Black Rail Research Articles

Black Rail Occupancy and Detectability in the Texas Mid-Coast National Wildlife Refuge

Black Rail Occupancy and Detectability in the Texas Mid-Coast National Wildlife Refuge

DOT-WINGED CRAKE PORZANA SPILOPTERA (RALLIDAE; DURNFORD, 1877) IN CHILE: NEW RECORDS AND A REVIEW OF THE STATUS OF PACIFIC POPULATIONS

We report new records of the Dot-winged Crake Porzana spiloptera in southern Chile, an almost unknown species distributed mainly in Argentina and recently discovered in Chile. The occasional capture of a juvenile of the species at Cruces River wetland (39°S), and the analysis of sound recordings obtained to explore the acoustic attributes of urban wetland soundscapes, made it possible to discuss the status of the Pacific populations of the species. The new records show that P. spiloptera has a resident status and suggest that the presence of the species in Chile went historically unnoticed, and that it has been confused with the Black Rail Laterallus jamaicensis. Comprehensive surveys and dedicated research that provide fundamental biological aspects such as the current distribution, population abundance, habitat requirements, and main threats for these secretive rails are urgently needed for their conservation.

Reference genome of the black rail, Laterallus jamaicensis.

The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.

Small rails from the late Quaternary of the Southern High Plains and their palaeoenvironmental context

The fossil record of birds from the Quaternary Period (2.58 mya to present) of North America sheds light on modern patterns of diversity and geographical distribution. Fossils from the late Pleistocene and early Holocene document the presence of multiple species of small rails on the Southern High Plains. Black Rails, Virginia Rails and Soras occurred throughout regional drainages from ~ 11 000 to 8500 years ago. Age and palaeoenvironmental data associated with the rail remains provide temporal and ecological context. Those data link the past populations to extant populations occurring as migrants to the region today. The total record reveals that Black Rails, Virginia Rails and Soras occur on the Southern High Plains today despite major changes in climate, environments, biota and habitats since the late Pleistocene–early Holocene. Anthropogenic changes to regional wetlands in the present day threaten the occurrence of small rails across the Southern High Plains.

Qualitative value of information provides a transparent and repeatable method for identifying critical uncertainty.

Conservation decisions are often made in the face of uncertainty because the urgency to act can preclude delaying management while uncertainty is resolved. In this context, adaptive management is attractive, allowing simultaneous management and learning. An adaptive program design requires the identification of critical uncertainties that impede the choice of management action. Quantitative evaluation of critical uncertainty, using the expected value of information, may require more resources than are available in the early stages of conservation planning. Here, we demonstrate the use of a qualitative index to the value of information (QVoI) to prioritize which sources of uncertainty to reduce regarding the use of prescribed fire to benefit Eastern Black Rails (Laterallus jamaicensis jamaicensis), Yellow Rails (Coterminous noveboracensis), and Mottled Ducks (Anas fulvigula; hereafter, focal species) in high marshes of the U.S. Gulf of Mexico. Prescribed fire has been used as a management tool in Gulf of Mexico high marshes throughout the last 30+ years; however, effects of periodic burning on the focal species and the optimal conditions for burning marshes to improve habitat remain unknown. We followed a structured decision-making framework to develop conceptual models, which we then used to identify sources of uncertainty and articulate alternative hypotheses about prescribed fire in high marshes. We used QVoI to evaluate the sources of uncertainty based on their Magnitude, Relevance for decision-making, and Reducibility. We found that hypotheses related to the optimal fire return interval and season were the highest priorities for study, whereas hypotheses related to predation rates and interactions among management techniques were lowest. These results suggest that learning about the optimal fire frequency and season to benefit the focal species might produce the greatest management benefit. In this case study, we demonstrate that QVoI can help managers decide where to apply limited resources to learn which specific actions will result in a higher likelihood of achieving the desired management objectives. Further, we summarize the strengths and limitations of QVoI and outline recommendations for its future use for prioritizing research to reduce uncertainty about system dynamics and the effects of management actions.

