the bar-backed partridge ( arborophila brunneopectus ) , also known as the brown-breasted hill-partridge , is a species of partridge in the family phasianidae .

it is found in southwestern china and southeast asia .

bar - backed partridge

select an image : 1 . bar - backed partridge > > foraging 2 . bar - backed partridge 3 . bar - backed partridge 4 . bar - backed partridge 5 . bar - backed partridge > > pair 6 . bar - backed partridge > > adult 7 . bar - backed partridge > > adult 8 . bar - backed partridge > > adult 9 . bar - backed partridge > > adult 10 . bar - backed partridge > > chick 11 . bar - backed partridge > > adult 12 . bar - backed partridge > > adult 13 . bar - backed partridge > > adult 14 . bar - backed partridge 15 . bar - backed partridge 16 . bar - backed partridge 17 . bar - backed partridge 18 . bar - backed partridge 19 . bar - backed partridge 20 . bar - backed partridge
markedly different to any other partridge occurring within its range . the extralimital bar - backed partridge
, the geographic distribution is relatively well understood . the widely distributed bar - backed partridge (
bar - backed partridge ( arborophila brunneopectus ) is a species of bird in the phasianidae family .
has narrower chestnut collar and smaller , pale chestnut ear - patch . from bar - backed partridge
crested partridge ( rollulus rouloul ) 2538463578 _ 9421428e54 _ b . jpg ( 1024×888 ) | faisanes y pavos reales ( peacock ) | pinterest | partridge and bird
26 - 32 cm . boldly - marked partridge with chestnut collar and tawny ear - patch .
mcgowan , p . j . k . & kirwan , g . m . ( 2018 ) . bar - backed partridge ( arborophila brunneopectus ) . 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 ) .
27 cm . well - marked partridge with bold , black - and - white head markings and orange neck flush .
) , especially the old world partridges , were separated and recombined in many situations . among the five hill partridge species ,
] constructed the relationships of 10 hill partridge species in china based on morphology and biogeographic distribution . chen et al . [
gene and eight trna genes ( trna - gln , trna - ala , trna - asn , trna - cys , trna - tyr , trna - ser ( tga ) , trna - pro , trna - glu ) . the base composition of the h strand of the bar - backed partridge mt - genome is : 30 . 40 % a ; 13 . 41 % g ; 24 . 86 % t ; 31 . 3 % c , which reflects the typical a - t rich pattern in vertebrate mitochondrial genomes . the length of the
diverged at 7 . 31 mya . all hill partridge species divergence events occurred during the miocene when global temperatures underwent gradual cooling .
, while it changed the topology of the five hill partridge species from type i to type ii . in an additional test , the
) . since extreme events have caused speciation of hill partridge species , the current habitat fragmentation and geographic isolation may prompt further speciation .
as the species is centrally distributed within an area covered by the distributions of 22 south - east asian hill partridge species . the complete mitochondrial genome ( mitogenome ) of
26 - 32 cm . medium sized forest partridge with chestnut collar and dirty - white ear - patch , lacks a clearly defined black necklace from lower throat to ear coverts .
species based on two mito - genes and six nuclear intron sequence . the relationships of the five hill - partridge species in our study are consistent with zheng et al . [
) . we propose that climate cooling forced hill partridges species from higher altitudes to lower and migrated to the margins of , and away from , the yungui and tibetan plateaus . migration to warmer climates during such extreme cooling events may explains why the five studied hill partridge species are isolated and distant from the tibetan and yungui plateaus , leaving a geographic zone devoid of hill partridge species (
was determined and compared with four other hill partridge species mitogenomes . nadh subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant . together with 44 other mitogenomes of closely related species , we reconstructed highly resolved phylogenetic trees using maximum likelihood ( ml ) and bayesian inference ( bi ) analyses and calculated the divergence and dispersal history of
the five studied hill partridge distributions have been assigned different colors while the others 17 are all colored midnight blue . elevation information ( altitude : meters above sea level ) is represented by different heat colors .
despite this study’s results , the location of hill partridge species’ root at the base of phasianidae is still controversial . some nuclear dna markers , such as cr1 or nuclear ovomucoid intron g place this lineage at a near crown status [
but it ' s not just about shorebirds and the nearby rice fields , pools and marshes also produced baillon ' s , ruddy - breasted and white - browed crakes , pheasant - tailed jacana , slender - billed gull , stork - billed kingfisher , pallas ' s grasshopper warbler , white - shouldered and purple - backed starlings , asian golden weaver and so much more .
this partridge is listed as near threatened because , despite its small population and very small range , it occurs at many sites and it is not thought to be declining rapidly owing to the reported tolerance that this species and congeners show to forest degradation .
distribution the orange - necked partridge , arborophila davidi , ( see remarks 1 ) is endemic to southern vietnam , occurring principally in the provinces of dong nai and lam dong in lower hill ranges north of ho chi minh city . details of the few records are as follows :
represented the west and east ( respectively ) . the geographic distributions of the other 17 south - east asian hill partridge species were usually across mountainous terrain in indochina and maritime southeastern asia , where human activities and disturbance can be uncommon . these 17 species only overlapped with the distributions of
breeding there is no information . none is kept in captivity . threats the orange - necked partridge is one of two threatened bird species that are entirely restricted to the ‘south vietnamese lowlands endemic bird area’ , threats and conservation measures in which are profiled by stattersfield et al . ( 1998 ) .
split with other phasianidae species in asia and further divided into the diverse hill partridge species . we notice that all four divergnece events happened in the miocene ( 23 . 03 to 5 . 33 mya ) where there was a moderately warm climate but with two major temperature decreases at 14 mya and 8 mya respectively [
this newly - split partridge has a disjunct distribution in lowland forest where logging is rapid and on - going , and trapping pressure is prevalent . this total population is likely to be small and comprised of isolated , very small subpopulations which are likely to be undergoing continuing population declines . it is therefore classified as vulnerable .
the road from dak lua to talai , the only one to cut through part of the orange - necked partridge’s range in the national park , was closed to public traffic in 1998 ( g . polet in litt . 1999 ) . wwf and care are currently implementing an integrated conservation and development project ( icdp ) at cat tien national park ( a . w . tordoff in litt . 2000 ) . a printed birdlist for cat tien national park , with an illustration of orange - necked partridge on the cover , was produced in 1999 and the species was due to appear on a vietnamese postage stamp in 2000 ( g . polet in litt . 1999 ) .
this partridge is listed as least concern because , despite its small range and suspected modest population declines , habitat remains contiguous through large parts of its range and it is not believed to approach any of the thresholds for classification as vulnerable . the impacts of selective logging do not appear to be adverse and the extent of clear - felling within its altitudinal range is low .
mcgowan , p . j . k . & kirwan , g . m . ( 2018 ) . hill partridge ( arborophila torqueola ) . 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 ) .
