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Home , Desert pupfish, Devils Hole pupfish, Leon Springs pupfish, Owens pupfish, Pupfish, Southern platyfish

Posted on Authorea 24 Nov 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160621932.29583857/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. atrso o eeoyoiyadhg nreigdpeso,dsiecnieal mut fdetected of amounts considerable despite ( populations depression, dog endangered inbreeding domesticated and high di- from threatened and genome-wide introgression of heterozygosity of historical history low incorporation demographic of the the patterns enabled of has context biology the (Leroy conservation within into metrics genomics versity of integration The efforts. 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U.S. and Salt populations the native and by two Mexico the Spring species New Malpais endangered Stockwell the markers, possible by locations: microsatellite a threatened distinct as as of ecologically IUCN, review two populations by under native at Endangered is Ancestral as and Service. listed Fish, Wildlife is and species Game The of against ( Department Mexico. pupfish hedge Sands New a White artificial Southern as the of or on or focuses listed facilities populations, paper breeding present wild species (Koike 2020). The captive declining populations pupfish (IUCN augmenting in natural vulnerable 12 or of maintained or currently reestablishing commonly threatened imminent for are are the as stock there species identified provide complex, pupfish others to many pupfish refugia 14 (e.g, this, and fishers the of recreational endangered Among by Because highly critically bait them or 1997). as makes endangered Echelle, used which as those and 1981), Nearc- as Echelle (Miller, Many (Black such springs ; loss congeners 1995). desert habitat introduced Wildekamp, 1979), isolated with (Deacon, 1986; small bridization withdrawal ( Miller, to groundwater fishes and restricted to salinity-tolerant (Smith are susceptible and distribution species temperature Neotropical of pupfish genera and tic differentiation 10 Nearctic population of broad and group a diversity a are of pupfishes patterns The (Lehmann detailing species image endangered resolution among high and within a achieve to approach 20)dmntae usata dpiebd hp aito ewe niiul olce rmthe from collected individuals between variation shape body adaptive substantial demonstrated (2005) eoefreiec fitorsinvahsoia neseichbiiainb siaigpairwise estimating by hybridization interspecific historical via introgression of evidence for genome tal. et tal. et 04.Adtoal,torfg ouain MudSrn n otRvr were River) Lost and Spring (Mound populations refuge two Additionally, 2004). 1998). 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No reuse without permission. | https://doi.org/10.22541/au.160621932.29583857/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. ompigteefaue oteasml ihbat(..0 Gertz (v.2.10; blast with assembly the from to obtained features were these mapping sequences to cDNA related 54,466 and from 2019) used Consortium, were sequences transcriptome transcriptome and maculatus protein and ( assembly, Minnow protein nuDNA Sheepshead translated the species: of annotate alignments help 2) To local and 2008). assembly 1) the performing: to by sequences accomplished then removed were were tation proteins known matching regions ( tularosa and 2008) library Hubley, the the and in Smit from identified (v.1.09; were families repeatmodeler element with transposable bly curation, genome draft After Annotation Genome Mitochondrial and Hahn Nuclear (v.1.8; mitobim with the assembly alongside genome used mtDNA and 2010) Hall, and ( Quinlan pupfish Hole mtDNA Devils al. the the Patil into et to (NUMTs) aligned (v.0.1; Translocations that coalqc Nuclear reads of Illumina used incorporation first inadvertent we the assembly, prevent help of To sequence reads. mtDNA complete The by genes. evaluated core was 3,640 the Completeness and of assembly). assembly set the the a Seppey in between alignments genes v.4.0.6; target local (busco; genome of performing curated Orthologs (proportion The comprehensiveness Single-Copy and removed. 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All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160621932.29583857/v1 | This a preprint and has not been peer reviewed. 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The (NC_028292.1). included (C. also pupfish was River species: Red following tularosa the the for and NCBI from KM985373.1) downloaded were diabolis 2020 August C. all 15 species, of pupfish as among ble relationship matrilineal Kimura, the (K2P; compare were differentiation. To parameter genomic distances Kimura-2 pairwise genetic the of alignments, patterns using package evaluate length) pairwise R to the in local with (>2Kb Following generated sequence 1). 1980) -max_target_seqs aligned -culling_limit 3, using each 1, -qcov_hsp_perc genome between masked 3, -max_hsp estimated (-perc_identity repeat 50, congeneric parameters -evalue each non-default 1, against following performed the then with were blastn alignments local the Pairwise using sections 2000). 