diversity

Article
Haemosporidians in Non-Passerine Birds of Colombia: An
Overview of the Last 20 Years of Research
Ingrid Astrid Lotta-Arévalo 1, *, Angie Daniela González 1 , Brayan Andrés Gamboa-Suárez 2 ,
M. Andreína Pacheco 3 , Ananías A. Escalante 3 , Carlos Moreno 2 , Oscar Rodríguez-Fandíño 4 , Andrés Cuervo 5
and Nubia E. Matta 1, *

1 Grupo Caracterización Genética e Inmunología, Departamento de Biología, Facultad de Ciencias, Universidad

Nacional de Colombia, Bogotá 111321, Colombia
2 Unidad de Rescate y Rehabilitación de Animales Silvestres—URRAS, Facultad de Medicina Veternaria y
Zootecnia, Universidad Nacional de Colombia, Bogotá 11321, Colombia
3 Biology Department, Institute of Genomics and Evolutionary Medicine (iGEM), Temple University,
Philadelphia, PA 19122-1801, USA
4 Dirección de Investigación, Universidad Internacional del Trópico Americano Unitrópico,
Yopal 850001, Colombia
5 Colección de Ornitología, Instituto de Ciencias Naturales, Universidad Nacional de Colombia,
Bogotá 111321, Colombia
* Correspondence: [email protected] (I.A.L.-A.); [email protected] (N.E.M.)

Abstract: The Neotropics are highly diverse in avian species. Neotropical countries contribute a large
part of the estimated diversity of haemosporidian parasites reported for the planet’s tropical zones.
However, sampling is limited and biased, illustrated by only 30% of the genetic records (barcodes)
from non-passerines, most of them not linked to a nominal species. This paper aimed to perform the
molecular and morphological characterization of the haemosporidians that infect non-passerine birds
from Colombia deposited in the biological collection named “Grupo de Estudio Relación Parásito
Citation: Lotta-Arévalo, I.A.;
Hospedero (GERPH)”. We analyzed 1239 samples from twelve biomes and two animal care facilities.
González, A.D.; Gamboa-Suárez,
Phylogenetic relationships using barcodes and mitochondrial genomes were estimated. In addition,
B.A.; Pacheco, M.A.; Escalante, A.A.;
Moreno, C.; Rodríguez-Fandíño, O.;
the reports of haemosporidian infections in non-passerine birds from the Neotropics recorded after
Cuervo, A.; Matta, N.E. 1978 were summarized. We reported the presence of thirteen morphological haemosporidian species,
Haemosporidians in Non-Passerine four potential new species deposited in GERPH, a host range expansion for two Plasmodium species,
Birds of Colombia: An Overview of and a barcode sequence for Haemoproteus caprimulgi. We confirmed the species associated with
the Last 20 Years of Research. 56 molecular lineages reported in other neotropical countries at the genus level. Thus, biological
Diversity 2023, 15, 57. https:// collections and curated databases such as MalAvi are essential to support integrative approaches
doi.org/10.3390/d15010057 demanded in modern taxonomy.
Academic Editors: Michael Wink,
Carolina Romeiro Fernandes Chagas Keywords: Neotropical birds; Plasmodium; Haemoproteus; Leucocytozoon; mtDNA; biological collections
and Francisco Ferreira

Received: 17 November 2022

Revised: 19 December 2022
1. Introduction
Accepted: 20 December 2022
Published: 3 January 2023 Haemosporidia are a highly diverse group of parasites hosted by reptiles, mammals,
and birds [1]. These protozoans have been confirmed to infect many avian families on all
continents [2]. Traditionally, research on avian haemosporidians relies on species that can
be captured using mist nets as a trapping method, thus skewing the information obtained
Copyright: © 2023 by the authors. towards passerine birds [3].
Licensee MDPI, Basel, Switzerland. The Neotropical region in about ten terrestrial ecoregions [4–6] harbors more than
This article is an open access article 4000 avian species, representing almost half of the world’s species [7]. In fact, the three
distributed under the terms and most biodiverse countries in the world’s Aves are found in this region [8]. Agreeing with
conditions of the Creative Commons this, the avian Haemosporida are highly diverse at low latitudes [9], where the Neotropical
Attribution (CC BY) license (https:// countries contribute about 40% of the unique lineages reported for tropical countries
creativecommons.org/licenses/by/
(Malavi database [10]). However, recent findings of new lineages [11–13] suggest that
4.0/).

Diversity 2023, 15, 57. https://doi.org/10.3390/d15010057 https://www.mdpi.com/journal/diversity

 Haemosporidian research in the Neotropics began at the dawn of the 20th century
with the characterization of the Haemoproteus columbae life cycle ([15] cit. [16]). White et al.
[17] published the first comprehensive compilation of studies on the avian haematozoa of
the Neotropics, including infection reports from 31 bird orders from Mexico to Argentina.
In that article, the haemosporidian genera Plasmodium, Leucocytozoon, and Haemoproteus
Diversity 2023, 15, 57 were reported in 22 of the 30 non-passerine orders of birds. Then, Gabaldon et al.2 of 28
[18]
reported the presence of a fourth parasite genus named Fallisia in a Columbiform species
for the first time. Later, Valkiūnas [2] reported fourteen Plasmodium, twelve Haemoproteus,
and three
higher Leucocytozoon
values of parasitespecies in non-passerine
diversity can be expected hosts forfound
to be this geographic
compared to area,
the most
known of
host
themdiversity
describedinbefore
Central
2000 and[16].
South
TheAmerican countriesbetween
findings reported [14]. 1908 and 2005 were made
usingHaemosporidian
blood smears asresearch in the tool
a diagnostic Neotropics
(Figurebegan at the dawn
1). Currently, of the 20th century
haemosporidian with
biodiver-
the
sitycharacterization
characterizationof uses Haemoproteus
thecombined columbae from
information life cycle
blood ([15] cit. [16]).
smears, White et al.line-
mitochondrial [17]
published the first comprehensive compilation of studies on the avian haematozoa
ages, host-parasite interactions, and ecological traits [16]. From the first studies in avian of the
Neotropics, including infection reports from 31 bird orders from
haemosporidians in the Neotropics until now, at least twenty-four species have been de- Mexico to Argentina.
In that article,
scribed the haemosporidian
in non-passerine genera Plasmodium, Leucocytozoon, and Haemoproteus
hosts [2,16,19–23].
wereThe
reported in 22 of athe
first record 30 non-passerine
PCR-based diagnosisorders of birds. Then,
of haemosporidian Gabaldon
parasites et al. [18]
in neotropical
reported the presence
non-passerine of adone
birds was fourth
byparasite
Durrantgenus named
et al. [24] Fallisia
in 2006 in a Columbiform
(Figure 1). Given thespecies
higher
for the first time. Later, Valki ūnas [2] reported fourteen Plasmodium,
detection rate of molecular methods over microscopy (e.g., [25]), the number of explored twelve Haemoproteus,
and
avianthree
ordersLeucocytozoon
has increased species in non-passerine
(Figure hosts for this
1). The first Leucocytozoon geographic
species area,
reported in most
Apodi-of
them described before 2000 [16]. The findings reported between
formes (Hummingbirds) came from Colombia, and was published in 2014 [20]. In that 1908 and 2005 were
made
report,using blood smears
the authors emphasize as aa diagnostic
change in thetooldistribution
(Figure 1). ofCurrently, haemosporidian
this parasitic genus, com-
biodiversity
monly foundcharacterization uses combined
only in the highlands. Then, information
several newfrom blood smears,
Leucocytozoon mitochondrial
lineages were re-
lineages, host-parasite interactions, and ecological traits [16]. From
ported in South America’s highlands for non-passerines [13,21,26,27], etc. To date, accord-the first studies in
avian haemosporidians in the Neotropics until now, at least twenty-four
ing to MalAvi [10], nearly 700 lineages that remain identified at the genus level have been species have been
described
reported for in neotropical
non-passerine hosts [2,16,19–23].
non-passerine hosts.

Figure 1. Schematic representation of the findings of haemosporidians in Neotropical non-passerine

birds since the last comprehensive revision in 1978. Over the timeline, the parasite species are
described with the host and references. Under the timeline, brown thin lines represent the time
periods for the number of studies carried out using only microscopy (represented by the figure of
the microscope), methods based on PCR (represented by the DNA molecule), or combined evidence
(represented by the letter i). The size of the icons represents the number of studies carried out
with each methodology. The thin blue lines represent the time spans for which the number of
orders studied is counted. At the bottom, the size of the name represents the number of records
associated with each order, the smallest being those with the fewest number of studies in the specified
time range.
Diversity 2023, 15, 57 3 of 28

Diversity 2023, 15, x FOR PEER REVIEW 3 of 29

The first record of a PCR-based diagnosis of haemosporidian parasites in neotrop-

ical non-passerine birds was done by Durrant et al. [24] in 2006 (Figure 1). Given the
Figure 1. Schematic representation of the findings of haemosporidians in Neotropical non-passerine
higher
birds detection
since the rate of molecular
last comprehensive revision inmethods
1978. Overover microscopy
the timeline, (e.g., species
the parasite [25]), the number of
are de-
explored
scribed with theavian
host andorders has increased
references. (Figurebrown
Under the timeline, 1). The linesLeucocytozoon
thinfirst represent the time species
periodsreported
forintheApodiformes
number of studies (Hummingbirds)
carried out using came from Colombia,
only microscopy andbywas
(represented the published
figure of the inmi-2014 [20].
croscope),
In thatmethods
report, based on PCR (represented
the authors emphasizeby the DNAin
a change molecule), or combined
the distribution ofevidence (rep- genus,
this parasitic
resented by the letter
commonly found i). The
onlysize
inofthe
the highlands.
icons represents the number
Then, severalofnewstudies carried out with
Leucocytozoon each
lineages were
methodology. The thin blue lines represent the time spans for which the number of orders studied
reported in South America’s highlands for non-passerines [13,21,26,27],
is counted. At the bottom, the size of the name represents the number of records associated with
etc. To date, ac-
cording to MalAvi [10], nearly 700 lineages that remain identified
each order, the smallest being those with the fewest number of studies in the specified time range.at the genus level have
been reported for neotropical non-passerine hosts.
In Colombia,
In Colombia, thethe biological
biological collection
collection namednamedGrupoGrupo de Estudio
de Estudio Relación
Relación Parásito Hos-
Parásito
pedero (GERPH)
Hospedero (GERPH)hosts hosts samples
samples from fromtwenty
twentynon-passerine
non-passerine bird
bird orders
orders collected
collected in atin at least
least
tenten different
different ecosystems
ecosystems since1999.
since 1999.This
Thisstudy
studyaimed
aimedtotoperform
performaamolecular
molecular and and morpho-
morphological
logical characterization of the Haemosporidians infecting non-passerine birdsde-
characterization of the Haemosporidians infecting non-passerine birds deposited
posited
in theinGERPH
the GERPH biological
biological collection.We
collection. We also
also present
presentan anupdate
update onon thethe
haemospor-
haemosporidian
idian infection
infection reports
reports in non-passerine
in non-passerine birds
birds fromfrom Mexico
Mexico to Argentina
to Argentina forfor
thethe
lastlast 40
40 years. That
years. That would provide a more accurate perception of the state of
would provide a more accurate perception of the state of Neotropical research, allowing Neotropical research,
allowing
futurefuture
studies studies
to focusto focus efforts
efforts on the
on the species
species andand ecosystemsless
ecosystems lesssampled
sampled to to date.
date.
2. Materials andand
2. Materials Methods
Methods
2.1.2.1.
Samples
Samples
This study
This analyses
study samples
analyses of 1239
samples of individuals belonging
1239 individuals to 178 species,
belonging 34 families,
to 178 species, 34 families,
and 20 orders of non-passerine birds deposited in the biological collection GERPH.
and 20 orders of non-passerine birds deposited in the biological collection GERPH. These These
samples
sampleshave been
have obtained
been mainly
obtained fromfrom
mainly wildwild
birdsbirds
collected in 23 in
collected localities distributed
23 localities distributed in
in 12 of the 32 continental biomes of Colombia (Table S1, Figure 2). There
12 of the 32 continental biomes of Colombia (Table S1, Figure 2). There are are also samples
also samples
from animals treated and housed in animal care facilities after being found injured or
from animals treated and housed in animal care facilities after being found injured or seized
seized from illegal traffickers. It is essential to highlight that these birds were sampled at
from illegal traffickers. It is essential to highlight that these birds were sampled at the time
the time of admission to the rescue center before receiving treatment or having contact
of admission to the rescue center before receiving treatment or having contact with other
with other specimens in the facilities. A detailed description of the sampling areas is pro-
specimens in the facilities. A detailed description of the sampling areas is provided in
vided in Table S1.
Table S1.

