Biology subjects

Matschiner, M.

Publications and source records attributed to Matschiner, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Patterns and drivers of cranial evolution in rhinos (Rhinocerotoidea; Perissodactyla): allometry, phylogeny and tempo of evolution

Despite their currently scarce taxonomic diversity, rhinocerotoids were among the most evolutionarily successful clades of large herbivorous mammals throughout the Caenozoic. Within an array of morphological adaptations, the cranial horn represents the clades most remarkable and name-giving feature, imposing significant morpho-functional demands on the skull. In this paper, patterns and drivers of the rhinos cranial evolution were investigated for the first time by compiling a three-dimensional geometric morphometric dataset of living and extinct species. Multiple aspects of morphological evolution were explored using phylogenetic comparative methods, including craniofacial evolutionary allometry (CREA - tendency of larger species to have longer faces), phylogenetic constraints, and tempo of evolution. Cranial shape variation linked to horn presence and size evolved under a phylogenetically constrained framework, with a notable transition from hornless to horned species. Rhinos significantly deviated from CREA, likely due to diversity of cranial forms and proportions that evolved independently across the clade in response to varying horn morphologies and dietary habits. Hornless and horned rhinos exhibited similar rates of cranial evolution, and shape variation was obtained through multiple episodes of accelerated evolution. This highlights the role of morphological innovations and Caenozoic global cooling events in the emergence of phenotypic diversity.

evolutionary biology↗

bioRxiv2026

Convergent genome streamlining accompanies independent miniaturization in the world's smallest fishes

Miniaturization, the reduction of adult body size to an extreme degree, has evolved repeatedly across vertebrates. Yet its genomic underpinnings remain poorly understood. Cypriniformes, the most species-rich order of freshwater fishes, contains multiple miniaturized lineages that have evolved contrasting developmental processes. Proportioned dwarfs are tiny-bodied but otherwise morphologically similar to larger relatives, while progenetic miniatures exhibit developmental truncation thus retaining larval-like anatomical features into adulthood. Using a new time-calibrated phylogeny of 309 cypriniform species and comparative genomic analyses of 33 high-quality genome assemblies, we investigated the evolutionary history and genomic correlates of miniaturization across this order. Ancestral state reconstruction revealed multiple independent origins of both miniature types, with transitions predominantly unidirectional and non-randomly distributed across the phylogeny. The origins of the two types of miniatures differed in their timing. Progenetic miniatures arose predominantly as early as the Eocene while proportioned dwarfs arose mainly within the Miocene period. Genome size variation across Cypriniformes has been overwhelmingly driven by polyploidy. However, progenetic miniatures but not proportioned dwarfs showed consistent genome size reduction. Comparative genomic analyses revealed that all three independently-evolved progenetic miniature lineages share convergent signatures of repeat loss alongside genome-wide intron shortening, patterns absent in proportioned dwarfs. Our study provides the broadest evidence to date that progenetic miniaturization, despite independent origins, is underpinned by predictable structural genomic changes, revealing a fundamental link between developmental truncation and genome architecture in vertebrates.

evolutionary biology↗

bioRxiv2026

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

Cypriniformes, the most species-rich order of freshwater fishes ([~]5,000 species), represents a key lineage for understanding vertebrate diversification in freshwater ecosystems. This clade includes several highly miniaturized and understudied lineages whose phylogenetic placements have long remained contentious. Here, we present the first phylogenomic analysis of Cypriniformes with complete family-level representation and broad genus-level coverage, encompassing 316 species comprising approximately 30% of all described genera. Our dataset integrates 257 newly assembled genomes with publicly available resources and analyzes multiple sets of genome-wide markers using both concatenation-based and coalescent-aware approaches. The general concordance among analytical frameworks indicates that the backbone topology of Cypriniformes is now established, allowing clear identification between well-supported clades and regions of persistent conflict. Our results strengthen the evolutionary relationships of several miniaturized lineages, while identifying recalcitrant relationships shaped by both biological processes and model artefacts that can yield superficially similar patterns of phylogenetic conflict. Our study substantially expands genomic representation and establishes a phylogenomic foundation for future comparative, developmental, and evolutionary research in this freshwater radiation.

evolutionary biology↗

bioRxiv2025

Museomics reveals the phylogenetic position of an enigmatic vertebrate family (Lophiiformes: Lophichthyidae)

