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Skeels A, Esquerré D, Lipsky D, Pellissier L, Boschman LM. Elevational Goldilocks zone underlies the exceptional diversity of a large lizard radiation (Liolaemus; Liolaemidae). Evolution 2023; 77:2672-2686. [PMID: 37756495 DOI: 10.1093/evolut/qpad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 01/05/2023] [Revised: 07/17/2023] [Accepted: 09/24/2023] [Indexed: 09/29/2023]
Abstract
Mountains are among the most biodiverse regions on the planet, and how these landforms shape diversification through the interaction of biological traits and geo-climatic dynamics is integral to understanding global biodiversity. In this study, we investigate the dual roles of climate change and mountain uplift on the evolution of a hyper-diverse radiation, Liolaemus lizards, with a spatially explicit model of diversification using a reconstruction of uplift and paleotemperature in central and southern South America. The diversification model captures a hotspot for Liolaemus around 40°S in lineages with low-dispersal ability and narrow niche breadths. Under the model, speciation rates are highest in low latitudes (<35°S) and mid elevations (~1,000 m), while extinction rates are highest at higher latitudes (>35°S) and higher elevations (>2,000 m). Temperature change through the Cenozoic explained variation in speciation and extinction rates through time and across different elevational bands. Our results point to the conditions of mid elevations being optimal for diversification (i.e., Goldilocks Zone), driven by the combination of (1) a complex topography that facilitates speciation during periods of climatic change, and (2) a relatively moderate climate that enables the persistence of ectothermic lineages and buffers species from extinction.
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Affiliation(s)
- Alexander Skeels
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra, Australia
| | - Damien Esquerré
- Research School of Biology, Australian National University, Canberra, Australia
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - Daria Lipsky
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Loïc Pellissier
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Lydian M Boschman
- Department of Environmental Systems Sciences, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pavón-Vázquez CJ, Esquerré D, Fitch AJ, Maryan B, Doughty P, Donnellan SC, Scott Keogh J. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex). Mol Phylogenet Evol 2022; 173:107516. [DOI: 10.1016/j.ympev.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
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Pavón-Vázquez CJ, Esquerré D, Keogh JS. Ontogenetic drivers of morphological evolution in monitor lizards and allies (Squamata: Paleoanguimorpha), a clade with extreme body size disparity. BMC Ecol Evol 2022; 22:15. [PMID: 35151266 PMCID: PMC8840268 DOI: 10.1186/s12862-022-01970-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Heterochrony, change in the rate or timing of development, is thought to be one of the main drivers of morphological evolution, and allometry, trait scaling patterns imposed by size, is traditionally thought to represent an evolutionary constraint. However, recent studies suggest that the ontogenetic allometric trajectories describing how organisms change as they grow may be labile and adaptive. Here we investigated the role of postnatal ontogenetic development in the morphological diversification of Paleoanguimorpha, the monitor lizards and allies, a clade with extreme body size disparity. We obtained linear and geometric morphometric data for more than 1,600 specimens belonging to three families and 60 species, representing ~ 72% of extant paleoanguimorph diversity. We used these data to undertake one of the largest comparative studies of ontogenetic allometry to date. Results Heterochrony is likely dictating morphological divergence at shallow evolutionary scales, while changes in the magnitude and direction of ontogenetic change are found mainly between major clades. Some patterns of ontogenetic variation and morphological disparity appear to reflect ontogenetic transitions in habitat use. Generally, juveniles are more similar to each other than adults, possibly because species that differ in ecology as adults are arboreal as juveniles. The magnitude of ontogenetic change follows evolutionary models where variation is constrained around an optimal value. Conversely, the direction of ontogenetic change may follow models with different adaptive optima per habitat use category or models where interspecific interactions influence its evolution. Finally, we found that the evolutionary rates of the ontogenetic allometric trajectories are phylogenetically variable. Conclusions The attributes of ontogenetic allometric trajectories and their evolutionary rates are phylogenetically heterogeneous in Paleoanguimorpha. Both allometric constraints and ecological factors have shaped ontogeny in the group. Our study highlights the evolutionary lability and adaptability of postnatal ontogeny, and teases apart how different evolutionary shifts in ontogeny contribute to the generation of morphological diversity at different evolutionary scales. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01970-6.
