the chilean woodstar ( eulidia yarrellii ) is a small bird in the hummingbird family , trochilidae .

it is restricted to northernmost chile with reports from southern peru .

its natural habitats are dry shrubland and rural gardens .

it is threatened by habitat loss and is classed as a critically endangered species .

it is usually classified in its own genus eulidia but is sometimes placed with the purple-collared woodstar in the genus myrtis .

in 2013 it was classed as endangered but recently , it was classed as critically endangered by the iucn red list .

chilean woodstar

chilean woodstar ( eulidia yarrellii ) is a species of bird in the trochilidae family .
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habitat loss , the chilean woodstar lives primarily in the desert climate where it is also threatened by the use of insecticides . more
the chilean woodstar is classified as endangered ( en ) , considered to be facing a very high risk of extinction in the wild .
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the chilean woodstar is a small hummingbird . it has iridescent olive - green plumage and white underparts . males are distinguished by their violet - red throat patch and both sexes possess short , black bills . . . more
the chilean woodstar is a small hummingbird . it has iridescent olive - green plumage and white underparts ( 2 ) . males are distinguished by their violet - red throat patch and both sexes possess short , black bills ( 2 ) .
based on available information , our preliminary proposal for the 2014 red list is to pend the decision on chilean woodstar eulidia yarrellii and keep this discussion open until early 2015 , while leaving the current red list category unchanged in the 2014 update .
the highly restricted range of the chilean woodstar represents a threat to its survival ; the species is confined to just two valleys in northern chile which are already heavily cultivated ( 2 ) . viable habitat for this species of hummingbird is therefore scarce .
listing three foreign bird species - andean flamingo ( phoenicoparrus andinus ) , the chilean woodstar ( eulidia yarrellii ) , and the st . lucia forest thrush ( cichlherminia lherminieri sanctaeluciae ) - from latin america and the caribbean as endangered throughout their range ; final rule
following further review , there has been a change to our preliminary proposal for the 2014 red list status of this species , and the recommended classification to be put forward to iucn is to treat chilean woodstar as critically endangered under criterion a2ac + 3c + 4ac .
the chilean woodstar , endemic to chile and peru , is a small hummingbird in the trochilidae family ( bli 2008 ) . no larger than the size of a moth ( johnson 1967 , p . 121 ) , the chilean woodstar is approximately 3 inches ( in ) ( 8 centimeters ( cm ) ) in length and has a short black bill ( bli 2008 ; del hoyo et al . 1999 , p . 674 ) . males have iridescent olive - green upperparts , white underparts , and a bright violet - red throat ( del hoyo et al . 1999 , p . 674 ; fjelds and krabbe 1990 , p . 296 ) . more
estades , c . f . , aguirre , j . , escobar , m . a . h . , tomasevic , j . a . , vukasovic , m . a . and tala , c . ( 2007 ) conservation status of the chilean woodstar eulidia yarrellii . bird conservation international 17 ( 2 ) : 163 - 175 .
a color photo of the chilean woodstar birdyarrellii - of the yarrellii species - and lists its size , weight , and number in existence at the time of the advertisement . azapa and lluta river valleys in chile , peru are stated as the animal ' s habitat range . luiz claudio marigo is the photographer . price : $ 10 . more
benoit - c . , i . l . , editor . 1989 . red book on chilean terrestrial flora ( part one ) . corporación nacional forestal ( conaf ) , santiago , chile .
description : the chilean woodstar is a small hummingbird about the size of a moth . this beautiful bird is no larger than three inches long , with iridescent , olive - green upperparts . males also have while underparts , accented by a bright violet - red throat . habitat : this hummingbird has varied habitat needs , from riparian thickets to arid scrub , agricultural lands , and gardens . more
the tiny , beautiful chilean woodstar is a hummingbird endemic to chile and peru . while it has always had a limited population distribution , it was once locally abundant . the 1970s marked a steep decline for the species due to both habitat loss and potential poisoning by dimethoate , a potent insecticide used to control mediterranean fruit flies . pesticides are still being used in the habitat of this hummingbird and continue to affect its reproduction . more
rest of day searching for chilean woodstar in azapa valley . in the evening return to tacna day 3 . mejia lagoons . drive to mejia lagoons and birding here . red - fronted coot is only found here in all peru , also good wetlands with many migrants . day 4 . mollendo pelagic . drive to arequipa . we will look out for raimondiā“s yellow - finch and grayish miner en route day 5 . chiguata and salinas . more
schuchmann , k . l . , kirwan , g . m . & sharpe , c . j . ( 2018 ) . chilean woodstar ( eulidia yarrellii ) . in : del hoyo , j . , elliott , a . , sargatal , j . , christie , d . a . & de juana , e . ( eds . ) . handbook of the birds of the world alive . lynx edicions , barcelona . ( retrieved from urltoken on 9 july 2018 ) .
chilean woodstar , peruvian sheartail , oasis hummingbird , tamarugo and cinereous conebills , vermillion flycatcher , peruvian meadowlark and the strange slender - billed finch . after our arrival we will visit the rocky coast where we expect to see a great array of its endemic seabirds including peruvian pelican , peruvian booby , guanay and red - legged cormorants , the stunning inca tern and band - tailed and gray gulls . along the desert coast we will look for flocks of willet , whimbrel , ruddy turnstone , surfbird , franklin ' s gull and elegant terns . more
chilean woodstar eulidia yarrellii is only known to breed regularly in the azapa and vitor valleys , arica department , extreme north chile ( estades 2007 ) . it is currently listed as endangered under criterion b1ab ( i , ii , iii , v ) because it has a very small range ( estimated extent of occurrence [ eoo ] = 2 , 200 km 2 ) with all viable populations apparently confined to remnant habitat patches in two desert river valleys ( collar et al . 1992 ) . as these valleys are heavily cultivated , the extent , area and quality of suitable habitat ( and therefore the population ) are likely to be declining .
cites appendix ii . all exports of hummingbirds from peru and chile are controlled . a ten - year species recovery plan was approved in 2004 and included plans for a public awareness campaign , a study of competition between the woodstar and peruvian sheartail , a permanent population monitoring programme , restoration of natural vegetation in the azupa and lluta valleys , incorporation of its conservation into the agenda of the local good agricultural practices committee , and a study of the feasibility of an
estades ( in litt . 2007 ) estimated the population to number 650 individuals in azapa , and 550 in chaca . this totals 1 , 200 individuals , roughly equivalent to 800 mature individuals . previously , estades et al . ( 2007 ) had calculated a chilean population of 1 , 539 individuals in september 2003 . recent information , however , suggests that the population of this species has since declined to around 500 individuals ( d . lebbin in litt . 2012 ) . this estimate is assumed to equate to a population of c . 335 mature individuals , rounded here to c . 350 mature individuals . trend justification : evidence from surveys and anecdotal observations indicates that this species is undergoing an extremely rapid decline . population estimates have shown that the azapa and chaca populations have reduced by 15 . 6 % annually ( 81 . 6 % ) in 10 years ( c . f . estades in litt . 2013 ) .
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sacc . 2005 and updates . a classification of the bird species of south america . available at : urltoken .
