038/nature13285 83-85. (7507), nulRve fEooy vlto,adSseais 43 Systematics, and Evolution, Ecology, of Review Annual EvoGenomics 1.doi:10.1186/1471-2105-12-246 (1). 1.doi:10.1002/0471250953.bi1110s43 (1). 12 1,115-135. (1), Posted on Authorea 29 Jun 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162495929.94655412/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. o . aik . i . dhbi . uye,S,&Rih .(05.N vdneta eeto has selection that evidence No Africans. (2015). in D. than Reich, Europeans & in S., mutations Sunyaev, doi:10.1038/ng.3186 deleterious The I., removing 126-131. (2011). Adzhubei, (2), at R. H., effective Durbin, less wild. Li, . been D., . the Balick, . R., A., in M. Do, DePristo, depression E., VCFtools. Banks, Inbreeding and A., C. format Albers, call G., variant Abecasis, (1999). A., Auton, P., A. Danecek, Population D. of Inference Roff, (2012). & doi:10.1038/sj.hdy.6885530 D. Falush, P., & S., Crnokrak, Myers, Data. G., Haplotype Hellenthal, Dense J., using D. (2010). Structure A. Lawson, A D. P., Nickerson, G. & (2014). Copenhaver, J., Shendure, M. J., D. M. Bamshad, Ruden, mutations. doi:10.1038/nmeth0410-250 A., Sidow, disease-causing . 250-251. (2015). B., highlight S. scores J. Ng, . constraint L., evolutionary J. SnpEff. D. Single-nucleotide . Goode, polymorphisms, Lee, L., M., nucleotide G. 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No reuse without permission. — https://doi.org/10.22541/au.162495929.94655412/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ri,D . esh . rc,T .(01.Seito naring. a in Speciation (2001). D. T. Price, & S., Bensch, doi:10.1038/35053059 E., D. Irwin, (2000). Proceedings. J. Symposium Quail R. (2007). National Olding, S. the & M. Whitley, R., & J. M., Heffelfinger, J. Mueller, A., history. D. life Holdermann, and 23-29. F., ecology Hernandez, H., quail T. Montezuma Allen, A., Proceedings. L. Symposium Harveson, Quail National the at presented predicts Paper heterozygosity (2009). “Individual A. on L. the Comment Harveson, tortoises”. Beyond (2021). desert Simulations C. threatened Genetic Oosterhout, in Forward van success & 3: E., translocation SLiM H. Morales, (2019). B., Hansson, R. Hernandez, & W., P. Model. Wright–Fisher through Messer, mutations . C., deleterious highly A., B. sequence of M. Haller, Purging reveals P. (2020). genome ibex. D. 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(ROH), (C) homozygosity heterozygous blue of U.S. less runs population. arrow), significantly (MX=4, the are AZ purple Texas Mexico in in (WTX=31, the populations Texas than and isolated populations West the circle), peripheral indicate arrow), estimates pink with heterozygosity orange genomic (AZ=28, Quail. Mexico (CTX=3, Arizona Montezuma in from Texas distributed genomes in Central whole predominantly inbreeding 66 gamebird analyzed and small We diversity a rescue. is Genomic the (inset) to rescue 1. Genetic Figure (2015). A. D. Tallmon, & C., 30 W. Evolution, Funk, & Ecology W., in S. relation- Trends Fitzpatrick, familial close R., of A. inference Whiteley, frequency-free data. Allele sequencing (2019). low-depth I. or genotypes Moltke, from & ships A., Albrechtsen, K., R. conservation.Waples, species of spectre (2019). the is K. alleles load 4 Mutation Guschanski, deleterious (2020). 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(1), idieSceyBlei,43 Bulletin, Society Wildlife h mrcnJunlo Human of Journal American The cec,370 Science, iRi.Rtivdfo htt- from Retrieved bioRxiv. . aueEooy&Evolution, & Ecology Nature A h otzm Quail Montezuma The (A) siae fgenetic of Estimates 62) 1086-1089. (6520), ROH .()Sliding (D) ). Conservation (4), Posted on Authorea 29 Jun 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162495929.94655412/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. niiilfeunyo /N hs eut eosrt htsalppltosieetvl ug enovo de Figure1.pdf purge ineffectively populations have file small always The Hosted mutations that new demonstrate increase. as results frequency size These small of panel) mutations. its 1/2N. rate (upper given deleterious of faster expected mutations frequency have is deleterious Texas initial population Texas West shared an West in for 2A) the panel) for trajectories (Fig. intercept (lower bottleneck similar higher mutations founding predict (age deleterious a around frequency private mutations to mutations but and due deleterious deleterious Texas of age recent West density privately mutation in the the are of in purging or of dip historic WTX The purging suggests Texas and (inset). inset) but West Arizona kya in the 25 between bar and shared size, (black kya are ˜17kya smaller 150 that much past mutations the its over deleterious Despite segregating of distributions line). age dotted ( The the younger by more contains (indicated originated population split (˜50%) load demographic contemporary the the of since Much 100kya. last the reveal load. over > Texas analysis West genetic and of Admixture Arizona AZ in dynamics (D) mutations between Temporal the populations. differentiation as ancestral (right). 