] to confirm that the chains had become stationary so that the ess values of our parameters were all high ( over 200 or so ) . the final analysis was run for 10 million generations with trees sampled every 1 , 000 generations . treeannotator was then used to discard the first 20 % trees and to generate the consensus tree . geographic data of endemic bird areas of the 22 hill partridge species and the other 23 birds were obtained from the birdlife database [
mcgowan , p . j . k . , kirwan , g . m . & boesman , p . ( 2018 ) . chestnut - bellied partridge ( arborophila javanica ) . 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 ) .
9088 species with videos ( 80 . 9 % ) 10386 with photos ( 92 . 4 % ) 6746 species with sounds ( 60 % ) view more statistics
this species has a very large range , and hence does not approach the thresholds for vulnerable under the range size criterion ( extent of occurrence < 20 , 000 km2 combined with a declining or fluctuating range size , habitat extent / quality , or population size and a small number of locations or severe fragmentation ) . despite the fact that the population trend appears to be decreasing , the decline is not believed to be sufficiently rapid to approach the thresholds for vulnerable under the population trend criterion ( > 30 % decline over ten years or three generations ) . the population size has not been quantified , but it is not believed to approach the thresholds for vulnerable under the population size criterion ( < 10 , 000 mature individuals with a continuing decline estimated to be > 10 % in ten years or three generations , or with a specified population structure ) . for these reasons the species is evaluated as least concern .
recommended citation birdlife international ( 2018 ) species factsheet : arborophila brunneopectus . 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 .
has sometimes been considered conspecific with a . orientalis and a . javanica ( with a . campbelli , a . rolli and a . sumatrana ) ; others attribute morphological similarities to convergent evolution . close relationship with a . rufipectus or a . hyperythra , or both , also suggested by some . birds in guangxi ( s china ) probably belong to race henrici , but sometimes ascribed to nominate race . races well marked , particularly in head pattern # r . three subspecies recognized .
( blyth , 1855 ) – cs china ( sw yunnan ) and e myanmar s to w thailand and n laos .
( oustalet , 1896 ) – n & c vietnam ; probably also s china ( guangxi ) .
occurrence and distribution in c & s laos , also race or races involved , uncertain .
c . 26–29 cm ; male c . 317 g , female c . 268 g . barring on back , greyish - brown or brown breast , and black - and - white spots on flanks are distinctive in combination . female . . .
advertising call is bisyllabic whistled “ti - hu , ti - hu , ti - hu” with a seesaw rhythm and . . .
dry evergreen , semi - evergreen and hill evergreen forests , including bamboo - dominated areas , up to . . .
no information on diet available , but forages in leaf litter in coveys of 4–9 birds .
only nest record is from early jun , near rangoon , burma : four white eggs in a scrape well filled with bamboo leaves and grass , in open . . .
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two birds foraging on an open space in the forest edge , later preening themselves .
two bird feeding eatch other , later they fleed away after an alarm call .
tomasz doroń , frédéric pelsy , josep del hoyo , henrik bringsøe , pedroyayadrums , mark . van . beirs , johannes pfleiderer , twitcher .
previously published on avocet as av4835 . certainty : 100 % . id determined by : in the hand . gps : for ke go , threatened birds of asia . recorded 14 - 19 jun 1994
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del hoyo , j . , collar , n . j . , christie , d . a . , elliott , a . and fishpool , l . d . c . 2014 . hbw and birdlife international illustrated checklist of the birds of the world . volume 1 : non - passerines . lynx edicions birdlife international , barcelona , spain and cambridge , uk .
justification : this species has a very large range , and hence does not approach the thresholds for vulnerable under the range size criterion ( extent of occurrence < 20 , 000 km2 combined with a declining or fluctuating range size , habitat extent / quality , or population size and a small number of locations or severe fragmentation ) . despite the fact that the population trend appears to be decreasing , the decline is not believed to be sufficiently rapid to approach the thresholds for vulnerable under the population trend criterion ( > 30 % decline over ten years or three generations ) . the population size has not been quantified , but it is not believed to approach the thresholds for vulnerable under the population size criterion ( < 10 , 000 mature individuals with a continuing decline estimated to be > 10 % in ten years or three generations , or with a specified population structure ) . for these reasons the species is evaluated as least concern .
the global population size has not been quantified , but the species is described as uncommon or localised throughout its range ( madge and mcgowan 2002 ) . trend justification : the population is suspected to be in decline owing to ongoing habitat destruction and unsustainable levels of hunting .
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arborophila charltonii , a . tonkinensis , and a . graydoni ( del hoyo and collar 2014 ) were previously lumped as a . charltonii following sibley and monroe ( 1990 , 1993 ) .
has narrower chestnut collar and smaller , tawny - stained white ear - patch with black spots .
by plainer upperside , heavy black breast markings , greenish to yellowish - green legs and distinctive ear - patch and collar . from extralimital scaly - breasted and annam partridges
( birdlife international 2001 ) . seems to tolerate disturbed forest with records from degraded sites in south thailand , but there are very few recent records anywhere on sumatra and it may only survive here in the north ( del hoyo et al . 1994 , birdlife international 2001 , madge and mcgowan 2002 ) .
the global population is thought to number fewer than 10 , 000 mature individuals ( perhaps fewer than 2 , 500 , as the nominate may number fewer than 1 , 000 individuals , and atjenensis fewer than 100 [ birdlife international 2001 , madge and mcgowan 2002 ] ) , with no subpopulations numbering more than 1 , 000 mature individuals . trend justification : there are no data on population trends ; however , habitat loss and degradation , in combination with trapping pressure , are suspected to be driving a moderately rapid decline .
forest destruction in the sundaic lowlands of indonesia and malaysia has been extensive ( sumatra lost almost 30 % of its forest cover 1985 - 1997 ) , because of a variety of factors , including the escalation of logging and land conversion , with deliberate targeting of all remaining stands of valuable timber including those inside protected areas , plus forest fires ( particularly in 1997 - 1998 ) . declines caused by habitat loss are compounded by trapping for the cage - bird trade .
survey to assess the size of all sub - populations . monitor trends in all sub - populations . research the species ' s tolerance of logged forest . protect large areas of primary and old secondary forest within its range .
by plainer upperside , heavy black breast markings , reddish bill with greenish tip , greenish to yellowish - green legs and distinctive ear - patch and collar . from extralimital scaly - breasted and annam partridges
benstead , p . , mahood , s . , taylor , j . , martin , r , symes , a . , westrip , j .
this species has a very large range , and hence does not approach the thresholds for vulnerable under the range size criterion ( extent of occurrence < 20 , 000 km 2 or area of occupancy < 2 , 000 km 2 combined with a declining or fluctuating range size , habitat extent / quality , or population size and a small number of locations or severe fragmentation ) . the population size has not been quantified , but it is not believed to approach the thresholds for vulnerable under the population size criterion ( < 10 , 000 mature individuals with a continuing decline estimated to be > 10 % in ten years or three generations , or with a specified population structure ) . despite the fact that the population trend appears to be decreasing , the decline is not believed to be sufficiently rapid to approach the thresholds for vulnerable under the population trend criterion ( > 30 % decline over ten years or three generations ) . for these reasons the species is evaluated as least concern .
