1
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Brennan IG, Lemmon AR, Moriarty Lemmon E, Hoskin CJ, Donnellan SC, Keogh JS. Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification. Syst Biol 2024; 73:1-11. [PMID: 37527840 DOI: 10.1093/sysbio/syad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/21/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups that vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas. [Anuran; adaptive radiation; Gondwana; phylogenetics].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32316, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
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2
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Turza F, Miler K. Small workers are more persistent when providing and requiring help in a monomorphic ant. Sci Rep 2023; 13:21580. [PMID: 38062073 PMCID: PMC10703799 DOI: 10.1038/s41598-023-49012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
The common sand-dwelling Formica cinerea ants possess monomorphic workers, yet with considerable and easily identified size variation. Considering the importance of body size in polymorphic ants and other animals, we test whether size-dependent differences in behaviour occur in this species. We focus on the behaviour of large and small foragers in the context of rescue occurring between nestmates when one of them is entrapped and requires help. We show that workers of different sizes are characterized by a similar frequency of rescue activity and time delay to the first act of rescue. However, small workers rescue for longer than large workers. These results indicate that, although there is no size-related rescue specialization in F. cinerea foragers, small rescuers behave differently than large ones in terms of rescue persistence. Additionally, we show that small workers are more active when trapped. We suggest that variation in behavioural persistence of differently-sized workers may increase the efficiency of rescue actions. This study is the first to find a connection between body size and rescue behaviour in ants and the first to quantify and analyze the behaviour of individuals in need of rescue. These findings add substantially to our understanding of social insects and, more generally, highlight the need to study among-individual behavioural variation in social animals, including those in which body size is judged minute and irrelevant.
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Affiliation(s)
- Filip Turza
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, 30-348, Kraków, Poland.
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
| | - Krzysztof Miler
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland.
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3
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Tiatragul S, Brennan IG, Broady ES, Keogh JS. Australia's hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes. Mol Phylogenet Evol 2023; 185:107812. [PMID: 37207892 DOI: 10.1016/j.ympev.2023.107812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/24/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023]
Affiliation(s)
- Sarin Tiatragul
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - Elizabeth S Broady
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra 2601, ACT, Australia.
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4
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Skeels A, Boschman LM, McFadden IR, Joyce EM, Hagen O, Jiménez Robles O, Bach W, Boussange V, Keggin T, Jetz W, Pellissier L. Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line. Science 2023; 381:86-92. [PMID: 37410831 DOI: 10.1126/science.adf7122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - L M Boschman
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
| | - I R McFadden
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | - E M Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, 80331 Munich, Germany
| | - O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - O Jiménez Robles
- Research School of Biology, Australian National University, Canberra 0200, Australia
- Institute of Biology, École Normale Supérieure, 75005 Paris, France
| | - W Bach
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - V Boussange
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - T Keggin
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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5
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [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: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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7
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Trethowan LA, Arvidsson C, Bramley GLC. Environmental stress influences Malesian Lamiaceae distributions. Ecol Evol 2022; 12:e9467. [PMID: 36340815 PMCID: PMC9627225 DOI: 10.1002/ece3.9467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Dual effects of spatial distance and environment shape archipelagic floras. In Malesia, there are multiple environmental stressors associated with increasing uplands, drought, and metal‐rich ultramafic soils. Here, we examine the contrasting impacts of multifactorial environmental stress and spatial distance upon Lamiaceae species distributions. We used a phylogenetic generalized mixed effects model of species occurrence across Malesia's taxonomic database working group areas from Peninsular Malaysia to New Guinea. Predictor variables were environmental stress, spatial distance between areas and two trait principal component axes responsible for increasing fruit and leaf size and a negative correlation between flower size and plant height. We found that Lamiaceae species with smaller fruits and leaves are more likely to tolerate environmental stress and become widely distributed across megadiverse Malesian islands. How global species distribution and diversification are shaped by multifactorial environmental stress requires further examination.
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Affiliation(s)
| | - Camilla Arvidsson
- Herbarium Kew Royal Botanic Gardens Kew London UK
- Department of Biosciences University of Exeter Exeter UK
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8
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Bernstein JM, Ruane S. Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.893088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops. Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops, and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes. A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA.Life Science Identifier (Hydrablabes periops)urn:lsid:zoobank.org:pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.
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9
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McCullough JM, Oliveros C, Benz BW, Zenil-Ferguson R, Cracraft J, Moyle RG, Andersen MJ. Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine radiation Corvides. Syst Biol 2022; 71:1423-1439. [PMID: 35703981 DOI: 10.1093/sysbio/syac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers-specifically isolated island systems and Wallace's Line-we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.
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Affiliation(s)
- Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Carl Oliveros
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
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10
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Pavón-Vázquez CJ, Brennan IG, Skeels A, Keogh JS. Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards. Evolution 2022; 76:476-495. [PMID: 34816437 DOI: 10.1111/evo.14403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 10/06/2021] [Accepted: 10/16/2021] [Indexed: 01/21/2023]
Abstract
How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.,Current Address: Department of Biological Sciences, New York City College of Technology, City University of New York, Brooklyn, New York, 11201
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alexander Skeels
- Landscape Ecology, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, CH-8092, Switzerland.,Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, CH-8903, Switzerland
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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11
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Galbraith JD, Ludington AJ, Sanders KL, Amos TG, Thomson VA, Enosi Tuipulotu D, Dunstan N, Edwards RJ, Suh A, Adelson DL. Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes. Genes (Basel) 2022; 13:genes13020217. [PMID: 35205262 PMCID: PMC8872380 DOI: 10.3390/genes13020217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs), also known as jumping genes, are sequences able to move or copy themselves within a genome. As TEs move throughout genomes they often act as a source of genetic novelty, hence understanding TE evolution within lineages may help in understanding environmental adaptation. Studies into the TE content of lineages of mammals such as bats have uncovered horizontal transposon transfer (HTT) into these lineages, with squamates often also containing the same TEs. Despite the repeated finding of HTT into squamates, little comparative research has examined the evolution of TEs within squamates. Here we examine a diverse family of Australo-Melanesian snakes (Hydrophiinae) to examine if the previously identified, order-wide pattern of variable TE content and activity holds true on a smaller scale. Hydrophiinae diverged from Asian elapids ~30 Mya and have since rapidly diversified into six amphibious, ~60 marine and ~100 terrestrial species that fill a broad range of ecological niches. We find TE diversity and expansion differs between hydrophiines and their Asian relatives and identify multiple HTTs into Hydrophiinae, including three likely transferred into the ancestral hydrophiine from fish. These HTT events provide the first tangible evidence that Hydrophiinae reached Australia from Asia via a marine route.
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Affiliation(s)
- James D. Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Alastair J. Ludington
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Kate L. Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Timothy G. Amos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Vicki A. Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Division of Immunity, Inflammation and Infection, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | | | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; (T.G.A.); (D.E.T.)
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
| | - David L. Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia; (J.D.G.); (A.J.L.); (K.L.S.); (V.A.T.)
- South Australian Museum, Adelaide, SA 5000, Australia
- Correspondence: (R.J.E.); (A.S.); (D.L.A.)
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12
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Zhang L, Sun K, Csorba G, Hughes AC, Jin L, Xiao Y, Feng J. Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats. BMC Ecol Evol 2021; 21:199. [PMID: 34732135 PMCID: PMC8565063 DOI: 10.1186/s12862-021-01926-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. RESULTS Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. CONCLUSIONS The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.
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Affiliation(s)
- Lin Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China.
| | - Gábor Csorba
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Alice Catherine Hughes
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla County, 666303, Yunnan, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
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13
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Martins A, Koch C, Joshi M, Pinto R, Machado A, Lopes R, Passos P. Evolutionary treasures hidden in the West Indies: Comparative osteology and visceral morphology reveals intricate miniaturization in the insular genera Mitophis Hedges, Adalsteinsson, & Branch, 2009 and Tetracheilostoma Jan, 1861 (Leptotyphlopidae: Epictinae: Tetracheilostomina). Anat Rec (Hoboken) 2021; 304:2118-2148. [PMID: 34296825 DOI: 10.1002/ar.24716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/16/2021] [Accepted: 06/01/2021] [Indexed: 11/07/2022]
Abstract
The genera Mitophis and Tetracheilostoma comprise two extant lineages of small-sized threadsnakes that exclusively inhabit several islands of the West Indies. Even though leptotyphlopids are known for their extremely reduced size, miniaturization has only been hypothesized to reflect insular dwarfism for the genus Tetracheilostoma. Herein, we aim to describe the comparative osteology and visceral morphology of both genera, investigating and discussing their several internal morphological simplifications and novelties. Our results indicate that these taxa exhibit several autapomorphies mostly concentrated in the dorsoposterior skull elements and maxillae, as well as in their axial skeleton and viscera. These novelties and simplifications are most likely a result of extreme miniaturization driven by the evolutionary constraints or ecological opportunities possibly imposed by the "island rule." Both Mitophis and Tetracheilostoma distinguish from all other Epictinae in lacking a dentigerous process in the maxillae, by having the prootic fused to the otooccipital, and by the lack (except in comparison to a few Epictia) of a cervical vertebrae intercentrum I. Additionally, Mitophis can be distinguished from other Epictinae by the participation of the unpaired supraoccipital in the dorsal border of the foramen magnum, by the absence of the pleurapophyses in the caudal vertebrae, by a higher number of liver segments, and by the extreme degeneration of the pelvic rudiments. Tetracheilostoma differs from other Epictinae by lacking a distinct supraoccipital, which is fused to the parietal. Thus, our results reinforce that morphological characters are extremely valuable for leptotyphlopid systematics given their extremely conserved external morphology.
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Affiliation(s)
- Angele Martins
- Departamento de Ciências Fisiológicas, Universidade de Brasília, Brasília, Brazil.,Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia Koch
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Mitali Joshi
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Roberta Pinto
- Laboratório de Diversidade de Anfíbios e Répteis, Museu de Arqueologia da Universidade Católica de Pernambuco, Universidade Católica de Pernambuco, Recife, Brazil
| | - Alessandra Machado
- Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa em Engenharia, Laboratório de Instrumentação Nuclear, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Lopes
- Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa em Engenharia, Laboratório de Instrumentação Nuclear, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Passos
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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14
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Csősz S, Seifert B, Mikó I, Boudinot BE, Borowiec ML, Fisher BL, Prebus M, Puniamoorthy J, Rakotonirina J, Rasoamanana N, Schultz R, Trietsch C, Ulmer JM, Elek Z. Insect morphometry is reproducible under average investigation standards. Ecol Evol 2021; 11:547-559. [PMID: 33437450 PMCID: PMC7790639 DOI: 10.1002/ece3.7075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/27/2020] [Accepted: 11/03/2020] [Indexed: 11/11/2022] Open
Abstract
Morphometric research is being applied to a growing number and variety of organisms. Discoveries achieved via morphometric approaches are often considered highly transferable, in contrast to the tacit and idiosyncratic interpretation of discrete character states. The reliability of morphometric workflows in insect systematics has never been a subject of focused research, but such studies are sorely needed. In this paper, we assess the reproducibility of morphometric studies of ants where the mode of data collection is a shared routine.We compared datasets generated by eleven independent gaugers, that is, collaborators, who measured 21 continuous morphometric traits on the same pool of individuals according to the same protocol. The gaugers possessed a wide range of morphometric skills, had varying expertise among insect groups, and differed in their facility with measuring equipment. We used intraclass correlation coefficients (ICC) to calculate repeatability and reproducibility values (i.e., intra- and intergauger agreements), and we performed a multivariate permutational multivariate analysis of variance (PERMANOVA) using the Morosita index of dissimilarity with 9,999 iterations.The calculated average measure of intraclass correlation coefficients of different gaugers ranged from R = 0.784 to R = 0.9897 and a significant correlation was found between the repeatability and the morphometric skills of gaugers (p = 0.016). There was no significant association with the magnification of the equipment in the case of these rather small ants. The intergauger agreement, that is the reproducibility, varied between R = 0.872 and R = 0.471 (mean R = 0.690), but all gaugers arrived at the same two-species conclusion. A PERMANOVA test revealed no significant gauger effect on species identity (R 2 = 0.69, p = 0.58).Our findings show that morphometric studies are reproducible when observers follow the standard protocol; hence, morphometric findings are widely transferable and will remain a valuable data source for alpha taxonomy.
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Affiliation(s)
- Sándor Csősz
- MTA‐ELTE‐MTM Ecology Research GroupBudapestHungary
- Evolutionary Ecology Research GroupCentre for Ecological ResearchInstitute of Ecology and BotanyVácrátótHungary
| | | | - István Mikó
- Department of Biological SciencesUniversity of New HampshireDurhamNHUSA
| | | | - Marek L. Borowiec
- Department of Entomology, Plant Pathology and NematologyUniversity of IdahoIDUSA
| | - Brian L. Fisher
- Department of EntomologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Matthew Prebus
- Department of Entomology, Plant Pathology and NematologyUniversity of IdahoIDUSA
| | | | - Jean‐Claude Rakotonirina
- Madagascar Biodiversity CenterAntananarivoMadagascar
- Département d'EntomologieUniversité d'AntananarivoAntananarivoMadagascar
| | | | - Roland Schultz
- Senckenberg Museum of Natural History GörlitzGörlitzGermany
| | | | | | - Zoltán Elek
- MTA‐ELTE‐MTM Ecology Research GroupBudapestHungary
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15
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Zaher H, Smith KT. Pythons in the Eocene of Europe reveal a much older divergence of the group in sympatry with boas. Biol Lett 2020; 16:20200735. [PMID: 33321065 DOI: 10.1098/rsbl.2020.0735] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extant large constrictors, pythons and boas, have a wholly allopatric distribution that has been interpreted largely in terms of vicariance in Gondwana. Here, we describe a stem pythonid based on complete skeletons from the early-middle Eocene of Messel, Germany. The new species is close in age to the divergence of Pythonidae from North American Loxocemus and corroborates a Laurasian origin and dispersal of pythons. Remarkably, it existed in sympatry with the stem boid Eoconstrictor. These occurrences demonstrate that neither dispersal limitation nor strong competitive interactions were decisive in structuring biogeographic patterns early in the history of large, hyper-macrostomatan constrictors and exemplify the synergy between phylogenomic and palaeontological approaches in reconstructing past distributions.
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Affiliation(s)
- Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, Ipiranga 04263-000, São Paulo, SP, Brazil
| | - Krister T Smith
- Department of Messel Research and Mammalogy, Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Faculty of Biological Sciences, Institute for Ecology, Diversity and Evolution, Max-von-Laue-Strasse 13, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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16
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Natusch DJD, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Lemmon EM, Riyanto A, Keogh JS, Donnellan S. Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade. Mol Phylogenet Evol 2020; 158:106960. [PMID: 32950680 DOI: 10.1016/j.ympev.2020.106960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 11/29/2022]
Abstract
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.
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Affiliation(s)
- Daniel J D Natusch
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; EPIC Biodiversity, Frogs Hollow, NSW 2550, Australia
| | - Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra 0200, Australia
| | | | - Amir Hamidy
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Gd. Widyasatwaloka, Jl. Raya Jakarta-Bogor km 46 Cibinong, Bogor, West Java, Indonesia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University, 319 Stadium Drive, P.O. Box 3064295, 17, Tallahassee, FL 32306-4295, USA
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Gd. Widyasatwaloka, Jl. Raya Jakarta-Bogor km 46 Cibinong, Bogor, West Java, Indonesia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra 0200, Australia
| | - Stephen Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia; School of Biological Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
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17
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Brennan IG, Lemmon AR, Lemmon EM, Portik DM, Weijola V, Welton L, Donnellan SC, Keogh JS. Phylogenomics of Monitor Lizards and the Role of Competition in Dictating Body Size Disparity. Syst Biol 2020; 70:120-132. [PMID: 32521014 DOI: 10.1093/sysbio/syaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here, we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological data sets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.[Character displacement; comparative methods; phylogenetics; trait evolution; Varanus.].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Alan R Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Daniel M Portik
- Department of Ecology and Evolution, University of Arizona, Biosciences West Rm 310, 1041 E. Lowell St, Tucson, AZ 85745 USA
| | - Valter Weijola
- Zoological Museum, Biodiversity Unit, FI-20014 University of Turku, Finland
| | - Luke Welton
- Univeristy of Kansas Biodiversity Institute & Natural History Museum, 1345 Jayhawk Blvd, Lawrence, KS 66045, USA
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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