8 cm . small hummingbird with short black bill . iridescent olive - green upperparts . male has violet - red throat . rest of underparts white . strongly forked tail . short , green central rectrices . longer outer rectrices blackish . female white tinged buff below , tail unforked , and rectrices tipped white .
estades , c . , fjeldså , j . , gonzalez - gomez , p . l . , howell , s . , jaramillo , a . & lebbin , d .
benstead , p . , capper , d . , sharpe , c j , symes , a . , taylor , j . & ashpole , j
this species is classified as critically endangered based on evidence that it is undergoing an extremely rapid population decline . urgent research and targeted conservation actions are now required to understand , halt and reverse this decline .
, and there is a historical record as far south as northern antofagasta province , but there are no recent records for peru ( estades 2007 ) . it was described as very common in the first half of the 20th century , with over 100 seen feeding together . in the late 1980s , the species was noted as common in gardens in arica and regular in the lluta valley ; however , it has since disappeared from these areas , and it is now rare in the azapa valley , where it was once regular and common ( estades 2007 , a . jaramillo
, while in 2007 the total population was estimated at around 1 , 200 individuals ( 55 % in azapa and 45 % in chaca ) ( c .
2007 ) . recent information , however , suggests that the population of this species has since declined to around 500 individuals ( d . lebbin
. 2012 ) . population estimates have shown that the azapa and chaca populations have reduced by 15 . 6 % annually ( 81 . 6 % ) in 10 years ( c . f . estades
. 2013 ) . monthly searches for the species in all tacna valleys ( southern peru ) during 2008 - 2009 did not yield any records of this species ( n . hidalgo
. 2013 ) . it has been speculated that the species could be lost from the azapa valley within a decade , and that the species could face extinction within two decades ( a . jaramillo
it inhabits small remnant patches of native scrub in desert river valleys up to 750 m , but birds are occasionally reported above 2 , 000 m and once as high as 3 , 000 m ( j . fjeldså
. despite the large numbers formerly seen feeding in flowering trees , it is usually a solitary feeder . active nests have been found in april , may , late august and september and there appear to be two annual peaks in breeding activity ( estades 2007 , estades
. 2007 ) . it is likely that males display at leks . courtship territories are placed above dense thickets which are now scarce in azapa and vítor ( clark
remaining native habitat in the narrow and heavily cultivated valleys inhabited by the species is confined to small patches , and the indigenous plants favoured by the species may be severely threatened . dense thickets , possibly used as courtship territories , are now scarce due to the spread of agricultural activities in azapa and vítor ( clark
. 2013 ) . although it has adapted to use introduced plants the presence of certain native species may still be a limiting factor ( estades 2007 ) . the ' chañar ' tree
may be an important food resource but is often destroyed by farmers who consider it invasive and believe it attracts mice ( estades 2007 ) . pesticides began to be heavily used in the azapa valley in the 1960s in order to control the mediterranean fruit fly and other crop pests , but the peruvian sheartail
has not suffered similar declines , suggesting that this may not be the primary cause of its decline ( estades 2007 ) . competition with peruvian sheartail has been suggested as a potential threat , although this has not been proven ( estades
. 2013 ) . the various threats of habitat destruction , pesticide use and competition with other hummingbirds are likely to be synergistic in their impacts on the species ( p . l . gonzalez - gomez
through their monopolisation of the new resource ( p . l . gonzalez - gomez
research genetic structure of populations . begin a habitat restoration program in the lluta , chaca and azapa valleys , ensuring that species whose flowers are visited regularly by
. 2014 ) . conduct an education campaign to emphasize the importance of native plants , and encourage the planting of appropriate trees and bushes . continue population monitoring , as detailed in species recovery plan . limit the amount of pesticides used in azapa and chaca valleys . as the vast majority of the species ' s range is now privately owned , it has been recommended that some of this land be purchased to create pesticide - free , native plant reserves , with perhaps one in each valley inhabited by the species ( a . jaramillo
( amended version of 2016 assessment ) . the iucn red list of threatened species 2017 : e . t22688244a112392683 .
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) , in neotropical birds online ( t . s . schulenberg , editor ) . cornell lab of ornithology , ithaca , ny , usa . retrieved from neotropical birds online :
recommended citation birdlife international ( 2018 ) species factsheet : eulidia yarrellii . downloaded from urltoken on 09 / 07 / 2018 . recommended citation for factsheets for more than one species : birdlife international ( 2018 ) iucn red list for birds . downloaded from urltoken on 09 / 07 / 2018 .
little is known about the natural ecology of this small hummingbird . it is a solitary feeder and has been observed in gardens feeding on flowers of lantana spp . and hibiscus spp . ( 2 ) . nests containing eggs and chicks have been recorded in late august ( 2 ) .
this bird is currently restricted to the extreme northern reaches of chile . it is thought to be confined to just two valleys that contain suitable habitat ( 2 ) .
found in scrub in desert river valleys up to 750 metres above sea level ( 2 ) .
classified as endangered ( en – b1 + 2abce ) on the iucn red list 2002 ( 1 ) , and listed on appendix ii of cites ( 3 ) .
further research into the natural ecology of this species is urgently required in order to understand the nature of resources needed to sustain the population . exports of hummingbirds from peru and chile are controlled ( 2 ) and this species is listed on appendix ii of the convention on international trade in endangered species ( cites ) ( 3 ) .
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relationships unclear ; usually placed in monotypic genus , as here , but external morphology and behaviour support treatment within myrtis . possible hybridization with thaumastura cora indicated # r . monotypic .
n chile in lluta , azapa and vitor valleys ( arica ) ; historical record as far s as n antofagasta . few sight records in s peru ( tacna and possibly moquegua ) # r .
7·5–8 cm ; 2·3–2·6 g . male has short black bill ; upperparts iridescent olive green ; throat shining violet - red , underparts white ; central tail . . .
cultivated desert river valleys and gardens from 200 m to 750 m , commonest below 400 m , with a . . .
little known . nesting records are available from may , aug and sept , while an immature was collected in nov , and juveniles and partially . . .
presumably sedentary for the most part , occasionally straggling s into n antofagasta , chile , but . . .
critically endangered . cites ii . a little - known , restricted - range species : present in peru - chile pacific slope eba . until 2000 ranked as vulnerable , and only uplisted to . . .
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molecular studies # r # r indicate that genera myrtis , eulidia , rhodopis , thaumastura and chaetocercus form a monophyletic group that includes also calypte , archilochus and selasphorus .
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the atacama desert is a narrow strip of desert along the northwest coast of chile . it extends nearly 1600 km and reaches a maximum width of 180 km . in many areas rainfall has never been recorded . consequently , an extremely arid , almost barren , landscape predominates . despite the aridity of this desert , some cacti ( eulychnia ) , perennials ( nolana ) and mesquite ( prosopis ) occur in basins where occasional water accumulation occurs . relatively few animal species have adapted to this arid environment and therefore , faunal diversity and density is extremely low . even bacteria are scarce , and in many portions of the desert insects and fungi are absent . the intrinsic value of the atacama desert ' s plant and animal communities lies in the unique nature of their composition , the high levels of endemism and some species ' remarkable adaptations for survival in some of the planet ' s most demanding conditions .
description location and general description the atacama desert ecoregion occupies a continuous strip for nearly 1 , 600 km along the narrow coast of the northern third of chile from near arica ( 18°24 ' s ) southward to near la serena ( 29°55 ' s ) ( dillon and a . e . hoffmann - j 1997 ) . this desert is a sparsely populated virtually rainless plateau , running east from the pacific ocean to the andes mountains . the average width is less than 100 km . the xeric conditions extend up to1 , 500 masl on the drier slopes ( börgel 1973 ) . the faulted coastal mountains ( mostly 500 - 1000 m high ) are composed of cretaceous sediments ( limestone and sandstone ) over more ancient masses of crystalline rocks ( lustig 1970 ) .
the atacama desert is considered to be one of the driest coastal deserts in the world . vegetation must contend with an annual rainfall of 0 . 6 mm in arica and 2 . 1 mm in iquique . the atacama becomes slightly less arid as it moves southward . the average monthly temperatures in iquique range from 14 . 5 oc in september to 21 oc in march ( dillon and a . e . hoffmann - j 1997 ) .
topography and substrate combine to influence the patterns of moisture availability and areas of suitable habitat . where isolated mountains or steep coastal slopes intercept the clouds , a fog zone develops with a stratus layer concentrated against the hillsides . the moisture allows the development of fog - zone plant communities termed
lomas
( small hills ) near the coast and in lower portions of numerous gorges (
quebradas
) between sea level and 1 , 100 m . these plant formations also have been called the fertile belt , fog oases or meadows on the desert . plant communities of the lomas consist of mixtures of annual and short - lived perennial and woody scrub vegetation .
the northern coastal zone has almost no vegetation . among some of the few plant species found in this zone are cacti growing over 500 m - eulychnia iquiquensis and copiapoa sp . near iquique , there is large community of tillandsia landbeckii growing at 990 - 1 , 100 m ( dillon and a . e . hoffmann - j 1997 ) . the valleys along streams support plant communities that are composed of trees prosopis chilensis , p . tamarugo , salix humboldtiana , schinus aareira , acacia macrantha and caesalpinia tinctoria and other shrubby and herbaceous plants ( roig 1999 ) . on slopes moistened by drizzle during the winter , sparse strands of tillandsia spp . may exist in association with a few lichens .
near the town of antofagastsa , the region is practically devoid of vegetation except for eulychnia iquiquensis and copiapoa sp . only some brush plants occur along the coastal plateaus , dependent for survival on the moisture of persistent fog , they include heliotropium pycnophyllum , ephedra breana and lycium deserti ( dillon and a . e . hoffmann - j 1997 ) . in places away from the area of fog formation , the desert is almost lifeless . in these areas , even decomposition does not occur . dead vegetation may be thousands of years old ( roig 1999 ) .
the southern atacama desert has a fog - zone vegetation with approximately 230 species of vascular plants . euphorbia lactiflua and eulychnia iquiquensis are dominant species in the central area of this zone . other shrubby species in the zone include echinopsis coquimbana , oxalis gigantea , lycium stenophyllum , proustia cuneifolia , croton chilensis , balbisia penduncularis and tillandsia geissei . bromeliads are also present along the coastal flats in this southern part , and include deuterocohni chrysantha and puya boliviensis ( dillon and a . e . hoffmann - j 1997 ) .
the southernmost area in the ecoregion is near chañaral . this area has communities of shrubs such as skytnathus acutus , encelia canescens , frankenia chilensis , and nolana rostrata . annuals and perennials include perityle emoryi , oenothera coquimbensis , ademia latistipula , atragalus coquimbensis , cruckshanksia verticillata , fagonia chilensis and tetragonia angustifolia ( dillon and a . e . hoffmann - j 1997 ) .
biodiversity features the intrinsic value of the atacama desert ' s plant and animal communities lies in the unique nature of their composition , the high levels of endemism and some species ' remarkable adaptations for survival in some of the planet ' s most demanding conditions . the highly endemic flora is of particular importance . there are some traditional uses of species by the local inhabitants ( aronson 1990 ; bittmann 1988 ) , e . g . food from oxalis spp . , medicinals from salvia tubiflora and ephedra spp .
there are approximately 550 species of vascular plants representing 225 genera and 80 families in the lomas formations . the most diverse families are the asteraceae , nolanaceae , cataceae , boraginaceae , and apiaceae . endemism can be very high ( over 60 % ) ( rundel et al . 1991 ) . most of the plant species mentioned earlier are endemic to the atacama desert . three cacti are endemic to the northern part of the atacama desert ; they are eulychnia iquiquensis , neoporteria sensu and copiapoa sp . endemic shurbs of the ecoregion include berberis litoralis , anisomeria littoralis , atriplex taltalensis , adesmia viscidissima , croton chilensis , balbisia peduncularis , nicotiana solanifolia , teucrium nudicaule , monttea chilensis , stevia hyssopifolia , senecio almeidae , gutierrezia taltalensis and haploppus desrticula . endemic plants near tocopilla are malesherbia tocopillana , mathewsia collina and nolana tocopillensis ( dillon and a . e . hoffmann - j 1997 ) .
understandably , very few animals have adapted to successfully inhabit this extremely dry habitat . the few scorpions and insects are the prey of lizards ( tropidurus spp . ) and of a small passerine of the genus geositta . an occasional bird of prey or vulture can be found scavenging on the carrion of domestic animals . mammals are equally few with a mouse ( phyllotis darwini ) and a fox ( pseudalopex griseus ) encountered periodically . the growth of a few scattered shrubs and herbaceous plants such as lichens enables certain specialized insects and poisonous spiders to colonize these deserts .
current status the region has been moderately affected by roads and mining operations . the northern area of the ecoregion has been especially affected by overgrazing of domestic livestock , collection of firewood , and commercial gathering of rare plants , including cacti and bulbs .
some nearby areas have archaeological importance . the beauty and rarity of the lomas formations provide opportunities for tourism combined with scientific studies . if the impact on the delicate communities is controlled through supervision , lomas formations can be enjoyed by the public and preserved . environmental education on the importance , rarity and the unusual characteristics of these natural resources is desperately needed . for example , quebrada el león needs some recuperation from overuse and could become a lasting and informative oasis as a nature reserve for residents of caldera and copiapó ( dillon and a . e . hoffmann - j 1997 ) .
three protected areas exist within the extreme desert region . pan de azúcar national park ( established in 1986 , iucn category ii ) covers 438 km² . it has been recommended ( anderson et al . 1990 ) that this park be expanded northward to include quebrada esmeralda ( 25°50 ' s ) and quebrada de las lozas ( 25°41 ' s ) , which would protect areas very rich in cacti . la chimba national reserve ( iucn category iv ) of 30 km² was recently established and lies approximately 15 km north of antofagasta . pampa del tamarugal national reserve ( iucn category iv ) , 1 , 023 km² in size , is one of the key areas for the conservation of the threatened tamarugo conebill ( conirostrum tamarugense ) .
types and severity of threats a few port towns exist in this desert . iquique , caldera , and antofagasta are located on precarious sea - eroded terraces at the base of coastal cliffs . these towns are the outlet for the numerous mining centers in the interior tectonic basins . the wealth of the region lies in its mineral resources ( copper , sodium chloride , sodium nitrate , iodine salts ) , not in its spare biotic resources ( roig 1999 ) .
most threats to this ecoregion are closely associated with the few human population centers . specifically , these include increased urbanization , pollution , road construction , livestock grazing – ( numerous goats ) , fuelwood gathering , commercial plant collecting , and erosion .
since many sites have become accessible by road only recently ( i . e . , within the past 12 years ) , atacama ' s specialized ecosystems remained well preserved until recent times . road construction in association with mining operations is increasing human occupation in the region . with the rise in copper prices during the 1980s , reactivation of mining activities utilizing large quantities of sulphuric acid has had an essentially undocumented impact on terrestrial and marine life ( anderson et al . 1990 ) .
