Biology subjects

Lutgen, D.

Publications and source records attributed to Lutgen, D..

5 recordsLinked to original sources

bioRxiv2026

Predominantly genetic determination and stable transmission of DNA methylation in an avian hybrid zone

The reshuffling of divergent genomes upon hybridization may disrupt co-evolved regulatory systems and contribute to epigenetic instability and, ultimately, reproductive isolation. While the genetic consequences of hybridization are well documented, insights into the consequences of hybridization for DNA methylation are currently limited. To obtain insights into the regulation of methylation and its transmission under hybridization, we here investigated genome-wide methylation in a natural hybrid zone of songbirds (wheatears of the Oenanthe hispanica complex) by integrating nearly 100 methylomes with population genomic data. Across 436,762 CpG sites, the population structure of methylation closely mirrors genetic population structure. Methylation quantitative trait locus analyses identify widespread associations of genetic with methylation variation, predominantly in trans, consistent with a regulatory architecture in which the genetic background determines methylation variation. Between species, methylation divergence is limited, with only 0.31% of CpGs differentially methylated. While at the level of chromosomes methylation divergence strongly correlates with genetic differentiation, the extent to which differentially methylated loci coincide with high genetic differentiation differs among chromosomes. A close-to-absent methylation divergence from promoters and coding regions indicates conservation of core regulatory architectures. Finally, CpGs with highest methylation divergence exhibit predominantly additive or dominant transition patterns in hybrids. In contrast, transgressive methylation is exceedingly rare, and we find no evidence for widespread hybrid-induced demethylation. Or results corroborate that DNA methylation primarily reflects underlying genetic variation in birds and remains robust to genome reshuffling, and at least for wheatears suggest a limited role for methylation divergence in hybrid dysfunction and reproductive isolation.

evolutionary biology↗

bioRxiv2022

An annotated chromosome-scale reference genome for Eastern Black-eared Wheatear (Oenanthe melanoleuca)

Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern Black-eared Wheatear (O. melanoleuca). This species is part of the O. hispanica-complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50: 12.6 Mb; scaffold N50: 70 Mb), with 96% of the genome assembled at chromosome level and 96% BUSCO completeness. The nuclear genome was annotated with 18160 protein-coding genes and 30730 mRNAs, and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern Black-eared Wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.

genomics↗

bioRxiv2022

Comparative transcriptomics reveals divergent paths of chitinase evolution underlying dietary convergence in ant-eating mammals

Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, hypertrophied salivary glands producing large amounts of saliva, and powerful claws for ripping open ant and termite nests. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functional CHIA paralogs (CHIA1-4), Asian pangolins (Manis spp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of different CHIA paralogs is observed in insectivorous species. Furthermore, convergently-evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin, CHIA5 is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels for CHIA1 and CHIA2 in the pancreas, and for CHIA3 and CHIA4 in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms within the chitinase acidic gene family underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin-digestive enzyme toolkit in this classic example of convergent evolution.

evolutionary biology↗

bioRxiv2022

Abundant Phenotypic Parallelism, Incomplete Lineage Sorting, and Introgression in Open-Habitat Chats

Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for a role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.

evolutionary biology↗

bioRxiv2020

Linked-read sequencing enables haplotype-resolved resequencing at population scale

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences - including the quantification and dating of admixture, introgression and demographic events, and the inference of selective sweeps - are still limited by the lack of high-quality haplotype information. In this respect, the newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x, and 5x) with high-coverage data (46-68x) of seven bird genomes suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15x coverage, phased haplotypes span about 90% of the genome assembly, with 50 and 90 percent of the phased sequence located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90), respectively. Phasing accuracy reaches beyond 99% starting from 15x coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x coverage), but only marginally improved phasing accuracy. Finally, phasing contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing data at population scale.

evolutionary biology↗