Marsupials exhibit unique biological features that provide fascinating insights into many aspects of mammalian development. These include their distinctive mode of reproduction, altricial stage at birth, and the associated heterochrony that is required for their crawl to the pouch and teat attachment. Marsupials are also an invaluable resource for mammalian comparative biology, forming a distinct lineage from the extant placental and egg-laying monotreme mammals. Despite their unique biology, marsupial resources are lagging behind those available for placentals. The fat-tailed dunnart (Sminthopsis crassicaudata) is a laboratory based marsupial model, with simple and robust husbandry requirements and a short reproductive cycle making it amenable to experimental manipulations. Here we present a detailed staging series for the fat-tailed dunnart, focusing on their accelerated development of the forelimbs and jaws. This study provides the first skeletal developmental series on S. crassicaudata and provides a fundamental resource for future studies exploring mammalian diversification, development and evolution.

Atrazine (ATZ) is one of the most widely used herbicides worldwide and is a common contaminant in human drinking water. It disrupts metabolic pathways in plants, and has metabolic and reproductive effects in vertebrates, including humans. Few studies have investigated the effects of exposure to low doses of ATZ, especially during sexual development in males. In this study, we exposed C57BL/6J male mice from weaning for 8 weeks to drinking water containing 0.5mgkg−1 bodyweight (BW) day−1 ATZ, the ‘no observed effect’ level used by the Australian government, or a 10-fold higher dose (5mgkg−1 BW day−1). Mice treated with the low dose of ATZ showed increased total and cumulative weight gain. At 12 weeks of age, there was a significant increase in the percentage of dead spermatozoa in both ATZ-exposed groups, as well as decreased epididymal sperm motility in the low-dose ATZ group. Significant changes in testis and liver gene expression were also observed following ATZ exposure. These data demonstrate that a low dose of ATZ can perturb metabolic and reproductive characteristics in male mice. A chronic reduction in sperm quality and increased weight gain could have negative consequences on the reproductive capacity of males, and further studies should consider the effects of long-term ATZ exposure on male reproductive health.

Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.

AbstractModern humans have substantially admixed with multiple archaic hominins. New Guineans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals, whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these events remain poorly understood. Here we investigate the function of archaic alleles of both Denisovan and Neanderthal ancestry characterised within a previously published set of 72 genomes from individuals of Papuan genetic ancestry living in the island of New Guinea. By comparing the distribution of archaic and modern human variants, we are able to assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We find that archaic alleles are often located within cis-regulatory elements and transcribed regions of the genome, suggesting that they are actively involved in a wide range of cellular regulatory processes. We identify 39,954 high-confidence Denisovan variants that fall within annotated cis-regulatory elements and have the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes in present-day humans. Additionally, we detect a consistent signal across Denisovan variants of strong involvement in immune-related processes. Lastly, we show how such regulatory effects might underlie some of the observed gene expression differences between multiple Indonesian populations carrying varying amount of Denisovan DNA. Together, these data provide support for the hypothesis that, despite their broadly deleterious nature, archaic alleles actively contribute to modern human phenotypic diversity and might have facilitated early adaptation to non-African environments.