Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. h ocnrto fsaae.Sc rdet r omnweefehadsawtrmx ihaeso lower of areas with mix, water beyond) sea even of the and or occasionally fresh match gradients where tolerant (and to broad common either to are tuned by gradients is up tolerance characterized Such plant concentrations with seawater. often a low of quantitative, are concentration relatively characteristic; the be environments from binary to Saline concentration, a likely salt is is 2013). environmental it halophytes (Cheeseman, though in environment as tolerance local used salt often However, is not. tolerance” study the “salt & for 2013). Brown, term models (Cheeseman, (Glenn, The evolution important estuaries to and become and managed have mechanisms have marshes, halophytes, 2%) tolerance salt called salt beaches, (ca. if collectively as of species toxic plants, such plant are These ecosystems terrestrial ions saline 1999). of Cl- Blumwald, in number the and of thrive Na+ small levels stresses, even a both High and abiotic addition, Nonetheless, colonize plants. in Among cells. for dehydration; in challenging to wide accumulate particularly leading stresses. extremely they environment, is an abiotic environments osmotic to salt the and adapt change high to biotic salt in species growing different plant of by of stress ability characterized physiological the environments been of has diversification range angiosperm of hallmark A a play may and in populations Introduction vary sampled the genotypes across triploid levels The salinity ocean strategy. adaptation. local local adaptive with in generalist associations role the more shows of composition a copies subgenome two to in or transition one a carry represent they whether may fine-textured and between genotypes hybridization diploid sexually and from textured both triploid derived wild clonally-propagating be the of to largely in appears unidentified consists reproduce ecotype ecotype to coarse-textured coarse-textured appears The the and contrast, genotypes. diploid in is Within propagation; ecotype variation. clonal genotyping-by-sequencing, fine-textured by ploidy employed and the and we collections differentiation of ecotypes: germplasm, wild genetic patterns distinct USDA identify >170 morphologically geographic existing to representing two influence cytometry plus accessions flow to States 218 and interact United Using sequencing may southern cpDNA levels. and coastal salinity wild the the environmental the throughout about to from in known response is occur little in to tools, particularly available appear adaptation, in composition increase an subgenome and and interest hybridization, recent of Despite populations wild grasses. in other present and diversity cereals in tolerance salt of ( paspalum Seashore Abstract 2020 17, August 3 2 1 Goad David halophyte model the ( in paspalum tolerance seashore salt and diversity of geographic patterns influence clonality and polyploidy Hybridization, ahntnUniversity Center Washington Science Plant Danforth Donald Louis Saint in University Washington Paspalum 1 vnBaxter Ivan , aplmvaginatum Paspalum pce.Teecoal rpgtn yrdgntpsaemr ral itiue hncoa fine- clonal than distributed broadly more are genotypes hybrid propagating clonally These species. 2 lzbt Kellogg Elizabeth , aplmvaginatum Paspalum .vaginatum P. wrz sahlpyi ufrs n mriggnmcmdlsse o h study the for system model genomic emerging and turfgrass halophytic a is Swartz) .vaginatum P. n t ls relative close its and ugnm,idctn utpeeouinr rgn.Ti variation This origins. evolutionary multiple indicating subgenome, 1 2 n ent Olsen Kenneth and , .distichum P. ) aito npod,coa propagation, clonal ploidy, in Variation . 3 .vaginatum P. .vaginatum P. hr are there , n an and Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. aito ntewl.Fut,i a enpooe oudrohbiiainwt lsl eae non-salt related closely genotypic a with of hybridization patterns undergo to geographical under proposed propagation affect been clonal may has of propagules it capable Fourth, clonal is wild. of the and almost in water stolons Duncan, dispersal is variation variation Carrow, by sea that this vegetatively Lee, including of suggesting 2005; spreads distribution and geographical cultivation, 2004, it to and Duncan, Third, basis up & genetic unknown. (Duncan tolerance, the Carrow, completely salinity although salt Lee, 2008), varying in 2004; Rieger, of variation & Carrow, habitats Eiteman, quantitative & across shows Duncan, variation distribution it (Lee, genotypic worldwide concentrations of Second, a patterns 2000). has shape Carrow, it to & First, interact gradients. polyploidy salinity and hybridization across ( clonality, how paspalum addressing 2016). parental seashore al. for each et grass If Tan from 2017; effects. halophytic received (Betto-Colliard, Glover, these examined copies & The Hansen, be untangle genome also Solberg, to of could Fjelldal, St¨ock, Harvey, numbers used phenotypes & 2018; other relative Perrin, be and interspecific the Sermier, potentially fitness Hofmann, of to on could effects respect effects have genotypes dosage with potential events whole-genome polyploid varied species, hybridization the and also natural with group diploid repeated confounded a of where such is mix Systems duplication a 2016). in al. genome 2004). et resulted Yannic, the halophytic (Fort & of most above Salmon, wild hybridiza- effect Baumel, described (Ainouche, interspecific the hybridization the genome through in cases non- entire However, arisen its such 2019). having in can contributes In Li,  genome) species Studies & parental allopolyploids its each Jiao, rather adaptation. doubling where Lin, but salinity (i.e. tion Wu, autopolyploids species 2013; in not al., diploid are role et a polyploids (Chao a in tolerance autopolyploidy play salt inducing increase also relative that may suggested the have duplication) and halophytes composition, niche whole-genome genomic adaptation. and (i.e. salinity their phenotypic Polyploidy for genotypes, for genomes High-throughput hybrid parental 2017). species identifying Barkai, their parental & in of 2002). Levy, different importance help Lupo, Rieseberg, (Bar-Zvi, can from a & question Welch techniques produce contributions (Gallego-T´evar, open Curado, 2009; genomic also an genomic parents al., remains can the hybrids et their It in of (Edelist 2016). differentiation to species roles Strong, relative parental relative & tolerance influenced non-halophytic Pakenham-Walsh, species The Ayres, two be in halophytic Lee, from to two decrease halophyte 2018; shown from novel or Castillo, derived been & hybrids increase has Figueroa, Specifically, environments relative Grewell, & saline niches systems. a Archer, to wild ecological show (Rieseberg, several Adaptation new may heterosis in to increasing 2009). hybridization and/or access Soltis, natural population by provide & a Soltis can into 1999; hybridization variation Wayne, interspecific genetic novel propagation, pattern introducing Coughlan, clonal one by follow 2018; to 2009). to Parker, Waycott, contrast & genotypes & In (Vrijenhoek lead Virnstein, understood that Calladine, poorly conditions environments Bricker, remain underlying multiple another The 1965; in or present (Baker, 2017). are range Dickinson, genotypes Stefanovi´c, & geographic generalist Han, few genotype” wide “general-purpose a a a whereby high, favored, is across if potential be Alternatively, dispersal 1979). instead and/or Vrijenhoek, to might infrequent 2015; reproductive niche” restricted is strategy (R´ois al., “frozen each genotypes two adapted et a new occur, locally of of is dispersal, populations production it clonal clonal the one which limited to distinct mutation), have area genetically geographical but multiple somatic small often whereby the arise or favored, genotypes which be reproduction at new might frequency If strategy sexual the expected. and through be propagules Rudmik, might clonal (e.g., & of strategies of Jefferies arise capacity patterns 2018; dispersal geographic genotypes Waycott, the for & on novel implications Virnstein, Depending 2015). Calladine, important al., (Bricker, R´ois has et adaptation 1991; and salinity halophytes local of in and characteristics diversity widely interspecific common occurs propagation, three propagation clonal below, are Clonal occurs adaptation described salinity adaptation As variation. local salinity local ploidy of unknown. patterns and local such largely hybridization shape are for whether Reager, could it that (Fournier, however, opportunities influence species rivers extensive halophytic species; that major forces offers halophytic of the variation aplmvaginatum Paspalum 2 Swartz ) rvdsa datgossystem advantageous an provides Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. itcacae hc sdsatyrltdt h te a 0 pce ntegns(usn 91 Scataglini, 1981; (Burson, genus the in species 300 ca. other the to related USDA distantly is the which programs, clade, Disticha 2015). fine- breeding 2000). (USDA-ARS, while Carrow, turf accessions & Florida, vaginatum fine-textured for (Duncan Paspalum and of samples Georgia entirely Coast stabilizer. to collecting almost dune Gulf Carolina composed on a North the is as from focus on collection use coast the found Atlantic limited typically to the seen on also is Due morphology, found has ecotype are ecotype leaf coarse-textured plants coarse-textured and makes the textured the leaves shoot smaller US, turfgrass; fine- and a in the The form as growth 2000). Within differ prostrate Carrow, use that its & for Duncan because valuable ecotypes important 1B; it economically (Fig. common more ecotypes two is ‘fine-textured’ ecotype by and textured ‘coarse-textured’ characterized the as is to It referred 2000). Carrow, & vaginatum Paspalum species. grass halophytic system model Study genomic this in tolerance salt composition of genome Methods basis of genetic roles in the the adaptation into vary into salinity investigations composition insight local future subgenome provide in inter- and findings propagation variation does Our and clonal ploidy salinity? extent differentiation and structure, wild, in genetic clonal