OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics.

To date, the databases built to gather information on gene orthology do not provide end-users with descriptors of the molecular evolution information and phylogenetic pattern of these orthologues. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian genomes. OrthoMaM version 12 includes 15,868 alignments of orthologous coding sequences (CDS) from the 190 complete mammalian genomes currently available. All annotations and 1-to-1 orthology assignments are based on NCBI. Orthologous CDS can be mined for potential informative markers at the different taxonomic levels of the mammalian tree. To this end, several evolutionary descriptors of DNA sequences are provided for querying purposes (e.g. base composition and relative substitution rate). The graphical web interface allows the user to easily browse and sort the results of combined queries. The corresponding multiple sequence alignments and ML trees, inferred using state-of-the art approaches, are available for download both at the nucleotide and amino acid levels. OrthoMaM v12 can be used by researchers interested either in reconstructing the phylogenetic relationships of mammalian taxa or in understanding the evolutionary dynamics of coding sequences in their genomes. OrthoMaM is available for browsing, querying and complete or filtered download at https://orthomam.mbb.cnrs.fr/.

Identification of constrained sequence elements across 239 primate genomes.

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Large-scale across species transcriptomic analysis identifies genetic selection signatures associated with longevity in mammals.

Lifespan varies significantly among mammals, with more than 100-fold difference between the shortest and longest living species. This natural difference may uncover the evolutionary forces and molecular features that define longevity. To understand the relationship between gene expression variation and longevity, we conducted a comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species. We found that few genes exhibit common expression patterns with longevity in the three organs analyzed. However, pathways related to translation fidelity, such as nonsense-mediated decay and eukaryotic translation elongation, correlated with longevity across mammals. Analyses of selection pressure found that selection intensity related to the direction of longevity-correlated genes is inconsistent across organs. Furthermore, expression of methionine restriction-related genes correlated with longevity and was under strong selection in long-lived mammals, suggesting that a common strategy is utilized by natural selection and artificial intervention to control lifespan. Our results indicate that lifespan regulation via gene expression is driven through polygenic and indirect natural selection.

Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.

Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). We identified 439,461 cCREs and 2,024,062 TFBSs under evolutionary constraint. Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. About 20% of TFBSs are transposable element-derived and exhibit intricate patterns of gains and losses during primate evolution whereas sequence variants associated with complex traits are enriched in constrained TFBSs. Our annotations illuminate the regulatory functions of the human genome.

Genomics expands the mammalverse.

Diverse mammal genomes open a new portal to hidden aspects of evolutionary history.

Medium and large-sized mammals of a private protected wetland in the Cerrado-Amazon biological corridor, Brazil / Mamíferos de médio e grande porte em uma área alagável protegida no corredor biológico Cerrado-Amazônia, Brasil

Brazil is the world’s richest country in biodiversity, including mammal species. In the Brazilian Cerrado biome, mammalian diversity is vast, with about 251 species, 32 of them are endemic and 22 listed as threatened species. In this work, we investigated species diversity of medium- and large-sized mammals in the private protected area RPPN Pontal do Jaburu (RPPN-PJ) and its surroundings, which is a flooded area located in an important biological corridor in the Cerrado-Amazon ecotone zone, a priority area for biodiversity conservation in Brazil. We used camera-trapping, active search (night and day), and track survey during dry season (Apr – Aug 2016). We recorded 29 mammal species, being the Carnivora order the most representative with 11 species. Regarding threat status, 35.7% of the recorded species were listed as threatened in Brazil and 32.1% worldwide. We highlight the high relative frequency of threatened species records such as Tapirus terrestris, Panthera onca, Blastocerus dichotomus, Pteronura brasiliensis, Priodontes maximus, and other, as well as the presence of the newly described aquatic mammal species Inia araguaiaensis. We stress the importance of RPPN-PJ and its surroundings for mammal conservation, which include complex habitats (wetlands) located in an important ecotone zone.

