Two novel qPCR assays to enhance black rail (Laterallus jamaicensis) eDNA surveys in the United States DOI Creative Commons
Sheena M. Feist, Xin Guan,

Madeleine P. Malmfeldt

et al.

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: April 26, 2022

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

Language: Английский

Evolutionary history of New World crakes (Aves: Rallidae) with emphasis on the tribe Laterallini DOI
Emiliano A. Depino,

Jorge L. Pérez‐Emán,

Elisa Bonaccorso

et al.

Zoologica Scripta, Journal Year: 2023, Volume and Issue: 52(4), P. 394 - 412

Published: April 7, 2023

Abstract New World crakes are intriguing, poorly known birds with cursorial cryptic habits; they belong to two unrelated tribes: Laterallini and Pardirallini. Recent genetic studies contributed the phylogenetic knowledge of these tribes, but a complete reconstruction is still missing. Here, we present most taxonomically dated gene‐based phylogeny crakes, an emphasis on Laterallini, including for first time sequences Coturnicops notatus , Laterallus levraudi L. jamaicensis tuerosi xenopterus . We used multilocus (mtDNA + nucDNA) analyses interpreted our results in light natural history group. Our novel show that: (1) sister leucopyrrhus ; (2) j. spilonota (3) C. clade that groups remaining black ( tuerosi, rogersi spilopterus ); (4) melanophaius conform recently diverged clade. Thus, indicate polyphyly this group, particularly and, time, some discrepancies previous stem from misidentified samples or Anurolimnas fasciatus. Finally, provide new preliminary insights into species limits taxa, specifically set stage integrative taxonomic assessments at generic level by incorporating (gene‐based) data.

Language: Английский

Citations

11
Galapagos Genetic Barcode: A Model for Island Economic Resilience During the COVID-19 Pandemic DOI
Jaime A. Chaves, Camille Bonneaud, Andrew F. Russell

et al.

Social and ecological interactions in the Galapagos Islands, Journal Year: 2023, Volume and Issue: unknown, P. 453 - 468

Published: Jan. 1, 2023

Language: Английский

Citations

2
Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs DOI

Daniel E Chavez,

Taylor Hains, Sebastian Espinoza‐Ulloa

et al.

Journal of Heredity, Journal Year: 2024, Volume and Issue: 115(4), P. 444 - 457

Published: March 15, 2024

Similar to other insular birds around the world, Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning entire width archipelago. were once common on with sufficiently high altitudes support shrubs in humid habitats. After humans introduced goats, this habitat was severely due overgrazing. Habitat loss devastated some populations, less than 50 individuals surviving, rendering genetic diversity a pressing conservation concern. Additionally, one enigma is reappearance island Pinta after they considered extirpated. Our approach investigate history and geographic distribution as well examine genome-wide effects historical population bottlenecks using 39 whole genomes across populations. We recovered an early divergence ancestors leading isolated populations second clade comprising rest islands, historically forming single landmass. Subsequently, separation landmass ~900 kya may led isolation Isabela more panmictic found Santa Cruz Santiago islands. that contain long runs homozygosity (>2 Mb) could be related introduction goats. Finally, our findings show modern eradication goats critical avoiding episodes inbreeding most

Language: Английский

Citations

0
Colonization record of the Galápagos’ vertebrate clades: Biogeographical issues plus a conservation insight DOI Creative Commons
Jason R. Ali, Uwe Fritz

Vertebrate Zoology, Journal Year: 2024, Volume and Issue: 74, P. 381 - 395

Published: May 16, 2024

Abstract Our focus is the colonization history of Galápagos’ vertebrate clades: 11 land-bound groups (eight reptiles, three rodents) and 13 taxa flyers swimmers (ten winged birds, two pinnipeds, one penguin). Using ‘colonization intervals’ profiles’, it clear that sets assembled very differently. The former includes older clades with between one, potentially eight, predating emergence oldest island (4 Mya). For origin some lineages, now-sunken landmasses associated Galápagos mantle-plume hotspot must have been involved, but for others could reflect taxonomic uncertainties. In contrast, are markedly younger, indicating either higher rates extirpation these sorts animal, or continued genetic influx from mainland populations, combination both factors. Concerning first, possible drivers environmental stressors El Niño–La Niña climate system; recent may be vulnerable to extreme events within oscillation sequence, perhaps on ≥10 4 -year timescales. Therefore, loose temporal thresholds might exist archipelago’s beyond which selection fortifies them most challenging seasonal states. Moreover, in a world uncertainty, findings appear relevant conservation initiatives suggesting focusing younger elements biota.