Preliminary assessment of thermal imaging equipped aerial drones for secretive marsh bird detection

Rails are a highly secretive group of marshland obligate species that are difficult to consistently survey and detect. Current survey efforts utilize either call–playback or autonomous recording devices, but the low detection probabilities for rails create challenges for long-term systematic monitoring. Between 8 April and 16 May 2022, we flew a small aerial drone equipped with a thermal camera to survey for six species of rail (Black Rail ( Laterallus jamaicensis), Yellow Rail ( Coturnicops noveboracensis), Sora ( Porzana carolina), Virginia Rail ( Rallus limicola), Clapper Rail ( Rallus crepitans), and King Rail ( Rallus elegans)) along the Gulf Coast of Texas to assess the feasibility of long-term drone monitoring. We successfully conducted 33 flights at 15 m above ground level and detected rails on the first visit at 42% of known occupied points. We achieved 27 total rail detections, including 12 Black Rail/Yellow Rail detections. Of the birds detected, 81% exhibited no response to the drone’s first approach. We intend for this preliminary data to shape future survey protocol for secretive species occupying difficult to navigate terrain.

Integrating habitat models for threatened species with landownership information to inform coastal resiliency and conservation planning

SummarySea-level rise threatens both human communities and vulnerable species within coastal areas. Joint spatial planning can allow conservation and social resiliency goals to work in synergy. We present a case study integrating distribution information of a threatened saltmarsh bird, the eastern black rail (Laterallus jamaicensis jamaicensis), with social information to facilitate such joint planning. We constructed a distribution model for the species within an urbanizing coastal region (New Jersey, USA) and integrated this with publicly available parcel and protected area data to summarize ownership patterns. We estimated that c. 0.3–2.8% (c. 260–2200 ha) of available saltmarsh is occupied by eastern black rail, most of which is publicly owned (79%). Privately owned saltmarsh was spread across nearly 5000 individual parcels, 10% of which contained areas with the highest likelihood of rail presence according to our model (top quartile of predicted occupancy probabilities). Compared with all privately owned saltmarsh, parcels with probable rail habitat were larger (median: 5 versus 2 ha), contained more marsh (87% versus 59%) and were less economically valuable (US$11 200 versus US$36 100). Our approach of integrating species distributions with landownership data helps clarify trade-offs and synergies in species conservation and coastal resiliency planning.

Large-scale distribution models for optimal prediction of Eastern black rail habitat within tidal ecosystems

Eastern black rails (Laterallus jamaicensis jamaicensis) are among the rarest and least-studied birds in North America and were recently listed as threatened under the U.S. Endangered Species Act. Spatial models that predict habitat quality across the subspecies range are therefore needed to inform conservation, recovery, and monitoring efforts for this rare bird. We used data from 47,585 call-broadcast surveys collected at 7906 sites over a 3-decade period (1990s, 2000s, 2010s; 23 total years) to build species distribution models for eastern black rails. We used hierarchical Bayesian occupancy models and predictive model selection to develop multi-scale models that optimally predict habitat suitability for eastern black rails within tidal wetlands while also accounting for imperfect detection of these cryptic birds during field surveys. We also used raster regression techniques to translate model predictions into 30-m resolution maps of habitat suitability for eastern black rails within tidal wetlands along the eastern seaboard of the United States. The model predicted suitability of breeding habitat as a function of wetland attributes (e.g., cover of high marsh and terrestrial border), hydrologic modification, and disturbance from human development measured over multiple spatial scales. We also found differences in habitat relationships for eastern black rails when compared to models that included both North American subspecies of black rail. Important results included negative effects of shrub-scrub wetlands, and strong positive effects of high marsh, terrestrial border, and impoundments on breeding season occupancy. Our study provides an example of integrating detection-non-detection data and modern statistical methods to build predictive distribution models for an extremely rare species, while also providing rigorous predictions of breeding habitat quality for the eastern black rail within tidal wetlands. These models will facilitate optimal monitoring, habitat conservation, and recovery planning efforts for eastern black rails and provide a foundation for future research and conservation of this imperiled bird.

Two novel qPCR assays to enhance black rail (Laterallus jamaicensis) eDNA surveys in the United States

Black rails (Laterallus jamaicensis) are a rare and protected bird species. They are also notoriously difficult to monitor. eDNA surveys have proven beneficial for the detection of this elusive species, but additional developments are needed to enhance eDNA survey utility (including reliability of outcomes) in light of black rail status and associated high-profile conservation actions. The use of multiple assays functions to increase eDNA detection confidence by increasing the probability of amplification in low concentration, highly degraded samples (i.e., reducing the risk of false negatives) and by providing a multiplicative test for ruling out contamination as the source of qPCR amplification (i.e., reducing the risk of false positives). The two eDNA assays developed, optimized, and validated in this study will prove valuable for the continued surveillance of the secretive black rail, offering data to measure its distribution and occurrence over time and as influenced by anticipated climate-change-induced disturbances and/or habitat restoration/creation initiatives. The assays are applicable to both Eastern black rails and California black rails, and do not exhibit qPCR amplification in non-target, co-distributed taxa (including other Rallidae species) in the United States.

