1
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Probst RS, Longino JT, Branstetter MG. Evolutionary déjà vu? A case of convergent evolution in an ant-plant association. Proc Biol Sci 2024; 291:20241214. [PMID: 38981524 PMCID: PMC11334994 DOI: 10.1098/rspb.2024.1214] [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: 10/01/2023] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.
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Affiliation(s)
- Rodolfo S. Probst
- Science Research Initiative (SRI), College of Science, University of Utah, Salt Lake City, UT84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112, USA
| | - John T. Longino
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112, USA
| | - Michael G. Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT84322, USA
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2
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Graham ZA, Padilla Perez DJ. Correlated evolution of conspicuous colouration and burrowing in crayfish. Proc Biol Sci 2024; 291:20240632. [PMID: 38981529 PMCID: PMC11335007 DOI: 10.1098/rspb.2024.0632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 05/02/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024] Open
Abstract
Conspicuous colours have fascinated biologists for centuries, leading to research on the evolution and functional significance of colour traits. In many cases, research suggests that conspicuous colours are adaptive and serve a function in sexual or aposematic signalling. In other cases, a lack of evidence for the adaptive value of conspicuous colours garners interest from biologists, such as when organisms that live underground and are rarely exposed to the surface are nevertheless colourful. Here, we use phylogenetic comparative methods to investigate colour evolution throughout freshwater crayfishes that vary in burrowing ability. Within the taxa we analysed, conspicuous colours have evolved independently over 50 times, and these colours are more common in semi-terrestrial crayfishes that construct extensive burrows. The intuitive but not evolutionarily justified assumption when presented with these results is to assume that these colours are adaptive. But contrary to this intuition, we discuss the hypothesis that colouration in crayfish is neutral. Supporting these ideas, the small population sizes and reduced gene flow within semi-terrestrial burrowing crayfishes may lead to the fixation of colour-phenotype mutations. Overall, our work brings into question the traditional view of animal colouration as a perfectly adapted phenotype.
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Affiliation(s)
- Zackary A. Graham
- Department of Organismal Biology, Ecology, and Zoo Science, West Liberty University, 208 University Drive, West Liberty, WV26074, USA
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3
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Saclier N, Duchemin L, Konecny-Dupré L, Grison P, Eme D, Martin C, Callou C, Lefébure T, François C, Issartel C, Lewis JJ, Stoch F, Sket B, Gottstein S, Delić T, Zagmajster M, Grabowski M, Weber D, Reboleira ASPS, Palatov D, Paragamian K, Knight LRFD, Michel G, Lefebvre F, Hosseini MJM, Camacho AI, De Bikuña BG, Taleb A, Belaidi N, Tuekam Kayo RP, Galassi DMP, Moldovan OT, Douady CJ, Malard F. A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database. Mol Ecol Resour 2024; 24:e13882. [PMID: 37864541 DOI: 10.1111/1755-0998.13882] [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: 04/19/2023] [Revised: 09/09/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species-rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large-scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade-offs during groundwater colonization.
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Affiliation(s)
- Nathanaelle Saclier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Louis Duchemin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Philippe Grison
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - David Eme
- INRAE, UR-RiverLY, Centre Lyon-Grenoble Auvergne-Rhône-Alpes, Villeurbanne, France
| | - Chloé Martin
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Cécile Callou
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Clémentine François
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Colin Issartel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Julian J Lewis
- Virginia Museum of Natural History, Martinsville, Virginia, USA
- Lewis and Associates, Cave, Karst and Groundwater Biological Consulting, Borden, Indiana, USA
| | - Fabio Stoch
- Evolutionary Biology & Ecology, Université libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Boris Sket
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sanja Gottstein
- Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Teo Delić
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zagmajster
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michal Grabowski
- Department of Invertebrate Zoology & Hydrobiology, Faculty of Biology & Environmental Protection, University of Lodz, Lodz, Poland
| | - Dieter Weber
- Musée National d'Histoire Naturelle de Luxembourg, Luxembourg City, Luxembourg
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Ana Sofia P S Reboleira
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dmitry Palatov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Georges Michel
- CWEPSS, Commission Wallonne d'Etude et de Protection des Sites Souterrains, Bruxelles, Belgium
| | | | - Mohammad-Javad Malek Hosseini
- Jovan Hadži Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts (ZRC-SAZU), Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology (NIB), Ljubljana, Slovenia