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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. .,Department of Biological Sciences, New York City College of Technology, City University of New York, Brooklyn, NY, 11201, USA.
| | - Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
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Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
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Melville J, Chapple DG, Keogh JS, Sumner J, Amey A, Bowles P, Brennan IG, Couper P, Donnellan SC, Doughty P, Edwards DL, Ellis RJ, Esquerré D, Fenker J, Gardner MG, Georges A, Haines ML, Hoskin CJ, Hutchinson M, Moritz C, Nankivell J, Oliver P, Pavón-Vázquez CJ, Pepper M, Rabosky DL, Sanders K, Shea G, Singhal S, Worthington Wilmer J, Tingley R. A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis. PLoS Biol 2021; 19:e3001210. [PMID: 34061821 PMCID: PMC8168848 DOI: 10.1371/journal.pbio.3001210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 11/19/2022] Open
Abstract
Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.
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Affiliation(s)
- Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, Australia
- Department of Biology, Washington University, St. Louis, MI, United States of America
- School of Biological Sciences, Monash University, Clayton, Australia
| | - David G. Chapple
- School of Biological Sciences, Monash University, Clayton, Australia
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Joanna Sumner
- Department of Sciences, Museums Victoria, Melbourne, Australia
| | - Andrew Amey
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | - Phil Bowles
- Snake & Lizard Red List Authority, CI-IUCN Biodiversity Assessment Unit, IUCN North America Office, Washington, DC, United States of America
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Patrick Couper
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
| | | | - Paul Doughty
- Collections & Research, Western Australian Museum, Welshpool, Australia
| | - Danielle L. Edwards
- Department of Life & Environmental Sciences, University of California, Merced, Merced, CA, United States of America
| | - Ryan J. Ellis
- Collections & Research, Western Australian Museum, Welshpool, Australia
- Biologic Environmental Survey, East Perth, Australia
| | - Damien Esquerré
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Jéssica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Michael G. Gardner
- South Australian Museum, North Terrace, Adelaide, Australia
- College of Science & Engineering, Flinders University, Adelaide, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | | | - Conrad J. Hoskin
- College of Science & Engineering, James Cook University, Townsville, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - James Nankivell
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Paul Oliver
- Biodiversity & Geosciences Program, Queensland Museum, Brisbane, Australia
- Environmental Futures Research Institute, Griffith University, Australia
| | - Carlos J. Pavón-Vázquez
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Mitzy Pepper
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Kate Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Glenn Shea
- School of Veterinary Science, University of Sydney, Sydney, Australia
- Australian Museum Research Institute, The Australian Museum, Sydney, Australia
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA, United States of America
| | | | - Reid Tingley
- School of Biological Sciences, Monash University, Clayton, Australia
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Esquerré D, Donnellan SC, Pavón-Vázquez CJ, Fenker J, Keogh JS. Phylogeography, historical demography and systematics of the world's smallest pythons (Pythonidae, Antaresia). Mol Phylogenet Evol 2021; 161:107181. [PMID: 33892100 DOI: 10.1016/j.ympev.2021.107181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022]
Abstract
Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.
| | | | - Carlos J Pavón-Vázquez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Jéssica Fenker
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Álvarez-Varas R, Heidemeyer M, Riginos C, Benítez HA, Reséndiz E, Lara-Uc M, Godoy DA, Muñoz-Pérez JP, Alarcón-Ruales DE, Vélez-Rubio GM, Fallabrino A, Piovano S, Alfaro-Shigueto J, Ortiz-Alvarez C, Mangel JC, Esquerré D, Zárate P, Medrano C, León Miranda F, Guerrero F, Vianna JA, Véliz D. Integrating morphological and genetic data at different spatial scales in a cosmopolitan marine turtle species: challenges for management and conservation. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractPatterns of genetic structure in highly mobile marine vertebrates may be accompanied by phenotypic variation. Most studies in marine turtles focused on population genetic structure have been performed at rookeries. We studied whether genetic and morphological variation of the endangered green turtle (Chelonia mydas) is consistent geographically, focusing on foraging grounds. An association between population genetic structure and body shape variation at broad (inter-lineage) and fine (foraging grounds) scales was predicted and analysed using mitochondrial DNA and geometric morphometrics. Although genetic and phenotypic differentiation patterns were congruent between lineages, no fine-scale association was found, suggesting adaptive divergence. Connectivity among Pacific foraging grounds found here suggests that temperatures of ocean surface currents may influence the genetic structure of C. mydas on a broad scale. Our results suggest that vicariance, dispersal, life-history traits and ecological conditions operating in foraging grounds have shaped the intraspecific morphology and genetic diversity of this species. Considering a range of geographic and temporal scales is useful when management strategies are required for cosmopolitan species. Integrating morphological and genetic tools at different spatial scales, conservation management is proposed based on protection of neutral and adaptive diversity. This approach opens new questions and challenges, especially regarding conservation genetics in cosmopolitan species.
