Puerto Rican Parrot Research Articles

Assessing population viability and management strategies for species recovery of the critically endangered Puerto Rican parrot

AbstractRecovery of endangered species is challenging and lengthy, especially when it involves reintroduction and dynamic environmental conditions. Because managers often need to decide between many management strategies with uncertain outcomes, periodically assessing progress toward recovery using population viability analysis (PVA) can help guide decision‐making. We developed a PVA for the critically endangered Puerto Rican parrot (Amazona vittata) to evaluate current status and potential future management strategies to reach goals set in the Recovery Plan. Having grown from their nadir of 13 birds in 1976 to 686 in 2021, the recovery effort has made great progress. Using 15 years of data, we built an individual‐based PVA that included interactions between two captive and three wild populations connected via annual releases. If management continues as planned, the wild populations have no to moderate risks of extinction (0–32%) over the next 100 years. However, wild populations remain dependent on releases to sustain growth, and recovery targets for stable population growth and connectivity have not yet been reached. Our analysis suggests that hurricanes are an impediment to reaching recovery targets and impact some wild populations more than others based on geography. Projections with climate‐change‐induced higher hurricane impact resulted in wild populations being less likely to stabilize. We identified demographic rates and associated management strategies that could positively impact wild populations: increasing reproduction (e.g., via increasing artificial nests, improving nest success) and decreasing first‐year mortality (e.g., via targeted predator control). Based on our current understanding of Puerto Rican parrot demographics, species recovery will continue to be management‐dependent unless demographic rates can be altered. As more data are gathered, especially for data‐sparse populations and in the face of environmental change, future iterations of this model can re‐evaluate progress, update management strategies, and provide support for deciding if and when to delist this iconic species.

Listening to Terrestrial Voices in Ted Chiang’s “The Great Silence”

Ted Chiang’s short story, “The Great Silence”, takes the perspective of a parrot living in the Rio Abajo forest in Puerto Rico, sharing its habitat with the Arecibo Observatory. The story first appeared as the textual component of a video installation by Allora & Calzadilla, a piece that emphasizes the entanglement of the forest habitat and the massive structure of the telescope). Chiang’s parrot-narrator wonders why humans demonstrate such a commitment to the possibility of interstellar communication while often ignoring the voices and interests of our terrestrial cohabitants. The parrot’s critically endangered species, the Puerto Rican parrot, once filled the forests of the island, and the narrator presents his/her narrative as a sort of final plea to humans, asking us to consider the speech of the nonhumans with whom we live. Bruno Latour’s notion of “the terrestrial” provides a useful framework for approaching the parrot’s narrative, specifically in terms of the demand to come “down to earth”, engaging in the politics of human and nonhuman agents who all have something at stake. The parrot asks that we turn more attention to terrestrial concerns, in order to communicate with those who are already speaking to us.

The Genomics Education Partnership As A Model of Course‐Based Undergraduate Experience (CURE) that Promotes Growth Mindset

The Genomics Education Partnership (GEP) is a community of practice aiming to integrate genomics research into undergraduate curriculum while providing support to faculty in the process. It consists of more than 200 members in over 180 undergraduate institutions across the United States. Following training, faculty can claim annotations from one or more distinct projects (F element, Pathways, Parasitoid Wasps, Puerto Rican parrot) to integrate in their classes. Students participating in these projects annotate previously unstudied genomes, which are then used in analyses to answer specific scientific questions by the project lead faculty. Each of these projects is facilitated by curated curricula and customized online Bioinformatics tools. This approach has several advantages, including enabling faculty to scale research experiences to whole classrooms (unlike the wet lab apprentice model), the lack of safety issues, and the ease of transition to online delivery. Importantly, mistakes in annotations are not costly, and students can revisit their annotations to correct them. This makes the research amenable to peer instruction. While students may initially experience some frustration, they can consult with their faculty, their peers, and/or virtual teaching assistants to amend their errors. Thus, the GEP model allows for learning gains through a growth mindset, where abilities are developed through the research process. Faculty report that struggles are beneficial to the students, and that they are more likely to allow students to fail in a GEP research project than in wet lab/field work. Student outcomes are routinely assessed by a pre/post quiz and survey. While positive outcomes are observed overall, our current research indicates that these can be enhanced by early interventions that reinforce the nature of science and the agency of individual student researchers. The GEP always looks to grow its network of faculty and increase the diversity of the community.