| | - Ana I Camacho
- Museo Nacional de Ciencias Naturales (CSIC). Dpto. Biodiversidad y Biología Evolutiva, Madrid, Spain
| | - Begoña Gartzia De Bikuña
- Anbiotek, Investigación científica y técnica del medio ambiente, Erandio, Bizkaia, Spain
- Anbiolab, BIC Bizkaia Astondo bidea, Derio, Spain
| | - Amina Taleb
- Laboratoire d'Écologie et Gestion des Ecosystèmes Naturels, University of Tlemcen, Tlemcen, Algeria
| | - Nouria Belaidi
- Laboratoire d'Écologie et Gestion des Ecosystèmes Naturels, University of Tlemcen, Tlemcen, Algeria
| | - Raoul P Tuekam Kayo
- Faculty of Science, Department of Zoology, University of Bamenda, Bambili, Cameroon
| | | | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Centro Nacional de Investigación sobre la Evolución Humana, Burgos, Spain
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
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4
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Bozza DC, Freire CA, Prodocimo V. A systematic evaluation on the relationship between hypo-osmoregulation and hyper-osmoregulation in decapods of different habitats. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:5-30. [PMID: 37853933 DOI: 10.1002/jez.2757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 09/06/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Decapods occupy all aquatic, and terrestrial and semi-terrestrial environments. According to their osmoregulatory capacity, they can be osmoconformers or osmoregulators (hypo or hyperegulators). The goal of this study is to gather data available in the literature for aquatic decapods and verify if the rare hyporegulatory capacity of decapods is associated with hyper-regulatory capacity. The metric used to quantify osmoregulation was the osmotic capacity (OC), the gradient between external and internal (hemolymph) osmolalities. We employ phylogenetic comparative methods using 83 species of decapods to test the correlation between hyper OC and hypo OC, beyond the ancestral state for osmolality habitat, which was used to reconstruct the colonization route. Our analysis showed a phylogenetic signal for habitat osmolality, hyper OC and hypo OC, suggesting that hyper-hyporegulators decapods occupy similar habitats and show similar hyper and hyporegulatory capacities. Our findings reveal that all hyper-hyporegulators decapods (mainly shrimps and crabs) originated in estuarine waters. Hyper OC and hypo OC are correlated in decapods, suggesting correlated evolution. The analysis showed that species which inhabit environments with intense salinity variation such as estuaries, supratidal and mangrove habitats, all undergo selective pressure to acquire efficient hyper-hyporegulatory mechanisms, aided by low permeabilities. Therefore, hyporegulation can be observed in any colonization route that passes through environments with extreme variations in salinity, such as estuaries or brackish water.
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Affiliation(s)
- Deivyson Cattine Bozza
- Departamento de Fisiologia, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Curitiba, Brazil
| | - Carolina Arruda Freire
- Departamento de Fisiologia, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Curitiba, Brazil
| | - Viviane Prodocimo
- Departamento de Fisiologia, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Curitiba, Brazil
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5
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Di Cicco M, Di Lorenzo T, Fiasca B, Galmarini E, Vaccarelli I, Cerasoli F, Tabilio Di Camillo A, Galassi DMP. Some like it hot: Thermal preference of the groundwater amphipod Niphargus longicaudatus (Costa, 1851) and climate change implications. J Therm Biol 2023; 116:103654. [PMID: 37478581 DOI: 10.1016/j.jtherbio.2023.103654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Abstract
Groundwater is a crucial resource for humans and the environment, but its global human demand currently exceeds available volumes by 3.5 times. Climate change is expected to exacerbate this situation by increasing the frequency of droughts along with human impacts on groundwater ecosystems. Despite prior research on the quantitative effects of climate change on groundwater, the direct impacts on groundwater biodiversity, especially obligate groundwater species, remain largely unexplored. Therefore, investigating the potential impacts of climate change, including groundwater temperature changes, is crucial for the survival of obligate groundwater species. This study aimed to determine the thermal niche breadth of the crustacean amphipod species Niphargus longicaudatus by using the chronic method. We found that N. longicaudatus has a wide thermal niche with a natural performance range of 7-9 °C, which corresponds to the thermal regime this species experiences within its distribution range in Italy. The observed range of preferred temperature (PT) was different from the mean annual temperature of the sites from which the species has been collected, challenging the idea that groundwater species are only adapted to narrow temperature ranges. Considering the significant threats of climate change to groundwater ecosystems, these findings provide crucial information for the conservation of obligate groundwater species, suggesting that some of them may be more resilient to temperature changes than previously thought. Understanding the fundamental thermal niche of these species can inform conservation efforts and management strategies to protect groundwater ecosystems and their communities.
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Affiliation(s)
- Mattia Di Cicco
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy.
