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Identification of an Australian pigeon in the NT

Identification of an Australian pigeon in the NT


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This pigeon was spotted in Darwin, NT, Australia. I am not able to solidly identify it using my books or google searches. My best bet is a Torresian Imperial Pigeon (Birds of the NT website).


Your bird appears to be an Imperial Pigeon of the Ducula genus. Based on the limited angle of the lone picture of your specimen, my best guess as to the species is the Torresian Imperial Pigeon (Ducula spilorrhoa).

The species is a relatively large, pied species of pigeon found in various habitats (forest, woodland, savanna, mangrove and scrub) in Australia (including in the Northern Territory where you saw your specimen), New Guinea and nearby islands.

You can see more pictures, videos, and calls here, as well as additional info here.

Your specimen is unlikely the closely related Pied Imperial Pigeon (Ducula bicolor) because:

  1. D. bicolor is a Southeast Asian species

  2. D. bicolor has a bluish grey beak, whereas your specimen and D. spilorrhoa both have a yellow beak.

    Note: Your specimen is also unlikely Ducula subflavescens because the feathers are white and not yellow, and it is unlikely Ducula luctuosa because that species is endemic to only a few islands.


Wonga Pigeon

When seen from above, the plumage of the Wonga Pigeon is a drab grey. However, when see front-on, the bird appears to be wearing a white scarf wrapped around its neck and when viewed from below, its white underparts are attractively patterned with row upon row of dozens of tiny crescentic shapes. Often, when the bird lands on a branch, it will tilt itself forward, raising its tail to reveal these half-moon markings, which are said to make the bird resemble a piece of broken dead wood.

Identification

Description

The Wonga Pigeon, or Wonga Wonga, is a large, plump, ground-dwelling pigeon with a small head, short, broad wings and a long tail. It is mainly grey above, with a pale face, a distinctive white V on the breast and white lower parts which are boldly marked with black-brown crescents and wedges. The eyes are dark red-brown with a pink eye-ring and black lores (area between the bill and the eye) and the bill, feet and legs are deep pink to red. Young Wonga Pigeons are browner above and the V is less distinct. A shy bird, except in areas where it has become used to humans, it will take off with explosive wing-claps if disturbed.

Location

Distribution

The Wonga Pigeon is found along the east coast of Australia, from south-eastern Queensland to Gippsland, Victoria.

Behaviour

Feeding

The Wonga Pigeon feeds on seeds of native and introduced plants as well as fallen fruit and the occasional insect. It forages exclusively on the ground, often walking long distances along well-defined routes. It mainly feeds in the early morning and late afternoon and sometimes forms large flocks where there is plenty of food.

Breeding

The Wonga Pigeon is monogamous, with breeding pairs defending the area around the nest. Threat displays include bowing and clicking while walking towards an intruder. Nests are built in large trees, usually high off the ground, and are a saucer-shaped platform of twigs and sticks, lined with small twigs, vine tendrils and other soft plant materials. Will sometimes use the abandoned nests of Topknot Pigeons or Tawny Frogmouths. Both sexes incubate the eggs and feed the young. They use a special 'cryptic posture' when sitting on the nest, keeping their patterned tail raised high and facing any observers, while peering over the tail to keep an eye on potential threats. This posture is also used when birds are flushed from cover and have flown to a perch. Adults feed the young by regurgitation and young birds will remain with the adults for some time after fledging but are fed less and less often.


10 Day Ultimate Top End Birding Adventure Tour

Darwin

  • Birdwatching focus
  • high
  • Wildlife focus
  • moderate
  • Photography focus
  • moderate | high
  • Culture focus
  • low | moderate
  • Walks rating
  • moderate
  • Number of boat cruises
  • Public 2 Private 1
  • Sleeping options
  • ensuite / camping

Tour notes & Add-ons

This tour starts in Darwin, Northern Territory and finishes in Kununurra, Western Australia. You can return to Darwin or Broome with a short flight with Air North or express transfer by road returning to Darwin.

Register for 2021 departures or book on our 7 day birding frenzy tours.

Tour Summary

NT Bird Specialists’ ‘Ultimate Top End Birding Adventure’ tour discovers some of the most remote and impressive landscapes and targeted bird and wildlife species in one fowl swoop! This one way bird watching tour departs Darwin, Northern Territory. Mouth-watering birds include: Yellow Chat, Spinifex Pigeon, Gouldian Finch, Purple-crowned Fairy-wren, Rainbow Pitta, Chestnut Rail, Rufous Owl, Red Goshawk, Banded Fruit-dove, White-lined Honeyeater, Chestnut and White-quilled Rock Pigeons, Hooded Parrot and honeyeaters galore.

Regions Visited

  • Darwin
  • Mary River
  • Kakadu
  • Katherine
  • Pine Creek
  • Timber Creek
  • Lake Argyle
  • Kununurra

Tour Route

Tour Gallery

Day by Day Itinerary

Day 1

We start by taking advantage of the early morning and scope out some of the best birding sites in Darwin. Numerous habitats surrounding the tropical city we explore include mangroves, monsoonal vine forests, garden parks, woodlands and coastal regions to enjoy the myriad of bird species that call these regions home. We look for species such as Mangrove Golden Whistler, Chestnut Rail, Rainbow Pitta, Rufous Owl, and Rufous-banded Honeyeater before returning to our accommodation in Darwin.

Day 2

A pre-dawn departure will lead us to heritage-listed Fogg Dam, a renowned wetland on the edge of the Adelaide River Floodplain. Home to a spectacle of birdlife including ducks, geese, ibis, egrets, kingfishers, cisticolas, finches, raptors, spoonbills, flycatchers, crane and stork species to name a few. We continue on to our accommodation in the Mary River region. Here we will relax and enjoy the birdlife within the grounds before taking to the restaurant for our evening meal.

Day 3

The morning starts with a dawn cruise along the fresh water reaches of the paperbark lined Mary River. Search for species such as Black Bittern, Great-billed Heron and various honeyeater species. We continue our journey in the heat of the day to the World Heritage Kakadu National Park, scanning the savannah woodlands and almighty South Alligator floodplains for Emu, Black-breasted Buzzard, Brolga and Radjah Shelduck. We visit Mamukala wetlands and bird hide before we travel to Jabiru for the rest of the afternoon and our accommodation. Jabiru gives us an opportunity to see Partridge Pigeon, known as ‘Ragul’ in the local aboriginal language.