O Brasil é o país mais rico em biodiversidade no mundo, incluindo espécies de mamíferos. No bioma Cerrado, a diversidade de mamíferos é enorme, com cerca de 251 espécies, sendo 32 delas endêmicas e 22 listadas como ameaçadas de extinção. Neste estudo, investigamos a diversidade de espécies de mamíferos de médio e grande porte da RPPN Pontal do Jaburu (RPPN-PJ) e seu entorno, que é uma floresta de inundação localizada em um importante corredor biológico na zona de ecótono Cerrado-Amazonia, uma área prioritária para conservação da biodiversidade no Brasil. Os dados foram coletados por armadilhas fotográficas, busca ativa (noturna e diurna) e identificação de pegadas durante a estação seca (abril - agosto de 2016). Registramos um grande número de espécies de mamíferos (n = 29), sendo a ordem carnívora a mais representativa com 11 espécies. Com relação ao status de ameaça, 34,5% das espécies registradas foram listadas como ameaçadas na lista vermelha do Brasil e 20,7% na lista vermelha da IUCN. Destacamos a alta frequência relativa de registros de espécies ameaçadas como Tapirus terrestris, Panthera onca, Blastocerus dichotomus, Pteronura brasiliensis, Priodontes maximus, bem como a presença da recém descrita espécie de mamífero aquático Inia araguaiaensis. Nós discutimos a importância da RPPN-PJ e seus arredores para a conservação de espécies de mamíferos, onde inclui habitats complexos (áreas de inundação) localizados em uma importante zona de ecótono. Os resultados reforçam a relevância desta área para a conservação de mamíferos.

Áreas en riesgo para los mamíferos marinos en Colombia / Areas at risk for marine mammals in Colombia

Resumen Introducción: Los mamíferos marinos se ven afectados por diversas amenazas que deben identificarse para los esfuerzos de mitigación. Objetivo: Cuantificar visualmente las amenazas a los mamíferos marinos en Colombia e identificar acciones de mitigación. Métodos: Georreferenciamos las amenazas con base en la literatura, cubriendo 35 especies en el período 1991-2020, y las superpusimos en mapas de distribución de especies. Resultados: 22 especies presentaron al menos una amenaza. La captura incidental y las interacciones con los artes de pesca afectaron a 16 especies, seguidas de la captura directa (8 especies), el tráfico/tránsito de embarcaciones (6 especies) y la alteración de la física oceánica (6 especies). Las especies más afectadas, en cuanto a mayor diversidad de amenazas, son: ballena jorobada (Megaptera novaeangliae), manatí antillano del Caribe (Trichechus manatus), el tucuxi marino (Sotalia guianensis) y el delfín nariz de botella (Tursiops truncatus). Casi todo el territorio marino de Colombia presenta algún grado de riesgo para los mamíferos marinos. Las áreas de alto riesgo son Buenaventura, Guapi, Golfo de Cupica y Tumaco en el Pacífico; y Golfo de Urabá, Golfo de Darién, Golfo de Morrosquillo, frente a Barranquilla, Ciénaga Grande de Santa Marta y Golfo de Coquivacoa en el Caribe. Conclusión: Los mamíferos marinos en Colombia se encuentran actualmente en riesgo debido a varias amenazas, especialmente relacionadas con actividades de pesca, caza/captura y transporte marítimo, principalmente en las zonas costeras. Se necesitan acciones urgentes de evaluación y gestión en las diez áreas de alto riesgo identificadas en este estudio.

Abstract Introduction: Marine mammals are affected by diverse threats that must be identified for mitigation efforts. Objective: To visually quantify threats to marine mammals in Colombia, and to identify mitigation actions. Methods: We georeferenced threats based on the literature, covering 35 species in the period 1991-2020, and superimposed them on species range maps. Results: 22 species had at least one threat. Bycatch and interactions with fishing gear affected 16 species, followed by direct capture (8 species), vessel traffic/transit (6 species) and alteration of ocean physics (6 species). The most affected species, in terms of the greatest diversity of threats, are: humpback whale (Megaptera novaeangliae), Caribbean West Indian manatee (Trichechus manatus), marine tucuxi (Sotalia guianensis) and bottlenose dolphin (Tursiops truncatus). Nearly all of Colombia's marine territory presents some degree of risk for marine mammals. High-risk areas are Buenaventura, Guapi, Cupica Gulf and Tumaco in the Pacific; and Urabá Gulf, Darién Gulf, Morrosquillo Gulf, off Barranquilla, Ciénaga Grande de Santa Marta and Coquivacoa Gulf in the Caribbean. Conclusion: Marine mammals in Colombia are currently at risk due to several threats, especially related to fishing, hunting/capture and shipping activities, mainly in coastal areas. Urgent evaluation and management actions are needed in the ten high-risk areas identified in this study.

The generality of cryptic dietary niche differences in diverse large-herbivore assemblages.

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families-grasses and legumes-accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

Climate change increases cross-species viral transmission risk.

