Jeff Allan Johnson

The Peregrine Fund

In the midst of the sixth mass extinction, limited resources are forcing conservationists to prioritize which species and places will receive conservation action. Evolutionary distinctiveness measures the isolation of a species on its phylogenetic tree. Combining a species’ evolutionary distinctiveness with its extinction risk creates a measure cal...

Feather quality in birds is considered an honest signal of individual health as feather appearance and function depend on an individual’s ability to maintain them. In addition to flight and insulation, feathers are essential for social interactions and sexual selection in the form of visual signals. Airborne particulate matter (PM) can accumulate o...

The south Florida subspecies of the Red-shouldered Hawk (Buteo lineatus extimus) is distinctly paler and smaller than other subspecies, reproduces at a lower rate, and can occupy very different habitats such as open marshes and grasslands with only scattered trees. We evaluated population differentiation between the south Florida population of Red-...

Across its range, the Atlantic Puffin (Fratercula arctica) is divided into four separate genetic clusters that correspond with geography and/or size differences. However, in the Western Atlantic High Arctic, there is a Puffin colony (“Thule”) that is comprised of two discrete size phenotypes. Using whole genome sequencing data of six Thule individu...

We examined long-term demography of an endangered subspecies, the Northern Aplomado Falcon (Falco femoralis septentrionalis), in South Texas, USA. The population has been managed and monitored since reintroductions began in 1993. Data spanning 1993–2018 enabled us to build an integrated population model (IPM) and a Cormack-Jolly-Seber model to esti...

A variety of conservation management strategies have been developed to address rapid, anthropogenically-driven biodiversity loss. The translocation of individuals from viable populations to those experiencing significant decline is one such strategy to increase genetic diversity and avoid extirpation, yet efficacy of this strategy has rarely been e...

The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of...

More than one-third of the bird species found in the Caribbean are endemic to a set of neighboring islands or a single island. However, we have little knowledge of the evolutionary history of the Caribbean avifauna, and the lack of phylogenetic studies limits our understanding of the extent of endemism in the region. The Sharp-shinned Hawk (Accipit...

Reintroductions are an important tool in conservation for preserving and enhancing biodiversity and preventing extinction, and post-release monitoring is essential to evaluate and inform conservation management and maximize recovery success. By quantifying genetic diversity levels and effective population size (Ne) over time, managers can gauge to...

Although the Atlantic puffin Fratercula arctica is well studied throughout its temperate and low Arctic breeding range, few have studied the species in its far northern distribution. This study is the first to present data on the migratory movements of the "large-billed" subspecies, F. a. naumanni, that breeds in the high Arctic and which has signi...

Zooarchaeologists have relied upon various approaches to study the impacts of harvest pressure and environmental change on ungulate populations, such as analysis of prey mortality patterns and morphometrics. Analysis of ancient DNA from ungulate bones and bone fragments from archaeological sites provides an additional means for studying prey popula...

Mercury (Hg) levels in the environment have substantially increased over the past century leading to increased concentrations in many high trophic level predators, including Arctic seabirds. From the Canadian high Arctic, research on seabird eggs has documented some of the greatest concentrations of egg Hg anywhere in the Arctic. Farther east, in h...

Birds can serve as effective biomonitors of air pollution, yet few studies have quantified external particulate matter accumulation on bird feathers. Biomonitoring of airborne elemental carbon (EC) is of critical significance because EC is a component of particulate matter with adverse effects on air quality and human health. To assess their effect...

Morphological measurements of 45 adult Atlantic puffins Fratercula arctica were collected in High-Arctic Greenland between 2010 and 2016. Measurements support that the population belongs to the F. a. naumanni subspecies and were significantly larger than those from populations found at lower latitudes, including F. a. grabae and F. a. arctica popul...

The southern boundary of prehispanic farming in South America occurs in central Mendoza Province, Argentina at approximately 34 degrees south latitude. Archaeological evidence of farming includes the recovery of macrobotanical remains of cultigens and isotopic chemistry of human bone. Since the 1990s, archaeologists have also hypothesized that the...

An accelerating decrease in summer sea-ice extent in the Arctic Ocean and Canadian Arctic Archipelago (North-west Passage) is predicted to increase the movement of species between the North Pacific and North Atlantic oceans. Here we report observations of two Subarctic North Pacific puffin species in the North Atlantic near the coast of north-west...

