Biology subjects

Grutzner, F.

Publications and source records attributed to Grutzner, F..

13 recordsLinked to original sources

bioRxiv2026

Monotreme transcriptomes shed light on evolution of lactation and placentation

Placentation and lactation are hallmark mammalian reproductive traits and key processes facilitating the transfer of nutrients from the mother to the offspring. The basal mammalian lineage of egg-laying monotremes features a short gestation period supported by a simple placenta and an elongated lactation, similar to marsupials. Eutherian mammals by contrast evolved longer gestation facilitated by extensive placentation and shorter lactation. To understand the gene expression underpinning maternal-foetal nutrient transfer across mammals, we generated transcriptome datasets for the monotreme reproductive tract and mammary gland and compared this to expression in representative species from the other mammalian clades: marsupials (Tammar wallaby) and eutherians (mouse). This revealed extensive overlapping gene expression between the therian placenta and monotreme reproductive tract, including the first observation of retroviral gene expression in the echidna reproductive tract. Interestingly, we discovered that transport and development functions supporting foetal growth are expressed in echidna mammary gland and eutherian placenta, likely a signature of the shift from prolonged lactation to longer placentation. Together, this demonstrates that diverse modes of maternal-foetal nutrient transfer are underpinned by similar gene networks across mammals.

evolutionary biology↗

bioRxiv2026

Monotremes provide novel insights into evolution of the DMRT gene family in vertebrates

Doublesex and mab-3 related (DMRT) genes encode a family of transcription factors central to sexual development across metazoa. DMRT genes are characterised by a highly conserved DNA binding domain (DM) while flanking regions may vary between species. Gene duplication and loss has shaped the diversity of the DMRT genes with several unresolved questions about their evolution. The most well characterised and conserved DMRT gene, DMRT1, functions as a sexual regulator universally in metazoans. In chicken, DMRT1 is located on the Z chromosome and acts as a dosage dependent primary sex determination gene. In therian mammals DMRT1 is autosomal, however, two copies are required for male development. Interestingly in the basal lineage of egg-laying mammals (monotremes), DMRT1 is localised on the X specific part of one of the X chromosomes. This provided the first evidence of a sex chromosome system with homology to the avian Z chromosome and raises questions about the function and evolution of DMRT1 in egg-laying mammals. To gain insight into the evolution of mammalian DMRT genes we performed sequence and expression analysis of monotreme DMRT genes and comparative analysis with other vertebrates. In monotremes, we identified DMRT genes 1-7, and show that DMRT8 is absent, suggesting that DMRT8 evolved in therian mammals after the divergence of monotremes. Sequence and expression analysis revealed multiple monotreme specific DMRT1 isoforms with additional protein-coding exons. The independent evolution of monotreme specific changes in DMRT1 may be the first indication of functional or regulatory differences in monotreme DMRT1. Article SummaryGenes in the Doublesex and mab-3 related (DMRT) family play important roles in sexual development across animals, but a comprehensive analysis of these transcription factors is lacking in the most basal mammalian lineage of monotremes. This comparative analysis of DMRT genes in monotremes and other vertebrates shows the conservation of DMRT genes 1- 7 but found no evidence of DMRT8 in monotremes or marsupial species, suggesting that this gene evolved in eutherians after the divergence of marsupials. The discovery of several monotreme specific isoforms and novel exons of the X linked DMRT1 reveals unique evolutionary changes in monotreme DMRT1.

genetics↗

bioRxiv2026

Undergraduate student practicals generate high-quality data for microbiome research