justification of ecoregion delineation the atacama desert is distinguished as being one of the driest places in the americas – and said to resemble a lunar landscape . inititial delineation’s followed di castri ( 1968 ) , however for the linework we followed simmonetti and montenegro ( 1994 ) to draw the northern and southern boundaries . eastern delineations follow the unesco ( 1980 ) boundary for the neighoring puna ecoregion in the high andes , and the western delineation is the pacific ocean .
references anderson , e . f . , m . bonilla - f . , a . e . hoffmann - j . , and n . p . taylor . 1990 . succulent plant conservation studies and training in chile . world wildlife fund - u . s . , washington , d . c .
aronson , j . 1990 . desert plants of use and charm from northern chile . desert plants 10 ( 2 ) : 79 - 86 .
bittmann , b . 1988 . recursos y supervivencia en el desierto de atacama . in masuda , s . , editors , recursos naturales andinos . tokyo : university of tokyo .
börgel , r . 1973 . the coastal desert of chile . pages 111 - 114 in d . h . k . amiran , and a . w . wilson , editors . coastal deserts : their natural and human environments . tucson : university of arizona press .
di castri , f . 1968 . esquisse ecologique du chili . biologique de l ' amerique australe 4 . cnrs , paris , france .
dillon , m . o . , and a . e . hoffmann - j . 1997 . lomas formations of the atacama desert northern chile . in s . d . davis , v . h . heywood , o . herrera - macbryde , j . villa - lobos , and a . c . hamilton , editors . centres of plant diversity : a guide and strategy for their conservation . wwf , iucn , oxford , u . k .
dorst j . 1967 . south america and central america : a natural history . hamish hamilton , london .
lustig , l . k . 1970 . appraisal of research on geomorphology and surface hydrology of desert environments . in w . g . mcginnies , b . j . goldman , and p . paylore , editors . deserts of the world : an appraisal of research into their physical and biological environments . university of arizona press , tucson .
roig , v . 1999 . atacama desert . page 54 in m . e . mares , editor , encyclopedia of deserts . university of oklahoma press , norman .
rundel , p . w . 1981 . the matorral zone of central chile . pages 175 - 201 in f . di castri , d . w . goodall , and r . l . specht , editors . ecosystems of the world vol . 11 . elsevier , amsterdam .
simmonetti , j . a . and g . montenegro . 1994 . conservation and use of biodiversity of the arid and semiarid zones of chile . presented at the international workshop
conservación y uso sostenible de la biodiversidad en zonas áridas y semiáridas de américa latina
, march 1994 , guadalajara , mexico . unpublished document .
world wildlife fund 1250 24th street , n . w . washington , dc 20037
this discussion was first published as part of the 2013 red list update , but remains open for comment to enable reassessment in 2014 .
further information is requested on the population trends , size and distribution of this species . comments on the proposed uplisting are welcome .
collar , n . j . , gonzaga , l . p . , krabbe , n . , madroño nieto , a . , naranjo , l . g . , parker , t . a . and wege , d . c . ( 1992 ) threatened birds of the americas : the icbp / iucn red data book . international council for bird preservation : cambridge , u . k .
we have conducted monthly additional searches for the species in all tacna valleys ( south peru ) during 2008 - 2009 , this species was not recorded in any census . regards .
there is now a period for further comments until the final deadline of 31 march , after which recommended categorisations will be put forward to iucn .
the final red list categories will be published on the birdlife and iucn websites in mid - 2014 , following further checking of information relevant to the assessments by both birdlife and iucn .
the final categorisation will be published later in 2014 , following further checking of information relevant to the assessment by birdlife and iucn .
with stark cliff walls over 1 , 600 meters high , the chicamocha canyon is the deepest in colombia . unfortunately for biologists , its difficult terrain houses a number of endemic species . it was in order to confirm the presence of one of these species – nicéforo’s wren thryophilus nicefori – that four biologists from calidris ( birdlife in colombia ) [ … ]
most businesses want to minimise their impact on the natural world – but it can be hard to know where to start . luckily , the process has just got a whole lot easier with the release of a new roadmap for companies operating in some of the most biologically significant places on the planet . the report , [ … ]
“a summit for the flyways” united 100 different organisations from 70 different countries to address one problem : how to protect migratory birds on their incredible journey . and with millions of migratory birds passing through the middle east , it was the perfect opportunity to tackle regional issues , too . birdlife took advantage of the fact that conservation [ … ]
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jasus paulensis , also commonly known as the st paul rock lobster , is a species of spiny lobster found in the waters around saint paul island in the southern indian ocean and around tristan da cunha in the southern atlantic ocean .

at one time the rock lobsters on tristan da cunha were believed to be a separate species known as the tristan rock lobster ( jasus tristani ) , but the use of mitochondrial dna sequencing has shown them to be identical .

some authorities , for example the iucn , retain them as separate species .

the tristan rock lobster features on the coat of arms and the flag of tristan da cunha .

jasus paulensis

afrikaans kreef [ from synonym ] for jasus ( jasus ) lalandii ( h . milne edwards , 1837 )
afrikaans kaapse kreef [ from synonym ] for jasus ( jasus ) lalandii ( h . milne edwards , 1837 )
english cape crawfish [ from synonym ] for jasus ( jasus ) lalandii ( h . milne edwards , 1837 )
english cape crayfish [ from synonym ] for jasus ( jasus ) lalandii ( h . milne edwards , 1837 )
jasus paulensis ( heller , 1862 ) : beurois ( 1971 ) [ statut pour les îles subantarctiques ] beurois , j . 1971 . régime alimentaire de la langouste jasus paulensis ( heller , 1862 ) des iles saint - paul et amsterdam ( ocean indien ) résultats préliminaires . téthys , 3 : 943 - 948 .
distribution of jasus spiny lobsters in the mid - latitude southern . . . | download scientific diagram
grua , p . , 1963 . maturité , cycle sexuel , soies ovigères des langoustes australes femelles jasus paulensis heller , 1863 . etude statistique . comité national français recherches antarctiques , 4 : i - viii , 1 - 35 , figs 1 , 2 , graphs 1 - 14
english australian crayfish [ from synonym ] for jasus ( sagmariasus ) verreauxi ( h . milne edwards , 1851 )
villacorta - rath c , et al . outlier snps enable food traceability of the southern rock lobster , jasus edwardsii .
to assess the probe efficiency in non - target species ( i . e . those not used for the initial probe design ) , we assessed the recovery of loci across the modern jasus samples including j . edwardsii , j . frontalis , j . lalandii , j . paulensis and j . tristani .
grua , p . , 1960 . les langoustes australes ( jasus lalandii ) . biologie - milieu - exploitation commerciale . terres australes antarctiques françaises , 10 : 15 - 40 , figs
morgan emj , green bs , murphy np , strugnell jm . investigation of genetic structure between deep and shallow populations of the southern rock lobster , jasus edwardsii in tasmania , australia .
for the target - capture experiment , we collected 87 samples of modern and museum specimens of jasus comprising six species j . edwardsii , j . caveorum , j . frontalis , j . lalandii , j . paulensis and j . tristani . specimens of s . verreauxi ( n = 16 ) were included to evaluate the custom probe set and the efficiency between ddrad and target - capture methods for the validated loci in both methods ( supplementary table s11 ) .
