Biology subjects

Dumbacher, J. P.

Publications and source records attributed to Dumbacher, J. P..

10 recordsLinked to original sources

bioRxiv2025

High-Quality De Novo Genome Assembly for the Galapagos Endemic Lava Gull Using Oxford Nanopore Technologies

High-quality reference genomes permit deeper investigation into species evolution and provide insight into species management and conservation. Next-generation sequencing technologies, such as Oxford Nanopore Technologies, allow researchers to generate high-accuracy long-read genetic data in real-time from anywhere in the world, increasing accessibility to sequence data. The lava gull (Leucophaeus fuliginosus), an endemic bird species of the Galapagos archipelago, is the worlds rarest gull with an estimated population of 300 to 600 individuals. Little genetic research has been done on this species due to its solitary nature and small population size. Here we present a chromosome-level reference genome assembly of an adult female lava gull, generated using ultra-long reads from the Oxford Nanopore Ultra-Long DNA Sequencing Kit and a PromethION 2 Solo device. Initial sequencing generated 1.78 million reads, consisting of 29.6 gigabases (Gbp), with a mean Q-score of 17.8 at an average 22.5x coverage. Our final assembly has a total length of 1.31 Gbp, with 450 scaffolds, and a scaffold N50 of 85.1 Mbp and contig N50 of 42.8 Mbp. The generation of a high-quality whole genome for the lava gull is an important step for investigation into the species phylogeography and population genetics.

genomics↗

bioRxiv2025

First Whole-Genome Assembly of the Galapagos Petrel (Pterodroma phaeopygia) Using Oxford Nanopore Sequencing to Advance Conservation Genomics in a Critically Endangered Seabird

The Galapagos petrel (Pterodroma phaeopygia) is a critically endangered procellariiform seabird endemic to the Galapagos Islands. Once abundant, its populations have sharply declined due to invasive predators, habitat degradation, and destruction of nest burrows. Although the species is distributed across several islands, the demographics of each population and their genetic relationships are poorly understood. To facilitate future studies of population structure and connectivity, we present the first high-quality reference genome for the Galapagos petrel. The genome was assembled from ultra-long Oxford Nanopore sequence data collected from an adult female sampled on San Cristobal Island. Sequencing was performed at the Galapagos Science Center, enabling local capacity-building and compliance with strict sample import-export regulations of endangered species. The final nuclear genome assembly spans 1.35 Gb in length, with average coverage of 36.07x, scaffold N50 of 74.2 Mb, and a BUSCO aves lineage completeness of 99.95%. The genome comprises 41 pseudo-chromosomes, with 23 spanning from telomere to telomere and 16, including W and Z chromosomes, containing a single telomere. Chromosomal-level scaffolding by reference was performed using the genome of Corys shearwater (Calonectris borealis) GCA_964196065.2 (Aranega et al., 2024), a related species. The Galapagos petrel reference genome represents a foundational tool for comparative genomics, conservation biology, and functional studies of island-endemic avifauna. It will also facilitate future efforts to characterize genetic diversity, structural variation, and adaptive responses in this critically endangered species.

genomics↗

bioRxiv2023

Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).

New Guinea, the largest tropical island, is topographically complex and is dominated by a large central mountain range surrounded by multiple smaller isolated mountain regions along its perimeter. The island is biologically hyper-diverse and harbours an avifauna with many species found only there. The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic differentiation, revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.

evolutionary biology↗

bioRxiv2022

DNA metabarcoding reveals the threat of rapidly expanding barred owl populations to native wildlife in western North America

Invasive predators can have detrimental impacts on native species and biological communities through direct consumptive effects and indirect effects on trophic interactions. As an invasive, apex predator achieving high densities, barred owls (Strix varia) may pose a substantial threat to native wildlife in western North American forests. Studies of the trophic ecology of barred owls in their invasive range, however, have involved morphological examinations of prey remains with limited taxonomic resolution. We conducted DNA metabarcoding using intestinal samples collected from barred owls at the leading edge of their range expansion in northeastern California. Using customized primers, we screened the intestinal contents of 124 barred owls and detected a broad diet of 78 unique prey types (48 vertebrates and 30 invertebrates), including many previously undetected prey types. Mammals were the most consumed vertebrate class (frequency of occurrence = 65%), followed by amphibians (32%), birds (22%), and reptiles (19%). Diets differed regionally but were similar among ages and sexes and exhibited limited variation in response to local environmental conditions. Our work highlights the generalist predatory strategy of invasive barred owls, indicates that they will not serve as ecological replacements for the congeneric spotted owls (S. occidentalis) they displace, and identifies numerous native species potentially threatened by their range expansion. Expanding currently limited barred owl removals could benefit native species and wildlife communities in western North America. More broadly, DNA metabarcoding provides a powerful tool for conducting detailed assessments of species consumed by invasive predators, potentially incentivizing conservation actions and improving outcomes.