what gradients the of do To geographical patterns How in 3) influence across 4) occurs system pattern? populations? a this wild discernible propagation strategy, in in no reproductive variation clonal diversity ploidy or niche” that and/or strategy, “frozen extent hybridization localized genotype” specific the a purpose the To suggest asked “general 2) distributions we widespread environmental clones? genoty- Specifically, and widespread of range. geographical nature geographically species do the few American investigate a North wild to the of Do germplasm in 1) USDA gradients questions: available salinity of following with wild specimens across together the wild distributions them in living pic analyzed of propagation collection and clonal largest date of the levels to undertook we actual study, the this quantify In Genotyping diversity. to 2017). genotypic Devos, required of & thus patterns Raymer, is stolons geographical Harrison, in aggressive and Bahri, material the propagation (Eudy, collected the as clonal pots occur newly whether neighboring natural easily invade of unclear represents can species is which collection the accessions, it of germplasm of samples, typical cross-contamination the the USDA post-collection in to or these redundancy due wild of Additionally, the genotypic genotyping 2000). of and Carrow, degree collection & high (Duncan the qualities between collection and turfgrass gap 2017) favorable decades-long Devos, and with & Raymer plants resources Harrison, towards Bahri, has (Eudy, biases accessions it also among such, redundancy is genotypic (USDA) As It to available due soils. publicly crops. of 2000). salt-affected cereal limitation Carrow, for current major & One turfgrass to (Duncan a mechanisms programs as tolerance breeding right et salt through available own (Morrone of economically germplasm sugarcane its several transfer and to in the sorghum related important facilitate maize, a closely economically could including is has Panicoideae, It which It 2019). subfamily 2012), al., the studies. al., et in analyses applied Qi genomic species 2017; for facilitate grass allowing Devos, important assembled, that & been Raymer, value recently Harrison, has economic Bahri, which (Eudy, genome and diploid tractability Mb ~600 experimental manageably-sized with features, system history life model these salinity to diploid local addition and both suggests In structure which 2017), population 2017), Devos, to Devos, contribute & & also Raymer, might Raymer, composition Harrison, Harrison, adaptation. subgenome Bahri, Bahri, and (Eudy, diploid Eudy, level predominantly reported ploidy 2000; be been that Carrow, to have and believed cytotypes is (Duncan triploid it and =20) although Finally, 2x tolerance. = salt (2n in variation phenotypic natural to ( species tolerant .distichum P. sdsrbtdtruhu rpcladsbrpclsln csseswrdie(Duncan worldwide ecosystems saline subtropical and tropical throughout distributed is n t lsl eae o-aohtcsse species sister non-halophytic related closely its and . Ed,Bhi arsn amr eo,21) hc ol contribute could which 2017), Devos, & Raymer, Harrison, Bahri, (Eudy, L.) .vaginatum P. aplmvaginatum Paspalum ouain ersn aydsic eoye rreplicates or genotypes distinct many represent populations .vaginatum P. 3 .vaginatum P. lopoie h eet fagenome-enabled a of benefits the provides also emls sisnro eei variability genetic narrow its is germplasm n a h eesr rudokfor groundwork necessary the lay and , .distichum P. .vaginatum P. .vaginatum P. oehrcmrs the comprise together and .distichum P. germplasm Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. ore n n-etrddpod,wt sue ouainnmesrnigfo -.Cosvalidation Cross 2-6. = K was from ranging PCA numbers comprising additional dataset population reduced assumed An further with only. a diploids, on genotypes fine-textured performed diploid was and unique data within analysis coarse- structure of missing 2009) Lange, population and consisting & assess Novembre, frequency dataset To (Alexander, allele v1.3.0 dataset. the minor this for genotype, on plink same performed the then in highest of the repeated collections with were multiple accession filters to the due only biases created prevent genotypes, then To similarity were duplicate datasets of group-specific variant a set Refined chose a S1). retained. each heuristically Fig. was produce and for coverage (see removed; To distances peaks of genotypes constructed. second histogram duplicate and was a component cluster with first created genotype matrix the principal then separated identified distance a we that visually genotypes, threshold genetic in each identical within included pairwise identify 2007); to were a al., threshold missing samples PCA, et were all (Purcell the that plink plants, in Individuals with collected frequency. performed among allele (PCA) for minor replicates analysis calls 0.01 removed. missing clonal were also than identify were there less To sites if had removed more or were or then and samples was Sites 50% 2009) which the 2007). at dataset Durbin, calls al. of SNP & et large 10% a (Li (Purcell than produced v0.7.12-r1039 v1.90b4.6 more This plink MEM 2014). BWA with al., et filtered with parameters (Rimmer further maps default v0.8.1 2011), Platypus 2011), with (Joshi, with (Martin, variants v1.000 pipeline sabre calls v1.14 Fast-GBS with cutadapt the demultiplexes which with using 2017), trims Belzile, performed & were Abed, Bastien, calling Laroche, variant (Torkamaneh, and processing Read University the at Center Biotechnology Carver Bioinformatics J. Roy the at Champaign-Urbana. reads Illinois 1x100 of with of platform digest which 2500 double (2018), HiSeq following a prepared Illumina Olsen using were & (2012), libraries D¨onmez, Rife (GBS) Beilstein, Brock, Genotyping-by-sequencing & (1990). of Poland Knapp protocol & Webb CTAB from the modified using was extracted was DNA Genomic Uruguay). Rep´ublica de genotyping-by-sequencing la de and (Universidad extraction Speranza DNA Pablo Dr. from Uruguay four from representing acquired extraction, wild- planting. DNA the before to for week 35 addition tissue one representing In than samples, greenhouses. longer 40 Center no of Science for five set Plant bag were plastic Danforth a which were a Donald material, stolons in samples the collected as placed harvested in three were then propagated Samples to and were clone. towel by One single Stolons paper separated a km. were damp of they a 1.5 collecting sampling locality, in replicated single least repeatedly minimize wrapped a at to from of m collected by chance 100 were least separated samples the multiple at were salt When reduce beaches, location. localities To included each to clone, lakes. in habitats Carolina collected Collection same and North S1). the rivers from Table 1A; freshwater States, of (Fig. representatives United and 2017 southeastern estuaries and the 2016 brackish of of marshes, coasts July and Gulf June and during Atlantic Texas, the along collected was coarse-textured 146 of set A Echarte, wild the in occasionally Sampling occurring diploid cytotypes 2017) 58) putative Devos, and & A 57, Raymer, 1992). and 54, Harrison, Sala, 52, cpDNA = Unlike & on (2n 2014). Clausen, based hyperpentaploid Morrone, distinguishable and 50) & are = often Denham, they and although Giussani, similar 1983), Zuloaga, very distichum morphologically Brummitt, (Scataglini, are 1968; sequences species Guest, nuclear two & The 2014). (Bor Morrone, confused & Denham, Giussani, Zuloaga, .distichum P. sblee ob rdmnnl eali 2 0,wt erpod(n=4) etpod(2n pentaploid 40), = (2n tetraploid with 60), = (2n hexaploid predominantly be to believed is eeotie rmteUD ainlGntcRsucsPorm diinly dried Additionally, Program. Resources Genetic National USDA the from obtained were , .vaginatum P. . 8fine-textured 18 , .distichum P. .vaginatum P. Pst and I 4 .vaginatum P. Msp ceso a lobe eotd(uy Bahri, (Eudy, reported been also has accession .vaginatum P. cesosadone and accessions .Smlswr eune ntrelnso the of lanes three on sequenced were Samples I. too hc r oretxue)and coarse-textured) are which of (two n 10 and .vaginatum P. .distichum P. .distichum P. .vaginatum P. ADMIXTURE , ceso,were accession, ln samples plant , P. Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. eeoyosgntp al eeas sdt ne ugnm dniyuigacso yhnscript python custom a using identity subgenome da- infer the to used we used analysis also this were For (https://github.com/david-goad/paspalum-hybridization/het_venn.py). calls genotype 2007). Heterozygous al., et (Purcell plink comparisons inbreeding in these individual Subgenome function employed the increase het as We the quantum calculated cytometry. was with flow a heterozygosity (F) showing on Genome-wide coefficient coverage. ap- the based as sequence in This identifiable size highest variation the genome are calls. with ploidy which in locus assess hybrids, increase heterozygous to diploid associated of additional strategies identify no number each to with levels, the used heterozygosity ploidy increase subgenome in be increasing any and At also genome, This differences reference loci. can 2017). diploid ‘heterozygous’ more proach Mock, a as to introduce & recorded mapped will (Gompert are be variation reads subgenome potentially will ploidy all can polyploids if identifying that in heterozygosity for rationale differences cytometry genome-wide the flow on of to based measures is complement approach ploidy, a in as vary used be that samples GBS-genotyped PI For for heterozygosity calculated genome-wide value with the 509022. estimates by PI Ploidy divided taking to by then compared calculated were accession then along calculations each were These of 1989) sizes propidium DNA. size Genome with Lucretti, B73 cytometer. stained (Doleˇzel, Binarov´a, & to flow were (the DNA LB01 C6 Nuclei 509022 sample Accuri standard. cold tested. an internal of mL were on an ratio run as genotypes 1 the were included unique in was samples each 24 which and blade of the tissue, iodide, accession razor B73 of one line two a from maize only collected with with was where chopped tissue samples leaf was fine-textured fresh Tissue ploidy, for and except variation genotype, size