Day 4

We embark on an early morning departure and explore around the Burrungkuy region to take in some of the more spectacular scenery of World Heritage Kakadu National Park. With easy walks up to 6km in length, it provides us with the best chances to view some of the endemic sandstone species such as White-lined Honeyeater, Banded Fruit-Dove and elusive Black Wallaroo. We continue to the north-east of Kakadu ‘stone country’ and take in the stunning vistas of the Arnhem Land Escarpment. Guided around the old occupational site of Ubirr ancient rock art and fascinating species such as Chestnut-quilled Rock Pigeon, and Wilkin’s Rock Wallaby. All before heading back to our accommodation in Jabiru.

Day 5

Today we rise before the sun to join the famous Yellow Water sunrise cruise. Yellow Water has Great-billed Heron, 6 species of kingfisher, Arafura Fantail, Buff-sided Robin, Black-necked Stork and Saltwater Crocodile. After breakfast, we’ll make our way to the Burrungkuy (Nourlangie) region, to look for endemic and sandstone specialists such as Banded Fruit-Dove and Helmeted Friarbird. We’ll travel south to our accommodation in Pine Creek, home to the endemic and illustrious Hooded Parrot.

Day 6

Another big day beckons as we pack our bags and head for Leliyn/Edith Falls in the iconic Nitmiluk National Park. The region is a hot spot for finch species including the much sought after Gouldian, Masked, Long-tailed, Crimson and Double-barred. We also keep an eye out for Northern Rosella and White-throated Gerygone. Continuing south on the Stuart Highway we travel to Katherine and spend the afternoon around the township, checking local birding sites.

Day 7

This morning we continue on the Victoria Highway heading west to our next accommodation at Victoria River Roadhouse. This is cattle farming country, prime finch and parrot territory as we check out the grasslands and watering holes we keep an eye out for mannikins (munias), parrots and bustards. We are welcomed with stunning views of various ranges including the Moray, Bynoe and Stokes. We scan the Cane Grass searching for one of Australia’s glorious fairywrens, the Purple-crowned Fairywren.

Day 8

A short journey leads us to a rocky walk heading up the escarpment, looking for sandstone specialties including White-quilled Rock Pigeon, Sandstone Shrike-thrush and Short-eared Rock Wallaby. Admiring the amazing morning view from this 3km return moderate walk is well worth the effort. We continue west past the Victoria River to our next destination, Timber Creek. This outback town is great for finches such as Gouldian, Star and Zebra. Before retiring to our accommodation and enjoying a well-deserved meal.

Day 9

We have time for a morning birding session after breakfast, before making our way to Keep River National Park. Here we check the local waterholes and stunning sandstone formations for a number of birds, including Spinifex Pigeon, White-quilled Rock Pigeon, Royal Spoonbill, Brolga, Grey-headed Honeyeater and Peregrine Falcon. We say goodbye to the Northern Territory and say hello to Australia’s largest mainland state, Western Australia and journey to Australia’s largest man-made lake, Lake Argyle. Having time to either enjoy the facilities or stroll around the grounds and enjoy the local birdlife.

Day 10

We board an early morning cruise and embark on an adventure in a truly remarkable environment, Lake Argyle. Enjoy a picnic breakfast out on the water then venture to one of the many islands within the lake in search for one of the more desired birds of the journey, the Yellow Chat. As we stroll around the island we keep an eye out not only for the Yellow jewels, but also Australian Bustard, Brown Songlark, Australian Pipit, Zebra Finch and various duck species. We head to our final destination being Kununurra and bid farewell.

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Results

Implementation and availability

Metagenomic reads (or contigs) are first mapped against a reference database with KMA [16], which implements the ConClave sorting scheme for better-informed and highly accurate alignments (Fig. 1). CCMetagen is then used to perform quality filtering and produce taxonomic classifications that can be explored in text or interactive visualization formats (Krona plots [17]). Our pipeline uses the NCBI taxonomic database (taxids) to produce ranked and updated taxonomic classifications, so that the ever-changing species nomenclature issue is minimized [18]. CCMetagen yields classifications at a taxonomic level that reflects the similarity between the query and reference sequences. This ranked classification means that species with only distant relatives in reference databases (e.g., undescribed genera) can be identified, as well as well-known microorganisms. The output of CCMetagen can be easily converted into a PhyloSeq object for statistical analyses in R [19]. The pipeline is sufficiently fast to use the entire NCBI nucleotide collection (nt) as a reference database [20], thereby enabling the inclusion of microbial eukaryotes—in addition to bacteria, viruses, and archaea—in metagenome surveys. Our program is implemented in Python 3 and is freely available at https://github.com/vrmarcelino/CCMetagen [21] or via the Python Package Index (PyPi) [22]. A web service to easily run the pipeline with default settings is available at https://cge.cbs.dtu.dk/services/ccmetagen/ [23].

Fungal classifications are more accurate with the CCMetagen pipeline

To test the performance of CCMetagen in identifying an important and diverse group of microbial eukaryotes, we simulated in silico a fungal metatranscriptome (15 species) and a fungal metagenome (30 species). We then benchmarked CCMetagen’s performance by comparing it with widely used metagenomic classification software, including Centrifuge [24], Kraken2 [25], and KrakenUniq [26]. These programs were chosen because they are compatible with custom-made reference databases, which is a desirable flexibility when working with microbial eukaryotes. KrakenUniq was recently shown to outperform eleven other classification methods when using the NCBI nucleotide collection (“nt” database), including Diamond/Blast + MEGAN [12, 27, 28], CLARK [29], GOTTCHA [30], PhyloSift [31], and MetaPhlAn2 [9]. KrakenUniq therefore provides a gold standard for the available tools. We evaluated precision, recall, and F1 scores of the benchmarked software in identifying fungal taxa in the simulated fungal metagenome and metatranscriptome (see the “Methods” section). The F1 score is the harmonic average of precision and recall high F1 scores can be interpreted as a good trade-off between precision and recall.

The CCMetagen pipeline achieved the highest precision and F1 scores of all the approaches tested (Fig. 2, Additional file 1: Figures S1 and S2, Additional file 2). KrakenUniq achieved higher precision than Kraken2 and Centrifuge when using an ideal database (i.e., RefSeq-bf, which contains only the complete and curated genomes of fungi and bacteria, containing all species from the test data set). However, the performance of KrakenUniq decreased substantially when the database was incomplete (i.e., RefSeq-f-partial, where a part of the reference sequences was removed to mimic the effects of handling species without reference genomes).

