W. Andrew Cox

A phylogenomic study of birds reveals their evolutionary history.

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

Landscape forest cover and edge effects on songbird nest predation vary by nest predator

Rates of nest predation for birds vary between and within species across multiple spatial scales, but we have a poor understanding of which predators drive such patterns. We video-monitored nests and identified predators at 120 nests of the Acadian Flycatcher (Empidonax virescens) and the Indigo Bunting (Passerina cyanea) at eight study sites in Missouri and Illinois, USA, during 2007–2010. We used an information-theoretic approach to evaluate hypotheses concerning factors affecting predator-specific and overall rates of predation at landscape, edge, and nest-site scales. We found support for effects of landscape forest cover and distance to habitat edge. Predation by Brown-headed Cowbirds (Molothrus ater) increased, and predation by rodents decreased as landscape forest cover decreased. Predation by raptors, rodents, and snakes increased as the distance to forest edges decreased, but the effect was modest and conditional upon the top-ranked model. Despite the predator-specific patterns we detected, there was no support for these effects on overall rates of predation. The interactions between breeding birds, nest predators, and the landscapes in which they reside are scale-dependent and context-specific, and may be resistant to broad conceptual management recommendations.

PHYLOGENETIC POSITION OF THE NEW WORLD QUAIL (ODONTOPHORIDAE): EIGHT NUCLEAR LOCI AND THREE MITOCHONDRIAL REGIONS CONTRADICT MORPHOLOGY AND THE SIBLEY-AHLQUIST TAPESTRY

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

Species and Temporal Factors Affect Predator-Specific Rates of Nest Predation for Forest Songbirds in the Midwest

ABSTRACT. Knowledge of the relative contributions of predator species to overall rates of nest predation can improve our understanding of why predation risk varies, but the identity of predators is seldom known. We used video technology to identify nest predators of the tree-nesting Acadian Flycatcher (Empidonax virescens) and the shrub-nesting Indigo Bunting (Passerina cyanea) in forests of Missouri and southern Illinois. Raptors, snakes, and nonraptorial birds were the most frequent nest predators; rodents depredated fewer nests; and mesopredators rarely depredated nests. We tested hypotheses concerning effects of songbird species, ordinal date, nest stage, height, and age on overall and predator-specific predation rates to determine whether variation in overall predation rates was attributable to a subset of nest predators. Overall predation rates were higher for Indigo Buntings than for Acadian flycatchers, were higher during the nestling stage than during incubation, and exhibited a midseason peak. Compared with Indigo Buntings, Acadian Flycatchers experienced significantly lower predation by raptors, nonraptorial birds, and snakes and were never depredated by a mesopredator. Nests of both species had higher predation rates during the nestling stage than during incubation because of increased predation by raptors and snakes. Raptors, nonraptorial birds, snakes, and rodents all exhibited a midseason peak in predation rates. Estimating the contribution of specific predators to overall predation rates can increase our mechanistic understanding of why predation risk varies and thus improve our understanding of antipredator behavior and increase our ability to predict how anthropogenic habitat and climate change will influence avian productivity.

THE EFFECTS OF TEMPERATURE ON NEST PREDATION BY MAMMALS, BIRDS, AND SNAKES

Abstract. Understanding how weather influences survival and reproduction is an important component of forecasting how climate change will influence wildlife population viability. Nest predation is the primary source of reproductive failure for passerine birds and can change in response to temperature. However, it is unclear which predator species are responsible for such patterns because predation events are rarely observed. We investigated whether temperature influenced predator-specific rates of nest predation by analyzing data from six prior studies conducted between 1997 and 2010 in Texas, Illinois, and Missouri that used constant-surveillance video systems to identify predators at the nests of Golden-cheeked Warblers (Setophaga chrysoparia), Blackcapped Vireos (Vireo atricapilla), Indigo Buntings (Passerina cyanea), and Acadian Flycatchers (Empidonax virescens). Rates of nest predation by snakes and birds increased as daily maximum temperatures increased, whereas predation by mammals was essentially invariant in response to temperature. The relative roles of physiological versus community-level mechanisms (e.g., abundance or behavior of predators and/or alternative prey) in driving the patterns we observed remain unclear, but our data point to the need to consider important biological interactions when forecasting the effects of climate change on songbird populations.

Breeding biology of the Three-striped warbler in Venezuela: A contrast between tropical and temperate parulids

Abstract We document reproductive life history traits of the Three-striped Warbler (Basileuterus tristriatus) from 146 nests in Venezuela and compare our results to data from the literature for other tropical and temperate parulid species. Mean (± SE) clutch size was 1.96 ± 0.03 eggs (n  =  96) and fresh egg mass was 2.09 ± 0.02 g. The incubation period was 15.8 ± 0.2 days (n  =  23) and the nestling period was 10.5 ± 0.3 days (n  =  12). Males did not incubate and rarely provided food for females during incubation. Females had 57 ± 2% (n  =  49) nest attentiveness (% of time on the nest incubating), which caused egg temperature to commonly become cold relative to development. Both adults fed nestlings and feeding rates increased with nestling age. The growth rate constant for nestlings based on mass was K  =  0.490, which is slower than for north temperate warblers. Predation was the primary source of nest failure and only 22% of nests were successful based on a Mayfield daily predation rate of 0.048 ± 0.006. Our literature review indicates parulids differ strongly in life histories between temperate and tropical/subtropical sites with species in the tropics having, on average, smaller clutches, longer incubation periods, lower nest attentiveness, longer off-bouts, and longer nestling periods.

