Genetic analysis of wild Scarlet Macaws from saliva they leave on fruits

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genetic-analysis-of-wild-scarlet-macaws-from-saliva-they-leave-on-fruits

To make a genetic
analysis of an organism, you need its DNA. In the case of animals, obtaining a
sample directly can be considered invasive to a greater or lesser degree. Some
individuals of animal species under human care can be trained to “donate” a
small sample, of blood for example, with little or no deviation from their
habitual routines. On the other hand, obtaining samples directly from
free-living animals in the wild can be much more challenging. Capture and
confinement, even if only for a very short time, might not only be very
difficult to achieve, but possibly also risky for both the animal and the
researcher.

A camera trap captures a pair of Scarlet Macaws at the nest entrance.

That is why, if
the objectives of the genetic analysis permit, it is preferable to obtain the
DNA in an indirect or non-invasive way. Some interesting methods give an
indication of how that can be achieved. For example, the presence of mammal
species in tropical forests in Côte d’Ivoire and Madagascar has
been confirmed by the analysis of DNA in the guts of carrion flies caught in
those forests. In zoo studies, DNA from individual mammals has been obtained by
using (disease-free) blood-sucking bugs, analysed upon retrieval. A study with common
terns (Sterna hirundo) shows that non-invasive blood collection from
bird species of various sizes is possible without disturbance. The technique
places in a nest a hollowed artificial egg containing a blood-sucking bug,
which can draw blood from the brood patch of breeding adults through a
gauze-covered hole in the egg.

Camera trap image of an open-winged Scarlet Macaw at the nest.

There is also the DNA that can be obtained from what
the animals leave within their environment without the need for intermediaries.
For example, Baus et al. (2019) have examined the non-invasive collection of
genetic samples to study bird populations in the Neotropics. Their analysis
showed that shed feathers were most frequently used (66.7% of studies),
followed by carcasses (14.2%), eggs (9.5%), non-invasively obtained blood
(4.8%) and both faeces and shed feathers (4.8%). Most studies addressed
population genetic issues (38.1%), followed by species identification (28.6%), evolutionary
relationships (14.3%), molecular sexing (9.5%), and parentage analyses (9.5%).

For many years, and with over US$204,250, the Loro
Parque Fundación has been supporting parrot conservation projects, which
include genetic analysis. One notable example of non-invasive collection of
genetic samples from the shed feathers of wild individuals has been with a
Scarlet Macaw (Ara macao) project in the area of the Tambopata
Research Centre in Peru. Analysis of the samples has revealed
important information about the genetics of the local population, as well as contributing
to knowledge about the evolutionary relationships between different
sub-populations of this species throughout its geographical distribution.

Forest extending to the beach, where Tropical almond trees are common.

The Loro Parque Fundación has also been supporting
Scarlet Macaw conservation projects in Mexico, Guatemala, Belize, Nicaragua and
Costa Rica, all countries where the subspecies A. m. cyanoptera is still
found, although seriously threatened by loss of forest habitat and illegal
trade. The projects include one managed by the NGO, Paso Pacífico, to save the
last remaining population on the Pacific coast of Nicaragua in the Cosigüina
Volcano forests of the far north-west of the country. In 2015, this isolated
population had diminished to only 14 individuals, but the protection measures
are now working. In 2017 the first successful nest in the area in over 20 years
was recorded and the population has increased.

Genetic analysis of this population could be very
useful to inform conservation measures in the future, and the chances that this
can happen could be increased by the use of a novel non-invasive method to
collect DNA. This method involves the collecting of residual saliva from fruits
partially consumed by the macaws (Monge et al. 2018). The researchers who
developed the method already knew that advances in the storage and processing of
DNA permit the recovery of genetic material from traces of saliva in food
remains. They therefore postulated that the feeding habits of canopy-dwelling
frugivorous birds, such as large macaws, could present an ideal opportunity to
obtain DNA from discarded fruits.

Scarlet Macaw feeding on Tropical almonds.

They tested this assumption by collecting tropical almond (Terminalia catappa) fruits which had been eaten and discarded by Scarlet Macaws in Costa Rica. This tree is common in the lowlands, and is also called the beach almond because it often prominently borders the beaches. In its fruiting season, Scarlet Macaws can frequently be observed feeding in these beach-side trees. The researchers used three different methods for the collection and storage of samples, and successfully isolated DNA molecules from saliva the macaws had left on the fruits. The best results were obtained for samples preserved in ethanol, and the researchers recommend the use of a combination of specialized collection swabs or ethanol-stored swabs along with commercial DNA extraction kits.

Tropical almond fruits partly eaten by Scarlet Macaws in Costa Rica. a) the fruit shows beak marks and the incision from where the edible flesh is extracted; b) shows traces of saliva left when using the tongue for support (enclosed in white circle).

Having demonstrated its success with the Scarlet Macaw, the researchers assert that DNA in saliva found in partially consumed food items is an underused non-invasive source of avian genetic material for analysis. In fact, such non-invasive genetic sampling can help tackle conservation problems and contribute to scientifically informed conservation policies for Scarlet Macaws and many other species in need.

Author: David Waugh, Correspondent, Loro Parque Fundación

Credits: title photo, photo 1 – 2 – Paso Pacífico; 3 – Almonds&corals; 4 – E. Chen; 5 – Monge et al 2020

Baus, I., Miño, C. &
Monge, O. (2019). Current trends in the
application of non-invasive genetic sampling to study Neotropical birds: Uses,
goals, and conservation potential. Avian Biology Research.
175815591984822. 10.1177/1758155919848229. 

Monge, O., Dumas, D.
& Baus, I. (2018). Environmental DNA from avian residual saliva in fruits
and its potential uses in population genetics. Conservation Genetics
Resources
. 12. 10.1007/s12686-018-1074-4.

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