porobić j , canales - aguirre cb , ernst b , galleguillos r , hernández ce . biogeography and historical demography of the juan fernández rock lobster , jasus frontalis ( milne edwards , 1837 )
the genus jasus encompasses six lobster species ( j . caveorum , j . edwardsii , j . frontalis , j . lalandii , j . paulensis and j . tristani ) that are distributed throughout the southern hemisphere 37 . j . edwardsii is the most widespread species within the genus , whilst the other species maintain limited geographical distributions , with some species known from only a single seamount ( e . g . j . caveorum ) . these species all support valuable fisheries , and have been exploited for more than one hundred years 38 .
pca across and within species based on snp genotypes , where no deamination filter was applied . for each dataset , the sample passed filters and snp pruning was adjusted to allow 0 . 10 maximum missing data per site and maf < 0 . 05 : ( a ) pca across six jasus species , 146 snps and 53 samples passed filters ; ( b ) pca of j . lalandii , 154 snps and 19 samples passed filter ; ( c ) pca of j . edwardsii , 748 variants and 12 samples passed filters ; ( d ) pca of j . paulensis , 124 variants and 14 samples passed filters .
deamination and transition / transversion ratio were calculated over filtered variants using vcftools 0 . 1 . 14 60 . snp pruning , diversity indices ( f st , heterozygosity and maf ) and pca were estimated for all jasus species using plink 1 . 9 61 .
booth , j . d . & ovenden , j . r . distribution of jasus spp . ( decapoda : palinuridae ) phyllosomas in southern waters : implications for larval recruitment . mar . ecol . prog . ser . 200 , 241–255 ( 2000 ) .
sample quality of modern and museum jasus specimens . ( a ) box - plot of mean gc content and year since sample collection . ( b ) linear regression between a 260 / a 280 ratio and gc content ; blue dots represent museum samples and red dots represent modern samples .
museum samples ( n = 47 ) were donated by the national institute of water and atmospheric research ( niwa ) and te papa museum ( new zealand ) . the samples were collected in 1967 ( j . lalandii and j . paulensis ) , 1991 ( j . edwardsii and j . lalandii ) and 1995 ( j . caveorum ) . samples were preserved in ethanol / isopropanol ( mostly evaporated ) . in some cases preservation methods were not indicated .
holthuis , l . b . and e . sivertsen . 1967 . the crustacea decapoda , mysidacea and cirripedia of the tristan da cunha archipelago with a revision of the
frontalis
subgroup of the genus jasus . results norwegian scientific expedition to tristan da cunha , 52 : 1 - 55 , text figs 1 - 9 , pls 1 - 5
a total of 40 lobsters samples were collected between 2010 and 2015 . the french southern and antarctic lands ( terres australes et antarctiques françaises - taaf ) provided j . paulensis pleopod tissue collected in 2014 . j . lalandii and j . tristani pereiopod samples , collected during in 2015 in south africa and tristan da cunha islands , respectively , were donated by the south african department of agriculture , fisheries and forestry . j . frontalis were sampled in juan fernandez archipelago in 2010 43 , these samples were donated by the universidad de concepcion ( chile ) .
the efficiency of the target capture experiment non - target jasus species was assessed using only modern samples ( n = 40 ) . the overall target coverage was given by the mean depth of targets for each species using bedtools 2 . 26 62 . mean coverage ( sample coverage depth ) , heterozygous read rate and gc content of samples were estimated from sample alignments using bbmap ( urltoken ) .
figure 1 . distribution of jasus spiny lobsters in the mid - latitude southern hemisphere based on booth ( 2006 ) . sampling locations for the present study were as follows : ( 1 ) st paul and amsterdam islands ; ( 2 ) seamount 150 ( located on the southwest indian ridge ) ; ( 3 ) gough and inaccessible islands ( tristan da cunha archipelago ) ; and ( 4 ) vema seamount .
principal component analysis and scatter plot of locus - specific f st vs observed heterozygosity of jasus species in modern samples . ( a ) and ( b ) 313 snps from the ddrad original probe set ; ( c ) and ( d ) 647 snps from the assembly - based reference . maximum missing data per site was set to 0 . 10 , maf < 0 . 05 , and overall f st was estimated according to weir & cockerham ( 1984 ) .
number of variable loci shared amongst each of six jasus species . ( a ) the left panel displays the number of loci shared among five ( 5 ) , four ( 4 ) , three ( 3 ) and two ( 2 ) species , or found only in a single species ( 1 ) in the assembly - based reference ( black and grey stacked column ) and the corresponding significant blast hits to the original probe set ( grey ) . ( b ) the right panel is a graphic representation of target enrichment hybridization reaction showing library size , captured fragments size and off - target reads . the grey lines represent the 120 - mer probes , the orange lines represent the library fragments and the black arrows represent overlapping / non - overlapping paired - end reads ( read 1 and read 2 ) .
in order to compare the target - genome divergence among species and its effects on target enriched sequencing , a nonparametric correlation was performed among sequencing yield ( given in number of processed reads ) , mapped reads , gc content , mean coverage and mapping quality for each species using spss v22 . 0 ( ibm corp . , ny , usa ) . univariate analysis of variance was applied to test whether gc content and mean coverage were significantly different among jasus species . the sequencing yield effect was included as a covariate , since it was previously explored as a random factor within a one - way anova analysis and found to be significant . data were checked with levene’s test and logarithm transformed to ensure normality and homogeneity of variance . principal component analysis ( pca ) including all variables was performed using past 3 . 12 ( urltoken ) .
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thank you for taking the time to provide feedback on the iucn red list of threatened species website , we are grateful for your input .
batchelor , a . , de silva , r . , dyer , e . , kasthala , g . , lutz , m . l . , mcguinness , s . , milligan , h . t . , soulsby , a . - m . & whitton , f .
has been assessed as data deficient . this species was formerly known from a very restricted range ( st paul and new amsterdam islands ) , however a few recent specimens have been collected from other seamounts along the south west indian ridge . this species faces a number of threats including intense harvesting within the st paul and new amsterdam islands eez , and intrinsic threats associated with its small range . the abundance of this species outside of the current fishing grounds is unknown therefore making it difficult to draw any conclusions on the impact of fishing to the global population . further surveys are needed for this species along the seamounts of the south west indian ridge before a more accurate assessment of conservation status can be made .
this species was originally only known from the st . paul and amsterdam islands in the southern indian ocean , with a single specimen has also been reported from the kerguelen islands ( holthuis 1991 ) , however recently additional specimens have been collected from seamounts along the south west indian ridge ( j . groeneveld pers . comm . 2011 ) . these indicate that the species is far more widely , but sparsely , distributed along the south west indian ridge than previously thought .
typically this species is found on rocky substrates at a depth range of 0 - 60 m , although is most commonly found in the kelp zone at a depth range of 10 - 35 m ( holthuis 1991 ) . females are most commonly taken from may to october , while males are most commonly taken from november to april ( holthuis 1991 ) .
this species is harvested as a food source and is taken using lobster pots ( holthuis 1991 ) . only a single ship harvests this fishery , and undertakes two trips per year with each trip lasting up to two months ( biais 2009 ) . recent information from the french rock lobster fishery in the st paul and amsterdam eez shows a consistent catch of around 350 - 400 t ( g . duhamel pers . comm . 2011 ) . “yields ( kg / pot ) are presently increasing along the period 2001 - 2010” ( g . duhamel pers . comm . 2011 ) .
the major threat to this species is high levels of exploitation . an intrinsic threat is this lobster ' s extremely restricted range . this species is also susceptible to environmental fluctuations for both adult and larval stages , and also to single catastrophic events .
an annual fishing quota of 400 tonnes is in place for this species . further surveys for this species are needed along the south west indian ridge in order to better understand both distribution and abundance .