Application of qualitative value of information to prioritize uncertainties about eastern black rail population recovery

AbstractNatural resource management decisions are often made in the face of uncertainty. The question for the decision maker is whether the uncertainty is an impediment to the decision and, if so, whether it is worth reducing uncertainty before or while implementing actions. Value of information (VoI) methods are decision analytical tools to evaluate the benefit to the decision maker of resolving uncertainty. These methods, however, require quantitative predictions of the outcomes as a function of management alternatives and uncertainty, in which predictions which may not be available at early stages of decision prototyping. Here we describe the first participatory application of a new qualitative approach to VoI in an adaptive management workshop for Atlantic Coast eastern black rail populations. The eastern black rail is a small, cryptic marsh bird that was recently listed as federally threatened, with extremely little demographic data available. Workshop participants developed conceptual models and nine hypotheses related to the effects of habitat management alternatives on black rail demography. Here, we describe the qualitative VoI framework, how it was implemented in the workshop, and the analysis outcomes, and describe the benefits of qualitative VoI in the context of adaptive management and co‐production of conservation science.

Interannual Winter Site Fidelity for Yellow and Black Rails

Yellow Rail (Coturnicops noveboracensis) is a species of conservation concern, while the Eastern Black Rail (Laterallus jamaicensis jamaicensis) has recently been listed as Threatened. Both species winter primarily in coastal areas from Texas through North Carolina. Between-year winter site fidelities of these species have not previously been reported, so we analyzed the recapture histories of Yellow Rails banded in southeastern Oklahoma (from 2008 to 2018) and coastal Texas (from 2006 to 2018), as well as Black Rails banded in Texas from 2006 to 2018. We banded 111 Yellow Rails in Oklahoma and 421 Yellow Rails in Texas during this time, as well as 94 Black Rails in Texas. Although Yellow Rails were routinely recaptured within season, only five individuals were recaptured between years. All recaptured birds were in Texas. Black Rails likewise exhibited low interannual site fidelity, with no interannual recaptures. The apparent low interannual site fidelity of Yellow Rails (1.1% in Texas, 0% in Oklahoma) and Black Rails (0%) is similar to that reported for other grassland species wintering in grasslands in this area (e.g., LeConte’s Sparrow (Ammodramus leconteii), Henslow’s Sparrow (A. henslowii), and Sedge Wren (Cistothorus stellaris)), and we speculate that low site fidelity could potentially be advantageous for species that use early successional habitats.

Status and Habitat Relationships of the Black Rail (Laterallus jamaicensis) in Coastal Louisiana, USA

The Eastern Black Rail (Laterallus jamaicensis jamaicensis) is a conservation priority species, yet distributional and habitat data continue to be lacking. In Louisiana, USA, the species is known from 13 documented records and scattered anecdotal reports. From May 2017 to April 2019, we conducted Louisiana's first systematic survey using point count and drag-line techniques. During breeding and non-breeding point counts, we detected one or more Black Rails during 3.1% (n = 1,239) of surveys across 13.8% (n = 152) of point locations at 33.3% (n = 33) of sites. Detection probability was highest from March to May (0.245 ± 0.055 SE) and occupancy was best explained by increasing Gulf cordgrass (Spartina spartinae) cover. During non-breeding season drag-line surveys, we tallied 36 detections at 43.8% (n = 16) of sites. We deployed VHF radios on 13 Black Rails between December 2018 and March 2019 and estimated a home range of 0.71 (± 0.13 SE) ha. These surveys provided the first evidence of a year-round Black Rail population in Louisiana. Additional study is urgently needed to understand habitat management needs, including prescribed fire, mechanical shrub removal, and cattle (Bos taurus) grazing intensities. Meanwhile, aggressive conservation actions are needed to preserve remaining habitat.