Figure 2. Geographical location of the sampling localities. Dot colors represent the biomes in each
locality. Then, Manaure (1) with a dark yellow spot is placed in the Tropical desert zonobiome of the
Diversity 2023, 15, 57 4 of 28

Guajira and Santa Marta; Cienaga (2) represented by a pale purple circle is located in the Caribbean
halobiome; and Barú (3) represented with a dark purple belongs to the Caribbean tropical dry
zonobiome. The dark green dots indicate the places included in the High orobiome of the Andes:
Los Nevados National Natural Park (NNP) (4), Chingaza National Natural Park (NNP) (5), and
Aldana (6). The localities sampled in the middle orobiomes of the Andes represented by light green
dots were Universidad Nacional de Colombia- Bogotá Campus (UNAL) (7), Ucumarí National Re-
gional Park (NRP) (8), El Cedral (9), and Quimbaya Flora and Fauna Sanctuary (FFS) (10); while in
the low orobiomes of the Andes, brown dots indicate the location of San Gil (11) and Medina (12).
The dark red dot represents San Agustín (13) in the upper Magdalena alternate hygric or subxero-
phytic zonobiome. Yopal (14), Villavicencio (15), and San Miguel (16) where the sampled places in
the Amazon-Orinoco peinobiome represented by light yellow dots, while La Macarena NNP (17)
represented in orange corresponds to the Macarena Orobiome. Sampling places in the helobiomes of
the Orinoco and the Amazon (18–20), and tropical humid Zonobiome of the Orinoco and Amazon
(21–22) are represented by dark and pale blue respectively. For helobiomes of the Cauca Valley, the
pink dot indicates the Sonso Lagoon (23). As for the animal care facilities, they are represented by a
white dot (URRAS–24) and a black dot (Ocarros–25).

2.2. Microscopic Examination

Microscopic examination was performed at low 400× and high magnification 1000×.
Positive smears were photographed using the CellSens software (Olympus Corporation).
We used the taxonomic keys provided in Valkiūnas [2], Valkiūnas and Iezhova [28] and the
original descriptions for parasite taxonomic identification. In addition, graphic material
from parasitic species deposited in the collection of Dr. G. Valkiūnas at the Institute
of Ecology (CDVA) and specimens from the International Reference Centre for Avian
Haematozoa (IRCAH) were revised to compare the parasite species morphologies observed
in these blood smears to corroborate species determinations.
Overall and individual parasite genus frequencies were calculated as the positive
individuals over the total sampled, expressed as a percentage.

2.3. DNA Extraction, Amplification of Cytochrome b (Cytb) Barcodes and mtDNA Genomes
DNA was extracted using the DNeasy blood and tissue kit (Qiagen, Hilden, Germany)
when collected samples were stored in EDTA, or the standard phenol chloroform proto-
col [29] for samples collected in ethanol or SET buffer. Molecular diagnosis was made
only for samples whose smears were positive (n = 108). It is important to mention that for
some of these positive samples, there was no blood available for molecular tests (n = 20).
Once DNA was obtained, amplification of cytochrome b (cytb) fragments was performed
using the primers and protocols suggested by Hellgren et al. [30] and Pacheco et al. [31]. To
check for non-patent coinfections with other haemosporidians, independent amplifications
were conducted using the primers of Pacheco et al. [31]. Amplicons were cleaned with
ammonium acetate [32] and sequenced in both senses on an ABI 3730xl System (Applied
Biosystems, Foster City, CA, USA). A total of 17 partial cytb gene sequences were reported
in this study and submitted to GenBank under accession numbers OL689174, OL689176,
OL689177, and OP087637-OP087649.
Second, for those positive samples with good DNA quality and parasitemia partial
parasite mtDNA genomes (≈6 kb) were amplified by a PCR protocol with Takara LA
Taq™ Polymerase (TaKaRa Mirus Bio, Madison, WI, USA) following Pacheco et al. (2018b)
using the oligos forward AE170-50 -GAGGATTCTCTCCACACTTCAATTCGTACTTC-30
and reverse AE171-50 -CAGGAAAATWATAGACCGAACCTTGGACTC-30 [33]. PCRs were
performed in 50 µL using 2 µL of total genomic DNA. PCR conditions were a partial
denaturation at 94 ◦ C for 1 min and 30 cycles with 30 s at 94 ◦ C and 7 min at 67 ◦ C,
followed by a final extension of 10 min at 72 ◦ C. PCR products (50 µL for each sample)
were visualized in agarose gels (1%). Excised bands (bands of ≈6 kb) were purified using a
QIAquick® Gel extraction kit (Qiagen, GmbH, Hilden, Germany). Finally, these products
were cloned using pGEM® -T Easy Vector systems (Promega, Madison, WI, USA) following
Diversity 2023, 15, 57 5 of 28

the manufacturer’s directions. A minimum of three to four clones per sample (both strands)
were sequenced at GENEWIZ from Azenta Life Sciences (Middlesex County, NJ, USA).
A total of five new mtDNA genomes for morphospecies were reported in this study and
submitted to GenBank under accession numbers OP701681-OP701685.

2.4. Phylogenetic Analysis

For cytb gene phylogenetic analysis, the partial sequences obtained from non-passerine
birds were manually edited in MEGA v7.0. [34]. Three alignments were constructed, one
for each of the three haemosporidian genera. Those alignments included lineages obtained
from the positive specimens deposited in the biological collection GERPH, along with
parasite sequences isolated from passerine and non-passerine birds deposited in GenBank
and MalAvi [10]. Thus, for Haemoproteus, an alignment of 465 bp composed of 15 se-
quences from GERPH specimens, 83 sequences from public databases, and 3 Leucocytozoon
species as outgroup was performed. In this alignment, 76 lineages were associated with
morphospecies.
For Plasmodium, 59 partial cytb gene sequences were used, 8 from GERPH specimens,
and 24 linked with morphospecies. Three Leucocytozoon lineages were added as an outgroup.
The total length for this alignment was 448 bp.
Leucocytozoon phylogenetic reconstruction included 48 lineages of this parasite’s genus,
along with 2 sequences of Plasmodium and 2 of Haemoproteus. Seven lineages were isolated
from specimens deposited in the GERPH collection, while the remaining forty-one were
obtained from public databases. Also, 23 lineages were associated with identified mor-
phospecies. The total length for this analysis was 456 bp. All sequences were aligned with
MAFFT (Ref. [35], available at https://www.ebi.ac.uk/Tools/msa/mafft/, accessed on 13
September 2022).
For the phylogenetic analysis, the general time-reversible model was used with
gamma-distributed substitution rates; a proportion of invariant sites (GTR + G + I) was
selected in Jmodeltest [36] as the best fit model of nucleotide substitution, according
to the Akaike information criterion. The phylogenetic relationships were estimated us-
ing maximum-likelihood (ML) implemented in W-IQ-TREE (Ref. [37], available at http:
//iqtree.cibiv.univie.ac.at/, accessed on 13 September 2022), performing a bootstrap of
1000 replicates. In addition, a Bayesian inference analysis was conducted with MrBayes v
3.2 [38] using two MCMC simulations 5 × 106 generations, with samplings every 100 gener-
ations. The convergence was checked by the average standard deviation of split frequencies
inferior to 0.01. A majority consensus rule was applied to obtain a phylogenetic hypothesis
of over 75,000 trees.
In addition, a fourth alignment was performed using 70 partial avian parasite mtDNA
genomes (5234 bp excluding gaps). The alignment included sequences from the Genbank
(N = 65) of the three genera (Leucocytozoon, Haemoproteus, and Plasmodium) and the new
mtDNA genome sequences (N = 5) obtained in this study for some well-identified mor-
phospecies using morphology. This alignment was done using MUSCLE, as implemented
in SeaView v4.3.5 [39], with manual editing. Then, using both the Bayesian (MrBayes)
and maximum likelihood (W-IQ-TREE) methods, phylogenetic relationships were inferred
using six partitions [33]. These partitions corresponded to the three non-protein coding
regions between the ORFs (fragmented SSU rRNA and LSU rRNA) and the three protein-
coding genes, keeping their order in the mtDNA genome. Also, a general time-reversible
model was used with gamma-distributed substitution rates and a proportion of invariant
sites (GTR + G + I) for each partition of the alignments. This model had the lowest Bayesian
information criterion (BIC) scores estimated by jModelTest [36]. The Bayesian support for
the nodes was inferred by sampling every 1000 generations from two independent chains
lasting 104 Markov chain Monte Carlo steps. Convergence between chains was assumed
once the average standard deviation of the posterior probability was <0.01, and the value
of the potential scale reduction factor was between 1.00 and 1.02 [38]. Then, as a ‘burn-in’,
25% of the sample was discarded once convergence was reached.
Diversity 2023, 15, 57 6 of 28

For each of the four alignments constructed in this investigation, genetic distances
were calculated using the Kimura 2 parameters (K2P) model of nucleotide substitution
implemented in MEGA v.7.0 [34].