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Affiliation(s)
- Rocío Álvarez-Varas
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
- Qarapara Tortugas Marinas Chile Non-governmental Organization, Santiago, Chile
| | - Maike Heidemeyer
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Hugo A Benítez
- Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, México
| | - Mónica Lara-Uc
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, México
| | - Daniel A Godoy
- Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Juan Pablo Muñoz-Pérez
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galapagos, Ecuador
- University of the Sunshine Coast USC, Queensland, Australia
| | - Daniela E Alarcón-Ruales
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galapagos, Ecuador
| | | | | | - Susanna Piovano
- School of Marine Studies, The University of the South Pacific, Suva, Fiji
| | - Joanna Alfaro-Shigueto
- ProDelphinus, Lima, Peru
- Facultad de Biología Marina, Universidad Científica del Sur, Lima, Peru
| | | | | | - Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Patricia Zárate
- Departamento de Oceanografía y Medio Ambiente, Instituto de Fomento Pesquero, Valparaíso, Chile
| | - Carol Medrano
- Qarapara Tortugas Marinas Chile Non-governmental Organization, Santiago, Chile
| | - Fabiola León Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Guerrero
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Qarapara Tortugas Marinas Chile Non-governmental Organization, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
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Medina I, Vega-Trejo R, Wallenius T, Esquerré D, León C, Perez DM, Head ML. No link between nymph and adult coloration in shield bugs: weak selection by predators. Proc Biol Sci 2020; 287:20201011. [PMID: 32576112 PMCID: PMC7329039 DOI: 10.1098/rspb.2020.1011] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/04/2020] [Indexed: 11/12/2022] Open
Abstract
Many organisms use different antipredator strategies throughout their life, but little is known about the reasons or implications of such changes. For years, it has been suggested that selection by predators should favour uniformity in local warning signals. If this is the case, we would expect high resemblance in colour across life stages in aposematic animals where young and adults share similar morphology and habitat. In this study, we used shield bugs (Hemiptera: Pentatomoidea) to test whether colour and colour diversity evolve similarly at different life stages. Since many of these bugs are considered to be aposematic, we also combined multi-species analyses with predation experiments on the cotton harlequin bug to test whether there is evidence of selection for uniformity in colour across life stages. Overall, we show that the diversity of colours used by both life stages is comparable, but adults are more cryptic than nymphs. We also demonstrate that nymphs and adults of the same species do not tend to look alike. Experiments on our model system suggest that predators can generalise among life stages that look different, and exhibit strong neophobia. Altogether, our results show no evidence of selection favouring colour similarity between adults and nymphs in this speciose clade.
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Affiliation(s)
- Iliana Medina
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Thomas Wallenius
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Damien Esquerré
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Constanza León
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Daniela M. Perez
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Megan L. Head
- Division of Ecology and Evolution, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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11
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Esquerré D, Donnellan S, Brennan IG, Lemmon AR, Moriarty Lemmon E, Zaher H, Grazziotin FG, Keogh JS. Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line. Syst Biol 2020; 69:1039-1051. [DOI: 10.1093/sysbio/syaa024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Lydekker’s line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promote morphological diversification in a formerly ecomorphologically conservative group. [Adaptive radiation; anchored hybrid enrichment; biogeography; morphometrics; snakes.]