genome unique assess to order In cytometry flow with 1999). estimation (Hall, aligned Ploidy BioEdit were the using Sequences compared at Analyzer. and performed DNA 2014) was 3730xl Morrone, products ABI PCR an purified the using of Center against The Biotechnology sequencing (2009). Wisconsin Sanger of al. Direct University et ecotypes. Giussani coarse-textured 10 in and described primers R1661 and httecas-etrdeoye r ato h itcacae(e eut) esqecdteito of intron the sequenced we Results), (see clade Disticha the of between part are subgenome the ecotypes three maternal coarse-textured All in the coast). differences that the for from look km To 40 > ocean collected sequencing the the gene sample of with the salinity Chloroplast one scaled the of for and (excluding identified 22.7% dataset centered and site and salinity then 2019) collection 50.9% al., where surface et explained each coordinates sea (Zweng PCs to average Atlas two Ocean the nearest World first downloaded water the the & we from the of (Fick 2005-2017 coordinate, using variables values years calculated third BioClim The the WorldClim were variance. the 19 components For unit the Principal respectively. scaled of variance locations. with PCA collection R a our in with in of function components each collection principal for each second 2017) three and Hijmans, in of first variables distan- the environmental coordinates as geographic for GPS ned distance pairwise Euclidian on the calculated calculated with based we dimensions we distance, genotype environmental wild, pairwise clonal the sure each from within collected the collections clones between multiple ce with genotypes. genotypes clonal For of dispersion K. environmental optimal and the Geographic determine to used was estimation error distHaversine rpl16 hools iooa ee f1 cesos(3 accessions 16 of genes ribosomal chloroplast .vgntmrpl16 vaginatum P. .vaginatum P. ucini 341(imn,Wlim,&Vne,21;RCr em 03.T mea- To 2013). Team, Core R 2019; Vennes, & Williams, (Hijmans, v3.4.1 R in function dist ucini ,a olw:codntsfrtefis n eoddmninwr obtai- were dimension second and first the for coordinates follows: as R, in function eeec eoeacsin .5 eaiet 7)t eemn eaiegenome relative determine to B73) to relative 0.259 accession, genome reference eune(ceso F507 ctgii uog,Gusn,Dna,& Denham, Giussani, Zuloaga, Scataglini, KF853027; (accession sequence Paspalum scale 5 ape,fcsn ngntpclyuiu accessions unique genotypically on focusing samples, ucini eoecluaigdistance. calculating before R in function .distichum P. .distichum P. .vaginatum P. 13 , and ape nldd3fine-textured 3 included samples .vaginatum P. .vaginatum P. sn h F71 the using ) n oconfirm to and prcomp Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. nqegntpsi h olcino 5acsin,too hc eeuiu oorwl olcin.The collections. wild our to unique were which of two accessions, 15 of For collection replicates. wild-collected the the clonal still in in multiple genotypes was eight genotypes by clonality So- of extensive unique represented ecotype. out Four but were this accessions. ecotype, 55 of accessions the in fine-textured populations fine-textured identified of the were wild >85% genotypes in in unique for found 24 occurs accounting was present; diversity propagation genotypes genotypic clonal widely-distributed greater extensive three mewhat that just indicates with (Supporting This accessions, accessions accessions. Methods; 148 identical (see the genotypically coarse-textured replicates among of the clonal number tected For identify large analy- S1). to a component Table criteria revealed Principal Information, threshold accessions. S1) similarity 218 Fig. genetic in Information, of SNPs Supporting application 127,282 by and characterized (PCA) was sis dataset GBS filtered The replicates the clonal because and of 201.09) Identification vs. (200.27 AIC included. lower was a it Results had when it significant because not interaction was an term salinity of without interaction number ocean model copy N the of local ~ chose effects in (salinity We the interaction differences test an to for perform with model to test linear models 2019) fixed-effects to a al., t-test used the et two-tailed we (Zweng both Then a dataset triploids. used Atlas and we diploids Ocean within between World First, salinity the comparisons. ocean from statistical local measurements two and salinity variation ocean genotypic local between the associations A). for alternate) is test 33.3% genome To reference genome, levels the reference salinity where respectively, (66.7% ocean AAB 2:1 with centered or the or ABB Correlations are matching ratio (e.g. alternate) that reads count composition 66.7% distributions of read subgenome return genome, 1:1 percent the a should reference on the Triploids on depending (33.3% for centered reads). was 1:2 histogram loci alternate locus either a of 50% count each distribution and on reads, at combined a counts reads genome return their raw alternate reference should if the and genome (50% reference for or diploid of plot The subgenome) number genome. scatter a The reference a identical depth). read). most to as was adequate two the based assignment reads visualized ensure the in unambiguous common file (to then variants compared most 20 ensure same two only of than (to the the we less position of genome was in singletons) neither the reference as if position identifies excluded the four manifested which the were all (often to file sites covering in Additionally, reads SAM type types. heterozygous low-quality the read as read of common of called each effect was column the of genotypically- locus (the remove number of a To string of number where the CIGAR cases each greatest counted their In from the we on be control). with individual the genotypes, 1:1 can coverage genotype of a the copies highest diploid distribution as subgenome of the the serve the of chose and (to on number We accessions genotypes Based the identical 2017). triploid S2). locus, Mock, putative (Fig. each & three file at the Gompert SAM reads 2019; a non-reference (Delomas, in vs inferred geno- reference loci coarse-textured of heterozygous triploid number at (https://github.com/david-goad/paspalum-hybridization/triploid_- in relative reads parent script counts each python fine-textured that from custom diploid comp.py) received a the copies used in subgenome we of present types, number not the is investigate di- To that and subgenome allopolyploid a of of case the sharing samples. In indicate loci. would ‘heterozygous’ subgenomes loci shared the that ( Following as groups. expected groups reflected between we hybrid shared be individuals, ploid two were would within that (the groups differences those subgenome between groups to reflect shared group morphological loci each ‘heterozygous’ three to the that unique our calculated logic calls We of heterozygous heterozygosity. with each <0.05 loci in of with heterozygous sites were and of that removal ecotypes loci after genotypes of unique number all comprising taset .vaginatum P. .distichum, P. .distichum P. ugnm (N subgenome xldn he uaieyamxdacsin) ete oprdtenumber the compared then We accessions). admixed putatively three excluding n coarse-textured and Pv Pv n h te ndnie ugnm (N subgenome unidentified other the and ) N + other .vaginatum P. N + 6 .vaginatum P. Pv :N other ctp,ol 2uiu eoye eede- were genotypes unique 12 only ecotype, n ihu t(aiiy~N ~ (salinity it without and ) e eut) ihnmeso shared of numbers high Results), see ; .distichum P. other .vaginatum, P. .W oprdthe compared We ). hr eefour were there , .vaginatum P. .vaginatum P. Pv N + eused we other ). Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. oa f6SP n n 0b ne,wt n diinlSPsgeaigwithin segregating SNP additional one with indel, 10-bp one and sequence, SNPs Within aligned 6 kb of 1.15 total the a In data. GBS two This the the S4). the between in (Fig. flow variation ecotypes gene SNP occasional fine-textured is and there coarse- that have between indeed suggests admixture individuals result with SNP coarse-textured consistent intermediate reduced genetically compositions a the created genetic that we shows analysis hypothesis, ADMIXTURE this diploid tes). test unique one admixture To only of possible ecotypes. clones containing suggests fine-textured were dataset genotypes which and these accessions coarse-textured of wild-collected placement the genotypes the intermediate between two of The These two S1). S3). and Table Fig. (coarse_05, 612771 3, genotype PI (Fig. accession PC2 GRIN along coarse-textured accessions to two coarse-textured corresponded clusters, and of fine- PCA the ecotypes main between fine-textured three termediate and the coarse- of to the addition groups separated In distinct primarily three and variance into the fell of separated accessions 20.2% vaginatum and most variance explained the 2 PCAs, groupings of PC same both 31.6% ; the For explained revealed 1 S3). PC genotypes Fig. to dataset, unique reduced-sample 3, corresponding 40 variant 177,954 of (Fig. accessions, in to set dataset clustered increase samples the tightly an total coverage on in the lower PCA resulting filter, in A the data dataset. as of missing highest-quality the Removal this pass genotype. for to sites sites per more accession allowed group reduced high-coverage a clonal one on each focused of analyses subsequent composed variation, clonal dataset of characterization and where identification the species locations Following and the genotypes in environments between particular differences on Genetic specializing the for not propagules clonal higher are that similarly occur. genotypes indicates were they dispersed this had measures was 2B); widely all distance genotype (Fig. these coarse_03) environmental accessions clonal restricted and of Pairwise fine-textured coarse-textured coarse_02 to 2A). was any compared (coarse_01, Fig. that ecotype genotypes of 1; coarse-textured genotype common (Fig. range most one km respect geographical three >1400 narrowest make with of the ranges the distributions genotypes exception and broad (coarse_06), (coarse_04), unique the showed area km of With genotypes 750 km handful variables. these more 1 a environmental