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broad and flattened , about as wide as long , much larger than the small spines .
type locality :
st . paul
, [ = st . paul island in the southern part of the western
. a report of the catch of a single lobster in kerguelen islands by aubert de la rüe ( 1954 : 119 ) seems very reliable and is well documented ( the specimen was brought up with algae entangled in the anchor of the ship
lozère
, a catch witnessed by a . berland ) ; but this evidently is a freak occurrence , as no lobster catches have been reported from the kerguelen either before or after this event .
the species lives at depths between 0 and 60 m , on rocky or gravel bottom , being most numerous in the kelp zone between 10 and 35 m . egg - layingstarts in may , and
females have been observed until november , or exceptionally early december . females are caught from may to october , while males dominate in most catches from november to april . the animals are nocturnal and feed on plants and ( dead ) animal matter .
cm ( females ) . the specimes from amsterdam island on the average are slightly smaller than those from st . paul island .
the fishing grounds are restricted to the islands of st . paul and amsterdam , the shorelines of which are respectively 12 and
heller , 1862 , verhandlungen zoologisch - botanischen gesellschaft wien , 12 : 525 .
aubert de la rüe , e . , 1954 . deux ans aux iles de la désolation , archipel de kerguelen : 1 - 316 , pls ( r . juliard , paris ) .
fischer , w . and g . bianchi ( eds ) , 1984 . fao species identification sheets for fishery purposes . western indian ocean ( fishing area 51 ) , vol . 5 : pag . var .
heller , c . , 1862b . neue crustaceen , gesammelt während der weltumseglung der k . k . fregatte navara . zweiter vorläufiger bericht . verhandlungen zoologisch - botanischen gesellschaft wien , 12 : 519 - 528 .
williams , a . b . , 1986 . lobsters - identification , world distribution , and u . s . trade . marine fisheries review , 48 ( 2 ) : 1 - 36 , figs 1 - 80
contains the volume of fish catches landed by country or territory of capture , by species or a higher taxonomic level , by fao major fishing areas , and year for all commercial , industrial , recreational and subsistence purpose . more > >
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en - st . paul rock lobster , fr - langouste de st . paul , sp - langosta de st . paul .
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disclaimer : itis taxonomy is based on the latest scientific consensus available , and is provided as a general reference source for interested parties . however , it is not a legal authority for statutory or regulatory purposes . while every effort has been made to provide the most reliable and up - to - date information available , ultimate legal requirements with respect to species are contained in provisions of treaties to which the united states is a party , wildlife statutes , regulations , and any applicable notices that have been published in the federal register . for further information on u . s . legal requirements with respect to protected taxa , please contact the u . s . fish and wildlife service .
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to cite this page : myers , p . , r . espinosa , c . s . parr , t . jones , g . s . hammond , and t . a . dewey . 2018 . the animal diversity web ( online ) . accessed at https : / / animaldiversity . org .
disclaimer : the animal diversity web is an educational resource written largely by and for college students . adw doesn ' t cover all species in the world , nor does it include all the latest scientific information about organisms we describe . though we edit our accounts for accuracy , we cannot guarantee all information in those accounts . while adw staff and contributors provide references to books and websites that we believe are reputable , we cannot necessarily endorse the contents of references beyond our control .
this material is based upon work supported by the national science foundation grants drl 0089283 , drl 0628151 , due 0633095 , drl 0918590 , and due 1122742 . additional support has come from the marisla foundation , um college of literature , science , and the arts , museum of zoology , and information and technology services .
holthuis , l . b . 1991 . fao species catalogue . vol 13 . marine lobsters of the world . an annotated and illustrated catalogue of species of interest to fisheries known to date . fao fisheries synopsis . 125 ( 13 ) : 292 p .
fao species catalogue . vol 13 . marine lobsters of the world . an annotated and illustrated catalogue of species of interest to fisheries known to date
english agassiz ' s lobsterette for nephropsis agassizii a . milne - edwards , 1880
english atlantic deep - sea lobster for acanthacaris caeca a . milne - edwards , 1881
english blind deep sea lobster for acanthacaris caeca a . milne - edwards , 1881
english blue spot rock lobster for panulirus longipes ( a . milne - edwards , 1868 )
english blunt slipper lobster for scyllarides squammosus ( h . milne edwards , 1837 )
deep sea between 122 and 1400 m , mostly between 122 and 900 m . [ details ]
deep sea between 878 and 2560 m , most common between 1100 and 1900 m . [ details ]
deep sea from 470 to 1804 m , mostly between 900 and 1400 m ; bottom mud . [ details ]
deep sea from 580 to 1160 m , bottom mud or sandy mud . [ details ]
deep - sea species from 640 to 1054 m depth . bottom very flat , of soft mud ( ooze ) . possibly a burrowing species . [ details ]
depth range from ( 205 - ) 260 to 373 ( - 390 ) m . [ details ]
depth range from 0 . 6 to 180m , usually between 0 . 6 and 64m [ details ]
found in deep water ( 406m ) , but also in 59 - 61m depth . [ details ]
in shallow water , from the sublittoral down to 15m depth , in coral reef areas , often on seaward edges of the reef . . . [ details ]
littoral zone to 0 . 5m deep , in sheltered bays and estuaries [ details ]
a deepsea species from 293 to 878 m depth ( mostly between 550 and 825 m ) . lives on soft mud bottoms in burrows . [ details ]
burrowing in muddy sand of the intertidal zone , sometimes under rocks . burrows y - shaped , and about 0 . 6 to 1 . 0m deep [ details ]
continental shelf between 0 and 150 m depth ; usually not deeper than 50 m . found on hard substrates : rock or hard . . . [ details ]
deep sea between 137 and 824 m , mostly between 200 and 600 m . bottom : mud or fine sand . [ details ]
deep sea between 170 and over 1060 m , usually between 500 and 750 m . on soft muddy substrates . [ details ]
deep sea between 420 and 1260 m , mostly between 500 and 800m . on muddy or sandy bottoms . [ details ]
deep sea between 655 and 1234 m , most catches between 800 and 1300 m ; substrate sand or mud , sometimes with rubble . [ details ]
deep sea between 786 and 2029 m , most catches between 1600 and 1900 m . substrate : mud . [ details ]
depth range between 230 and 360 ( - 400 ) m . soft substrate ( mud or coralfine rubble ) . [ details ]
depth range from 140 to 640 m ; substrate mud or sandy mud , firm enough for burrowing . [ details ]
depth range from 230 to 700 m , most common between 300 and 500 m ; on a substrate of sand or mud . [ details ]
depth range from 250 to 750 m , but mostly between 300 and 450 m . substrate of hard mud ; the species possibly lives . . . [ details ]
found at 560 m depth ; bottom solid bluish grey mud overlaid by softer brown mud . [ details ]
in shallow , sometimes slightly turbid coastal waters , from 1 to 8 m depth , with a few records from depths as great . . . [ details ]
shallow coastal waters , rock pools , etc . the extreme rarity of the species is the cause that very little is known . . . [ details ]
the species lives at depths between 0 and 60 m , on rocky or gravel bottom , being most numerous in the kelp zone . . . [ details ]
the species lives in coastal waters at depth between 0 and 46 m , on rocky bottoms , sometimes with patches of sand . . . [ details ]
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holthuis , l . b . 1991 . fao species catalogue . vol 13 . marine lobsters of the world . an annotated and illustrated catalogue of species of interest to fisheries known to date . fao fisheries synopsis . 125 ( 13 ) : 292 p . [ details ]
habitat the species lives at depths between 0 and 60 m , on rocky or gravel bottom , being most numerous in the kelp zone between 10 and 35 m . [ details ]
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carla a . souza , 1 nicholas murphy , 1 cecilia villacorta - rath , 2 laura n . woodings , 1 irina ilyushkina , 3 cristian e . hernandez , 4 bridget s . green , 2 james j . bell , 3 and jan m . strugnell 5 , 1
open access this article is licensed under a creative commons attribution 4 . 0 international license , which permits use , sharing , adaptation , distribution and reproduction in any medium or format , as long as you give appropriate credit to the original author ( s ) and the source , provide a link to the creative commons license , and indicate if changes were made . the images or other third party material in this article are included in the article’s creative commons license , unless indicated otherwise in a credit line to the material . if material is not included in the article’s creative commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use , you will need to obtain permission directly from the copyright holder . to view a copy of this license , visit urltoken .