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library Tallahassee, FL 32306-4120, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, CEP 04263-000, São Paulo, SP, Brazil
- CR2P – Centre de Recherche em Paléontologie – MNHN – Sorbonne Université – CNRS, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, SP, Brazil
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
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12
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Natusch DJ, Esquerré D, Lyons JA, Hamidy A, Lemmon AR, Moriarty Lemmon E, Riyanto A, Keogh JS, Donnellan S. Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia. Mol Phylogenet Evol 2020; 142:106640. [DOI: 10.1016/j.ympev.2019.106640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/30/2019] [Accepted: 10/05/2019] [Indexed: 02/01/2023]
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13
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Jehl F, Désert C, Klopp C, Brenet M, Rau A, Leroux S, Boutin M, Lagoutte L, Muret K, Blum Y, Esquerré D, Gourichon D, Burlot T, Collin A, Pitel F, Benani A, Zerjal T, Lagarrigue S. Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach. BMC Genomics 2019; 20:1033. [PMID: 31888468 PMCID: PMC6937963 DOI: 10.1186/s12864-019-6384-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
Background Production conditions of layer chicken can vary in terms of temperature or diet energy content compared to the controlled environment where pure-bred selection is undertaken. The aim of this study was to better understand the long-term effects of a 15%-energy depleted diet on egg-production, energy homeostasis and metabolism via a multi-tissue transcriptomic analysis. Study was designed to compare effects of the nutritional intervention in two layer chicken lines divergently selected for residual feed intake. Results Chicken adapted to the diet in terms of production by significantly increasing their feed intake and decreasing their body weight and body fat composition, while their egg production was unchanged. No significant interaction was observed between diet and line for the production traits. The low energy diet had no effect on adipose tissue and liver transcriptomes. By contrast, the nutritional challenge affected the blood transcriptome and, more severely, the hypothalamus transcriptome which displayed 2700 differentially expressed genes. In this tissue, the low-energy diet lead to an over-expression of genes related to endocannabinoid signaling (CN1R, NAPE-PLD) and to the complement system, a part of the immune system, both known to regulate feed intake. Both mechanisms are associated to genes related polyunsaturated fatty acids synthesis (FADS1, ELOVL5 and FADS2), like the arachidonic acid, a precursor of anandamide, a key endocannabinoid, and of prostaglandins, that mediate the regulatory effects of the complement system. A possible regulatory role of NR1H3 (alias LXRα) has been associated to these transcriptional changes. The low-energy diet further affected brain plasticity-related genes involved in the cholesterol synthesis and in the synaptic activity, revealing a link between nutrition and brain plasticity. It upregulated genes related to protein synthesis, mitochondrial oxidative phosphorylation and fatty acid oxidation in the hypothalamus, suggesting reorganization in nutrient utilization and biological synthesis in this brain area. Conclusions We observed a complex transcriptome modulation in the hypothalamus of chicken in response to low-energy diet suggesting numerous changes in synaptic plasticity, endocannabinoid regulation, neurotransmission, lipid metabolism, mitochondrial activity and protein synthesis. This global transcriptomic reprogramming could explain the adaptive behavioral response (i.e. increase of feed intake) of the animals to the low-energy content of the diet.
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Affiliation(s)
- F Jehl
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - C Désert
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - C Klopp
- SIGENAE Plateform, INRA, 31326, Castanet-Tolosan, France
| | - M Brenet
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - A Rau
- GABI UMR 1313, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - S Leroux
- GenPhySE UMR 1388, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - M Boutin
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - L Lagoutte
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - K Muret
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - Y Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, 75013, Paris, France
| | - D Esquerré
- GENOTOUL Plateform, INRA, 31326, Castanet-Tolosan, France
| | | | - T Burlot
- NOVOGEN, Mauguérand, 22800, Le Foeil, France
| | - A Collin
- BOA UMR, INRA, Université de Tours, 37380, Nouzilly, France
| | - F Pitel
- GenPhySE UMR 1388, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - A Benani
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université de Bourgogne, Dijon, France
| | - T Zerjal
- SIGENAE Plateform, INRA, 31326, Castanet-Tolosan, France.
| | - S Lagarrigue
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France.