The CCMetagen pipeline has a higher F1 score than other metagenomic classification methods for all taxonomic ranks. The two points for each program and taxonomic rank represent the results using a simulated metagenome and a metatranscriptome sample of a fungal community. a Results using the whole NCBI nt collection as a reference database. b Results using the RefSeq-bf (bacteria and fungi) database, containing all bacterial and fungal genomes available. c Partial RefSeq database containing only some of the fungal species currently present in the RefSeq-bf database, mimicking the effects of dealing with species without representatives in reference data sets. In this case, Kraken2, Centrifuge, and KrakenUniq have overlapping results. Refer to Additional file 1: Figures S1 and S2 and Additional file 2 for more information, including precision and recall

Centrifuge, Kraken2, and KrakenUniq yielded many more taxa than the number included in the test data sets: for example, Centrifuge, when used with the nt database, reported 6950 species in the simulated metagenome containing 30 species, while CCMetagen yielded only 15. Naturally, their recall was very high—Centrifuge and KrakenUniq recovered 100% of the taxa present in the test data set when using the RefSeq-bf and nt reference databases (Additional file 1: Figure S2). The species-level recall of Kraken2 decreased when using the nt database. CCMetagen recovered between 50 and 100% of the species when used with RefSeq-bf and nt databases (Additional file 2).

We also tested CCMetagen with assembled sequence reads (Additional file 3). When using the NCBI nt collection, precision ranged from 67 to 71% for species-level classifications, while recall ranged from 53 to 100% (Additional file 4), indicating that our pipeline is suited to processing long sequences.

The fastest processing time was achieved by Kraken2 (Table 1). The combined CPU time of KMA and CCMetagen (i.e., the CCMetagen pipeline) was faster than Centrifuge and KrakenUniq when using the whole NCBI nt database, but it was the slowest approach when using the RefSeq database. The KMA indexing of the nt database was limited to only include k-mers with a two-letter prefix, which on average corresponds to only saving non-overlapping k-mers. This prefixing substantially increases the speed and could also be applied to the RefSeq database if a faster processing time is required (Additional file 3). Choosing a longer prefix will result in gaps in the database which in turn will result in lower precision and recall. With a prefix of two, this is relatively limited. When the NCBI nt data set was used, CCMetagen required

15 min to process a sample (

5 Gb, 7.8M reads on average).

9M PE reads) and a fungal metagenome (mtg,

Bacterial communities are best depicted with the CCMetagen pipeline

We assessed the performance of the CCMetagen pipeline when applied to 10 bacterial communities simulated at different levels of complexity [32, 33]. Using the NCBI nt collection as a reference, CCMetagen achieved the highest precision and F1 scores at all taxonomic ranks (Fig. 3). Recall was highest for Centrifuge and KrakenUniq. In this data set, the recall of Kraken2 was higher than CCMetagen from phylum- to family-level classifications, but lower than CCMetagen at the genus and species level.

CCMetagen pipeline performance for bacterial classifications, compared with Kraken2, Centrifuge, and KrakenUniq. Precision (% of true positives), recall (% of taxa identified), and F1 scores represent averages across 10 simulated metagenome samples. Shaded areas indicate 75% confidence intervals

The complete CCMetagen pipeline (KMA + CCMetagen) required an average of 2.1 min to process the bacterial metagenomes (± 0.26 SD). It was slower than Kraken2 (average 0.27 m, ± 0.21 SD) and faster than KrakenUniq (average 2.56 m, ± 2.60 SD) and Centrifuge (average 9.19 m, ± 0.80 SD).

Biological data set 1: Experimentally seeded fungal metatranscriptome

We validated the CCMetagen pipeline with a fungal community previously generated in vitro by culturing, processing, and sequencing 15 fungal species ([34], Additional file 5). The analyses were performed using the NCBI nt collection as a reference. Our pipeline correctly retrieved 13 of the 15 fungal species sequenced, in addition to identifying a small component of other eukaryotic (0.4%) and bacterial (3%) RNA, which likely represent laboratory contaminants (Fig. 4, Additional file 5).

Snapshot of CCMetagen results for a spiked fungal community. This Krona graph shows the relative abundance of taxa at various taxonomic levels that are color-coded according to their taxonomic classification at lower-ranks—here, we see fungal taxa in shades of red, and bacterial taxa in shades of green. The Krona html file can be opened and interactively inspected in a web browser. Each circle represents a taxonomic level, where the user can click for a representation of the relative abundance at a given taxonomic rank. For a detailed list of taxa, refer to Additional file 5

As this data set contains the same 15 fungal species as those simulated in silico, it is possible to tease apart classification errors from laboratory-related confounders such as contamination. Accordingly, we were able to retrieve all 15 species when using the in silico data set, suggesting that the two false negatives (Schizosaccharomyces pombe and Debaryomyces hansenii) were missing due to laboratory-related issues, such as RNA extraction biases, gene [under] expression, and imprecise cell counts. We also identified seven times more false positives in the seeded fungal metatranscriptome (44 species, including bacteria, while the simulated data yielded only 6). These additional 38 species were present at low abundance and possibly represent reagent and laboratory contaminants [35, 36] as they were not identified in the analysis of the equivalent simulated metatranscriptome.