The increasing prominence and accessibility of microbiomics has provided an opportunity for authentic research experiences in the undergraduate practical classroom. In recent years, this approach has contributed to published research projects. However, there is little information evaluating the quality of student-generated data compared to that of trained researchers. To investigate this, we designed an undergraduate practical component in which 37 final-year genetics students generated microbial profiles of 22 echidna scats using matched samples that were also profiled by an experienced researcher. DNA yield, 16S PCR success, sequencing library size and microbial diversity were compared between the groups in order to assess both the ability and accuracy of students in characterising faecal microbiota. Our research revealed that students were able to produce research-grade microbiome data comparable to a postgraduate researcher. Importantly, we found that students did not introduce contamination at a higher rate than the trained researcher. These findings reinforce that the undergraduate classroom is a valuable approach for microbiome research in addition to its benefits for student engagement and experience. The design and successful implementation of these practicals provide a template for a variety of research-led microbiome teaching.

scientific communication and education↗

bioRxiv2025

Large-Scale Restructuring of the Caspase-1 Gene Cluster Region in Mammals

The inflammatory response is an important component of the host immune defence mechanism against pathogens. Activation of the NLRP3 inflammasome has been shown to have a wide range of triggers including fungal, bacterial and viral components, cellular stress and environmental irritants. The NLRP3 inflammasome has been well characterised in mouse and humans but limited information is available from other mammalian species. In order to gain a better understanding of the evolution of genes involved in the NLRP3 inflammasome pathway, we examined them in mammalian species representing the three major groups (eutheria, metatheria and prototheria) and in chicken as an outgroup. Our results show that the inflammasome pathway machinery is generally well conserved though chicken appears to lack several key components and monotremes have a duplication of Syk. Analysis of the proinflammatory caspase cluster and neighboring genes revealed massive reorganisation as well as the previously described multiple duplications that occurred during mammalian evolution. Our data suggest that Caspase-1 moved to a new chromosomal region in early mammalian evolution. This was followed by expansion of the cluster and accumulation of additional genes regulating inflammatory responses such as Card16, Card17, Card18 and the Birc genes. The expansion of key gene families flanking Caspase-1 may have led to an expansion of inflammasome pathways and a more regulated immune system in humans through the CARD genes.

genetics↗

bioRxiv2025

Evolution and expression of Glial Cells Missing (GCM1 and GCM2) in monotremes suggests an ancient role in reproduction and placentation

The Glial Cells Missing (GCM) genes were first discovered in Drosophila and encode transcription factors important for gliogenesis. In placental mammals, GCM1 regulates several genes that are important for early placenta development, while its paralog GCM2 is important for parathyroid gland development. The egg-laying monotremes, which represent the most diverged extant mammalian lineage, undergo a short period of intrauterine development and form a simple placenta. To gain more insight into the evolution of GCM genes we analysed the sequence, expression, and genomic localization of GCM1 and GCM2 genes in the platypus and echidna. We found that the chromosomal localisation of GCM1 changed after the divergence of therian mammals, coinciding with the evolution of a complex placenta. Expression analysis revealed the presence of GCM transcripts in male and female monotreme gonads, as well as expression of GCM1 in the female reproductive tract. GCM binding sites in target genes associated with placental development in therian mammals were also present in the monotremes and the chicken. Together, this suggests that the role of GCM1 in the placenta emerged early in mammalian evolution.

evolutionary biology↗

bioRxiv2025

Structural evolution of the estrogen receptor regulatory domain

Estrogen receptors (ERs) , {beta} and {gamma} are ligand-dependent transcription factors that regulate vertebrate reproduction, cell survival and other physiological processes. Here, we report an integrative analysis of mammalian and teleost receptors, including the first structure of an ER{gamma} ligand binding domain (LBD), showing that structural divergence acquired during evolution is accommodated by different strategies within functional regions to preserve intrinsic regulatory mechanisms. Supervised-learning and comparative Markov modelling uncover highly constrained network structures essential for allostery and protein folding, revealing a fundamental regulatory architecture and source of selective pressure in ER+ breast cancer and reproductive disorders. Finally, cross-referencing molecular constraints to genome sequencing reveal evolutionary origins underlying natural genetic variation in humans and widespread disruption of constraints. This work provides structural insights into the conservation of gene regulation by essential transcription factors and has implications for precision medicine.