There are currently four world bird lists referenced by different stakeholders including governments, academic journals, museums and citizen scientists. Consolidation of these lists is a conservation and research priority. In reconciling lists, care must be taken to ensure agreement in taxonomic concepts—the actual groups of individual organisms ci...

As we sit in the vortex of the Covid‐19 outbreak, individual energies are focused on staying safe and juggling the personal, social and financial impacts of the pandemic and political responses to it. These impacts are profoundly re‐shaping our lives, with many commentators suggesting that ‘normality’ will be permanently redefined for all sectors o...

While collating contributions and comments from 36 researchers, the coordinating authors accidentally omitted Dr. Suzanne Carrière from the list of contributing co-authors. Dr. Carrière's data are described in Tables 1 and 3, Figure 2 and several places in the narrative.The new author list is thus updated in this article.

The peregrine falcon (Falco peregrinus) and the gyrfalcon (Falco rusticolus) are top avian predators of Arctic ecosystems. Although existing monitoring efforts are well established for both species, collaboration of activities among Arctic scientists actively involved in research of large falcons in the Nearctic and Palearctic has been poorly coord...

The peregrine falcon (Falco peregrinus) and the gyrfalcon (Falco rusticolus) are top avian predators of Arctic ecosystems. Although existing monitoring efforts are well established for both species, collaboration of activities among Arctic scientists actively involved in research of large falcons in the Nearctic and Palearctic has been poorly coord...

Rheas have been an important food source to human communities in South America, providing meat and especially eggs, and thus playing a crucial role in the development of South American societies. Two extant species currently exist: Rhea americana (greater rhea) and Rhea pennata (lesser rhea). Both species occupy distinct geographic ranges except fo...

The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this...

Raptors provide critical ecosystem services, yet there is currently no systematic, global synthesis of their conservation status or threats. We review the International Union for the Conservation of Nature's Red List to examine the conservation status, distributions, threats, and conservation recommendations for all 557 raptor species. We further a...

Genes of the major histocompatibility complex (MHC) are a critical part of the adaptive immune response, and the most polymorphic genes in the vertebrate genome, especially in passerine birds. This diversity is thought to be influenced by exposure to pathogens which can vary in relation to numerous factors. Migratory behaviour may be a particularly...

Birds are useful bioindicators of environmental contamination around the globe, but avian studies in the high Arctic have been primarily limited to a few abundant species. This study was designed to assess mercury (Hg) concentrations in both abundant and less-abundant marine and terrestrial avian species on breeding grounds in northwest Greenland u...

An ideal taxonomy for organisms incorporates comprehensive knowledge of existing species diversity and their phylogenetic relationships. This knowledge is used in developing consistent criteria for recognizing and naming species as well as monophyletic groups (clades) above the species level, including genera, families, and orders. This provides we...

Gene polymorphisms shared between recently diverged species are thought to be widespread and most commonly reflect introgression from hybridization or retention of ancestral polymorphism through incomplete lineage sorting. Shared genetic diversity resulting from incomplete lineage sorting is usually maintained for a relatively short period of time,...

Non-native invasive species threaten Galápagos’ endemic biodiversity, and increasing efforts are underway to protect its species from further harm. One such project is focused on the eradication of invasive rodents using rodenticide bait on Floreana, the archipelago’s sixth largest island. Short-eared owls (Asio flammeus galapagoensis) that consume...

The northern bobwhite (Colinus virginianus; hereafter, bobwhite) population decline has prompted several studies over the past decade investigating bobwhite population genetics and overall connectivity. The zeitgeist of current quail conservation is that bobwhite populations have become increasingly fragmented, leading to their decline as a result...

Gastrointestinal microbiota is increasingly recognized as an important component of individual health, and therefore, our ability to quantify its diversity accurately is central for exploring different ways to improve health. Non-invasive sampling methods, such as cloaca swabs, are often used to measure gastrointestinal microbiota diversity within...

Isolation-by-distance is recognized as a useful model for describing the spatial distribution of gene frequencies depending on dispersal characteristics of the species under study. However, some species may have populations that occupy the same geographic distribution during the breeding season yet reproduce at different time periods resulting in i...

Since their emergence in the early 1990s, neonicotinoid use has increased exponentially to make them the world's most prevalent insecticides. Although there has been considerable research concerning the lethality of neonicotinoids, their sub-lethal and developmental effects are still being explored, especially with regards to non-mammalian species....

