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Parrots (1 Viewer)

l_raty

laurent raty
cyanogaster and malachitacea are not applied to the same species?
Psittacus cyanogaster Vieillot 1818 ([OD], current valid name Triclaria malachitacea (Spix 1824)) is a junior primary homonym of Psittacus cyanogaster Shaw 1812 (current valid name Trichoglossus moluccanus (Gmelin 1788)).
Junior primary homonyms are permanently invalid.
 

Peter Kovalik

Well-known member
Slovakia
Mulga Parrot

Kerensa McElroy, Keira Beattie, Matthew R. E. Symonds & Leo Joseph. Mitogenomic and nuclear diversity in the Mulga Parrot of the Australian arid zone: cryptic subspecies and tests for selection. Emu - Austral Ornithology, Published online: 17 Dec 2017

Abstract:

The Australian arid zone is well recognised as a source of evolutionary novelty and diversity. Roles for selection vs. drift in the region remain less understood. We surveyed mitogenomic diversity and genome-wide nuclear markers in the Mulga Parrot (Psephotellus varius) to add to phylogeographic data from arid zone species. We found structured diversity either side of the Flinders Ranges–Lake Eyre Basin (Eyrean barrier; net nucleotide divergence 1.92% for ND2). Coalescent analysis suggests that this arose during the mid-Pleistocene approximately 402 000 years ago. In both phylogroups, however, the mitogenome is under pervasive purifying selection. Purifying selection in the context of consistent environments either side of the Eyrean barrier may have maintained ancestral plumage and morphological traits, though in other plumage traits there is some plumage divergence that is geographically concordant with the phylogeographic structure. This leads to the essentially ‘cryptic’ genetic diversity uncovered here, despite indications of ongoing adaptation to aridity in P. varius as evidenced by increasing bill surface area (shown by earlier work to have increased relative to body size by 10.4% since 1871), a result we affirm here across the species as a whole. This study also demonstrates the utility of shallow ‘genome skimming’ sequencing for population analyses.
 

Peter Kovalik

Well-known member
Slovakia
Parrots of Oceania

George Olah, Jörn Theuerkauf, Andrew Legault, Roman Gula, John Stein, Stuart Butchart, Mark O’Brien & Robert Heinsohn. Parrots of Oceania – a comparative study of extinction risk. Emu - Austral Ornithology Vol. 0 , Iss. 0,0

[abstract]

Australia, New Zealand, New Guinea, Wallacea, and the islands of the Pacific Ocean collectively possess 42% of the world’s parrot species, including half of all Critically Endangered species. We used comparative methods to review the factors related to extinction risk of 167 extant and 5 extinct parrot species from this region, subsequently referred to as ‘Oceania’. We tested a range of ecological and socio-economic variables as predictors of extinction risk for parrots in the region while controlling for phylogeny. Parrot species were most likely to be threatened if they had small historical ranges, large bodies, or a high dependency on forest, or if they were endemic to a single country, or native to a country with high unemployment. Our analysis identifies invasive species as an especially severe threat to the parrots of Oceania. We present maps of parrot species’ diversity and draw attention to regions of conservation concern. Our comparative analysis presents an important overview of the factors contributing to the decline of parrots in Oceania, and provides a strong basis for comparison with other parts of the world.
 

l_raty

laurent raty
Barros de Araujo, Marques, Vielliard. 2017. Flight-call as species-specific signal in South American parrots and the effect of species relatedness in call similarity. Rev. Bras. Ornitol. 23:143-151.
[pdf]
 

Daniel Philippe

Well-known member
Eclectus Parrot and Rainbow Lorikeet

Braun M.P., Reinschmidt M., Datzmann T., Waugh D., Zamora R., Häbich A., Neves L., Gerlach H., Arndt T., Mettke-Hofmann C., Sauer-Gürth H. & Wink M., 2017. Influences of oceanic islands and the Pleistocene on the biogeography and evolution of two groups of Australasian parrots (Aves: Psittaciformes: Eclectus roratus, Trichoglossus haematodus complex). Rapid evolution and implications for taxonomy and conservation. Eur. J. Ecol. 3 (2): 47-66.