3. Results
A total of 108 specimens from 11 avian orders were found infected with haemosporid-
ian parasites. Such infected individuals were distributed in nine of the twelve biomes
studied and from the two rescue centers. For Haemoproteus, there were 82 positive birds
(6.62%), while for Plasmodium and Leucocytozoon there were 15 and 11 (1.21% and 0.89%),
respectively.
Haemoproteus parasites were distributed in all the biomes except for those located in
the Caribbean region (tropical desert zonobiome–I; Caribbean halobiome–II; and Caribbean
tropical dry zonobiome–III). Meanwhile, Plasmodium was found only for middle orobiomes
of the Andes (V), the helobiomes of the Orinoco and the Amazon (X), and the tropical humid
zonobiome of the Orinoco and Amazon (XI). Leucocytozoon was restricted to places whose
altitudes exceeded 2100 m asl; then, the genus was found only in the Andean mountains in
the high altitude (IV) middle altitude (V) orobiomes and in the Upper Magdalena alternate
hygric or subxerophytic zonobiome (VII). For the rescue centers, only the infections caused
by Plasmodium and Haemoproteus are registered (Table 1).

Table 1. Non-passerine bird samples deposited in the “Grupo de estudio relación parásito hospedero”
biological collection (GERPH). The number of tested specimens is indicated as nT . Localities and
biomes are as in Figure 2 and Table S1. P: Plasmodium, H: Haemoproteus, L: Leucocytozoon. Lineages
obtained are provided. a : cytb fragments (478 pb), b : Mitochondrial complete genomes, *: New
lineages reported in this study. The remaining negative birds are registered at the end of the table,
along with the biome (super index), and number of sampled specimens in parenthesis.

Haemosporidian
Species nT Biome Locality Parasite Species Lineage
P H L
Accipitriformes
Accipitridae
Rupornis magnirostris 4 1 V, VI, X, IX 6, 12, 17, 18 Haemoproteus sp. -
Buteo platypterus 1 1 24 Haemoproteus nisi -
Anseriformes
Anatidae
Anas discors 13 2 II, XII 2, 23 Haemoproteus sp. -
OL456193
a /OP701681
Cairina moschata 18 2 V, VI 11,12 H. gabaldoni b -OP701682
b -CAIMOS01

KJ592828
Dendrocygna autumnalis 33 14 X 19 H. macrovacuolatus a /KJ499987
b -DENAUT01

Apodiformes
Trochilidae
KF309188
Adelomyia melanogenys 24 1 V, VII 5, 8, 10, 13 L. qyunzae a -HEAME01

Boissonneaua flavescens 3 1 IV, V 4, 5, 10 H. witti

Chalybura buffonii 2 1 VI, VII, VIII 1, 7, 15 Haemoproteus sp. -
KF309189
Coeligena helianthea 16 1 V, IV 2, 7, 13 L. qyunzae a -COHEL01

KY653794
Ensifera ensifera 9 2 IV 4, 5, 7 H. witti a -TROAED20
Diversity 2023, 15, 57 7 of 28

Table 1. Cont.

Haemosporidian
Species nT Biome Locality Parasite Species Lineage
P H L
KY653794
Eriocnemis cupreoventris 14 1 IV 5, 7, 8 H. witti a -TROAED20

KY653794
Eriocnemis derbyi 51 1 IV, V 4, 10 H. witti a -TROAED20

KY653794
Eriocnemis vestita 33 3 IV 7 H. witti a -TROAED20

Plasmodium OP087644
Glaucis hirsutus 17 1 1 VIII, X, XI 16, 20, 21 a -DENPET03
nucleophilum,
KF309188
Heliangelus a /KF479480
6 1 IV, V 5, 7, 8,9 L. qyunzae
amethysticollis b -HEAME01

1 IV, V Haemoproteus sp. -

Heliangelus exortis 37 4, 5, 7
KF309188
1 L. quynzae a -HEAME01

Lafresnaya lafresnayi 19 1 IV, V 4, 5, 7 H. witti -

KF309188
Metallura tyrianthina 56 6 IV, V 4, 5, 7, 10 L. qyunzae a -HEAME01

Opisthoprora euryptera 2 1 IV 5, 7 L. qyunzae -

Caprimulgiformes
Caprimulgidae
OP087649
Chordeiles acutipennis 3 1 X 19 H. caprimulgi a /OP701683
b -CHOACU01 *
OL689174
2 H. caprimulgi, a -NYCTALB02 *
Nyctidromus albicollis 3 VIII, XI 14, 21
OP087647
1 Plasmodium sp. a -NYCTALB03 *

OL689174
Nyctipolus nigrescens 1 1 IX 17 H. caprimulgi a -NYCTALB02 *

Charadriiformes
Scolopacidae
Numenius phaeopus 13 1 II, III, XII 2, 3,23 H. contortus -
Columbiformes
Columbidae
OL689177
Claravis pretiosa 6 3 VIII, IX 14, 17 Haemoproteus sp. a -COSQU01

KY653761
Columba livia 40 16 IV, V, VI 7, 8, 12 H. columbae a -HECOL01

Columbina minuta 4 1 IX, X 17, 18 Haemoproteus sp. -

Columbina passerina 3 2 VIII 16 Haemoproteus sp. -
Columbina squammata 6 2 VIII, X 14, 16, 18 Haemoproteus sp.
OL689176
a /OP701685
14, 17, 18, H. paramultipigmen- b -COLPAS03
Columbina talpacoti 13 6 I, VIII, X
19 tatus
OP087648
a -COPIC01

14, 15, 17,

Leptotila rufaxilla 12 1 VIII, IX, X Haemoproteus sp. -
18
10, 14, 16,
Leptotila verreauxi 11 2 V, VIII, X Haemoproteus sp. -
20
Patagioenas cayennensis 1 1 VIII 14 Haemoproteus sp. -
IV, V, VIII, 8, 10, 16, 17,
Zenaida auriculata 30 4 Haemoproteus sp. -
IX, XI 22
Zentrygon frenata 1 1 VII 13 Haemoproteus sp. -
Diversity 2023, 15, 57 8 of 28

Table 1. Cont.

Haemosporidian
Species nT Biome Locality Parasite Species Lineage
P H L
Galbuliformes
Galbulidae
OL689171
Galbula ruficauda 8 1 VIII, X 14, 18 P. tejerai a /OP701684
b -SPMAG04

Bucconidae
OP087643
Monasa nigrifrons 2 1 XI 21 Haemoproteus sp. a -MONNIG02

Gruiformes
Rallidae
Plasmodium OP087639
9 a -GRW06
Porphyrio martinica 30 V, - 7, 8, 23, 24 elongatum,
OP087637
1 Plasmodium sp. a -CYCYA01

Pelecaniformes
Ardeidae
OP087640
Butorides striata 5 1 V, XII, 8, 23, 24 Plasmodium sp. a -BUSTR03 *
Strigiformes
Strigidae
Haemoproteus OP087641
Megascops choliba 1 1 24 a -PSDIS01
syrnii-like
Haemoproteus OP087645
Asio clamator 4 4 25 a -ASICLA01
syrnii-like *
Trogoniformes
Trogonidae
KF537290
a -TROPER01
Trogon personatus 4 1 V 4, 6, 7, 9 Plasmodium sp.
KY653806
b -TROPER02

Total infected 15 82 11
Non infected 1131
Negative birds: Accipitriformes: Accipitridae: Accipiter striatus IV (1), Anseriformes: Anatidae: Amazonetta
brasiliensis VIII (2), Anas andium IV (2), Anas georgica XI,XII (7) Anas platyrhynchos V (4), Anser anser V (1), Cairina
moschata V,VI (16), Dendrocygna bicolor XII (1), Oressochen jubatus X (1), Apodiformes: Trochilidae: Aglaeactis
cupripennis IV (3), Aglaiocercus kingii V (2), Amazilia sp. IX (2), Amazilia fimbriata VI,VIII,X (5), Amazilia franciae V
(12), Amazilia versicolorVI,VIII (4), Chaetocercus mulsant V (1), Chalcostigma herrani IV (1), Chalcostigma heteropogon
V (8), Chionomesa fimbriata X (8), Chlorestes notata X (2), Chlorostilbon mellisugus IV,VIII,IX,X (6), Coeligena bonapartei
IV (1), Coeligena coeligena V (13), Coeligena lutetiae IV (13), Colibri thalassinus V (3), Coeligena torquata IV,V (12),

Colibri coruscans IV,V (67), Discosura conversii IX (1), Doryfera ludovicae V (2), Eriocnemis derbyi (50), Eriocnemis
mosquera IV (1), Glaucis sp. X (1), Haplophaedia aureliae V (3), Heliangelus exortis IV,V (35), Heliodoxa leadbeateri
IV (1), Heliodoxa rubinoides V (2), Heliomaster longirostris IX (3), Heliothryx auritus X (1), Metallura williami IV (9),

Ocreatus underwoodii V (1), Oxypogon guerinii IV (4), Phaethornis augusti VI,IX (5), Phaethornis anthophilus VIII,X (8),
Phaethornis bourcieri X (1), Phaethornis hispidus VI,VIII,X (8), Phaethornis guy V (7), Phaethornis malaris X (4), Phaethornis
syrmatophorus V (7), Polytmus guainumbi VIII (6), Pterophanes IV (2), Pterophanes cyanopterus IV (2), Ramphomicron
microrhynchum IV (6), Schistes geoffroyi V (1), Thalurania furcata X (2), Threnetes leucurus X (1), Threnetes ruckeri IX (1);
Caprimulgiformes: Caprimulgidae: Chordeiles sp. X (3), Systellura longirostris IV (2), Charadriiformes: Burhinidae:
Burhinus bistriatus I,- (2), Charadriidae: Charadrius semipalmatus III (6), Pluvialis squatarola XII (3), Vanellus cayanus
VIII (1), Vanellus chilensis III,V,VIII,X,XI,XII (63), Vanellus resplendens IV (2), Jacanidae: Jacana jacana VIII,X,XII (22),

Laridae: Gelochelidon nilotica II (4), Leucophaeus atricilla II (3), Sterna hirundo II (2), Thalasseus sandvicensis II (3),
Recurvirostridae: Himantopus mexicanus I,II,III,XII (15), Scolopacidae: Actitis macularius I,XII (4), Calidris mauri III (6),
Calidris melanotos III (3), Calidris minutilla I,III,XII (42), Calidris pusilla I (2), Gallinago nobilis IV (1), Gallinago delicata
XII (1), Limnodromus griseus I,II (5), Tringa flavipes I,XII (14), Tringa melanoleuca I,XII (5), Tringa solitaria III,X,XII (7),