Seasonal Variation in Fecal Glucocorticoid Levels and Their Relationship to Reproductive Success in Captive Populations of an Endangered Parrot

Many species are threatened with extinction, and captive breeding programs are becoming more common to avoid this outcome. These programs serve to prevent extinction and produce individuals for eventual reintroduction to natural populations in historical habitat. Captive animals experience different energetic demands than those in the wild, however, and as a result may have different levels of glucocorticoid hormones. Glucocorticoids help with responses to energetically expensive and potentially stressful situations. Elevated glucocorticoid levels can also potentially alter reproduction and other key behaviors, thus complicating successful captive breeding. The Puerto Rican parrot (Amazona vittata) is a critically endangered parrot that currently exists in only two wild and two captive populations. Its recovery program provides a good platform to better understand how glucocorticoid levels may relate to reproductive success under captive conditions. We validated a corticosterone assay in this species and used non-invasive techniques of measuring fecal glucocorticoid metabolites of males and females from two captive populations (Rio Abajo and El Yunque) of Puerto Rican parrots over two consecutive breeding seasons, 2017 and 2018, and the pre-breeding season of 2018, which occurred just after Hurricane Maria struck Puerto Rico. Our results show that levels of fecal glucocorticoid metabolites of males measured during the breeding season of 2018 negatively correlated to the number of total eggs and fertile eggs laid by pairs. In contrast, there was a positive relationship of female fecal glucocorticoid metabolite levels during the pre-breeding season of 2018 with total eggs laid. In males from the Rio Abajo population, we found seasonal differences in fecal glucocorticoid metabolite levels, with higher levels during the pre-breeding season of 2018 compared to both 2017 and 2018 breeding seasons. There was no difference in the mean value of male fecal glucocorticoid metabolites between the 2017 breeding season and 2018 breeding season which started four months after Hurricane Maria struck Puerto Rico. We did find sex differences during the pre-breeding season of 2018 in birds from the Rio Abajo population. Adjustments in the care routine of both populations that could reduce circulating baseline glucocorticoids and avoid frequent, sudden elevations of glucocorticoids should be considered. These results provide a baseline for future comparison with reintroduced populations of this endangered species and other species with captive breeding programs.

Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles.

Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean.

Minimizing Potential Allee Effects in Psittacine Reintroductions: An Example from Puerto Rico

The family Psittacidae is comprised of over 400 species, an ever-increasing number of which are considered threatened with extinction. In recent decades, conservation strategies for these species have increasingly employed reintroduction as a technique for reestablishing populations in previously extirpated areas. Because most Psittacines are highly social and flocking species, reintroduction efforts may face the numerical and methodological challenge of overcoming initial Allee effects during the critical establishment phase of the reintroduction. These Allee effects can result from failures to achieve adequate site fidelity, survival and flock cohesion of released individuals, thus jeopardizing the success of the reintroduction. Over the past 20 years, efforts to reestablish and augment populations of the critically endangered Puerto Rican parrot (Amazona vittata) have periodically faced the challenge of apparent Allee effects. These challenges have been mitigated via a novel release strategy designed to promote site fidelity, flock cohesion and rapid reproduction of released parrots. Efforts to date have resulted in not only the reestablishment of an additional wild population in Puerto Rico, but also the reestablishment of the species in the El Yunque National Forest following its extirpation there by the Category 5 hurricane Maria in 2017. This promising release strategy has potential applicability in reintroductions of other psittacines and highly social species in general.

Thinking Like a Parrot: A Wide‐Ranging Synthesis of the Current State of Research on Wild Parrot Biology

Thinking Like a Parrot: A Wide‐Ranging Synthesis of the Current State of Research on Wild Parrot Biology

Conservation practices and the formation of vocal dialects in the endangered Puerto Rican parrot, Amazona vittata

Captive breeding is a conservation strategy that often results in behavioural changes in animals born and reared in captivity. Culturally transmitted behaviours, such as learned vocal signals, are particularly prone to the effects of captive breeding because captive animals have limited opportunities to learn these behaviours from wild animals. Changes in learned behaviour could affect the success of reintroduction programmes once captive animals are released into the wild. We tested for vocal divergence of learned calls in Puerto Rican parrots, Amazona vittata. We recorded parrots from two captive populations and two wild populations, representing all extant populations of this species. We also recorded parrots that had been translocated between populations and evaluated changes in their vocal signals over time. Fine-scale acoustic analysis revealed vocal divergence in all four populations. The geographical variation in vocal signals evolved over a time span of 10–40 years, demonstrating that cultural traits can evolve rapidly in managed parrot populations. Parrots that were translocated between populations adopted the new vocal signals. Vocal divergence in this species likely resulted from a combination of historical rearing practices, cultural drift and geographical separation. Managers should consider strategies to facilitate the acquisition of foreign vocal signals prior to release.

Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation.

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean.