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14
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Esquerré D, Ramírez-Álvarez D, Pavón-Vázquez CJ, Troncoso-Palacios J, Garín CF, Keogh JS, Leaché AD. Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae). Mol Phylogenet Evol 2019; 139:106524. [DOI: 10.1016/j.ympev.2019.106524] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/30/2022]
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15
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Cádiz FJ, Esquerré D, Cádiz VH, Martins FM. Phylogeography of
Plectostylus
Beck, 1837 (Gastropoda: Stylommatophora: Orthalicoidea): Origin and isolation of the Fray Jorge forest relicts in northern Chile. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco J. Cádiz
- Department of Zoology Biosciences Institute University of São Paulo São Paulo Brazil
| | - Damien Esquerré
- Ecology and Evolution, Research School of Biology The Australian National University Canberra ACT Australia
| | - Victor H. Cádiz
- Escuela de Terapia Ocupacional Facultad de Medicina Edificio de Ciencias Biomédicas Universidad Austral de Chile Valdivia Chile
| | - Felipe M. Martins
- Ecology and Evolution, Research School of Biology The Australian National University Canberra ACT Australia
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16
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Esquerré D, Brennan IG, Catullo RA, Torres‐Pérez F, Keogh JS. How mountains shape biodiversity: The role of the Andes in biogeography, diversification, and reproductive biology in South America's most species‐rich lizard radiation (Squamata: Liolaemidae). Evolution 2018; 73:214-230. [DOI: 10.1111/evo.13657] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/04/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
| | - Renee A. Catullo
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
- School of Science & Health and Hawkesbury Institute for the EnvironmentWestern Sydney University 2751 Perth New South Wales Australia
| | - Fernando Torres‐Pérez
- Instituto de BiologíaPontificia Universidad Católica de Valparaíso 2950 Valparaíso Chile
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of BiologyThe Australian National University 0200 Canberra Australian Capital Territory Australia
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17
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Maroilley T, Berri M, Lemonnier G, Esquerré D, Chevaleyre C, Mélo S, Meurens F, Coville JL, Leplat JJ, Rau A, Bed'hom B, Vincent-Naulleau S, Mercat MJ, Billon Y, Lepage P, Rogel-Gaillard C, Estellé J. Immunome differences between porcine ileal and jejunal Peyer's patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues. Sci Rep 2018; 8:9077. [PMID: 29899562 PMCID: PMC5998120 DOI: 10.1038/s41598-018-27019-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/18/2018] [Indexed: 01/09/2023] Open
Abstract
The epithelium of the intestinal mucosa and the gut-associated lymphoid tissues (GALT) constitute an essential physical and immunological barrier against pathogens. In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer’s patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genes FOXP3, GATA3, STAT4, TBX21 and RORC were less expressed in IPPs compared to JPPs, whereas the transcription factor BCL6 was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specific cis-genetic control of gene expression.
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Affiliation(s)
- T Maroilley
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - M Berri
- ISP, INRA, Université de Tours, 37380, Nouzilly, France
| | - G Lemonnier
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - D Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castenet-Tolosan, France
| | - C Chevaleyre
- ISP, INRA, Université de Tours, 37380, Nouzilly, France
| | - S Mélo
- ISP, INRA, Université de Tours, 37380, Nouzilly, France
| | - F Meurens
- ISP, INRA, Université de Tours, 37380, Nouzilly, France.,BIOEPAR, INRA, Oniris, La Chantrerie, 44307, Nantes, France
| | - J L Coville
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J J Leplat
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,LREG, IRCM, DRF, CEA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - A Rau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - B Bed'hom
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - S Vincent-Naulleau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,LREG, IRCM, DRF, CEA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - M J Mercat
- BIOPORC and IFIP-Institut du porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu, France
| | - Y Billon
- GENESI, INRA, 17700, Surgères, France
| | - P Lepage
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - C Rogel-Gaillard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - J Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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18