Columbiformes: Columbidae: Geotrygon montana XI (1), Coraciiformes: Alcedinidae: Chloroceryle aenea VIII,X (3),
Chloroceryle amazona VIII,X (3), Chloroceryle americana III,VIII (6), Chloroceryle inda VIII (8), Megaceryle torquata VIII,XII (2),
Momotidae: Momotus momota V,IX (5), Cuculiformes: Cuculidae: Coccycua minuta VIII,X (2), Coccyzus americanus VIII
(10), Coccyzus melacoryphus V (1), Crotophaga ani VIII,IX,X,XII (10), Crotophaga major X (2), Falconiformes: Falconidae:
Falco sparverius X (1), Galbuliformes: Galbulidae: Galbula tombacea VIII (3), Bucconidae: Bucco macrodactylus X (1),
Bucco tamatia X (1) Galliformes: Odontophoridae: Colinus cristatus VIII,X (4), Phasianidae: Coturnix coturnix VI (2),
Gallus gallus IV,V,VI,VIII,X (13), Gruiformes: Rallidae: Fulica ardesiaca IV (3), Gallinula galeata XII (2), Pelecaniformes:
Diversity 2023, 15, 57 9 of 28

Ardeidae: Bubulcus ibis XII (4), Egretta rufescens II (2), Egretta tricolor I,III (3), Egretta thula I,XII (4), Nyctanassa violácea
II (1), Nycticorax nycticorax I (7), Threskiornithidae: Platalea ajaja I (5), Phimosus infuscatus XII (6), Plegadis falcinellus
XII (1), Piciformes: Capitonidae: Capito aurovirens XI (4), Picidae: Colaptes punctigula VI,VIII (2), Colaptes rivolii IV (7),

Melanerpes cruentatus VIII (1), Melanerpes rubricapillus X (2), Picumnus olivaceus V (1), Picumnus squamulatus X (2),
Ramphastidae: Andigena nigrirostris IV (1), Andigena hypoglauca IV (4), Aulacorhynchus albivitta VII (2), Aulacorhynchus
haematopygus V (1), Aulacorhynchus prasinus V (1), Pteroglossus pluricinctus IX,XI (2), Pteroglossus castanotis VI (1),
Podicipediformes: Podicipedidae: Podilymbus podiceps XII (2), Psittaciformes: Psittacidae: Amazona amazónica -
(4), Amazona ochrocephala - (4), Ara macao - (1), Brotogeris versicolurus - (2), Eupsittula pertinax X (1), Psittacidae VIII
(1), Pyrrhura calliptera IV (2), Touit huetii IX (4), Strigiformes: Strigidae: Athene cunicularia IX,X (3), Megascops sp. -
(1), Suliformes: Phalacrocoracidae: Phalacrocorax brasilianus XII (1), Sulidae: Sula nebouxii XII (2), Tinamiformes:
Tinamidae: Nothocercus julius IV (1), Trogoniformes: Trogonidae: Trogon collaris V (1).

Regarding the avian orders, the largest number of available samples of non-passerine
birds in the GERPH biological collection corresponded to the Apodiformes and the Columb-
iformes, while less than five individuals were from Falconiformes, Tinamiformes, Podici-
pediformes, and Suliformes (Tables 1, S1 and S2).
Thirteen haemosporidian morphological species (Figures 3 and 4) were identified in
the positive specimens (n = 108 specimens). In addition, four specimens should be studied
in more detail for taxonomic confirmation, since they do not fit into previously described
morphospecies (Table 1). To date, twenty-two parasite cytb gene lineages and eight partial
mtDNA genomes (including the five new mtDNA genomes reported in this research) were
obtained from non-Passeriformes blood samples deposited in the biological collection
GERPH. Such sequences were associated with ten of the thirteen morphospecies identified
in this study. We also report for the first time two new lineages of Plasmodium and three of
Haemoproteus in Strigiformes, Pelecaniformes, and Caprimulgiformes (Table 1, Figures 5–8).
Detailed information on the infections detected in each order explored is presented below.

3.1. Accipitriformes
Six individuals from three species were analyzed (Table 1), and only two infections
caused by Haemoproteus were found. One of them was in a Roadside Hawk (Rupornis
magnirostris, n = 1) from the eastern plains, and the other in a specimen of a Broad-winged
Hawk (Buteo platypterus, n = 1) from URRAS (Table 1). The infection registered in the
Rupornis magnirostris was caused by an Haemoproteus buteonis-like parasite (Figure 3A,B)
that needs to be further studied in more detail (when more positive samples are available)
in order to determine if it corresponds to a new species, since this parasite differed from
H. buteonis in one of its main diagnostic characters. Young parasites adhere to the host
cell nucleus, growing longitudinally along it. Outlines are usually even; then, they may
form angular terminals at the tips of the gametocytes (Figure 3A). Also, wavy or ameboid
margins were observed (Figure 3A). Host-cell nucleus displacement was observed in nearly
mature or mature gametocytes. Although mature gametocytes are closely appressed to the
envelope and host cell nucleus, they do not encircle it completely.
Buteo platypterus showed infection by Haemoproteus nisi [40]. The parasite’s cytoplasm
was granular; outlines were ameboid developing small projections (Figure 3C). Growing
gametocytes do not or only slightly touch the erythrocyte membranes (Figure 3D), and
parasites are closely appressed to both envelope and nucleus, displacing it (Figure 3E). Fully
grown gametocytes encircling the host cell nucleus were not observed. Unfortunately, we
could not obtain the cytb lineages from these Haemoproteus species infecting these raptors
(n = 2).
 parasites are closely appressed to both envelope and nucleus, displacing it (Figure 3E).
Fully grown gametocytes encircling the host cell nucleus were not observed. Unfortu-
Diversity 2023, 15, 57 nately, we could not obtain the cytb lineages from these Haemoproteus species infecting
10 of 28
these raptors (n = 2).

Figure 3. Haemoproteidae of non-passerine birds of Colombia: (A) macrogametocyte; (B) microgame-

Figure 3. Haemoproteidae of non-passerine birds of Colombia: (A) macrogametocyte; (B) microga-
tocyte of Haemoproteus (H.) buteonis-like in Rupornis magnirostris; (C,D) immature microgametocytes;
metocyte of Haemoproteus (H.) buteonis-like in Rupornis magnirostris; (C,D) immature microgameto-
cytes;nearly
(E) mature
(E) nearly macrogametocyte
mature macrogametocyte of H. nisi Buteo
of H.ofnisi of platypterus; (F) young
Buteo platypterus; gametocyte
(F) young and (G)
gametocyte ma-
and
ture gametocyte of H. gabaldoni in Cairina moschata; (H) macrogametofyte of H.
(G) mature gametocyte of H. gabaldoni in Cairina moschata; (H) macrogametofyte of H. macrovacuola-in macrovacuolatus
Dendrocygna
tus autumnalis;
in Dendrocygna (I) fully
autumnalis; (I) grown gametocyte
fully grown of H. nettionis
gametocyte in Anasindiscors;
of H. nettionis (J) microgametocyte
Anas discors; (J) microga-
metocyte ofin
of H. witti H.E.witti in E.(K)
vestita; vestita;
micro(K)andmicro and (L) macrogametocyte
(L) macrogametocyte of H. caprimulgi
of H. caprimulgi from Lyncornis
from Lyncornis macrotis in
macrotis in the specimen IRCAH G403126_9396; (M) nearly mature macro
the specimen IRCAH G403126_9396; (M) nearly mature macro and microgametocytes and (N) mature and microgametocytes
and (N) mature macrogametocyte
macrogametocyte of H. caprimulgi fromof H.Nyctidromus
caprimulgi from Nyctidromus
albicollis; and (O,P)albicollis; and of
gametocytes (O,P) gameto-in
H. contortus
cytes of H. contortus in Numenius phaeopus. Black arrowheads: cleft between
Numenius phaeopus. Black arrowheads: cleft between parasite and nucleus membranes; black parasite and nucleus
arrows:
membranes; black arrows: parasite nucleus; white arrow: hemozoin granules; white arrowhead:
parasite nucleus; white arrow: hemozoin granules; white arrowhead: parasite membrane; asterisk:
parasite membrane; asterisk: vacuole; black double arrowheads: host cell nucleus. Giemsa-stained
vacuole; black double arrowheads: host cell nucleus. Giemsa-stained blood films. Scale bar = 10 µm.
blood films. Scale bar = 10 μm.
Diversity 2023, 15, x FOR PEER REVIEW 11 of 29
Diversity 2023, 15, 57 11 of 28

Figure 4. Haemosporidia of non-passerine birds of Colombia: (A) mature microgametocyte of Haemo-

Figure 4. Haemosporidia of non-passerine birds of Colombia: (A) mature microgametocyte of Haem-
proteus (H.) columbae in Columba livia; (B,C) young macro and microgametocytes; (D) nearly mature
oproteus (H.) columbae in Columba livia; (B,C) young macro and microgametocytes; (D) nearly mature
macrogametocyte
macrogametocyte of H. H. paramultipigmentatus
of paramultipigmentatus fromfrom Columbina
Columbina talpacoti;
talpacoti; (E,F) gametocytes
(E,F) young young gametocytes
of H of
H syrnii-like
syrnii-like in Asio
in Asio clamator;
clamator; (G) Erythrocytic
(G) Erythrocytic meront;
meront; andgametocyte
and (H) (H) gametocyte of Plasmodium
of Plasmodium (P.) nucle-
(P.) nucle-
ophilum
ophilum from
fromGlaucis hirsutus;
Glaucis (I) young
hirsutus; gametocyte
(I) young of Plasmodium
gametocyte sp. from
of Plasmodium Nyctidromus
sp. albicollis; albicollis;
from Nyctidromus (J)
erythrocytic meront
(J) erythrocytic of P. of
meront tejerai in Galbula
P. tejerai ruficauda;
in Galbula (K) fan-shaped
ruficauda; and (L)
(K) fan-shaped androundish erythrocytic
(L) roundish erythrocytic
meronts; (M,N) gametocytes of P. elongatum in Porphyrio martinica; (O) parasite stage of Plasmodium
meronts; (M,N) gametocytes of P. elongatum in Porphyrio martinica; (O) parasite stage of Plasmodium
sp. in Butorides striata; (P) macrogametocyte of Leucocytozoon (L.) quynzae from Heliangelus exortis.
sp. in Butorides striata; (P) macrogametocyte of Leucocytozoon (L.) quynzae from Heliangelus exortis.
Black arrowheads: cleft between parasite and nucleus menbranes; black arrows: parasite nucleus;
Blackarrow:
white arrowheads:
hemozoincleft betweenwhite
granules; parasite and nucleus
arrowhead: menbranes;
parasite membrane; black arrows:
asterisk: parasite
vacuole; blacknucleus;
white arrowheads:
double arrow: hemozoin granules;
host cell nucleus; white arrowhead:
white double parasitevolutin
arrowheads: membrane; asterisk:
granules. vacuole; black
Giemsa-stained
blood
doublefilms. Scale bar =host
arrowheads: 10 μm.cell nucleus; white double arrowheads: volutin granules. Giemsa-stained
blood films. Scale bar = 10 µm.
3.2. Anseriformes
3.2.Currently,
Anseriformesthere are 82 individuals of nine species of Anatidae deposited in the
GERPH biologicalthere
Currently, are 82 (Tables
collection individuals
2 andofS2).
nine species oftoAnatidae
According Gonzálezdeposited
et al. [41],intwo
the in-
GERPH
dividuals are infected with Haemoproteus gabaldoni (Ref. [19]—Figure 3F,G), fourteen with are
biological collection (Tables 1 and S2). According to González et al. [41], two individuals
infected with
Haemoproteus Haemoproteus (Ref.
macrovacuolatus gabaldoni (Ref. [19]—Figure
[20]—Figure 3H), and two3F,G),
withfourteen with Haemoproteus
Haemoproteus nettionis
macrovacuolatus
(Ref. (Ref.
[42]—Figure 3I). [20]—Figurefor
Unfortunately, 3H),theand two with
specimen Haemoproteus
infected nettionis
with H. nettionis, there(Ref.
was[42]—
Figure 3I). Unfortunately, for the specimen infected with H. nettionis, there was no blood
available for molecular diagnosis. Haemoproteus gabaldoni (lineage OL456193-CAIMOS01)
and H. macrovacuolatus (KJ592828-DENAUT01) were placed in a well-supported clade
 Diversity 2023, 15, x FOR PEER REVIEW 12 of 29