The Genomics Education Partnership: Course‐based Research Experiences for Undergraduates

The Genomics Education Partnership (GEP) is a collaboration between faculty from over 100 diverse institutions with the goal of providing authentic course‐based undergraduate research experiences (CUREs) in bioinformatics and genomics for undergraduate students. The GEP faculty have developed curricula for undergraduates at all levels that allow faculty to implement bioinformatics instruction and research within their courses. The research projects have primarily focused on the comparative genomics of the Muller F element (dot chromosome) in several Drosophila species. This chromosome is unusual in that it is largely heterochromatic, but contains ca. 80 genes that are expressed at levels similar to those found in euchromatin. Our students have focused on sequence improvement (finishing), and the annotation of protein‐coding genes and transcription start sites. Through these evolutionary comparisons, we are gaining insights into the regulation of gene expression within this heterochromatic environment. Our most recent paper on the expansion of the Drosophila ananassae F element includes 239 undergraduate students and 31 faculty co‐authors. Our faculty and student surveys, pre/post‐quiz results, and focus groups suggest that students gain the most from CUREs when faculty treat them like members of a research team. They also learn through formative failures — when challenges arise that must be resolved. In addition to research projects, we are developing new curricula, such as the “Understanding Eukaryotic Genes” modules, designed to familiarize beginning students with genome browsers while teaching eukaryotic gene structure, and units on Hidden Markov Models and Dynamic Programming for more advanced students. The GEP is collaborating with Galaxy to create G‐OnRamp (http://gonramp.org), a workflow that constructs UCSC Assembly Hubs and JBrowse genome browsers for newly sequenced eukaryotic genomes. G‐OnRamp enables faculty to engage students in novel annotation projects from a variety of organisms (e.g., Puerto Rican parrot, parasitoid wasps). If interested in participating in a grant‐supported workshop either June 12–15 or July 16–19, 2018 to learn to use G‐OnRamp, contact Sarah Elgin (selgin@wustl.edu).Support or Funding InformationSupported by NSF IUSE #1431407 and NIH R25GM119157 to SCRE.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Health and Reproductive Assessment of Selected Puerto Rican Parrots ( Amazona vittata ) in Captivity.

The Puerto Rican parrot ( Amazona vittata ) has become an iconic and high-profile conservation species. The cornerstone of the recovery plan for this critically endangered species is an active captive breeding program, management of the wild population, and a long-term reintroduction program. In 2002, 40 adult Puerto Rican parrots that had not produced viable offspring were selected for reproductive assessment at 2 aviary populations in Puerto Rico (Iguaca and Río Abajo), which are the only sources of parrots for release. The goal was to enhance reproductive potential and produce productive pairings in an attempt to augment the population growth and provide ample individuals for reintroduction. Seven Hispanolian Amazon parrots ( Amazona ventralis ) that were used as surrogate parents for the Puerto Rican parrots were also included in the study. This assessment included physical examination, endoscopic evaluation, hematologic and plasma biochemical profiles, viral screening, and hormonal assays. Results of general physical examination and hematologic and plasma biochemical testing revealed overall good health and condition of this subset of the population of Puerto Rican parrots; no major infectious diseases were found. Endoscopic examination also revealed overall good health and condition, especially of females. The apparent low fertility of male birds warrants further investigation. The findings helped to define causes of reproductive failure in the selected pairs and individual birds. New pairings resulting from the assessment helped to augment reproduction of this critically endangered species.

Isolation and characterization of microsatellite loci in the critically endangered Puerto Rican parrot (Amazona vittata)

The Puerto Rican parrot (Amazona vittata) is one of the most endangered avian species in the world. Its dramatic decline to near extinction in 1975 was thwarted only by the establishment of two captive breeding programs. To date, conservation efforts resulted in a significant population recovery with over 400 living birds either at the two captive breeding sites, or released into the wild. However, despite nearly 40 years of conservation efforts, very few specific tools are available to study genetic diversity of this species. Here we present 18 highly polymorphic microsatellite markers developed using the genome sequence of A. vittata and verified in a population sample. The markers cross-amplify in two sister species from other islands: the Hispaniolan (A. ventralis) and the Cuban (A. leucocephala) parrots. The primer pairs we developed will eventually aid the breeding efforts by providing unique identifiers for individual birds, and in the population studies monitoring recovery of critically endangered A. vittata.

The Puerto Rican parrot reintroduction program: Sustainable management of the aviary population

The cornerstone of the recovery plan for the critically endangered Puerto Rican parrot (Amazona vitatta) is an actively managed, long-term reintroduction program. One captive population distributed across two aviaries in Puerto Rico is the sole source for release but its ability to persist as a managed resource has not been evaluated since 1989. We conducted an assessment for sustainable management of the aviary population while harvesting for release. To assess demographic rates such as population growth, vital rates, and age/sex structure, we compiled a studbook database on all living, dead, and released individuals in the aviary population. Using an individual-based risk assessment model we applied population specific data based on the management period from 1993 to 2012 to simulate future aviary population dynamics and evaluate future potential production. We modeled four potential management strategies to harvest parrots for proposed releases; these scenarios vary the number of parrots and the life stage. Our simulations revealed that the aviary population can be simultaneously managed for sustainability and harvesting of parrots for release. However, without cautious management, overharvesting can jeopardize sustainability of the aviary population. Our analysis of the aviary breeding program provides a rare opportunity to review progress relative to conservation program objectives after four decades of active management. The successful growth of the aviary population and its ability to serve as a sustainable source for reintroductions supports the 1973 decision to build a breeding program from a small population of 13 parrots.