4. pronounced of Plateau and Figure shown no. MX, Mexican Oriental also K= and Central Madre form is AZ populations. the to Sierra lineages between TX showing and two west coancestry the schematic Arizona, the the along A within between in expansion subdivisions Occidental barrier (left). eastern ring to Madre landscape populations smaller a proportional Texas Sierra major of a is modern the that and size resembles the along of small arrow population quail forming expanding series maintained Montezuma quail; Arizona of population a have Montezuma contemporary phylogeography ancestral after for populations The the year an formed Texas (C) 1 TX. with (NAZ) of and populations kya. species, AZ time Arizona 17 between generation rate contemporary split a migration whereas assumed a We split demographic by underwent their followed bottlenecks. (NA0) since kya population demographic (NTX) ancestral 90 Our the sizes (B) around indicates isolation. samples (NA1) populations term Texas Mexico long expansion and and between indicates Arizona within Arizona co-ancestry diagonal) Both of shown of right Lack are box. model (bottom heterogeneous. clades dotted populations more the Arizona are major in quail and three Texas Texas shown co-ancestry; The are population samples within (right). Texas higher populations Central share sampled the Quail. and for Montezuma boxes map of black heat history Texas co-ancestry West demographic and small and (left) the Phylogeography p in (* small higher 3. proportion in depression. is the Figure inbreeding genomes, higher load, to individual significantly Realized contribute in (C) was may homozygotes frequency and MAF as mutations. allele exist population deleterious expected, minor that weakly bar) As mutations and (error deleterious deleterious SE interquartileof populations. both and 1.5x two for (circle) represent in Mean population whiskers mutations Texas (B) quartiles; deleterious lower outliers. boxplots, represent of and In points upper (MAF) mutations. black are deleterious Texas solid weakly edges West and unpurged smaller box range of and median; load Arizona indicates potential larger line greater the between a center overall has similar Arizona is but Quail. deleterious, Montezuma population, are in that load mutations realized genic and all load range Potential interquartile 2. 1.5x p Figure center represent (* boxplots, whiskers BirdsInFocus. In quartiles; outliers. Gress, database. lower average, Bob represent IUCN and on points courtesy: the upper ROHs, from represents black are longer acquired solid (break have edges was and populations map box population CTX Range genomes median; WTX and individual individuals. indicates across WTX MX the line length in or ROH in Individuals AZ of distribution to heterozygosity x-axis). The compared the genomic (E) along chromosomes). in column all for reduction (each S2 overall Fig. see an chromosome chicken centromere; reveal to corresponding also windows 1kb non-overlapping 1 across heterozygosity of analysis window 0kai h neta ouain hra 3%o h eeeiu lee rs ntels 02 kya 10-25 last the in arose alleles deleterious the of ˜30% whereas population, ancestral the in kya 50 vial at available https://authorea.com/users/311018/articles/528252-an-evolutionary- < y)dltrosmttosta aeaie env rdbr.(B) bar). (red novo de arisen have that mutations deleterious kya) 5 < .5 *p ** 0.05, 17 A h g itiuino otmoaydeleterious contemporary of distribution age The (A) < ka a enls ffiin.()Lna model Linear (C) efficient. less been has 5kya) < .1 * p *** 0.01, < .5 *p ** 0.05, A oeta od h rprinof proportion the load, Potential (A) < < .0) otzm ui image Quail Montezuma 0.001). .1 * p *** 0.01, A eelgcltree Genealogical (A) < 0.001) Posted on Authorea 29 Jun 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162495929.94655412/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. conservation-efforts perspective-on-contemporary-genetic-load-in-threatened-species-to-inform-future- (A) (B) (A) (A) AZ MX WTX CTX Potential Load