Biological data set 2: Australian birds

We used the CCMetagen pipeline to characterize the gut microbiome represented in 9 metatranscriptome libraries from wild birds sampled at various sites across Australia [37, 38]. These samples were collected as part of a long-term avian influenza study and were stored in Viral Transport Medium (brain-heart infusion broth containing 2 × 10 6 IU/l penicillin, 0.2 mg/ml 383 streptomycin, 0.5 mg/ml gentamicin, 500 U/ml amphotericin B, Sigma), possibly simplifying microbiome composition and abundance, but not necessarily eliminating microbial genetic material. Indeed, fungal and bacterial transcripts were observed in all libraries (Additional file 6). Eukaryotic microbes accounted for 60% of the family-level diversity of the bird microbiome samples (taxa unclassified at family-level were not taken into account). Notably, fungi represented 12 of the 20 most abundant microbial families (Fig. 5). Among the fungal transcripts with a species-level classification, those attributed to the basidiomycete Cystofilobasidium macerans (Tremellomycetes) were the most abundant and were present in all bird libraries. Transcripts from species of filamentous fungi (e.g., Mucor, Cladosporium, Fusarium) and yeasts (e.g., Cryptococcus, Metschnikowia) were common. The high diversity of fungi associated with birds is unsurprising, as birds are known to play an important role in the ecology and distribution of yeasts and fungal spores [39, 40]. Bird excrement is a natural niche for species of the opportunistic pathogen Cryptococcus [41, 42], and several studies have reported Mucor, Cladosporium, and Cryptococcus associated with birds [43,44,45]. Species of Fusarium and Metschnikowia are often associated with plants and may be transient microbes in the avian microbiome, following ingestion of plant materials containing spores or dormant yeast cells [40, 46]. Other microbial eukaryotes were also observed, including the trichomonad Simplicimonas and the Apicomplexan Eimeria. Archaeal and viral transcripts were also detected. The methanogenic archaea Methanobrevibacter woesei, which was previously reported in chicken guts [47], was observed in two duck libraries. Influenza A virus was detected and confirmed with PCR-based methods [37]. The CCMetagen results were parsed with PhyloSeq for a graphical representation of the most abundant microbes, and the R script to reproduce Fig. 5 is available on the CCMetagen website [48].

Microbial families in the microbiome of wild birds. The 20 most abundant families are shown, with fungal families indicated in bold. For a full list of taxa, refer to Additional file 6. A tutorial and R scripts to reproduce these analyses are available on the CCMetagen website


Abstract

Australia hosts approximately 10% of the world’s reptile species, the largest number of any country. Despite this and evidence of widespread decline, the first comprehensive assessment of the conservation status of Australian terrestrial squamates (snakes and lizards) was undertaken only recently. Here we apply structured expert elicitation to the 60 species assessed to be in the highest IUCN threat categories to estimate their probability of extinction by 2040. We also assessed the probability of successful reintroduction for two Extinct in the Wild (EW) Christmas Island species with trial reintroductions underway. Collation and analysis of expert opinion indicated that six species are at high risk (>50%) of becoming extinct within the next 20 years, and up to 11 species could be lost within this timeframe unless management improves. The consensus among experts was that neither of the EW species were likely to persist outside of small fenced areas without a significant increase in resources for intense threat management. The 20 most imperilled species are all restricted in range, with three occurring only on islands. The others are endemic to a single state, with 55% occurring in Queensland. Invasive species (notably weeds and introduced predators) were the most prevalent threats, followed by agriculture, natural system modifications (primarily fire) and climate change. Increased resourcing and management intervention are urgently needed to avert the impending extinction of Australia’s imperilled terrestrial reptiles.

Additional keywords: anthropogenic mass extinction crisis, Australia, biodiversity conservation, Delphi, expert elicitation, IDEA, lizard, reptile, snake, squamate, terrestrial, threatening processes.


Animal Diversity Web

Wild Columba livia are native to Europe, North Africa, and southwestern Asia. Feral pigeons are found worldwide, including throughout all of North America. It should be noted that occurrence within this range is not evenly distributed (see habitat).

  • Biogeographic Regions
  • nearctic
    • introduced
    • native
    • introduced
    • introduced
    • native
    • introduced
    • introduced
    • introduced
    • Other Geographic Terms
    • cosmopolitan

    Habitat

    Wild rock doves nest in crevices along rocky seaside cliffs, close to agriculture or open shrub vegetation. Feral pigeons live in old farm buildings in rural areas. In cities, the skyscrapers tend to take the place of their natural cliff surroundings.

    Physical Description

    The rock dove has a dark bluish-gray head, neck, and chest with glossy yellowish, greenish, and reddish-purple iridescence along its neck and wing feathers. Females tend to show less iridescence than the males. The bill is dark grayish-pink. Two dark bands across the wings are seen in most pigeons, and one bluish-gray band across the tail. Rock doves and feral pigeons can be divided into a large number of different phenotypes, or groups based on outward characteristics. Some of these classifications are the blue-bar, blue checker, dark checker, spread, and red phenotypes.

    Reproduction

    Pairs may be formed at any point during the year. These pairs are formed for life. Each bird works cooperatively on most aspects of reproduction and young-rearing. The male builds the nest, and the eggs are laid shortly after the nest is finished. Both males and females incubate the eggs. Eggs hatch approximately 19 days after being laid.

    • Key Reproductive Features
    • iteroparous
    • gonochoric/gonochoristic/dioecious (sexes separate)
    • sexual
    • oviparous
    • Average eggs per season 2 AnAge
    • Average time to hatching 19 days
    • Average time to hatching 18 days AnAge
    • Average age at sexual or reproductive maturity (female)
      Sex: female 140 days AnAge
    • Average age at sexual or reproductive maturity (male)
      Sex: male 140 days AnAge

    Lifespan/Longevity

    Behavior

    Pigeons generally walk or run while bobbing their heads forward and backward. They fly with a steady and direct path. Pigeons are most often seen during daylight, seeking cover at night and in during the heat of the day, according to the climate. They flock while roosting, sunning, and feeding, but no play has been observed. In the nesting territory, both sexes are aggressive, pecking intruders on the head.

    Communication and Perception

    Food Habits

    Rock doves feed in the early morning and in the mid-afternoon on the open ground. They eat mainly seeds. Studies of pigeons in a semi-rural part of Kansas found that their diet includes the following: 92% corn, 3.2% oats, 3.7% cherry, along with small amounts of knotweed, elm, poison ivy, and barley. In cities, feral pigeons also eat popcorn, cake, peanuts, bread, and currants. Female rock doves need to eat a diet somewhat higher in protein and calcium in order to have the nutritional resources to lay eggs.

    Predation

    Some common predators of feral pigeons in the North America are opossums (Didelphis virginiana), raccoons (Procyon lotor), great horned owls (Bubo virginianus), and eastern screech-owls (Otus asio). Other predators include the golden eagle (Aquila chrysaetos), American kestrels (Falco sparverius), and peregrine falcons (Falco peregrinus).

    • Known Predators
      • Virginia opossums (Didelphis virginiana)
      • raccoons (Procyon lotor)
      • great horned owls (Bubo virginianus)
      • eastern screech-owls (Otus asio)
      • golden eagles (Aquila chrysaetos)
      • American kestrels (Falco sparverius)
      • peregrine falcons (Falco peregrinus)

      Economic Importance for Humans: Positive

      Eaten by humans and used for laboratory research.