but a patterns did 1), and to showed (Table only geography ecotype accessions Not both wild coarse-textured strategy. to of the genotype” majority of purpose the genotypes “general up ecotype, a fine-textured with the consistent “frozen-niche” to a contrast with a consistent S1; In indicated generally (Table Methods) are environ- km see patterns fine-textured pairwise 126 conditions; These for of salinity of 2B). strategy and assessments (Fig. range reproductive climatic dispersion maximum distributions, environmental local a geographical of on had level narrow (based low restricted locations their locations genotypes multiple with among had in Consistent four distances found the mental 2A). multiple two of Fig. two with the ranges; 1; genotypes while geographic four Fig. location, small genotype” the relatively single ecotype, have “general-purpose a to fine-textured to a tended the wild For or the clones). “frozen-niche” in clones) distributed a clones broadly restricted with consistent few environmentally patterns (a showed and strategy they geographically collec- which wild to (multiple our in extent strategy genotype the same investigated the we of Specifically, clones between tions. wild-collected distances environmental the and geographic among of distribution clonality extensive detected Having occurs propagation propagation clonal clonal of that patterns suggest US- and results Geographic wild-collected these Together including 1). species, wild (Table both in genotypes across extensively 40 samples unique totaled genotypically samples, all DA for dataset SNP final .vaginatum P. . .vaginatum P. rpl16 cesoso h n-etrdeoyecridtouiu Nsta distinguished that SNPs unique two carried ecotype fine-textured the of accessions , nrno h hools eoecnre h he ao rusietfidby identified groups major three the confirmed genome chloroplast the of intron and .distichum P. .vaginatum P. .vaginatum P. .distichum P. .distichum P. populations. 7 . eoye 3 cesosad1728plmrhcsi- polymorphic 117,218 and accessions (33 genotypes n h w ctpsof ecotypes two the and iee rmbt ctpsof ecotypes both from differed .vaginatum P. .vaginatum P. .vaginatum P. .distichum P. ape,w etasse the assessed next we samples, eoye eepae sin- as placed were genotypes ecotypes. .distichum P. .vaginatum. P. from .vaginatum P. .vaginatum P. TbeS2). (Table o the For by P. Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. eeoyoslcsclsfrhridctdta nadto opod aito,teewr losubgenome also were there variation, ploidy to addition in that indicated that further indicating calls in locus S3) Heterozygous Fig. coarse-textured 3, triploid (Fig. from the subgenome results Thus, distinct PCA genotypes. with fine-textured coarse-textured consistent to to are unique patterns were loci These additional to distichum heterozygous unique S5). the 28,881 were (Fig. whether Whereas loci assess case. species heterozygous the to 33,585 not groups and is individuals these this between that sharing indicate sharing SNP heterozygous polyploid coarse-textured of in subgenomes levels both examined in we identified were , genotypes be allopolyploid can hybrids Because ecotype and coarse-textured allopolyploids diploid the of the that composition of but Subgenome origin ecotype, variation. the to ploidy in by according that hybridization subdivided subgroups inference with further distinct the consistent genetically support potentially and despite two findings is -0.520 genotypes, into these size, fine- coarse-textured = Collectively genome and the F ecotype. coarse- in in (average coarse-textured heterozygosity diploid difference diploids between greater of F-value to the lack in 0.541); relative a consistent difference and triploids were large (-0.278 F-values putative a accessions triploids, was in textured and there heterozygosity diploids Unexpectedly, of in respectively). combination increase coarse-textured -0.279 a slight the be respectively) For a to -1.241 0.541). indicated with = and data cytometry F -1.323 flow of (average = which calls cluster F heterozygosity fine-textured (average genome-wide the lowest genotypes in Conversely, & allopentaploid occurred 1). Gompert and F-values) (Table (see allohexaploid negative heterozygosity genotypes to genome-wide of more all highest expected combination The for to are subgenome. ploidy additional allopolyploids) (corresponding each estimate (e.g. with values to heterozygosity subgenomes in able multiple increase were containing an show we individuals conjunction Specifically, above, in 2017). results plink) by Mock, cytometry generated the (F-values flow dataset than SNP the smaller the with ~11% from calls likely heterozygosity is genome-wide using species By latter hexaploid the and of pentaploid size genome genome. for basal reference expectations the that numerical and that match that genotypes, genotypes, suggest triploid closely results and these diploid values Together of 1). primarily (Table the respectively) 3.03, reference, and (2.53 of genomes point 2.69, and the (2.25 as hexaploids and pentaploids distichum putative P. between a size genome suggests in respectively) difference the Unlike Instead, 1992). genome. For Sala, & (1.56). Clausen, triploids (Echarte, pentaploid and samples, and (1.04) hexaploid predominantly diploids is the of species as this mix designated a ploidy is with extensive 1.0 consistent distichum when identified were (1.01, we samples diploidy coarse-textured samples, with for our consistent diploid size of the genome of subset estimated size average a Within groups. an on differentiated had genetically size ecotype three genome the with estimate associated to variation cytometry flow Using hybridization and recognizing variation taxonomy Ploidy current the with consistent variants. are results within These variation groups. two other vaginatum the from them .distichum P. ape a ihraeaerltv eoesz siae vrl,cnitn ihpeitosthat predictions with consistent overall, estimates size genome relative average higher had samples , sn oecoeyrltdt coarse-textured to related closely more no is and eaiegnm ie eercluae suigabslgnm ieo .9isedo 1.0 of instead 0.89 of size genome basal a assuming recalculated were sizes genome relative .distichum P. .vaginatum P. .vaginatum P. eoesz siae i o omovosmlilso the of multiples obvious form not did estimates size genome .distichum P. .vaginatum P. .distichum P. stodsic pce Bumt,18) nadto,tepteno SNP of pattern the addition, In 1983). (Brummitt, species distinct two as niae httefietxue ctp scaatrzdb nqe derived unique, by characterized is ecotype fine-textured the that indicates eeec eoe Tbe1.I otat h eaiegnm ieestimates size genome relative the contrast, In 1). (Table genome) reference aa eoesz hti 1%salrthan smaller ~11% is that size genome basal rma nnw source. unknown an from ih esae with shared be might .distichum P. .vaginatum P. 8 .vaginatum P. .distichum P. slreycmoe fpnali n hexaploid and pentaploid of composed largely is .distichum P. .vaginatum P. .distichum P. cmoe nieyo ilis a the had diploids) of entirely (composed eoye rgrls fpod)than ploidy) of (regardless genotypes ny31 oiwr hrdbetween shared were loci 3713 only , .vaginatum P. atrso eeoyoslocus heterozygous of Patterns . .vaginatum P. eoye pert ar a carry to appear genotypes n eecnitn iha with consistent were and .vaginatum P. .vaginatum P. .vaginatum P. .vaginatum P. .vaginatum P. n in and h fine-textured the , .vaginatum P. o nyfalls only not .vaginatum P. .distichum P. scomposed is Paspalum reference When . group, P. P. Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. ye htaeec dpe oaseicgorpial oaie niomn Rose l,21;Vrijenhoek 2015; geno- al., (R´ois multiple et environment by localized characterized geographically is specific a strategy to geographic niche” explain adapted “frozen can each The that are strategies that genotypes. proposed types clonal two individual are there of clonally, distributions reproduce commonly that salinity. species For varying propagation of environments clonal across in of roles widely patterns key grow Differing play to these variation Collectively species ploidy adaptation. this hybridization-associated salinity of of and on number propagation ability genome Increasing clonal species’ the 4) halophytic both the and that of and suggest S6); effect diploids findings S5, direct including a Fig. variation, suggesting 1; 5), ploidy (Table (Fig. extensive niche” composition “frozen by subgenome a vaginatum characterized and their is P. former in system the vary environment for The strategy that the 3) adaptive to allotriploids latter; genotype” respect the purpose with “general for and a strategy geographically suggesting 2), the both Fig. ecotype, include 1; fine-textured (Fig. findings the Our than both with distributed species. species, in widely widespread this extensively in species of occurs sister adaption composition propagation halophytic salinity genomic Clonal several and of make 1) to structure mechanisms following: us throughout population for allowed widely diversity, has implications collected ecotypes, genetic (fine-textured) broader samples the turf-like wild toward into new bias insights a using key without analyses, and genomic US, southern population the Our species. 