biochemistry↗

bioRxiv2024

Evolution of the Jawed Vertebrate (Gnathostomata) Stomach through Gene Repertoire Loss: Findings from Agastric Species

Independent and convergent gene loss, such as the loss of gastric enzymes (Pga, Pgc) and proton pump subunits (Atp4a, Atp4b) in monotremes and polyphyletic teleost species have been associated with the agastric phenotype - stomachs lacking gross morphology, gastric glands and acid secretion. The loss of the key gastric hormone gastrin (Gast) has been observed in monotremes, but not corroborated in agastric teleosts. Furthermore, it is unclear how this loss affects the evolution and selection of the native receptor (Cckbr), gastrin releasing peptide (Grp) and receptor (Grpr), or if there are further gene losses associated with the agastric phenotype. We investigated the evolution, selection and conservation of the gastrin physiological pathway and novel gastric genes in a broad range of gastric and agastric vertebrates. Our analyses showed no correlation between the losses of Gast and Grpr with the agastric phenotype in vertebrate lineages. We identified genes implicated in gastric mucosal maintenance and development (Gkn1, Gkn2, Tff1, Tff2, Vsig1, Anxa10) that are lost in agastric species except the echidna, which retained some of them (Gkn1, Tff2, Vsig1). Our findings demonstrate a convergent repertoire of gastric genes lost in agastric species, partial retention of gastric functionality in the echidna, and the diversified roles of gastrin pathway constituents in vertebrate lineages.

evolutionary biology↗

bioRxiv2024

Pseudogenisation of NK3 Homeobox 2 (Nkx3.2) in Monotremes Provides Insight into Unique Gastric Anatomy and Physiology

Development of the vertebrate antral stomach and pyloric sphincter (antropyloric region) - involved in enzymatic breakdown and thoroughfare of food - is underpinned by a highly conserved developmental pathway involving the hedgehog, bone morphogenetic protein (BMP) and Wingless/Int-1 (Wnt) protein families. Monotremes are a unique lineage where acid-based digestion has been lost, and this correlates with a lack of genes for gastric acid and enzymes in the genomes of the platypus (Ornithorhynchus anatinus) and short-beaked echidna (Tachyglossus aculeatus). Furthermore, these species feature unique gastric phenotypes, both with truncated and aglandular antral stomachs and the platypus with no pylorus. Here, we explore the genetic underpinning of monotreme gastric phenotypes, investigating genes important in antropyloric development using the newest monotreme genome sequences (mOrnAna1.pri.v4 and mTacAcu1) together with RNA-seq data. We found that the pathway is generally conserved but, NK3 homeobox 2 (Nkx3.2) was pseudogenised in both platypus and echidna. We speculate that pyloric-like restriction in the echidna may correlate with independent evolution of Grem1 and Bmp4 sequences, and that the convergent loss of gastric acid and stomach size genotypes and phenotypes in teleost and monotreme lineages may be a result of eco-evolutionary dynamics. These findings reflect the effects of gene loss on phenotypic evolution and further elucidate the genetic control of monotreme stomach anatomy and physiology.

evolutionary biology↗

bioRxiv2024

Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus)

Monotreme and marsupial early development is characterised by a short gestation, the birth of the young at an early stage of development, and a long lactation in the pouch or pseudo-pouch. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich world. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiome during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Swab samples were obtained from wild and captive echidna pseudo-pouches outside of breeding season, during courtship and breeding, and during lactation. 16S rRNA gene metabarcoding revealed that the pseudo-pouch microbiome undergoes dramatic changes during lactation, with a reduction in bacterial taxa that may be pathogenic. These changes were not observed in samples taken outside of breeding season or during courtship and mating. This showed that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. This study pioneers pouch microbiome research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.

