Posted on Authorea 26 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160373183.39716449/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. Masaoki Daisuke AOKI Author: iii. migrant Japanese a for scenario Divergence title: running short A mi- archipelago ii. a Japanese for the in divergence species dispersal-driven bird long-distance gratory supports phylogeography integrated Migration-tracking of Title: new understanding i. a our provides improve for framework should inferred Our models was vicariance Vicariance population. species. and Japanese migratory LDD population. of the discriminating histories new from and phylogeographic the continent the region, the of Asian of this expansion northeast isolation and in the Shrinkage and approach scenario in integrative Shrike. colonisation phylogeographic Brown subspecies Our successful the the for conclusions: of of CRECS Main responsible subspecies present divergence ECS. Japanese been subspecies the the the have Japanese and of the across may ECS divergence for archipelago ECS for the route Japanese migratory hypothesis of the LDD major shelf and A the continental diverged LGM. CRECS supported emerged subspecies the the was the during Japanese between of route, subspecies that the inferred Japanese area colonisation inferred the was that source SDM past for candidate suggest The areas candidate the breeding networks CRECS. a suitable infer phylogenetic the reflects were to in Molecular possibly (LGM) population which maximum Results: a subspecies, glacial from Japanese last geolocators. A the light-level the maximum of of by the diverged. route climate tracked under subspecies variables the migratory Location: Japanese bioclimatic to A using (ECS). the projected constructed Sea colonisation. population was was China continental It subspecies East Japanese which algorithm. the the from entropy over for diverged examine LDD (SDM) to subspecies model via distribution (CRECS) reconstructed bird species Sea were migratory China subspecies ( Japanese East integrative three Shrike a the an its Brown of that conducted We region Taxon: predicts coastal Asia previous which species. the However, East bird hypothesis, in migratory divergence. LDD population in genetic a the to speciation from test vicariant contributes to from range approach process species’ this a phylogeographic discriminated outside not (LDD) have dispersal studies long-distance theory, In Aim: Abstract 2020 26, October 3 2 1 Takagi Aoki Daisuke archipelago Japanese the bird in migratory species a for divergence dispersal-driven long-distance supports phylogeography integrated Migration-tracking okioUiest aut fSineGaut colo Science of School Graduate Science of Branch Faculty Eastern University Far Hokkaido Sciences of Academy Russian University Hokkaido 3 4,* 1 1 AAOOHaruna SAKAMOTO , auaSakamoto Haruna , aiscristatus Lanius 1 ueioKitazawa Munehiro , 1 IAAAMunehiro KITAZAWA , ehd:Bt altp ewr n ut-ou eentokof network gene multi-locus a and network haplotype a Both Methods: ) 1 1 lxyKryukov Alexey , 2 RUO lxyP Alexey KRYUKOV , 2 n Masaoki and , 3 TAKAGI & Posted on Authorea 26 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160373183.39716449/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. aaeesbpce a nerdbtenteCESadteJpns rhplg costeECS. the the CRECS for across present route archipelago migratory the Japanese major and the A ECS and LGM. the CRECS the of the during between shelf subspecies inferred continental Japanese was emerged the subspecies the for Japanese that areas inferred breeding suitable SDM were The CRECS. reflects the possibly in geolocators. which light-level subspecies, the by Japanese infer tracked the Results to was of (LGM) route, maximum route species colonisation glacial migratory last past A A the candidate the of colonisation. a under climate diverged. of variables the area bioclimatic to subspecies source using projected Japanese candidate constructed was was It the subspecies algorithm. Japanese population entropy maximum the continental for which (SDM) model from distribution examine to constructed Methods Taxon China East (ECS). the of Sea region China coastal East the Location predicts the in bird which over population hypothesis, migratory LDD a LDD from via in diverged the (CRECS) speciation subspecies test Sea bird vicariant to migratory approach from Japanese phylogeographic a process integrative that this an conducted discriminated We not species. have studies previous However, Japanese the Aim from 19J21406) keywords: for (no. grant-in-aid and DA a Abstract to (JSPS). of and vi. Science support 16H04737) a of and with Promotion 16K14796 conducted the partly (no. for was MT Society Mari study to Nishida, This (C) Yusuke Kawahara, Chiba. Research Takayuki considerable Riku Scientific Kawaji, the Kajihara, and for Noritomo grateful Sato Hiroshi assistants: are greatly Ryotaro We field Professor Esashi, were daily use. Koizumi, to many Analyses us from Itsuro allowed various received kindly University. Professor Kakui help from Keiichi Hokkaido which Professor shrikes and course, computers, Kato Toru of Biodiversity throughput Professor M. the samples Keisuke high Ivan Koizumi, of with using Itsuro Red’kin, members Professor improved us from A. laboratory comments providing valuable Yaroslav and by for improved Nagata, Atsumi, greatly Ornithology Junco was manuscript for Endo, The Institute Sachiko regions. Yamashina Hara, and Seiichi Matsumiya, Tiunov, Hiroaki thank We Acknowledgements v. 0000-0001-7010-7338 P, Alexey KRYUKOV 0000-0001-8308-899X Masaoki, TAKAGI 0000-0002-5780-8487 Daisuke, +81(11)706-4464 AOKI number ORCID: telephone [email protected], address email Correspondence: * Russia 690022, Japan Vladivostok 060-0810, Sciences, of Academy Russian the 4 of Branch Eastern Far Biodiversity, 3 Japan 060-8589, Sapporo 2 Japan 060-0810, Sapporo 1 affiliations institutional Author’s iv. eateto aua itr cecs aut fSine okioUiest,N08 iak,Sapporo Kita-ku, Terrestrial N10W8, University, Asia Hokkaido Science, East of Faculty the Sciences, History of Natural Center of Department Scientific Federal Genetics, and Zoology Evolutionary of Laboratory Kita-ku, N9W9, University, Hokkaido Agriculture, of School Graduate Sciences, Environmental in Frontiers Kita-ku, N10W8, University, Hokkaido Science, of School Graduate Sciences, History Natural of Department nter,ln-itnedsesl(D)otieaseis ag otiue ogntcdivergence. genetic to contributes range species’ a outside (LDD) dispersal long-distance theory, In : rw hie( Shrike Brown : oeua hlgntcntok ugs htteJpns useisdvre rmapopulation a from diverged subspecies Japanese the that suggest networks phylogenetic Molecular : atAsia East : ohahpoyentokadamlilcsgn ewr fistresbpce eere- were subspecies three its of network gene multi-locus a and network haplotype a Both : aiscristatus Lanius ) 2 Posted on Authorea 26 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160373183.39716449/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. h iapaac fteln rdeldt iain pcain eefe aldteVcrac Hypothesis Vicariance the called hereafter that speciation; implies vicariant Strait), Tsushima to the led a currently LDD-driven over bridge is shift 1b). implying land there more range (Figure CRECS, (where the a is Japan of the of to hypotheses means from disappearance by Peninsula following the Colonisation Korean (ECS) two 2) the Sea 1a). from the route (Figure China bridge which of Hypothesis land East et along LDD which the open Saitoh and called indicate the 2011; population different hereafter help regional al., divergence; across P¨ackert where or which will et Colonisation 2015; from (CRECS) Russia), colonized, 1) al., predicting Sea was plausible. East system, et China archipelago This Far Dong 2017). East Japanese to (e.g. al., the the ranges et China of breeding Zhao northern region 2015; their al., Peninsula, occupy coastal populations Korean the Moreover, or (the on species 2017). glacial continent either Motokawa, during 2012; be Asian continent (McKay, could Asian endemics northeast animal East Japanese populations terrestrial the as Most continental from diverged 1998). source archipelago subsequently Ota, the they 1990; colonized and Ohshima, separated Japan periods, 2019; remained in Tada, parts the occurring & other of currently Itaki, while parts Matsuzaki, bridges, some of species levels, land 2015; periods sea via al., glacial lower continent et to During the due (Gallagher to lineage. present), connected migratory the system were breeding to a suitable archipelago ago of of a years Japanese speciation provides million endemism of 2.7 archipelago (approximately mode high Japanese Quaternary biogeographic the the relatively a 2015), identify and 2010, to al., paleogeography, which et within well-documented (Saitoh nature, lineages of passerine assumption insular migratory the its without 2018), to inferred Manica, 2017). be Owing & many Duke-Sylvester, hardly & because Rodrigues, have Tagliacollo, be could (Somveille, Schoolmaster, paleogeographical might speciation widespread (Albert, a This of and vicariance that processes continental tested.  