      Economic Importance for Humans: Negative

      A large number of pigeons living in a small area can be a nuisance to farmers. Some diseases (e.g., histoplasmosis) may be spread in pigeon droppings.

      Conservation Status

      Since pigeons are often fed by well-meaning city dwellers, their numbers are high. Wild rock doves also have no special status.

      • IUCN Red List Least Concern
        More information
      • IUCN Red List Least Concern
        More information
      • US Migratory Bird Act No special status
      • US Federal List No special status
      • CITES No special status
      • State of Michigan List No special status

      Other Comments

      Feral pigeons have been used extensively in laboratories because they are domesticated and found in abundance throughout the world. These studies include flight mechanisms, thermoregulation, water metabolism, genetics of color patterns, and Darwinian evolutionary biology.

      Contributors

      Jennifer Roof (author), University of Michigan-Ann Arbor.

      Glossary

      Living in Australia, New Zealand, Tasmania, New Guinea and associated islands.

      living in sub-Saharan Africa (south of 30 degrees north) and Madagascar.

      living in the Nearctic biogeographic province, the northern part of the New World. This includes Greenland, the Canadian Arctic islands, and all of the North American as far south as the highlands of central Mexico.

      living in the southern part of the New World. In other words, Central and South America.

      living in the northern part of the Old World. In otherwords, Europe and Asia and northern Africa.

      uses sound to communicate

      having body symmetry such that the animal can be divided in one plane into two mirror-image halves. Animals with bilateral symmetry have dorsal and ventral sides, as well as anterior and posterior ends. Synapomorphy of the Bilateria.

      Found in coastal areas between 30 and 40 degrees latitude, in areas with a Mediterranean climate. Vegetation is dominated by stands of dense, spiny shrubs with tough (hard or waxy) evergreen leaves. May be maintained by periodic fire. In South America it includes the scrub ecotone between forest and paramo.

      uses smells or other chemicals to communicate

      having a worldwide distribution. Found on all continents (except maybe Antarctica) and in all biogeographic provinces or in all the major oceans (Atlantic, Indian, and Pacific.

      in deserts low (less than 30 cm per year) and unpredictable rainfall results in landscapes dominated by plants and animals adapted to aridity. Vegetation is typically sparse, though spectacular blooms may occur following rain. Deserts can be cold or warm and daily temperates typically fluctuate. In dune areas vegetation is also sparse and conditions are dry. This is because sand does not hold water well so little is available to plants. In dunes near seas and oceans this is compounded by the influence of salt in the air and soil. Salt limits the ability of plants to take up water through their roots.

      animals that use metabolically generated heat to regulate body temperature independently of ambient temperature. Endothermy is a synapomorphy of the Mammalia, although it may have arisen in a (now extinct) synapsid ancestor the fossil record does not distinguish these possibilities. Convergent in birds.

      forest biomes are dominated by trees, otherwise forest biomes can vary widely in amount of precipitation and seasonality.

      referring to animal species that have been transported to and established populations in regions outside of their natural range, usually through human action.

      offspring are produced in more than one group (litters, clutches, etc.) and across multiple seasons (or other periods hospitable to reproduction). Iteroparous animals must, by definition, survive over multiple seasons (or periodic condition changes).

      having the capacity to move from one place to another.

      the area in which the animal is naturally found, the region in which it is endemic.

      islands that are not part of continental shelf areas, they are not, and have never been, connected to a continental land mass, most typically these are volcanic islands.

      found in the oriental region of the world. In other words, India and southeast Asia.

      reproduction in which eggs are released by the female development of offspring occurs outside the mother's body.

      rainforests, both temperate and tropical, are dominated by trees often forming a closed canopy with little light reaching the ground. Epiphytes and climbing plants are also abundant. Precipitation is typically not limiting, but may be somewhat seasonal.

      scrub forests develop in areas that experience dry seasons.

      reproduction that includes combining the genetic contribution of two individuals, a male and a female

      uses touch to communicate

      A terrestrial biome. Savannas are grasslands with scattered individual trees that do not form a closed canopy. Extensive savannas are found in parts of subtropical and tropical Africa and South America, and in Australia.

      A grassland with scattered trees or scattered clumps of trees, a type of community intermediate between grassland and forest. See also Tropical savanna and grassland biome.

      A terrestrial biome found in temperate latitudes (>23.5° N or S latitude). Vegetation is made up mostly of grasses, the height and species diversity of which depend largely on the amount of moisture available. Fire and grazing are important in the long-term maintenance of grasslands.

      uses sight to communicate

      References

      Johnston, Richard F. Birds of North America No. 13, 1992. The American Ornithologists' Union.


      Crested Pigeon

      When flying,a whistling sound is produced by the air passing over a modified primary feather on the Crested Pigeon's wing.

      The Crested Pigeon is a stocky pigeon with a conspicuous thin black crest. Most of the plumage is grey-brown, becoming more pink on the underparts. The wings are barred with black, and are decorated with glossy green and purple patches. The head is grey, with an pinkish-red ring around the eye. If startled, this pigeon takes to the air with a characteristic whistling flight, and glides with down turned wings. The whistling sound is produced by the air passing over a modified primary feather on the wing. Upon landing, the pigeon swings its tail high in the air.

      The Crested Pigeon is one of only two Australian pigeons that possess an erect crest. The Spinifex Pigeon, Geophaps plumifera, markedly smaller (20 cm - 24 cm) than the Crested Pigeon, has cinnamon coloured plumage and a bright red facial patch. The much larger (40 cm - 46 cm) Topknot Pigeon, Lopholaimus antarcticus, has a shaggy, reddish brown drooping topknot.

      The Crested Pigeon is native to Australia and is common throughout most of the mainland.

      The Crested Pigeon is found in lightly wooded grasslands in both rural and urban areas. It is usually found in the vicinity of water, as it has to drink every day, and is absent from the denser forests.

      The Crested Pigeon's diet consists mostly of native seeds, as well as those of introduced crops and weeds. Some leaves and insects are also eaten. Feeding is in small to large groups, which also congregate to drink at waterholes. Birds arrive in nearby trees, and often sit for long periods before descending to drink. Drinking and feeding are most common in morning and evening, but can occur at any time.

      The Crested Pigeon builds a delicate nest of twigs, placed in a tree or dense bush. Both sexes share the incubation of the eggs, and both care for the young.


      Hundreds of Australian lizard species, barely known to science, may face extinction

      Credit: E Vanderduys, Fourni par l'auteur

      Most of the incredible diversity of life on Earth is yet to be discovered and documented. In some groups of organisms—terrestrial arthropods such as spiders and scorpions, marine invertebrates such as sponges and molluscs, and others—scientists have described fewer than 20% of species.

      Even our knowledge of more familiar creatures such as fish and reptiles is far from complete. In our new research, we studied 1,034 known species of Australian lizards and snakes and found we know so little about 164 of them that not even the experts know whether they are fully described or not. Of the remaining 870, almost a third probably need some work to be described properly.

      Documenting and naming what species are out there—the work of taxonomists—is crucial for conservation, but it can be difficult for researchers to decide where to focus their efforts. Alongside our lizard research, we have developed a new "return on investment" approach to identify priority species for our efforts.

      We identified several hotspots across Australia where research is likely to be rewarded. More broadly, our approach can help target taxonomic research for conservation worldwide.

      Why we need to look at species more closely

      As more and more species are threatened by land clearing, climate change and other human activities, our research highlights that we are losing even more biodiversity than we know.

      Return on investment for taxonomic research on lizards and snakes in Australia. Red areas have high numbers of species and high conservation value. Hotspots include the Kimberley in WA, northern tropical savannas and also far north eastern QLD. Credit: R. Tingley, Author provided

      Conservation often relies on species-level assessments such as those conducted by the International Union for Conservation of Nature (IUCN) Red List, which lists threatened species. Although new species are being discovered all the time, a key problem is that already named "species" may harbor multiple undocumented and unnamed species. This hidden diversity remains invisible to conservation assessment.

      One such example are the Grassland Earless Dragons (Tympanocryptis spp.) found in the temperate native grasslands of south-eastern Australia. These small secretive lizards were grouped within a single species (Tympanocryptis pinguicolla) and listed as Endangered on the IUCN Red List.

      But recent taxonomic research split this single species into four, each occurring in an isolated region of grasslands. One of these new species may represent the first extinction of a reptile on mainland Australia and the other three have a high probability of being threatened.

      Scientists call documenting and describing species "taxonomy." Our research shows the importance of prioritizing taxonomy in the effort to conserve and protect species.

      The Roma Earless Dragon (Tympanocryptis wilsoni), described in 2014, lives only in grasslands in the western Darling Downs QLD and has recently been listed as Vulnerable in Queensland. Credit: A. O'Grady, Author provided

      Many government agencies do take some account of groups smaller than species in their conservation efforts, such as distinct populations. But these are often ambiguously defined and lack formal recognition, so they are not widely used. That's where taxonomists come in, to identify species and describe them fully.

      Our new research was a collaboration of 30 taxonomists and systematists, who teamed up to find a good way of working out which species should be a priority for taxonomic research for conservation outcomes. This new approach compares the amount of work needed with the likelihood of finding previously unknown species that are at risk of extinction.

      The research team, who are experts on the taxonomy and systematics of Australia's reptiles, implemented this new approach on Australian lizards and snakes. This group of reptiles is ideal as a test case because Australia is a global hotspot of lizard diversity—and we also have a strong community of taxonomic experts.

      Barrier Range Dragon (Ctenophorus mirrityana), described in 2013, is restricted to rocky ranges in western NSW and is listed as Endangered in NSW. Credit: S. Wilson, Author provided

      Australia's lizards and snakes

      Of the 1,034 Australian lizard and snake species, we were able to assess whether 870 of them may contain undescribed species. This means we know so little about the remaining 164 species that even the experts could not make an informed opinion on whether they contain hidden diversity. There is so much still to learn!

      Of the 870 species experts could assess, they determined 282 probably or definitely needed more taxonomic research. Mapping the distributions of these species indicated hotspot regions for this taxonomic research, including the Kimberley, the Tanami Desert region, western Victoria and offshore islands (such as Tasmania, Lord Howe and Norfolk Islands). Some areas in the Kimberley region had more than 60 species that need further taxonomic research.

      We found 17.6% of the 282 species that need more taxonomic research contained undescribed species that would probably be of conservation concern, and 24 had a high probability of being threatened with extinction. Taxonomists know that there are undescribed species because there is some data available already but the description of these species—the process of defining and naming—has not been done.

      These high-priority species belong to a range of families including geckos, skinks and dragons found across Australia.

      The high number of undescribed species, especially those with significant likelihood of being endangered, was a shock to even the experts. The IUCN currently estimates only 6.3% of Australian lizards and snakes require taxonomic revision, but this is obviously a significant underestimate.

      In this map, red hotspot areas have lower species diversity but still a very high average return on investment. National hotspots include Tasmania, western Victoria and the Tanami Desert region in WA and NT. Credit: R. Tingley, Author provided

      A race against extinction

      Beyond lizards, there is a huge backlog of species awaiting description.

      Recent projects have used genetic analyses to discover unknown species, including a $180 million global BIOSCAN effort aiming to identify millions of new species. However, genetics is only a first step in the formal recognition of species.

      The taxonomic process of documenting, describing and naming species requires multiple further steps. These steps include a comprehensive diagnostic assessment using a combination of evidence, such as genetics and morphology, to uniquely distinguish each species from another. This process requires a high level of familiarity and scholarship of the group in question.

      Among the Australian lizards and snakes alone, there is a backlog of 59 undescribed species for which only the final elements of taxonomic research are awaiting completion.

      The Mt Elliot Sunskink (Lampropholis elliotensis), described in 2018, is found in leaf litter of highland rainforest above 600m on Mt Elliot in Bowling Green Bay National Park. Queensland, and is probably Vulnerable. Credit: C. Hoskin, Author provided

      To work through these taxonomic backlogs—let alone species that are so far entirely unknown—resources need to be invested in taxonomy, including research funding and increased provision of viable career paths.

      Without taxonomic research, the conservation assessment of these undocumented species will not proceed. There are untold numbers of species needing taxonomic research that are already under threat of extinction. If we don't hurry, they may go extinct before we even know they exist.

      This article is republished from The Conversation under a Creative Commons license. Read the original article.


      The Passenger Pigeon

      At the start of the nineteenth century, Passenger Pigeons were perhaps the most abundant birds on the planet, numbering literally in the billions. The flocks were so large and so dense that they blackened the skies, even blotting out the sun for days at a stretch. Yet by the end of the century, the most common bird in North America had vanished from the wild. In 1914, the last known representative of her species, Martha, died in a cage at the Cincinnati Zoo.