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Maroilley T, Lemonnier G, Lecardonnel J, Esquerré D, Ramayo-Caldas Y, Mercat MJ, Rogel-Gaillard C, Estellé J. Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis. BMC Genomics 2017; 18:967. [PMID: 29237423 PMCID: PMC5729405 DOI: 10.1186/s12864-017-4354-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. The objective of this work was to study the genetic architecture of variation in gene expression in the blood of healthy young pigs using two approaches: an expression genome-wide association study (eGWAS) and allele-specific expression (ASE) analysis. RESULTS The blood transcriptomes of 60-day-old Large White pigs were analyzed by expression microarrays for eGWAS (242 animals) and by RNA-Seq for ASE analysis (38 animals). Using eGWAS, the expression levels of 1901 genes were found to be associated with expression quantitative trait loci (eQTLs). We recovered 2839 local and 1752 distant associations (Single Nucleotide Polymorphism or SNP located less or more than 1 Mb from expression probe, respectively). ASE analyses confirmed the extensive cis-regulation of gene transcription in blood, and revealed allelic imbalance in 2286 SNPs, which affected 763 genes. eQTLs and ASE-genes were widely distributed on all chromosomes. By analyzing mutually overlapping eGWAS results, we were able to describe putative regulatory networks, which were further refined using ASE data. At the functional level, genes with genetically controlled expression that were detected by eGWAS and/or ASE analyses were significantly enriched in biological processes related to RNA processing and immune function. Indeed, numerous distant and local regulatory relationships were detected within the major histocompatibility complex region on chromosome 7, revealing ASE for most class I and II genes. CONCLUSIONS This study represents, to the best of our knowledge, the first genome-wide map of the genetic control of gene expression in porcine peripheral blood. These results represent an interesting resource for the identification of genetic markers and blood biomarkers associated with variations in immunity traits in pigs, as well as any other complex traits for which blood is an appropriate surrogate tissue.
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Affiliation(s)
- T Maroilley
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - G Lemonnier
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - D Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Y Ramayo-Caldas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - M J Mercat
- IFIP - Institut du porc/BIOPORC, La Motte au Vicomte, BP 35104, 35651, Le Rheu, France
| | - C Rogel-Gaillard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - J Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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19
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Esquerré D, Sherratt E, Keogh JS. Evolution of extreme ontogenetic allometric diversity and heterochrony in pythons, a clade of giant and dwarf snakes. Evolution 2017; 71:2829-2844. [DOI: 10.1111/evo.13382] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology The Australian National University Canberra Australia
| | - Emma Sherratt
- Division of Ecology and Evolution, Research School of Biology The Australian National University Canberra Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology The Australian National University Canberra Australia
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20
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Coyral-Castel S, Ramé C, Cognié J, Lecardonnel J, Marthey S, Esquerré D, Hennequet-Antier C, Elis S, Fritz S, Boussaha M, Jaffrézic F, Dupont J. KIRREL is differentially expressed in adipose tissue from 'fertil+' and 'fertil-' cows: in vitro role in ovary? Reproduction 2017; 155:183-198. [PMID: 29170164 DOI: 10.1530/rep-17-0649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 11/18/2017] [Accepted: 11/23/2017] [Indexed: 01/10/2023]
Abstract
We have previously shown that dairy cows carrying the 'fertil-' haplotype for one quantitative trait locus affecting female fertility located on the bovine chromosome three (QTL-F-Fert-BTA3) have a significantly lower conception rate and body weight after calving than cows carrying the 'fertil+' haplotype. Here, we compared by Tiling Array the expression of genes included in the QTL-F-Fert-BTA3 in 'fertil+' and 'fertil-' adipose tissue one week after calving when plasma non-esterified fatty acid concentrations were greater in 'fertil-' animals. We observed that thirty-one genes were overexpressed whereas twelve were under-expressed in 'fertil+' as compared to 'fertil-' cows (P < 0.05). By quantitative PCR and immunoblot we confirmed that adipose tissue KIRREL mRNA and protein were significantly greater expressed in 'fertil+' than in 'fertil-'. KIRREL mRNA is abundant in bovine kidney, adipose tissue, pituitary, and ovary and detectable in hypothalamus and mammary gland. Its expression (mRNA and protein) is greater in kidney of 'fertil+' than 'fertil-' cows (P < 0.05). KIRREL (mRNA and protein) is also present in the different ovarian cells with a greater expression in granulosa cells of 'fertil+' than 'fertil-' cows. In cultured granulosa cells, recombinant KIRREL halved steroid secretion in basal state (P < 0.05). It also decreased cell proliferation (P < 0.05) and in vitro oocyte maturation (P < 0.05). These results were associated to a rapid increase in MAPK1/3 and MAPK14 phosphorylation in granulosa cells and to a decrease in MAPK1/3 phosphorylation in oocyte. Thus, KIRREL could be a potential metabolic messenger linking body composition and fertility.