phylogeographic are empirically their scenario be species thus alternative never bird an for has migratory explanations species,  sufficient currently migratory divergence provided of LDD-driven has Schluter, divergence facilitated vicariance & known change genetic While Weir previously of 2006). (e.g. that cases Drovetski, populations vicariance many & assumed new i.e. Rohwer, Pavlova, population, anecdotally and continuous Zink, Many have source formerly 2004; 1986). however, a the O’Connor, subdivided species, 2014; between barriers Gilroy, migratory barrier biogeographical & example, (Lees of For geographic distance population studies 2014). a increasing new Claramunt, phylogeographic with when a & et decreases (Weeks of vagrancy frequency (Harvey timescales divergence because divergence geological in expands, allows over genetic decrease that LDD preclude mechanism will of hence candidate frequency vagrancy and the a changes population is the 2014), it new change Gilroy, increase since effect & Paleogeographical the may Lees its vagrancy of see 2019). of of but isolation frequency determinant 1986; al. prevent high key (O’Connor, may A population their a it allopatric during 2000). is an whereas Polis, wind vagrancy of & by establishment of (Rose successful influenced vagrants frequency of destinations, receives chance the anticipated that instance theory, their population for In overshot have, a or that on 2008). past populations (Newton, drifted migratory migration range. birds, from known seasonal Weeks, mostly of species’ is & derives a case Pegan, outside speciation, and the well Auteri, vagrancy to in (LDD) Winger, called dispersal contribute long-distance 2005; is they to phenomenon Marra, leads how This & often ability and (Greenberg dispersal biogeography behaviour, High of migratory 2019). area animal studied to infrequently due an propensities dispersal High Introduction: vicariance text archipelago, Main Japanese vii. the Shrike, Brown the modelling, of bution understanding our improve should Keywords: species. models migratory vicariance in of phylogeographic and subspecies new histories LDD the a phylogeographic discriminating of provides and the framework divergence Our region, for this inferred population. successful in was Japanese for the scenario Vicariance responsible from been continent population. have Asian new may northeast ECS the the the of of isolation expansion and and Shrinkage colonisation Shrike. Brown the of subspecies conclusions Main ih-ee elctr ogdsac ipra,mgaoyrue hlgorpy pce distri- species phylogeography, route, migratory dispersal, long-distance geolocator, Light-level u nertv prahspotdteLDhptei o iegneo h Japanese the of divergence for hypothesis LDD the supported approach integrative Our : 3 Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. h yku n h hlpie r cuidol ynnbedn ie irtn n wintering) and migrating Since (i.e. 1c). non-breeding (Figure by range distribution only wider occupied its are and of GenBank Philippines coverage from the a genes mitochondrial for and of 2007) Ryukyus sequences Hebert, database the used & for also (Ratnasingham We East BOLD Far obtained. Russian was samples the genetic from for samples prefectures blood 2019, Nagano and in site tissue confirmed). the collected to not We was return not geolocator did bird’s haplotyping and this and 2018 procedure of Laboratory in (2003) presence Takagi breeding (the by before uncaptured report disappeared remained previous rings the it Deployment a leg of 2018. so with 5% with in compared marked exceed site when not male study rate did breeding One return independence; g) the the 1.1 for to change (< returned test significantly system (chi-square (32%) not the birds strings did Eight of harness tags 2013). mass leg-loop al., of total with et the (BioTrack) (Bridge that tags mass ensured geolocator We birds’ MK5740 1991). attached Tipton, We & rings. (Rappole leg of with them routes marked migratory the track To procedure field species. paleogeographical and migratory species a the Study of discuss divergence on we genetic based scenario, the Methods: Shrike to and this Brown contributed Materials From have dated the approach. could a of integrative LDD With divergence which 1997). our the Worfolk, in from of & context scenario Lefranc obtained phylogeographic 1c; results (Figure a the Island provided Sakhalin we subspecies. of tree, three most phylogenetic its and continent of Asian archipelago, distribution northeast breeding Japanese the the ( to the Shrike given and Brown in hypotheses from the these Peninsula passerine, Korean test migratory the to over long-distance expected a is studied route We migratory during a suitable 1b). and been (Figure have between SDM, to archipelago the bridge predicted archipelagic Japanese by are land the Peninsula For period the is Korean disappeared. glacial the because or and or a continent, route (Figure within, formed China Asian northern repeatedly likely migratory nests current archipelago northeast been either genetically a Japanese the have population, the population and in to and archipelagic SDM, Peninsula population expected the Korean the the is the that by from, CRECS predicts divergent period the well hypothesis and glacial population, not vicariance archipelago the archipelagic The Japanese the during (2) population For the suitable in networks. archipelagic 1a). between phylogenetic hypotheses been the ECS by between have vicariance the inferred split to and across be genetic LDD predicted will a CRECS the is that the from CRECS predicts in predicted population hypothesis be differently a LDD may be and The colonisation system. can (1) past this components framework. in of three this barrier modes 2008; the sea both Newton, present of Therefore, 2014; a Results 2019). Smith, migratory over the & al., route Fuller, Second, migratory et (Alvarado, 2019). the Winger range in al., in 2006; breeding LDD et reflected Moritz, the reflect Winger in & may 2008; for shifts (Newton, barrier Hijmans, archipelago past absent geographic Ruegg, Japanese retraces or large the & smaller partly a to was also (Zink over barrier route route route occurred the colonisation migration when Asian colonisation past existing the suitable past which the an and the also for from archipelago First, candidate Japanese was reasons. area the a following that between potential as the barrier range a interpreted sea continental a be as over (20 may Any interpreted route continent ago migratory 2011). be years avian al., An 20,000 may 2017). ca. et period Gardner, (LGM), (Elith glacial maximum infer distributions a glacial can SDMs species last during 2012). the present genetic Mardulyn, during 2006; from Japanese intraspecific species Bryant, the kya) & of of of (Huson distributions relationships data colonisation breeding multi-locus disentangling past suitable and the for haplotype in infer informative model both to are distribution variations geolocators, networks species light-level a Phylogenetic using networks, archipelago. tracking phylogenetic migration of and means by (SDM), phylogeography integrative conducted We .c superciliosus c. L. .c lucionensis c. L. .c superciliosus c. L. χ 2 .1 f=1 .4.Fu ae ottertg eoerecapture. before tags their lost males Four 0.74). = p 1, = df 0.11, = n rmteRuysfor Ryukyus the from and resi h RC,and CRECS, the in breeds 4 ecpue 5autml hie nHkad and Hokkaido in shrikes male adult 25 captured we , aiscristatus Lanius .c cristatus c. L. .c lucionensis c. L. .c cristatus c. L. .c superciliosu c. L. ,a u rtattempt first our as ), rmHkad and Hokkaido from , oa f95 of total A . resi the in breeds breeds s L. Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. fteaalbeWrdlmdt vrin14 imn ta.20) nyoevral rmec arof pair each from variable one only the domain. 2005), of modelling distribution al. the present et as the Hijmans defined include was 1.4; to data (version ( environmental data variables data the environmental this correlated WorldClim in available the and that integrated the subspecies clipped area be We continental Of to of need the regardless 2011). area infer Shrike continental al., to Brown the et is and (Elith purpose archipelago current Our model the between data. for differences coordinate ecological suitable final been the occurrence have migrating with one of might S1.1). model only integration (Figure include a avoid archipelago to constructed to Japanese thinned We August) the were covering to coordinates square (May final km season processes, 20 breeding quality-checking per few the a to After only limited birds. hereafter were In- Biodiversity prep.) Records Global (in data. from bounding of colleagues data polygon downloaded distribution his by we A presumed conducted and 2019 the http://doi.org/10.15468/dl.igj5uw). May Surveys Kitazawa https://www.gbif.org/, 12 National (M (GBIF; on the Additionally, Facility literature on formation data’). and based ‘review Japan localities as of to breeding referred Environment of of summary a Ministry from the obtained were of Japan range in breeding the settings. modelled other We for (2018) Xie, Drummond, al. modelling (Rambaut, et software distribution Aoki Species 1.7.1 chains. followed We pre-burn-in v. thousand Tracer 2018). Markov 100 Suchard, through with 2008). checked & states Schluter, was Baele, million & parameter Weir 50 each 2016; for Fuchs, for proceeded & Convergence sampling ( Lanfear, (MCMC) gene (Nabholz, each Carlo passerines for Monte bychain selected are was shrikes determined G since models + justified HKY substitution twowas 7; analysis, best BEAST v. the the MEGA with In on cytb Criterion partitions 2014). Information different al., Bayesian lowest et to (Bouckaert the assigned 2.4.8 independently v. consisting were BEAST the dataset genes using for A method file of (BI) sequences. sequences input inference mitochondrial Bayesian concatenated an two of as the haplotypes used using unique by was of phylogeny which mitochondrial 2006), reconstructed Bruneau, We & uncorrected (Joly calculated 1.03 and analysis. v. loci NeighborNet POFAD four using of all samples network four of individual multi-locus the sequences a combined with we constructed individuals Then, also included We only ( We samples. pairwise 108 2006). & from Bryant, Forster, bp) & Bandelt, (521 5.0.0.3; ( COI NETWORK loci (using partial four network using haplotype 1999) (MJ) Rohl, median-joining analysis. the a PHASE in constructed and used al., We reactions, not et PCR were (Stephens primers, 0.5 ABI3130 about 2.1.1 below details analyses or values v. Phylogenetic for ABI7130 support S1 PHASE with an Appendix used inferred a See either we determine Haplotypes To for analyses. sites, on 2003). 2009). following heterozygous Donnelly, only run (Filatov, multiple & software sequenced was 3.5 Stephens with were sequencing 2001; v. introns ProSeq introns nuclear Automated using of autosomal aligned haplotypes were S1.1). The Sequences (Table (ABI). (PCR). Analyzer samples (TGFb2)) reaction Genetic intron-5 the chain 2 of beta polymerase factor subset growth by transforming amplified (MB), (Qiagen). intron-2 Kit were (myoglobin Tissue introns & autosomal Blood ( two DNeasy b and using cytochrome samples (complete tissue genes and mitochondrial blood Two from extracted was DNA genomic Total lucionensis lucionensis c. n .9frCI.Apiaino h tnadaincokrt for rate clock avian standard the of Application COI). for 0.19 and p cytb itne mn eune nec ou sn EAv Kmr tce,&Tmr,2016). Tamura, & Stecher, (Kumar, 7 v. MEGA using locus each in sequences among distances ) e al 11frdtisaotsmlsadsequences. and samples about details for S1.1 Table See . O,M n Gb)udrteNihoNtagrtm(sn pisTe .44 Huson 4.14.4; Tree Splits (using algorithm NeighborNet the under TGFb2) and MB COI, , Lfac&Wrok 97 eeigas 96,te eeue srpeettvsof representatives as used were they 1996), Severinghaus, 1997; Worfolk, & (Lefranc | r | > .)wsue,rsligi ee aibe:bo,2 ,5 2 4ad15. and 14 12, 5, 3, 2, bio1, variables: seven in resulting used, was 0.7) p .c superciliosus c. L. .c superciliosus c. L. dsac arcst rdc tnadzdgntcdsac arxamong matrix distance genetic standardized a produce to matrices -distance .c superciliosus c. L. codn oLfac&Wrok(97 a sdt lpthe clip to used was (1997) Worfolk & Lefranc to according sisbedn aia uigteLM hrfr,any Therefore, LGM. the during habitat breeding its as cytb cytb 5 n O a rprdfrte eosrcinb the by reconstruction tree for prepared was COI and n rjce tit h G.Dt noccurrence on Data LGM. the into it projected and ,adprilctcrm xds uui (COI)) I subunit c oxidase cytochrome partial and ), cytb .15lnaemlinyears 0.0105/lineage/million , α .0for 0.10 = .c. L. Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. tsooe ie hna nisatnospitaogamgaoypt,tefre ilb niae with indicated be analyses will Phylogenetic former time the past more path, of spend migratory route a birds Results: the latter. along Because retrace the point tracks. to than instantaneous migratory birds probabilities an three expect higher at the we relatively than presented where of we sites interest paths and stopover of median of individuals, we-at region inferred three in probabilities a paths the also involved posterior in final among We uncertainties the distribution means the colonisation. probability large standardized their and a calculated we Regarding iterations, cell, as 2019), iterations. raster them three al., 0.08 each three with et between on with chains estimates (Lisovski value samples 120,000 location geolocators ‘tol’ 15,000 ran by a last we estimations setting the tuning, migration by by fine autumn periods determined and the equinox burn-in re slightly during the As We recording around 0.1. periods. estimations stopped and movement latitudinal geolocator for interpolated allowed its details). We were for because S1 areas #V5604-025 only Appendix land designed (see bird and was and period archipelago for periods sea equinox Japanese stationary analysis both for the movement our mask while between no spatial thus sea land modified a the location, terrestrial Therefore, single cross land. include a must on to model, at stopover birds group must records mask, the and as probability for In continent of treated a S1.2). the m/s are For (Table periods 12.9 results period defined. for the of stationary was distribution of a speed model interpretation gamma for air our grouped a influence average times greatly with the twilight not prior for did allowing priors speed that determined flight found 0.3), a = set was discrimination rate we collurio for 13, model, threshold = movement probability the (shape applied A was movement For data. twilight ‘GeoLight’ 0.9. fitted spatial the in We and to from function model period. ChangeLight set periods movement the of calibration these a twilight between the periods, define periods To movement discriminate as The twilight. and to calibration deployment of stationary masks. geolocator detection in for of spatial after times separately distribution days and masks twilight error 26 an model, actual of as movement data distribution and twilight gamma a determined locations used model, We between estimated tag. twilight the deviation each refines the the model components: incorporates This ‘SGAT’. the three model called in of approach, for implemented modelling transitions framework means statistical sunrise Bayesian a by and a incorporated sunset We in determined script 0.5. We model’ of R (2019). thresholds ‘group an intensity al. prepared light We et by 2015). Lisovski (Lisovski dates Lisovski, by 2.0.0 specific & provided version Sumner, manual ‘GeoLight’ (Wotherspoon, the package 0.1.3 following R version by ‘SGAT’ the and in 2012) analysed Hahn, were & geolocators light-level detailed from the retrieved for Data S1 Appendix (See analysis analysis extrapolation route this and Migratory from calculated analysis). values also SDM negative the was by on (MESS) indicated system procedures surface regions climate (MIROC-ESM, to similarity community model F environmental restricted climate it the Multivariate was Max-Planck-Inst. on then 2013). models: research the interdisciplinary and Lo, climate and for different predicted, & 2004) model three was Emori, the data from 2011), & environmental distribution (2005) al., LGM Hasumi present et The The Gent al. transformation. (CCSM, et cloglog model Hijmans AICc. using regularization by data lowest a environmental drawn with the LGM were feature, by the hinge to selected The model projected assesses the was 2014). was were it as al., since 1.5, points et used cross-validation background of for (Muscarella was data 10,000 methods multiplier option partition other regularization above, ‘maxent.jar’ to than and used defined The entropy better was hinge) domain transferability maximum method tested. and modelling ‘block’ Combina- were the The quadratic, geographical 0.5) randomly. execute and settings. the of sampled From linear several to (increments of 3 of 2014) algorithm. combination to range al., model a 0.5 a et (linear, from across ranging classes (Muscarella 2006) multipliers feature 0.3.0 Schapire, three & of v. Anderson, tions ‘ENMeval’ (Phillips, package algorithm R (MaxEnt) the used We Buee od,20) ecnutdasniiiyaayi o h am itiuin n we and distribution, gamma the for analysis sensitivity a conducted We 2001). Boldt, & (Bruderer 6 rMtoooi lmt oe MIEMP Liepert (MPI-ESM-P, model climate Meteorologie ur ¨ Lanius Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. tpigsoemne ln h ykuilnsfo h RC rTia a lob eslkl.This likely. less be also in may colonisation Taiwan LDD or 3). CRECS (Figure the SDM from our islands projected et separating Ryukyu we Matsuzaki gulf which the 5; the to (Figure along LGM estimated, wide manner the relatively was stepping-stone to was divergence a compared CRECS the 1998), the Ota, which and 2019; landscape. Peninsula around terrestrial al., Korean periods a the 4). over glacial archipelago, (Figure dispersal Japanese the normal ECS the via during the for population across because, a habitat archipelago ar- is of Japanese breeding expansion This and the gradual glacial and reflect southern suitable cannot CRECS the results the 2), Our between between (Figure observed Brown split was networks the route phylogenetic gene of migratory A the divergence 5a-b). genetic in 1a, for inferred superciliosus hypothesis (Figure was LDD archipelago clades the Japanese chipelagic supported the approaches in three both Shrike the that from revealed results geolocators The Flores. and retrieved Java detour successfully on not two specifically did Islands, the and Discussion: Sunda median regions from the two the data in these and wintered between The map had ECS probability of Peninsula. shrikes the The part Korean Taiwan. across western migrated northern the the birds to in over cell that CRECS both to suggest the individuals mean tracks due three along higher migratory continent the and estimates, the among archipelago location observed on Japanese with were recording the involved locations stopped uncertainties migratory tag Despite for individual deployment. One probabilities three after routes. months for spring three inferred and failure were autumn their routes between migration observed spring and superciliosus autumn c. framework, Bayesian model. predicted the our not Under on were based islands LGM, Ryukyu analysis the the route during of Migratory species Most habitat the LGM. breeding for suitable the which suitable during within be archipelago, remained to Japanese of largely the area but in present for coastal southwards than the lower the habitat receded to relatively that breeding corresponding be inferred suitable range to 3b-d) continental estimated be was (Figure inner to LGM an predicted the and were of shelf, known CRECS, continental models taxon’s ECS climatic submerged the three currently to reflected the model 3a) the (1997). (Figure of without Worfolk Projection areas habitat & suitable suitable Lefranc presence estimate to to of training evaluated according prediction was Minimum range model present breeding 3). the The and (Figure 1.9% overfitting. were algorithm problematic localities MaxEnt test for the rates using omission variables bioclimatic non-correlated of distribution within breeding present (numbers The Pleistocene the S1.2). Middle and (Figure northern the modelling tree the during distribution density). BI while Species Mya, posterior Pleistocene the 0.47] highest Middle 1.10] by 95% [0.20, to [0.55, indicate Shrike 0.32 Early 0.80 brackets Brown late around around square the clades, the diverged archipelagic/northern to of clade the corresponding archipelagic lineage and (Mya), southern basal ago the years the between million as occurred split inferred to first was appeared The 2b). clade individuals (Figure Two clusters supported by southern loci. was northern only The nuclear structure and separated and similar southern was mitochondrial A the (H1) the between haplotypes. haplotype both intermediate major clade including major be archipelagic network northern its the multi-locus The and of the gaps. clade one by mutational southern from nine positions the with subspecies, mutational from observed two three distant was the most clades phylogenetic reflected genetically archipelagic BI was possibly and the clades southern in southern 2a). the clades (Figure between and distinct range northern, superciliosus as species’ archipelagic, c. supported the were L. the from which S1.2); sequences groups, 108 (Figure genetic using tree three constructed was inferred COI network of This network haplotype MJ An a siae ohv xse rudteCESb h D Fgr ) n t current its and 3), (Figure SDM the by CRECS the around existed have to estimated was Fgr ,Fgr 14.Fl nuldt eertivdfo w as n iiaiywas similarity and tags, two from retrieved were data annual Full S1.4). Figure 4, (Figure , .c cristatus c. L. and , .c superciliosus c. L. .c lucionensis c. L. 7 a oeldbsdo rsneol aaadseven and data presence-only on based modelled was epciey(iue1) nti ewr,asplit a network, this In 1c). (Figure respectively , .c superciliosus c. L. utblt o hs regions these for Suitability . .c. L. L. Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. Lfac&Wrok 97.Atog hi atpplto yaisadgn o ed ob directly be for scenario to new needs a flow least, at gene provides, and our approach integrative dynamics in continent our shown population the scenario, pair, past hypothetical on our clade introgression their refine distant presumed Although to with most 1997). estimated contact Saitoh the Worfolk, 2018; secondary between & al., their individuals et and (Lefranc reflect Aoki archipelagic intermediate 5d; possibly the genetically (Figure network, of its distribution The multi-locus expansion vicariant expanded northward 2010). present 2003; subsequently and the al., (Hikida bridge in and predicts et resulted land hypothesis period, have the colonisation could glacial of reverse clades Disappearance a the northern 2015). as during Kim, 5c), Peninsula bridge population Korean (Figure & the land Nishiumi period small colonised interglacial interglacial a have a subsequent an may over suggests the during population archipelago network a range during that northwards, Japanese haplotype suggest probably pattern we the this star-like Therefore, range, of from a 1987). its al., and structure expanded et Russia, The nor- (Avise that in the period 2a). localities period of of (Figure glacial range haplotype found the wide COI was during a major population from clade a archipelagic samples this Moreover, the among of China. of shared was part northern suitable (H1) that current highly clade implies and be thern This Peninsula to China). Korean (current predicted the coast were ar- continental colonized time, southern the China, the or northern from at east current continent diverging the and the clade peninsula to northern Korean connected present the for archipelago the for of Japanese LGM, hypothesis size the the During the a with vicariance. regions. in supports by changes these description clade between Thus, chipelagic