      This stunningly illustrated book tells the astonishing story of North America’s Passenger Pigeon, a bird species that—like the Tyrannosaur, the Mammoth, and the Dodo—has become one of the great icons of extinction. Errol Fuller describes how these fast, agile, and handsomely plumaged birds were immortalized by the ornithologist and painter John James Audubon, and captured the imagination of writers such as James Fenimore Cooper, Henry David Thoreau, and Mark Twain. He shows how widespread deforestation, the demand for cheap and plentiful pigeon meat, and the indiscriminate killing of Passenger Pigeons for sport led to their catastrophic decline. Fuller provides an evocative memorial to a bird species that was once so important to the ecology of North America, and reminds us of just how fragile the natural world can be.

      Published in the centennial year of Martha’s death, The Passenger Pigeon features rare archival images as well as haunting photos of live birds.

      Awards and Recognition

      • Honorable Mention for the 2015 National Outdoor Book Awards, Nature and the Environment, NOBA Foundation
      • One of The Independent’s Best Nature Books of 2014
      • Selected for the American Scientist Science Book Gift Guide 2014
      • One of The Seattle Times 8 Books to Put under a Bird-Lover’s Tree 2014
      • One of The Globe and Mail 75 Book Ideas for Christmas 2014
      • One of TheAustralian.com’s "In the Good Books" 2014

      "Lavishly illustrated with rare photographs of the birds. . . . This book provides a general introduction to the history of the passenger pigeon through its collection of rare photographs and other visual materials that most people have not seen before."—Devorah Bennu, The Guardian

      "Visually beautiful. . . . Gives a fine account of the species, its biology and its demise."—Adrian Barnett, New Scientist

      "A handsome, well-produced volume concentrating on paintings and photographs of the long-lost birds."—Rob Hardy, Columbus Dispatch

      "A beautifully illustrated, elegantly written 'celebration' of the passenger pigeon and the artists who illustrated and photographed the species. . . . It is a haunting tale, and if you want a readable, engrossing but not lengthy account, I highly recommend this book."—Donna Schulman, 10,000 Birds

      "Informative. . . . A celebration of this departed species through a mix of prose, paintings and photographs. . . . Filled with interesting tidbits."—Herb Wilson, Portland Press Herald

      "A timely reminder of just how tenuous life can be for a species, regardless of how numerous they might be. This hardback book is beautifully illustrated. Mr. Fuller has put together a complete natural history of the passenger pigeon drawing upon historical illustrations, photographs, specimens, poems, ornithological journal articles and historical accounts."—Penny Miller, A Charm of Finches

      "A must have for anyone with an interest in this species."—Ian Paulsen, Birdbooker Report

      "Beautifully illustrated, this easy-to-read book will appeal to anyone who wishes to understand the concept of extinction."—Jennifer J. Meyer, Orange County Register

      "From start to finish, the text is informative and entertaining and the photos and artwork are fascinating. Whether you've studied the Passenger Pigeon for years or haven't even heard of the species, I would highly recommend this book."—Rob Ripma, Nutty Birder

      "Beautifully illustrated, including rare archival images as well as haunting photographs of live birds, this is an evocative memorial to one of the great icons of extinction."—Leslie Geddes-Brown, Country Life

      "If a picture is worth a thousand words, then Errol Fuller's slim book, The Passenger Pigeon, is surely stuffed full of them. . . . It will probably appeal to younger readers, it is a fast read and it could be a satisfying companion volume to the other two passenger pigeon books that have been recently published."Grrl Scientist

      "The most visually beautiful [of recently published books on the passenger pigeon] is Errol Fuller's The Passenger Pigeon, which gives a fine account of the species, its biology and its demise."—Adrian Barnett, New Scientist

      "[It] is THE monograph for the passenger pigeon. I imagine everyone would learn something from this book. I personally was left with a feeling that we should not stand idle and allow mankind to eradicate any other living species. An excellent read, recommended."—Mike King, Gloster Birder

      "Written with both clarity and feeling. Most impressive is the breadth and depth of research crammed into what is a relatively slim volume. . . . A masterful summary of what we know about this remarkable bird. To read it is a joy, but one tinged with sadness and regret."—Andy Stoddart, Birdwatch

      "I would highly recommend reading The Passenger Pigeon by Errol Fuller. . . . Beautifully illustrated."—David Lewis, Birds from Behind

      "The Passenger Pigeon is an excellent introduction to this bird, what made it so special, and the tragedy of its extinction. If you want to learn about the Passenger Pigeon, or just enjoy the art and photographs, then I'd highly recommend it."—Grant McCreary, Birder's Library

      "This is a book that should be on every reader's shelf as a reminder as to what we have missed and to help ensure such an avian tragedy does not occur again."—David Saunders, Bird Watching

      "[I]f you want to learn more about the Passenger Pigeons, this is a great book to have and to share."North Durham Nature Newsletter

      "The heartbreaking illustrated history of a bird that, having once numbered in the billions, vanished from the planet in 1914. On the centenary of the species' extinction Fuller, an expert on extinct birds, reflects on what we lost."Globe and Mail

      "A book about a long extinct bird could easily have been a dry, academic tome full of dull facts and figures, but Errol Fuller has managed to avoid this, and instead has produced an engaging book to fire the imagination, to encourage empathy with Martha, alone in her cage for the last four years of her life, to provoke outrage that the species was driven to extinction, and above all, a desire to fight to prevent the same fate befalling others."—Andy Mackay, Grebe

      "A sad and gorgeous book."—Stephen Romei, Australian

      "Sumptuously illustrated."—Michael McCarthy, Independent

      "Passenger Pigeon takes just the opposite approach. Though there is an informative and gracefully written text, this handsome volume tells its stories most eloquently in pictures."—Rick Wright, ABA Blog

      "Writing in a clear, conversational tone, artist/writer Fuller highlights important aspects of this bird's natural history and its remarkable downhill spiral into oblivion. He provides fascinating accounts of the last wild birds of ‘Martha,' the last of her species, who died in the Cincinnati Zoo and historical testimony from people who observed the birds' enormous flocks firsthand. Illustrated with numerous historical photographs and exquisite artwork (modern and period), this lasting tribute to one of the most magnificent birds to have ever lived will interest anyone who cares about conservation of the natural world."Choice