Declining Brown-Headed Cowbird (Molothrus ater) Populations Are Associated with Landscape-Specific Reductions in Brood Parasitism and Increases in Songbird Productivity

Many songbird species have experienced significant population declines, partly because of brood parasitism by the Brown-headed Cowbird (Molothrus ater), which is positively associated with increasing landscape forest cover in the midwestern United States. However, cowbirds are also experiencing long-term population declines, which should reduce parasitism pressure and thus increase productivity of host species. We used 20 years of nest monitoring data from five sites in Missouri across a gradient of landscape forest cover to assess temporal trends in the rate and intensity of brood parasitism for Acadian Flycatchers (Empidonax virescens), Indigo Buntings (Passerina cyanea), and Northern Cardinals (Cardinalis cardinalis). We evaluated whether there were concomitant changes in fledging brood size, nest survival, a combination of the two metrics (i.e., host young produced per nest attempt), and whether such changes were more substantial with decreasing landscape forest cover. Parasitism rates and intensities declined substantially during 1991–2010. Fledging brood size and nest survival rates were positively associated with landscape forest cover, confirming the fragmentation hypothesis for Midwest forest birds. Declining parasitism rates were associated with increased fledging brood sizes, with more pronounced increases as landscape forest cover decreased. Nest survival increased insubstantially across time during laying and incubation, but not during the nestling stage. The best predictor of nest survival was parasitism status, with parasitized nests surviving at lower rates than unparasitized nests. Overall, productivity increased during 1991–2010, with more pronounced increases associated with lower levels of landscape forest cover. The negative effects of cowbirds on nest survival in addition to fledging brood size in less forested landscapes suggest that cowbirds may be a primary cause of forest fragmentation effects on songbird productivity in the Midwest. Our results underscore the dynamic nature of demographic parameters, which should be accounted for in predictive models of wildlife responses to future environmental conditions.

Development of a Survey Protocol for Monitoring Reddish Egrets (Egretta rufescens) in Florida, USA

Abstract The Reddish Egret (Egretta rufescens) is North Americas rarest heron, and roughly 10% of its population resides in Florida. Its dark plumage, subcanopy nesting, and rarity make it difficult to count with aerial surveys, and assessments of ground- and boat-based methods for estimating the abundance of nesting pairs at breeding sites in Florida are lacking. The efficacy of flight-line surveys (boat-based counts of adults flying to and from colonies) and direct counts (ground- or boat-based counts of nests) were compared using data collected by multiple observers during repeated visits to 16 Reddish Egret colonies in three core breeding areas in the State of Florida, USA. Detection rates on direct counts were 77% for a single observer and 89% for two observers combined. Variance between repeated flight-line surveys was high (61%) for 1-hr surveys but substantially lower for 2-hr (18%) and 3-hr (14%) surveys. Estimated nest counts from flight-line surveys were substantially greater than those produced during direct counts, with mean differences of 85% for 1-hr counts, 134% for 2-hr counts, and 133% for 3-hr counts. Overestimates from flight-line surveys may be related to factors that can be mitigated by avoidance of sites for which use of the method is likely inappropriate (e.g., where breeding is substantially asynchronous or when a site includes an interior foraging lagoon). Survey recommendations are presented for monitoring the Reddish Egret on a large spatial scale.

Timing of Songbird Nest Predation as Revealed by Video Surveillance

ABSTRACT The use of video to monitor nests has increased in frequency over the past 25 years and new research using this technology has shed light on many aspects of the interactions between predators and nesting birds. We used video cameras to describe the timing of nest predation events for Acadian Flycatchers (Empidonax virescens), Indigo Buntings (Passerina cyanea), and other forest-dwelling songbird species. Seventy-four percent (111 of 151) of nest predation events occurred during diurnal hours for both focal species. Although some of our observations were unexpected (e.g., Barred Owls [Strix varia] were primarily diurnal nest predators), many of the predator-specific temporal patterns we observed were consistent with prior knowledge. Understanding diel patterns of nest predation in conjunction with identification of the suite of predators that contribute to overall predation rates will improve our understanding of how birds recognize and respond to the risk of nest predation across ecological and evolutionary time scales.

Threat of climate change on a songbird population through its impacts on breeding

Understanding global change processes that threaten species viability is critical for assessing vulnerability and deciding on appropriate conservation actions1. Here we combine individual-based2 and metapopulation models to estimate the effects of climate change on annual breeding productivity and population viability up to 2100 of a common forest songbird, the Acadian flycatcher (Empidonax virescens), across the Central Hardwoods ecoregion, a 39.5-million-hectare area of temperate and broadleaf forests in the USA. Our approach integrates local-scale, individual breeding productivity, estimated from empirically derived demographic parameters that vary with landscape and climatic factors (such as forest cover, daily temperature)3, into a dynamic-landscape metapopulation model4 that projects growth of the regional population over time. We show that warming temperatures under a worst-case scenario with unabated climate change could reduce breeding productivity to an extent that this currently abundant species will suffer population declines substantial enough to pose a significant risk of quasi-extinction from the region in the twenty-first century. However, we also show that this risk is greatly reduced for scenarios where emissions and warming are curtailed. These results highlight the importance of considering both direct and indirect effects of climate change when assessing the vulnerability of species.Individual and metapopulation models together project that—under an unabated climate change scenario—warming could reduce breeding productivity of a currently abundant songbird enough to pose a risk of quasi-extinction this century.