following divergence 2014). LDD-driven Gilroy, the for & contrast, responsible (Lees archipelagic In been increases distance the the have island of as may the rare isolation barrier increasingly of to facilitated geographic becomes breadth have area islands a 5a; the could source to vagrancy continental This (Figure period, since the 5b). CRECS interglacial CRECS the from (Figure subsequent in the km a that 1,000 from from During propagule population almost 1967). sufficient shrike archipelago et to Wilson, in (Senzaki Japanese expanded & resulted CRECS ECS the MacArthur have the the 2012; in may from al., therefore, arrived et 2008) landmasses, provides which Gillespie Newton, two which migrants), conditions; the 2010), (accidental anticyclonic of Liu, numbers and traveling proximity (birds & winds Increased overshooting Wu favourable to many 2019). due Lu, of to al., probably records (Xu, are due vagrancy continental spring Present forest far emergent during 1997). archipelago Worfolk, sparse the too Japanese al., & with analysis; the (Lefranc et sea in Shrike grassland SDM (Matsuzaki lower species Brown by Pleistocene migratory our the the Middle covered for with to because habitat was line breeding Early periods ECS suitable in late ECS the glacial the are the in of records during Meanwhile, shelf Paleopalynological shelf history. barrier continental 1998). the species’ biogeographic of Ota, the a emergence 2019; throughout as the period to effective glacial led less level a became during and open shrank remained has different across ECS that be processes The can is divergence interpretation results different divergence an involves the Such suggesting that twice. of the scenario barriers. possibly least interpretation hypothetical from geographic at our 2), following distant occurred Therefore, the continent (Figure most by the population. clade be explained and archipelagic this continent, archipelago archipelagic to the from the Asian found the from between the diverged was divergence clade to have of clade northern close part may northern the the genetically eastern The population of that and the Pleistocene. archipelagic suggesting in clade Early the S1.2), located late southern hypothesis, (Figure the been Shrike LDD have around Brown the may population the Given species of CRECS. this lineage of including basal area the breeding represented ancestral clade southern reflect The Shrike results ECS. Brown our the the aligns across that of migration since subspecies imply scenario inferred phylogeographic Meanwhile, migratory we Hypothetical the 2016). Japanese framework, 5), a Higuchi, hypothesis-testing (Figure of Hijikata, our period divergence Koike, within LDD-driven this 2006; the Therefore, unlike during al., 4), CRECS prediction. (Figure et the our them unsuitable (Shiu to along with been inferred connected have species not was to other was Taiwan predicted route for were northern migratory islands reported the Ryukyu and routes the 3b-d), the .c cristatus c. L. Fgr 13.TeJpns rhplg a rdce ob oesial hneither than suitable more be to predicted was archipelago Japanese The S1.3). (Figure 8 Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. h rdtoa iaineseai ugssta h 0 mwd tatbtenteKra eisl and Peninsula Korean the example, For between strait it. by wide km explained 100 be the adequately suitable that not provided suggests may has scenario events scenario vicariance divergence this traditional While some gene- the 2004). cases, in Schluter, many vicariance & assumed Weir for that 2004; explanations species (Hewitt, migratory populations for shrikes scenario isolated divergence as rating a such illustrated have passerines studies speciesPrevious for migratory also of process 2017). unfavourable divergence Thorup, conditions, LDD-driven Arisawa, be & Yamaguchi, wind Possible Klassen, would 2016; spring Onrubia, al., conditions for Pederson, et suitable These Tøttrup, (Nourani unstable 2001; specifically 2012). were It (Alerstam was ECS Higuchi, 2016). Strait the Higuchi, & Tsushima over & the cross strengths Shimada, Manda, over and to Yamaguchi, Peninsula directions route (Nourani, wind Korean a archipelago when the that Japanese around shown the detours enter for been route to shown has migration channel been spring sea has route its spring narrow phenomenon whereas a ancestral which migration ECS Buzzard one in the loop Honey retaining crossing This Oriental migration, involves by the 2001). 2008). loop (Newton, of evolved (Alerstam Generally, conditions population have determinant environmental current a 2012). important to to an al., adjust thought to is et is other Wind the the divergent, Tøttrup deriving with independently are while 2012; optimized colonisation should routes is al., retracing seasons route migration et different migratory autumn a in (Stanley focal and If passages route route. the upon the focal the that pressures the across shape selection migration of implies routes spring conservatism different This idiosyncratic and the environment, autumn that support 3b-d). present between view may similarity our (Figure 4) Second, supporting conserved. (Figure LGM population LGM, been ECS have archipelagic the the barrier present the before large during change the for a distribution even over to habitat a breeding expansion archipelago traces suitable post-LGM route Japanese that migratory the the shown was trace have in which should we throughout remained glaciation, routes contrast, labile to migratory be By to response and range. needed migration LGM breeding history major that the implied evolutionary a This glaciation. during species’ 2017). probably Gardner, severe sheets from a was & Reverting (Zink ice residents experienced 2018). analyses al., sedentary by SDM that by et covered becoming inferred Sokolovskis region 2006; previously to al., any plausible regions migratory et more include Ruegg inhabit being be 2006; Wayne, not that to & Mil´a, interpretation species does Smith, 2017; our al., (Hach´e used system and et have (2019) our studies al.’s First, et Previous the counterview. Winger to believe the optimization we Helbig, of than 2017). reasons, Berthold, two Gardner, result 2011; following & a (Alerstam, the Zink is For colonisation 1998; ECS migratory Sutherland, past the 2019). consider 1992; reflect al., across to Querner, et not route & Winger is does migratory 2007; Mohr, view and (Pulido, observed of dominant selection conditions the part natural environmental the that interpret to However, present claim to subjected colonisation. easily could order are past one in that Thus, of traits 2019) labile route al., highly the et as highly routes as (Winger are data species histories migratory tracking evolutionary long-distance our obligate their least of at throughout routes is idiosyncratic traits that route persistent view crossing population. recent sea the archipelagic taken focal the have We the for that routes guarantees major further statement the Although their statement. during of their needed, observation one with is concur direct data geolocators on geolocator of Our based deployment Islands. that, Zhoushan the stated or (1997) Province Worfolk Jiangsu & population- geolocators Lefranc light-level many for of However, limitations migration, analysis 2019). limited methodological the the al., recognized too from of et is because inferred far (Lisovski routes 4) routes (Figure is migratory Migratory uncertainties in large ECS 2012). variation Stutchbury, included individual the also & entire because McKinnon, across the required Fraser, for Shrike is MacPherson, (Stanley, route data Brown tracking pathway the the our colonisation of of of past universality interpretation the the route for thus migratory proxy inference, the a level as on route data migratory Shrike. Our a Brown the of of use interpretation the phylogeographic for better Justification a and 2017) (Motokawa, region this .c superciliosus c. L. ya es 0 mars h e rmJpnt h os fChina’s of coast the to Japan from sea the across km 700 least at fly ensptilorhynchus Pernis 9 .c superciliosus c. L. reigi aa.Isatm migration autumn Its Japan. in breeding ean nla.Careful unclear. remains Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. rbblte flcto siae ftetrebrsfrec atrcl r niae yclu rdto from gradation colour