Diversity 2023, 15, 57 12 of 28

no blood available for molecular diagnosis. Haemoproteus gabaldoni (lineage OL456193-
CAIMOS01) and H. macrovacuolatus (KJ592828-DENAUT01) were placed in a well-sup-
ported clade (clade D, Figure 5), closely related to clades B and C, that contained haemo-
(clade D, Figure
proteids 5), closely
from nightjars, related to clades
woodpeckers, frigateBbirds,
and C,and thatowls.
contained haemoproteids
The genetic distance be- from
nightjars,
tween the taxa in clade D and clades B and C ranged between 0.031 and 0.056 (Table S4). in
woodpeckers, frigate birds, and owls. The genetic distance between the taxa
clade Regarding
D and cladestheBmtDNA
and C ranged
genome between
analysis,0.031 and
three 0.056 parasite
partial (Table S4).
mtDNA genomes
Regarding the mtDNA genome analysis, three partial
were obtained for H. macrovacuolatus (n = 1, KJ592828-DENAUT01) and parasite mtDNA genomes
H. gabaldoni (n were
=
obtained for H. macrovacuolatus (n = 1, KJ592828-DENAUT01) and
2, OP701681 and OP701682-CAIMOS01). Both parasites appeared as a sister taxon and H. gabaldoni (n = 2,
OP701681 and OP701682-CAIMOS01).
shared a common Both parasites
ancestor with a Haemoproteus appeared
sp. (Figure as a sister
8) detected taxon and
in Colinus shared
virgini-
aanus
common ancestor
ridgwayi with a Haemoproteus
from Arizona sp. (Figure
(KY653798-COLVIR01; Ref.8)[43]).
detected in Colinus
The genetic virginianus
distance be-
ridgwayi
tween H.from Arizona (KY653798-COLVIR01;
macrovacuolatus and H. gabaldoni was 0.008Ref.(Table
[43]). S5).
TheAlthough
genetic distance cytb H.
between
both partial
macrovacuolatus
sequences (480 bp) H.H.
andfor gabaldoni
gabaldoniwas 0.008
were (Tableand
identical S5).identified
Although asboth partial cytblineage,
the CAIMOS01 sequences
(480 bp) for H.
the mtDNA gabaldoni
genome weredistance
genetic identicalbetween
and identified
both was as0.002,
the CAIMOS01 lineage,
indicating some the mtDNA
population
differences.
genome genetic distance between both was 0.002, indicating some population differences.

Figure 5. Phylogenetic reconstructions of Haemoproteus sp. obtained with the Cytochrome b (cytb)
barcode fragments of 479 bp. Bold tip labels correspond to sequences obtained from specimens
of GERPH biological collection. Parasites isolated from passerines are indicated by grey tip labels,
while lineages for non-passerine birds are in black. The nodal support values are indicated above the
branches as BI/ML. Nodal supports below 0.8/80 not shown.
Diversity 2023, 15, 57 13 of 28

3.3. Apodiformes
There are 546 samples from 59 Trochilidae species deposited in the biological collection
GERPH, and 14 of them are infected with Haemosporidians. Previously, a specimen of
the White-vented Plumeleteer (Chalybura buffonii) was reported infected with Haemopro-
teus sp. [44]. Unfortunately, for this sample there was no blood for molecular diagnosis
(Tables 1 and S2). Haemoproteus witti [23] morphology was characterized in the Black-
thighed Puffleg (Eriocnemis derbyi) that was associated with the TROAED02 lineage in
González et al. [45]. In the same report, this species was found infecting two more species
of the same genus—the Coppery-bellied Puffleg (E. cupreoventris) and the Glowing Puffleg
(E. vestita) (Table S2).
In this study, three more species were positive for H. witti (Figure 3J): the Buff-tailed
Coronet (Boissonneaua flavescens), the Sword-billed Hummingbird (Ensifera ensifera), and the
Mountain Velvetbreast (Lafresnaya lafresnayi) (Tables 1 and S2). Furthermore, a Haemoproteus
that could not be identified by morphology or molecular methods because of the low
parasitemia, and an absence of mature parasites was reported for Rufous-breasted Hermit
(Glaucis hirsutus) (Tables 1 and S2).
Haemoproteus witti (KY653794-TROAED02) has been identified in other hummingbirds
as well as in passerine birds [13,46] (Table S6). In the phylogenetic reconstructions, this
species (Clade A, Figures 3 and 8) is located basal to other lineages from parasites isolated
from passerine species.
Currently, three valid species of haemoproteids infect hummingbirds: H. witti, H.
archilochus and H. trochili [23]. Recent records of H. archilochus (Clade G, Figure 5) are
for Colombia and the United States [47,48] associated with the lineages KY560444, and
MW548594-SETGRA01 (Table S2). Cytb genetic distances between H. witti and H. archilochus
were estimated as 0.073 (Table S4).
In addition, the Rufous-breasted Hermit was infected with P. nucleophilum (Ref. [49]—
Figure 4G,H). Although scarce, trophozoites were seen in a subpolar position. Such struc-
tures had tiny pigment granules and two small vacuoles with even contours. Further stages
were observed to adhere to the host cell nucleus growing longitudinally from subpolar
positions. Pigment granules increased to four, and outlines became wavy. Scanty nearly
mature meronts with up to eight merozoites and pigment granules were clumped in a big
spot at the periphery of the meront. The outline was ameboid (Figure 4G). Gametocytes
were slender and macrogametocytes with irregular cytoplasm were located lateral to the
parasite nucleus to which they discontinuously adhere, as well as to the host cell membrane,
possibly due to the scalloped edges of the parasite. The pigment granules were rounded to
ovoid and numbered about 10. They were grouped towrds the center of the gametocyte
(Figure 4H). In contrast, in microgametocytes the cytoplasm seemed more homogeneous,
with wavy contours and pigment granules clumped in two or three spots of different sizes.
All the development was observed in mature erythrocytes. The lineage obtained from this
hummingbird (OP087644-DENPET03) was identical to that reported by Chagas [50] in the
Egyptian Goose (Alopochen aegyptiaca—JX467689-DENPET03) and was placed in clade B
(Figure 6) along with the Plasmodium parasites MK695452-AMABRA01 from Anseriformes
(Genetic distance 0.006) and MN458617-COLTAL05) from Columbiformes (Genetic distance
0.01) (Table S4).
Leucocytozoon quynzae (Ref. [21], Figure 5P) was the only leucocytozoid detected before
in the non-passerine birds deposited in the GERPH biological collection. However, in this
study, in addition to the host species reported by Matta et al. [21], two more species were
found infected: the Speckled Hummingbird (Adelomyia melanogenys) and the Tourmaline
Sunangel (Heliangelus exortis). All infections were detected in localities that exceeded 2100 m
in altitude (Tables 1 and S2).
Diversity 2023, 15,
Diversity 2023, 15, 57
x FOR PEER REVIEW 14 of
14 of 28
29

Figure 6. Phylogenetic reconstructions of Plasmodium sp. obtained with the Cytochrome b (cytb) bar-
Figure 6. Phylogenetic reconstructions of Plasmodium sp. obtained with the Cytochrome b (cytb)
code fragments of 479 bp. Bold tip labels correspond to sequences obtained from specimens from
barcode fragments of 479 bp. Bold tip labels correspond to sequences obtained from specimens from
the GERPH biological collection. Parasites isolated from passerines are indicated by grey tip labels,
the GERPH
while biological
lineages collection. Parasites
from non-passerine birds areisolated from
in black. Thepasserines are indicated
nodal support byindicated
values are grey tip labels,
above
while lineagesasfrom
the branches non-passerine
BI/ML. birdsbelow
Nodal supports are in 0.8/80
black. not
Theshown.
nodal support values are indicated above
the branches as BI/ML. Nodal supports below 0.8/80 not shown.
Leucocytozoon quynzae (Ref. [21], Figure 5P) was the only leucocytozoid detected be-
fore in thenew
The infections reported
non-passerine here were
birds deposited identical
in the GERPH to biological
the lineagecollection.
KF479480-HEAME01
However, in
isolated from the type specimen of the species Amethyst-throated Sunangel
this study, in addition to the host species reported by Matta et al. [21], two more (Heliangelus
species
amethysticollis) [21]. This lineage was also reported in a White-tufted Sunbeam (Aglaeactis
were found infected: the Speckled Hummingbird (Adelomyia melanogenys) and the Tour-
castelnaudii) from Peru, while the lineage KF309189-COHEL01 from L. quynzae was found
maline Sunangel (Heliangelus exortis). All infections were detected in localities that ex-
in the White-bearded Hermit (Phaethornis hispidus) from Peru [13] (Clade C, Figure 8).
ceeded 2100 m in altitude (Tables 2 and S1).
Leucocytozoon quynzae was placed basal to the parasites of non-passerine birds such
The new infections reported here were identical to the lineage KF479480-HEAME01
as ducks, raptors, toucans, and woodpeckers in clades A and B (Figure 7). The median
isolated from the type specimen of the species Amethyst-throated Sunangel (Heliangelus
genetic distances between those clades were 0.061 (A vs. C) and 0.062 (B vs. C). Al-
amethysticollis) [21]. This lineage was also reported in a White-tufted Sunbeam (Aglaeactis
though Leucocytozoon polynuclearis was placed in clade A (Gen dist KF471028-HEAME01 vs.
castelnaudii) from Peru, while the lineage KF309189-COHEL01 from L. quynzae was found
MW626894-COLAUR01: 0.06, Table S4), the closest species to L. quynzae was L. schoutedeni
in the White-bearded Hermit (Phaethornis hispidus) from Peru [13] (Clade C, Figure 8).
in clade D (gen dist 0.05) (Table S4). In the mtDNA phylogenetic tree (Figure 8), L. quynzae
Leucocytozoon quynzae was placed basal to the parasites of non-passerine birds such
(from Heliangelus amethysticollis, KF479480-HEAME01) appeared as the sister taxon of Leu-
cocytozoon raptors,
as ducks, sp. (fromtoucans, and woodpeckers
Turdus fuscater, in clades A
KT162002-TFUS14); andshared
both B (Figure 7). Theancestor
a common median
genetic distances between those clades were 0.061 (A vs. C) and 0.062 (B vs. C). Although
Leucocytozoon polynuclearis was placed in clade A (Gen dist KF471028-HEAME01 vs.
 MW626894-COLAUR01: 0.06, Table S4), the closest species to L. quynzae was L. schoutedeni
in clade D (gen dist 0.05) (Table S4). In the mtDNA phylogenetic tree (Figure 8), L. quynzae
Diversity 2023, 15, 57 (from Heliangelus amethysticollis, KF479480-HEAME01) appeared as the sister taxon 15 of of
Leu-
28
cocytozoon sp. (from Turdus fuscater, KT162002-TFUS14); both shared a common ancestor
with L. majoris (from Zonotrichia leucophrys oriantha, FJ168563-ZOLEU02). Genetic dis-
tances
with L. between theseZonotrichia
majoris (from species are shown inoriantha,
leucophrys Table S5.FJ168563-ZOLEU02). Genetic distances
between these species are shown in Table S5.

