Homeward bound: canopy cover and species identity influence non-breeding season homing success and speed in forest birds

Background Efficient and safe movement is fundamental for wild birds to thrive in their environments. For arboreal forest animals, especially birds, canopy cover has a large impact on birds’ daily movements and is a crucial component of conservation strategies seeking to retain avian population in disturbed or urban habitats. Methods We translocated woodland bird species utilizing different forest strata during two non-breeding seasons in Gainesville, FL, USA. We used linear model and generalized linear model to examine the effects of canopy cover and species identity on homing success and speed. Results Among our study species of Tufted Titmouse (Baeolophus bicolor), Carolina Chickadee (Poecile carolinensis), and Northern Cardinal (Cardinalis cardinalis), we found that Carolina Chickadees and Tufted Titmice were more likely to return than Northern Cardinals. Among birds that successfully returned, homing speed is significantly affected by forest canopy cover and species identity (titmice had higher homing speed than cardinals). Birds return much faster in landscape with higher canopy cover. Conclusions This study presented evidence of species identity’s effect on homing success and speed in common feeder bird species in Southeast US and provided further evidence that bird movements in the suburban land cover are constrained by low canopy cover.

Count data as response variable.

This chapter is devoted specifically to count data for three reasons: (i) they are common in ecological studies (e.g. clutch sizes, numbers of fledglings from a nest, numbers of seeds per pod...); (ii) they are simple to collect and are therefore often the data collected by students (e.g. numbers of beetles in a pitfall trap, number of pollinator visits to flowers...); and (iii) they pose numerous issues that linear models with their normal error structure cannot deal with. Two studies will be examined with the response variable being counts, starting with one that nearly fits the ideals of a Poisson distribution well, the other less so. Example 1 deals with fledgling numbers in relation to clutch initiation date. The data are on the northern cardinal bird, Cardinalis cardinalis, and were collected to test the hypothesis that birds that start their clutches later may suffer higher pre-fledging offspring mortality. Example 2 focuses on pollinator flower visits in Passiflora speciosa in relation to flower size.

Count data as response variable.

This chapter is devoted specifically to count data for three reasons: (i) they are common in ecological studies (e.g. clutch sizes, numbers of fledglings from a nest, numbers of seeds per pod...); (ii) they are simple to collect and are therefore often the data collected by students (e.g. numbers of beetles in a pitfall trap, number of pollinator visits to flowers...); and (iii) they pose numerous issues that linear models with their normal error structure cannot deal with. Two studies will be examined with the response variable being counts, starting with one that nearly fits the ideals of a Poisson distribution well, the other less so. Example 1 deals with fledgling numbers in relation to clutch initiation date. The data are on the northern cardinal bird, Cardinalis cardinalis, and were collected to test the hypothesis that birds that start their clutches later may suffer higher pre-fledging offspring mortality. Example 2 focuses on pollinator flower visits in Passiflora speciosa in relation to flower size.

Airborne point counts: a method for estimating songbird abundance with drones

Using drones to conduct airborne bioacoustic surveys is a potentially useful new way to estimate the abundance of vocal bird species. Here we show that by using two recording devices suspended from a quadcopter drone it is possible to estimate distances to birds with precision. In an experimental test, the mean error of our estimated distances to a broadcast song across 11 points between 0 and 100 m away was just 3.47 m. In field tests we compared 1-minute airborne counts with 5-minute terrestrial counts at 34 count locations. We found that the airborne counts yielded similar data to the terrestrial point counts for most of the 10 the songbirds included in our analysis, and that the effective detection radii were also similar. However, airborne counts significantly under-detected the Northern Cardinal (χ29 = 22.8, post-hoc test P = 0.007), which we attribute to a behavioral response to the drone. Airborne counts work best for species that vocalize close to the ground and have high frequency-range songs. Under those circumstances, airborne bioacoustics could have several advantages over ground-based surveys, including increased precision, increased repeatability, and easier access in difficult terrain. Further, we show that it is possible to do rapid surveys using airborne techniques, which could lead to the development of much more efficient survey protocols than are possible using traditional survey techniques.Lay SummaryWe show that it is possible to estimate the distance of singing birds from a drone, which then allows bird counts to be converted to true abundance or population densities.Using drones to count birds allows researchers to survey areas that may be difficult or dangerous to access on foot.Airborne counts are potentially a highly efficient and highly repeatable way to estimate populations of vocal bird species.

De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly-contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.

Species-Specific Responses of Bird Song Output in the Presence of Drones

Drones are now widely used to study wildlife, but applications for studying bioacoustics have been limited. Drones can be used to collect data on bird vocalizations, but an ongoing concern is that noise from the drones could change bird vocalization behavior. To test this behavioral impact we conducted an experiment using 30 sound localization arrays to track the song output of seven songbird species before, during, and after a 3-minute flight of a small quadcopter drone hovering at 50 m above ground level. We analyzed 8,303 song bouts, of which 2,285 song bouts of 184 individual birds were within 50 meters of the array centers. We used linear mixed effect models to assess patterns in song output showed patterns that could be attributed to the drone’s presence. We found no evidence of any effect of the drone for five species: American Robin Turdus migratorius, Common Yellowthroat Geothlypis trichas, Field Sparrow Spizella pusilla, Song Sparrow Melospiza melodia, and Indigo Bunting Passerina cyanea. However, we found a substantial decrease in Yellow Warbler Setophaga petechia song detections during the 3-minute drone hover, such that there was an 81% drop in detections in the 3rd minute (Wald-test, p<0.001), compared with before the drone’s introduction. In contrast, the number of singing Northern Cardinal Cardinalis cardinalis increased after the drone was introduced, and remained almost five-fold higher for 4-minutes after the drone departed (P<0.001). Further, we found an increase in cardinal contact/alarm calls when the drone was overhead, with the elevated calling-rate sustaining for 2 minutes after the drone had departed (P<0.001). Our study suggests that responses of songbirds to drones may be species-specific, an important consideration when proposing the use of drones in avian studies. We note that recent advances in drone technology have resulted in much quieter drones, which makes us hopeful that the impacts that we detected could be greatly reduced.

De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.