Evolutionary History of the Galápagos Rail Revealed by Ancient Mitogenomes and Modern Samples

Abstract

The biotas of the Galápagos Islands are one of the best studied island systems and have provided a broad model for insular species’ origins and evolution. Nevertheless, some locally endemic taxa, such as the Galápagos Rail Laterallus spilonota, remain poorly characterized. Owing to its elusive behavior, cryptic plumage, and restricted distribution, the Galápagos Rail is one of the least studied endemic vertebrates of the Galapagos Islands. To date, there is no genetic data for this species, leaving its origins, relationships to other taxa, and levels of genetic diversity uncharacterized. This lack of information is critical given the adverse fate of island rail species around the world in the recent past. Here, we examine the genetics of Galápagos Rails using a combination of mitogenome de novo assembly with multilocus nuclear and mitochondrial sequencing from both modern and historical samples. We show that the Galápagos Rail is part of the “American black rail clade”, sister to the Black Rail L. jamaicensis, with a colonization of Galápagos dated to 1.2 million years ago. A separate analysis of one nuclear and two mitochondrial markers in the larger population samples demonstrates a shallow population structure across the islands, possibly due to elevated island connectivity. Additionally, birds from the island Pinta possessed the lowest levels of genetic diversity, possibly reflecting past population bottlenecks associated with overgrazing of their habitat by invasive goats. The modern and historical data presented here highlight the low genetic diversity in this endemic rail species and provide useful information to guide conservation efforts.

Evolutionary history of New World crakes (Aves: Rallidae) with emphasis on the tribe Laterallini

“…Our results are in broad agreement with previous studies in showing that New World crakes are not a monophyletic group (Garcia-R et al, 2014a(Garcia-R et al, , 2020Kirchman et al, 2021). We confirmed and expanded on the phylogenetic placement of New World crakes in two different and distantly related lineages: (1) the tribe Laterallini, which is composed of the crake genera Coturnicops, Laterallus, Hapalocrex, Rufirallus and one species traditionally placed in Anurolimnas [fasciatus] but recently placed in Rufirallus (Chaves et al, 2020;Garcia-R et al, 2014aGarcia-R et al, , 2020Kirchman et al, 2021;Stervander et al, 2019) and (2) the tribe Pardirallini, which encompasses the crake genera Amaurolimnas, Mustelirallus and Anurolimnas castaneiceps, together with Cyanolimnas, Pardirallus rails and the Aramides wood rails.…”

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

“…erythrops and M. albicollis, but less so to the three species of Pardirallus, in partial congruence with prior predictions (Olson 1973, Livezey 1998, Garcia-R & Matzke 2021. Although it is now rather well established that plumage is not necessarily a reliable character for inferring phylogenetic relationships within the Rallidae (e.g., Garcia-R et al 2014, Stervander et al 2019, Chaves et al 2020, in the present case morphology appears to be rather informative.…”

“…Employing a birth-death speciation model, we set the prior for death rate to follow an exponential distribution with mean 1. We enforced monophyly of the clades Rallidae, Ralloidea, and Gruoidea, and employed dating calibration priors on Gruiformes and stem Rallidae following Chaves et al (2020). We then ran two iterations of 10 million generations, sampling every 1,000 generations, and optimized tuning parameters and operator weights to produce the final xml specification used for our analyses (see Data Availability).…”

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

“…Within this grouping, the species appears to be most closely related to N. erythrops and M. albicollis, but less so to the three species of Pardirallus, in partial congruence with prior predictions (Olson 1973;Livezey 1998;Garcia-R & Matzke 2021). Although it is now rather well established that plumage is not necessarily a reliable character for inferring phylogenetic relationships within the Rallidae (e.g., Garcia-R et al 2014;Stervander et al 2019;Chaves et al 2020), in the present case morphology appears to be rather informative.…”

“…Employing a birth-death speciation model, we set the prior for death rate to follow an exponential distribution with mean 1. We enforced monophyly of the clades Rallidae, Ralloidea, and Gruoidea, and employed dating calibration priors on Gruiformes and stem Rallidae following Chaves et al (2020). We then ran two iterations of 10 million generations, sampling every 1000 generations, and optimized tuning parameters and operator weights to produce the final xml specification used for our analyses (see "Data availability").…”