Access to PDF
 

Peter Kovalik

Well-known member
Slovakia
Poicephalus gulielmi

Adam Dawid Urantówka, Aleksandra Kroczak & Paweł Mackiewicz (2017) The complete mitochondrial genome of red-fronted parrot (Poicephalus gulielmi) revealed a new gene rearrangement within the order Psittaciformes, Mitochondrial DNA Part B, 2:2, 833-835, DOI: 10.1080/23802359.2017.1407691

[pdf]
 

Peter Kovalik

Well-known member
Slovakia
Poicephalus rufiventris

Subir Sarker, Shubhagata Das, Seyed A. Ghorashi, Jade K. Forwood, Karla Helbig & Shane R. Raidal (2018) The first complete mitogenome of red-bellied parrot (Poicephalus rufiventris) resolves phylogenetic status within Psittacidae, Mitochondrial DNA Part B, 3:1, 195-197, DOI: 10.1080/23802359.2018.1437818

[pdf]
 

Melanie

Well-known member
Clarkona

Is the genus name Clarkona for the Mulga parrot still in use or it is just a syonym for Psephotellus.
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
A new species of Mexican parrot? Reasonable doubt on the status of Amazona gomezgarzai (Psittaciformes: Psittacidae)
PATRICIA ESCALANTE, ABIGAIL EUNICE ARTEAGA-ROJAS, MAURICIO GUTIÉRREZ-SÁNCHEZ-RÜED

Abstract

We present arguments against the recognition of Amazona gomezgarzai Silva et al., 2017 as a valid species. This putative new species was stated to have been discovered in Becanchén town in the central Yucatan Peninsula by a veterinarian, who presented two live individuals to the authors for description. This description has numerous weaknesses, as follows: 1) the Yucatan Peninsula avifauna is well-known, having been extensively explored by collectors and other ornithologists; 2) the authors were never in the relevant field area, nor did they verify that the two individuals obtained for the description came from a natural population; 3) our field trip to the type locality and distribution area failed to verify the existence of the putative new species there; instead, inhabitants of these localities denied that such a person was there and denied having given anyone the birds, nor did they recognize that there were parrots matching the “new” species in the area; 4) the description was prepared without proper voucher specimens; 5) comparisons in existing museum collections were highly inadequate; 6) the characters on which the description is based fail to support that it represents a valid taxon, instead strongly supporting an hypothesis of hybrid origin, which was untested by nuclear DNA markers; and 7) no collecting permits were mentioned in the paper. Although earlier reviewers pointed out weaknesses of the original manuscript, the authors failed to rigorously address these questions and the paper was nevertheless published.

Keywords

Aves, invalid species, questionable description, Neotropical parrots

http://www.mapress.com/j/zt/article/view/zootaxa.4420.1.9
 

Daniel Philippe

Well-known member
Rosellas

Shipham A., Joseph L., Schmidt D.J., Drew A., Mason I. & Hughes J.M., in press. Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and Platycercus eximius. Heredity

There
 

l_raty

laurent raty
Loriini

Smith, Mauck, Benz, Andersen. 2018. Uneven missing data skews phylogenomic relationships within the lories and lorikeets. [BioRxiv preprint]

Abstract

Resolution of the Tree of Life has accelerated with massively parallel sequencing of genomic loci. To achieve dense taxon sampling within clades, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. A particular challenge that arises with this type of sampling scheme is an expected systematic bias in DNA sequences, where older material has more missing data. In this study, we evaluated how missing data influenced phylogenomic relationships in the brush-tongued parrots, or the lories and lorikeets (Tribe: Loriini), which are distributed across the Australasian region. We collected ultraconserved elements from modern and historical material representing the majority of described taxa in the clade. Preliminary phylogenomic analyses recovered clustering of samples within genera, where strongly supported groups formed based on sample type. To assess if the aberrant relationships were being driven by missing data, we performed an outlier loci analysis and calculated gene-likelihoods for trees built with and without missing data. We produced a series of alignments where loci were excluded based on Δ gene-wise log-likelihood scores and inferred topologies with the different datasets to assess whether sample-type clustering could be altered by excluding particular loci. We found that the majority of questionable relationships were driven by particular subsets of loci. Unexpectedly, the biased loci did not have higher missing data, but rather more parsimony informative sites. This counterintuitive result suggests that the most informative loci may be subject to the highest bias as the most variable loci can have the greatest disparity in phylogenetic signal among sample types. After accounting for biased loci, we inferred a more robust phylogenomic hypothesis for the Loriini. Taxonomic relationships within the clade can now be revised to reflect natural groupings, but for some groups additional work is still necessary.