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Affiliation(s)
- S Coyral-Castel
- INRAUMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRSUMR7247, Nouzilly, France.,Université François Rabelais de ToursTours, France.,IFCENouzilly, France.,Département GIPSIEInstitut de l'Elevage, Paris Cedex 12, France
| | - C Ramé
- INRAUMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRSUMR7247, Nouzilly, France.,Université François Rabelais de ToursTours, France.,IFCENouzilly, France
| | - J Cognié
- INRAUMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRSUMR7247, Nouzilly, France.,Université François Rabelais de ToursTours, France.,IFCENouzilly, France
| | - J Lecardonnel
- INRAUMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.,AgroParisTechUMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - S Marthey
- INRAUMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.,AgroParisTechUMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - D Esquerré
- INRAUMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.,AgroParisTechUMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | | | - S Elis
- INRAUMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France.,CNRSUMR7247, Nouzilly, France.,Université François Rabelais de ToursTours, France.,IFCENouzilly, France
| | - S Fritz
- ALLICEParis Cedex 12, France
| | - M Boussaha
- INRAUMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.,AgroParisTechUMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - F Jaffrézic
- INRAUMR1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France.,AgroParisTechUMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - J Dupont
- INRAUMR85 Physiologie de la Reproduction et des Comportements, Nouzilly, France .,CNRSUMR7247, Nouzilly, France.,Université François Rabelais de ToursTours, France.,IFCENouzilly, France
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Giuffra E, Munyard KA, Goubil A, Vincent-Naulleau S, Esquerré D, Djebali S, Foissac S. P3038 Chromatin accessibility in the liver and circulating immune cells of pigs, goats and chickens. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement471a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Letaief R, Grohs C, Fritz S, Rocha D, Boussaha M, Esquerré D, Barbieri J, Fritz S, Klopp C, Philippe R, Blanquet V, Boichard D. P8006 Identification and characterization of copy number variations in cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4183a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Esquerré D, Scott Keogh J. Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas. Ecol Lett 2016; 19:800-9. [DOI: 10.1111/ele.12620] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/11/2016] [Accepted: 04/26/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Damien Esquerré
- Division of Evolution, Ecology and Genetics Research School of Biology The Australian National University Canberra ACT 0200 Australia
| | - J. Scott Keogh
- Division of Evolution, Ecology and Genetics Research School of Biology The Australian National University Canberra ACT 0200 Australia
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Esquerré D, Troncoso-Palacios J, Barros R. Liolaemus riodamas Esquerré, Núñez & Scolaro, 2013 (Reptilia: Squamata: Liolaemidae): new record for the Maule Region in Chile. cl 2016. [DOI: 10.15560/12.2.1871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Liolaemus riodamas is a recently described lizard, only known from a very restricted river canyon in the Andes of the O’Higgins Region in Chile. The species is particular for being one of the few Liolaemus lacking the pheromone secreting glands known as precloacal pores. Here we document a second locality for this species located 30 km southwest of the type locality. This is also 500 m higher than the type locality, therefore a considerable altitudinal extension. This is a very positive discovery since the type locality of L. riodamas is intervened by a hydroelectric project, and gives hope to the conservation of this unique taxon.