1:1 plant and other 2:1 to (2:0 vaginatum well Paspalum as ploidy changes necessarily subgenome Discussion of other number the remove the of entirely for not number accounting 1:2). could copy after we to the because that however, in analysis species noted, halophytic change this be the from (P a should from salinity ploidy subgenomes It decreased of of adaptation. that effect with salinity proportion the relative associated revealed on the weakly effect two) that was detectable suggests or genome a finding unknown has one, This the 5). (zero, of Fig. copy 0.033, subgenomes additional = unidentified an having the while of of ), number number the tolerance. the salinity two both in and having incorporated variation ploidy) adaptive that to of each model 0.5328, contribute independent = of obviously linear (P not location a individuals does we triploid contrast, collection alone and tolerance, In variation diploid the salt of ploidy to locations to thus, the nearest 5); adaptation between Fig. significantly ocean in differ the composition not did of subgenome levels Salinity salinity and ploidy surface of the roles subgenome compared each potential of the copies investigate infer of To to number us salinity the allows that ocean genotypes but with Our coarse-textured them, Correlations tested pattern. of the reverse all of the in four have present all to are in subgenomes differs. appear loci two genotypes heterozygous same among two of the difference other set that one the same This specifically, the whereas More C-D). of source, composition. fine-textured S6 use unknown subgenome the DG120, Fig. an same of and from copy C-D; the 107 one have copies 4 carry 4B; DG not Fig. to accessions Fig. do appears reads; one they by reads; genotype that represented genotypes, reference reference indicates coarse_04, triploid of (33.3% (66.6% genotypes and ratio three ratio ratios triploid (coarse_02 1:2 the 2:1 1:1 two a Among showed other a showed S6A). respectively) the DG117) of Fig. while accession pattern 4A; S6B), by Fig. expected Fig. represented reference; the (coarse_01, a (50% them followed within reads of S1), subgenomes alternate haploid Table to of (coarse_03; number reference genotype the estimate coarse-textured could diploid we from loci, are that heterozygous genotype at reads alternate versus coarse-textured the within differences composition .vaginatum P. ugnmswti eoyeaeascae ihocrec nmr aieenvironments saline more in occurrence with associated are genotype a within subgenomes sapoiignwgnmcmdlsse o h td fsl oeac ncrasand cereals in tolerance salt of study the for system model genomic new promising a is .vaginatum P. .distichum P. ugnmswssrnl soitdwt ihrlcloenslnt P=7.6e-11 = (P salinity ocean local higher with associated strongly was subgenomes rsm te ore(e ehd) ceso G7,arepresentative a DG076, Accession Methods). (see source other some or Tbe1 al 1;2 lnso h oretxue ctp r more are ecotype coarse-textured the of Clones 2) S1); Table 1; (Table .vaginatum P. 9 .vaginatum P. .vaginatum P. ru.B onigtenme freference of number the counting By group. .vaginatum P. eeec eoeadtosubgenome two and genome reference ctps swl si h non- the in as well as ecotypes, .vaginatum P. ugnms(n s two, vs. (one subgenomes .vaginatum P. subgenomes, sample. Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. hsdffrnei ugnm opsto stu ieytersl fhbiiainbetween hybridization of result the likely thus different two is least composition at subgenome and in between difference wild This the in vaginatum hybridization P. interspecific fine-textured for between hybridization evidence find not vaginatum did we While flow. gene distichum of P. ecotypes ecotypes fine-textured two and the coarse- that found We vaginatum 2017). P. Devos, & Raymer, re- Harrison, between potentially of Bahri, admixture can (Eudy, apparent levels which identified salinity work population, termediate Previous a conditions. into environmental alleles novel salt-tolerant introduce to can adaptation in flow sult gene between and differentiation hybridization genetic Interspecific drives “general-purpose the allopolyploids explain and could hybrids groups factors of these by composition plasticity of maintain Subgenome clones. Both to coarse-textured serve hybrids. in can coarse-textured seen in for propagation pattern heterozygosity difficult (Fig. clonal it Additionally, possible) genotype” of make is location. could loss it recombination given the that post-hybridization a preventing suggests of in lack individuals genotypes This specialize admixed unique to of S4). of plants presence Sexual number Fig. the S3, low 2000). (although the Carrow Fig. rare however, Parker, & likely 3, tested; & (Duncan is been (Vrijenhoek it propagation not that pattern clonal has indicate vegetative “frozen-niche” ecotypes to coarse-textured a addition of in geno- in fine-textured reproduction resulting fit reproduction strategy, most sexual it, proposed the of dominate this pable of then with Clones will Consistent genotypes. location Recombination propagating 2009). given strategy. clonally a propagation novel clonal in produce influence type more can also even may reproduction are to reproduction sexual genotypes access sexual during have of widespread rate allopolyploids and the that in common assumption Differences hybrids. the most diploid with two consistent than the is alleles as This adaptive diploids potentially 1). to (Fig. “frozen relative triploids plasticity a both strategy to follow propagation clonal plants boost coarse- in additional transition fine-textured hybrid a the while induced have that may pattern in hybridization in that prediction genotype” indicates this This “general-purpose have with pattern. consistent Stefanovi´c, a should niche” are Han, follow findings genotypes Coughlan, the Our ecotypes follow 1965; plasticity to (Baker, 1984). textured likely high Lynch, species more 2017; parental Since be Dickinson, either thus & may than alleles 2017). genotypes strategy access hybrid al., environments, genotypes” can multiple “general-purpose they et in as survive (Shimizu-Inatsugi plasticity, to phenotypic ability species increased increased parental with genotypes both yield from to expected is Hybridization of genotypes. collection clonal our of parental With ranges the coarse-textured 2017). as hybrid Dickinson, rare Stefanovi´c, the are & vaginatum, Han, species both (Coughlan, parental investigate from sexual its to clones obligately and opportunities hybrid however, often distribution; a are between clonal species are an of strategies asexual, patterns reproduction be obligately investigate often clonal could to are differential hybridization which system 2018; Hybrids, interspecific model Waycott, strategy. of common & propagation a occurrence Virnstein, clonal determining Calladine, The in Bricker, wide- factor 1965; 2017). are important (Baker, Dickinson, that environments Stefanovi´c, genotypes & of few Han, a range Coughlan, by a characterized across is strategy distributed genotype” ly purpose “general the Conversely, 1979). .vaginatum P. .vaginatum. P. ohtecas-etrdand coarse-textured the both , ewr bet xlctyts o n ofimdffrne ntegorpi n environmental and geographic the in differences confirm and for test explicitly to able were we .vaginatum P. 5 n x and 6x) and (5x and and and utemr,wti h yrdcas-etrdgntps lorpod a rvd an provide may allotriploidy genotypes, coarse-textured hybrid the within Furthermore, .distichum P. .distichum P. .distichum P. Paspalum n non-tolerant and .vaginatum P. ontapa osaetesm non- same the share to appear not do Fg ,Fg 3,atog eddietf iie eeflwbtenthe between flow gene limited identify did we although S3), Fig. 3, (Fig. omddsic eei rus ihn intrso eeflwbetween flow gene of signatures no with groups, genetic distinct formed species. .vaginatum P. .vaginatum P. .distichum P. 2 n x ersn ucetrpoutv are oprevent to barrier reproductive sufficient a represent 3x) and (2x .distichum P. .vaginatum P. n other and Fg S4) (Fig. 10 rusapa ohv enfre rminterspecific from formed been have to appear groups hc ol rdc eoye dpe oin- to adapted genotypes produce could which , Paspalum n n fisprn pce,fine-textured species, parent its of one and . .vaginatum P. ti osbeta liydffrne between differences ploidy that possible is It pce.Itrsigy coarse-textured Interestingly, species. .vaginatum P. eoye r nw ob ca- be to known are genotypes ugnm Fg S5). (Fig. subgenome .distichum P. .vaginatum P. and P. P. Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. iie oasalnme fseis e fwihaegass(a,22;Msr an,21) hsis This 2017). Tanna, & Mishra salt- in 2020; tolerance been highly (Fan, increased have for grasses of halophytes breeding are studies and in which worldwide, limited tolerance of fields crop with salt agricultural few from affects of tolerant, species, salinity comes basis of soil salt tolerance because number genetic not problematic salt small the generally a of on are to underpinnings studies limited Additionally, that physiological species. species and plant genetic model tolerant the plant of and knowledge species our of Most geographic the breeding temporal across plant areas, estuary comparison for coastal an for Implications some in unsuited for example, them exist study. (for make data this wild salinity datasets of the resolution scale between in higher variation plants resolution While methodological the by gradient). have and salinity experienced not history steep likely does introduction a dataset variation or salinity with microhabitat demographic surface unknown the sea our that identify Additionally, possible to salt patterns. controlled also these with to is confirmed contribute It be could transcriptomics. must and and nature assays in tolerance maternal correlational necessarily out are between associations rule environmental observe the can we implying trend haplotype, we the cpDNA cross. also triploids, Although same each but the for reciprocal lower, carry species hybrids only of parent coarse-textured not maternal studies the is same of other salinity all because ocean most effects local unlike subgenome their Furthermore, because variable. genotypes” polyploids more “general-purpose that predictions likely or of are ploidy of opposite number hybrids increased the the to is of of effect it due large then effect is The ocean effect The effect ploidy less tolerant. weaker triploids). a (slightly salt this is 1:2 more direction it whether be and opposite If certain should both. diploids the for or in (1:1 say effects, and cannot copy dosage We weaker subgenome one copy). was only each subgenome with with unknown salinity those the than of counts higher is increasing ~15% as average environments on was saline ecotype coarse-textured for the in adapted present vaginatum copies subgenome as unknown two other not received the that they is hypothesis 2013). which the similar Birchler, from support each & results 2:1), parent from Our Auger, the vs Gray, 2017; received Glover, Yao, to 1:2 & they 2016; similar Hansen, al., more subgenomes Solberg, (e.g. et Fjelldal, often St¨ock, Harvey, of hybrids Tan & 2018; are halophytes number Perrin, allotriploid which Sermier, in the reciprocal