1
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Van Der Wal C, Ahyong ST, Adams MWD, Ewart KM, Ho SYW, Lo N. Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Mol Phylogenet Evol 2023; 178:107629. [PMID: 36191898 DOI: 10.1016/j.ympev.2022.107629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.
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Affiliation(s)
- Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia; Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia.
| | - Shane T Ahyong
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, NSW 2010, Australia; School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maxim W D Adams
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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2
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The Impact of Fast Radiation on the Phylogeny of Bactrocera Fruit Flies as Revealed by Multiple Evolutionary Models and Mutation Rate-Calibrated Clock. INSECTS 2022; 13:insects13070603. [PMID: 35886779 PMCID: PMC9319077 DOI: 10.3390/insects13070603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
Several true fruit flies (Tephritidae) cause major damage to agriculture worldwide. Among them, species of the genus Bactrocera are extensively studied to understand the traits associated with their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but several nodes of the Bactrocera phylogeny are still controversial, especially concerning the reciprocal affinities of the two major pests B. dorsalis and B. tryoni. Here, we analyzed a newly assembled genomic-scaled dataset using different models of evolution to infer a phylogenomic backbone of ten representative Bactrocera species and two outgroups. We further provide the first genome-scaled inference of their divergence by calibrating the clock using fossil records and the spontaneous mutation rate. The results reveal a closer relationship of B. dorsalis with B. latifrons than to B. tryoni, contrary to what was previously supported by mitochondrial-based phylogenies. By employing coalescent-aware and heterogeneous evolutionary models, we show that this incongruence likely derives from a hitherto undetected systematic error, exacerbated by incomplete lineage sorting and possibly hybridization. This agrees with our clock analysis, which supports a rapid and recent radiation of the clade to which B. dorsalis, B. latifrons and B. tryoni belong. These results provide a new picture of Bactrocera phylogeny that can serve as the basis for future comparative analyses.
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3
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Wang D, Huang Z, Billen J, Zhang G, He H, Wei C. Complex co-evolutionary relationships between cicadas and their symbionts. Environ Microbiol 2021; 24:195-211. [PMID: 34927333 DOI: 10.1111/1462-2920.15829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022]
Abstract
Previous evidence suggests that cicadas lacking Hodgkinia may harbour the yeast-like fungal symbionts (YLS). Here, we reinforce an earlier conclusion that the pathogenic ancestor of YLS independently infected different cicada lineages instead of the common ancestor of Cicadidae. Five independent replacement events in the loss of Hodgkinia/acquisition of YLS and seven other replacement events of YLS (from an Ophiocordyceps fungus to another Ophiocordyceps fungus) are hypothesised to have occurred within the sampled cicada taxa. The divergence time of YLS lineages was later than that of corresponding cicada lineages. The rapid shift of diversification rates of YLS and related cicada-parasitizing Ophiocordyceps began at approximately 32.94 Ma, and the diversification rate reached the highest value at approximately 24.82 Ma, which corresponds to the cooling climate changes at the Eocene-Oligocene boundary and the Oligocene-Miocene transition respectively. Combined with related acquisition/replacement events of YLS occurred during the cooling-climate periods, we hypothesise that the cooling-climate changes impacted the interactions between cicadas and related Ophiocordyceps, which coupled with the unusual life cycle and the differentiation of cicadas may finally led to the diversification of YLS in Cicadidae. Our results contribute to a better understanding of the evolutionary transition of YLS from entomopathogenic fungi in insects.
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Affiliation(s)
- Dandan Wang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhi Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Johan Billen
- Zoological Institute, University of Leuven, Naamsestraat 59, Leuven, B-3000, Belgium
| | - Guoyun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hong He
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
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4
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Arab DA, Lo N. Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts. J Mol Evol 2021; 89:238-248. [PMID: 33730185 DOI: 10.1007/s00239-021-10001-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/20/2021] [Indexed: 10/21/2022]
Abstract
The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such correlations between the mitochondrial genomes of cockroaches and the genomes of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of the bacterial endosymbionts Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses showed a highly significant correlation of molecular rates between the genomes of Buchnera and the mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.
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5
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Zadra N, Rizzoli A, Rota-Stabelli O. Chronological Incongruences between Mitochondrial and Nuclear Phylogenies of Aedes Mosquitoes. Life (Basel) 2021; 11:life11030181. [PMID: 33669100 PMCID: PMC7996624 DOI: 10.3390/life11030181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/12/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
One-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing on the disentanglement between nuclear and mitochondrial phylogenetic signals. We first show that there are some phylogenetic discrepancies between nuclear and mitochondrial markers which may be caused by wrong taxa assignment in samples collections or by some stochastic effect due to small gene samples. We indeed show that the concatenated dataset is model and framework dependent, indicating a general paucity of signal. Our Bayesian calibrated divergence estimates point toward a mosquito radiation in the mid-Jurassic and an Aedes radiation from the mid-Cretaceous on. We observe, however a strong chronological incongruence between mitochondrial and nuclear data, the latter providing divergence times within the Aedini significantly younger than the former. We show that this incongruence is consistent over different datasets and taxon sampling and that may be explained by either peculiar evolutionary event such as different levels of saturation in certain lineages or a past history of hybridization throughout the genus. Overall, our updated picture of Aedini phylogeny, reveal a strong nuclear-mitochondrial incongruence which may be of help in setting the research agenda for future phylogenomic studies of Aedini mosquitoes.