( 2016 ) estimated the maximum area of occupancy ( calculated as the remaining tree area within the species’s range ) to be c . 2 , 322 km
the global population size has not been quantified owing to recent taxonomic splits . trend justification : there are no data on population trends ; however , despite its tolerance for disturbed and modified habitats , habitat loss and degradation , in combination with trapping pressure , are suspected to be driving an overall population decline .
but differs primarily by broader black band through eye , black gorget , orange neck flush , broader supercilium behind eye , grey on underparts and larger black flank markings .
browne , s . , evans , t . , pollard , e . , samnang , c . , tordoff , j . & tran vy , n .
( nguyen xuan dang and osborn 2004 ) and dak o sfe . it is predicted to occur in a number of other sites and may be widespread in southern lam dong , dong nai , binh duong and binh phuoc provinces , where suitable habitat remains
. 2009 ) . the species is apparently rare ( or perhaps just elusive ) in some areas . a slow decline is suspected owing to on - going pressures placed on forest habitats , but the apparent ability of this species ( as well as many congeners ) to tolerate degraded habitats suggests that current forestry operations are unlikely to represent a major threat .
the species is now known from many sites in southern vietnam and one in cambodia . the area of suitable habitat has been found to be more extensive than was previously thought and given the population densities recorded in several congeners and their ability to persist in degraded habitats it seems likely that the population approaches 10 , 000 individuals , and it is thus placed in the band 2 , 500 - 9 , 999 individuals . this equates to 1 , 667 - 6 , 666 mature individuals , rounded here to 1 , 500 - 7 , 000 mature individuals .
this species is assumed to have declined owing to clearance within its very small range , but it is probably tolerant to some degree of forest degradation . declines are thought to be continuing as forest clearance continues .
it is resident in evergreen forest in lowlands and foothills , from 120 m to at least 600 m , particularly hills covered with non - thorny bamboo . it also thrives in a variety of secondary habitats including tall scrub , bamboo ,
, logged evergreen and semi - evergreen forest plantations , perhaps preferring bamboo - covered slopes with a thick leaf - litter layer . thus it appears to be able to tolerate considerable habitat disturbance and modification . pairs call in duet . calling reportedly peaks in march but has been recorded in november in cambodia .
of the protected area are in the process of being degazetted to allow further clearance . there is currently extensive legal collection of bamboo in the sbca , although the impact of this on the species is unknown
( e . c . s . baker , 1921 ) – w himalayan foothills ( himachal pradesh in india to w nepal ) .
( valenciennes , 1825 ) – w nepal e in foothills to se tibet and n yunnan ( sc china ) and extreme n myanmar .
( ogilvie - grant , 1906 ) – n & w myanmar and sc china ( w yunnan ) .
28–30 cm ; male 325–430 g , female 227–386 g . head pattern distinctive . female differs mainly on crown and throat ; lacks male ' s head pattern and neckband . . .
most vocal early morning and evening . advertising call is far - carrying ( audible over 1 km ) , . . .
evergreen forest and scrub , usually between 1500 m and 3000 m , but higher and lower in some areas ( . . .
seeds , shoots , berries , insects and small molluscs ; also larvae . scratches for food amongst leaf litter , foraging in groups of 5–10 . . .
considered to be monogamous . season apr–jul in india , earlier at lower altitudes ; feb–may in race
no altitudinal movements definitely reported , but in bhutan not recorded above 3000 m in winter ( to . . .
not globally threatened ( least concern ) . considered fairly common in nepal . no information on abundance or trends in indian subcontinent , other than density of 14·5 . . .
from obc bulletin 33 , june 2001 , reproduced from threatened birds of asia : the birdlife international red data book , with kind permission of birdlife international .
vietnam bu kroai , binh phuoc province , may 1927 ( specimen in mnhm , delacour and jabouille 1931 ) ; c . 64 km east of phu rieng , binh phuoc province , c . 250 m ) , february 1927 ( specimen in bmnh , delacour et al . 1928 ; see remarks 2 ) ; cat tien national park , dong nai , lam dong and binh phuoc provinces , three on a small isolated hill at c . 150 - 200 m near dak lua substation , 37 km south - east of bu kroai , june 1991 ( eames and robson 1992 , mcgowan 1992 , robson et al . 1993 , nguyen cu in litt . 1997 ) , with several subsequent sightings at the same location ( oriental bird club bull . 18 [ 1993 ] : 67 - 70 , oriental bird club bull . 24 [ 1996 ] : 59 - 65 , nguyen tran vy in litt . 1997 ) , groups of 2 - 5 recorded during fieldwork in february - april 1997 ( atkins and tentij 1998 ) , up to 27 recorded in the cat loc sector , february - april 1997 ( j . c . eames in litt . 1997 , atkins and tentij 1998 ) , up to three pairs on nearby elephant mountain , april 1997 ( nguyen tran vy in litt . 1997 ) , and subsequently recorded by many observers ( e . g . b . wright in litt . 1999 ) .
population before its rediscovery , the global population of this species was estimated at below 1 , 000 ( mcgowan et al . 1994 ) . despite intensive searching , only small numbers were initially observed in cat tien national park and the species was presumed scarce at this site ( eames and robson 1992 , nguyen cu in litt . 1997 ) . however , it has more recently been described as occurring ‘everywhere on hills’ in the park and ‘common’ in its cat loc sector , with 27 sightings in four days ( atkins and tentij 1998 ) .
food there is no information , although diet and foraging behaviour are presumably similar to related arborophila partridges .
loss of habitat is compounded by high levels of hunting by local ethnic groups such as the chau ma and s’tieng and by immigrants from northern vietnam ( nguyen cu in litt . 1997 ) . as pheasants and partridges are commonly snared by people working in the forest in vietnam ( eames et al . 1989a , b , c , eames and robson 1992 ) , it is likely that hunting poses a significant threat to surviving populations of this species , at least outside cat tien national park .
measures taken the species occurs in cat tien national park , a site considered irreplaceable to the long - term conservation of east asian galliforms ( mcgowan et al . 1999 ) . the park originally covered 383 km2 ) but , with recent extensions to include the tay cat tien and cat loc sectors , now covers 738 km2 ) ( atkins and tentij 1998 , g . polet in litt . 2000 ) . as a result , protection of the cat loc sector is much improved , with 30 forest guards now stationed there , an increase from seven in 1998 ( g . polet in litt . 1999 ) . in 1998 , 110 park guards were stationed in the nam cat tien sector of the park ( which excludes the cat loc and tay cat tien sectors ) ; not only has the number of guards increased in the last few years , but the level of protection is much higher , a circumstance leading to a marked decline in poaching incidents ( g . polet in litt . 2000 ) .
fieldwork should be targeted towards identifying new populations of the species . remaining habitat in lam dong , dong nai , binh duong and binh phuoc provinces should receive immediate attention . for example , the species might occur at bu gia map nature reserve and a survey of this protected area should be undertaken at the earliest opportunity ( nguyen cu in litt . 1997 , atkins and tentij 1998 ) . the species responds strongly to playback of taped vocalisations ( atkins and tentij 1998 ) and this method should be used judiciously in surveys for the species .
oriental bird club , uk registered charity 297242 , is for people around the world who are interested in birds of the oriental region and their conservation .