ecology↗

bioRxiv2020

Sodium channel toxin-resistance mutations do not govern batrachotoxin (BTX) autoresistance in poison birds and frogs

Poisonous organisms carry small molecule toxins that alter voltage-gated sodium channel (Na{checkmark}) function. Among these, batrachotoxin (BTX) from Pitohui toxic birds and Phyllobates poison frogs, stands out because of its lethality and unusual effects on Nav function. How these toxin-bearing organisms avoid autointoxication remains poorly understood. In poison frogs, a Nav DIVS6 pore-forming helix N[->]T mutation has been proposed as the BTX resistance mechanism. Here, we show that this variant is absent from Pitohui and poison frog Navs, incurs a strong cost that compromises channel function, and fails to produce BTX-resistant channels when tested in the context of poison frog Navs. We further show that captive-raised poison frogs are BTX resistant, even though they bear BTX-sensitive Navs. Hence, our data refute the hypothesis that BTX autoresistance is rooted in Nav mutations and instead suggest that more generalizable mechanisms such as toxin sequestration act to protect BTX-bearing species from autointoxication.

biophysics↗

bioRxiv2020

Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls

Spotted owls (SO, Strix occidentalis) are a keystone species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (subspecies S. o. caurina) has been listed as "threatened" under the Endangered Species Act since 1990. Here we present a comprehensive look at genetic variation to elucidate the population histories of SO and invading western BO. Specifically, we present an improved SO genome assembly, based on 10x and Bionano Genomics data, along with 51 high-coverage whole-genome sequences including 11 SO from two subspecies (caurina and occidentalis), 25 BO, 2 confirmed and 13 potential hybrids. We identified potential hybrids based on intermediate morphology and found them to be a mixture of pure BO, F1 hybrids, and F1 x BO backcrosses. Unlike previous studies reporting asymmetries in the species-specific genders of the parents of F1 hybrids, we did not observe any significant asymmetry. Within species, we found that Western BO genetic variation is not simply a subset of the genetic variation in Eastern BO, suggesting that the two groups have been genetically isolated for longer (thousands of years) than previously suspected (80-130 years). Similarly, we found evidence of substantial genetic differentiation between the two SO subspecies. Finally, our analyses suggest that Northern SO experienced a moderate population bottleneck around the end of the last glaciation, while BO population sizes have always been large.

evolutionary biology↗

bioRxiv2019

Speciation with gene flow across an elevational gradient in New Guinea kingfishers

Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high elevation and low elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modeling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that while in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.

evolutionary biology↗

bioRxiv2018

Whole-genome analysis of introgression between the spotted owl and barred owl (Strix occidentalis and Strix varia, respectively; Aves: Strigidae) in western North America

As the barred owl (Strix varia; Aves: Strigiformes: Strigidae) expands throughout western North America, hybridization between barred and spotted owls (Strix varia and S. occidentalis, respectively), if abundant, may lead to genetic swamping of the endangered spotted owl. We analyzed low-coverage, whole-genome sequence data from fifty-one barred and spotted owls to investigate recent introgression between these two species. Although we obtained genomic confirmation that these species can and do hybridize and backcross, we found no evidence of widespread introgression. Plumage characteristics of western S. varia that suggested admixture with S. occidentalis appear unrelated to S. occidentalis ancestry and may instead reflect local selection.

genomics↗

bioRxiv2018

Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California

We analyzed whole-genome data of four spotted owls (Strix occidentalis) to provide a broad-scale assessment of the genome-wide nucleotide diversity across S. occidentalis populations in California. We assumed that each of the four samples was representative of its population and we estimated effective population sizes through time for each corresponding population. Our estimates provided evidence of long-term population declines in all California S. occidentalis populations. We found no evidence of genetic differentiation between northern spotted owl (S. o. caurina) populations in the counties of Marin and Humboldt in California. We estimated greater differentiation between populations at the northern and southern extremes of the range of the California spotted owl (S. o. occidentalis) than between populations of S. o. occidentalis and S. o. caurina in northern California. The San Diego County S. o. occidentalis population was substantially diverged from the other three S. occidentalis populations. These whole-genome data support a pattern of isolation-by-distance across spotted owl populations in California, rather than elevated differentiation between currently recognized subspecies.

genomics↗

bioRxiv2017

Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens

Laboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens (Suchan et al. 2016). The hyRAD method employs fragments produced in a restriction site associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affects sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing, but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.

genomics↗