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Affiliation(s)
- Nicola Zadra
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige (TN), Italy; (N.Z.); (A.R.)
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Povo (TN), Italy
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige (TN), Italy; (N.Z.); (A.R.)
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige (TN), Italy; (N.Z.); (A.R.)
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Povo (TN), Italy
- Center Agriculture Food Environment—C3A, University of Trento, 38010 San Michele all Adige (TN), Italy
- Correspondence:
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6
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Yu D, Deharveng L, Lukić M, Wei Y, Hu F, Liu M. Molecular phylogeny and trait evolution in an ancient terrestrial arthropod lineage: Systematic revision and implications for ecological divergence (Collembola, Tomocerinae). Mol Phylogenet Evol 2021; 154:106995. [PMID: 33164871 DOI: 10.1016/j.ympev.2020.106995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 01/05/2023]
Abstract
Phylogenetic assessments of functional traits are important for mechanistically understanding the interactions between organisms and environments, but such practices are strongly limited by the availability of phylogenetic frameworks. The tomocerin springtails are an ancient, widespread and ecologically important group of terrestrial arthropods, whereas their phylogeny and trait evolution remained unaddressed. In the present study, we conducted the first comprehensive phylogenetic reconstruction of Tomocerinae, based on a multi-loci molecular dataset covering all major lineages within the subfamily, using Bayesian inference (BI), maximum-likelihood (ML) and maximum-parsimony (MP) approaches. Divergence time was estimated and ancestral character state reconstruction (ACSR) was performed to trace the evolutionary history of five ecomorphological traits correlated with sensory and locomotory functions. Our results support the monophyly of Tomocerinae, and indicate that current classification of Tomocerinae only partially reflects evolutionary relationships, notably the commonest and speciose genus Tomocerus is polyphyletic. The subfamily probably originated in Early Cretaceous and diversified in two Cretaceous and one Eocene radiation events. As indicated by the evolutionary patterns of functional traits, multiple ecological divergences took place during the diversification of Tomocerinae. The study suggests a potential underestimation of ecological divergence and functional diversity in terrestrial arthropods, calls for an update of present trait databases, and demonstrates the value of macroevolutionary knowledge for improving the trait-based ecology. In addition, Tomocerus, Tomocerina and Tritomurus are redefined, a new genus Yoshiicerusgen. n. and new subgenera Coloratomurussubgen. n., Ciliatomurussubgen. n., Striatomurussubgen. n. and Ocreatomurussubgen. n. are described in the appendix.
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Affiliation(s)
- Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, 210095 Nanjing, China.
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France.
| | - Marko Lukić
- Croatian Biospeleological Society, Zagreb, Croatia; Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Yiming Wei
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, 210095 Nanjing, China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, 210095 Nanjing, China.
| | - Manqiang Liu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Jiangsu Key Laboratory for Solid Organic Waste Utilization, 210095 Nanjing, China.
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7
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Guzik MT, Stevens MI, Cooper SJB, Humphreys WF, Austin AD. Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia. Genome 2020; 64:181-195. [PMID: 32552081 DOI: 10.1139/gen-2019-0199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 (COI) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella, indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.
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Affiliation(s)
- Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia
| | - Mark I Stevens
- Biological and Earth Sciences, South Australian Museum, SA 5000, Australia.,University of South Australia, Clinical and Health Sciences, SA 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - William F Humphreys
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia, Affiliate.,School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, the University of Adelaide, SA 5005, Australia.,South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
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8
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Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates. Mol Biol Evol 2020; 36:1793-1803. [PMID: 31004175 PMCID: PMC6657730 DOI: 10.1093/molbev/msz094] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many factors complicate the estimation of time scales for phylogenetic histories, requiring increasingly complex evolutionary models and inference procedures. The widespread application of molecular clock dating has led to the insight that evolutionary rate estimates may vary with the time frame of measurement. This is particularly well established for rapidly evolving viruses that can accumulate sequence divergence over years or even months. However, this rapid evolution stands at odds with a relatively high degree of conservation of viruses or endogenous virus elements over much longer time scales. Building on recent insights into time-dependent evolutionary rates, we develop a formal and flexible Bayesian statistical inference approach that accommodates rate variation through time. We evaluate the novel molecular clock model on a foamy virus cospeciation history and a lentivirus evolutionary history and compare the performance to other molecular clock models. For both virus examples, we estimate a similarly strong time-dependent effect that implies rates varying over four orders of magnitude. The application of an analogous codon substitution model does not implicate long-term purifying selection as the cause of this effect. However, selection does appear to affect divergence time estimates for the less deep evolutionary history of the Ebolavirus genus. Finally, we explore the application of our approach on woolly mammoth ancient DNA data, which shows a much weaker, but still important, time-dependent rate effect that has a noticeable impact on node age estimates. Future developments aimed at incorporating more complex evolutionary processes will further add to the broad applicability of our approach.