| | - Tiziana Di Lorenzo
- National Biodiversity Future Center, Palermo, Italy; IRET-CNR, Istituto di Ricerca Sugli Ecosistemi Terrestri Del CNR, Florence, Italy; Racovitza Institute of Speleology, Romanian Academy, Clinicilor 400006 Cluj Napoca, Romania; Departamento de Biologia Animal, Faculdade de Ciências, Centre for, Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal. 4 Natural History Museum of Denmark
| | - Barbara Fiasca
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Emma Galmarini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Ilaria Vaccarelli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy; University Institute of Higher Studies in Pavia, Pavia, Italy
| | - Francesco Cerasoli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
| | - Agostina Tabilio Di Camillo
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy; IRET-CNR, Istituto di Ricerca Sugli Ecosistemi Terrestri Del CNR, Florence, Italy
| | - Diana Maria Paola Galassi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Via Vetoio, 67100 L'Aquila, Italy
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6
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Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol 2023; 40:msac269. [PMID: 36508357 PMCID: PMC11249980 DOI: 10.1093/molbev/msac269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/14/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Interspecies RNA-Seq datasets are increasingly common, and have the potential to answer new questions about the evolution of gene expression. Single-species differential expression analysis is now a well-studied problem that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available methods in various settings. However, synthetic dataset simulation tools are still missing in the interspecies gene expression context. In this work, we develop and implement a new simulation framework. This tool builds on both the RNA-Seq and the phylogenetic comparative methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the usefulness of this new framework through a targeted simulation study, that reproduces the features of a recently published dataset, containing gene expression data in adult eye tissue across blind and sighted freshwater crayfish species. Using our simulated datasets, we perform a fair comparison of several approaches used for differential expression analysis. This benchmark reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for interspecies differential expression analysis, and allows for a reanalysis of the crayfish dataset. The tool has been integrated in the R package compcodeR, freely available on Bioconductor.
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Affiliation(s)
- Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David B Stern
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
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7
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Horváth G, Kerekes K, Nyitrai V, Balázs G, Berisha H, Herczeg G. Exploratory behaviour divergence between surface populations, cave colonists and a cave population in the water louse, Asellus aquaticus. Behav Ecol Sociobiol 2023. [DOI: 10.1007/s00265-022-03288-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Abstract
Behaviour is considered among the most important factors in colonising new
habitats. While population divergence in behaviour is well-documented, intraspecific
variation in exploratory behaviour in species with populations successfully colonising and
adapting to extreme (compared to the ‘typical’) habitats is less understood. Here, by studying
surface- vs. cave-adapted populations of water louse (Asellus aquaticus), we tested whether (i)
adaptation to the special, ecologically isolated cave habitat includes a decrease in
explorativeness and (ii) recent, surface-type cave colonists are more explorative than their
surface conspecifics from the source population. We repeatedly tested dispersal related novel
area exploration and dispersal speed in both the presence and absence of light. We found that
surface populations showed higher behavioural activity in dark than in light, and they were
more explorative and dispersed faster than their cave conspecifics. Recent colonists showed a
trend of higher dispersal speed compared to their source surface population. We suggest that
extreme and isolated habitats like caves might work as ‘dispersal traps’ following successful
colonisation, because adaptation to these habitats includes the reduction of explorativeness.
Furthermore, we suggest that individuals with higher explorativeness are likely to
colonise markedly new environments. Finally, we provide experimental evidence about
surface A. aquaticus moving more in dark than in light.
Significance statement
Environmental conditions in caves are differing drastically from those of the surface. Consequently, animals colonising subterranean habitats are subject to different selective forces than those experienced by the ancestral surface-living population. Behaviour is believed to be a key factor in successful colonisation to novel habitats; however, intraspecific behavioural variation in species with both surface- and cave-adapted populations is less known. Here, we compared dispersal related novel area exploration and dispersal speed across surface and cave-adapted populations of the freshwater crustacean Asellus aquaticus. Our results show that cave-adapted A. aquaticus are significantly less explorative and disperse slower than surface-type populations, indicating that caves may act as ‘dispersal traps’, where adaptation includes the loss of explorativeness. Also, recent cave colonists show a trend to be faster dispersers than peers from the surface source population, suggesting that individuals with higher explorativeness are likely to colonise markedly different new environments.
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8
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Diehl KM, Storer NM, Wells HD, Davis DA, Loughman ZJ, Graham ZA. On the surface or down below: Field observations reveal a high degree of surface activity in a burrowing crayfish, the Little Brown Mudbug (Lacunicambarus thomai). PLoS One 2022; 17:e0273540. [PMID: 36240144 PMCID: PMC9565396 DOI: 10.1371/journal.pone.0273540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 08/10/2022] [Indexed: 11/07/2022] Open
Abstract
Opposed to most crayfish species that inhabit permanent bodies of water, a unique burrowing lifestyle has evolved several times throughout the crayfish phylogeny. Burrowing crayfish are considered to be semi-terrestrial, as they burrow to the groundwater—creating complex burrows that occasionally reach 3 m in depth. Because burrowing crayfishes spend most of their lives within their burrow, we lack a basic understanding of the behavior and natural history of these species. However, recent work suggests that burrowing crayfishes may exhibit a higher level of surface activity than previously thought. In the current study, we conducted a behavioral study of the Little Brown Mudbug, Lacunicambarus thomai using video surveillance to determine their degree of surface activity and behavioral patterns. Throughout 664 hrs of footage, we observed a surprisingly high amount of activity at the surface of their burrows—both during the day and night. The percentage of time that individual crayfish was observed at the surface ranged from 21% to 69% per individual, with an average of 42.48% of the time spent at the surface across all crayfish. Additionally, we created an ethogram based on six observed behaviors and found that each behavior had a strong circadian effect. For example, we only observed a single observation of foraging on vegetation during the day, whereas 270 observations of this behavior were documented at night. Overall, our results suggest that burrowing crayfishes may exhibit higher levels of surface activity than previously thought. To increase our understanding of burrowing crayfish behaviors ecology, we encourage the continued use of video-recorded observations in the field and the laboratory.