Lophichthys boschmai, the only member of the family Lophichthyidae, is an elusive lophiiform fish whose phylogenetic associations are debated. This family is among the last three vertebrate families lacking DNA sequence data, primarily due to the species rarity, lack of fresh material and challenges associated with sequencing formalin-treated museum specimens. In this study, we provide mitochondrial and nuclear DNA sequences obtained from two museum specimens of Lophichthys boschmai. Employing ancient DNA techniques, we successfully extracted and analyzed the degraded and fragmented DNA. Our findings, derived from both mitochondrial genomes and nuclear ultra-conserved elements (UCE), reveal the Lophichthyidae as sister lineage to Tathicarpidae within the Antennarioidei. This study showcases the use of whole-genome "shotgun" sequencing data from formalin-fixed museum specimens in the context of an available UCE dataset. Given the enhanced versatility in data reusability this approach offers, we suggest it should be a favored approach when studying rare specimens.

zoology↗

bioRxiv2024

Museomics analyses inform about Channichthys icefish species diversity

The rapid diversification of notothenioid fishes in the waters surrounding the Antarctic continent is a prime example of the process of adaptive radiation. Within around 10 million years, Antarctic notothenioids have diversified into over 100 species with a broad range of lifestyles and ecological adaptations. However, the exact number of species within this radiation has long been unclear. Particularly challenging is the taxonomy of the genus Channichthys, for which between one and nine species have been recognized by different authors. The putative species from this genus are known from a limited number of representative specimens, of which most were sampled decades ago. Here, we investigated the mitochondrial genomes of museum specimens representing the four recently recognized species Unicorn Icefish (C. rhinoceratus), Red Icefish (C. rugosus), Sailfish Pike (C. velifer), and Charcoal Icefish (C. panticapaei), complemented by morphological analyses. All analyzed specimens were collected in the 1960s and 1970s and fixed in formaldehyde, and their DNA has thus been heavily degraded. Applying ancient-DNA protocols for DNA extraction and single-stranded library preparation, we were nevertheless able to obtain sufficient endogenous DNA to reconstruct the mitochondrial genomes of one specimen of each species. These mitochondrial genome sequences were nearly identical for the three specimens assigned to Unicorn Icefish, Red Icefish, and Sailfish Pike, while greater mitochondrial divergence was observed for the Charcoal Icefish specimens. We discuss possible explanations of the contrast between these molecular results and the recognizable morphological variation found among the four species, and recommend that at least the Charcoal Icefish be included the list of valid icefish and notothenioid species.

evolutionary biology↗

bioRxiv2024

Hemoglobin gene repertoire in teleost and cichlid fishes shaped by gene duplications and genome rearrangements

Hemoglobin is a crucial element of the oxygen transport system in vertebrates. It exhibits remarkable gene diversity across teleost fishes, reflecting their evolutionary adaptations for thriving in various aquatic environments. In this study, we present the dynamic evolution of hemoglobin subunit genes based on a comparison of high quality long-read genome assemblies of 24 vertebrate species, including 16 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain between five (fugu) and 43 (salmon) hemoglobin genes, representing the largest hemoglobin gene repertoire among vertebrates. We find evidence that the ancestor of teleosts had at least four Hb and three or four Hb{beta} subunit genes, and that the current gene diversity emerged during subsequent teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organization of hemoglobin clusters, revealing the parallel origin of multiple clusters in tetrapods and in teleosts. Importantly, we show that the presence of paralogous rhbdf1 genes flanking both teleost hemoglobin clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environments has been shown to play roles in species diversification. Our analysis of six cichlid genomes, including the Pungu maclareni from crater lake Barombi Mbo, for which we sequenced the representative genome, reveals 18 to 31 copies of the Hb genes, and elevated rates of non- synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how hemoglobin genes contribute to the adaptive and diversification potential of teleosts.

evolutionary biology↗

bioRxiv2024

First chromosome-level genome assembly of a ribbon worm from the Hoplonemertea clade, Emplectonema gracile, and its structural annotation

Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome of a Hoplonemertea species is crucial. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well-suited for laboratory experimentation. The genome is 157.9 Mbp in span. Hi-C scaffolding yielded 15 putative chromosomes with a scaffold N50 of 10.0 Mbp and a BUSCO completeness score of 95.3%. Structural annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50. These data will be highly useful for future investigations towards a better understanding of the evolution, development, morphology, and toxicology of Nemertea. SignificanceThe genome of Emplectonema gracile is highly contiguous, well annotated, and shorter than those of the other two ribbon worm species sequenced to date. This genome is a valuable resource for studies on molecular ecology, venom evolution, and regeneration in marine invertebrates.

genomics↗

bioRxiv2023

Among-species rate variation produces false signals of introgression

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression - the exchange of genetic material through hybridization and backcrossing - are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression" - referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome, and implemented this test in the program Dsuite.