by indicated are cell raster each for birds three the of estimates terrestrial location level. of the probabilities sea that lowered the Note multivariate 4 to by coastlines. the Figure indicated due present whereas extrapolation LGM indigo, indicate strict the to of lines during green that Black expanded Glacial yellow, is Last landmass analysis. from area the black increases surface for The grid similarity models absence. min environmental climate as 2.5 different determined a three was for (b-d) area Suitability and grey kya). climate, present 20 the (LGM, (a) Maximum to projected was haplotypes model mitochondrial under their 3 loci (Figure which four Figure tree to the inference using clades black Bayesian Shrike to a Brown the correspond and the in shades for bar, belong. circles found Coloured constructed one of network algorithm. clades by Colours multi-locus NeighborNet to indicated The samples. the analogous was (b) of Clusters indicated. gap number vector. are mutational the S1.2) median to One a proportional collected. indicates is were size node samples its where and regions haplotype indicate unique subspecies. a between indicates median- zone circle hybrid the subspecies presumed presumed in a 2 of indicates ranges inferred Figure indicate region breeding breeding haplogroups indicate lines striped from colours indicate The dotted Land samples (2000). 2a). colours represent and Worfolk (Figure following their triangles COI Pleistocene, of and and network Middle Circles haplotype respectively, the joining localities. localities, to sampling the non-breeding Early for DNA and (c) possibilities the various coastlines. during are present areas there the Because terrestrial predicted 2007). represent We al., 1c. regions et Figure of (Zhang in gene position Asia subspecies genetic Predicted South-east to Shrike. around correspond (coloured Brown distributed regions Colours are the glacial shown. suitable in are and hypotheses hypotheses circles), that two open vicariance with the (b) (lines under routes and circles) migratory (LDD) panes), left dispersal (upper distance networks long (a) in 1 of animals. importance Figure text: other relative the and the in birds 2018). embedded of migratory Figures al., of understanding our LDD ix. speciation of our et the the usability facilitate taking Sun the in revisited will of vicariance 2004; be verification species to (Hewitt, Further continental should LDD several 2008). barriers history in Fadeev, among these & ranges) geological approach over Drovetski, mountain their integrative Reeves, species and (e.g. migratory during account deserts, in the into shape divergence Like seas, hypothesis genetic and 2017). as the al., size (such of et changed barriers Some Winkler also geographic 2015; speciation Attention have some Marra, and diversified. & distribution system, areas have for Studds, our phenomenon species Dudash, in important (Rushing, migratory an ECS as species most colonisation migratory where and continental regions LDD of to continental paid for consideration comprehensive been that important more recently believe We has a also region. benefited is this framework in LDD our species of migratory in of vicariance species. mechanisms from diversification migratory a of LDD of understanding discriminating divergence a that to provided contributed showed have successfully to also We paleogeography which framework. We and within testing LDD system hypothesis how a for suitable under scenario a divergence hypothetical provided genetic explanati- species of bird alternative mode migratory have 2015). the its Japanese discriminate al., species be a et migratory using to (Warren a approach most likely integrative it of for is Our test establishment distribution LDD to and continental of opportunities 1990), the consequence the Graves, on a hindered & based as probably Gotelli frameworks area (e.g. traditional distant However, species more ineffectively on. bird the a would volant from from barrier highly small mammals population a a of new such of populations perspective, movement ecological archipelagic the an of From restrict divergence 2017). Sato, genetic 2012; deep (McKay, continent caused archipelago Japanese the .c lucionensis c. L. irtr otso he individual three of routes Migratory a einjiighpoyentokcntutduig51b fteprilCIgn.Each gene. COI partial the of bp 521 using constructed network haplotype joining median A (a) siae utbedsrbto for distribution suitable Estimated rdce ooiainrue(lc ros n xetdrslsfo nertv approaches integrative from results expected and arrows) (black route colonisation Predicted .c cristatus c. L. ersnstebsllnaeo h rw hiesnecoerltvso hsspecies this of relatives close since Shrike Brown the of lineage basal the represents nteLDhptei,w i o rsn ti iue1.Ge coloured Grey 1a. Figure in it present not did we hypothesis, LDD the in .c superciliosus c. L. .c.superciliosus L. 10 rudteEs hn e.Ma posterior Mean Sea. China East the around o ieettm eid;aconstructed a periods; time different for Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. iue2 Figure pane arrows and each 1 route migration Figure in and circles the Coloured lines indicate archipelagic circles (1998). populations. hatched open the Ota of with The following movements Lines both periods, lineage. indicate distributions. each inter/glacial of of geographical previous populations vicariance the present Korean ancestral in caused indicate the their coastlines colonised expansions predicted in population Northward the archipelagic resulted indicate the archipelagic (d) and of the bridge. part clades of retrace China land period, to northern isolation glacial shaped East a Increased was later (b) the over route a migratory Pleistocene. In across Peninsula Its (c) Early divergence. LDD its route. late facilitated via colonisation the ECS the archipelago the around of Japanese period expansion through glacial the population a colonised in population (ECS) ancestral Sea migrations The spring (a) and Shrike. Autumn respectively). respectively. 5 sites, lines, Figure hatched stationary and and routes solid migratory migrating by inferred their indicate indicated of are dots tracks median red indicate segments and line with (white Dots (low). indigo to (high) yellow ceai rsnaino h yohtclpyoegahcseai fdvrec nteBrown the in divergence of scenario phylogeographic hypothetical the of presentation Schematic 11 Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. iue3 Figure 12 Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. iue5 Figure 4 Figure 13 Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. yaiso irtr iie clg n vlto,41) 3456–3469. 4(17), evolutionary Evolution, the elucidate and methods Ecology tracking Integrative divide. (2014). migratory B. S5–S23. a T. 152, Smith, of Ornithology, & dynamics L., of T. Journal Fuller, 319–331. H., revisited. 209(3), A. Alvarado, migration Biology, bird Theoretical Optimal of Journal (2011). T. migration. 167-182. Alerstam, bird 66(2), on Biology, in displacement Systematic Detours Barrier biogeography. (2001). (2017). continental M. T. of S. Alerstam, theory Duke-Sylvester, a & Toward V., Tagliacollo, landscape: R., neutral D. a Schoolmaster, S., J. Albert, data (submitted raw repository the data and References: at scripts available xi. R are S1.1). modelling https://doi.org/10.5061/dryad.cfxpnvx2j). Table distribution DOI in species with listed DRYAD and are to analyses numbers route (accession DDBJ migratory at for available is data Genetic statement: availability Data x. 14 Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. nteseito rcs.Ana eiwo clg,Eouin n ytmtc,50:75-95. controls Systematics, Demographic and isolation: Evolution, reproductive Ecology, Beyond of (2019). Review temperate L. Annual of D. process. Diversity Rabosky, speciation Palaeovegetation. & the (2001). S., on Singhal, C. G., I. M. 129-130. Prentice, Harvey, 413(6852), & Nature, H., Alexandra, Asia. Takahara, east for . G., . in Implications . plants Yu, range: D., P., breeding Stralberg, S. Canadian S., 6078–6088. its Harrison, C. 7, across Davis, Evolution, songbird T., and migratory M. Ecology a Hallworth, units. of conservation H., Phylogeography Maryland: Proctor, (2017). 