Hofmann, here, tolerance whole (Betto-Colliard, investigated in describe a have salt we vary on studies those of occur that to also evolution Other hybrids can increased the of number and species. copy in phenotypes populations gene parental implicated on in in Variation influence been salinity level dramatic 2012). has ocean genome a Cheeseman, genes have & local salt al., Bohnert, can tolerance in Dassanayake, et effects increased salt (Oh, difference Yang dosage with of 2019; detectable Gene al., number associated no factor. et copy is be driving Wu there the to 2013; be alone, al., tends may considered triploid et ploidy and is (Chao diploid in ploidy species between related when increase However, closely an between that 2014). and salinity within indicate ocean both systems local tolerance other with associated in is Studies ploidy not but composition Subgenome in non- the between tolerance o rswtrevrnet.Hptee o h hsmgthv curdicuelwrepeso of expression lower include occurred have might this why for Hypotheses the environments. freshwater for non- these non- textured of the contribution that genomic likely the is to it due be could vaginatum groups hybrid P. two these between differentiation Niche .distichum P. .vaginatum P. .vaginatum P. ugnm fietxue,ad21tilis eefudi oain hr h oa ca salinity ocean local the where locations in found were triploids) 2:1 and (fine-textured, subgenome aet.T u nweg,no knowledge, our To parents. . ugnm in subgenome .vaginatum P. agl anandishg attlrnewhile tolerance salt high its maintained largely .vaginatum P. .vaginatum P. .vaginatum P. .distichum P. aetlseiso ohgop r o aohtc ept hs coarse- this, Despite halophytic. not are groups both of species parental .vaginatum P. aet,adps-yrdzto eeto o rswtradaptations freshwater for selection post-hybridization and parents, Fg ) nta,cp ubro the of number copy Instead, 5). (Fig. Paspalum ugnmsi ossetwt u nigta coarse-textured that finding our with consistent is subgenomes eaiet coarse-textured to relative .vaginatum P. 11 ugnm oynme n oa aiiyi striking, is salinity local and number copy subgenome pce sa attlrn as salt-tolerant as is species Fg5.Pat ihtocpe fthe of copies two with Plants 5). (Fig .vaginatum P. .distichum P. .vaginatum P. .vaginatum P. ieecsi salt in differences , hw adaptations shows subgenome therefore, ; P. Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. ho .Y,Dle,B,Lo . oga,A,Ykbv,E,Lhe,B,&Sl,D .(03.Polyploids (2013). E. D. Salt, & Arabidopsis. B., in Lahner, tolerance E., salinity Yakubova, and A., uptake Douglas, potassium H., higher Luo, exhibit B., Dilkes, D.-Y., Chao, diploid four among relations 10.1086/337261 doi: Genome 592–596. (1981). L. B. 25. Burson, Spermatophyta: for Committee the of 10.2307/1221981 Report doi: (1983). of K. Phylogenetics R. (2018). Brummitt, M. K. ( Olsen, gold-of-pleasure of & origin A., Evolution the M. on insights Beilstein, and A., poten- (Brassicaceae) D¨onmez, planta A. aquatic R., an J. in Brock, clonality environment. Mega changing (2018). a M. in Waycott, strategy & survival R., tial Virnstein, A., Gramineae. Calladine, 9. E., Vol. Bricker, Iraq, of Flora (1968). https://www.cabdirect.org/cabdirect/abstract/19690700617 E. Guest, from & toads. L., N. polyploid Sciences Bor, in Biological speciation B: hybrid Society of Royal and hallmarks divergence the genetic as of Profound contributions St¨ock, genomic (2018). & a M. genome N., or parental Perrin, parents, R., asymmetric both Sermier, of S., best Hofmann, The C., vigor: Betto-Colliard, (Eds.), Hybrid Stebbins (2017). L. N. Barkai, G. & & A., Baker, A. clash? Levy, G. O., H. Lupo, In D., weeds. Bar-Zvi, of origin species of unrelated colonizing modes in of and ancestry Characteristics Genetics of (1965). estimation G. H. model-based Fast Baker, (2009). K. Lange, in & speciation J., individuals. Novembre, and H., polyploidy Hybridization, D. (2004). Alexander, G. Yannic, & A., Salmon, A., Spartina Baumel, L., M. Ainouche, Science Plant Danforth States H. reference United References William the the the by by providing funded supported for was been JGI work has for This at DMG Fellowship. Speranza amplification. 2016-35-605). the team Pablo cpDNA (project assembly and project; performing Association the the WUSTL for Golf of and Small at stages Schmutz Linda staff early and, Jeremey the greenhouse genome; advice; Uruguay; in the collection discussions from providing of useful tissue for for rest Griffin) sending Science) Georgia the Crop of (Bayer (University and Raymer Eudy Wolk Paul Doug care; Aileen plant Fabbri, providing Sally for DDPSC Dyer, required. be Mike will thank ecotypes We coarse- coarse-textured the from in traits them identify for with to useful Acknowledgments programs associated work breeding Future of markers turf ecotypes. genetic introgression in fine-textured and relevant, diversity of traits economically genetic more these of possibility between but source crosses valuable depauperate, the in a genetically natural diversity to provide the of genetic could presence points This of apparent populations. ecotypes lack The textured the study. coarse-textured by this and in hampered effects of confirmed been fine tolerance. expression as have dosage salt or germplasm, turfgrass whole-genome crop number available paspalum improving copy with publicly seashore to to associated key for changes the programs that be be tolerant Breeding and may may salt insufficient pathways wild more be and develop may the genes approach to interacting in salt knowledge gene multiple in tolerance that single involved a transfer salt genes that to and that indicates us mechanisms finding allow the may Understanding Our slow. species cereals. been grass has halophytic grasses, in all tolerance are which crops, cereal urn pno nSsesBiology Systems in Opinion Current (Poaceae). , 127 eoeResearch Genome 3–4.di 10.1016/j.ympev.2018.06.031 doi: 834–842. , e Phytologist New p.137–172) (pp. , 19 9,15–64 o:10.1101/gr.094052.109 doi: 1655–1664. (9), , 161 1,1512 o:10.1046/j.1469-8137.2003.00926.x doi: 165–172. (1), , . , 285 6 e ok cdmcPress. Academic York: New 22.di 10.1016/j.coisb.2017.08.004 doi: 22–27. , rnir nPatScience Plant in Frontiers 17) 0767 o:10.1098/rspb.2017.2667 doi: 20172667. (1872), 12 Paspalum aeiasativa Camelina lr fIa,Vl .Gramineae. 9. Vol. Iraq, of Flora species. Science Taxon , 9 ). o:10.3389/fpls.2018.00435 doi: . oaia Gazette Botanical oeua hlgntc and Phylogenetics Molecular , , 341 32 2,2924 JSTOR. 279–284. (2), 64) 5–5.doi: 658–659. (6146), Camelina Proceedings , Retrieved 142 Crantz. (4), Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. alT .(99 iEi:aue-redybooia euneaineteio n nlsspormfor program analysis and editor alignment sequence biological user-friendly genotyping-by-sequencing a with levels BioEdit: 95/98/NT. ploidy (1999) Windows individual A. of T. Detection Hall (2017). E. halophytes. K. of analysis. Mock, potential (GBS) crop & and Z., tolerance Salt Gompert, (1999). E. Sciences Blumwald, Plant & in J., Reviews J. and Brown, niche P., Realized E. Glenn, (2018). M. hybrids. J. halophyte Castillo, & exotic E., and 018-4251-y M. native Figueroa, of J., pattern B. spatial Grewell, Mexico. G., of Curado, Gulf B., the Gallego-Tevar, in influence” freshwater of of “regions mapping land/ocean Statistical Oceans as Research: (2019). signatures J. Vazquez-Cuervo, fate & and B., origin Dzwonkowski, T., Disaggre- J. (2016). Reager, in C. S., heterosis Spillane, Fournier, & to R., contributions Sulpice, hybridity global G., and M. for dosage Aarts, . surfaces genome C., climate parental Wijnen, resolution polyploidy, C., P. spatial gating McKeown, 1-km P., new Ryder, A., 2: Fort, WorldClim (2017). J. R. areas. Hijmans, land & E., S. halophytes. Fick, in responses stress 10.1080/15592324.2019.1704528 salt doi: of 1704528. diversity genetic mechanisms (1), and Genetic level (2020). Ploidy (2017). C. M. Fan, K. Devos, & P., Raymer, genus L., the M. in Harrison, A., B. Bahri, D., Eudy, Diffe- 10.3732/ajb.0900067 (2009). halophyte S. Karrenberg, the & in H., genes L. progenitors salt-tolerance Rieseberg, candidate D., Sicard, of C., expression Dillmann, rential M., Falque, de X., Raffoux, morfologica C., variabilidad Edelist, y cromosomicos Numeros JSTOR. & (1992). from A. Wiley Retrieved C. JSTOR. John Sala, turfgrass. & environmental M., distichum A. Paspalum the Clausen, paspalum: M., flow Seashore A. by Echarte, (2000). cells N. plant R. in Carrow, content & Sons. DNA R., nuclear R. of Duncan, Analysis (1989). S. Lucretti, cytometry. & Binarov´a, P., Doleˇzel, J., polymorphisms nucleotide are single sequencing. using 0998.13073 clones individuals amplicon triploid generalist and by diploid Widespread genotyped Differentiating (2019). ( A. (2017). Hawthorns T. Northwest A. Delomas, Pacific T. of allopolyploids Dickinson, in & expansion Ecology perspectives. niche Molecular Stefanovi´c, S., and and S., range problems with Han, environments: associated M., saline J. in activity Coughlan, of integration Biology The Plant (2013). Functional M. J. Cheeseman, 10.1126/science.1240561 e Phytologist New ilgaPlantarum Biologia nentoa ora fClimatology of Journal International .annuus H. Paspalum oeua clg Resources Ecology Molecular , , , 209 124 Paee nl rvni eBeo ie (Argentina). Aires Buenos de provincia la en (Poaceae) 26 uli cd ypsu series symposium acids Nucleic ru Disticha. group , and 2) 4459.di 10.1111/mec.14331 doi: 5484–5499. (20), 2,5059 o:10.1111/nph.13650 doi: 590–599. (2), 7,45–93 o:10.1029/2018JC014784 doi: 4954–4973. (7), , , .petiolaris H. 40 18 9,7974 o:10.1071/FP12285 doi: 759–774. (9), 2,2725 o:10.1080/07352689991309207 doi: 227–255. (2), , 31 2,1310 https://doi.org/10.1007/BF02907241 113–120. (2), oeua clg Resources Ecology Molecular rpScience Crop (Asteraceae). , 17 , 37 6,15–17 o:10.1111/1755-0998.12657 doi: 1156–1167. (6), 13 1 95–98. 41, , , mrcnJunlo Botany of Journal American 1) 3241.di 10.1002/joc.5086 doi: 4302–4315. (12), 57 Oecologia 6,31–32 o:10.2135/cropsci2017.04.0241 doi: 3319–3332. (6), , , einhsparadoxus Helianthus 19 188 6,14–51 o:10.1111/1755- doi: 1545–1551. (6), 3,8982 o:10.1007/s00442- doi: 849–862. (3), Darwiniana ln inln Behavior & Signaling Plant , 96 ora fGeophysical of Journal 1) 8013.doi: 1830–1838. (10), rbdpi thaliana Arabidopsis , 31 n t glycophyte its and 14,185–197. (1/4), Crataegus Critical , L.). 