De‐extinction sensu stricto is the resurrection of phenotypic traits once possessed by extinct species to create extant functional proxies. To realise the ecological benefit of de‐extinction, self‐sustaining (genetically viable) populations of functional proxies are required. It is often implied, yet rarely stated, that the genetic challenges assoc...

Arctic Terns Sterna paradisaea are an understudied species in Greenland. Outside of the largest colonies, little is known about their current population status and no long-term annual monitoring program has been established. Previous surveys outside of key breeding colonies have been limited to a small number of colonies for single-season studies....

The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the varia...

The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie...

In a recent review, Pimm et al. (2015) highlight emerging technologies in protecting biodiversity. While their list is noteworthy, the authors’ exclusion of innovations in genomic research, with the exception of single-species DNA barcoding methods, was surprising given recent advances in genome-editing technology and its potential application to c...

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two class...

Captive breeding programs often use a pedigree to identify breeding pairs that maintain genetic diversity and limit inbreeding. However, unintentional breeding of closely related individuals can occur when errors exist in the pedigree and may subsequently result in inbreeding depression. In this study, a DNA-based approach was used to identify pare...

Immune-receptor genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognizing specific pathogens and are known to have high rates of adaptive evolution, presumably as a consequence of rapid coevolution between hosts and pathogens. In contrast, many 'mediating' genes of the immune system do not...

Mercury (Hg) is a ubiquitous and highly toxic contaminant that can have negative effects on wildlife. Only a few studies have measured Hg concentrations in birds from the south central United States, and the potential threat of Hg contamination to birds in this region is largely unknown. In the present study, we assess Hg concentrations in blood an...

[Extract] Governments, businesses, financial institutions and local communities are increasingly using biodiversity offsets, also known as compensatory mitigation, as a putative mechanism to achieve 'no net loss' (NNL) of biodiversity as a result of specific development projects (McKenney & Kiesecker, 2010; Quetier & Lavorel, 2011; Gardner et al.,...

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with...

Identifying small, isolated populations is a conservation priority, not only because isolation may result in negative fitness consequences, but these populations may also harbor unique genetic diversity. The Greater Sage-Grouse (Centrocercus urophasianus) is a widespread obligate species of the sagebrush biome in western North America that has expe...

Captive breeding and ex situ conservation have become important tools in species conservation programmes. The effectiveness of the management of captive populations can be hampered by the absence of pedigree data, but molecular markers can be used to inform conservation objectives and reduce inbreeding in the captive population. Using microsatellit...

Breeding populations of Nearctic and Palearctic waterfowl have undergone significant changes in abundance and distribution over the past 50 years. The Avanersuaq District in northwest Greenland is home to an assemblage of waterfowl from both geographic areas; however, minimal historic or current information is available on species abundance. In 200...

We isolated and characterized a total of 24 microsatellite loci from the orange-breasted falcon (Falco deiroleucus). Loci were screened in 32 individuals currently maintained as a captive population: 13 wild-caught individuals from Panama and four from Belize, and the remaining 15 were first generation F1 offspring. The number of alleles per locus...

[Extract] Biodiversity is being lost at an ever increasing rate (Butchart et al., 2010), leading to the degradation of ecosystems services to levels that threaten human well-being. There are significant global efforts to address this situation: spending on conservation in 2006 by major international organizations and non-governmental organizations...

The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initia...

Plumage colour variation exists among Gyrfalcons throughout their Arctic and sub-Arctic circumpolar distribution, ranging from white through silver and grey to almost black. Although different colour variants coexist within many populations, a few geographical regions, such as northern Greenland, possess a single variant, suggesting that local envi...

Common eider (Somateria mollissima) populations in Greenland severely declined throughout the 20th century. As a result, in 2001, harvest regulations were changed and the length of the hunting season was reduced. Recent data suggest that these changes have been successful, and population regrowth is occurring. In the Avanersuaq District, northwest...

The Polyborinae is the most diverse subfamily of the Falconidae in terms of both morphology and behaviour, and includes falconet-shaped birds (Spiziapteryx), arboreal omnivores (Daptrius, Ibycter), as well as terrestrial generalists and scavengers (Caracara, Milvago and Phalcoboenus). The Polyborinae are endemic to the New World, with all but one s...

Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in a few reported vertebrates. In Gyrfalcon (Falco rusticolus), plumage color variation exists throughout their arctic and subarctic circumpolar distribution, from white to gray and almost black. Multiple color variants do exist within the majori...