[Related: https://www.birdforum.net/showthread.php?p=3441265#post3441265 ]
 

Jim LeNomenclatoriste

Taxonomy and zoological nomenclature
France
Taxonomic theory:
Cardeos Verheyen, 1956 - Cardeos cardinalis (Gray, 1849)

Chalcopsitta Bonaparte, 1850 - Chalcopsitta atra (Scopoli, 1786), Chalcopsitta duivenbodei Dubois, 1884, Chalcopsitta scintillata (Temminck, 1835)

Charminetta Iredale, 1956
Charminetta wilhelminae (Meyer, 1874)

Charmosyna Wagler, 1832 - Charmosyna josefinae (Finsch, 1873, Charmosyna multistriata (Rothschild, 1911), Charmosyna pulchella Gray, 1859, Charmosyna papou (Scopoli, 1786), Charmosyna stellae Meyer, 1886, Charmosyna toxopei (Siebers, 1930)

Coriphilus Wagler, 1832 - Coriphilus amabilis (Ramsay, 1875), Coriphilus australis (Gmelin, 1788), Coriphilus kuhlii (Vigors, 1824), Coriphilus margarethae (Tristam, 1879), Coriphilus meeki (Rothschild & Hartert, 1901), Coriphilus palmarum (Gmelin, 1788), Coriphilus peruvianus (Statius Müller, 1776), Coriphilus rubrigularis (Sclater, 1881), Coriphilus solitarius (Suckow, 1800), Coriphilus stepheni (North, 1908), Coriphilus ultramarinus (Kuhl, 1820)

Glossopsitta Bonaparte, 1854 - Glossopsitta concinna (Shaw, 1791)

Glossoptilus Hartert, 1896 - Glossoptilus goldiei (Sharpe, 1882)

Hypocharmosyna Salvadori, 1891- Hypocharmosyna diadema (Verreaux & Des Murs, 1860) (tentative), Hypocharmosyna placentis (Temminck, 1835), Hypocharmosyna rubronotata (Wallace, 1862)

Parvipsitta Mathews, 1916
Parvipsitta porphyrocephala (Dietrichsen, 1837), Parvipsitta pusilla (Shaw, 1790)

Pseudeos Peters, 1935 - Pseudeos fuscata (Blyth, 1858)

Psitteuteles Bonaparte, 1854 - Psitteuteles versicolor (Lear, 1831) –

Trichoglossus Stephens, 1826 (included Eos Wagler, 1832) - Trichoglossus bornea (Linnaeus, 1758) comb. nov., Trichoglossus capistratus (Bechstein, 1811), Trichoglossus chlorolepidotus (Kuhl, 1820), Trichoglossus cyanogenius (Bonaparte, 1850) comb. nov.,Trichoglossus euteles (Temminck, 1835), Trichoglossus flavoviridis Wallace, 1863, Trichoglossus forsteni Bonaparte, 1850, Trichoglossus haematodus (Linnaeus, 1771), Trichoglossus histrio (Statius Müller, 1776) comb. nov., Trichoglossus iris (Temminck, 1835), Trichoglossus johnstoniae Hartert, 1903, Trichoglossus meyeri Walden, 1871, Trichoglossus moluccanus (Gmelin, 1788), Trichoglossus ornatus (Linnaeus, 1758), Trichoglossus reticulatus (Müller, 1841) comb. nov., Trichoglossus rosenbergii Schlegel, 1871, Trichoglossus rubiginosus (Bonaparte, 1850), Trichoglossus rubritorquis Vigors & Horsfield, 1827, Trichoglossus semilarvatus (Bonaparte, 1850) comb. nov., Trichoglossus squamatus (Boddaert, 1783) comb. nov., Trichoglossus weberi (Büttikofer, 1894)

The other genera don't change
 
Last edited:

Daniel Philippe

Well-known member
Urantowka A.D., Kroczak A., Silva T., Zamora Padrón R., Fernández Gallardo N., Blanch J., Blanch B. & Mackiewicz P., in press. New insight into parrots’ mitogenomes indicates that their ancestor contained a duplicated region. Mol. Biol. Evol.

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Peter Kovalik

Well-known member
Slovakia
BirdLife's Globally Threatened Bird Forums

Eclectus Parrot (Eclectus roratus) is being split: assessment of newly recognised taxa.