15 Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. ucl,S,Nae . odBon . hms . eria .A . edr . hm .C (2007). C. P. files. Sham, . . FastQ . analyses. linkage D., population-based Bender, Genetics and for R., Human association A. of whole-genome M. nal for Ferreira, tool set L., tool Thomas, A K., genetics. Todd-Brown, trimming PLINK: and B., breeding Neale, plant S., and for Purcell, from Genotyping-by-Sequencing lessons (2012). demultiplexing extreme: W. the T. at Rife, barcode Genome Life & A., (2012). J. a M. Poland, J. Cheeseman, & J., H. genome. Sabre: Bohnert, the M., Dassanayake, D.-H., Oh, and (2011). sequences DNA plastid https://github.com/najoshi/sabre N. integrating Zuloaga, Panicoideae): . . . Joshi, (Poaceae: A., Paniceae classification. M. Chemisquy, new the S., a S. of into Denham, Phylogeny L., morphology D. (2012). Salariato, A., O. M. F. Scataglini, L., promoters. Aagesen, and O., genes Morrone, tolerance stress salt for Science resources potential Plant Halophytes: in reads. Frontiers (2017). sequencing B. Tanna, high-throughput & A., from Mishra, sequences adapter removes Cutadapt parthenogene- net.Journal geographic (2011). M. genotypesand transform. Martin, Burrows–Wheeler general-purpose 257–290. Biology,59(3), with hybridization, of alignment Destabilizing Review read Quarterly short sis.The (1984). organic accurate of M. and Synthesis Fast Lynch, (2008). (2009). salin- W. R. M. to Durbin, Bioinformatics Rieger, & responses & H., relation A., Li, M. water Eiteman, and R., in Growth R. mechanisms , tolerance Duncan, salt N., and (2005). R. osmolytes Carrow, R. G., R. ecotypes. Lee, Duncan, paspalum seashore & halophytic halophytic of N., 10.1016/j.scienta.2004.08.011 stress in R. salinity stress to Carrow, ity responses Photosynthetic G., (2004). Lee, R. R. Duncan, shoot ecotypes. & ecotypes: paspalum N., seashore paspalum R. seashore Carrow, of G., tolerance Lee, Salinity http://agris.fao.org/agris-search/search.do?recordID=US201301013363 (2004). from N. Retrieved R. . Carrow, criteria. & and R., responses growth R. Duncan, of salinity G., ( to Lee, Responses California (2016). Bay, R. Francisco D. Strong, Invasions San & Biological R., in M. Pakenham-Walsh, formed R., halophytes. hybrids D. in Ayres, allocation K., 1.5-10). resource A. and Lee, (Version reproduction trigonometry Growth, spherical (1991). T. geosphere: Rudmik, Botany & L., (2019). R. C. Jefferies, Vennes, whole- a & elicits E., https://CRAN.R-project.org/package=geosphere Ploidy from Williams, maternal Retrieved (2017). second J., the A. of R. K. origin genetic Glover, Hijmans, the & to linked T., is Hansen, salmon Atlantic F., set. triploid M. chromosome of growth Solberg, effect: G., dosage P. genome Fjelldal, C., A. Harvey, 63 1,1–7 o:10.1016/j.envexpbot.2007.10.009 doi: 19–27. (1), , , 39 5 , 3,9–0.di 10.3835/plantgenome2012.05.0005 doi: 92–102. (3), 1,31.di 10.1016/0304-3770(91)90018-Z doi: 3–16. (1), eoeBiology Genome 17 , 25 1,1–2 o:10.14806/ej.17.1.200 doi: 10–12. (1), M Genetics BMC 1) 7416.di 10.1093/bioinformatics/btp324 doi: 1754–1760. (14), , 18 , 8,20–29 o:10.1007/s10530-015-1011-3 doi: 2207–2219. (8), 81 , ln Science Plant 8 3,5955 o:10.1086/519795 doi: 559–575. (3), otcec ulcto fteAeia oit o otclua Science Horticultural for Society American the of Publication A : HortScience , o:10.3389/fpls.2017.00829 doi: . 13 , 3,21 o:10.1186/gb-2012-13-3-241 doi: 241. (3), 18 1,3.di 10.1186/s12863-017-0502-x doi: 34. (1), Cladistics , aplmvgntm niomna n xeietlBotany Experimental and Environmental vaginatum. Paspalum 166 , 6,11–45 o:10.1016/j.plantsci.2003.12.029 doi: 1417–1425. (6), 28 .atrioaxfoliosa x alterniflora S. 14 4,3336 o:10.1111/j.1096-0031.2011.00384.x doi: 333–356. (4), cetaHorticulturae Scientia and , .dnioaxfoliosa) x densiflora S. 104 h mrcnJour- American The 2,2126 doi: 221–236. (2), h Plant The Spartina Aquatic EMB- . Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. u .Q,Ln .Y,Ja,Q,&L,S-.(09.Ttali xiismr oeatt aiiyta diploid than salinity to tolerant more exhibits Tetraploid (2019). S.-J. ( Li, beet & sugar Q., in Jiao, L.-Y., Lin, species, G.-Q., sunflower Wu, hybrid homoploid a genus. between plant divergence recalcitrant Habitat 10.3732/ajb.89.3.472 previously (2002). H. a paradoxus L. from Helianthus Rieseberg, extraction & E., DNA M. Welch, (1990). J. S. Reporter Knapp, Biology (Eds.), Molecular & and Dijk M., P. genotypes D. & purpose Webb, general Martens, K. parthenogenesis: Schon, Geographical I. (2009). In Parthenogenesis D. variation. E. niche Parker, frozen & C., coexistence. R. and Vrijenhoek, diversity clonal affecting Factors Biology (1979). C. R. Data Vrijenhoek, Ag (GRIN). Network Information Resources Germplasm https://doi.org/10.15482/USDA.ADC/1212393 the Commons. (2015). for Service. pipeline Research Agricultural new USDA a Fast-GBS: data. 10.1186/s12859-016-1431-9 genotyping-by-sequencing (2017). from doi: F. SNPs Belzile, 5. of & (1), calling A., accurate Abed, highly M., and imbalance efficient Bastien, dosage J., gene/genome Laroche, Genome-wide D., Torkamaneh, (2016). Z. Li, Science & X., Plant synthetic Ge, in in Y., speciation. expressions Xiang, plant gene C., in regulates Cui, hybridization Q., of Pan, role C., Tan, The (2009). E. D. Soltis, adaptiveBiology & Plant S., (2017). P. K. Soltis, K. transcriptomes. Shimizu, in & J., plasticity Sese, polyploid 10.1111/mec.13738 H., by Kudoh, mediated K., new Hirose, of radiation Phylogeny A., Terada, (2014). R., O. Shimizu-Inatsugi, Morrone, D. & A. S., S. Caperta, Denham, Evolution M., and L. . . Giussani, . O., F. D., world Zuloaga, Espirito-Santo, A., P., M. Scataglini, A. Paes, parthenogenesis. 10.1093/aob/mcv138 geographical of G., halophytes of doi: Teixeira, tetraploid pattern 50. and a S., diploid for in O. evidence reproduction Paulo, of (Plumbaginaceae): modes F., and Phylogeography Sadio, (2016). S., A. Rois, imr . hn . aheo,I,Ibl . wg,S .F,Cnotu,W,...Lne,G (2014). G. Lunter, . . . W., sequencing Consortium, clinical F., in variants R. calling S. for Twigg, approaches Z., haplotype-based Iqbal, applications. and I., specia- assembly- Mathieson, and mapping-, adaptation H., Integrating segregation, Phan, Transgressive A., (1999). Rimmer, K. R. Wayne, & A., M. Statistical tion. Archer, for Foundation H., R L. computing. Rieseberg, statistical for environment http://www.R-project.org/. and Austria.URL genetic language Vienna, density A Computing, R: High the (2013). (2019). to Team M. Core relationship K. R their Devos, & and L., genotyping-by-sequencing P. using Raymer, paspalum J., genome. Schmutz, seashore C., of J. maps Schnable, D., Eudy, P., Qi, Heredity Paspalum , , cetfi Reports Scientific 19 60 3,7777 o:10.1093/icb/19.3.787 doi: 787–797. (3), 10.1146/annurev.arplant.043008.092039 doi: 561–588. (1), aueGenetics Nature eavulgaris Beta , , 83 300 Paee aioda,Psaee ae npatdadncermarkers. nuclear and plastid on based Paspaleae) Panicoideae, (Poaceae, p.9–3) odeh:Srne ehrad.di 10.1007/978-90-481-2770-2_6 doi: Netherlands. Springer Dordrecht: 99–131). (pp. , 7 4,3332 o:10.1038/sj.hdy.6886170 doi: 363–372. (4), 5,15–00 o:10.1007/s00606-013-0944-1 doi: 1051–1070. (5), o:10.3389/fpls.2016.01432 doi: . Atrca) n t progenitors. its and (Asteraceae), , , L.). 8 9 , 3,10 o:10.1007/BF02669514 doi: 180. (3), 1,11.di 10.1038/s41598-019-48257-3 doi: 1–10. (1), 46 caPyilga Plantarum Physiologiae Acta 8,9298 o:10.1038/ng.3036 doi: 912–918. (8), rsianapus Brassica 15 n eiaie A,AC C,CCAA). CCA, AAC, (AC, derivatives and mrcnJunlo Botany of Journal American , 41 oeua Ecology Molecular 4,5.di 10.1007/s11738-019-2844-7 doi: 52. (4), otSx h vltoayBooyof Biology Evolutionary The Sex: Lost naso Botany of Annals nertv n Comparative and Integrative M Bioinformatics BMC , nulRve fPlant of Review Annual 26 , 89 1,1327 doi: 193–207. (1), Limonium ln Systematics Plant 3,4248 doi: 472–478. (3), ogu bicolor Sorghum , 117 Frontiers 1,37– (1), species Plant , 18 Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. rus h eaieysalnme flc htaehtrzgu nbt coarse-textured both in heterozygous are that loci coarse-textured of number small and relatively The groups. S5 Figure 1-7. = K for error rate heterozygosity.validation heterozygosity lower of ( indicate genome-wide (two K=2 blue its individuals at of indicates admixed shades individual Darker three S4 each F). as Figure of coefficient well inbreeding color individual as The assessment. the definitive groups as overlap). a defined (reported and make well to clonal three wide are genome into which trend accessions the Disticha at subgroup look to necessary S3 is Figure of ~2:1 it copies the sequencing so haploid to chance two be Due with to each to triploid reads). due to considered a reference ratio identical represent of are could be percentages types example or to read hypothetical ratios expected vaginatum location two this calculating are reads same common in reference locus the included most of a not at the ratio at start (i.e. to allele reads ignored identical each and GBS not representing errors Because reads reads genotype. Therefore, site, triploid cut other. hypothetical restriction a the for to locus due a at reads counts S2 Figure genotypes. clonal identifying for ( , 2014). S1 al. Figure et (Scataglini KF853027 accession GenBank to S2 Table ploidy article. infer this to of used version on-line the S1 in Table found be may information supporting Additional interpre- and manuscript. analysis manuscript. at Information the data the study, Supporting drafted occur writing the and and designing will figures, to proposals contributed grant generated scripts authors writing data, All of tation, analyzed sequences. development work, cpDNA Future lab aligned KMO performed plants, dryad. collected to snapshots DMG submitted and datasets be Contributions SNP will The Author project publication. MT361665). the before MT361650- in SRA (accessions https://github.com/david-goad/paspalum-hybridization/. NCBI used GenBank to code on submitted of available be V. will are A. reads sequences Mishonov, trimmed & E., and H. Demultiplex Garcia, A., R. salinity. Locarnini, Accessibility 2, P., Volume Data T. triploid Boyer, in 2018. D., heterosis atlas Seidov, on ocean R., effects World dosage J. (2018). Genomic Reagan, M., (2013). M. A. Zweng, J. Birchler, physiological & of L., Evolution D. Auger, (2014). maize. D., B. A. Liu, Gray, H., Yao, . . . wheat. S., hexaploid 10.1073/pnas.1412839111 Wen, in H., doi: Wang, stress 11882–11887. Z., salt Yang, to H., Zhang, responses L., Zhao, C., Yang, B .distichum P. Coarse-textured ) rceig fteNtoa cdm fSciences of Academy National the of Proceedings A nomto o l ape nldn olcinlcto,txnmcadgntp aes n data and labels, genotype and taxonomic location, collection including samples all for Information oyopi ie nteito fteclrpatgene chloroplast the of intron the in sites Polymorphic . ugnm n n rmteukonpoeio;hwvr igelcscudhv skewed a have could locus single a however, progenitor; unknown the from one and subgenome DITR lt hwn ouainasgmn f3 nqediploid unique 33 of assignment population showing plots ADMIXTURE itga fpiws eei itne ewe ape ihn( within samples between distances genetic pairwise of Histogram ubro N akr hr eeoyosclsaeuiu ogvngopo hrdbetween shared or group given to unique are calls heterozygous where markers SNP of Number n = ( K=3 and ) rnia opnn nlss(C)soigtegntcsprto falsampled all of separation genetic the showing (PCA) analysis component Principal ( A h ai oko ftili_opp.