At least 10,000 virus species have the ability to infect humans but, at present, the vast majority are circulating silently in wild mammals1,2. However, changes in climate and land use will lead to opportunities for viral sharing among previously geographically isolated species of wildlife3,4. In some cases, this will facilitate zoonotic spillover-a mechanistic link between global environmental change and disease emergence. Here we simulate potential hotspots of future viral sharing, using a phylogeographical model of the mammal-virus network, and projections of geographical range shifts for 3,139 mammal species under climate-change and land-use scenarios for the year 2070. We predict that species will aggregate in new combinations at high elevations, in biodiversity hotspots, and in areas of high human population density in Asia and Africa, causing the cross-species transmission of their associated viruses an estimated 4,000 times. Owing to their unique dispersal ability, bats account for the majority of novel viral sharing and are likely to share viruses along evolutionary pathways that will facilitate future emergence in humans. Notably, we find that this ecological transition may already be underway, and holding warming under 2 °C within the twenty-first century will not reduce future viral sharing. Our findings highlight an urgent need to pair viral surveillance and discovery efforts with biodiversity surveys tracking the range shifts of species, especially in tropical regions that contain the most zoonoses and are experiencing rapid warming.

Demographic and life history traits explain patterns in species vulnerability to extinction.

As ecosystems face disruption of community dynamics and habitat loss, the idea of determining ahead of time which species can become extinct is an important subject in conservation biology. A species' vulnerability to extinction is dependent upon both intrinsic (life-history strategies, genetics) and extrinsic factors (environment, anthropogenic threats). Studies linking intrinsic traits to extinction risk have shown variable results, and to our knowledge, there has not been a systematic analysis looking at how demographic patterns in stage-specific survival and reproductive rates correlate to extinction risk. We used matrix projection models from the COMPADRE and COMADRE matrix databases and IUCN Red List status as our proxy of extinction risk to investigate if some demographic patterns are more vulnerable to extinction than others. We obtained data on demographic rates, phylogeny, and IUCN status for 159 species of herbaceous plants, trees, mammals, and birds. We calculated 14 demographic metrics related to different aspects of life history and elasticity values and analyzed whether they differ based on IUCN categories using conditional random forest analysis and phylogenetic generalized least square regressions. We mapped all species within the database, both with IUCN assessment and without, and overlaid them with biodiversity hotspots to investigate if there is bias within the assessed species and how many of the non-assessed species could use the demographic information recorded in COMPADRE and COMADRE for future IUCN assessments. We found that herbaceous perennials are more vulnerable when they mature early and have high juvenile survival rates; birds are more vulnerable with high progressive growth and reproduction; mammals are more vulnerable when they have longer generation times. These patterns may be used to assess relative vulnerability across species when lacking abundance or trend data.

Cancer risk across mammals.

Cancer is a ubiquitous disease of metazoans, predicted to disproportionately affect larger, long-lived organisms owing to their greater number of cell divisions, and thus increased probability of somatic mutations1,2. While elevated cancer risk with larger body size and/or longevity has been documented within species3-5, Peto's paradox indicates the apparent lack of such an association among taxa6. Yet, unequivocal empirical evidence for Peto's paradox is lacking, stemming from the difficulty of estimating cancer risk in non-model species. Here we build and analyse a database on cancer-related mortality using data on adult zoo mammals (110,148 individuals, 191 species) and map age-controlled cancer mortality to the mammalian tree of life. We demonstrate the universality and high frequency of oncogenic phenomena in mammals and reveal substantial differences in cancer mortality across major mammalian orders. We show that the phylogenetic distribution of cancer mortality is associated with diet, with carnivorous mammals (especially mammal-consuming ones) facing the highest cancer-related mortality. Moreover, we provide unequivocal evidence for the body size and longevity components of Peto's paradox by showing that cancer mortality risk is largely independent of both body mass and adult life expectancy across species. These results highlight the key role of life-history evolution in shaping cancer resistance and provide major advancements in the quest for natural anticancer defences.

A species-level timeline of mammal evolution integrating phylogenomic data.

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1-3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6, and thus the timescale of placental mammal evolution remains contentious7-10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.

The cost of sequencing the genome is dropping at a much faster rate compared to assembling and finishing the genome. The use of lightly sampled genomes (genome-skims) could be transformative for genomic ecology, and results using k-mers have shown the advantage of this approach in identification and phylogenetic placement of eukaryotic species. Here, we revisit the basic question of estimating genomic parameters such as genome length, coverage, and repeat structure, focusing specifically on estimating the k-mer repeat spectrum. We show using a mix of theoretical and empirical analysis that there are fundamental limitations to estimating the k-mer spectra due to ill-conditioned systems, and that has implications for other genomic parameters. We get around this problem using a novel constrained optimization approach (Spline Linear Programming), where the constraints are learned empirically. On reads simulated at 1X coverage from 66 genomes, our method, REPeat SPECTra Estimation (RESPECT), had 2.2% error in length estimation compared to 27% error previously achieved. In shotgun sequenced read samples with contaminants, RESPECT length estimates had median error 4%, in contrast to other methods that had median error 80%. Together, the results suggest that low-pass genomic sequencing can yield reliable estimates of the length and repeat content of the genome. The RESPECT software will be publicly available at https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_shahab-2Dsarmashghi_RESPECT.git&d=DwIGAw&c=-35OiAkTchMrZOngvJPOeA&r=ZozViWvD1E8PorCkfwYKYQMVKFoEcqLFm4Tg49XnPcA&m=f-xS8GMHKckknkc7Xpp8FJYw_ltUwz5frOw1a5pJ81EpdTOK8xhbYmrN4ZxniM96&s=717o8hLR1JmHFpRPSWG6xdUQTikyUjicjkipjFsKG4w&e=.

