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Hartley GA, Frankenberg SR, Robinson NM, MacDonald AJ, Hamede RK, Burridge CP, Jones ME, Faulkner T, Shute H, Rose K, Brewster R, O'Neill RJ, Renfree MB, Pask AJ, Feigin CY. Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution. Commun Biol 2024; 7:636. [PMID: 38796620 PMCID: PMC11128018 DOI: 10.1038/s42003-024-06251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/26/2024] [Indexed: 05/28/2024] Open
Abstract
The eastern quoll (Dasyurus viverrinus) is an endangered marsupial native to Australia. Since the extirpation of its mainland populations in the 20th century, wild eastern quolls have been restricted to two islands at the southern end of their historical range. Eastern quolls are the subject of captive breeding programs and attempts have been made to re-establish a population in mainland Australia. However, few resources currently exist to guide the genetic management of this species. Here, we generated a reference genome for the eastern quoll with gene annotations supported by multi-tissue transcriptomes. Our assembly is among the most complete marsupial genomes currently available. Using this assembly, we infer the species' demographic history, identifying potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely underpins pelage color differences between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii).
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Affiliation(s)
- Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | | | - Natasha M Robinson
- Fenner School of Environment & Society, Australian National University, Canberra, ACT, 2601, Australia
| | - Anna J MacDonald
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, TAS, 7050, Australia
| | - Rodrigo K Hamede
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | | | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Tim Faulkner
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Hayley Shute
- Australian Reptile Park & Aussie Ark, Somersby, NSW, 2250, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW, 2088, Australia
| | - Rob Brewster
- WWF-Australia, PO Box 528, Sydney, NSW, 2001, Australia
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Andrew J Pask
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Sciences, Museums Victoria, Carlton, VIC, 3053, Australia
| | - Charles Y Feigin
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
- Department of Environment and Genetics, La Trobe University, Bundoora, VIC, 3086, Australia.
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Menzies BR, Tarulli GA, Frankenberg SR, Pask AJ. Therian origin of INSL3/RXFP2-driven testicular descent in mammals. Front Cell Dev Biol 2024; 12:1353598. [PMID: 38380341 PMCID: PMC10877632 DOI: 10.3389/fcell.2024.1353598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
Introduction: During early development in most male mammals the testes move from a position near the kidneys through the abdomen to eventually reside in the scrotum. The transabdominal phase of this migration is driven by insulin-like peptide 3 (INSL3) which stimulates growth of the gubernaculum, a key ligament connecting the testes with the abdominal wall. While all marsupials, except the marsupial mole (Notoryctes typhlops), have a scrotum and fully descended testes, it is unclear if INSL3 drives this process in marsupials especially given that marsupials have a different mechanism of scrotum determination and position relative to the phallus compared to eutherian mammals. Methods: To understand if INSL3 plays a role in marsupial testicular descent we have sequenced and curated the INSL3 gene and its receptor (RXFP2) in a range of marsupials representing every order. Furthermore, we looked at single cell RNA-seq and qPCR analysis of INSL3 in the fat-tailed dunnart testis (Sminthopsis crassicaudata) to understand the location and timing of expression during development. Results: These data show a strong phylogenetic similarity between marsupial and eutherian orthologues, but not with monotreme INSL3s which were more similar to the ancestral RLN3 gene. We have also shown the genomic location of INSL3, and surrounding genes is conserved in a range of marsupials and eutherians. Single cell RNA-seq and qPCR data show that INSL3 mRNA is expressed specifically in Leydig cells and expressed at higher levels during the testicular descent phase in developing marsupials. Discussion: Together, these data argue strongly for a therian origin of INSL3 mediated testicular descent in mammals and suggests that a coordinated movement of the testes to the abdominal wall may have preceded externalization in marsupials and therian mammals.
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Affiliation(s)
- Brandon R. Menzies
- School of BioSciences, Faculty of Science, The University of Melbourne, Melbourne, VIC, Australia
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Kyomen S, Murillo-Rincón AP, Kaucká M. Evolutionary mechanisms modulating the mammalian skull development. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220080. [PMID: 37183900 PMCID: PMC10184257 DOI: 10.1098/rstb.2022.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Mammals possess impressive craniofacial variation that mirrors their adaptation to diverse ecological niches, feeding behaviour, physiology and overall lifestyle. The spectrum of craniofacial geometries is established mainly during embryonic development. The formation of the head represents a sequence of events regulated on genomic, molecular, cellular and tissue level, with each step taking place under tight spatio-temporal control. Even minor variations in timing, position or concentration of the molecular drivers and the resulting events can affect the final shape, size and position of the skeletal elements and the geometry of the head. Our knowledge of craniofacial development increased substantially in the last decades, mainly due to research using conventional vertebrate model organisms. However, how developmental differences in head formation arise specifically within mammals remains largely unexplored. This review highlights three evolutionary mechanisms acknowledged to modify ontogenesis: heterochrony, heterotopy and heterometry. We present recent research that links changes in developmental timing, spatial organization or gene expression levels to the acquisition of species-specific skull morphologies. We highlight how these evolutionary modifications occur on the level of the genes, molecules and cellular processes, and alter conserved developmental programmes to generate a broad spectrum of skull shapes characteristic of the class Mammalia. This article is part of the theme issue 'The mammalian skull: development, structure and function'.