Mapping Habitat Quality and Threats for Eastern Black Rails (Laterallus jamaicensis jamaicensis)

Documenting the spatial distribution of high-quality habitat patches, the distributions of threats and protected areas, and the vulnerability of habitat patches to changes in environmental conditions is vital for conservation of rare species. Range-wide species distribution models were developed for Black Rails (Laterallus jamaicensis) to predict the distribution of high-quality habitat patches for breeding Eastern Black Rails (L. j. jamaicensis). Overlay analyses were conducted to quantify the distribution of habitat relative to human development and existing protected areas, as well as the vulnerability of the best habitat to future sea level rise. The amount of high-quality habitat varied among states (0.4-7.6% of area) and was relatively rare throughout the subspecies' range (3.3% of area). Human development was common but the amount varied spatially among states (2.2-15.3% of area). Higher-quality breeding habitat was more common on federal lands (9.4% of area) and protected areas (6.4% of area), yet 33-42% of the highest-quality habitat patches were vulnerable to sea level rise of 0.61-1.83 m. Our results imply that even though many of the highest-quality habitat patches may be less likely sites for development they are often vulnerable to rising seas, and thus maintenance of existing high-quality habitat patches may be difficult without management that takes into account the likelihood of future inundation.

Decline of Eastern Black Rails (Laterallus jamaicensis jamaicensis) within the Chesapeake Bay Region, USA

Eastern Black Rails (Laterallus jamaicensis jamaicensis) were surveyed during 1990, 2007, 2014 within the Chesapeake Bay region in Maryland and Virginia, USA. A network of point count locations (n = 182) was established and surveyed within tidal salt marshes. Occupancy declined during the study period from 0.84 ± 0.13 (ψ ± SE) in 1990 to 0.06 ± 0.02 in 2014. The annualized rate of decline was estimated to be 6.5%. Extinction and colonization rates between 1990 and 2014 were 0.81 ± 0.09 and 0.04 ± 0.02 respectively. Abundance declined from 1.98±0.05 Black Rails/point in 1990 to 0.26 ± 0.02 in 2014 with a 3.2% annualized rate of decline. Recruitment was 1.32 ± 1.35 between 1990 and 2007 and 0.003 ± 0.05 between 2007 and 2014. Species detection was negatively influenced by advancing season and waxing moon phase while individual detection was most strongly influenced by survey year and advancing season. Anecdotal observations of range-wide strongholds within the Chesapeake Bay suggest that sites have experienced significant declines with birds being extirpated by 2016. Declines throughout the core breeding area and within individual strongholds in the Chesapeake Bay are consistent with Black Rail declines in tidal habitats throughout the broader Northeast region.

Eastern Black Rail (Laterallus jamaicensis jamaicensis) Home Range and Habitat Use in Late Winter and Early Breeding Season in Coastal Texas, USA

Habitat use by the Eastern Black Rail (Laterallus jamaicensis jamaicensis) in coastal Texas, USA is poorly understood. To provide data for effective management of the subspecies in Texas, home range size was estimated and habitat use was examined. From February-May of 2017 and 2018, regular locations of 13 radio-transmitted Eastern Black Rails were obtained at San Bernard National Wildlife Refuge, Texas. The mean fixed kernel home range for birds with ≥ 24 relocations was 2.3 ha, with a mean core area of 0.43 ha. Average 95% MCP home range was 0.98 ha with a mean core area of 0.12 ha. During radio tracking, an Eastern Black Rail nest was found on 19 March 2018, the earliest on record for the state. Birds used the Salt and Brackish High Tidal Marsh, Salty Prairie, and Baccharis (Baccharis spp.) Shrubland, and avoided Salt and Brackish Low Tidal Marsh. Home ranges contained a gently sloping elevation gradient suggesting the importance of on-foot access to higher ground. Protection and restoration of Salty Prairie, and Salt and Brackish High Tidal Marsh is recommended for maintaining Eastern Black Rail populations in coastal Texas.

A Window into the Breeding Ecology and Molt of the Eastern Black Rail (Laterallus jamaicensis jamaicensis)

Knowledge of the ecology of the Eastern Black Rail (Laterallus jamaicensis jamaicensis) has remained nearly as elusive as the rail itself. Camera trapping methods facilitated the first study of breeding phenology and chick development, courtship and brood rearing behaviors, and flightless molt phenology and duration. Broods (n = 33) were observed between August 2015 - September 2019. Chicks were capable of flight at approximately 40 days after hatching. Nesting was initiated as early as 17 April 2019 ( x̄ = 5 June ± 30.0 SD) and fledging occurred as late as 30 September 2019 (x̄ = 10 August). Behavioral observations combined with phenology data provided evidence of pairs raising two or more broods during a breeding season. Flightless molt (n = 10 adults in molt), which was initiated as early as 15 August 2019 and completed as late as 11 October 2019, was completed within approximately 21 days of initiation. Conservation and management strategies should take into consideration periods of vulnerability, which coincide with increasingly severe and frequent coastal flooding events and hurricanes. It is necessary to understand factors key to fecundity and survival to effectively develop conservation strategies to ensure the persistence of the subspecies.