Posted on May 23, 2019 by Red List Team (BirdLife International)

Following a taxonomic reassessment investigating the findings of Braun et al. (2016), Eclectus Parrot is being split into four species; Moluccan Eclectus Eclectus roratus, Papuan Eclectus E. polychloros, Sumba Eclectus E. cornelia and Tanimbar Eclectus E. riedeli.

The pre-split species was listed as Least Concern. The population was judged to be declining due to the dual impacts of trapping for the cage bird trade and high rates of habitat loss in parts of the species’s large range. Nevertheless, the overall rate of this decline was not thought to approach the thresholds for listing as threatened under Criterion A, the range greatly exceeded the thresholds for Criterion B, and the total population size was unknown but thought to considerably exceed the thresholds under Criteria C and D. Despite being legally protected in Indonesia, trade continues to be noted throughout the range (Cottee-Jones et al. 2014, Collar et al. 2019).

The reduced range size, and likely population sizes of the newly defined taxa may result in one or more qualifying for listing as threatened. For the newly recognised Moluccan and Papuan Eclectus, an initial assessment (see below) suggests that while they are considered to be declining, they are not considered to approach the thresholds for listing as threatened under the IUCN Red List (IUCN 2001, 2012). Constructive comments are still welcome on these judgements. However, Sumba Eclectus and Tanimbar Eclectus meet initial thresholds for listing as threatened, hence are assessed against all criteria.

Of importance is that there is a revised estimate for the generation length of the pre-split species of 12.7 years (BirdLife International in prep.). Here this is used for each of the newly recognised species to define the three-generation period over which to assess population decline, rounded to 38 years.

Moluccan Eclectus (E. roratus) – The new nominate species includes the two subspecies voesmaeri and roratus, and is restricted to the Moluccas, being known from the islands of Morotai, Halmahera, Ternate, Bacan and Obi (including some smaller islands), and Buru, Seram, Ambon, Haruku and Saparua (Collar et al. 2019). The newly calculated Extent of Occurrence (EOO; IUCN 2001, 2012, Joppa et al. 2016) is 234,950 km2, greatly exceeding the range-size criterion for listing as threatened under Criterion B1 (EOO < 20,000 km2).

A recent survey within the range indicates that the population remains large: on Halmahera, the population just in the Aketajawe-Lolobata National Park was estimated at 4,463 individuals in 2012 (Bashari 2012), which suggests that the overall population on Halmahera is close to 10,000 individuals. The density estimate here was 5.9 individuals/km2, which is similar to the density recorded on Seram (7.4-13 individuals/km2; Marsden 1998, 1999), and Buru (1.9 – 13 inds/km2; Marsden 1999). All populations together likely exceed the population size thresholds for listing as threatened (< 10,000 mature individuals for Criterion C, < 1,000 mature individuals for Criterion D).

However, there are concerns over the impact of trade in parts of the range. While a status assessment of the threat to parrots within the Moluccas in the 1990s did not consider Eclectus to be a priority (Widodo et al. 1999), a recent estimate of 810 (± 153) individuals harvested annually for trade on the island of Obi (Cottee-Jones et al. 2014) appears rather high. The species was found to be uncommon on Obi (Mittermeier et al. 2013; Cottee-Jones et al. 2014), and it was traded at almost double the price of any other parrot species in the bird market. While Obi is a small part of the range and the species persists there, this population appears severely threatened (Cottee-Jones et al. 2014). Lambert (1993) reported that the species was far rarer on Obi than on Bacan or Halmahera, so this may represent a real suppression of numbers by trapping. With densities elsewhere being higher, the concerning situation on Obi indicates that it is reasonable to infer that the population is declining, but that overall the rate of decline is unlikely to approach the threshold for listing as threatened under Criterion A (>30% decline in three generations). Consequently, Moluccan Eclectus is proposed to be listed as Least Concern.

Papuan Eclectus (E. polychloros) – Papuan Eclectus (E. polychloros)includes the subspecies aruensis, biaki, macgillivrayi, and solomonensis. Its range extends from the west Papuan islands (Gebe [Rothschild and Hartert 1901] including Gag Island [Johnstone 2006], Kai Islands, Aru Islands and Biak throughout lowland New Guinea, the Admiralty Islands through the Bismarck Archipelago and the Solomon Islands (except St Matthias, Nissan and Rennell), to the extreme north of Queensland, Australia (Collar et al. 2019). The EOO is 3,770,141 km2. It is considered that while the population may be declining due to trapping and habitat loss, the rate of decline is unlikely to approach the thresholds for listing the species as threatened under Criterion A (>30% decline in three generations).

