Novel statistical methods for integrating genetic and stable isotope data to infer individual‐level migratory connectivity

Methods for determining patterns of migratory connectivity in animal ecology have historically been limited due to logistical challenges. Recent progress in studying migratory bird connectivity has been made using genetic and stable‐isotope markers to assign migratory individuals to their breeding grounds. Here, we present a novel Bayesian approach to jointly leverage genetic and isotopic markers and we test its utility on two migratory passerine bird species. Our approach represents a principled model‐based combination of genetic and isotope data from samples collected on the breeding grounds and is able to achieve levels of assignment accuracy that exceed those of either method alone. When applied at large scale the method can reveal specific migratory connectivity patterns. In Wilson's warblers (Wilsonia pusilla), we detect a subgroup of birds wintering in Baja that uniquely migrate preferentially from the coastal Pacific Northwest. Our approach is implemented in a way that is easily extended to accommodate additional sources of information (e.g. bi‐allelic markers, species distribution models, etc.) or adapted to other species or assignment problems.     

Stable‐hydrogen isotope turnover in red blood cells of two migratory thrushes: application to studies of connectivity and carry‐over effects

ABSTRACT Understanding turnover rates of stable isotopes in metabolically active tissues is critical for making spatial connections for migratory birds because samples provide information about pre‐migratory location only until the tissue turns over to reflect local values. We calculated stable‐hydrogen isotope (δ²H) turnover rate in the red blood cells of two long‐distance migratory songbirds, Bicknell's Thrushes (Catharus bicknelli) and Swainson's Thrushes (Catharus ustulatus), using samples collected at a breeding site in New Brunswick, Canada. Blood from both species captured early in the breeding site was more positive in δ²H than blood sampled later in the summer, but did not match blood values for wintering Bicknell's Thrushes. An asymptotic exponential model was used to estimate turnover of red blood cell δ²H and yielded a half‐life estimate of 21 days and 14 days for Bicknell's and Swainson's thrushes, respectively. Red blood cells of both species approached the local breeding site value one month after the first individuals were detected at the site. For Bicknell's Thrushes, estimated δ²H in blood at arrival (?72‰) was closer to blood collected at wintering sites (mean ?61‰) than to expected breeding site δ²H (?120‰). Discrimination values calculated for red blood cells collected at the breeding site for both species were greater than expected based on studies using keratin. Turnover during migration currently limits the use of blood sampled early in the breeding season for connectivity/carry‐over effect studies. However, direct tracking technology such as geolocators can provide information about migration duration, timing, and stopovers that can be used to improve isotopic turnover equations for metabolically active tissues.     

Geolocators reveal migratory connectivity between wintering and breeding areas of Golden‐winged Warblers

The conservation of migratory songbirds is often impeded by a lack of understanding of how populations in breeding and wintering areas are geographically linked (migratory connectivity). In recent years, light‐level geolocators have improved our understanding of migratory connectivity. Such information is valuable for evaluating how conservation efforts align between the breeding and non‐breeding areas of at‐risk species, and help to more effectively prioritize the allocation of conservation funding. Golden‐winged Warblers (Vermivora chrysoptera) are imperiled migratory songbirds, but the extent to which conservation efforts in their breeding and non‐breeding areas coincide with patterns of migratory connectivity are not well known. We used light‐level geolocators to evaluate the extent to which conservation actions targeting Golden‐winged Warblers in Nicaragua and in their breeding range in North America align with patterns of migratory connectivity. We recovered six of 22 geolocators that had been deployed on male Golden‐winged Warblers at the El Jaguar Reserve during the winter of 2015–2016. All six males migrated to breeding areas in the western Great Lakes region that includes eastern Minnesota, northern Wisconsin, southwestern Ontario, and Michigan's Upper Peninsula. All six males also had similar migration routes, with spring stopovers in southern Mexico, Guatemala, and Belize, a trans‐Gulf flight, and a stopover in the region of Louisiana, Arkansas, eastern Oklahoma, and Texas. Our results, in combination with those of previous studies, demonstrate strong migratory connectivity between portions of the breeding and winter distributions of Golden‐winged Warblers currently targeted for conservation. However, additional studies are needed to improve our understanding of the stopover ecology of Golden‐winged Warblers, especially in areas where they remain for extended periods of time. Finally, patterns of migratory connectivity revealed in our study should be used in combination with existing demographic parameters for Golden‐winged Warblers in the western Great Lakes and Nicaragua to help inform full life cycle population models for this imperiled songbird.     