Breeding phenology of the Eastern Black Rail (Laterallus jamaicensis)

The Eastern Black Rail (Laterallus jamaicensis jamaicensis) is listed as Threatened under the United States Endangered Species Act and as Endangered in 6 states along the Atlantic Coast. Black Rails are difficult to observe and documentation of definitive breeding evidence is limited. This, along with perceived overlaps between the breeding and migratory periods, has led to uncertainty about the breeding status of calling birds across a large portion of their range. To delineate breeding and migratory periods, I examined the phenology of breeding records (N = 170) and documented “presumed migrants” (N = 55) based on rails that hit radio towers, lighthouses, and buildings or were found in inner cities, on ships-at-sea, or on offshore islands. Nesting in Eastern Black Rails extends 3 months from mid-May to mid-August and peaks during the third week of June. Based on the available sample there is no evidence that egg dates vary with latitude along the Atlantic Coast. Presumed migrants were recorded from early March to early May and from early September to early November. Breeding observations and records of presumed spring migrants overlapped during the first 2 weeks of May. The overlap includes only 2.4% of breeding records. There was no overlap between records of presumed fall migrants and the breeding season.

An eDNA diagnostic test to detect a rare, secretive marsh bird

We describe a novel method to detect a rare, secretive marsh bird using environmental DNA (eDNA). The Black Rail (Laterallus jamaicensis) occurs in visually concealing habitats and is most commonly surveyed by auditory callback. This method does not detect unresponsive individuals, is constrained seasonally and temporally, and requires significant personnel effort. New minimally invasive detection methods are needed to determine distribution and habitat use of this threatened species. We developed a highly species-specific quantitative PCR assay. We conducted callback surveys targeting Black Rails at sites on the mid-Atlantic coastal plain to collect samples for validation of eDNA diagnostics. Our assay reliably produced a signal when sufficient copies of Black Rail template were present. We successfully amplified Black Rail eDNA from 47% of the environmental samples taken from locations with detections. We tested whether environmental factors (water depth, salinity, air temperature), or sampling and handling procedures (time between collection and DNA extraction, storage temperature before filtering, field detection method, time between detection and sample collection) affected eDNA detectability. Only water depth had a significant positive effect on amplification success, emphasizing the importance of small pools as reservoirs of eDNA for terrestrial vertebrates. Our technique can be used in combination with other conservation strategies such as measuring occupancy in conjunction with habitat restoration efforts and resurveying coastal marshes after extreme weather events. It is adaptable to other elusive species of concern.

California Black Rail (<i>Laterallus jamaicensis</i> <i>coturniculus</i>) Response to Marsh Enhancement at Point Pinole Regional Shoreline, California

California Back Rail (<i>Laterallus jamaicensis</i> <i>coturniculus</i>) is the smallest rail in North America and is largely a resident of fresh, brackish and saltwater wetlands. Due to habitat degradation and destruction, this species is listed as a threatened species in California. Protecting and managing its breeding habitat and restoring adjacent suitable marsh sites are strategies to help its population recover. Habitat enhancement efforts by staff and volunteers of the East Bay Regional Park District at Giant Marsh in Richmond, California have been improving conditions for this native species since 2004. Analysis of systematically obtained call count data, collected there during the breeding seasons of 2013 through 2021 is showing a positive trend of increasing California Black Rails, as compared to the first baseline information collected in 1977 at this location. Field research also is showing that the rail population is now four times higher at this site and that they are typically confined to high marsh habitat, at the upper limits of tidal flooding. Analyzing these trends occurring within Giant Marsh at Point Pinole Regional Shoreline is providing important information that will aid recovery efforts designed to preserve and manage breeding habitat for this threatened species.

Mapping habitat suitability for the Eastern Black Rail throughout its Atlantic coastal range using maximum entropy (MaxEnt)

Neice, A. A. and S. B. McRae. 2021. Mapping habitat suitability for the Eastern Black Rail throughout its Atlantic coastal range using maximum entropy (MaxEnt). Avian Conservation and Ecology 16(1):23. https://doi.org/10.5751/ACE-01919-160123