Biology subjects

Gyllenhaal, E. F.

Publications and source records attributed to Gyllenhaal, E. F..

7 recordsLinked to original sources

bioRxiv2026

A multi-tissue transcriptome strategy for genomic resource development in Pinus edulis

Premise:: Conifers comprise one-sixth of global forests and landscape genomic studies are urgently needed to understand their biology, yet relatively few conifer species have reference genomes. Targeted exon-capture is a practical alternative to whole-genome sequencing, but selecting loci without a reference genome remains a barrier. We developed a multi-tissue reference transcriptome for pi non pine (Pinus edulis) to ask how multi-tissue sampling improves probe design, and what is lost under a conventional single-tissue approach. Methods: We assembled a reference transcriptome from four diploid tissues (needle, phloem, root, vegetative bud) and one haploid tissue (megagametophyte), using the latter as a pseudo-guide. We designed a target-capture probe-set by prioritizing highly expressed P. edulis transcripts and transcripts matching a conifer exon database. Results: We recovered 76% of conserved plant genes with few duplicated transcripts. Filtering yielded 15,664 transcripts totaling 31.4 Mb, ~0.1% of the genome. Tissue-specific expression was substantial: 27.4% of transcripts occurred exclusively in non-needle tissues. Functional annotation confirmed complementary contributions, including seed-desiccation and germination genes from megagametophytes, and defense- and stress-associated genes from roots and phloem. Discussion: We built a transcriptome and efficient probe set using a roadmap suitable for other non-model plants with large genomes; keys to success were prioritizing complementary tissues and using expression-based filtering.

genomics↗

bioRxiv2026

Asymmetric gene flow across a desert contact zone in a riparian songbird

Secondary contact is a key point in the speciation process, and fine-scale geography can shape its outcomes. This is especially true for species restricted to fragmented habitats, such as riparian corridors through arid regions. Here we examine the role of disjunct riparian habitat in shaping secondary contact in Bells Vireo (Vireo bellii), a North American songbird species that contains distinct eastern and western forms. We recovered a unique, discontinuous contact zone along the Rio Grande in New Mexico, where two populations with greater nuclear and mitochondrial genetic affinity for the eastern lineage are separated by a population with an affinity for the western lineage. This point of primarily western ancestry on the Rio Grande corresponded with a stretch where several intermittently flowing tributaries join from the west and may have acted as gene flow corridors. Using a combination of empirical analyses of divergence and diversity across the genome and population genetic simulations, we uncovered evidence of neutral, genome-wide admixture driving the genomic architecture of divergence, rather than evidence for local adaptation or selective sweeps. In sum, this genomic study showed us how fine-scale dispersal corridors can cause idiosyncratic patterns of admixture when habitat is limiting in zones of secondary contact.

evolutionary biology↗

bioRxiv2025

Spatially heterogeneous gene flow may hinder linking phylogeographic data to macroevolutionary patterns

How microevolutionary processes translate to macroevolutionary patterns is a central question in evolutionary biology. Macroevolutionary and biogeographic studies often rely on species trees to make inferences about diversification, but gene flow can lead to incorrect phylogenetic inference. Under a range of biogeographic conditions, gene flow may not occur uniformly across space during diversification, which could lead to macroevolutionary misinferences. For example, whenever a "peripheral" population is relatively isolated and inferred as sister to a "core" clade of populations that exchange migrants, it might solely reflect gene flow, as opposed to macroevolutionary processes such as the order of biogeographic dispersal events. We use simulations of the hypothetical case of spatially heterogeneous gene flow described above and found that relatively low levels of gene flow led to monophyly of the adjacent populations, with longer branches for peripheral taxa, regardless of the true divergence history. We highlight an empirical example wherein lowland antbirds (Family: Thamnophilidae)-a clade known for dynamic gene flow in Amazonia-tend to be young in Amazonia, but older at Amazonias periphery. Although it is challenging to know if the simulated bias applies here, our work suggests a distinguishability problem for any nodes stemming from radiations in geographically heterogeneous environments.

evolutionary biology↗

bioRxiv2024

Waves of Colonization and Gene Flow in a Great Speciator

Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones--where reproductive isolation can further develop via reinforcement or phenotypic displacement--or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayrs foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.

evolutionary biology↗

bioRxiv2024

Taxonomy and nomenclature of the giant hummingbirds (Patagona spp.) (Aves: Trochilidae)