evolutionary biology↗

bioRxiv2023

Genomic repeat landscape evolution across the teleost fish lineages

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity have coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we found that TE content, the degree of parental care and short tandem repeat (STR) content contributed to genome size variability. In contrast to TEs, STR content showed a negative relationship with genome size. STR content did not correlate with TE content, which implies independent evolutionary paths. Last, marine and freshwater fish have large differences in STR content. The most extreme propagation was found in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.

evolutionary biology↗

bioRxiv2022

Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)

Currents are unique drivers of oceanic phylogeography and so determine the distribution of marine coastal species, along with past glaciations and sea level changes. Here, we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Multiple west to east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present since [~]208 Kya (thousand years ago). Mediterranean populations were founded [~]53 Kya while extant distributions along western and eastern Atlantic shores coincide with the end of the Last Glacial Maximum ([~]20 Kya). The recent colonization and 5-to 7-fold lower genomic diversity of Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

evolutionary biology↗

bioRxiv2022

The mitochondrial genome of the red icefish (Channichthys rugosus) casts doubt on its species status

Antarctic notothenioid fishes are recognized as one of the rare examples of adaptive radiation in the marine system. Withstanding the freezing temperatures of Antarctic waters, these fishes have diversified into over 100 species within no more than 10-20 million years. However, the exact species richness of the radiation remains contested. In the genus Channichthys, between one and nine species are recognized by different authors. To resolve the number of Channichthys species, genetic information would be highly valuable; however, so far, only sequences of a single species, C. rhinoceratus, are available. Here, we present the nearly complete sequence of the mitochondrial genome of C. rugosus, obtained from a formalin-fixed museum specimen sampled in 1974. This sequence differs from the mitochondrial genome of C. rhinoceratus in no more than 27 positions, suggesting that the two species may be synonymous.

zoology↗

bioRxiv2022

Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use long-read sequencing data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Finally, we show that both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.

genomics↗

bioRxiv2022

The history and organization of the Workshop on Population and Speciation Genomics

With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks. Here, we describe our experience with the organization of a course in one of the longest-running extended bioinformatics series of work-shops, the Evomics Workshop on Population and Speciation Genomics that takes place biennially in the UNESCO world heritage town of [C]esky Krumlov, Czech Republic. We list the key ingredients that make this workshop successful in our view, and describe the routine for workshop organization that we have optimized over the years. We report the results of a survey conducted among past workshop participants that quantifies measures of effective teaching and provide examples of how the workshop setting has led to the cross-fertilisation of ideas and ultimately scientific progress. We expect that our account may be useful for other groups aiming to set up their own extended bioinformatics courses.

scientific communication and education↗

bioRxiv2021

Efficient ancestry and mutation simulation with msprime 1.0

Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and tskit library. We summarise msprimes many features, and show that its performance is excellent, often many times faster and more memory efficient than specialised alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.

genetics↗

bioRxiv2021

Origin and fate of supergenes in Atlantic cod

Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here, we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate that chromosomal inversions underlie all four supergenes, and show that they originated at different times between 0.40 and 1.66 million years ago. While we found no evidence for a role of introgression in the origin of the four supergenes, we reveal gene flux between supergene haplotypes with derived and ancestral arrangements, occurring both through gene conversion and double crossover. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the purging of introduced genetic variation.

evolutionary biology↗

bioRxiv2020

Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes

Sex is a fundamental trait that is determined, depending on the species, by different environmental and/or genetic factors, including various types of sex chromosomes. While the functioning and emergence of sex chromosomes have been explored in species scattered across the eukaryotic tree of life, little is known about tempo and mode of sex chromosome evolution in closely related species. Here, we examine the dynamics of sex chromosome evolution in an archetypical example of adaptive radiation, the cichlid fishes of African Lake Tanganyika. Through inspection of male and female genomes from 244 cichlid taxa and the analysis of transcriptomes from 66 taxa, we identify signatures of sex chromosomes in 79 taxa, involving 12 different linkage groups. We estimate that Tanganyikan cichlids have the highest rates of sex chromosome turnover and heterogamety transitions known to date. We further show that the recruitment of chromosomes as sex chromosomes is not at random and that some chromosomes have convergently emerged as sex chromosomes in cichlids, which provides empirical support to the "limited options" hypothesis of sex chromosome evolution.

evolutionary biology↗

bioRxiv2019

Genome sequencing of the nine-spined stickleback (Pungitius pungitius) provides insights into chromosome evolution.

The Gasterostidae fish family hosts several species that are important models for eco-evolutionary, genetic and genomic research. In particular, a wealth of genetic and genomic data have been generated for the three-spined stickleback (Gasterosteus aculeatus), the ecologys supermodel, while the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2 Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and ca. 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromeric-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years (MYA) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 MYA. Compared to the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.

genomics↗

bioRxiv2019

Stable species boundaries despite ten million years of hybridization in tropical eels

Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.

evolutionary biology↗