Population genetic connectivity of an endemic New Zealand passerine after large‐scale local extirpations: a model of re‐colonization potential

Little is known about how a 70% loss of native forests has affected the genetic connectivity of remnant bird populations in New Zealand. We use the common and widely distributed New Zealand Bellbird Anthornis melanura as an indicator species of population connectivity for well‐flighted birds. Using eight microsatellite loci, we identified five main genetic populations in the North Island, South Island, sub‐Antarctic Auckland Islands and two small remnant island populations adjacent to a large region of avian extirpations in northern North Island. Only one remnant island population, on a 30‐year‐old conservation reserve at Tiritiri Matangi, displayed a clear signature of recent genetic bottleneck. The 7% migration rate at Tiritiri Matangi indicates that bottlenecks can be maintained despite habitat rehabilitation, possibly through behavioural barriers to gene flow. Adjacent to the same extirpation zone, Bellbirds on the Poor Knights Islands were found to have low genetic diversity and low re‐colonization potential. Two gaps concordant with deforestation patterns separated the Kapiti Coast of southern North Island from populations to both the north and the south. In summary, we identified linked avian habitats, as well as isolated and inbred populations and suggest that Bellbirds are good re‐colonizers. We emphasize the importance of genetic studies that assess animal dispersal among newly rehabilitated habitat patches.     

Flexibility and constraints in the molt schedule of long‐distance migratory shorebirds: causes and consequences

Molt is a major component of the annual cycle of birds, the timing and extent of which can affect body condition, survival, and future reproductive success through carry‐over effects. The way in which molt is fitted into the annual cycle seems to be a somewhat neglected area which is both of interest and of importance. Study of the causes of annual variation in the timing of molt and its potential consequence in long‐distance migratory birds was examined using the Curlew Sandpiper, Calidris ferruginea, as a model species. Using the maximum likelihood molt models of Underhill and Zucchini (1988, Ibis 130:358–372), the relationship between annual variability in the start dates of molt at the population level with conditions on the breeding area was explored. Adult males typically started early in years when temperature in June on the Arctic breeding grounds were high compared to cold years while adult females molted later in years of high breeding success and/or warm July temperature and vice versa. When molt started later, the duration was often shorter, indicating that late completion of molt might have fitness consequences, probably jeopardizing survival. Evidence of this was seen in the low body condition of birds in years when molt was completed late. The results indicate that these migratory shorebirds follow a fine‐tuned annual life cycle, and disturbances at a certain stage can alter next biological events through carry‐over effects.     

Using gap‐crossing capacity to evaluate functional connectivity of two Atlantic rainforest birds and their response to fragmentation

Abstract One of the main consequences of habitat loss and fragmentation is the increase in patch isolation and the consequent decrease in landscape connectivity. In this context, species persistence depends on their responses to this new landscape configuration, particularly on their capacity to move through the interhabitat matrix. Here, we aimed first to determine gap‐crossing probabilities related to different gap widths for two forest birds (Thamnophilus caerulescens, Thamnophilidae; and Basileuterus culicivorus, Parulidae) from the Brazilian Atlantic rainforest. These values were defined with a playback technique and then used in analyses based on graph theory to determine functional connections among forest patches. Both species were capable of crossing forest gaps between patches, and these movements were related to gap width. The probability of crossing 40 m gaps was 50% for both species. This probability falls to 10% when the gaps are 60 m (for B. culicivorus) or 80 m (for T. caerulescens). Actually, birds responded to stimulation about two times more distant inside forest trials (control) than in gap‐crossing trials. Models that included gap‐crossing capacity improved the explanatory power of species abundance variation in comparison to strictly structural models based merely on patch area and distance measurements. These results highlighted that even very simple functional connectivity measurements related to gap‐crossing capacity can improve the understanding of the effect of habitat fragmentation on bird occurrence and abundance.     

Effects of point‐count duration on estimated detection probabilities and occupancy of breeding birds

Increasingly, point‐count data are used to estimate occupancy, the probability that a species is present at a given location; occupancy accounts for imperfect detection, the probability that a species is detected given that it is present. To our knowledge, effects of sampling duration on inferences from models of bird occupancy have not been evaluated. Our objective was to determine whether changing count duration from 5 to 8 min affected inferences about the occupancy of birds sampled in the Chesapeake Bay Lowlands (eastern United States) and the central and western Great Basin (western United States) in 2012 and 2013. We examined the proportion of species (two doves, one cuckoo, two swifts, five hummingbirds, 11 woodpeckers, and 122 passerines) for which estimates of detection probability were ≥ 0.3. For species with single‐season detection probabilities ≥ 0.3, we compared occupancy estimates derived from 5‐ and 8‐min counts. We also compared estimates for three species sampled annually for 5 yr in the central Great Basin. Detection probabilities based on both the 5‐ and 8‐min counts were ≥ 0.3 for 40% ± 3% of the species in an ecosystem. Extending the count duration from 5 to 8 min increased the detection probability to ≥ 0.3 for 5% ± 0.5% of the species. We found no difference in occupancy estimates that were based on 5‐ versus 8‐min counts for species sampled over two or five consecutive years. However, for 97% of species sampled over 2 yr, precision of occupancy estimates that were based on 8‐min counts averaged 12% ± 2% higher than those based on 5‐min counts. We suggest that it may be worthwhile to conduct a pilot season to determine the number of locations and surveys needed to achieve detection probabilities that are sufficiently high to estimate occupancy for species of interest.