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the birdwatching tours overview page has complete background information , including lodging and food details and a list of key species , for all our birdwatching tours .
day 1 - depart khon kaen at 5am and arrive at nam nao national park around 7am .
day 2 - return to khon kaen in the late afternoon . optional visit to a handicraft village or historic temple on the way back .
if our itinerary doesn ' t fit your exact needs and desires , please let us know .
add 600 / 1 , 200 / 1 , 800 baht ( 1 - 2 / 3 - 6 / 7 - 8 people ) for each friday , saturday , sunday , and holiday night spent in nam nao national park .
all sightseeing and activities as specified in the itinerary with an english - speaking guide and a local park ranger , entrance fees , transportation in an air - conditioned vehicle , snacks and cold water in the vehicle , hotel transfers , accommodation , accident insurance , taxes , and pre - departure travel consultation .
transportation to khon kaen , meals and drinks , travel and medical insurance , personal expenses ( such as laundry , souvenirs , snacks , etc . ) , tips / gratuities , visa fees ( thai visas are free or not required for most international visitors . ) , and any additional expenses incurred due to airline schedule changes , natural disasters , political actions , or other factors beyond our control .
for tours longer than one day , a non - refundable deposit of 30 % is required as soon as possible after making your reservation .
the full payment is due before the tour begins . this can be done after you arrive in thailand , as long as you have access to sufficient funds before you depart on your tour .
we accept payment via cash ( thai baht , us dollars , british pounds , and euros ) , atm transfer and counter deposit to siam commercial bank , wire transfer ( bank - to - bank or through western union and moneygram ) , and credit / debit card ( through western union and moneygram ) . note that the new western union and moneygram online service is far cheaper than the original same - day counter agent service , and also most likely cheaper than your bank .
if local taxes and / or fuel prices increase significantly , we reserve the right to add comparable surcharges .
copyright © 2011 - 2018 isan explorer , khon kaen , thailand . all rights reserved .
day 3 - return to khon kaen in the late afternoon . optional visit to a handicraft village or historic temple on the way back .
[ ecological distribution and spatial niche of pheasants in the karst mountains of southwest guangxi province , china ] . - pubmed - ncbi
warning : the ncbi web site requires javascript to function . more . . .
[ ecological distribution and spatial niche of pheasants in the karst mountains of southwest guangxi province , china ] .
college of animal sciences and technology , guangxi university , nanning 530005 , china .
( j . f . gmelin , 1789 ) – mountains of w java .
, quite dissimilar to any of congeners . crown and nape orange - rufous , streaked and mottled dark grey . . .
song typically in duet , one bird emitting a fast series of loud piping whistles , gradually . . .
forest between 300 m and 3000 m , though recent records are all from altitude between 600 m and 2500 . . .
season apparently extended , with records from jan–apr and jul–nov . lays up to four eggs . in captivity , male constructs domed . . .
not globally threatened ( least concern ) . mace lande : vulnerable . little direct information ; species considered threatened due to habitat loss , and forest clearance has . . .
this pair of scaly - breasted partridges were displaying an interesting behaviour when frightened , by crouching down back - to - back , as if to watch for danger from both directions . i only caught them on video doing it once , but wonder if this is a natural behaviour in the wild against predators ?
ok ok so i ' ve posted lots of photos from this place over the years but the truth is that this is such a great site and such an awesome experience . whether you are taking photos with your slr or bridge camera , you just can ' t fail to get some impressive shots .
this visit turned up a few new species that i ' ve never come across before and i managed to get some reasonable pics of all of them , apart from a grey - faced woodpecker . . . . . .
of course there were the usual birds present , so here ' s a section of my best pics . . . . . . . .
have been playing around with the video function of my nikon d7200 whilst spending time at the numerous feeding stations and water holes on my recent thailand tour . see what you think . . . . . . ?
this dark - sided thrush was seen every time we walked along the boardwalk at the top of doi inthanon . it ' s a bona fide zoothera thrush and gets my pulse racing every time .
now who can ' t be moved by this siberian rubythroat . . . . . ?
loved this northern red - flanked bluetail . . . a bit brief but it ' s such a sexy bird . . . . !
and best of all , the rusty - naped pitta from doi ang khang . a little too close i ' m afraid . . . !
the shorebird heaven of phetchaburi province is home to a small wintering population of spoon - billed sandpipers and that is obviously the major draw here . and quite right too ! classified as critically endangered by birdlife international they state that there are only 240 - 400 mature individuals left in the wild and this site is undoubtedly the ' easiest ' place for visiting birders to go and see this very special bird . we found 3 spoonies , one of which had a green leg flag from the reintroduction project . the worrying thing here is that the owner of these salt pans is considering closing them to visiting birders due to a few instances of bad behaviour . . . . . . . .
the other major target species here is nordmann ' s greenshank , classified as endangered by birdlife international with a reputed 330 - 670 mature individuals . they are always difficult to get close too but this year we had our best views ever of several groups and enjoyed watching them on repeated occasions .
asian dowitchers have been rather more erratic this year and it wasn ' t until our last morning in the area that we caught up with them , thanks to nick upton ' s local knowledge . although a little distant we watched 3 birds at a range of some 50m through the scope and felt a little relieved ! here ' s a photo of a different group from a tour we did a couple of years ago .
) - a new bird for thailand and previously found by nick upton some 6 weeks earlier .
a huge variety of other shorebirds were seen on our tour and on one day we saw 40 species out of a total tour count of 46 . . . ! so we saw oriental pratincole , 100 ' s of great knots , long - toed stints , red - necked phalaropes , broad - billed sandpiper , far eastern curlew , greater sandplover , greater painted snipe and thousands of red - necked stints . for anyone with an interest in shorebirds , this is the place to be . and if you ' re not . . . . oh well . . ! but the spectacle of seeing so many birds is something to behold .
thailand never disappoints and our tours seem to get better and better every year . take a look a nick upton ' s blog
so i can ' t wait to return . next year ' s tour is already full , but looks like i will be back in june for our thai pita tour where we hope to see blue , blue - winged , hooded and hopefully the ever elusive eared pitta . we might also make a detour to get mangrove and malayan banded pittas as well . if you fancy joining us then take a look at our itinerary -
i ' m the owner of zoothera birding , a uk based birding holiday company . our emphasis is on seeing all birds and wildlife well and , like most birders , we really like the endemics , rare , scarce , speciality and skulking species a lot ! we believe our small group sizes greatly increase the tour quality . it is my hope that you find these blog posts of interest and you can see what species are being seen and also get a flavour of what happens on a zoothera tour . but this blog only covers my tours and we have plenty of other tours to destinations such as colombia , costa rica , brazil , guyana , madagascar , south korea , chile , guatemala , armenia and many others . just go to urltoken for a full tour programme . happy birding !
a gray - headed chickadee delivers food to a nest full of hungry chicks . photo aaron lang . an incredible opportunity awaits ! in june i’ll be leading a group . . .
juvenile baird ' s sandpiper at cuckmere haven . today i did a dawn - to - dusk , 260 - mile birding loop of kent and east sussex , logging 97 species in the process . . . .
by yoav perlman mandtii black guillemot featured on birding frontiers in the past – see here and here . it also featured in martin’s challenge series – wint . . .
camel estuary : 19 mediterranean gull on the main channel between padstow / porthilly . ( s grose ) marazion marsh rspb : 2 mute swan , 24 mallard , 1 gadwall , 13 . . .