in order to obtain a ddrad loci catalogue . this was used as a template to design the mybait
assembly , using liberal similarity thresholds ( 75 % ) , revealed putative paralogous loci , which were discarded . redundant loci ( present in multiple assemblies ) were synonymized into single loci as described in the methods section . across all three assemblies only 123 loci were shared between the two species , and 2 , 267 were species - specific ( 1 , 219 were from
. the percentage of missing loci over all samples was 52 . 4 ± 19 . 2 for
histograms displaying the number of shared loci among samples in ddrad libraries of j . edwardsii ( a ) and s . verreauxi ( c ) samples . overlapping histograms of target - capture and ddrad representing the percentage of missing data among validated loci in j . edwardsii ( b ) and s . verreauxi i ( d ) .
) . the enriched loci were sequenced on a single 250 x 2 illumina miseq sequencing run , generating 4 . 6 gbp ( giga base pairs ) of sequence data ( 1 . 29 % sequencing error rate and 84 . 49 % of data above q30 score ) . subsequent trimming and removal of low quality reads and external contaminants resulted in 800 and 174 mbp high - quality data for modern and museum specimens , respectively . the lower sequencing output for museum samples is likely due to low yield dna extracts , which were highly fragmented and possessed a low a
museum samples ( n = 8 ) generated sequencing data sufficient to enable variant calling and were excluded from downstream analysis .
as the probes were developed with j . edwardsii and s . verreauxi ddrad libraries , we initially examined the probe capture efficiency in these two taxa .
. in addition , the target - capture approach resulted in less missing data within each species than the ddrad sequencing approach ( fig .
target - capture enriched sequencing and genotyping efficiency between j . edwardsii and s . verreauxi sampling .
we were able to re - sequence and validate 54 loci reported in villacorta - rath et al . 15 in eight j . edwardsii samples replicates . besides , the average level of missing data among these loci in our target - capture experiment was 15 . 96 % within j . edwardsii species . it means that the ddrad loci outliers discovered in a previous study 15 were successfully re - sequenced and could be enriched and sequenced in range of populations to investigate genome signatures of selection .
species and a further 112 were shared across at least three species . only two loci were detected from a single species ( fig .
number of reads mapped to original probe set ( ddrad loci ) and assembly - based reference with corresponding levels of similarity threshold ( * ) .
* overall loci counts across species . * * ( maq ≥ 5 ) .
) . after discarding snps in linkage disequilibrium , those with greater than 10 % missing data or a minor allele frequency ( maf ) lower than 0 . 05 , 313 informative snps remained across all modern
samples . these snps had a mean heterozygosity of 0 . 32 ± 0 . 16 and a global
of 0 . 15 . pca analyses of this data revealed three main clusters ( fig .
) , which is unsurprising given that these snps are testing species level differences , however , the remaining snps allow population - level assessment within multiple taxa .
species , including ‘off - target’ loci ( i . e . flanking regions adjacent to the targeted ddrad loci ) . all
) . the new assembly - based reference comprised 5 , 940 loci , of which 1 , 773 loci were assigned as off - target reads , rather than artefacts ( fig .
) , and therefore , an alternative source of informative sequencing data . blast analysis of off - target loci showed 925 significant hits to a
the assembly - based reference increased mapping success from 34 . 86 % to 49 . 23 % across the 40 modern
) . mapping results showed that 1 , 475 ( among 5 , 940 ) loci were monomorphic among specimens . among the variable loci , we found 1 , 731 homologous loci were consistently shared across the five species , 4 , 026 were shared across at least three species and 112 loci were found in only a single species ( fig .
) . employing an assembly - based reference maximised the use of available reads because it permitted the mapping of loci that were too divergent - in the non - targtet species - to be efficiently mapped to the original probe set .
descriptive statistics of mapped data based on the new assembly for modern and museum samples .
mean coverage and gc content ( gc % ) per sample was compared across species in modern samples . data expressed as mean ( sem ) . a , b , c different superscripts within a column denote significant differences ( p < 0 . 01 ) . adjustment for multiple comparisons : bonferroni .
) . for example , the heterogeneous mean coverage ( 0 . 631 ; p < 0 . 01 ) and gc content ( 0 . 346 ; p < 0 . 01 ) across species , for example , were both positively correlated with sequencing yield ( supplementary table
) . however , mean coverage and gc content were not reciprocally correlated . the mean coverage was significantly reduced in
) , the latter presented the greatest gc content . this implies that , unlike
genome was the most divergent as evidenced by higher sequence dissimilarities to the assembly - based reference . in line with this observation , differences in average sequence coverage have been reported in target - capture experiments for species with more than 5 % sequence divergence
overall 23 , 555 cross - species variants were identified within the 1 , 731 shared loci ( fig .
) from the assembly - based reference . the diversity of this reference is in accordance with the patterns in the original mapped loci ( table
( 4 , 106 ) . after removing snps with missing data greater than 10 % , maf lower than 0 . 05 and linked snps , a total of 647 informative snps remained ( 2x increase from the original mapped loci ) . this snp subset displayed a high proportion of polymorphic loci ( 0 . 42 ± 0 . 22 mean heterozygosity ) and low differentiation level ( global
) . this indicates that they are potentially more informative within species rather than among species comparisons , when compared with those from the mapped probe set . for example , in fig .
st among species equal to 0 . the pca analyses based on 647 snps revealed four main clusters : ( 1 )
should be synonymized ) . the assembly - based data set provided greater separation than the mapped probes , placing
species . this result indicates that differentiation levels among non - target species can be more accurately achieved by building an assembly - based reference of target - enriched sequencing data ; because it takes into account the full diversity of the sequencing dataset .
) were mapped to the assembly - based reference . the alignments were then compared with modern samples in terms of mean coverage , gc content , read heterozygous rate and snp diversity . prior to this comparison , dna damage patterns were established for each museum sample by tracking and quantifying cumulative substitutions frequencies of c to t at the 5′end and g to a at the 3′end in mapped reads using the mapdamage 2 . 0 software
( data not shown ) . no evidence of base mis - incorporation bias due to dna damage was found in any of the museum samples .
in contrast to the modern samples , a significant correlation between gc content and mean coverage ( 0 . 24179 ; p < 0 . 032 ) was found , suggesting that museum samples were highly impacted by sequencing coverage ( supplementary table
) . the overall gc content among museum samples were quite heterogeneous ( fig .