Giant hummingbirds (Patagona spp.) are extraordinarily large hummingbirds whose taxonomy has been muddled for two centuries. Patagona systematics were recently redefined in a study of migration, physiology, and genomics, revealing two species: the Southern Giant Hummingbird and Northern Giant Hummingbird. Here, we re-evaluate taxonomy and nomenclature of the genus in light of its newly-clarified biology and species limits, analyzing data from 608 specimens and wild-caught individuals spanning 1864-2023. The forms gigas and peruviana were both described based on multiple syntypes. No adequate syntypes for P. gigas are extant, so we designate a neotype for this taxon. We then critically consider the identity and usage of gigas and peruviana, respectively, and examine identification challenges that have fostered taxonomic uncertainty. We endorse the names Patagona gigas for the Southern Giant Hummingbird and P. peruviana for the Northern Giant Hummingbird. The genetic identity of the peruviana lectotype remains untested, but its plumage appears to match the northern species. We found that [~]33% of Patagona gigas specimens in major museum collections are misidentified as peruviana; we provide this list to correct the historical record. To facilitate identification and future study of these two cryptic species, we provide comprehensive information on plumage, measurements, and seasonal ranges.

zoology↗

bioRxiv2023

Extraordinary levels of per- and polyfluoroalkyl substances (PFAS) in vertebrate animals at a New Mexico desert oasis: multiple pathways for wildlife and human exposure

Per- and polyfluoroalkyl substances (PFAS) threaten human and wildlife health, but their movement through food webs remains poorly understood. Contamination of the physical environment is widespread, but particularly concentrated at military installations. Here we measured 17 PFAS in wild, free-living mammals and migratory birds at Holloman Air Force Base (AFB), New Mexico, USA, where wastewater catchment lakes form biodiverse oases. PFAS concentrations were among the highest ever reported in animal tissues, and high levels have persisted for at least three decades. The hazardous long carbon-chain form, perfluorooctanosulfonic acid (PFOS), was most abundant, with liver concentrations averaging tens of thousands of ng/g wet weight (ww), reaching as high 97,000 ng/g (ww) in a 1994 specimen of white-footed mouse (Peromyscus leucopus) and 38,000 ng/g ww in a duck, the American wigeon (Mareca americana). Perfluorohexanesulfonic acid (PFHxS) averaged thousands of ng/g ww in the livers of birds and house mice, but one order of magnitude lower in the livers of upland desert rodent species. PFAS levels were strikingly lower at control sites, even for highly mobile migratory species. Tissue concentrations were correlated within individuals, and consistently higher in liver than in muscle or blood. Twenty of 23 vertebrate species sampled at Holloman AFB were heavily contaminated, representing multiple trophic levels and microhabitats, and implicating a range of pathways for PFAS spread: ingestion of surface water, sediments, and dust; foraging on aquatic invertebrates and plants by secondary consumers; and preying upon small vertebrates by higher level consumers, including consumption of game species by hunters. Unlike in other aquatic systems, piscivory was not an important pathway of PFAS uptake. In sum, legacy PFAS at a desert wetland have permeated the local food web across a period of decades, severely contaminating resident and migrant animals, and likely exposing humans via game meat consumption and outdoor recreation. Five highlightsO_LIA biodiverse, wetland food web at a military base is heavily contaminated with PFAS. C_LIO_LILittoral-zone mice and aquatic birds had high liver PFOS, up to 97,000 ng/g ww. C_LIO_LISpecies and ecological variation were high among 16 PFAS detected in animal tissues. C_LIO_LIGame species had dangerously contaminated meat and can transport it long distances. C_LIO_LIBiorepositories provide key temporal and spatial sampling for contaminant studies. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/561778v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@96a640org.highwire.dtl.DTLVardef@7cd7f4org.highwire.dtl.DTLVardef@45fb67org.highwire.dtl.DTLVardef@7c33a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2022

PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea-level change on island archipelagos

O_LIPleistocene sea-level change played a significant role in the evolution and assembly of island biotas. The formation of land bridges between islands during Quaternary glacial maxima, when sea levels were up to 120 metres below present-day sea levels, often facilitated historical dispersal and gene flow between islands that are today geographically disconnected. C_LIO_LIDespite this, relatively few studies have attempted to quantify the effects of Pleistocene sea-level change on the evolution of island species assemblages. C_LIO_LIHere we present PleistoDist, an R package that allows users to visualise and quantify the effects of Pleistocene sea-level change on islands over time, and test multiple temporally explicit hypotheses of inter-island dispersal and community assembly. C_LIO_LIRe-analysing published datasets, we demonstrate how using PleistoDist to account for historical sea-level change can provide greater explanatory power when analysing extant island communities, and show how population genetic simulations can be used to generate spatiotemporally explicit neutral expectations of population genetic structure across island archipelagos. C_LI

bioinformatics↗