30Kb into ( genome each genome breaking reference available an with sis), species with pupfish visualized related For were results divergence The genomic >20. and mitochondrial quality and removed base Nuclear were and 30 length of in quality mapping >100Kb minimum Scaffolds Korneliussen (v.093; S1). angsd (Table using analyses downstream from tec iei ahrfrnegnm,gna v130 Pockrandt (v.1.3.0; Smit (v.4.07; genmap the repeatmasker genome, mismatches. two reference to up each allowing in site each at ( heterozygosity Genome-wide diversity Genomic .rerio D. n o context for and 08.EtmtdmDAdvrec ie eete noae oteN re xotdi Nexus in exported tree, NJ the to annotated then were times divergence mtDNA Estimated 2018). tN sebyrpre een h rvosyarchived previously the herein, reported assembly mtDNA (KX061747.1), eBs irr sarfrne ie ihmpaiiy< n eetdrgoswr excluded were regions repeated and <1 mappability with Sites reference. a as library RepBase tal. et Cyprinodontidae .maculatus X. 08.Mlclrtm siae eeotie rmTmte (Kumar Timetree from obtained were estimates time Molecular 2018). .nvdni amargosa nevadensis C. H a siae o six for estimated was ) tal. et n notru.Mlil euneaineto ullnt mitogenome length full of alignment sequence Multiple outgroup. an and GF027251,hmlgu uN ein eeietfidb first by identified were regions nuDNA homologous (GCF_002775205.1), ape Cyprinodontidae 04 sn h noddst rqec pcrm(F) eurn a requiring (SFS), spectrum frequency site unfolded the using 2014) .maculatus X. v541 Paradis (v.5.4.1; tal. et rubrofluviatilis splitter 06.I diint raigatmte,ma pairwise mean timetree, a creating to addition In 2016). 5 tN seby(C017.)wsue sa out- an as used was (NC_011379.1) assembly mtDNA K833.) h eetpps ( pupfish Desert the (KU883631.1), Cyprinodontiformes hlgn,btt rvd vltoaycnetfor context evolutionary provide to but phylogeny, ucinipeetdi mos(..0 Rice (v.6.60; emboss in implemented function tal. et tal. et tal. et C092) nadto otenew the to addition In NC_009125). ; 05 a hnue oietf eet using repeats identify to used then was 2015) .tlrs,C variegatus C. tularosa, C. 04.Rslswr iulzdwith visualized were Results 2004). Cyprinodontidae tal. et 94 n egbrJiig(J di- (NJ) Joining Neighbor a and 1994) .tularosa C. 00 a u using run was 2020) is,t eemn mappability determine to First, . reltime-ML .variegatus C. eSqmDAassembly mtDNA RefSeq tN eoe availa- genomes mtDNA ggplot2. H ucin(Tamura function and .macularius C. tal. et a calculated was (KT288182.1), 100-mers .nevaden- C. .tularosa C. 07 and 2017) ggplot2 tal. et and C. ; Posted on Authorea 24 Nov 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160621932.29583857/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 1.Dvriyvle mn l i pce lutae that illustrated ( species 0.00003049 six to all ) among values Diversity S1). ( heterozygosity Genome-wide diversity Genomic differentia- of levels (p-values=0) tularosa significant C. illustrated F loci (WSP-2, these at tion G-test exact An (p-values=0.195-1.00). (Stockwell demarcation H R to p-value=0.953; related SE=0.103, negatively was p-value distance genic SE=0.092, that SE=0.082, found Estimate=0.265, we Intercept: heterozy- 50Kb, 2A; reported (Figure previously ESU R microsatellite had or value=0.850; mapped between which gene were relationship loci nearest three significant 11/16 the and p no to Using genes distance suggested 2). more and (Table regression or heterozygosity one comprehensive gene of any our 10-100Kb from estimates, between gosity >100Kb located location were five a gene(s), to a of characterize 10Kb to within used the previously in microsatellites cated 16 the of Each Identification Microsatellite to the than similar over lower 1%), improved moderately F was values, 95%; these (C upon the based in completeness, 95%) Genome the (Table (C 1%). the 1.36Mb genes (F Using single-copy of fragmentation complete inherent 1). N50 3,452 Table identified a N50=31.5Mb; busco and size=35.3Mb; orthologs, 8.12Mb contig chromosome-level of max the 5Kb size (contigs=97; than than contiguous contig less greater max but (those reticulata N50=0.0843Mb) a contigs size=4.51Mb; 1.086Mb, contig 1,995 max of on (contigs=4,093; new length statistics the total assembly Thus, a genome, 1). showed draft length) pupfish similarityin Sands sequence White A the region. 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(Table genome .tularosa C. 2 ST 005 =.5;D=,9.Uo iiigorrgeso omcoaelt oita were that loci microsatellite to regression our limiting Upon DF=2,19). F=0.050; =0.005; .maculatus X. seby( 66;F03) qiaett h chromosome-level the to equivalent 0.3%), F 96.6%; (C assembly < .nevadansis C. 030 S-1 F WSP-11, =0.350; .tularosa C. siae000 E000 p-value=0.780; SE=0.000, Estimate=0.000, : or , 0.001; .tularosa C. tal. et Chytribiomycota eoeasml.Trewr on ihna nrno ee v eelocated were five gene, a of intron an within found were Three assembly. genome Distance .variegatus C. 2 032 =.29 F21) ohmcoaelt akr sdt nomESU inform to used markers microsatellite Both DF=2,15). 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