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Affiliation(s)
- Jade Vincent Membrebe
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Fogarty International Center, National Institutes of Health, Bethesda, MD
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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9
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Arab DA, Bourguignon T, Wang Z, Ho SYW, Lo N. Evolutionary rates are correlated between cockroach symbionts and mitochondrial genomes. Biol Lett 2020; 16:20190702. [PMID: 31910734 DOI: 10.1098/rsbl.2019.0702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
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Affiliation(s)
- Daej A Arab
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Thomas Bourguignon
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.,Okinawa Institute of Science and Technology Graduate University, Tancha, Onna-son, Okinawa, Japan.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Zongqing Wang
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
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10
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Goodman KR, Prost S, Bi K, Brewer MS, Gillespie RG. Host and geography together drive early adaptive radiation of Hawaiian planthoppers. Mol Ecol 2019; 28:4513-4528. [PMID: 31484218 DOI: 10.1111/mec.15231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022]
Abstract
The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.
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Affiliation(s)
- Kari Roesch Goodman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California, Berkeley, CA, USA.,LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Frankfurt/Main, Germany
| | - Ke Bi
- Computational Genomics Resource Laboratory (CGRL), California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.,Ancestry, San Francisco, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Michael S Brewer
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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11
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Striedter GF. Variation across Species and Levels: Implications for Model Species Research. BRAIN, BEHAVIOR AND EVOLUTION 2019; 93:57-69. [PMID: 31416083 DOI: 10.1159/000499664] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/08/2019] [Indexed: 11/19/2022]
Abstract
The selection of model species tends to involve two typically unstated assumptions, namely: (1) that the similarity between species decreases steadily with phylogenetic distance, and (2) that similarities are greater at lower levels of biological organization. The first assumption holds on average, but species similarities tend to decrease with the square root of divergence time, rather than linearly, and lineages with short generation times (which includes most model species) tend to diverge faster than average, making the decrease in similarity non-monotonic. The second assumption is more difficult to test. Comparative molecular research has traditionally emphasized species similarities over differences, whereas comparative research at higher levels of organization frequently highlights the species differences. However, advances in comparative genomics have brought to light a great variety of species differences, not just in gene regulation but also in protein coding genes. Particularly relevant are cases in which homologous high-level characters are based on non-homologous genes. This phenomenon of non-orthologous gene displacement, or "deep non-homology," indicates that species differences at the molecular level can be surprisingly large. Given these observations, it is not surprising that some findings obtained in model species do not generalize across species as well as researchers had hoped, even if the research is molecular.
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Affiliation(s)
- Georg F Striedter
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA,
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12
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Singer D, Mitchell EAD, Payne RJ, Blandenier Q, Duckert C, Fernández LD, Fournier B, Hernández CE, Granath G, Rydin H, Bragazza L, Koronatova NG, Goia I, Harris LI, Kajukało K, Kosakyan A, Lamentowicz M, Kosykh NP, Vellak K, Lara E. Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists. Mol Ecol 2019; 28:3089-3100. [DOI: 10.1111/mec.15117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/26/2022]
Affiliation(s)
- David Singer
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Department of Zoology, Institute of Biosciences University of São Paulo São Paulo Brazil
| | - Edward A. D. Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Jardin Botanique de Neuchâtel Neuchâtel Switzerland
| | | | - Quentin Blandenier
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Real Jardín Botánico CSIC Madrid Spain
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
| | - Leonardo D. Fernández
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS) Universidad Bernardo O'Higgins Santiago Chile
| | - Bertrand Fournier
- Community and Quantitative Ecology Laboratory, Department of Biology Concordia University Montreal QC Canada
| | - Cristián E. Hernández
- Facultad de Ciencias Naturales y Oceanográficas, Departamento de Zoología Universidad de Concepción Barrio Universitario de Concepción Chile
| | - Gustaf Granath
- Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Håkan Rydin
- Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Luca Bragazza
- WSL Swiss Federal Institute for Forest, Snow and Landscape Research Lausanne Switzerland
- Laboratory of Ecological Systems (ECOS), Ecole Polytechnique Féderale de Lausanne (EPFL) School of Architecture, