Geology topics

Andreanna J. Welch

Publications and source records attributed to Andreanna J. Welch.

9 recordsLinked to original sources

USGS2024

Carotenoid skin ornaments as flexible indicators of male foraging behavior in a marine predator: Variation among Mexican colonies of brown booby (Sula leucogaster)

Carotenoid-dependent ornaments can reflect animals’ diet and foraging behaviors. However, this association should be spatially flexible and variable among populations to account for geographic variation in optimal foraging behaviors. We tested this hypothesis using populations of a marine predator (the brown booby, Sula leucogaster ) that forage across a gradient in ocean depth in and near the Gulf of California. Specifically, we quantified green chroma for two skin traits (foot and gular color) and their relationship to foraging location and diet of males, as measured via global positioning system tracking and stable carbon isotope analysis of blood plasma. Our three focal colonies varied in which foraging attributes were linked to carotenoid-rich ornaments. For gular skin, our data showed a shift from a benthic prey-green skin association in the shallow waters in the north to a pelagic prey-green skin association in the deepest waters to the south. Mean foraging trip duration and distance of foraging site from coast also predicted skin coloration in some colonies. Finally, brown booby colonies varied in which trait (foot versus gular skin color) was associated with foraging metrics. Overall, our results indicate that male ornaments reflect quality of diet and foraging–information that may help females select mates who are adapted to local foraging conditions and therefore, are likely to provide better parental care. More broadly, our results stress that diet-dependent ornaments are closely linked to animals’ environments and that we cannot assume ornaments or ornament signal content are ubiquitous within species, even when ornaments appear similar among populations.

Marine Biology↗

USGS2021

Palaeoceanographic changes in the late Pliocene promoted rapid diversification in pelagic seabirds

Aim Palaeoceanographic changes can act as drivers of diversification and speciation, even in highly mobile marine organisms. Shearwaters are a group of globally distributed and highly mobile pelagic seabirds. Despite a recent well-resolved phylogeny, shearwaters have controversial species limits, and show periods of both slow and rapid diversification. Here, we explore the role of palaeoceanographic changes on shearwaters' diversification and speciation. We investigate shearwater biogeography and the evolution of a key phenotypic trait, body size, and we assess the validity of their current taxonomy. Location Worldwide. Taxa Shearwaters (Order Procellariiformes, Family Procellariidae, Genera Ardenna , Calonectris and Puffinus ). Methods We generated genomic (ddRAD) data to infer a time-calibrated species tree for the shearwaters. We estimated ancestral ranges and evaluated the roles of founder events, vicariance and surface ocean currents in driving diversification. We performed phylogenetic generalised least squares to identify potential predictors of variability in body size along the phylogeny. To assess the validity of the current taxonomy, we analysed genomic patterns of recent shared ancestry and differentiation among shearwater taxa. Results We identified a period of high dispersal and rapid speciation during the Late Pliocene–early Pleistocene. Species dispersal appears to be favoured by surface ocean currents, and founder events are supported as the main mode of speciation in these highly mobile pelagic seabirds. Body mass shows significant associations with life strategies and local conditions. The current taxonomy shows some incongruences with the patterns of genomic divergence. Main Conclusions A reduction of neritic areas during the Pliocene seems to have driven global extinctions of shearwater species, followed by a subsequent burst of speciation and dispersal probably promoted by Plio-Pleistocene climatic shifts. Our findings extend our understanding on the drivers of speciation and dispersal of highly mobile pelagic seabirds and shed new light on the important role of palaeoceanographic events.

Journal of Biogeography↗

USGS2021

Integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of pelagic seabirds

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.

Systematic Biology↗

USGS2018

Carotenoid-based skin ornaments reflect foraging propensity in a seabird, Sula leucogaster

Carotenoid-based ornaments are common signalling features in animals. It has long been proposed that such ornaments communicate information about foraging abilities to potential mates. However, evidence linking foraging with ornamentation is largely missing from unmanipulated, free-ranging populations. To investigate this relationship, we studied a coastal population of brown booby ( Sula leucogaster brewsteri ), a seabird with a carotenoid-based gular skin ornament. δ 13 C values from both feathers and blood plasma were negatively correlated with male gular colour, indicating birds that consumed more pelagic prey in offshore locations had more ornamented skin than those that fed on nearshore, benthic prey. This relationship was supported by our GPS tracking results, which revealed longer, more offshore foraging trips among highly ornamented males. Our data show that brown booby ornaments are honest indicators of foraging propensity; a link consistent with the rarity hypothesis and potentially driven by the concentration of carotenoids found in phytoplankton versus benthic algae. Carotenoid-based ornaments may reflect foraging tendencies in animals such as coastal predators that use food webs with distinct carotenoid profiles.

Biology Letters↗

USGS2018

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6 , three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Mitochondrial DNA Part A↗

USGS2018

Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae)

Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura . Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura . We recommend that C. viridipennis , currently generally treated as specifically distinct from C. chapmani , be returned to its former status as C. chapmani viridipennis , and that C. andrei , now generally regarded as synonymous with C. vauxi aphanes , again be recognized as a valid species. Widespread Neotropical species C. spinicaudus is paraphyletic with respect to more range-restricted species C. fumosa , C. egregia , and C. martinica . Geographically structured genetic variation within some other species of Chaetura , especially notable in C. cinereiventris , suggests that future study may lead to recognition of additional species in this genus. Biogeographic analysis indicated that Chaetura originated in South America and identified several dispersal events to Middle and North America following the formation of the Isthmus of Panama.

Molecular Phylogenetics and Evolution↗

USGS2014

Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the Arctic environment

Polar bears ( Ursus maritimus ) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear ( U. arctos ). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate if polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex, and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide, which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of nitric oxide as an adaptive response to control trade-offs between energy production in the form of ATP versus generation of heat (thermogenesis).

Genome Biology and Evolution↗

USGS2012

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Proceedings of the National Academy of Sciences↗

USGS2011

Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird

Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels ( Pterodroma sandwichensis ) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (δ 13 C, δ 15 N and δD, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with Φ ST = 0.50 ( p < 0.0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower δ 13 C and δ 15 N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated δ 15 N values at the food web base. δ 15 N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather δD varied from −69 to 53‰. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies.

Hawaii↗