[ image : oystercatcher12 ] virtually every area of bird habitat in north kent is under threat , from unsympathetically placed proposals for a solar farm at gra . . .
three * mediterranean gull * , two adults and a first summer , flew over the spit and upriver with 120 + * black - headed gull * feeding in the beach . elsewhere the . . .
* exilerating day at sea * * monterey bay national marine sanctuary * this is a trip report for shearwater journeys ' august 25 , 2017 monterey bay pelagic trip . . .
with over 378 , 000 birds ringed by fibo , there have been some remarkable movements logged , with ringed birds recovered as far away as brazil , canada , russia . . .
* baltimore oriole * - barton cove , franklin co . , ma . may 3rd , 2018 . other passerines in the boat ramp area included warbling and red - eyed vireos , and severa . . .
[ all photographs copyright , gary nunn 2017 ] – i was just getting into my car at fort rosecrans national cemetery about 8 : 30am this morning , to head downhil . . .
below are some images of mixed auks moving west off pendeen late last year . they mostly include guillemot , but there are also a few razorbills . pendeen i . . .
peter clarke lived for holme bird observatory in north norfolk - it ' s birds , mammals & butterflies filled his life of that environ for the best part of 50 . . .
the last day of the season was quite busy ! it was a nice warm day topping out around 52 degrees , with southeast and south winds that produced over 4000 bi . . .
* had a couple of visits on forest with an all - dayer at the tail end of last week and a couple of hours again tail end of this weekend , highlights being t . . .
during my week in sweden i had some wildlife other than birds . as with birds , no unexpected levels of excitement were reached , but overall it was enjoyable . . .
this is one of the major reasons why i only take small groups to thailand , but read on . . . . . . . . spent the first few hours of . . .


donax trunculus ( abrupt wedge shell , wedge clam ) , is a bivalve species in the family donacidae .

it is native to the mediterranean and atlantic coasts of western europe .

it is locally known as tellin , tellina , telline or " tenille " in french , tellina or coquina in spanish , and conquilha or cadelinha in portuguese , and is consumed as a food in these countries .

there is a very similar shellfish in australia locally known as " pippies "

donax trunculus

nathan wilson changed the thumbnail image of
conquilha ; cadelinha / / lovely donax ( donax trunculus )
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eduard solà added the catalan common name
tellina
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donax trunculus linnaeus , 1758
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eduard solà added the catalan common name
tellerina
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donax trunculus linnaeus , 1758
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eduard solà added the catalan common name
escopinya francesa
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donax trunculus linnaeus , 1758
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hans - martin braun added the french common name
donace tronquée
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donax trunculus linnaeus , 1758
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en - truncate donax , fr - flion tronqué , sp - coquina truncada .
the reports of donax trunculus done by pelseneer ( 1881b ) and vonck ( 1933 ) are probably wrong according to dumoulin ( 1984 ) .
species of donax often dislodge and rebury between wave surges using their foot ( mikkelsen and bieler , 2007 : pages 341 - 342 ) . while d . trunculus does not actively migrate , it can be carried to different parts of the shore by waves and the tide .
d . trunculus has an observed maximum lifespan of 6 years , but 4 years is more typical ( deval , 2009 : pages 551 - 558 ) .
d . trunculus is commercially explored and consumed in spain , italy , and other countries ( ramon et al . 1999 , pages 37 - 46 ) .
displayed behaviors are related to reproduction , feeding , locomotion , and basic reactions . most of every year is spent preparing for reproduction , with spawning occuring during the summer . as suspension feeders , species of donax feed on loose organic particles and plankton that float nearby . locomotion is provided by a large and muscular foot , which helps species of donax reburrow between wave surges . it also responds to light in spite of a lack of eyes ( mikkelsen and bieler , 2007 : pages 341 - 342 ) .
d . trunculus is commercially explored in spain and italy , but because of its large natural population , it is able to withstand the impacts of this activity ( ramon et al . 1999 , pages 37 - 46 ) . there is virtually no risk of d . trunculus becoming an endangered or protected species in the near future .
d . trunculus is a suspension feeder that eats seston , a mixture of live plankton and floating organic material ( ramon et al . 1999 , pages 37 - 46 ) .
the sex ratio of d . trunculus is 1 : 1 . it reaches sexual maturity by its second spring / summer ( deval , 2009 : pages 551 - 558 ) .
the shell of d . trunculus is wedge - shaped , equivalve , no longer than 150mm , with the posterior longer than the anterior . exterior coloring varies , but is usually muted when compared to the polychromic shell interior . the interior is smooth and the pallial line is strong . d . trunculus has two cardinal teeth in each valve and a heterodont hinge plate .
a 18s rna fragment of d . trunculus was sequenced as part of a study that identified different bivalve species in food using molecular data . this method is useful because shells are not available for species determination in most cases when d . trunculus is presented as food . it was found that seafood products are often mislabeled ( espineira et al . , 2009 : pages 495 - 502 ) .
d . vittatus is easily mistaken for d . trunculus , but the latter has a larger shell and its inner margin is smooth below the ligament , as opposed to d . vittatus , which is notched .
in great britain d . trunculus is found on the southern coast ( jeffreys , 1863 ) . south of great britain it occurs along coasts including western europe and western africa down to senegal , as well as in the mediterranean , the aegean , the black , and the red seas ( jeffreys , 1863 ; dillwyn , 1817 ) . while d . trunculus is common in north - eastern france and the channel islands , it is comparatively rare in britain ( cockerell , 1888 ) . d . trunculus ' presence in the red sea means that it has colonized the area in spite of the invasive species that have been entering the mediterranean through the suez canal ( mooney and cleland , 2001 ) .
while the landmarks along the road to sexual maturity are the same for all d . trunculus , the timing is slightly different from population to population . the gametogenic development of d . trunculus in the sea of marmara may occur as early as march , but usually comes later . spawning is from april to july , with a peak in may and june . from then until november , d . trunculus enters a resting period where the gonad cannot be distinguished ( deval , 2009 : pages 551 - 558 ) . however , off the coast of israel gonadal development begins in january or february , with oocyte maturity occuring in june or july . the mass spawning is in august and sexual development then regresses until winter ( neuberger - cywiak et al . , 1989 ) .
recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves . null alleles have been associated with heterozygous deficits in many studies . while several studies have tested for its presence using different analytical tools , few have empirically tested for its consequences in estimating population structure and differentiation . we characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam , donax trunculus . we carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles . we tested the robustness of microsatellite genotyping for population assignment by showing that well - recognised biogeographic regions of the south atlantic and south mediterranean coast of spain harbour genetically different populations .