( triploid_comp.py. of workflow basic The ) .vaginatum P. u o fine-texture not but .vaginatum P. B .Pttv n-oreamxdidvdasaeidctdwt tr.( stars. with indicated are individuals admixed fine-coarse Putative ). ieyd o hr non- a share not do likely n ( and , P.vaginatu C rceig fteNtoa cdm fSciences of Academy National the of Proceedings ) .distichum P. lgtbu ein niae that indicates region) blue (light m 16 , .vaginatum P. 110 7,26–69 o:10.1073/pnas.1221966110 doi: 2665–2669. (7), B otdrdln niae itnethreshold distance indicates line red Dotted . nilsrto fhwtriploid_comp.py how of illustration An ) rpl16 subgenome. oiin r ae nalignment on based are Positions . A fine-textured ) .vaginatum P. .distichum P. rpl16 .vaginatum P. .vaginatum P. C , genotypes Paspalum 111 Cross- ) cpDNA h P. the (32), and Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. ftems omncoa eoye dtce n6o oeacsin) ( accessions). more or 6 in (detected locations geographical genotypes indicate clonal Shapes variants. common distichum, ploidy most and subgroups the genetic of major indicate Colors States. 1 Figure § (N heterozygosity. size wide genome Relative ++ geno-types unique No. + sampled accessions No. ploidy Esti-mated distichum P. Ecotype vaginatum P. the than Species for smaller estimates 11% size is genome the that for relative size 1.0 indicate genome = brackets basal 2x in a of values size 509022); genome PI haploid diploid (accession two a assuming or calculated one were having estimates reflects triploids 1 the Table in 2:1 or Figures 1:2 and either Tables toward bias A the of 2:1. copies and 1:2 at triploids ( DG076) by ( represented DG120) ( (coarse_03, DG117) coarse-textured genotype coarse_01(accession hybrid four genotypes: diploid in common SNPs most heterozygous the covering alternate) is other S6 Figure nldstrepttv orefietxue die ape seFg n al S1). Table and 2 Fig. (see samples admixed coarse/fine-textured putative three Includes . ubro cesosmaue ihtrerpiae e accession per replicates three with measured accessions of Number = N niiulibedn offiin Prele l 07;mr eaievle niaehge genome- higher indicate values negative more 2007); al. et (Purcell coefficient inbreeding individual = F D) nerdcoaiyadpod aito o sampled for variation ploidy and clonality Inferred ( fine-textured A h a onso h w otcmo ed weeoei dnia oterfrneadthe and reference the to identical is one (where reads common most two the of counts raw The P e ie niaeepce ai frfrnet lent ed o ilisa : n reciprocal and 1:1 at diploids for reads alternate to reference of ratio expected indicate lines Red . a fU olcin of collections US of Map ) . ietxue x5 410 2 0.541 (2) 1.01 24 55 2x 2x Coarse-textured Fine-textured vaginatum .vaginatum P. ugnm respectively. subgenome x16315 3 -0.520 (3) 1.56 3 116 3x x6226 30]()-1.323 -1.241 (2) [3.03] 2.69 (2) [2.53] 2.25 2 2 6 9 6x 5x § n coarse-textured and B) Paspalum ore0 acsinD17 ( DG107) (accession coarse_02 , .vaginatum P. 17 ru itcaacsin ntesuhatr United southeastern the in accessions Disticha group 2910 9 -0.278 (9) 1.04 9 32 Paspalum eeec genome. reference .vaginatum P. cesos eaiegnm size genome Relative accessions. .vaginatum P. C B n ore0 (accession coarse_04 and ) A rmlf oright: to left From ) n h he triploid three the and ) .distichum P. ape representing samples eeec genome reference assuming P. + vrg F Average ) ++ Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. ae nsbeoecmoiin lc n rybr ersn oynme fhpodsbeoe from subgenomes haploid ploidy. of indicates number Color copy represent error. bars standard grey and vaginatum Black P. composition. subgenome on based 5 Figure in-the-model-halophyte-seashore-paspalum-paspalum-vaginatum polyploidy-and-clonality-influence-geographic-patterns-of-diversity-and-salt-tolerance- image5.emf file Hosted from subgenomes haploid (grey). of number species the progenitor indicate corner right ( top the DG076) by ( DG117) represented (accession (coarse_03, coarse-textured genotype four in hybrid loci heterozygous at 4 Figure in-the-model-halophyte-seashore-paspalum-paspalum-vaginatum the polyploidy-and-clonality-influence-geographic-patterns-of-diversity-and-salt-tolerance- as admixed (reported putatively two image4.emf rate heterozygosity. as heterozygosity lower well genome-wide indicate as blue its file formed of indicates Hosted shades are individual Darker groups F). each defined coefficient of well inbreeding color individual Three The group. clonal individuals. each from sample 3 Figure in-the-model-halophyte-seashore-paspalum-paspalum-vaginatum polyploidy-and-clonality-influence-geographic-patterns-of-diversity-and-salt-tolerance- image3.emf is coordinates) genotype GPS a (with level. file wild whether ploidy the Hosted indicate indicates in IDs Color collected genotype n. genotype Unique each by of indicated genotype. number is that The for fine-textured. distance or pairwise coarse-textured in propagating variation clonally no each is from clones of locations 2 Figure in-the-model-halophyte-seashore-paspalum-paspalum-vaginatum polyploidy-and-clonality-influence-geographic-patterns-of-diversity-and-salt-tolerance- image2.emf file Hosted vaginatum. P. oa ca aiiyi rcia aiiyuis(S)frec forwild our of each for (PSU) units salinity practical in salinity ocean Local itiuin fpiws egahc( geographic pairwise of Distributions itiuino h ecn frasta r dnia othe to identical are that reads of percent the of Distribution rnia opnn nlss(C)of (PCA) analysis component Principal vial at available at available at available at available (N Pv n h nnw rgntrseis(N species progenitor unknown the and ) B) ore0 acsinD17 ( DG107) (accession coarse_02 , https://authorea.com/users/351065/articles/475745-hybridization- https://authorea.com/users/351065/articles/475745-hybridization- https://authorea.com/users/351065/articles/475745-hybridization- https://authorea.com/users/351065/articles/475745-hybridization- .vaginatum P. A .vaginatum P. n niomna ( environmental and ) 18 Paspalum C A n ore0 acsinD10 ( DG120) (accession coarse_04 and ) n h he rpodgntps coarse_01 genotypes: triploid three the and ) ape ersnigtems omndiploid common most the representing samples other ru itcaacsin ae nasingle a on based accessions Disticha group eoye igedtidctsta there that indicates dot single A genotype. epciey oe niaema and mean indicate Boxes respectively. ) .vaginatum P. B .vaginatum P. itne ewe collection between distances ) bak ra unidentified an or (black) .vaginatum P. eeec genome reference D) collections asin Bars . Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary. A ● ● ● ● ● ● ● Geographic distance (km) ● ● ● ● ● ● ● 1000 1500 ● ● ● ● 500 ● ● ● ● ● ● ● ● 0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● n=36 ● ● ● ● ●

coarse_01 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● n=68 ● ● ● ● ● ● ● ● ● ● ●

coarse_02 ● ● ● ● n=20 coarse_03 ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● B ● nqegntp ID genotype Unique n=7 coarse_04 n=2 ● ● ● ● coarse_06 ● ● ● n=3

coarse_07 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● n=3 ● ● ● ● ● fine_05 ● ● ● ● ● ●● ● n=3 ● ● ● fine_06 ● ● ● ● ● ● ● ● ● ● ● ● ● n=6 fine_07 Ploidy n=2 A

fine_08 3X 2X 19 ● ● ● ● Environmental distance 0 1 2 3 4 5 n=36 coarse_01 ● ● ● ● ● ● ● ● ● ● ● n=68 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

coarse_02 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● n=20 ● ● ● ● ● ● ●

coarse_03 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● n=7 ● ● ● ● ● ● ● ● ● coarse_04 ● ● ● ● ● ● ● ● ● ● ● ● ● nqegntp ID genotype Unique ● ● ● ● ● ● ● ● ● ● n=2 coarse_06 n=3 coarse_07 ● ● n=3 ● ● ● ● ● ● ● ● ● ● omncoa genotypes clonal Common groups Major fine_05 ● Pd_02 fne_07 (3x) coarse_04 (2x) coarse_03 (3x) coarse_02 (3x) coarse_01 distichum P. Admixed Fine-textured 2x Coarse-textured 3x Coarse-textured ● ● n=3 fine_06 n=6 fine_07 Ploidy n=2 B

fine_08 3X 2X Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary.

Num ber of loc i PC2 (20.2% variance explained) 100 200 300 400 500 600 200 400 600 800 0 0 ● ● ● ● ● ● ● ● ● ● 0. 0. C A 0 0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Coarse-textured vaginatuP. ecn frasietclto identical reads of Percent 0. 0. 2 2 Admixed vaginatuP. Fine-textured vaginatuP. 0. 0. 4 4 m C 3.%vrac explained) variance (31.6% PC1 0. m 0. 6 6 m 0. 0. 8 8 1. 1. 0 0 20 .vaginatumP. 100 200 300 400 500 100 200 300 400 500 600 700 0 0 0. 0. D B 0 0 0. 0. eeec genomereference 2 2 ● 0. 0. .distichuP. 4 4 ● 0. 0. 6 6 m ● ● 0. 0. 8 8 Individual 1. 1. 0 0 − − 0. 0. 1. 0. 0 5 0 5 F Posted on Authorea 17 Aug 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159769014.45599887 | This a preprint and has not been peer reviewed. Data may be preliminary.

Local ocean salinity (PSU) 28 30 32 34 36 1:2 aetlsbeoecp ubr(N number copy subgenome Parental 1:1 21 2:1 Pv N : other ) 2:0 Ploidy 3X 2X