Figure 7. Phylogenetic reconstructions of Leucocytozoon sp. obtained with the Cytochrome b (cytb)
Figure 7. Phylogenetic reconstructions of Leucocytozoon sp. obtained with the Cytochrome b (cytb)
barcode fragments of 479 bp. Bold tip labels correspond to sequences obtained from specimens of
barcode
the GERPHfragments of 479
biological bp. BoldParasites
collection. tip labels correspond
isolated to sequences
form passerines areobtained
indicatedfrom specimens
by grey of
tip labels,
the GERPH biological collection. Parasites isolated form passerines are indicated by grey
while lineages form non-passerine birds are in black. The nodal support values are indicated abovetip labels,
while lineagesas
the branches form non-passerine
BI/ML. birds below
Nodal supports are in black.
0.8/80 The nodal
are not support values are indicated above
shown.
the branches as BI/ML. Nodal supports below 0.8/80 are not shown.
3.4. Caprimulgiformes
Fourteen individuals of six species were evaluated for haemosporidian infections.
The presence of the Haemoproteus sp. and Plasmodium sp.—registered here in the blood of
the Lesser Nighthawk (Chordeiles acutipennis), the Pauraque (Nyctidromus albicollis), and
the Blackish or Roraiman Nightjar (Nyctipolus nigrescens)—constituted the first report of
Diversity 2023, 15, 2023,
Diversity 57 15, x FOR PEER REVIEW 17 of 29 16 of 28

Figure 8. Phylogenetic reconstructions of Haemosporida using mtDNA genomes. The Bayesian and
maximum likelihood phylogenetic analyses were performed using 70 partial avian parasite mtDNA
genomes (5234 bp excluding gaps). The values above branches are posterior probabilities/bootstraps.
Parasites reported in non-passerines are indicated in black and bold, and parasites in passerines
are indicated in gray. The new mtDNA genomes (N = 5) reported in this study are marked with an
asterisk. Sequences obtained from samples deposited in the biological collection named “Grupo de
estudio relación parásito hospedero” (GERPH) are indicated by colored rectangles.
Diversity 2023, 15, 57 17 of 28

3.4. Caprimulgiformes
Fourteen individuals of six species were evaluated for haemosporidian infections.
The presence of the Haemoproteus sp. and Plasmodium sp.—registered here in the blood of
the Lesser Nighthawk (Chordeiles acutipennis), the Pauraque (Nyctidromus albicollis), and
the Blackish or Roraiman Nightjar (Nyctipolus nigrescens)—constituted the first report of
infection caused by haemosporidians for each species. The Haemoproteids observed in
these three species (Figure 3M,N) fit the description of Haemoproteus caprimulgi [51]. Indeed,
the comparison of these specimens with the paratype of H. camprimulgi (IRCAH specimen
G403126_9396, Figure 3K,L) from the Great-Eared Nightjar (Lyncornis macrotis) indicated
that the macrogametocytes were slightly longer in the IRCAH specimen than in the speci-
mens in the Colombian samples (media specimen IRCAH: 16.4 ± 2.01, media specimen N.
nigrescens: 15.17 ± 1.42). For the reviewed specimens from the wild (Figure 3M,N), growing
parasites often partially touch the host cell nucleus, but some spaces are left between those
two membranes (Figure 3M macrogametocyte), particularly in gametocytes with slightly
ameboid contours. Parasites in the IRCAH reference material (Figure 3K,L) showed even
outlines in the different stages of the development of the parasite, while the specimens
in C. acutipennis and N. albicollis sometimes showed ameboid outlines. Fully grown ga-
metocytes were found in mature erythrocytes. Pigment granules are either scattered (see
the macrogametocyte in Figure 3M) in the cytoplasm or grouped at the tips (Figure 3M
microgametocytes), or different places of the parasite (Figure 3N). For the IRCAH material,
small roundish white spots grouped at the tips of the parasites (Figure 3L) could correspond
to what once were pigment granules.
Here, we reported for the first time the cytb and mtDNA genome sequences associated
with H. caprimulgi. The cytb lineages obtained in this study for this morphospecies were
placed in a well-supported clade along with the sequence CHOMIN01-MK216058 obtained
from the Common or Antillean Nighthawk (Chordeiles minor) from the USA (clade B,
Figure 5). Genetic distances between the last-mentioned sequence and the sequences
obtained in this study ranged from 0.013 to 0.02 (Table S4). Interestingly, in the mtDNA
genomic analysis (Figure 8), H. caprimulgi appeared to share a common ancestor with
parasites found in other non-passerine birds (Anseriformes, Galliformes, Columbiformes,
and Strigiformes). Indeed, all Haemoproteus (except H. witti) mtDNA genomes available
from species found in non-Passeriformes are part of a monophyletic group with high
posterior probability and bootstrap at the node (1.0/100). The genetic distance between
these parasites is shown in Table S5.
Nyctidromus albicollis, additionally, was found infected with Plasmodium sp. Although
the morphospecies of this infection could not be identified because of the low number
of parasite stages in the peripheral blood (Figure 4I). Molecular tests indicated that the
lineage OP087647-NYCTALB03 shared a common ancestor with the parasites of the clade
G (Figure 6) that included the lineage OL598516 of P. elongatum, which differed by 0.037,
and a lineage of Plasmodium sp. (AY733088) isolated from an African Penguin (Spheniscus
demersus) separated by a genetic distance of 0.034. There is only one additional record of a
Plasmodiidae infecting a Caprimulgiform species in Myanmar, the lineage COPMAL02
(EF380144) isolated from Caprimulgus macrurus (clade A, Figure 6) that differed from
OP087647-NYCTALB03 by 0.067 (Table S4).

3.5. Charadriiformes
As for Charadriiformes, 228 individuals from six families and twenty-four species
were screened for haemosporidian parasites. Only one was found infected. Haemoproteus
contortus [52] was the only parasite detected in a Whimbrel (Numenius phaeopus), the same
host species in which this parasite was described [52]. The cytoplasm was homogeneous
and faintly stained, so the macrogametocytes were recognized by the more compact nucleus
and a slightly more bluish tone of cytoplasm (Figure 3P). Growing and fully mature gameto-
cytes showed highly ameboid outlines (Figure 3O,P) that makes the parasite touch the host
cell nucleus at some points but leave the characteristic cleft between them (Figure 3P). We
Diversity 2023, 15, 57 18 of 28

did not find ring-like, fully closed parasites as published in the original description, but all
mature forms did completely encircle the host cell nucleus (Figure 3O). Unfortunately for
this specimen (infected Whimbrel), there was no material available for molecular analysis.
Currently, there is only one lineage from a haemoproteid species isolated from N.
phaeopus in Japan (NUMPHA01 GenBank Acc. num LC230122) that lies basal in clade E
(Figure 5).

3.6. Columbiformes
One hundred and thirty Columbiformes representing twelve species were analyzed
(Table 1), from which thirty-nine individuals from eleven species were infected with H.
columbae [53], H. paramultipigmentatus [54] or Haemoproteus sp.
The Rock Pigeon (Columba livia), an introduced species in Colombia, showed a preva-
lence of 41% (16/39, Table 1) of H. columbae. Most of the specimens infected with H. columbae
(Ref. [53] Figure 4A) had high parasitemia, with 8% as the maximum parasitemia recorded
for a host in our biological collection [55]. All the sampled specimens had the lineage
HAECOL01 (KY653761) that share a common ancestor with H. multipigmentatus [54] (clade
J, Figure 5), differing with a genetic distance of 0.098 (Table S4).
Haemoproteus paramultipigmentatus (Ref. [54] Figure 4B–D), was detected in the Ruddy
Ground Dove (Columbina talpacoti). Young or nearly mature stages predominate (Figure 4B)
in the individuals infected with this species of parasite. Very early stages were seen in sub-
polar positions. The young parasites were located lateral to the host cell nucleus touching
it in some portions (Figure 4B). Outlines were predominantly ameboid, and the cytoplasm
was irregular with some small vacuoles visible. In nearly mature gametocytes, outlines
were wavy. Few pigment granules were observed, particularly for microgametocytes that
seem to aggregate in clumps throughout the cytoplasm or at the poles of the parasites
(Figure 4C). The more mature parasites observed fill the erythrocyte to the poles, displacing
the host cell nucleus considerably. However, gametocytes still showed clefts between the
membranes of gametocytes and the host cell nucleus (Figure 4D), and the contours were
still slightly wavy. However, from the early stages, macrogametocytes may show multiple
pigment granules scattered throughout the cytoplasm that was a distinctive character of
the species [54].
Four sequences were obtained from the Ruddy Ground Dove specimens sampled
in Colombia (n = 13). Two of them were identical to the lineage obtained from the type
specimen of H. paramultipigmentatus (JN788934-COLPAS03) in Mexico, while the other
(OP087648-COPIC01) differed by a genetic distance of 0.002 (clade H, Figure 5; Table S4).
In addition, a Haemoproteus sp. was detected in a Claravis pretiosa (Blue Ground Dove)
with low parasitemia. This lineage (OL689177-COSQU01) lay basal to H. paramultipigmenta-
tus, along with JX029921-COSQU01, a Haemoproteus parasite that was found in the Scaled
Dove (Columbina squamata) in Brazil, which was identical (clade I, Figure 5; Table S4). In ad-
dition, the mtDNA lineage obtained in this study (OP701685) was identified as COLBUC01
and appeared as a sister taxon of H. columbae from Columba livia (KY653761-COLIV07,
Colombia). The genetic distance for all the subgenus Haemoproteus species are shown in
Table S5.
A White-throated Quail-Dove (Zentrygon frenata) was found infected with Haemopro-
teus sp.; however, given the few stages observed and the small additional sample available,
molecular analysis and further determination were not possible.