437–443). M., C. (pp. B. E. migration M. of E. evolution and Villard, Hach´e, ecology S., Greenberg the Press. R. worlds: University In two synthesis. Hopkins of A Johns biology: Birds islands. bird The (Eds.), land-bridge migratory Marra on of P. renaissance species P. The Long- avian (2005). & P. of (2012). P. Marra, occurrence K. & the R., G. and Greenberg, size Roderick, Body 315-325. 47-56. R., (1990). 17(3), 27(1), M. Nikula, Biogeography, R. Evolution, of Zhang, G. I., and Graves, Journal Ecology C. . & in . Fraser, J., . Trends N. M., R., testing. Gotelli, J. hypothesis S. Waters, for Jayne, framework 4973–4991. G., C., a 24(19), B. E. dispersal: Climate, Hunke, Baldwin, distance of M., G., Journal M. 4. R. version Holland, Gillespie, model J., system L. climate Planetary Donner, community and The G., Earth (2011). Danabasoglu, in recent R., Progress to P. Pliocene approach. Gent, The multi-proxy (2015). a W. P. Currents: Hoiles, 1–23. Tsushima & 2(1), and I., Science, Koizumi, Kuroshio T., the Itaki, soft- Y., of ProSeq3 Iryu, history with A., Kitamura, datasets J., multigenic S. of Gallagher, analysis explanation genetic statistical 3189–3190. population A 25(23), and (2011). Bioinformatics, Processing J. ware. (2009). C. 43–57. Yates, A. 17(1), & D. Distributions, E., Filatov, and Y. Diversity Chee, Dud´ık, ecologists. M., T., for Hastie, MaxEnt J., of S. Phillips, J., 312–325. Elith, 157(2), Ibis, data. DNA multilocus and 143, Ibis, Flycatcher speeds. Alstr Narcissus of M., measurements Wei, radar L., (2013). I. Dong, W. birds: of D. Field characteristics Winkler, Flight of (2001). & Journal A. 178–204. B., geolocation. Boldt, light-level R. & MacCurdy, of B., Bruderer, review M., technical R. A Gabrielson, birds: 121–137. A., migratory 84(2), Contina, Ornithology, small F., tracking 1–6. J. in 10(4), Kelly, Biology, Advances Computational S., PLoS E. analysis. evolutionary Bridge, Bayesian for platform behaviour software migratory K A of 2: J., microevolution BEAST Heled, Rapid 668–670. R., (1992). 360, U. Nature, Bouckaert, Querner, species. & bird G., wild Mohr, a J., in A. Helbig, phylogenies. P., intraspecific Berthold, inferring 37–48. for 16(1), networks Median-joining Evolution, N. and (1999). Saunders, and A. Biology & Rohl, genetics Molecular A., 489-552. & P., population C. 18, Forster, Reeb, between Systematics, J., H. E., and bridge Bandelt, J. Evolution, DNA Ecology, Neigel, mitochondrial of T., Lamb, Review the E., Annual phylogeography: Bermingham, Quaternary-related systematics. Intraspecific M., R. (2018). (1987). Ball, H. J., C. Arnold, Suzuki, ( C., 1087–1097. & Jay J. 159(4), S., Avise, Ornithology, Eurasian of Lee, the Journal of I., region. dynamics Nishiumi, Sea population P., circum-Japan parallel A. and Kryukov, differentiation G., genetic Kinoshita, D., Aoki, ieuanarcissina Ficedula m . un,X,Oso,U,Siea . hn,G 21) aooyo the of Taxonomy (2015). G. Zheng, . . . Y., Shigeta, U., Olsson, X., Huang, P., ¨ om, het . aga,T,W,C . i,D,...Dumn,A .(2014). J. A. Drummond, . . . D., Xie, H., C. Wu, T., Vaughan, D., uhnert, ¨ ope:A nertv prahuigmrhlgcl bioacoustic morphological, using approach integrative An complex: 15 arlsglandarius Garrulus nthe in ) Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ucrla . aat,P . oe-uri,M,Bra .A,Ks,J . rat,M,&Adro,R. 1198–1205. 5(11), Anderson, Evolution, & and M., Ecology optimal Uriarte, in estimating Methods M., and models. J. H. evaluations niche independent Kass, ecological & spatially Maxent A., Motokawa conducting for R. for complexity M. package Boria, model R In M., An Soley-Guardia, Japan. ENMeval: (2014). perspective J., in 3–23). P. P. new (pp. animals Galante, Japan A R., terrestrial in Muscarella, diversification: Animals of of affect diversity Diversity shift” Species species of (Eds.), “elevation evolution high Kajihara and the the drives emergence” understanding expansion “Land toward population (2017). Postglacial 2403–2409. M. 60(11), (2006). Motokawa, Evolution, K. songbird. R. a Wayne, in & migration long-distance B., Biogeography, of T. Journal Smith, mammals. Mil´a, Japan’s B., of diversification and the Earth for in timeframe 1134–1143. new Progress 39(6), A U1429). (2012). Sea Site D. China (IODP B. East McKay, assemblages Northern radiolarian the from in inferred 6(1). changes as Paleoceanographic Science, kyr (2019). Planetary 400 R. Molecular Tada, last variation? & the T., sequence during Princeton Itaki, DNA Jersey: M., intraspecific K. New Matsuzaki, display biogeography. to island networks of 3385-3390. and/or 21, theory Trees Ecology, The (2012). P. (1967). Bridge, Mardulyn, O. . 221-236. . . 89(1), E. Ecology, T., Wilson, Animal M. of Press. & Hallworth, University Journal L., R. H., guide. K. in user’s R. Dhanjal-Adams, A data MacArthur, C., analyses: geolocator S. geolocator Davidson, Light-level light-based (2019) M., analysing S. Briedis, E. and S., Bauer, processing water S., – global 1055–1059. Lisovski, 3, the GeoLight Evolution, of (2012). and biases Ecology S. and in 8–11. Hahn, variability Methods 8(2), Press. “Inter-model & Letters, Pica of Research S., Sussex: Environmental update East Lisovski, models.” CMIP5 world. climate the (2013). coupled of F. CMIP3 shrikes Lo, in the cycle & to G., guide Ecology a B. Global Shrikes: Liepert, islands. (1997). oceanic T. of Worfolk, colonisation & predict N., to Lefranc, fails Vagrancy (2014). 405–413. J. 23(4), J. Biogeography, Gilroy, and 7.0 & 1870–1874. version C., analysis 33(7), A. genetics Evolution, Lees, evolutionary and Molecular Biology MEGA7: Molecular (2016). datasets. K. bigger Tamura, & for G., Stecher, S., Kumar, Starlings Chestnut-cheeked of wintering and of Migration history (2016). H. evolutionary philippensis Higuchi, the & N., reconstructing Hijikata, S., for Koike, variation from allelic example an Incorporating genes: (2006) multiple from A. Molecular organisms Bruneau studies. & evolutionary in S., networks Joly, phylogenetic of 254–267. of views 23, Application Evolution, from (2006). and D. distribution Bryant, Biology Japanese) Geographic & (in – H., inter- 205–220. Asia D. resolution 54, East Huson, high Kagaku, in Very Seibutsu islands (2005). studies. 1965–1978. in A. morphological 25(15), reptiles Jarvis, and Climatology, of molecular of & Biogeography Journal G., (2003). International P. T. areas. Jones, Hikida, land L., global J. for Parra, surfaces E., Tran- climate S. Philosophical polated 183–195. Cameron, Quaternary. 359(1442), J., the Sciences, R. in Biological Hijmans, oscillations B: 1–34. climatic Society Report, Royal Technical of the K-1 consequences of description. Genetic (MIROC) sactions (2004). model M. coupled G. K-1 Hewitt, (2004). S. Emori, & H., Hasumi, rihlgclSine 5 63–74. 15, Science, Ornithological . Rosa 16 nNrhAeia ytmtcBooy 54,623–636. 55(4), Biology, Systematic America. North in Agropsar Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hlgntc.I .Mtkw .Kjhr Es) pce iest fAiasi Japan. molecular in from Animals Insights of Japan: Diversity in Species (2015). assembly (Eds.), faunal I. Kajihara mammalian Nishiumi, H. of Japanese process & the Motokawa the M. around of . . review In and . A phylogenetics. in H., (2017). candidates J. Kamigaichi, species J. Old S., bird Sato, 177–186. Kobayashi, cryptic 15(1), (2010). Resources, as Y., Ecology lineages K. Iwami, Molecular distinct Ueda, S., Archipelago. 24 & reveals Someya, Biology, barcoding U., Evolutionary N., DNA BMC Olsson, Sugita, Ages. T., D., Ice the Saitoh, Williams, through Y., survival long-term Shigeta, supports long-distance 35. I., bird 10, in boreal Ecography, variation Nishiumi, a Annual P., bird. in divergences migratory Alstrom, (2015). a P. T., in P. conditions Saitoh, Marra, climatic & season E., non-breeding C. 1006-1014 and in Studds, 38(10), pathways breeding R., migratory by of M. driven origin Dudash, dispersal the S., and change C. 693–701. Climate Rushing, 23, (2006). Ecography, C. islands. Moritz, of & thrush, stepping-stone insularity J., Swainson’s a the R. the On imply Hijmans, C., data (2000). K. A. DNA Ruegg, G. Mitochondrial Polis, & (2008). D., V. M. I. Rose, 7:355–364. warbler Fadeev, Notes arctic & Ecology by V, Molecular Beringia S. of system. small Drovetski, colonisation data to life B., transmitters of A. radio barcode of Reeves, The attachment (2007) for PDN design Hebert harness S, 335–337. New Ratnasingham 62(3), in Ornithology, (1991). summarization Field R. Posterior of A. Journal (2018). Tipton, A. passerines. & M. H., 901–904. Suchard, 67(5), J. & Biology, Rappole, G., Systematic 165–174. Baele, 57(2), 1.7. Tracer D., Science, using Xie, Bio phylogenetics J., Migration. Bayesian A. Avian Drummond, of A., Evolution geographic Rambaut, and species Genetics of The modeling (2007). entropy Maximum F. Pulido, (2006). 