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Affiliation(s)
- Kaine M. Diehl
- Department of Organismal Biology, Ecology & Zoo Science, West Liberty University, West Liberty, WV, United States of America
| | - Nicoleena M. Storer
- Department of Organismal Biology, Ecology & Zoo Science, West Liberty University, West Liberty, WV, United States of America
| | - Hogan D. Wells
- Department of Organismal Biology, Ecology & Zoo Science, West Liberty University, West Liberty, WV, United States of America
| | - Destinee A. Davis
- Department of Organismal Biology, Ecology & Zoo Science, West Liberty University, West Liberty, WV, United States of America
| | - Zachary J. Loughman
- Department of Organismal Biology, Ecology & Zoo Science, West Liberty University, West Liberty, WV, United States of America
| | - Zackary A. Graham
- Department of Organismal Biology, Ecology & Zoo Science, West Liberty University, West Liberty, WV, United States of America
- * E-mail:
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9
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Dooley KE, Niemiller KDK, Sturm N, Niemiller ML. Rediscovery and phylogenetic analysis of the Shelta Cave Crayfish (Orconectes sheltae Cooper & Cooper, 1997), a decapod (Decapoda, Cambaridae) endemic to Shelta Cave in northern Alabama, USA. SUBTERRANEAN BIOLOGY 2022. [DOI: 10.3897/subtbiol.43.79993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Shelta Cave Crayfish (Orconectes sheltae) is a small, cave-obligate member of the genus Orconectes (family Cambaridae) endemic to a single cave system—Shelta Cave—in northwest Huntsville, Madison Co., Alabama, USA. Although never abundant, this stygobiont was regularly observed in the 1960s and early 1970s before the population and aquatic community in general at Shelta Cave collapsed likely in response to groundwater contamination and the loss of energetic inputs from a Grey Bat (Myotis grisescens) maternity colony that abandoned the cave after installation of a poorly designed cave gate. We conducted 20 visual surveys of aquatic habitats at Shelta Cave between October 2018 and July 2021. Although the aquatic community has not recovered, we did confirm the continued existence of O. sheltae, which had not been observed in 31 years, with observations of an adult female on 31 May 2019 and an adult male on 28 August 2020. We conducted the first phylogenetic analyses of O. sheltae and discovered that the species is most closely related to other geographically proximate stygobiotic crayfishes in the genus Cambarus in northern Alabama than members of the genus Orconectes. We advocate for recognition of this species as Cambarus sheltae to more accurately reflect evolutionary relationships of this single-cave endemic and offer recommendations for its management, conservation, and future research, as this species remains at high risk of extinction.
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10
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Stratton CE, Reisinger LS, Behringer DC, Bojko J. Revising the Freshwater Thelohania to Astathelohania gen. et comb. nov., and Description of Two New Species. Microorganisms 2022; 10:636. [PMID: 35336214 PMCID: PMC8951847 DOI: 10.3390/microorganisms10030636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 01/25/2023] Open
Abstract
Crayfish are common hosts of microsporidian parasites, prominently from the genus Thelohania. Thelohania is a polyphyletic genus, with multiple genetically distinct lineages found from freshwater and marine environments. Researchers have been calling for a revision of this group for over a decade. We provide evidence that crayfish-infecting freshwater Thelohania are genetically and phylogenetically distinct from the marine Thelohania (Clade V/Glugeida), whilst also describing two new species that give further support to the taxonomic revision. We propose that the freshwater Thelohania should be transferred to their own genus, Astathelohania gen. et comb. nov., in a new family (Astathelohaniidae n. fam.). This results in the revision of Thelohania contejeani (Astathelohania contejeani), Thelohania montirivulorum (Astathelohania montirivulorum), and Thelohania parastaci (Astathelohania parastaci). We also describe two novel muscle-infecting Astathelohania species, A. virili n. sp. and A. rusti n. sp., from North American crayfishes (Faxonius sp.). We used histological, molecular, and ultrastructural data to formally describe the novel isolates. Our data suggest that the Astathelohania are genetically distinct from other known microsporidian genera, outside any described family, and that their SSU rRNA gene sequence diversity follows their host species and native geographic location. The range of this genus currently includes North America, Europe, and Australia.