density 0.0925 0.0950 0.0975 0.1000 0.1025 0e+00 2e-05 4e-05 density6e-05 8e-05 0e+00 2e-05 4e-05 6e-05 8e-05 0.57 0.57 WTX Deleterious AZ 0.54 0.57 ZWTX AZ 0 0.46 50 00 75000 50000 25000 0 ns E8948 E8947 E8949 E8946 E8032 E8025 E8024 E7146 E7031 E8013 E8017 E7946 E7934 E6536 E8031 E7747 E7969 E7125 E6609 E6877 E8030 E6628 E7208 E7563 E8142 E6846 E7927 E7751 E7746 E7752 E7932 E7220 E9050 E9048 E9051 E9046 E9058 E9059 E9057 E9056 E8954 E9041 E9040 E9054 E9055 E9037 E9570 E9569 E9067 E9034 E9032 E9043 E9042 E9052 E9047 E9053 E9049 E9045 E9044 E9035 E9030 E9036 E9031 E9039 E9038 E9033 E9033 E9038 E9039 E9031 E9036 E9030 E9035 E9044 E9045 E9049 E9053 E9047 E9052 E9042 E9043 E9032 E9034 E9067 E9569 E9570 E9037 E9055 E9054 E9040 E9041 E8954 E9056 E9057 E9059 E9058 E9046 E9051 E9048 E9050 E7220 E7932 E7752 E7746 E7751 E7927 E6846 E8142 E7563 E7208 E6628 E8030 E6877 E6609 E7125 E7969 E7747 E8031 E6536 E7934 E7946 E8017 E8013 E7031 E7146 E8024 E8025 E8032 E8946 E8949 E8947 E8948 0.54 * 0.46