Genomic convergence between Akkermansia muciniphila in different mammalian hosts.

BACKGROUND: Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut. However, A. muciniphila 16S rRNA gene sequences have also been found in the intestines of many vertebrates. RESULTS: We detected A. muciniphila-like bacteria in the intestines of animals belonging to 15 out of 16 mammalian orders. In addition, other species belonging to the Verrucomicrobia phylum were detected in fecal samples. We isolated 10 new A. muciniphila strains from the feces of chimpanzee, siamang, mouse, pig, reindeer, horse and elephant. The physiology and genome of these strains were highly similar in comparison to the type strain A. muciniphila MucT. Overall, the genomes of the new strains showed high average nucleotide identity (93.9 to 99.7%). In these genomes, we detected considerable conservation of at least 75 of the 78 mucin degradation genes that were previously detected in the genome of the type strain MucT. CONCLUSIONS: The low genomic divergence observed in the new strains may indicate that A. muciniphila favors mucosal colonization independent of the differences in hosts. In addition, the conserved mucus degradation capability points towards a similar beneficial role of the new strains in regulating host metabolic health.

Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe.

The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5' untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission.

No evidence for parallel evolution of cursorial limb adaptations among Neogene South American native ungulates (SANUs).

During the Neogene, many North American ungulates evolved longer limbs. Presumably, this allowed them to move more efficiently or quickly in open habitats, which became more common during this interval. Evidence suggests that open habitats appeared even earlier in South America, but no study to date has investigated whether the ungulate-like mammals of South America (South American native ungulates or SANUs) evolved similar limb adaptations. We analyzed limb elongation in the two predominant SANU groups, notoungulates and litopterns, by compiling genus-level occurrences from the late Oligocene to the Pleistocene and calculating metatarsal/femur ratio (Mt:F). None of the groups or subgroups we analyzed show a pronounced increase in Mt:F across this interval, with the possible exception of proterotheriid litopterns. Proterotheriids are thought to have inhabited forested environments rather than open ones, which raises questions about the selective forces responsible for limb elongation in ungulates. Conversely, notoungulates, which are traditionally thought to have lived in open habitats, show no strong trend of increasing Mt:F across this interval. Our study suggests that the macroevolutionary trend of limb elongation in ungulate-like mammals is not universal and is highly influenced by the evolutionary affinities of the groups being analyzed.

Less need for differentiation? Intestinal length of reptiles as compared to mammals.

Although relationships between intestinal morphology between trophic groups in reptiles are widely assumed and represent a cornerstone of ecomorphological narratives, few comparative approaches actually tested this hypothesis on a larger scale. We collected data on lengths of intestinal sections of 205 reptile species for which either body mass (BM), snout-vent-length (SVL) or carapax length (CL) was recorded, transforming SVL or CL into BM if the latter was not given, and analyzed scaling patterns with BM and SVL, accounting for phylogeny, comparing three trophic guilds (faunivores, omnivores, herbivores), and comparing with a mammal dataset. Length-BM relationships in reptiles were stronger for the small than the large intestine, suggesting that for the latter, additional factors might be relevant. Adding trophic level did not consistently improve model fit; only when controlling for phylogeny, models indicated a longer large intestine in herbivores, due to a corresponding pattern in lizards. Trophic level effects were highly susceptible to sample sizes, and not considered strong. Models that linked BM to intestine length had better support than models using SVL, due to the deviating body shape of snakes. At comparable BM, reptiles had shorter intestines than mammals. While the latter finding corresponds to findings of lower tissue masses for the digestive tract and other organs in reptiles as well as our understanding of differences in energetic requirements between the classes, they raise the hitherto unanswered question what it is that reptiles of similar BM have more than mammals. A lesser effect of trophic level on intestine lengths in reptiles compared to mammals may stem from lesser selective pressures on differentiation between trophic guilds, related to the generally lower food intake and different movement patterns of reptiles, which may not similarly escalate evolutionary arms races tuned to optimal agility as between mammalian predators and prey.