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Affiliation(s)
- Cheyenne E. Stratton
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA; (C.E.S.); (L.S.R.); (D.C.B.)
| | - Lindsey S. Reisinger
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA; (C.E.S.); (L.S.R.); (D.C.B.)
| | - Donald C. Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL 32653, USA; (C.E.S.); (L.S.R.); (D.C.B.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
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11
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Graham ZA, Diehl K, Davis D, Loughman Z. Death from below: Sit-and-wait predatory behavior in a burrowing crayfish (Lacunicambarus thomai). FOOD WEBS 2022. [DOI: 10.1016/j.fooweb.2022.e00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Flórez JS, Cadena CD, Donascimiento C, Torres M. Repeated colonization of caves leads to phenotypic convergence in catfishes (Siluriformes: Trichomycterus) at a small geographical scale. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Across various animal groups, adaptation to the challenging conditions of cave environments has resulted in convergent evolution. We document a Neotropical cavefish system with ample potential to study questions related to convergent adaptation to cave environments at the population level. In the karstic region of the Andes of Santander, Colombia, cave-dwelling catfish in the genus Trichomycterus exhibit variable levels of reduction of eyes and body pigmentation relative to surface congeners. We tested whether cave-dwelling, eye-reduced, depigmented Trichomycterus from separate caves in Santander were the result of a single event of cave colonization and subsequent dispersal, or of multiple colonizations to caves by surface ancestors followed by phenotypic convergence. Using mitochondrial DNA sequences to reconstruct phylogenetic relationships, we found that caves in this region have been colonized independently by two separate clades. Additional events of cave colonization – and possibly recolonization of surface streams – may have occurred in one of the clades, where surface and cave-dwelling populations exhibit shallow differentiation, suggesting recent divergence or divergence with gene flow. We also identify potentially undescribed species and likely problems with the circumscription of named taxa. The system appears promising for studies on a wide range of ecological and evolutionary questions.
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Affiliation(s)
| | | | - Carlos Donascimiento
- Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Villa de Leyva, Colombia
| | - Mauricio Torres
- Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Colombia
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13
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Premate E, Borko Š, Kralj-Fišer S, Jennions M, Fišer Ž, Balázs G, Bíró A, Bračko G, Copilaş-Ciocianu D, Hrga N, Herczeg G, Rexhepi B, Zagmajster M, Zakšek V, Fromhage L, Fišer C. No room for males in caves: Female-biased sex ratio in subterranean amphipods of the genus Niphargus. J Evol Biol 2021; 34:1653-1661. [PMID: 34424594 DOI: 10.1111/jeb.13917] [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: 06/11/2021] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 12/16/2022]
Abstract
Sex allocation theory predicts that the proportion of daughters to sons will evolve in response to ecological conditions that determine the costs and benefits of producing each sex. All else being equal, the adult sex ratio (ASR) should also vary with ecological conditions. Many studies of subterranean species reported female-biased ASR, but no systematic study has yet been conducted. We test the hypothesis that the ASR becomes more female-biased with increased isolation from the surface. We compiled a data set of ASRs of 35 species in the subterranean amphipod Niphargus, each living in one of three distinct habitats (surface-subterranean boundary, cave streams, phreatic lakes) representing an environmental gradient of increased isolation underground. The ASR was female-biased in 27 of 35 species; the bias was statistically significant in 12 species. We found a significant difference in the ASR among habitats after correction for phylogeny. It is most weakly female-biased at the surface-subterranean boundary and most strongly female-biased in phreatic lakes. Additional modelling suggests that the ASR has evolved towards a single value for both surface-subterranean boundary and cave stream-dwelling species, and another value for 9 of 11 phreatic lake dwellers. We suggest that a history of inbreeding in subterranean populations might lower inbreeding depression such that kin selection favours mating with siblings. This could select for a female-biased offspring sex ratio due to local mate competition among brothers. The observed patterns in sex ratios in subterranean species make them a group worthy of more attention from those interested in sex allocation theory.