Parrots over Puerto Rico by Susan L. Roth (review)

Reviewed by: Parrots over Puerto Rico by Susan L. Roth Thaddeus Andracki Roth, Susan L. Parrots over Puerto Rico; written by Susan L. Roth and Cindy Trumbore; illus. by Susan L. Roth. Lee & Low, 2013. 44p. ISBN 978-1-62014-004-8 $19.95 R 6-9 yrs. In this cross-disciplinary picture book, Roth and Trumbore trace the history of the Puerto Rican parrot, the only parrot indigenous to the United States and its territories, linking the bird to the history of the island itself. The book examines the ways humans have affected the environment for the parrot, from the early Taíno people to European settlers to the current populace. The parrot nearly became extinct by the mid-twentieth century due to habitat destruction and competition from invasive species and both historical and contemporary efforts to protect the parrot are described. The book is notable for its parallel treatment of both social and ecological histories, offered in engaging and descriptive prose—hardly a page goes by without the refrain of the parrots’ call (Iguaca!). The paper and fabric collage illustrations are lush with texture, using fine detail to show off the verdant landscape and dramatic unfolding of events; the book’s vertical format highlights the flight of the birds over Puerto Rico, with visual depictions of the parrots and their lives displayed above text about the island’s development and colonization. This can certainly serve as a crossover between social studies and science classrooms, but the story’s vivid enough to stand on its own as a grand environmental narrative. An afterword includes photographs and additional information about conservation efforts, while additional back matter includes a timeline and bibliography. Copyright © 2014 The Board of Trustees of the University of Illinois

Optimal allocation of captive-reared Puerto Rican parrots: Decisions when divergent dynamics characterize managed populations

Reintroduction programs often face the challenge of sustaining multiple populations, each with unique demographic rates. Decision makers must determine how to allocate afinite number of captive-reared animals among these populations to achieve the fundamental objective of the program. We explored the optimal allocation of captive-reared Puerto Rican parrots (Amazona vittata) to 3 distinct populations: a struggling relict (population 1), a successfully reintroduced population (population 2), and a potential (new) population (population 3). We illustrate decision tradeoffs using 4 hypothetical scenarios of demographic performance created using the parrot literature and expert opinion and find the optimal decision by formulating the problem as a Markov decision process. Across all scenarios, our analysis favored releasing parrots into population 2 first when population sizes were small, followed by releases into population 3, and subsequently to population 1. The point in the decision space at which these transitions occurred was a function of location demographic rates. Releasing parrots in a location harboring an extant population versus a location that does not is advisable if differences in environmental conditions that promote population growth between locations are small. If management actions cannot ameliorate limiting factors in a location, decisions will favor translocations from such locations and allocations to locations where growth is more likely. When the cost of conducting a release is considered, managers should occasionally postpone releases to avoid these costs. This is optimal whenever the weighted contribution of the additional parrots to the sum of the discounted additional expected future population levels is less than the size of the fixed costs. This was most often the case for population 1 as costs increased. 2013 The Wildlife Society.

Erratum to: Genome empowerment for the Puerto Rican parrot – Amazona vittata

In the article 'Genome empowerment for the Puerto Rican parrot - Amazona vittata. GigaScience 2012 1:13' [1] the leadership of avian phylogenomic project [2] mentioned in commentary should have been Guojie Zhang, Erich Jarvis, and Tom Gilbert [2]. We regret this omission.

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education.

BackgroundAmazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale.FindingsIn a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50 = 6,983 bp, longest = 75,003 bp), which was further scaffolded into 148,255 fragments (N50 = 19,470, longest = 206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences.ConclusionsThe current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts.

Genome empowerment for the Puerto Rican parrot – Amazona vittata

A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large sequencing centers.

A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort

AbstractThe genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico. This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled. A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (<500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a longest contig at 75,003, and 148,255 long fragment library of scaffolds with N50=19,470 with the longest at 206,462 bp length. Further sequencing is needed to generate enough coverage of the genome and close the assembly gaps. To our knowledge, this is the first genome project to be initiated and supported by local community fundraising efforts, and represents a model for the future of de novo genome projects for conservation genetics of nonhuman species.

A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort

A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort