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Winterhoff ML, Achmadi AS, Roycroft EJ, Handika H, Putra RTJ, Rowe KMC, Perkins SL, Rowe KC. Native and Introduced Trypanosome Parasites in Endemic and Introduced Murine Rodents of Sulawesi. J Parasitol 2020; 106:523-536. [PMID: 32931567 DOI: 10.1645/19-136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The Indonesian island of Sulawesi is a globally significant biodiversity hotspot with substantial undescribed biota, particularly blood-borne parasites of endemic wildlife. Documenting the blood parasites of Sulawesi's murine rodents is the first fundamental step towards the discovery of pathogens likely to be of concern for the health and conservation of Sulawesi's endemic murines. We screened liver samples from 441 specimens belonging to 20 different species of murine rodents from 2 mountain ranges on Sulawesi, using polymerase chin reaction (PCR) primers targeting the conserved 18S rDNA region across the protozoan class Kinetoplastea. We detected infections in 156 specimens (10 host species) with a mean prevalence of 35.4% (95% confidence interval [CI] = 30.9-39.8%). Sequences from these samples identified 4 infections to the genus Parabodo, 1 to Blechomonas, and the remaining 151 to the genus Trypanosoma. Within Trypanosoma, we recovered 17 haplotypes nested within the Trypanosoma theileri clade infecting 117 specimens (8 host species) and 4 haplotypes nested within the Trypanosoma lewisi clade infecting 34 specimens (6 host species). Haplotypes within the T. theileri clade were related to regional Indo-Australian endemic trypanosomes, displayed geographic structuring but with evidence of long-term connectivity between mountains, and had substantial phylogenetic diversity. These results suggest T. theileri clade parasites are native to Sulawesi. Conversely, T. lewisi clade haplotypes were recovered from both endemic and introduced rodents, demonstrated complete geographic separation between clades, and had low genetic diversity. These results suggest that the T. lewisi clade parasites invaded Sulawesi recently and likely in 2 separate invasion events. Our results provide the first records of metakinetoplastids in Sulawesi's rodents and highlight the need for more extensive sampling for pathogens in this biodiversity hotspot.
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Affiliation(s)
- Monique L Winterhoff
- School of Biosciences, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
- Sciences Department, Museums Victoria, Carlton, Melbourne, Victoria 3053, Australia
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biology-LIPI, Jl. Raya Jakarta-Bogor Km. 46, Cibinong 16911, Indonesia
| | - Emily J Roycroft
- School of Biosciences, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
- Sciences Department, Museums Victoria, Carlton, Melbourne, Victoria 3053, Australia
| | - Heru Handika
- School of Biosciences, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
- Sciences Department, Museums Victoria, Carlton, Melbourne, Victoria 3053, Australia
- Department of Biology and Museum of Natural Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | | | - Karen M C Rowe
- School of Biosciences, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
- Sciences Department, Museums Victoria, Carlton, Melbourne, Victoria 3053, Australia
| | - Susan L Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York 10024
- The City College of New York, 160 Convent Avenue, New York, New York 10031
| | - Kevin C Rowe
- School of Biosciences, The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
- Sciences Department, Museums Victoria, Carlton, Melbourne, Victoria 3053, Australia
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Ramm T, Roycroft EJ, Müller J. Convergent evolution of tail spines in squamate reptiles driven by microhabitat use. Biol Lett 2020; 16:20190848. [PMCID: PMC7058953 DOI: 10.1098/rsbl.2019.0848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2023] Open
Abstract
The repeated evolution of convergent or analogous traits is often used as evidence for adaptive evolution. Squamate reptiles show a high degree of convergence in a variety of morphological traits; however, the evolutionary mechanisms driving these patterns are not fully understood. Here, we investigate the evolution of tail spines, a trait that evolved multiple times in evolutionarily independent clades of lizards. Taking a comparative phylogenetic approach, we use 2877 squamate species to demonstrate that the evolution of spiny tails is correlated with microhabitat use, with species that live in rocky habitats significantly more likely to have evolved spiny tails. In the light of previous behavioural observations, our results suggest that spiny-tailed lizards have an advantage in rocky habitats through predation avoidance, where tail spines are used to prevent extraction from rocky crevices. In concordance with previous research on lizard body armour, our results suggest that the evolution of tail spines is coupled to both a rock-dwelling lifestyle and predator avoidance strategies, and highlight a complex interplay between different selective pressures on the evolution of defensive morphologies in reptiles.
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Affiliation(s)
- Till Ramm
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3052, Australia
- Sciences Department, Museums Victoria, Carlton, Victoria 3053, Australia
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin 10115, Germany
| | - Emily J. Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3052, Australia
- Sciences Department, Museums Victoria, Carlton, Victoria 3053, Australia
| | - Johannes Müller
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin 10115, Germany
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Roycroft EJ, Nations JA, Rowe KC. Environment predicts repeated body size shifts in a recent radiation of Australian mammals. Evolution 2019; 74:671-680. [PMID: 31595503 DOI: 10.1111/evo.13859] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022]
Abstract
Closely related species that occur across steep environmental gradients often display clear body size differences, and examining this pattern is crucial to understanding how environmental variation shapes diversity. Australian endemic rodents in the Pseudomys Division (Muridae: Murinae) have repeatedly colonized the arid, monsoon, and mesic biomes over the last 5 million years. Using occurrence records, body mass data, and Bayesian phylogenetic models, we test whether body mass of 31 species in the Pseudomys Division can be predicted by their biome association. We also model the effect of eight environmental variables on body mass. Despite high phylogenetic signal in body mass evolution across the phylogeny, we find that mass predictably increases in the mesic biome and decreases in arid and monsoon biomes. As per Bergmann's rule, temperature is strongly correlated with body mass, as well as several other variables. Our results highlight two important findings. First, body size in Australian rodents has tracked with climate through the Pleistocene, likely due to several environmental variables rather than a single factor. Second, support for both Brownian motion and predictable change at different taxonomic levels in the Pseudomys Division phylogeny demonstrates how the level at which we test hypotheses can alter interpretation of evolutionary processes.
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Affiliation(s)
- Emily J Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Sciences Department, Museums Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
| | - Jonathan A Nations
- Museum of Natural Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Sciences Department, Museums Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
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Roycroft EJ, Moussalli A, Rowe KC. Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents. Syst Biol 2019; 69:431-444. [DOI: 10.1093/sysbio/syz044] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.
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Affiliation(s)
- Emily J Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Science, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Adnan Moussalli
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Science, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Science, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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Roycroft EJ. Digest: Colonizing rodents overcome ecological incumbency in an island system. Evolution 2019; 73:1496-1497. [PMID: 31131440 DOI: 10.1111/evo.13770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 11/26/2022]
Abstract
Do primary radiations inhibit the persistence and diversification of secondary colonizers? Rowsey et al. test predictions of this "incumbency effect" by contrasting patterns of morphological variation in two murine rodent clades on the Philippine island of Luzon. They find that in this system, primary colonizers may impose constraints via biotic filtering, and may also restrict size evolution in secondary colonists.
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Affiliation(s)
- Emily J Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Carlton, Victoria, Australia
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Roycroft EJ, Le Port A, Lavery SD. Population structure and male-biased dispersal in the short-tail stingray Bathytoshia brevicaudata (Myliobatoidei: Dasyatidae). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01167-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Potter S, Xue AT, Bragg JG, Rosauer DF, Roycroft EJ, Moritz C. Pleistocene climatic changes drive diversification across a tropical savanna. Mol Ecol 2017; 27:520-532. [DOI: 10.1111/mec.14441] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/20/2017] [Accepted: 10/31/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sally Potter
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
| | - Alexander T. Xue
- Department of Biology City University of New York New York NY USA
- Department of Genetics Rutgers University Piscataway NJ USA
| | - Jason G. Bragg
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
| | - Dan F. Rosauer
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
| | - Emily J. Roycroft
- School of Biosciences The University of Melbourne Parkville Vic. Australia
- Sciences Department Museums Victoria Melbourne Vic. Australia
| | - Craig Moritz
- Research School of Biology The Australian National University Acton ACT Australia
- Centre for Biodiversity Analysis Acton ACT Australia
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