231–259. E. 190, R. Schapire, Modelling, & Ecological P., R. distributions. forest Anderson, Asian J., 556–573. Southeast S. 39, and Phillips, Biogeography, Himalayan of of Journal patterns Passeriformes). phylogeographic elevational (Aves: and passerines Horizontal (2012). T. D. Population Ryukyu on the Research of implications. P reptiles paleogeographical and their amphibians to in 189–204. reference speciation 40(2), Ecology, special and Quaternary endemism with The of Late-Quaternary. Japan, patterns archipelago, the Geographic in (1998). Japanese H. the Ota, around straits Philosophical of 193–208. Britain. History 29(3), Research, in The 583-598. species (1990). 314, B, bird K. London. Ohshima, among of invaders Society of Royal characteristics the Biological of seasonal Transactions (1986). the J. facilitate R. conditions O’Connor, Wind (2016). H. Higuchi, Honey-buzzards 506–518. & Oriental 168, A., of by Manda, birds behaviour M., Japanese water-crossing S325–S331. among N. 1), Yamaguchi, colonization 156(Suppl reverse E., Ornithology, for Nourani, of potential Journal the data. Assessing (2015). barcode Elsevier. H. DNA London: C. mining edition). Kim, mitochondrial (1st & birds bird I., of for Nishiumi, ecology rate migration molecular The (2008). mass-corrected I. Body Newton, (2016). 4438–4449. J. 25(18), Fuchs, Ecology, & Molecular R., DNA. Lanfear, B., Nabholz, cet . atn,J,Sn .-. eeigas .L,Nzrno .A,Tn,J,Tpe,T n Tietze, and T. Topfer, J., Ting, A., A. Nazarenko, L., L. Severinghaus, -H., Y. Sun, J., Martens, M., ¨ ackert, ahrsustulatus Catharus hlocpsborealis Phylloscopus ora fBoegah,3() 1172–1182. 33(7), Biogeography, of Journal . 17 ensptilorhynchus Pernis ora fAinBooy 9 567–575. 39, Biology, Avian of Journal . vrteEs hn e.Ibis, Sea. China East the over Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. igr .M,Atr,G . ea,T . ek,B .(09.Aln itrfrteRdQueen: Red the for winter long A (2019). C. B. 737–752. 17(10), Weeks, 94(3), Ecology, & Reviews, Molecular M., Biological T. migration. Pegan, clock. seasonal of G., molecular evolution G. avian the Auteri, rethinking the M., Calibrating B. Royal Winger, (2008). the of D. Proceedings Schluter, birds. & 2321–2328. boreal T., in speciation J. promote Weir, 1881–1887. sheets 271, Ice B, (2004). London. D. of Schluter, Society & 20141257. archipela- 281, T., Australasian B, J. in Weir, diversification Society avian Royal inhibited the MacArthur-Wilson. C. has of Thebaud, after Dispersal Proceedings (2014) years S. . gos. fifty . Claramunt, . Prospects & D., C., evolution: Gravel, B. Weeks, L., and F. ecology Condamine, 200–217. in 18(2), R., 149–154. systems Letters, Aguilee, 48, model Ecology Biology, E., as Avian red-backed R. Islands of of Ricklefs, Migration Journal D., (2015). (2017). Simberloff, detour? K. H., sub-optimal Thorup, or B. & Warren, optimal G., Peninsula: H. R. Iberian Klassen, the A., . from . Biological Onrubia, . shrikes L., B: S., Pederson, Society P., P. Royal Different A. Jorgensen, the Tottrup, migrant: of W., passerine Proceedings African M. – migration. Kristensen, 1008-1016. Eurasian spring 279, K., trans-equatorial and Sciences, Thorup, a autumn of Field R., for cycle strategies of Strandberg, annual spatio-temporal Journal The G., H. (2012). shrikes. T. R. Brown Alerstam, Klaassen, and P., Bull-headed A. Avian in Tottrup, early of selection Journal since habitat and 45–52. deposits systems. 74(1), Philopatry Loess migration Ornithology, in (2003). constraint (2018). M. and Takagi, Y. flexibility Qiao, for Earth Asian & Evidence 441–446. of 29(4), L., Journal (1998). Biology, Qi, J. China. east W. Z., in Sutherland, He, evolution desert R., for 164–173. Liu, implications 155, and M., Sciences, China Tian, northeast in X., from 1162–1169. Pleistocene reconstruction Zhang, 73, haplotype Genetics, for M., Human methods of Sun, Bayesian Journal of American comparison A data. genotype (2003). from P. population reconstruction 978–989. Donnelly, haplotype 68, & for Genetics, M., method Human Stephens, statistical of new A Journal Repeat American (2001). P. (2012). data. Donnelly, M. population & N., J. 7(7), seasonal Smith, ONE, B. M., PLoS Stutchbury, global Stephens, & route. the in A., flexibility drives E. but timing efficiency McKinnon, migration C., consistent Energy 5–10. reveals K. songbirds Fraser, individual (2018). M., of tracking MacPherson, A. 962–969. Q., 2(6), Manica, Evolution, C. & Stanley, and Ecology L., Nature S. birds. A. of distribution Rodrigues, 1–10. 6(1), M., and Ecology, grams Somveille, Movement Ten warblers Africa. (2018). willow S. East in Akesson, to choice & route Russia S., - East Bensch, wing D., the Solovyeva, on M., 13,000km Willemoes, G., Bianco, site K., and Sokolovskis, Route 151–156. (2006). 5, H. Higuchi, Science, H., Buzzards Ornithological Nakamura, Grey-faced Y., . Wu, raptors: E., migratory Hiraoka, two E., of Morishita, fidelity K., Tokita, shrike J., H. brown Shiu, migratory the Migratory of Japanese). (2019). (in strategy S. Shuppan Territory 460–465. Hara, Sogo & (1996). Bun-ichi B., Tokyo: L. Nishizawa, Severinghaus, guide. S., Takagi, field H., a Senzaki, Japan: Y., of Odaya, birds Y., Umegaki, M., Senzaki, 18 uatrindicus Butastur hlocpstohlsyakutensis trochilus Phylloscopus n Honey-buzzards and aiscristatus Lanius irtn rmFar from migrating ensapivorus Pernis bs 138(3), Ibis, . Posted on Authorea 26 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160373183.39716449/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. P olce ape nRsi;D n P odce aoaoypoeue;D nlsdtedata; the analysed APK. DA and and procedures; MT fieldwork MK, laboratory the from conducted conducted assistance MT APK with and and writing MK DA the HS, Russia; led DA, DA in ideas; genus samples the the conceived collected of MT APK ecology and conservation University. Hokkaido DA and at contributions: evolutionary course Author master’s on a collaborate for thesis authors dispersal his higher other on with based and taxa is of He work speciation This and species. distribution avian between population especially relationship abilities, the barns: in interested before is swallows Aoki Daisuke Barn 1245–1251. (2006). 273, V. B, 1–9. S. Society Biosketch: Royal 3(9), Drovetski, xii. Advances, of & Science Proceedings S., switch. colonisation. Rohwer, intercontinental migratory and a A., Pavlova, histories as Glaciation M., (2017). R. S. Zink, A. Gardner, & M., R. Zink, Taxonomic Rufous-headed Kriˇst´ın, (2007). endangered & the A. J., of distribution H. and Wang, F. Alstr H. M., Zhao, Zhao, H. Z. ( Yin, 173–180. species G., 42(2), shrike Liang, Asian the eight M., reveals 1–10. of F. status analysis 30, Ethology, weather Lei, of Real-time W., Journal (2011). Zhang, raptors. H. China by Higuchi, East sea-crossing & the 53–60. direct Y., around 227, change of Shimada, International, climate adaptability Y., Quaternary and Arisawa, vegetation record. M., 000-Year N. pollen 30 Yamaguchi, high-resolution (2010). a Z. from Liu inferred & shelf N., Wu, Sea tracking. H., animal Lu, for D., geolocation Xu, Solar/satellite SGAT: 323–362. 22, (2015). Birding, S. https://github.com/SWotherspoon/SGAT established Lisovski, Dutch from newly & Retrieved Hobson, shrikes. M., a brown & Sumner, and in J., S., isabelline Wotherspoon, K. migration red-backed, 1080–1084. Kardynal, of of 27(7), Identification E., adjustment Biology, Current (2000). Rakhimberdiev, rapid T. Argentina. J., and Worfolk, in M. expansion breeding Iliff, Swallows range I., Barn Long-distance of J. population Areta, (2017). A., A. F. Gandoy, K. W., D. Winkler, m . u . ho . a,Y,Li . u .(07.Pyoeei eainhp,song relationships, Phylogenetic (2017). Y. Qu, & F., Lei, Y., Hao, C., Zhao, R., Hu, P., ¨ om, Lanius :Pyoeei nlssbsdo Cyt on based analysis Phylogenetic ): oi avvr ruficeps Larvivora Robin 19 bs 5() 204–216. 159(1), Ibis, . b n o eesequences. gene CoI and Lanius .