Several estimates of population density exist, of which many indicate relatively high densities in excess of 10 individuals/km2. For example, densities on New Britain were estimated at 16 individuals/km2 in primary forest and 25-72 individuals/ km2 in logged forest and forest gardens (Marsden and Pilgrim 2003). In lowland rainforest on mainland New Guinea, densities were 10 individuals/km2 (Bell 1982), while the density in hillforest (between 430-950 m) was 11.3 individuals/km2 (Marsden and Symes 2006). The population on New Britain alone would therefore likely exceed thresholds for listing under the population size criterion. Overall, Papuan Eclectus is considered to have a large population and is not believed to approach the thresholds for listing as threatened. Papuan Eclectus is therefore proposed to be listed as Least Concern.

The other two newly-defined taxa have restricted ranges. Sumba Eclectus E. cornelia is only found on the island of Sumba in the western Lesser Sundas, and Tanimbar Eclectus E. riedeli on at least Yamdena Island and Larat (Bishop and Brickle 1999). As they meet the initial thresholds for listing as threatened, they are here assessed against each Red List criterion in turn.
 

Peter Kovalik

Well-known member
Slovakia
BirdLife's Globally Threatened Bird Forums

Maroon-tailed Parakeet (Pyrrhura melanura) is being split: assessment of newly recognised taxa.

Posted on May 23, 2019 by Red List Team (BirdLife International)

Following a taxonomic reassessment, Maroon-tailed Parakeet (Pyrrhura melanura) has been split into Maroon-tailed Parakeet (P. melanura) and Upper Magdalena Parakeet (P. chapmani). The newly defined Upper Magdalena Parakeet occurs in the Upper Magdalena Valley on the eastern slope of the Central Andes in the departments Tolima and Huila (Donegan et al. 2016, Collar et al. 2019). It is found in cloud forest at an elevation of 1,600-2,800 m (Collar et al. 2019). Upper Magdalena Parakeet is known from a small number of localities (Donegan et al. 2016), including the La Riviera and Los Yalcones reserves (Calderón 2005, Bradley 2015).

The pre-split species was listed as Least Concern, undergoing a slow decline due to forest loss and trapping (BirdLife International 2019). It is highly unlikely that the removal of the Upper Magdalena Parakeet from the pre-split taxon will have large effects on the overall population size, distribution range and trend of the newly defined Maroon-tailed Parakeet; thus, unless new information becomes available, Maroon-tailed Parakeet will be retained as Least Concern.
 

Peter Kovalik

Well-known member
Slovakia
Psephotellus

Martin Irestedt, Per G. P. Ericson, Ulf S. Johansson, Paul Oliver, Leo Joseph and Mozes P. K. Blom. No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus). Diversity 2019, 11(4), 58; https://doi.org/10.3390/d11040058

Abstract:

The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.

[pdf]
 

Peter Kovalik

Well-known member
Slovakia
Ara macao

Kari L Schmidt, Matthew L. Aardema & George Amato. Genetic analysis reveals strong phylogeographic divergences within the Scarlet Macaw Ara macao. Ibis, First Published: 17 June 2019. https://doi.org/10.1111/ibi.12760

Abstract:

Scarlet Macaws Ara macao have the largest geographic distribution of any Neotropical psittacine, occupying a variety of lowland forest habitats from Mexico to Brazil. Two subspecies, A. m. macao and A. m. cyanoptera, are currently recognized based on wing chord length and plumage colouration, with formal descriptions suggesting genetic introgression in southern Nicaragua and northern Costa Rica. The present study aimed to investigate the extent of genetic diversification within A. macao by analysing mitochondrial sequence data from contemporary and historical samples. Phylogenetic reconstruction and population aggregation analysis confirmed two distinct phylogeographic groups, with a high degree of intraspecific genetic structure and no evidence of a putative hybrid zone. Whole mitochondrial genome sequencing further confirmed substantial divergence (~1.8%) between the cyanoptera and macao lineages. These results demonstrate a separation of A. macao into two distinct evolutionary entities and highlight a non‐uniform distribution of intraspecific diversity, suggesting current conservation designations may warrant re‐evaluation.
 

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