Biology subjects

Catalan, A.

Publications and source records attributed to Catalan, A..

8 recordsLinked to original sources

bioRxiv2025

Impact of Partition Models on Phylogenetic Inference and Divergence Times of Lampyridae from Mitochondrial Genomes

Mitochondrial genomes are frequently used for phylogenetic inference due to their availability and cost-efficient sequencing. In most mitogenomic phylogenetic analyses, only the two ribosomal RNA and 13 protein coding genes are used. For such multi-locus datasets it has long been established that appropriate data partition models, e.g., partitioning by gene type and/or codon position, are necessary for robust phylogenetic inference. While most studies focused on the impact of partition models on the tree topology, little is known about the impact on divergence time estimation. Furthermore, although modeling among site rate variation within a partition is common practice, the extent of substitution rate variation among partitions is less explored. Here we study the impact of four partition model strategies: (i) no subdivision of the data (uniform), (ii) partitioning by gene, (iii) partitioning by codon position, and (iv) partitioning by both gene and codon position (combined). We explore the impact of partition models on divergence time estimation in fireflies (Coleoptera: Lampyridae). To this end, we sequenced mitochondrial genomes from 22 firefly species from Europe and Central America and combined these with 82 published mitochondrial genomes. Our results represent the most comprehensive time-calibrated phylogeny of fireflies to day. While the partition models had an impact on the inferred tree topology, the divergence times were almost not affected. Furthermore, we observed up to 3-fold substitution rate variation across genes and additionally more than to 10-fold substitution rate variation across codon positions. Our study gives insights into best practices of performing partitioned-data time-calibrated phylogenetic inference from mitochondrial genomes and multi-locus datasets in general.

evolutionary biology↗

bioRxiv2025

Filling the gap in the Neotropics: new firefly species provide insights into Central American biodiversity

Tropical ecosystems, particularly in the Neotropics, remain vastly understudied, especially regarding the biodiversity of many taxa such as fireflies. This study investigates the biodiversity and phylogenetic relationships of fireflies in Guatemala, focusing on the genera Photinus, Photuris, and Bicellonycha. Using genetic barcoding we generate time-calibrated phylogenetic trees, revealing deep divergent times between Guatemalan and North American fireflies and potentially multiple colonialization events. Using morphometric information, taxonomic keys and species delimitations models (mPTP) we identified four new Photinus species: P. hunahpu, P. helodermensis, P. schusteri, and P. semetabajense. This work highlights the significant firefly biodiversity in Nuclear Central America and the potential for future species discovery. Biodiversity research is necessary for conservation efforts of key ecosystems and will broaden our understanding of general evolutionary processes.

evolutionary biology↗

bioRxiv2024

Sex-biased migration and demographic history of the big European firefly Lampyris noctiluca

Differential dispersion between the sexes can impact population structure and connectivity between populations, which in turn, can have an effect on the evolvability capability of a species. Here we explored the demographic history of the big European firefly, Lampyris noctiluca, which exhibits female neoteny. L. noctiluca distribution extends throughout Europe, but nothing is known on how its colonization processes. To investigate this, we produced the first Lampyris genome (653Mb), including an IsoSeq annotation and the identification of the X chromosome. We collected 115 individuals from six populations of L. noctiluca (Finland to Italy) and generated whole genome re-sequencing for each individual. We inferred several population expansions and bottlenecks throughout the Pleistocene that correlate with glaciation events. Surprisingly, we uncovered strong population structure and low gene-flow. We reject a stepwise, south to north, colonization history scenario and instead uncovered a complex demographic history with a putative eastern European origin. Analyzing the evolutionary history of the mitochondrial genome as well as X-linked and autosomal loci, we found evidence of a maternal colonialization of Germany, putatively from a western European population, followed by male-only migration from south of the Alps (Italy). Overall, investigating the demographic history and colonization patterns of a species should form part of an integrative approach of biodiversity research. Our results provide evidence of sex-biased migration which is important to consider for demographic, biogeographic and species delimitation studies.

evolutionary biology↗

bioRxiv2021

A Time-calibrated Firefly (Coleoptera: Lampyridae) Phylogeny: Using Genomic Data for Divergence Time Estimation

Fireflies (Coleoptera: Lampyridae) consist of over 2,000 described extant species. A well-resolved phylogeny of fireflies is important for the study of their population genetics, bioluminescence, evolution, and conservation. We used a recently published anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) and state-of-the-art statistical methods (the fossilized birth-death-range process implemented in a Bayesian framework) to estimate a time-calibrated phylogeny of Lampyridae. Unfortunately, estimating calibrated phylogenies using AHE and the latest and most robust time-calibration strategies is not possible because of computational constraints. As a solution, we subset the full dataset by applying three different strategies: (i) using the most complete loci, (ii) using the most homogeneous loci, and (iii) using the loci with the highest accuracy to infer the well established Photinus clade. The estimated topology using the three data subsets agreed on almost all major clades and only showed minor discordance within less supported nodes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust as long as the topology inference is robust and any well selected data subset suffices. Additionally, we observed an un-expected amount of gene tree discordance between the 436 AHE loci. Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci which is likely to bias phylogenetic inferences. We performed a simulation study to explore the impact of (a) incomplete lineage sorting, (b) uniformly distributed and systematic missing data, and (c) systematic bias in the position of highly variable and conserved sites. For our simulated data, we observed less gene tree variation which shows that the empirically observed amount of gene tree discordance for the AHE dataset is unexpected and needs further investigation.