however , a natural threat to the species that could possibly destablilize populations is the trematode bacciger bacciger . this parasite embeds itself in the gonadal tissue of d . trunculus and eventually leads to castration and lack of physical sexual differentiation ( ramon et al . 1999 , pages 37 - 46 ) .
occurs near the shore as well as between 0 and 2 meters below the surface ( neuberger - cywiak et al . , 1989 ) . d . trunculus prefers to live in high - energy environments with suspended particles and wave action ( ramon et al . 1999 , pages 37 - 46 ) .
d . trunculus accumulates trace amounts of metals such as cd , cu , fe , mn and zn and is useful as a bioindicator for these materials . this ability may be useful in detecting and preventing water contamination or pollution ( romeo and gnassia - barelli , 1988 : pages 223 - 227 ) .
anterior and posterior pedal retractor muscles , as well as pedal protractors and elevators , are all present in d . trunculus . the foot is large , muscular , and bladelike . incurrent and excurrent water flows are at the posterior end . the digestive system includes a stomach with a posterodorsal gastric appendix and a coiled midgut . from here food passes through the hindgut and exits at a sessile rectum ( mikkelsen and bieler , 2007 : pages 341 - 342 ) .
samples of d . trunculus were collected from three sites , two located in the atlantic coast and one in the mediterranean sea . in the southwest atlantic coast of spain , we collected samples from two adjacent localities , isla canela ( n = 66 ; 37°10′11 . 334″n , 7°22′14 . 25″w ) and doñana national park ( n = 77 ; 36°55′6″n , 6°28′20″w ) , in the province of huelva . the third sample was obtained from the mediterranean coast of spain from caleta de vélez , malaga ( n = 52 ; 36°44′49″n , 4°4′32″w ) . the euclidean geographic distance between the first 2 sites over coast line is 85 km ; while between the second and the third site is 287 km ( 128 km from doñana national park to the strait of gibraltar and 158 km from there to the third site ) . the first two samples are separated from the third one by the strait of gibraltar which is well - recognised as a major geographical barrier to dispersal among marine taxa ( perez - losada et al . , 2007 ; sá - pinto et al . , 2012 ) . permit of sampling was approved by the consejeria de medio ambiente ( permit number 2011107300001463 ) .
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shell acutely triangular , inequilateral and bright looking . the longitudinal striae are fine and there are no transverse or concentric striae . the color varies from olive , blended with chestnut with white rays , to yellow - orange or near - white . in addition , the posterior margin is abruptly truncate and the lateral teeth are often rudimentary or indistinct ( jeffreys , 1863 ) .
depth range based on 1 specimen in 1 taxon . environmental ranges depth range ( m ) : 20 - 20 note : this information has not been validated . check this * note * . your feedback is most welcome .
in portuguese , and is consumed as a food in these countries . there is a very similar shellfish in australia locally known as
pippies
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biological and ecological features of the species : a bivalve mollusc with an oblique shaped shell that is very thin , slightly flattened with a smooth surface . the front is rounded , the back is shorter . it is yellowish or brownish - purple on the outside , whitish inside .
nutritional qualities : bivalve mollusks belonging to the family tellinidae are appreciated for their delicate taste and tender meat . they may be used in several recipes in place of clams , especially in first courses . like clams , these mollusks are a low source of calorie , fat and omega - 3 fatty acids . the protein content is not high . they are a good source of minerals .
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the smooth shell shows thin radial streakings . it is light coloured and covered by a bright brown periostracum .
it is a sought after prey by carnivorous gastropods : for these reasons it is often possible to find perforated shells on the beach .
# 365papers ( 84 / 365 ) : rico et al . show that null alleles in usats do not effect population str analysis urltoken
this is an open access article distributed under the terms of the creative commons attribution license , which permits unrestricted use , distribution , reproduction and adaptation in any medium and for any purpose provided that it is properly attributed . for attribution , the original author ( s ) , title , publication source ( peerj ) and either doi or url of the article must be cited .
rico c , cuesta ja , drake p , macpherson e , bernatchez l , marie ad .
simulation studies suggest that null alleles with frequencies between 5 % and 8 % should have only minor effects on classical estimates of population differentiation , but that higher frequencies would bias such parameters ( chapuis & estoup , 2007 ) . null alleles have been associated with heterozygous deficits in many studies and several have tested their presence and effects in population structure estimates using various analytical and simulation tools ( e . g . , dąbrowski et al . , 2015 and references therein ) . however , to the best of our knowledge no study has empirically tested for its consequences in estimating differentiation using population samples separated by well characterised biogeographic barriers .
dna was extracted from different tissues using a slightly modified version of aljanabi & martinez ( 1997 ) salting out method . namely , after addition of the saline solution , the mixture was centrifuged for 30 min at 10 , 000 g . also , dna precipitation was achieved by incubation at −20 °c with 600 µl isopropanol for 30 min . then , after washing out the pellet with 70 % ethanol , we centrifuged at 10 , 000 g for 10 min .
for the preparation of the ssr enriched library we followed the protocol of santana et al . ( 2009 ) . in brief , we started with 20 µg of high molecular weight genomic dna ( gdna ) to enrich for ssr with issr - pcr method ( zietkiewicz , rafalski & labuda , 1994 ) , but without using the final stage of cloning in a bacterial vector . the primers used were : issr1 ( 5′ - ddb ( gtc ) 5–3′ ) , issr2 ( 5′ - dhb ( atc ) 5 - 3′ ) , issr3 ( 5′yhy ( gt ) 5g - 3′ ) , issr4 ( 5′ - hvh ( cat ) 5 - 3′ ) , issr5 ( 5′ - ndb ( tgt ) 7c - 3′ ) , issr6 ( 5′ - ndv ( ct ) 8–3′ ) , and issr7 ( 5′ - hbdb ( aac ) 4–3′ ) . for each trial microsatellite - enriched dna we analysed in 5 µg in the pyrosequencing platform roche 454 gs - flx . for each sample , a single - lane sequencing run using portioned sections of the picotiterplate was performed according to the manufacturer’s protocol preparation . sample preparation and analytical processing such as base calling , were also performed on site according to the manufacturer’s protocol .
to uncover sequences containing microsatellites in the pyrosequence reads , we used the mreps software which has been designed to isolate and characterise highly polymorphic microsatellite loci ( kolpakov , bana & kucherov , 2003 ) . for the purpose of evaluating the number of microsatellite - containing reads from the dataset , we defined two filtering steps . in the first step , we included loci containing di - and tri - , nucleotides ssr with 20 to 60 base pairs of repeated units ( i . e . , at least 10 tandem repeats for di - , and seven for tri - nucleotides ) , and a maximum proportion of non - perfect repeats of 0 . 333 .
since hundreds of potential loci were detected in this filtering step and only loci with sufficiently large flanking sequences around the microsatellite are potentially useful for primer design for successful pcr amplification , we selected loci with a minimum of 40 flanking nucleotides on each side of the tandem repeated units . these loci are referred as “potentially amplifiable loci” , or pal ( castoe et al . , 2012 ) . from the 85 pal identified , we selected 52 sequences for subsequent analyses . primer design was performed using the on - line version of primer 3 ( rozen & skaletsky , 2000 ) . a total of 52 primer pairs were thus designed and synthesised with the universal m13 primer in the 5′ end of the forward primer for their later analysis using a fluorescently labelled m13 primer according to schuelke ( 2000 ) .