3.7. Galbuliformes
Only one specimen of the individuals of Galbulidae had a Haemosporidian infection
(Table 1). A specimen of Rufous-tailed Jacamar (Galbula ruficauda) had an infection caused
by Plasmodium tejerai [56]. Few morphological stages were found in the smear; however, the
erythrocytic meront observed (Figure 4J) in a polar position of the erythrocyte was elongate
with even outlines. Although appressed with the host nucleus and outer membrane, no
displacement of it or perceptible deformation was evident. The large vacuole was not
Diversity 2023, 15, 57 19 of 28

evident in this species, however. Such structures fade as meronts mature. In addition,
pigment granules were clumped, as in P. tejerai, once the large vacuoles disappeared [2]. In
addition, 10 merozoites were observed, fitting the description of P. tejerai, since this species
of parasite usually showed 10 to 15 nuclei. Yet, the parasite cytoplasm was not basophilic as
has been reported for the species. In any case, the lineage obtained (OL689171-SPMAG04)
was identical to KJ575552 and MF953290 (SPMAG04) (clade E, Figure 6), and both were
related to P. tejerai, detected in Spheniscus magellanicus [57,58] and Galbula ruficauda [59] from
Brazil (Table S2). These lineages were placed in a well-supported clade (clade F, Figure 6)
along with Plasmodium species found in Gruiformes in Colombia and Pelecaniformes n
Guyana. Genetic distances between these taxa were 0.0021 in both cases (Table S4). In
the mtDNA phylogenetic analysis, P. tejerai appeared as a sister taxon of Plasmodium sp.
found in Opisthocomus hoazin from Venezuela (KY653749-OH2A; Ref. [60]); it was part
of the monophyletic group that contains P. lutzi, P. elongatum, and Plasmodium sp. of a
Trogon personatus from Colombia (KY653806-TROPER02). The genetic distances among
these parasites can be found in Table S5.
In addition to the three species of Bucconidae deposited in the GERPH biological
collection (Table 1), only one infection caused by a Haemoproteus parasite was found in
a Black-fronted Nunbird (Monasa nigrifrons). The morphology of this parasite must be
studied in more detail since it does not fit completely with the previously described species
(Haemoproteus bucconis) for this family [2]. Yet, the lineage OP087643 was identical to the
sequence MONNIG02-MG598390 found in Brazil in the same host species. Such lineages
were placed as the sister group of H. syrnii (clade E, Figure 5). The genetic distance
between the lineage CULKIB01 of H. syrnii and the lineage found in M. nigrifrons was 0.038
(Table S4).

3.8. Gruiformes
Thirty-six individuals from three families of Gruiformes were screened for haemo-
sporidian parasites (Table 1). Two Plasmodium species were detected in the American Purple
Gallinule (Porphyrio martinica). The first of the Plasmodium species was compatible with P.
elongatum (Ref. [61] Figure 4K–N). Erythrocytic meronts were found in only one specimen
and developed predominantly in mature erythrocytes containing six or nine merozoites
arranged in a fan (Figure 4K) or a circumference (Figure 4L) with no displacement of the
host cell nucleus. Gametocytes located in a lateral position had even (Figure 4M) or highly
ameboid (Figure 4N) outlines; in contrast to those reported by [62], they were slightly sepa-
rated from the envelope of the erythrocyte (Figure 4M). None or only a few medium-sized
pigment granules were observed clumped in the parasite cytoplasm (Figure 4N). The am-
plified lineage OP087639-GRW06 was identical to OL598516, identified as P. elongatum and
reported by Harl et al. [63]. It was closely related to the Plasmodium sp. lineage AY733088
from Sphenciformes, while differed from lineages of Passeriformes and Caprimulgiformes
(clade G, Figure 6) by a genetic distance ranging between 0.0021 and 0.036 (Table S4).
The second species of Plasmodium sp. needs to be studied in more detail, since few
diagnostic characters could be seen due to the low parasitaemia. The lineage (CYACYA02-
OP087637) was placed in clade F (Figure 6), closely related to the lineage SPMAG04
(OP087638) P. tejerai found in Galbuliformes (genetic distance of 0.0021—Table S4).

3.9. Pelecaniformes
From the ten sampled species of Pelecaniformes, only the Striated Heron (Butorides
striata) showed infection by a Plasmodium sp. species. However, it could not be identified
due the low parasitemia (Figure 4O), where only a few immature parasite stages were
found. Yet, the lineage OP087640-BUTSTR03 was placed in a well-supported clade, along
with AB477128-CXPIP10 that was isolated from a Yellow Bittern (Ixobrychus sinensis)—a
Pelecaniform species in Japan (clade C, Figure 6). Both lineages showed a genetic distance
of 0.03 (Table S4). Another, the lineage of Plasmodium was isolated from B. striata in Guyana
Diversity 2023, 15, 57 20 of 28

(DQ241528-BUTSTR01, clade F, Figure 6); however, it is distantly related to BUTSTR

(OP087640), differing from it with a genetic distance of 0.052 (Table S4).

3.10. Strigiformes
Two of the three species of Strigiformes sampled were positive for haemosporidians
(Table 1). A species closely similar to Haemoproteus syrnii, henceforth H syrnii-like, was
detected in the Striped Owl (Asio clamator) and the Tropical Screech-Owl (Megascops choliba).
Most of the parasites in Asio clamator (Figure 4E,F) were immature. Early stages were
observed in lateral or polar position to the host cell nucleus. Young gametocytes were iden-
tified by the presence of a space between the host cell nucleus and the parasite membrane,
and by the spaces at the host cell poles (Figure 4E). Even (Figure 4E) or slightly ameboid
(Figure 4F) outlines were observed in equal proportions. Parasites caused a slight to moder-
ate displacement of the host cell nucleus without encircling it completely (Figure 4F) as has
been reported by [64]. The specimen in M. choliba was slightly different from that of Asio
clamator, so it needs to be studied in more detail to confirm the parasite species’ identity.
Two closely related cytb lineages were obtained from the infected owls—OP087645-
ASICLA010 from A. clamator and OP087641-PSDIS01 from Megascops choliba. (genetic
distance 0.0084—Table S4)—the last one identical to the lineage KJ575554 identified as H.
syrnii, isolated from Megascops choliba in Brazil [58].
The lineage of H. syrnii was located in two distantly related clades (clade E and clade
F, Figure 5). The sequences OP087645-ASICLA01 and OP087641-PSDIS01 were placed in
the well-supported clade F (Figure 6) along with the lineages KF279523-STAL2 (H. syrnii)
and KF747371-STVAR01 (Haemoproteus sp.). Both infections were isolated from owls from
Europe and North America. The genetic distances between the lineages in the Colombian
hosts and the group comprising KF279523-STAL2 and KF747371-STVAR01 were 0.0127 and
0.0084 (Table S4). Meanwhile, the genetic distance with the lineage MK330144-CULKIB01
in clade E was 0.0322.
The lineages OP087645-ASICLA01 and OP087641-PSDIS01 differed from the two other
recognized species of Haemoproteus infecting Strigiformes, H. noctuae and H. syrnii (lineage
CIRCUM01, clade C, and KF279523-STAL2, clade F; Figure 5) by 0.032 (Table S4).

3.11. Trogoniformes
Only one out of the six Trogoniformes samples analyzed was found infected. The
sample showed the two Plasmodium species (Table 1) already reported by González et al. [45].
A blood smear of a Masked Trogon (Trogon personatus) showed parasite stages of Plasmodium
(Huffia) sp. along with a Plasmodium (Novyella) sp. which was found in coinfection. The
sequences TROPER01 (KF537290) and TROPER02 (KY653806) obtained for this specimen
have no other known host. Such sequences were placed in clade D (Figure 6; see also
Figure 8 for comparison), along with the other lineages isolated from Peruvian T. personatus
(MH457281-TROPER03, MH457292-TROPER04, and MN458765-TROPER05) that differed
by genetic distances ranging from 0.0021 to 0.023. The most closely related species identified
in the phylogenetic tree was P. matutinum in clade E (MK652235-LINN1), separated by
genetic distances of 0.034 and 0.036 (Table S4).

4. Discussion
At a global scale, the diversity patterns of avian haemosporidian species seem similar
to those of their hosts [9,65]. Thus, the Neotropics, as the world’s most diverse area for
birds, is expected to harbor diverse haemosporidian parasite communities. However, at
the regional level, biodiversity patterns are also driven by ecological and biogeographical
contexts resulting from the local and regional evolutionary histories. Thus, as expected, the
diversity of these hematozoa is unevenly distributed throughout the continent and along
elevational gradients in mountainous areas [13,14,45,59]. In general, such patterns have
been studied using data from passerine birds. Thus, due to the scarcity of information, esti-
mates of diversity, distribution, and life cycles, as well as the characterization of prevalence
Diversity 2023, 15, 57 21 of 28

