Biology subjects

Palsboll, P. J.

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

10 recordsLinked to original sources

bioRxiv2026

DNA methylation correlates with lifespan and predicts remaining lifespan in the zebra finch

Biomarkers that correlate with age are essential tools for understanding aging and lifespan variation. DNA methylation (DNAm) changes predictably with age in parts of the genome. In humans, epigenetically 'old' individuals relative to their chronological age also have a reduced life expectancy but whether the link between epigenetic age and lifespan is a general feature remains an open question. We explored age-related changes in DNAm in the zebra finch (Taeniopygia castanotis), a key avian model species, using 100 longitudinal whole genome methylomes from 50 captive adults monitored until their natural death. We found genome-wide hypomethylation with age, with DNAm decreasing faster in individuals with shorter lifespans and identified 29 CpG sites where DNAm changed significantly with age. We developed an epigenetic aging clock based on 119 CpG sites, that predicted chronological age with high accuracy (median absolute deviation=0.68 years, 8.2% of maximum lifespan in our dataset). Females raised in large broods, which have shorter lifespans, showed increased epigenetic age acceleration, consistent with faster biological aging. However, epigenetic age acceleration did not predict lifespan or remaining lifespan. In contrast, the within-individual rate of change in epigenetic age significantly predicted lifespan: faster epigenetic aging was associated with a shorter lifespan. Moreover, a 'doom' clock, trained to predict post-sampling lifespan, successfully predicted remaining lifespan. Our findings provide the first evidence that DNAm provides a window into biological aging in birds, showing how early-life environments shape the aging trajectory via the epigenome and underscore the value of longitudinal data in aging studies.

molecular biology↗

bioRxiv2025

Inferences from epigenetic information in an ecological context: a case study of early-life environmental effects on DNA methylation in zebra finches

DNA methylation (DNAm) plays a key role in mediating phenotypic responses to environmental variation. Various approaches exist to link DNAm variation to phenotypes, ranging from single nucleotide resolution to the development of composite indexes ( epigenetic clocks). We here discuss the conceptual differences between these approaches through a case study using whole genome, longitudinal DNAm data from adult zebra finches raised in experimentally created small or large broods. Specifically, we (i) identified sex and age-specific CpG sites where DNAm was affected by brood size, and (ii) developed two DNAm-based indexes of the early-life environment (DMSi: based on differentially methylated sites with respect to rearing brood size; SMLmi: supervised machine learning-derived index optimized to predict brood size). We also compared results obtained by either merging or analyzing longitudinal DNAm samples separately and discussed how the permanence or transience of DNAm changes shapes responses to environmental variation through life. Our findings confirm that early-life environment leaves lasting DNAm signatures detectible in adulthood, and this effect is stronger later in life. Importantly, both indexes predicted early-life growth rates, demonstrating that DNAm-based indexes can be leveraged to retroactively quantify aspects of early-life conditions, providing a powerful novel tool in the study of wild populations.

evolutionary biology↗

bioRxiv2025

Long-term effects of early-life adversity on DNA methylation in zebra finches

Early-life experiences can have profound and long-lasting effects on adult phenotype and thereby Darwinian fitness, though the mechanisms driving these effects remain poorly understood. Epigenetic alterations, especially DNA methylation which affects gene expression, potentially mediate developmental condition effects on adult phenotype. We tested for such effects using captive zebra finches that were reared in either small or large broods, a manipulation that is known to have pleiotropic phenotypic effects. Analyzing whole genome DNA methylation patterns in erythrocytes from 50 individuals sampled in adulthood, we found 0.8% of all CpG sites after filtering to be differentially methylated after correction for multiple testing. We identified 149 non-transiently differentially methylated sites (DMSs) where the DNA methylation difference between treatments was larger than 25%. These DMSs were located in 19 autosomal chromosomes, in or near genes involved in critical biological processes such as cell growth, division, and differentiation, regulation of immune response, muscle contraction, and neuronal signaling. These findings suggest that epigenetic modifications such as DNA methylation potentially mediate long-term effects of early-life adversity via differential gene expression, but follow-up studies are needed to identify the extent to which the observed DMSs are functionally related to the previously observed phenotypic effects.

ecology↗

bioRxiv2024

Sex-chromosome-dependent aging in female heterogametic methylomes

Recent research in humans and both model and non-model animals has shown that DNA methylation (DNAm), an epigenetic modification, is one of the mechanisms underlying the aging process. DNAm-based indices predict mortality and provide valuable insights into biological aging mechanisms. Although sex-dependent differences in lifespan are ubiquitous and sex chromosomes are thought to play an important role in sex-specific aging, they have been largely ignored in epigenetic aging studies. We characterized the genome-wide distribution of age-related CpG sites from longitudinal samples in two avian species (zebra finch and jackdaw), including for the first time the avian sex chromosomes (Z and the female-specific, haploid W). In both species, we find a small fraction of the CpG sites to show age-related changes in DNAm with the majority of them being located on the haploid, female-specific W chromosome where DNAm levels predominantly decrease with age. Age-related CpG sites were overrepresented on the zebra finch but underrepresented on the jackdaw Z chromosome. Our results highlight distinct age-related changes in sex chromosome DNAm compared to the rest of the genome in two avian species, suggesting this previously understudied feature of sex chromosomes may be instrumental in sex-dependent aging. Moreover, studying the DNAm of sex chromosomes might be particularly useful in aging research, facilitating the identification of shared (sex-dependent) age-related pathways and processes between phylogenetically diverse organisms.