we carried out a high number of tests to find optimal multiplexes , grouping several markers of different allelic sizes in a single reaction and adjusting the concentration of the primers according to the strength of the signal . for the multiplex reactions , we used the qiagen ® multiplex pcr kit ( qiagen , toronto , can ) . final volumes and concentrations of the master mixes were optimised to reduce the total genotyping cost ( guichoux et al . , 2011 ) . pcr reactions were done in a final volume of 10 µl for all multiplexes , with 3 µl of primer mix , 5 µl of qiagen multiplex mix , and 2 µl of gdna template ( 10–15 ng / µl ) . the cycling conditions for the four multiplexes differed only in the annealing temperature ( table 1 ) : an initial step at 95 °c for 15 min ; then 35 cycles at 94 °c for 30 s , 54 to 61 °c for 3 min and 72 °c for 1 min ; and a final elongation step at 60 °c for 30 min . only 16 loci produced codominant fragments ( i . e . , one allele of maternal and one of paternal origin ) in the 48 samples analysed . table 1 summarises the information about the primers sequences , concentrations in the primer premix ( µm ) , genbank accession numbers , and multiplex panel annealing temperatures .
one hundred ninety - five individuals were used for this analysis . locus identity , type of florescence dye in the forward primer , panel numbers ( mp ) indicate groupings of loci sharing a multiplex in the pcr reaction , primer sequences , repeat motif ssr , primer concentrations ( [ c ] µm ) in the primer mix , number of alleles ( n a ) found , range of allele sizes ( range , bp ) , observed ( h o ) and expected ( h e ) heterozygosity , f is , departure from hardy–weinberg equilibrium ( hwe ) , polymorphism information content ( pic ) , and genbank accession numbers . annealing temperatures for each panel were as follows : kit 3 = 60° c , kits 1 , 2 , 4 = 58°c .
we also estimated null allele frequencies and f st using the software freena ( chapuis & estoup , 2007 ) with a number of replicates fixed to 25 , 000 . we ran this analysis using the ena correction method to efficiently correct for the positive bias induced by the presence of null alleles on f st estimation and so , to provide an accurate estimation of f st . we ran both software programs in order to see if the presence of high frequencies of null alleles can affect the f st estimates knowing that arlequin does not take into account the presence of null alleles compared to freena .
the possibility of genotyping artefacts was examined in several ways . first , a subset of samples (
= 94 ) were re - amplified for each of the 16 loci under relaxed annealing temperatures ( 4 °c lower ) to verify that additional alleles had not been missed . second , we used the software
) to test for stuttering and large allele drop - out and to obtain various estimates of the expected frequency of null alleles ( r ) . these , in turn , were used to calculate the expected number of null homozygotes ( i . e . , when both alleles remain undetected ) using the 4 ( nr
) so that we could compare these estimates to the actual number of individuals that fail to amplify systematically in repeated pcr reactions . the analysis yielded a close match between the expected and observed number of null homozygous . third , we estimated the frequency of null alleles using ml - nullfreq (
) . therefore it is reasonable to hypothesise that the samples from the atlantic coast separated by 85 km of continuous shoreline would not be genetically distinct from each other , but would be differentiated from the mediterranean population . to test this hypothesis even when the presence of null alleles in our loci was already confirmed , we took advantage of the algorithm introduced by
) assuming no a priori structure and allows for the presence of null alleles in the dataset . to test the effects of null alleles in the population structure depicted by these loci , we first estimated the most likely number of populations (
) assuming no null alleles and using the locprior option and subsequently , we repeated the analysis but incorporating the recessivealleles as well as the locprior options in structure . in this case , the program assumes that the recessive allele is never observed in homozygous state but it might be present . this analysis , partitions multilocus genotypes into clusters , while minimising departure from hardy–weinberg expectations and linkage disequilibrium among loci , and it estimates individual ancestry proportions to each putative cluster . we therefore investigated the most likely
running ten independent simulations . all simulations were run using default parameters in the admixture model and with correlated allele frequencies . each run included 100 , 000 iterations of burnin , followed by 500 , 000 mcmc iterations used for parameter estimation . the most likely value of
= 1–3 , despite knowing that the maximum number of populations between atlantic and mediterranean samples is likely 2 . then , potential admix individuals in each of the proposed clusters were identified using posterior probabilities calculated for each individual in structure .
because of the high frequencies of null alleles , we also ran structure with the complete data but removing a different locus at a time for each new run using the same parameters as described above ( and including the recessivealleles option ) . this analysis was performed in order to identify the level of information provided by each locus on the level of assignment . then , we selected the most informative loci and ran again structure with and without the recessivealleles options still using the same parameters . we selected the most informative loci from the run using the recessivealleles option . for that , we created a reference assignment’s level from the average level of individuals’ assignment of the south - atlantic coast of spain and the south - mediterranean coast of spain respectively . if the average level of individuals’ assignment of a run ( run when removing a locus ) was under the reference one , then , we considered that the locus we removed for this run was very informative .
a total of 18 , 795 reads with an average length of 232 bp were obtained from 454 pyrosequencing of a microsatellite enriched library and assembled into 595 contigs . we identified 267 contigs ( 44 . 9 % ) that contained microsatellite loci with at least 10 di - or seven tri - nucleotide repetitions . of these , there were a total of 85 contigs ( 31 . 8 % ) we identified as pal of di - or tri - nucleotide microsatellites and 182 contigs ( 68 . 2 % ) as nonpal ( i . e . , contigs containing di - or trinucleotide microsatellites without suitable flanking pcr - primer sites ) . comparing across the two classes of repeats in pal sequences , di - nucleotide repeats represented 66 . 8 % and tri - nucleotides 33 . 2 % .
from the microsatellite containing sequences , we selected 52 loci for testing their usefulness in multiplex genotyping and 37 produced pcr amplification when visualised on agarose gels and ethidium bromide staining . of these 37 loci , nine gave multiple bands , faint bands , or fragments clearly defined but of a different size than the one expected from the original sequence . these loci were discarded from subsequent analyses . of the remaining 28 , 21 could be genotyped and displayed polymorphism in 48 individuals . these 21 loci were deposited in genbank under accession numbers
. five loci , d . tru28 , 30 , 31 , 39 and 46 , amplified two or three loci simultaneously and were discarded from further analyses . for the remaining loci , the number of alleles per locus ranged from eight to 28 (
= 5 . 86 ) . expected and observed heterozygosities , and polymorphic information content ranged from 0 . 15 to 0 . 82 (
) . there was no evidence of large allele dropout or genotyping errors due to stutter peaks for the 16 loci . however , all loci but two ( d . tru4 and d . tru16 ) , showed a significant excess of homozygotes ( deviation from hardy–weinberg equilibrium ,
< 0 . 001 ) . there was no evidence of linkage disequilibrium between any pair of loci . genotyping was consistent across the 48 samples , which were each tested twice yielding the same genotypes . the multiplex optimisation yielded a total of four panels for the 16 primer pairs . the numbers of possible multiplex combinations was limited due to the allele size ranges of the markers and differences in the annealing temperatures of the primers . we were thus able to design two 3 - plex , and two 5 - plex multiplex reactions after excluding the duplicated loci .