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Affiliation(s)
- Ester Premate
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Špela Borko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Simona Kralj-Fišer
- Research Centre of the Slovenian Academy of Sciences and Arts, Jovan Hadži Institute of Biology, Ljubljana, Slovenia
| | - Michael Jennions
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Žiga Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Gergely Balázs
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Anna Bíró
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gregor Bračko
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Denis Copilaş-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Nuša Hrga
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Gábor Herczeg
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Behare Rexhepi
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Lutz Fromhage
- Department of Biological and Environmental Science, University of Jyvaskyla, Finland
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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14
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Amador L, Victoriano PF, D’Elía G. Molecular species delimitation reveals hidden specific diversity within a freshwater burrowing crayfish (Decapoda: Parastacidae) from southern Chile. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2020.1865471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luis Amador
- Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
- Universidad Laica Vicente Rocafuerte, Guayaquil, 090514, Ecuador
| | - Pedro F. Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, 4030000, Chile
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
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15
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Villastrigo A, Abellán P, Ribera I. Habitat preference and diversification rates in a speciose lineage of diving beetles. Mol Phylogenet Evol 2021; 159:107087. [PMID: 33545273 DOI: 10.1016/j.ympev.2021.107087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022]
Abstract
The long-term geological stability of aquatic habitats has been demonstrated to be a determinant in the evolution of macroinvertebrate fauna, with species in running (lotic) waters having lower dispersal abilities, smaller ranges and higher gene flow between populations than species in standing (lentic) environments. Lotic species have been hypothesized to be more specialised, but the diversification dynamics of both habitat types have not been studied in detail. Using a speciose lineage of water beetles we test here whether diversification rates are related to the habitat preference of the species and its consequences on turnover, which we expect to be higher for lotic taxa. Moreover, we tested whether life in lotic environments is acting as an evolutionary dead-end as it is considered an ecological specialisation. We built a comprehensive molecular phylogeny with 473 terminals representing 421 of the 689 known species of the tribe Hydroporini (Coleoptera, Dytiscidae), using a combination of sequences from four mitochondrial and two nuclear genes plus 69 mitogenomes obtained with NGS. We found a general pattern of gradual acceleration of diversification rate with time, with 2-3 significant diversification shifts. However, habitat is not the main factor driving diversification in Hydroporini based on SecSSE analyses. The most recent common ancestor of Hydroporini was reconstructed as a lotic species, with multiple shifts to lentic environments. Most frequent transitions were estimated from lentic and lotic habitats to the category "both", followed by transitions from lotic to lentic and lentic to lotic respectively, although with very similar rates. Contrary to expectations, we found little evidence for differences in diversification dynamics between habitats, with lotic environments clearly not acting as evolutionary dead-ends in Hydroporini.
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Affiliation(s)
- Adrián Villastrigo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | | | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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16
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Mammola S, Amorim IR, Bichuette ME, Borges PAV, Cheeptham N, Cooper SJB, Culver DC, Deharveng L, Eme D, Ferreira RL, Fišer C, Fišer Ž, Fong DW, Griebler C, Jeffery WR, Jugovic J, Kowalko JE, Lilley TM, Malard F, Manenti R, Martínez A, Meierhofer MB, Niemiller ML, Northup DE, Pellegrini TG, Pipan T, Protas M, Reboleira ASPS, Venarsky MP, Wynne JJ, Zagmajster M, Cardoso P. Fundamental research questions in subterranean biology. Biol Rev Camb Philos Soc 2020; 95:1855-1872. [DOI: 10.1111/brv.12642] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS) University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
- Molecular Ecology Group (MEG) Water Research Institute (IRSA), National Research Council (CNR) Corso Tonolli, 50 Pallanza 28922 Italy
| | - Isabel R. Amorim
- cE3c – Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Faculty of Agrarian and Environmental Sciences, Rua Capitão João d'Àvila Pico da Urze Angra do Heroísmo Azores 9700‐042 Portugal
| | - Maria E. Bichuette
- Laboratory of Subterranean Studies Federal University of São Carlos Rodovia Washington Luís km 235 São Carlos São Paulo 13565‐905 Brazil
| | - Paulo A. V. Borges
- cE3c – Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores, Faculty of Agrarian and Environmental Sciences, Rua Capitão João d'Àvila Pico da Urze Angra do Heroísmo Azores 9700‐042 Portugal
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science Thompson Rivers University 805 TRU Way Kamloops British Columbia Canada
| | - Steven J. B. Cooper
- Evolutionary Biology Unit South Australian Museum North Terrace Adelaide South Australia 5000 Australia
- Australian Centre for Evolutionary Biology and Biodiversity, and Environment Institute, School of Biological Sciences University of Adelaide Adelaide South Australia 5005 Australia
| | - David C. Culver
- Department of Environmental Science American University 4400 Massachusetts Avenue, N.W. Washington DC 20016 U.S.A
| | - Louis Deharveng
- UMR7205 – ISYEB Museum national d'Histoire naturelle 45 rue Buffon (CP50) Paris 75005 France
| | - David Eme
- IFREMER Centre Atlantique Unité Ecologie et Modèles pour l'Halieutique Rue de l'Île d'Yeu Nantes 44980 France
| | - Rodrigo Lopes Ferreira
- Center of Studies in Subterranean Biology, Biology Department Federal University of Lavras Campus Universitário Lavras Minas Gerais CEP 37202‐553 Brazil