and their relationship with life histories, environmental conditions, and specific traits, are
unknown for the vast majority of parasites found in non-passerine birds (see [66]).
There are five major results from this study. (1) It added valuable information on
the hosts, morphology, barcode sequences, and phylogenetic relationships of parasites
infecting non-passerine birds of 11 bird orders and 41 species, of which 34 are endemic in
the Neotropical region. In addition, we reported the barcode sequence for H. caprimulgi
while reporting the host range expansion for P. elongatum, and P. nucleophilum, reported for
the first time infecting Porphyrio martinica (Gruiformes) and Glaucis hirsutus. (2) From the
22 lineages isolated from samples deposited in the biological collection at GERPH, five are
newly reported in this study. In this repository, we have identified thirteen morphological
species, and four more need to be investigated in the future since they seem to constitute
new species. (3) Furthermore, 14 of the 22 lineages amplified in this study were identical
to 78 cytb sequences previously reported in GenBank (Table S6), which have been isolated
from 274 host species around the globe. Due to the tremendous volume of information
published today, compilations such as the one presented here greatly aid to avoid the
duplication of information released in public databases. (4) Also, we are reporting for the
first time five new parasite mtDNA genomes for the morphospecies P. tejerai, H. gabaldoni
(n = 2), H. caprimulgi, and H. paramultipigmentatus and their phylogenetic relationships.
(5) In this study, we present a summary of all the reports on non-passerine birds examined
for haemosporidians over the last 40 years for the Neotropics (Tables S2 and S3).
Following the general tendencies observed in the last 40 years of research from
Neotropical countries, Haemoproteus parasites were the most prevalent in the study. Indeed,
these parasites were found in most of the biomes sampled, with Columbiformes being the
most infected birds, followed by the Anseriformes and the Apodiformes (Trochilidade).
This data should be interpreted with precaution since the Apodiformes and Columbiformes
are the non-passerine birds most sampled using mist nets.
According to our results, the Columbiformes sampled in the Amazon-Orinoco peino-
biome (VIII) were in the bird order where Haemoproteus is the most frequent parasite genus,
similar to what has been reported by [59]. In that article, the prevalence in doves was high
in Amazonia and in the tropical and subtropical grassland great biome located close to the
area of the Amazon-Orinoco peinobiome [5,59,67]. Most of the species of Columbiformes
exhibit a gregarious behavior that may facilitate the vector to easily locate and feed on
different individuals of the group [55,68].
In the case of Trochilidae, our results indicate the highest frequency of infections by
Haemoproteus in the high altitude orobiomes of the Andes (IV). Fecchio et al. [59] reported
the Peruvian Andes as one of the biomes with the highest prevalence of these parasites in
hummingbirds; McNew et al. [13] reported the highest prevalence at altitudes that fit with
the high and middle altitude orobiomes of the Andes (IV and V respectively).
Meanwhile, Plasmodium was found in biomes under 2500 m asl. In all these places,
plenty of breeding places for Culicidae vectors are available, from bromeliads in the middle
altitude orobiomes of the Andes to large tracts of flooded land in the helobiomes of the
Orinoco and the Amazon. Temperatures in these areas exceed 12 ◦ C, which is suitable for
Plasmodium development [69].
As for Leucocytozoon, our results contrast the recent findings where this parasite has
been reported to infect resident birds under 2100 m asl in Brazil [70,71]. Gametocytes from
in situ captured birds have not corroborated these infections, and they may correspond
to non-patent chronic infections that were probably overlooked on blood smears, or they
may correspond to abortive infections. However, the fact that those reports are in territorial
species suggests the presence of a competent vector that is maintaining the infection
from either migratory birds or resident chronically infected hosts in such places, defying
the proposed theory of the existence of an altitudinal gradient of distribution of these
parasites [21,27,72].
Current research of haemosporidian diversity, particularly in non-passerine birds,
faces three methodological challenges to be resolved. First, mist nets of medium-size mesh
Diversity 2023, 15, 57 22 of 28

reaching less than three meters of height above the ground (i.e., ref. [73,74]) are the usual
method for host sampling [3]. Such methodology biases the capture towards small non-
passerine birds such as Columbiformes and Trochilidae. There is a paucity of studies using
alternative methods like bow-nets [75] rocket nets, and swim-in bait traps [76] that are used
by hand at nests during the breeding season [3,77], as opposed to samples obtained from
animals collected by guns [78] and collisions with different objects [79]. They may bias the
information obtained towards the orders under investigation that can be collected using
these methods (i.e., raptors and ducks). The joint work with animal protection entities such
as rescue centers represents an alternative for obtaining samples of rare specimens that
are not regularly captured in mist nets, or for which there is some restriction on sampling.
Valuable information has been obtained from these specimens in different recent studies
(i.e., ref. [21,61,62]). However, parasite transmission can occur at these facilities, and the
captive birds can become “accidental hosts” of parasites with which they are not infected
in their natural environment [80–83]. So, it is essential to settle protocols of sampling that
lead us to detect the infections truly acquired in the wild.
Second, the low parasitemias common in birds with chronic infections represent a
challenge for estimating the prevalence and diversity of haemosporidians in wild birds
using morphology. Although the association of parasite lineages with a morphological
parasite species was the main aim of this investigation, particularly for this study, such
values were underestimated since the molecular determination was made only on samples
whose smear was positive. As PCR methods are more sensitive than microscopy [25,84],
they can detect infections that are non-patent and might be part of the transmission cy-
cles [25]. This is common in other vertebrates, such as humans, where asymptomatic
patients with submicroscopic infections can infect malaria vectors [85]. However, detection
based only on PCR may compromise the reliability of the host–parasite relationships since
such methodologies can detect the parasite DNA at any development stage, even if the
life cycle was interrupted before the parasite reaches the gametocyte stage [86]. Despite
the fact that molecular methods to detect specific Haemosporidian developmental stages
such as gametocytes are more reliable than microscopy [87], those are not available in avian
Haemosporida due to limited genomic information.
Third, according to recent molecular characterizations, the haemosporidian parasites
infecting non-passerine birds are highly diverse [22,64,68,88,89].The Neotropics may harbor
a great diversity of haemosporidian lineages that might be overlooked due to the mis-
priming of the oligonucleotides routinely used for the detection of these parasites [63,90,91].
Indeed, in this study we failed to amplify the Haemoproteus parasites of raptors, probably
due to a mismatch between the primers and the cytb sequence of the parasites. To overcome
this issue different primer sets have been developed aiming to characterize the genetic
diversity of particular areas and hosts [31,63,91,92].
Biological collections constitute large information banks on the specimens deposited
in these repositories [93]. In this sense, the specimens stored in collections such as the
“GERPH collection” have allowed for the obtaining of informative molecular data linked
to morphospecies. Furthermore, multiple parasite mtDNA genomes from morphospecies
found in non-passerine and passerine birds deposited in biological collections have yielded
phylogenies with a better resolution (Figure 8). Although mtDNA phylogenetic hypothesis
lacks sequences of species that are available only for cytb fragments, which may affect
branch length in some of the taxa, the main topologies are similar to those obtained with
478 bp. lineages (for example, the clade of Haemoproteus (Haemoproteus) parasites and their
position regarding the Haemoporteus (Parahaemoproteus) species or lineages included in
both analyses). Thus, future directions of research with this repository will encompass the
molecular screening of all samples and will increase the efforts to get more mitochondrial
genomes. These perspectives will provide new insights into diversity and more robust
phylogenetic hypotheses of haemosporidian parasites [33,94].
For the Neotropics, 1779 species of non-passerine birds have been reported [95]. To
date, about 30% of these species have been explored for haemosporidian infections. In the
Diversity 2023, 15, 57 23 of 28

case of Colombia, 195 of a total of 878 non-passerine bird species have been tested for avian
malaria and related parasites. Many host taxa have been tested with only a handful of
individuals that do not represent the species’ geographic range nor allow for the estimation
of the prevalence of haemosporida parasites. This number of taxa is equivalent to only 22%
of the biodiversity of non-passerine hosts in the country. Although significant advances
have been made in the last twenty years, there are still nine bird orders under-sampled.
Then, for a more precise understanding of parasite diversity and dynamics in Colombia
and the Neotropics, deeper sampling of the great host biodiversity reported for this area
will be needed.
We confirmed infections using morphology that were previously reported using only
PCR in other neotropical countries. So, the use of collections allows the implementation
of integrative approaches prevailing in modern taxonomy. Although limited in number
of sampled individuals per host species, our findings exemplify the importance of the
information deposited in repositories and collections as data sources to support the study
of the geographic distribution of host-parasite diversity associations. Indeed, surveys
directed to inform biodiversity assessments of vertebrates can better provide insights into
regional processes by considering parasites and other symbionts in order to document
host-symbiont species assemblages. Biological collections where specimens are curated
with their associated metadata are indispensable for incorporating neglected symbiont taxa
such as haemosporidian parasites into biodiversity science.

Supplementary Materials: The following supporting information can be downloaded at https:

//www.mdpi.com/article/10.3390/d15010057/s1: Table S1: Biomes and specific localities of origin
of the non-passerine bird samples deposited in the GERPH biological collection included in this study.
Table S2: Non-passerine species found infected with Haemosporidian parasites in the Neotropics
after the comprehensive review of White et al. [17]. Table S3: Non-passerine species explored and
found negative for Haemosporidian parasites in the Neotropics after the comprehensive review of
White et al. (1978). Table S4: Kimura-two-parameters pairwise genetic distances between lineages
in Figures 5–7. Table S5: Estimates of evolutionary divergence between haemosporidian parasites’
mtDNA genome sequences (5234 bp excluding gaps). Table S6: Lineages identified in this study as
identical with others previously reported. Table S7: Database of papers reviewed for data compilation
of Haemosporidian parasite infections in neotropical birds after 1978. References [96–108] are cited in
Supplementary Materials.
Author Contributions: Conceptualization, I.A.L.-A., A.D.G., M.A.P., A.A.E. and N.E.M.; method-
ology, I.A.L.-A., A.D.G., M.A.P. and N.E.M.; formal analysis, I.A.L.-A., A.D.G., M.A.P. and N.E.M.;
investigation, I.A.L.-A., M.A.P., A.C., B.A.G.-S., A.D.G. and N.E.M.; resources, N.E.M., A.D.G.,
I.A.L.-A., B.A.G.-S., C.M., O.R.-F. and A.C.; data curation, I.A.L.-A., A.D.G., N.E.M. and M.A.P.;
writing—original draft preparation, I.A.L.-A., M.A.P. and N.E.M.; writing—review and editing,
A.D.G., M.A.P., A.A.E., B.A.G.-S., C.M., O.R.-F., A.C. and N.E.M.; visualization, I.A.L.-A. and M.A.P.;
funding acquisition, N.E.M., A.D.G., O.R.-F., C.M. and I.A.L.-A. All authors have read and agreed to
the published version of the manuscript.
Funding: This compilation was supported by Minciencias contract No 572-2020.
Institutional Review Board Statement: All the assays described in this study were performed using
blood samples and smears deposited and stored over the years in the “Grupo de Estudio Relación
Parásito Hospedero—GERPH” biological collection. The methods for sample collection used by the
GERPH research group were approved by the bioethics committee of the Department of Animal
Health Sciences of the Faculty of Veterinary Medicine of the National University of Colombia (Permit
number CBE-FMVZ-016), the Bioethics Committee of the Sciences Faculty of the National University
of Colombia (Act number: 04 of 2017 and 03 of 2018), and the institutional bioethics committee of the
UNITROPICO University (Permit number 431-CI-2019-121).
Informed Consent Statement: Not applicable.
Data Availability Statement: The sequence data produced in this study are available in the Gen-
Bank database under accession numbers OL689174, OL689176, OL689177, OP087637-OP087649, and
OP701681-OP701685. Also, this lineage information was submitted to the MalAvi database.
Diversity 2023, 15, 57 24 of 28

Acknowledgments: The authors would like to thank the past and present members of GERPH for
their collaboration in the field and laboratory. Through their efforts, the biological collection of the
Host Parasite Relationship Study Group (GERPH) has been maintained. Special thanks to Gustavo
Fuentes, Natalia Basto, David Pinto and Jhon Macías. Also, we would like to thank the URRAS staff,
especially Miguel Nova, Juan Guerrero, Libny Bolaños and Kelly Diaz, WCS and Ocarros Biopark. A
special thanks to Gypsy G. Lotta of the Galactic Monkey Collective for illustration of the birds used
in all the figures in this article, and Thomas Defler for language editing.
Conflicts of Interest: The authors declare no conflict of interest.

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