Mammal type specimens in the Macleay Collections, University of Sydney.

Type material of 12 mammal taxa originally proposed as species or subspecies are housed in the former Macleay Museum (now Macleay Collections, Chau Chak Wing Museum), University of Sydney and consist of seven holotypes and 12 syntypes. These were published from 1875 to 1887, five by N.N. Miklouho-Maclay and seven by E.P. Ramsay, of which six are currently considered valid taxa. Six type specimens are identified in the Collection for the first time. This includes rediscovery of the holotype skull of the New Guinean forest wallaby Dorcopsis chalmersii Miklouho-Maclay not reported since its description in 1884, a likely syntype of the bandicoot Perameles macroura torosa Ramsay, and three additional syntypes of the flying fox Pteropus (Epomops?) epularius Ramsay. The holotype of the dasyurid Antechinus (Podabrus) froggatti Ramsay, housed at the Australian Museum since before 1959, is also discussed. Limited specimen data currently prevents validation of an additional six specimens identified here as suspected syntypes of four further names: the macropodoids Halmaturus mastersii Krefft, Halmaturus crassipes Ramsay and Hypsiprymnodon moschatus Ramsay, and the bandicoot Perameles moresbyensis Ramsay. Individual accounts are given for a total of 21 proposed names. Type material of four of these remain unlocated in world collections and it is not known if they were ever in the Macleay Collections: the bandicoot Brachymelis garagassi Miklouho-Maclay, 1884; the wallaby Macropus tibol Miklouho-Maclay, 1885; the cuscus Cuscus chrysorrhous var. goldiei Ramsay and the giant rat Hapalotis papuanus Ramsay. The nomenclatural status of the possum Phalangista pinnata Ramsay, 1877, a possible nomen nudum, is also discussed. No nomenclatural actions are taken in this paper.

The role and impact of Zootaxa in mammalogy in its first 20 years.

Zootaxa came as a new and innovative publication medium for taxonomy, amidst a scenario of devaluation of this important biological science. After 20 years, it has ascertained itself as one of the main journals in animal taxonomy. However, the contribution of the journal to the taxonomy of Mammalia (mammals), one of the most studied groups of animals with a long-standing, dedicated spectrum of specialized journals (mammalogy), could have been expected as minor. All the current and former editors of the Mammalia section of Zootaxa analyzed the relative contribution of the journal to the description of new species of mammals since 2001. We also analyzed the contribution of Zootaxa by taxon, geographic origin of taxa, and geographic origin of first authors. The taxonomic methodology of authors in species description is described as well as the temporal trends in publications and publication subjects. We highlight the editors' picks and eventually, the challenges for the future. We found that Zootaxa has had a significant contribution to mammalogy, being the second journal (the first being Journal of Mammalogy) in terms of number of new species described (76; 10.6% of the new mammalian species described between 2001 and 2020). The majority of the new species were described following an integrative taxonomic approach with at least two sources of data (86%). The analysis of published taxa, their geographic origin, and the country of origin of first authors shows a wide coverage and exhaustive representation, except for the species from the Nearctic. We conclude that Zootaxa has likely responded to a repressed demand for an additional taxonomic journal in mammalogy, with as possible appeals the absence of publication fees and an established publication speed. With 246 articles published in the past 20 years, the Mammalia section of Zootaxa embraces a large spectrum of systematic subjects going beyond alpha taxonomy. The challenges for the future are to encourage publications of authors from the African continent, still poorly represented, and from the palaeontology community, as the journal has been open to palaeontology since its early days.

Divide-and-conquer: machine-learning integrates mammalian and viral traits with network features to predict virus-mammal associations.

Our knowledge of viral host ranges remains limited. Completing this picture by identifying unknown hosts of known viruses is an important research aim that can help identify and mitigate zoonotic and animal-disease risks, such as spill-over from animal reservoirs into human populations. To address this knowledge-gap we apply a divide-and-conquer approach which separates viral, mammalian and network features into three unique perspectives, each predicting associations independently to enhance predictive power. Our approach predicts over 20,000 unknown associations between known viruses and susceptible mammalian species, suggesting that current knowledge underestimates the number of associations in wild and semi-domesticated mammals by a factor of 4.3, and the average potential mammalian host-range of viruses by a factor of 3.2. In particular, our results highlight a significant knowledge gap in the wild reservoirs of important zoonotic and domesticated mammals' viruses: specifically, lyssaviruses, bornaviruses and rotaviruses.