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Žiga Fišer
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Daniel W. Fong
- Department of Biology American University 4400 Massachusetts Avenue, N.W. Washington DC 20016 U.S.A
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, Division of Limnology University of Vienna Althanstrasse 14 Vienna 1090 Austria
| | - William R. Jeffery
- Department of Biology University of Maryland College Park MD 20742 U.S.A
| | - Jure Jugovic
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies University of Primorska Glagoljaška 8 Koper SI‐6000 Slovenia
| | - Johanna E. Kowalko
- Harriet L. Wilkes Honors College Florida Atlantic University 5353 Parkside Dr Jupiter FL 33458 U.S.A
| | - Thomas M. Lilley
- BatLab Finland, Finnish Museum of Natural History University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
| | - Florian Malard
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés Univ. Lyon 1, ENTPE, CNRS, Université de Lyon, Bat. Forel 6 rue Raphaël Dubois Villeurbanne cedex 69622 France
| | - Raoul Manenti
- Department of Environmental Science and Policy Università degli Studi di Milano Via Celoria 26 Milan 20113 Italy
| | - Alejandro Martínez
- Molecular Ecology Group (MEG) Water Research Institute (IRSA), National Research Council (CNR) Corso Tonolli, 50 Pallanza 28922 Italy
| | - Melissa B. Meierhofer
- BatLab Finland, Finnish Museum of Natural History University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
- Department of Rangeland, Wildlife and Fisheries Management Texas A&M University 534 John Kimbrough Blvd. College Station TX 77843 U.S.A
| | - Matthew L. Niemiller
- Department of Biological Sciences The University of Alabama in Huntsville 301 Sparkman Drive NW Huntsville AL 35899 U.S.A
| | - Diana E. Northup
- Department of Biology University of New Mexico Albuquerque NM 87131‐0001 U.S.A
| | - Thais G. Pellegrini
- Center of Studies in Subterranean Biology, Biology Department Federal University of Lavras Campus Universitário Lavras Minas Gerais CEP 37202‐553 Brazil
| | - Tanja Pipan
- ZRC SAZU Karst Research Institute Novi trg 2 Ljubljana SI‐1000 Slovenia
- UNESCO Chair on Karst Education University of Nova Gorica Vipavska cesta Nova Gorica 5000 Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics Domenicas University of California 50 Acacia Avenue San Rafael CA 94901 U.S.A
| | - Ana Sofia P. S. Reboleira
- Natural History Museum of Denmark University of Copenhagen Universitetsparken 15 Copenhagen 2100 Denmark
| | - Michael P. Venarsky
- Australian Rivers Institute Griffith University 170 Kessels Road Nathan Queensland 4111 Australia
| | - J. Judson Wynne
- Department of Biological Sciences, Center for Adaptable Western Landscapes Northern Arizona University Box 5640 Flagstaff AZ 86011 U.S.A
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical Faculty University of Ljubljana Jamnikarjeva 101, PO BOX 2995 Ljubljana SI‐1000 Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS) University of Helsinki Pohjoinen Rautatiekatu 13 Helsinki 00100 Finland
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17
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Wolfe JM, Breinholt JW, Crandall KA, Lemmon AR, Lemmon EM, Timm LE, Siddall ME, Bracken-Grissom HD. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Proc Biol Sci 2020; 286:20190079. [PMID: 31014217 DOI: 10.1098/rspb.2019.0079] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
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Affiliation(s)
- Joanna M Wolfe
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA.,2 Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology , Cambridge, MA 02139 , USA.,3 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
| | - Jesse W Breinholt
- 4 Florida Museum of Natural History, University of Florida , Gainesville, FL 32611 , USA.,5 RAPiD Genomics , Gainesville, FL 32601 , USA
| | - Keith A Crandall
- 6 Computational Biology Institute, The George Washington University , Ashburn, VA 20147 , USA.,7 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC 20012 , USA
| | - Alan R Lemmon
- 8 Department of Scientific Computing, Florida State University , Dirac Science Library, Tallahassee, FL 32306 , USA
| | - Emily Moriarty Lemmon
- 9 Department of Biological Science, Florida State University , Tallahassee, FL 32306 , USA
| | - Laura E Timm
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
| | - Mark E Siddall
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA
| | - Heather D Bracken-Grissom
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
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18
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Mammola S, Arnedo MA, Fišer C, Cardoso P, Dejanaz AJ, Isaia M. Environmental filtering and convergent evolution determine the ecological specialization of subterranean spiders. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13527] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Stefano Mammola
- Molecular Ecology Group (MEG) IRSA—Water Research Institute National Research Council Verbania Pallanza Italy
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Miquel A. Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute University of Barcelona Barcelona Spain
| | - Cene Fišer
- Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
| | - Andrea J. Dejanaz
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Marco Isaia
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
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19
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Stern DB, Crandall KA. The Evolution of Gene Expression Underlying Vision Loss in Cave Animals. Mol Biol Evol 2019; 35:2005-2014. [PMID: 29788330 PMCID: PMC6063295 DOI: 10.1093/molbev/msy106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms. Here, we analyze gene expression variation in adult eye tissue across the freshwater crayfish, representing four independent vision-loss events in caves. Species and individual expression patterns cluster by eye function rather than phylogeny, suggesting convergence in transcriptome evolution in independently blind animals. However, this clustering is not greater than what is observed in surface species with conserved eye function after accounting for phylogenetic expectations. Modeling expression evolution suggests that there is a common increase in evolutionary rates in the blind lineages, consistent with a relaxation of selective constraint maintaining optimal expression levels. This is evidence for a repeated loss of expression constraint in the transcriptomes of blind animals and that convergence occurs via a similar trajectory through genetic drift.