Language: Английский

Citations

0
Reference genome of the black rail, Laterallus jamaicensis DOI Creative Commons
Laurie A. Hall, Ian Wang, Merly Escalona

et al.

Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(4), P. 436 - 443

Published: April 29, 2023

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

Language: Английский

Citations

1
First genetic data for the critically endangered Cuban endemic Zapata Rail Cyanolimnas cerverai, and the taxonomic implications DOI Creative Commons

Alex F. Brown,

Yvonne Lawrie, Thomas Shannon

et al.

Journal of Ornithology, Journal Year: 2022, Volume and Issue: 163(4), P. 945 - 952

Published: July 8, 2022

Abstract The taxonomic affinity of the near-flightless Zapata Rail Cyanolimnas cerverai , a critically endangered and highly localized species endemic to Cuba, has long been debated. Morphological analyses have suggested that this species, which constitutes monotypic genus, could be related either extinct Tahitian Cave Rails ( Nesotrochis sp.) or South American rail tribe Pardirallini, i.e., genera Neocrex Mustelirallus Pardirallus . While pronounced phenotypic convergence—and divergence—among rails repeatedly proven morphology-based phylogenies unreliable, thus far no attempt sequence DNA from enigmatic succeeded. In study, we extracted historic museum specimen collected in 1927 sequenced multiple short fragments allowed us assemble partial mitochondrial cytochrome oxidase I gene. Phylogenetic confirm belongs Pardirallini as sister genus it diverged about 6 million years ago. Their divergence was estimated at 9 Based on morphology our phylogeny, conclude is unjustified retain tentatively recommend C. two are ascribed

Language: Английский

Citations

2
The Role for Scientific Collections and Public Museums in Island Conservation DOI
John P. Dumbacher, Jaime A. Chaves

Social and ecological interactions in the Galapagos Islands, Journal Year: 2023, Volume and Issue: unknown, P. 391 - 413

Published: Jan. 1, 2023

Language: Английский

Citations

0
First genetic data for the Critically Endangered Cuban endemic Zapata RailCyanolimnas cerverai, and the taxonomic implications DOI Creative Commons

Alex F. Brown,

Thomas Shannon, J. Martin Collinson

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

ABSTRACT The taxonomic affinity of the near-flightless Zapata Rail Cyanolimnas cerverai , a Critically Endangered and highly localized species endemic to Cuba, has long been debated. Morphological analyses have suggested that this species, which constitutes monotypic genus, could be related either extinct Tahitian Cave Rails ( Nesotrochis sp.) or South American rail tribe Pardirallini, i.e., genera Neocrex, Mustelirallus Pardirallus . Whilst pronounced phenotypic convergence–and divergence–among rails repeatedly proven morphology-based phylogenies unreliable, thus far no attempt sequence DNA from enigmatic succeeded. In study, we extracted historic museum specimen collected in 1927 sequenced multiple short fragments allowed us assemble partial mitochondrial cytochrome oxidase I gene. Phylogenetic confirm belongs Pardirallini as sister genus Neocrex it diverged about six million years ago. Their divergence was estimated at eight Based on morphology our phylogeny, conclude is unjustified retain tentatively recommend C. two are ascribed Abstract Figure

Language: Английский

Citations

0
Two novel qPCR assays to enhance black rail (Laterallus jamaicensis) eDNA surveys in the United States DOI Creative Commons
Sheena M. Feist, Xin Guan,

Madeleine P. Malmfeldt

et al.

Research Square (Research Square), Journal Year: 2022, Volume and Issue: unknown

Published: April 26, 2022

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

Language: Английский

Citations

0