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Troncoso-Palacios J, Díaz HA, Esquerré D, Urra FA. Two new species of the Liolaemuselongatus-kriegi complex (Iguania, Liolaemidae) from Andean highlands of southern Chile. Zookeys 2015:83-109. [PMID: 25987873 PMCID: PMC4432242 DOI: 10.3897/zookeys.500.8725] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/18/2015] [Indexed: 11/26/2022] Open
Abstract
The elongatus-kriegi complex is one of the most diverse clades of the Liolaemus (sensu stricto) subgenus of lizards. There are currently 29 species recognized in this group distributed between Chile and Argentina. Based on molecular evidence, there seem to be five main clades nested within this complex: the elongatus, leopardinus, kriegi, petrophilus and punmahuida clades. Liolaemusbuergeri and Liolaemuskriegi, both of the kriegi clade, were believed to inhabit the surroundings of the Laja Lagoon, in the Biobío Region of Chile. Moreover, this Chilean population of Liolaemuskriegi was recently recognized as an undescribed taxon called “Liolaemus sp. A” based on molecular phylogenetics. In this work, we studied these two populations of the Laja Lagoon and provided the morphological diagnosis to describe them as two new species: Liolaemusscorialissp. n. and Liolaemuszabalaisp. n., previously considered Liolaemusbuergeri and “Liolaemuskriegi/Liolaemus sp. A” respectively. Additionally, we identified another population of Liolaemusscorialis in the vicinity of La Mula Lagoon in the Araucanía Region of Chile. Liolaemusscorialis differs from almost all of the species of the elongatus-kriegi complex by its considerably smaller size. Nevertheless, without molecular data we cannot assign it to any particular subclade. Liolaemuszabalai belongs to the kriegi clade based on published molecular phylogenies. Finally, we provide some natural history data on both species and we document for the first time the presence of Liolaemusneuquensis in Chile from a museum specimen from La Mula Lagoon.
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Affiliation(s)
- Jaime Troncoso-Palacios
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Hugo A Díaz
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile ; Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile
| | - Damien Esquerré
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Felix A Urra
- Programa de Fisiología y Biofísica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile ; Programa de Farmacología Molecular y Clínica, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
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Roux PF, Marthey S, Djari A, Moroldo M, Esquerré D, Estellé J, Klopp C, Lagarrigue S, Demeure O. Comparison of whole-genome (13X) and capture (87X) resequencing methods for SNP and genotype callings. Anim Genet 2014; 46:82-6. [PMID: 25515399 DOI: 10.1111/age.12248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2014] [Indexed: 12/30/2022]
Abstract
The number of polymorphisms identified with next-generation sequencing approaches depends directly on the sequencing depth and therefore on the experimental cost. Although higher levels of depth ensure more sensitive and more specific SNP calls, economic constraints limit the increase of depth for whole-genome resequencing (WGS). For this reason, capture resequencing is used for studies focusing on only some specific regions of the genome. However, several biases in capture resequencing are known to have a negative impact on the sensitivity of SNP detection. Within this framework, the aim of this study was to compare the accuracy of WGS and capture resequencing on SNP detection and genotype calling, which differ in terms of both sequencing depth and biases. Indeed, we have evaluated the SNP calling and genotyping accuracy in a WGS dataset (13X) and in a capture resequencing dataset (87X) performed on 11 individuals. The percentage of SNPs not identified due to a sevenfold sequencing depth decrease was estimated at 7.8% using a down-sampling procedure on the capture sequencing dataset. A comparison of the 87X capture sequencing dataset with the WGS dataset revealed that capture-related biases were leading with the loss of 5.2% of SNPs detected with WGS. Nevertheless, when considering the SNPs detected by both approaches, capture sequencing appears to achieve far better SNP genotyping, with about 4.4% of the WGS genotypes that can be considered as erroneous and even 10% focusing on heterozygous genotypes. In conclusion, WGS and capture deep sequencing can be considered equivalent strategies for SNP detection, as the rate of SNPs not identified because of a low sequencing depth in the former is quite similar to SNPs missed because of method biases of the latter. On the other hand, capture deep sequencing clearly appears more adapted for studies requiring great accuracy in genotyping.
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Affiliation(s)
- P F Roux
- INRA, UMR1348 PEGASE, Saint-Gilles, F-35590, France; Agrocampus Ouest, UMR1348 PEGASE, Rennes, F-35000, France; Université Européenne de Bretagne, Rennes, France
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Esquerré D, Keogh JS, Schwanz LE. Direct effects of incubation temperature on morphology, thermoregulatory behaviour and locomotor performance in jacky dragons (Amphibolurus muricatus). J Therm Biol 2014; 43:33-9. [DOI: 10.1016/j.jtherbio.2014.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/19/2014] [Accepted: 04/26/2014] [Indexed: 11/26/2022]
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