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Affiliation(s)
- David B Stern
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
| | - Keith A Crandall
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
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20
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Emerling CA. Regressed but Not Gone: Patterns of Vision Gene Loss and Retention in Subterranean Mammals. Integr Comp Biol 2019; 58:441-451. [PMID: 29697812 DOI: 10.1093/icb/icy004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Regressive evolution involves the degradation of formerly useful traits as organisms invade novel ecological niches. In animals, committing to a strict subterranean habit can lead to regression of the eyes, likely due to a limited exposure to light. Several lineages of subterranean mammals show evidence of such degeneration, which can include decreased organization of the retina, malformation of the lens, and subcutaneous positioning of the eye. Advances in DNA sequencing have revealed that this regression co-occurs with a degradation of genomic loci encoding visual functions, including protein-coding genes. Other dim light-adapted vertebrates with normal ocular anatomy, such as nocturnal and aquatic species, also demonstrate evidence of visual gene loss, but the absence of comparative studies has led to the untested assumption that subterranean mammals are special in the degree of this genomic regression. Additionally, previous studies have shown that not all vision genes have been lost in subterranean mammals, but it is unclear whether they are under relaxed selection and will ultimately be lost, are maintained due to pleiotropy or if natural selection is favoring the retention of the eye and certain critical underlying loci. Here I report that vision gene loss in subterranean mammals tends to be more extensive in quantity and differs in distribution from other dim light-adapted mammals, although some committed subterranean mammals demonstrate significant overlap with nocturnal microphthalmic species. In addition, blind subterranean mammals retain functional orthologs of non-pleiotropic visual genes that are evolving at rates consistent with purifying selection. Together, these results suggest that although living underground tends to lead to major losses of visual functions, natural selection is maintaining genes that support the eye, perhaps as an organ for circadian and/or circannual entrainment.
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Affiliation(s)
- Christopher A Emerling
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Institut des Sciences de l'Evolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, 34090 Montpellier, France
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21
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Stern DB, Crandall KA. Phototransduction Gene Expression and Evolution in Cave and Surface Crayfishes. Integr Comp Biol 2019; 58:398-410. [PMID: 29762661 DOI: 10.1093/icb/icy029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the absence of light in caves, animals have repeatedly evolved reduced eyes and visual systems. Whether the underlying genetic components remain intact in blind species remains unanswered across taxa. The freshwater crayfish have evolved to live in caves multiple times throughout their history; therefore, this system provides an opportunity to probe the genetic patterns and processes underlying repeated vision loss. Using transcriptomic data from the eyes of 14 species of cave and surface crayfishes, we identify the expression of 17 genes putatively related to visual phototransduction. We find a similarly complete repertoire of phototransduction gene families expressed in cave and surface species, but that the expression levels of those transcripts are consistently lower in cave species. We find statistical support for episodic positive selection, increased and decreased selection strength in caves, depending on the gene family. Analyses of gene expression evolution suggest convergent and possibly adaptive downregulation of these genes across eye-reduction events. Our results reveal a combination of evolutionary processes acting on the sequences and gene expression levels of vision-related genes underlying the loss of vision in caves.
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Affiliation(s)
- David B Stern
- The George Washington University, Milken Institute School of Public Health, Computational Biology Institute, 800 22nd St NW, Washington, DC 20052, USA.,Birge Hall, Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Keith A Crandall
- The George Washington University, Milken Institute School of Public Health, Computational Biology Institute, 800 22nd St NW, Washington, DC 20052, USA
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22
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Nguyen HN, Lu CW, Chu JH, Grismer LL, Hung CM, Lin SM. Historical demography of four gecko species specializing in boulder cave habitat: Implications in the evolutionary dead end hypothesis and conservation. Mol Ecol 2018; 28:772-784. [PMID: 30580492 DOI: 10.1111/mec.14985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022]
Abstract
Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by unsuitable floodplain habitats, these boulder-dwelling geckos are among the most narrowly distributed Squamata in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results reveal long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have greatly impacted population divergence and declines. The habitat specialization of these geckos has led to fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.
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Affiliation(s)
- Hung N Nguyen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Zoology, Southern Institute of Ecology, Vietnam Academia of Science and Technology, Ho Chi Minh City, Vietnam.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Wei Lu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Si-Min Lin
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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23
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Cyriac VP, Kodandaramaiah U. Digging their own macroevolutionary grave: fossoriality as an evolutionary dead end in snakes. J Evol Biol 2018; 31:587-598. [DOI: 10.1111/jeb.13248] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023]
Affiliation(s)
- V. P. Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology; Indian Institute of Science Education and Research Thiruvananthapuram; Thiruvananthapuram India
| | - U. Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology; Indian Institute of Science Education and Research Thiruvananthapuram; Thiruvananthapuram India
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