) and significantly correlated to the year of collection ( 0 . 483 ; p < 0 . 01 ) and a
) . we suggest that sequencing coverage was affected by dna fragmentation in museum samples leading to non - uniform representation of targets and heterogeneous gc content in sequencing libraries . however , patterns are difficult to interpret . for example , the highest overall coverage was observed in 50 - year - old
) . in both sample groups , the mean gc content significantly deviated from the mean of corresponding modern samples ( p < 0 . 01 in both cases ; supplementary table
museum samples were the only samples that demonstrated an increased read heterozygous rate ( p < 0 . 0066 ; in supplementary table
. it may also be related to the museum preservation methods applied to the specimens .
ratios as low as 1 . 01 and moderate dna concentration above 30–40 ng / µl ( as determined from the a
values ) exhibited acceptable average target coverage with no significant gc % deviations ( fig .
ratio greater than 1 . 0 and spectrophotometric quantification greater than 30 ng / µl are more likely to generate acceptable sequencing coverage . the a
ratio and dna spectrophotometric quantification cutoff , both prior to sequencing , and when assessing the results of sequencing .
because of the limitations of the museum samples used in this study , the amount of missing data was much higher in these samples . this is likely because the fragmentation bias of dna templates in library preparation led to uneven enrichment and sequencing coverage of targeted loci . the number of loci in each species ranged from 3 , 828 in 25 - year - old
) when compared with the modern samples . the loci also seem to be less variable , as determined by the number of snp per locus in all species . whilst cumulative substitution bias was not evident in museum samples , the overall deamination level in museum samples of
) . thus , in order to examine the usefulness of the target capture approach for incorporating museum samples into population genomic studies , we modified the variant - filtering settings to avoid false positive variants as a precaution . strand biased variants , heterozygous snps at the end of reads and snps with deamination pattern found towards the 5′ and the 3′ reads’ ends were filtered out resulting in a slightly different snp set from that used for the modern samples .
st estimates ( from 0 . 0589 to 0 . 0653 after filtering ) and pca distributions ( supplementary fig .
st values , suggesting that base modifications due to dna damage are not severe enough to influence overall differentiation or are not present among the variants called . thus , provided historic samples with extreme low coverage ( < 2 . 0x ) are removed , variant call accuracy can be adjusted to diminish base mis - incorporation bias to a negligible level .
here , ddrad libraries from two closely related lobster species , j . edwardsii and s . verreauxi were used as genome resources to design probes to capture and enrich genomic libraries of other five closely related species . the target - enriched sequencing generated thousands of informative markers for population genomics application with a small sequencing effort of 4 . 6 gbp only . the enriched sequencing of previously discovered ddrad loci enabled the recovery of 1 , 250 out of 2 , 366 ddrad loci in the species from which the probes were designed , including sample replicates between both methods . thus , it could potentially be used to enrich and re - sequence ddrad loci outliers discovered in previous studies 15 in a range of populations to investigate genome signatures of selection . also , this method circumvents one of the main disadvantages of ddradseq , that being the high level of missing data due to allele dropout .
remaining ddrad reads were assembled in pyrad 3 . 0 . 4 19 and used to build ddrad loci catalogues within and between species . samples were assembled in three datasets as follows : ( 1 ) j . edwardsii only ; ( 2 ) s . verreauxi only ; and ( 3 ) all samples from both species . for assemblies 1 and 2 we adopted a 95 % similarity threshold within species and for assembly 3 we established an 85 % similarity threshold . a maximum of three mismatches and a maximum of 0 . 5 site heterozygosity were allowed per cluster . to avoid clusters of paralogous loci we discarded all clusters with excessive shared heterozygous snps in more than four individuals and the paralogous filter was set to three . the ddrad loci were considered for probe design ( candidate ddrad loci ) only if they were shared across 10 individuals in assemblies 1 and 2 or 20 individuals in assembly 3 . pyrad assemblies’ settings and outputs are detailed in the supplementary methods s1 .
, and contigs with more than 90 % similarity across at least 55 % of the fragment length were discarded . highly similar clusters with spurious alignments resulting from low complexity dna sequences ( comprised by mononucleotide repeats ) were also discarded . as capture probes are known to support up to about 12 % sequence divergence
, 75 % similarity among ddrad loci was used as a limit . remaining repetitive regions among ddrad loci were identified and removed using repeatmasker web server
a total of 2 , 366 loci were finally selected as templates for bait manufacturing : 2 , 358 nuclear loci and eight mitochondrial loci . the mybaits ® set were estimated to cover 322 kb from 5 . 3 gb of j . edwardsii genome , including 80 loci identified as outlier snps putatively under selection in j . edwardsii 15 . in total , 4 , 732 120 - mer mybaits ® probes ( mycroarray ) were manufactured with 2x tiling density and an overlap of 60 bp between probes . probes sequences were deposited at the dryad data repository ( urltoken ) .
dna was extracted from adult lobsters ( pleopod clip or pereiopod muscle ) and phyllosoma larvae ( leg ) . all dna extractions were performed with the dneasy qiagen kit using spin columns econospin ( epoch life sciences ) . as the museum specimens resulted in low dna yield and purity levels , the isolation protocol was optimized accordingly . for these samples , dna recovery was improved by overnight incubation , final dna elution in 30 µl of ae buffer with three consecutive washes followed by column centrifugation . dna extraction and library preparation using museum specimens was performed using consumables dedicated to the museum specimens only with different batches for each species .
sequencing data was processed using the locally developed pipeline carlaseq ( urltoken ) described in detail in supplementary methods s4 . briefly , it involved the first four steps of the pipeline that consisted of adapter trimming , removal of contaminants ( human and microorganisms ) , merging of paired - end reads and de - multiplexing . the paired - end filtered reads were merged and trimmed to fragments up to 220 bp long . reads with average phred score lower than 33 were discarded .
processed reads were mapped to the reference ddrad loci , using bowtie 2 21 with ‘–very - fast - local’settings . samtools ( urltoken ) was used to sort alignments ( maq ≥ 5 ) . picard 2 . 6 . 0 ( urltoken ) was used to mark pcr duplicates from alignments by identifying fragments that are identical in insert length and related sequence composition . the capture reaction ensures that single strand fragments at a given locus are unlikely to be of equal length unless they are duplicates .
the efficiency of the target capture experiment was firstly assessed for the two species ( j . edwardsii and s . verreauxi ) from which the original probes were designed . this data set included 11 j . edwardsii specimens and 16 s . verreauxi , of which eight and 16 samples , respectively , were replicates of the original ddrad libraries sequenced . the number of on - target reads between species was compared using blast . then , mapping success ( bowtie 2 ) and the amount of missing data ( loci counts ) per number of samples were compared between ddrad and target - capture methods for both species .
c . a . s . wrote the main text , generated the data and performed the analyses . c . a . s . , n . m . and j . m . s . designed the study . c . a . s . , n . m . , j . m . s . , j . j . b . and b . g . conceived the idea and reviewed the manuscript . c . v . r . , l . n . w . , i . i . and c . e . h . collected the samples and contributed to data interpretation . c . a . s . and l . n . w . performed the laboratory work . c . a . s . , n . m . and j . m . s . led the writing of the manuscript with contributions from all authors .
supplementary information accompanies this paper at doi : 10 . 1038 / s41598 - 017 - 06582 - 5
publisher ' s note : springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations .
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