      "In The Passenger Pigeon, Erroll Fuller brings his artist's eye to a recently popular, much-covered, yet little-understood phenomenon. . . . Fuller's vivid account is the one new book on the species you must buy."Living Bird Magazine

      "It is easy to read and thought-provoking, and will be of interest to anyone concerned about conservation today."—Ian Woodward, BTO News

      "Fuller's book will appeal to a much larger audience and is worth the price just for the photos and illustrations. . . . The Passenger Pigeon should make us vow to never lose another species because of our own greed or neglect."—D.R.K., Wildlife Activist

      "[L]yrical and artistic. Short enough to hold your attention, detailed enough to convey the essential facts, and elegantly presented."—Alan Knox, Scottish Birds

      Related Books


      Methods

      Phenotyping

      Pigeon pea accessions were phenotyped at three locations, in years 2013–14 and 2014–15 at Gulbarga and ICRISAT 2014–15 at Tandur. The phenotyping data from ICRISAT used in the present study have been taken from (Varshney et al., 2017 ). In order to generate reliable phenotyping data, all the accessions were planted in two replications in an alpha-lattice design. In each replication, data were recorded from three plants from each accession. All the accessions were phenotyped for nine yield and yield-related traits, including days to 50% flowering, days to 75% maturity, plant height, number of primary branches, number of secondary branches, pods per plant, number of seeds per pod, 100 seed wt and seed yield per plant. The phenotyping was conducted following standard procedures described in the GenBank manual (Upadhyaya and Gowda, 2009 ).

      Pangenome assembly and annotation

      Whole-genome sequence data of 89 pigeon pea accessions having more than 9.5x coverage from Varshney et al. ( 2017 ) were used for pangenome assembly using the iterative mapping and assembly approach. The majority of the diversity present in the original dataset is present in the pangenome dataset. The pangenome data contain 64 landraces, 24 breeding lines and 1 unknown, compared with 167 landraces, 117 breeding lines, 14 wild types and 2 unknowns in Varshney et al. ( 2017 ). All regions present in the original data are present in the pangenome, with a focus on India. Of the pangenome individuals, 67 come from India, 4 from the Philippines and 17 additional countries including Uganda (1 individual), Kenya (2 individuals) and Zaire (1 individual).

      The pangenome was constructed by mapping of the sequence reads individually to the reference genome (Varshney et al., 2012 ), using bowtie2 v2.3.0 (Langmead and Salzberg, 2012 ), followed by assembly of pooled unmapped using MaSuRCA v3.2.3 (Zimin et al., 2013 ) to produce additional reference sequence. The assembled contig sequences were compared with the NCBI nt database (downloaded 2 May 2018) using BLAST v2.5.0. Contigs with best hits to non-green plants, chloroplast or mitochondrial sequences were removed. The remaining newly assembled contigs >1 Kb in length were annotated using MAKER2 (Holt and Yandell, 2011 ). De novo gene prediction was performed with SNAP (Schmid et al., 2003 ) and Augustus (Stanke et al., 2006 ). Publicly available ESTs (24 177), as well as 43 pigeon pea RNA-seq data sets (Table S10) and proteins (48 450) from NCBI, were used as evidence. The functional annotations were assigned by BLAST comparison with UniProt 90 of A. thaliana. Gene ontologies (GO terms) were assigned based according to GO terms of the best hit of each gene by home-made python scripts. GO enrichment was performed using Fisher’s exact test as implemented in topGO package (Alexa et al., 2006 ) with method ‘elim’ used to adjust for multiple comparisons. REVIGO (Supek et al., 2011 ) was used to remove redundant GO categories from all GO terms enriched with a P-value below 0.05, and CirGO (Kuznetsova et al., 2019 ) was used to visualize the results.

      Gene presence/absence variation and pangenome modelling

      Whole-genome sequence data for all 89 pigeon pea accessions were mapped to the reference genome using bowtie2 v2.2.5 (--end-to-end --sensitive -I 0 -X 1000 Langmead and Salzberg, 2012 ). SGSGeneLoss (Golicz et al., 2015b ) was used to determine whether a gene is present or absent. Curves describing pangenome size and core genome size were fitted in R (R Core Team, 2018 ) using the nls function (nonlinear least squares) from package stats, part of R. Points used in regression corresponded to all the possible combinations of genomes, similar to Hirsch et al. ( 2014 ).

      SNP discovery and annotation

      Whole-genome sequence reads were mapped to the pangenome using Bowtie2 v2.2.9 (-I 0 -X 1000) (Langmead and Salzberg, 2012 ). Parallel jobs were run using GNU parallel 20160622 (Tange, 2011 ). The resulting SAM files were converted to BAM format using samtools (Li et al., 2009 ), followed by the removal of duplicate reads using picard tools v2.14 (http://broadinstitute.github.io/picard/). SNPs were called using UnifiedGenotyper in GATK 3.8.0 (McKenna et al., 2010 ) and functionally annotated using SnpEff v4.3T (Cingolani et al., 2012 ).

      After removing SNPs with a minor allele frequency below 1%, a SNP quality score (QUAL) below 20 and a SNP depth (DP) below 10, we used BLINK v0.01 (standard settings Huang et al., 2019 ) for association analysis and rMVP to plot Manhattan and QQ-plots (https://github.com/XiaoleiLiuBio/rMVP). The P-value significance cut-off was set to 1.35e-08 (=0.05/3 713 723 SNPs).

      The GWAS with the 4635 variable genes instead of SNPs using the SNP-based principal components as covariates was performed using FarmCPU as implemented in rMVP (standard settings) with a significance cut-off set to 1.08e-5 (0.05/4635). The presence/absence matrix was encoded as SNPs, where ‘presence’ was the minor and ‘absence’ was the major allele.

      ANOVA was carried out using the R v3.5.1 function aov by grouping all locations and time points for each of the nine phenotypes using the formula phenotype

      location/year. P-values were adjusted for multiple comparisons by using R’s p.adjust method.

      Genes upstream or downstream from candidate SNPs were mined using bedtools2 v2.27.1 closest (Quinlan and Hall, 2010 ). All candidate genes were aligned with the Glycine max Williams-82 Wm82.a2.v1 reference annotation (Schmutz et al., 2010 ) using blastp (options: -evalue 1e-10 Camacho et al., 2009 ) and annotations for these genes were extracted from SoyBase (Grant et al., 2010 ).


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