genomics↗

bioRxiv2023

Bushfire alters the gut microbiome in endangered Kangaroo Island echidnas (Tachyglossus aculeatus multiaculeatus)

Kangaroo Island experienced extensive bushfires in December 2019 and January 2020, affecting almost half of the island. This impacted several threatened species including the Kangaroo Island echidnas (Tachyglossus aculeatus multiaculeatus). Echidnas can often survive fires, however, changes in soil chemistry and food availability raises questions about the impact on echidna gut health and foraging behaviours. Due to local participation in the citizen science project, EchidnaCSI, echidna scats were collected before and after the fires to directly assess how fire affects their gut microbiomes. Metabarcoding of scat microbiota (n = 13) revealed substantial changes in bacterial composition of echidna faeces post-bushfire when compared to samples collected prior to bushfires. Before the fires, echidna gut microbiomes were more variable and contained mostly soil-associated bacteria, whereas post-fire samples shifted to uniform bacterial communities consisting of lactic acid and gut commensal bacteria. Interestingly, changes were observed in scats collected in both burnt and unburnt regions of the island, suggesting echidnas are foraging between these areas. This is the first study to document changes in gut microbiome of any mammal following bushfires. More work is needed to investigate if the gut bacterial communities continue to change as areas recover from fires.

genomics↗

bioRxiv2023

Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation.

Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.

evolutionary biology↗

bioRxiv2021

Microchromosomes are building blocks of bird, reptile and mammal chromosomes

Microchromosomes, once considered unimportant shreds of the chicken genome, are gene rich elements with a high GC content and few transposable elements. Their origin has been debated for decades. We used cytological and whole genome sequence comparisons, and chromosome conformation capture, to trace their origin and fate in genomes of reptiles, birds and mammals. We find that microchromosomes as well as macrochromosomes are highly conserved across birds, and share synteny with single small chromosomes of the chordate amphioxus, attesting to their origin as elements of an ancient animal genome. Turtles and squamates (snakes and lizards) share different subsets of ancestral microchromosomes, having independently lost microchromosomes by fusion with other microchromosomes or macrochromosomes. Patterns of fusions were quite different in different lineages. Cytological observations show that microchromosomes in all lineages are spatially separated into a central compartment at interphase and during mitosis and meiosis. This reflects higher interaction between microchromosomes than with macrochromosomes, as observed by chromosome conformation capture, and suggests some functional coherence. In highly rearranged genomes fused microchromosomes retain most ancestral characteristics, but these may erode over evolutionary time; surprisingly de novo microchromosomes have rapidly adopted high interaction. Some chromosomes of early branching monotreme mammals align to several bird microchromosomes, suggesting multiple microchromosome fusions in a mammalian ancestor. Subsequently multiple rearrangements fueled the extraordinary karyotypic diversity of therian mammals. Thus microchromosomes, far from being aberrant genetic elements, represent fundamental building blocks of amniote chromosomes, and it is mammals, rather than reptiles, that are atypical. Significance StatementGenomes of birds and reptiles, but not mammals, consist of a few large chromosomes and many tiny microchromosomes. Once considered unimportant shreds of the genome, microchromosomes are gene rich and highly conserved among bird and reptiles, and share homology with one or more of the tiny chromosomes of an invertebrate that diverged from the vertebrate lineage 684 million years ago. Microchromosomes interact strongly and crowd together at the centre of cells, suggesting functional coherence. Many microchromosomes have been lost independently in turtles, snakes and lizards as they have fused with each other, or with larger chromosomes. In mammals they have completely disappeared, yet some chromosomes of the basal platypus line up with several microchromosomes, suggesting that they are the building blocks of the atypically variable chromosomes of mammals.

genomics↗

bioRxiv2017

Insights into platypus population structure and history from whole-genome sequencing

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly-improved reference genome, we called over 6.7M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative amongst other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0x10-9/bp/generation (95% CI 4.1x10-9 - 1.2x10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

genomics↗