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Affiliation(s)
- Stella Kyomen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Andrea P Murillo-Rincón
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
| | - Markéta Kaucká
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, Plön 24306, Germany
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Zhu M, Tabin CJ. The role of timing in the development and evolution of the limb. Front Cell Dev Biol 2023; 11:1135519. [PMID: 37200627 PMCID: PMC10185760 DOI: 10.3389/fcell.2023.1135519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023] Open
Abstract
The term heterochrony was coined to describe changes in the timing of developmental processes relative to an ancestral state. Limb development is a well-suited system to address the contribution of heterochrony to morphological evolution. We illustrate how timing mechanisms have been used to establish the correct pattern of the limb and provide cases where natural variations in timing have led to changes in limb morphology.
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Newton AH. Marsupials and Multi-Omics: Establishing New Comparative Models of Neural Crest Patterning and Craniofacial Development. Front Cell Dev Biol 2022; 10:941168. [PMID: 35813210 PMCID: PMC9260703 DOI: 10.3389/fcell.2022.941168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Studies across vertebrates have revealed significant insights into the processes that drive craniofacial morphogenesis, yet we still know little about how distinct facial morphologies are patterned during development. Studies largely point to evolution in GRNs of cranial progenitor cell types such as neural crest cells, as the major driver underlying adaptive cranial shapes. However, this hypothesis requires further validation, particularly within suitable models amenable to manipulation. By utilizing comparative models between related species, we can begin to disentangle complex developmental systems and identify the origin of species-specific patterning. Mammals present excellent evolutionary examples to scrutinize how these differences arise, as sister clades of eutherians and marsupials possess suitable divergence times, conserved cranial anatomies, modular evolutionary patterns, and distinct developmental heterochrony in their NCC behaviours and craniofacial patterning. In this review, I lend perspectives into the current state of mammalian craniofacial biology and discuss the importance of establishing a new marsupial model, the fat-tailed dunnart, for comparative research. Through detailed comparisons with the mouse, we can begin to decipher mammalian conserved, and species-specific processes and their contribution to craniofacial patterning and shape disparity. Recent advances in single-cell multi-omics allow high-resolution investigations into the cellular and molecular basis of key developmental processes. As such, I discuss how comparative evolutionary application of these tools can provide detailed insights into complex cellular behaviours and expression dynamics underlying adaptive craniofacial evolution. Though in its infancy, the field of "comparative evo-devo-omics" presents unparalleled opportunities to precisely uncover how phenotypic differences arise during development.
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Feigin C, Frankenberg S, Pask A. A Chromosome-Scale Hybrid Genome Assembly of the Extinct Tasmanian Tiger (Thylacinus cynocephalus). Genome Biol Evol 2022; 14:evac048. [PMID: 35349647 PMCID: PMC9007325 DOI: 10.1093/gbe/evac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
The extinct Tasmanian tiger or thylacine (Thylacinus cynocephalus) was a large marsupial carnivore native to Australia. Once ranging across parts of the mainland, the species remained only on the island of Tasmania by the time of European colonization. It was driven to extinction in the early 20th century and is an emblem of native species loss in Australia. The thylacine was a striking example of convergent evolution with placental canids, with which it shared a similar skull morphology. Consequently, it has been the subject of extensive study. While the original thylacine assemblies published in 2018 enabled the first exploration of the species' genome biology, further progress is hindered by the lack of high-quality genomic resources. Here, we present a new chromosome-scale hybrid genome assembly for the thylacine, which compares favorably with many recent de novo marsupial genomes. In addition, we provide homology-based gene annotations, characterize the repeat content of the thylacine genome, and show that consistent with demographic decline, the species possessed a low rate of heterozygosity even compared to extant, threatened marsupials.
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Affiliation(s)
- Charles Feigin
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Molecular Biology, Princeton University, New Jersey, USA
| | - Stephen Frankenberg
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Sciences, Museums Victoria, Carlton, Victoria, Australia
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