the results of the re - amplification of a subsample of individuals under lower stringency mostly confirmed the above findings . however , only 10 loci produced codominant fragments ( i . e . , one allele of maternal and one of paternal origin ) under relaxed annealing temperatures ( table s1 : original annealing temperature , new annealing temperature ) . locus d . tru16 , which initially had not deviated from hwe , amplified multiple loci and thus could not be used for this comparison . furthermore , two additional loci showed null allele frequencies not different from zero ( d . tru6 and d . tru23 ) . this result suggests that non - amplifying alleles can be detected by reducing the stringency of the annealing temperature . for the remaining eight loci , no differences were observed in the heterozygous deficit or the null allele frequencies supporting the presence of null alleles in the wedge clam genome ( table 2 ) .
characteristics of the 10 microsatellite markers with original ( oa ) and new ( na ) annealing temperature for 94 individuals ( isla canela : 27 ; doñana : 37 ; caleta de vélez : 30 ) including the number of alleles ( n a ) , range of allele sizes ( range , bp ) , observed ( h o ) and expected ( h e ) heterozygosity , polymorphism information content ( pic ) and null - allele frequency ( naf ) .
the fact that most loci had large heterozygous deficits was an intriguing result which deserves a thorough discussion . the first consideration that needs to be evaluated in addition of the occurrence of null alleles , is the presence of large allele dropout . another consideration is the level of stuttering as it may hamper the reliable scoring of alleles differing within one or two repeated units in some loci . another possible explanation could be the differences in allele size as reported by previous studies that have found that loci with longer alleles tend to have higher dropout rates than those with shorter alleles (
) . this will artificially increase the frequency of null alleles even in the absence of true null alleles .
the analysis of null allele frequencies per population using the maximum likelihood estimates implemented in ml - nullfreq confirmed the presence of null alleles in all loci but d . tru4 and d . tru16 . for these loci , null - allele frequencies estimates ranged between 0 % and 31 . 2 % (
= 0 . 098 ) and all loci but d . tru4 , d . tru16 and d . tru23 had a null - allele frequencies above 5 % (
) . results from freena showed lower null allele frequencies for each locus ( except for the locus d . tru19 ) than results obtained using ml - nullfreq . null allele frequencies estimates ranged between 0 % and 29 . 3 % (
) . it is plausible that the mutagenic action of some pollutants such as heavy metals ( e . g . , mercury or cadmium ) (
) can be responsible for an increased mutation rate in clams . this could be further investigated by comparing samples representing genetically distinct populations where organisms are either heavily exposed to pollutants in beaches adjacent to major urban areas or those occupying habitats in remote locations where the level of pollution is likely to be low and far from industrial pollution .
the maximum likelihood and the ena correction methods were used , using ml - nullfreq and freena respectively .
individuals are represented as vertical bars , where the amount of each colour indicates the proportion of each inferred cluster . a represents the clusters obtained in the simulations considering the absence of null alleles while b represents those assuming them . isla canela and doñana are represented by the label “south - atlantic coast of spain” , and caleta de vélez by the label “south - mediterranean coast” .
when running structure with the complete data set without a different locus at a time for each run , our results also showed that three microsatellite loci were very informative ( d . tru4 , d . tru29 and d . tru32 ; fig . s1 , table s2 ) . indeed , compared to the reference average level of individuals’ assignment ( 84 . 7 % ± 2 . 5 and 90 . 6 % ± 1 . 7 for the south atlantic coast of spain and the south mediterranean coast of spain , respectively ) , without these three loci , the average level of individuals’ assignment dropped to 65 . 5 % ± 6 . 5 , 68 . 2 % ± 3 . 7 and 77 . 9 % ± 2 . 6 in the south atlantic coast of spain and to 38 . 2 % ± 5 . 4 , 89 . 5 % ± 2 . 2 and 89 . 9 % ± 2 . 8 in south mediterranean coast of spain , respectively , when excluding either locus d . tru4 , d . tru29 or d . tru32 . surprisingly , two of these loci ( d . tru29 and d . tru32 ) have large frequencies of null alleles ( 0 . 311 ± 0 . 030 and 0 . 228 ± 0 . 027 for the locus d . tru29 and d . tru32 respectively ; table 3 ) confirming that even when microsatellite loci display a large frequencies of null alleles , they can , nevertheless , be useful to identify the genetic structure of populations . this conclusion was also corroborated with the f st results using freena and arlequin , which showed that the use of the null allele’s correction option had no effect in the f st estimates .
the results issued from the software structure present the average of the level of individuals’ assignment ( percentage ±sd ) using the 16 loci and when removing a different locus for each run .
we provide three databases : the database we used for the analyses ( 16 loci ) , the database with the original annealing temperature ( 10 loci ) , and the database with the new annealing temperature ( 10 loci ) .
we are grateful for the support given , throughout the project , by the coordination office of donana national park and the consejeria de agricultura , pesca y desarrollo rural of the andalusian government . cr also acknowledges mi rico , f hiraldo cano , jj negro balmaseda , e normandeau and g côté for their support during his stay in canada . we gratefully acknowledge the associate editor and the two referees , mariah scott and patrick gaffney , for their relevant comments which allowed us to considerably improve the manuscript .
ciro rico conceived and designed the experiments , performed the experiments , analyzed the data , wrote the paper , reviewed drafts of the paper .
jose antonio cuesta , pilar drake and enrique macpherson contributed reagents / materials / analysis tools , wrote the paper , reviewed drafts of the paper .
louis bernatchez contributed reagents / materials / analysis tools , wrote the paper , reviewed drafts of the paper , laboratory and sequencing facilities .
amandine d . marie analyzed the data , wrote the paper , prepared figures and / or tables , reviewed drafts of the paper .
the following information was supplied relating to field study approvals ( i . e . , approving body and any reference numbers ) :
permit of sampling was approved by the consejeria de medio ambiente ( permit number 2011107300001463 ) .
the locus described here are accessible via genbank accession numbers : hg792255 , hg792256 , hg792257 , hg792258 , hg792259 , hg792260 , hg792261 , hg792262 , hg792263 , hg792264 , hg792265 , hg792266 , hg792268 , hg792271 , hg792273 , hg792275 .
cr was supported by the spanish ministry of education ( grant no pr2010 - 0601 ) and the spanish scientific research council ( csic ) . this research was financially supported by organismo autonomo de parque nacionales grant oapn122 _ 2010 to cr , em , jac and pd . adm was supported by the strategic research themes of the university of the south pacific . the funders had no role in study design , data collection and analysis , decision to publish , or preparation of the manuscript .
de novo transcriptome characterization and development of genomic tools for scabiosa columbaria l . using next - generation sequencing techniques
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