evolutionary biology↗

bioRxiv2021

Epigenetic mechanisms of partial dosage compensation in an avian, female heterogametic system

The evolution of genetic sex determination is often accompanied by degradation of one of the proto sex chromosomes. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf ZWf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5<Zf:ZZm<1). The underlying mechanism remains largely elusive. Here, we quantified gene expression for a total of 15 male and female Eurasian crows (Corvus (corone) spp.) raised under common garden conditions. In addition, we characterized aspects of the regulatory landscape quantifying genome-wide ATAC-seq and 5mC methylation profiles. Partial dosage compensation was explained by female upregulation of Z-linked genes accompanied by increased chromatin accessibility on the female Z chromosome. 5mC methylation was strongly reduced in open chromatin-regions and GC islands and showed chromosome-, but no sex-specific variation. With the exception of the pseudo-autosomal region (PAR), female upregulation of gene expression was evenly spread across the Z chromosome without evidence for regional epigenetic regulation, as has for example been suggested for the male hypermethylated region (MHM) in chicken. Our results support the hypothesis that partial dosage compensation in female heterogametic systems is subject to chromosome-wide, epigenetic control mediated by differential chromatin accessibility between the sexes.

genomics↗

bioRxiv2019

On the inference of a southern origin of the North American firefly Photinus pyralis

The firefly Photinus pyralis inhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Its ample geographic distribution makes this species an ideal system for the study of local adaptation and demographic inference of wild populations. Therefore, in this study we modelled and inferred different demographic scenarios for North American populations of P. pyralis, collected from Texas to New Jersey. To do this, we used a combination of ABC techniques (for multi-population/colonization analyses), and likelihood inference (dadi) for single-population demographic inference, which proved useful with our RAD data.We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. Our results suggest that P. pyralis originated in Central- or South America, followed by migration events that populated northern latitudes. Finally, modelling the demographic history of North American P. pyralis serves as a null model of nucleotide diversity patterns, which will inform future studies of adaptation, not only in P. pyralis, but also in other North American taxa.

evolutionary biology↗

bioRxiv2019

The population genomics of structural variation in a songbird genus

Structural variation (SV) accounts for a substantial part of genetic mutations segregating across eukaryotic genomes with important medical and evolutionary implications. Here, we characterized SV across evolutionary time scales in the songbird genus Corvus using de novo assembly and read mapping approaches. Combining information from short-read (N = 127) and long-read re-sequencing data (N = 31) as well as from optical maps (N = 16) revealed a total of 201,738 insertions, deletions and inversions. Population genetic analysis of SV in the Eurasian crow speciation model revealed an evolutionary young (~530,000 years) cis-acting 2.25-kb retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth of SV segregating in natural populations and demonstrate its evolutionary significance.

genomics↗

bioRxiv2018

Drift and directional selection are the evolutionary forces driving gene expression divergence in eye and brain tissue of Heliconius butterflies

Investigating gene expression evolution over micro- and macroevolutionary timescales will expand our understanding of the role of gene expression in adaptation and speciation. In this study, we characterized which evolutionary forces are acting on gene expression levels in eye and brain tissue of five Heliconius butterflies with divergence times of ~5-12 MYA. We developed and applied Brownian motion and Ornstein-Uhlenbeck models to identify genes whose expression levels are evolving through drift, stabilizing selection, or a lineage-specific shift. We find that 81% of the genes evolve under genetic drift. When testing for branch-specific shifts in gene expression, we detected 368 (16%) shift events. Genes showing a shift towards up-regulation have significantly lower gene expression variance than those genes showing a shift leading towards down-regulation. We hypothesize that directional selection is acting in shifts causing up-regulation, since transcription is costly. We further uncover through simulations that parameter estimation of Ornstein-Uhlenbeck models is biased when using small phylogenies and only becomes reliable with phylogenies having at least 50 taxa. Therefore, we developed a new statistical test based on Brownian motion to identify highly conserved genes (i.e., evolving under strong stabilizing selection), which comprised 3% of the orthoclusters. In conclusion, we found that drift is the dominant evolutionary force driving gene expression evolution in eye and brain tissue in Heliconius. Nevertheless, the higher proportion of genes evolving under directional than under stabilizing selection might reflect species-specific selective pressures on vision and brain necessary to fulfill species-specific requirements.

evolutionary biology↗