Age of deleterious mutation (years)

E9033 E9033 E9033 E9038 E9039 E9031 E9036 E9030 E9035 E9044 E9045 E9049 E9053 E9047 E9052 E9042 E9043 E9032 E9034 E9067 E9569 E9570 E9037 E9055 E9054 E9040 E9041 E8954 E9056 E9057 E9059 E9058 E9046 E9051 E9048 E9050 E7220 E7932 E7752 E7746 E7751 E7927 E6846 E8142 E7563 E7208 E6628 E8030 E6877 E6609 E7125 E7969 E7747 E8031 E6536 E7934 E7946 E8017 E8013 E7031 E7146 E8024 E8025 E8032 E8946 E8949 E8947 E8948 1250 E9038

002000 1000 0 E9038

E9039 E90391250

E9031 E9031

E9036 E9036 E9030 E9030 0.210 0.215 0.220 0.225 0.230 0.235

E9035 E9035

E9044 E9044 1870

E9045

0.0e+00 E90451870 2.5e-05 5.0e-05 7.5e-05 1.0e-04 E9049 E9049

E9053 E9053 E9047

E9047 Weakly Deleterious

E9052 E9052

E9042 E9042 E9043

2490

E9043 WTX AZ E9032

E90322490 E9034

E9034 E9067

0010000 5000 0 E9067 E9569

E9569 E9570 **

E9570 E9037 E9037 E9055 3110

50000

E9055 E9054 3110

E9054 E9040

E9040 E9041 E9041 E8954 Age of deleterious mutation (years)

Median Median Median

E8954 E9056 E9056 E9057

3730 E9057 E9059

3730

E9059 E9058 Pre E9058 E9046

0040 006000 5000 4000 3000

E9046 E9051 E9051 E9048

-

E9048 E9050 (B) bottleneck E9050 E7220

4350

E7220 E7932

4350

age age age E7932 E7752

E7752 E7746

E7746 E7751 E7751 E7927

0.57

E7927 E6846 privateWTX privateAZ shared 0.54 E8142

4970 E6846 Minor allele frequency (MAF) E7563

100000 E81424970

E7563 0.54 E7208 0.57 E6628 0.1 0.12 0.14 0.16

E7208

E6628 E8030

50 00 25000 20000 15000 Realized Load per individual

4e-04 5e-04 6e-04 7e-04 8e-04 E6877

No. of deleterious SNPs E8030 0.46 E6609

E6877

5590 0.46 E7125

E6609

E7969 E71255590 Deleterious

E7969 E7747 Weakly Deleterious Deleterious E8031

100000 E7747 = = =

E8031 E6536 WTX AZ

E6536 E7934 50 E7946 9

8 0.57

E7934 6210 E8017 ****

E79466210

, , 18 E8013 Private_WTX Private_AZ Shared 743 328 E8017

, E8013 E7031 068 E7146 E7031

E7146 E8024

E8024 E8025 E8032

6830 E8025 years E8946 years

6830 Realized Load per individual

E8032 4e-04 5e-04 6e-04 7e-04 8e-04 E8949

years E8946 E8947 0.0027 0.0018 0.0021 0.0024 E8949 E8948 E8947 Deleterious 0.46 E8948 0.54 Weakly Deleterious N 0.46 ZWTX AZ 0.57 0.54 A0 1250 1870 2490 3110 3730 4350 4970 5590 6210 6830 ZWTX AZ 0.57 =117,735 **** 0080 0010000 9000 8000 7000 (C) (B) (D) 0.57 T **** 1 (C) Post WTX AZ 87,301 - 0.0018 0.0021 0.0024 0.0027 150000 bottleneck K= 3 0.0060 0.0065 0.0070 0.0075 Weakly Deleterious 0.0 0.4 0.8 Synonymous ZWTX AZ (C) N ZWTX AZ ****

Allele frequency (MAF) Allele frequency (MAF) A1

Time (in years) Realized Load (C) =1,199,304 0.05 0.06 0.04

0.04 0.05 0.06 0.07 0.08 0.02 0.06 0.1 0.14 **** T 10 5 0 10 5 0 2 AZ Deleterious β β β WTX 0.0060 0.0065 0.0070 0.0075 ZWTX AZ WTX AZ s β Age of Deleterious Mutation (Kya) Age of Deleterious Mutation (Kya) WTX s AZ = 1.82x10 = = 1.87x10 = AZ Synonymous **** = 4.29x10 = = 1.67x10 = = 20% = 80% MX ZWTX AZ 16,539 **** Shared Private Mexico Arizona - - 4x10 3 3 11000 - 4 - 4 0.09 0.06 0.07 0.08 - 5 52 25 20 15 52 25 20 15 WTX 4x10 T 3 Weakly Deleterious Plateau Mexico Central - 4 ZWTX AZ Present Time (kya) **** N AZ N TX CTX 50-100 25-50 15-25 10-15 5-10 0-5 TX TX AZ WTX AZ WTX AZ = 27,325 = 35,523 Texas