evolutionary biology↗

bioRxiv2024

Before and after delisting: population dynamics of North Atlantic humpback whales over two decades in the Gulf of Maine

Whales are long-lived, slow-reproducing species that were decimated by commercial whaling. Although some populations seem close to recovery, others are challenging to assess. We studied humpback whales (Megaptera novaeangliae) in the Gulf of Maine, an area of the North Atlantic (NA) with well-documented threats. Long-term studies and mark-recapture data were used to estimate humpback whale apparent survival, abundance and population growth from 2000 through 2019. Estimates were derived from a hierarchical, Bayesian state-space model with sex, age, and random time effects on survival while accounting for individual capture probability. Abundance increased from 744 (95% CI: 726-762) in 2000 to 1,706 (95% CI: 1,639-1,771) in 2019, with 4.6% mean annual growth. However, adult males exhibited higher survival and outnumbered adult females by the end of the study. Over time, fewer calves were observed, calf survival varied and the juvenile class declined. These are rare insights into the dynamics underlying whale abundance trends and they revealed similarities to an endangered species that is declining due to environmental and human impacts. The results inform a listing change under the U.S. Endangered Species Act, a mortality event of unprecedented magnitude off the U.S and humpback whale recovery from historical whaling in the NA.

ecology↗

bioRxiv2023

Universal baleen whale microsatellite panel for individual identification and power to detect parentage

Highly polymorphic single tandem repeat loci (STR, also known as microsatellite loci) remain a familiar, cost efficient class of markers for genetic analyses in ecology, behavior and conservation. We characterize a new universal set of ten STR loci (from 28 potential candidate loci) in seven baleen whale species, which are optimized for PCR amplification in two multiplex reactions along with a Y chromosome marker for sex determination. The optimized, universal set of STR loci provides an ideal starting point for new studies in baleen whales aimed at individual-based and population genetic studies, and facilitates data sharing among research groups. Data from the new STR loci were combined with genotypes from other published STR loci to assess the power to assign parentage (paternity) using exclusion in four species: fin whales, humpback whales, blue whales and bowhead whales. We argue that parentage studies should present a power analysis to demonstrate that the specific data are sufficiently informative to assign parentage with statistical rigor.

genetics↗

bioRxiv2022

Direct estimation of genome mutation rates from pedigrees in free-ranging baleen whales

Current low germline mutation rate () estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to methodological errors and uncertainty. We estimated directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Petos Paradox). We demonstrate the feasibility of estimating from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on .

genetics↗

bioRxiv2022

PHFinder: Assisted detection of point heteroplasmy in Sanger sequencingchromatograms

O_LIHeteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. C_LIO_LIHere, we present PHFinder, a Python-based, open source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whale (Megaptera novaeangliae) tissue samples with known heteroplasmies. C_LIO_LIPHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible, enabling explicit specification of key parameters to infer double peaks (i.e., heteroplasmies). C_LI

bioinformatics↗

bioRxiv2018

Strong and lasting impacts of past global warming on baleen whale and prey abundance

AbstractThe demography of baleen whales and their prey during the past 30 thousand years was assessed to understand the effects of past rapid global warming on marine ecosystems. Mitochondrial and genome-wide DNA sequence variation in eight baleen whale and seven prey species revealed strong, ocean-wide demographic changes that were correlated with changes in global temperatures and regional oceanographic conditions. In the Southern Ocean baleen whale and prey abundance increased exponentially and in apparent synchrony, whereas changes in abundance varied among species in the more heterogeneous North Atlantic Ocean. The estimated changes in whale abundance correlated with increases in the abundance of prey likely driven by reductions in sea-ice cover and an overall increase in primary production. However, the specific regional oceanographic environment, trophic interactions and species ecology also appeared to play an important role. Somewhat surprisingly the abundance of baleen whales and prey continued to increase for several thousand years after global temperatures stabilized. These findings warn of the potential for dramatic, long-term effects of current climate changes on the marine ecosystem.\n\nOne Sentence SummaryThe effects of past global warming on marine ecosystems were drastic, system-wide and long-lasting.

evolutionary biology↗

bioRxiv2018

Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

HighlightsO_LIMitochondrial monophyly is commonly employed to define evolutionary significant units.\nC_LIO_LIMonophyly may be caused by insufficient sampling or a recent common ancestor.\nC_LIO_LIMitogenomic studies are generally based on few samples and prone to sampling issues.\nC_LIO_LIExpanded mitogenome sampling negates previous monophyly in fin whales.\nC_LI\n\nAbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively \"trivial\" aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC=\"FIGDIR/small/488130v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1e38e54org.highwire.dtl.DTLVardef@9533eborg.highwire.dtl.DTLVardef@183b5b5org.highwire.dtl.DTLVardef@eae09_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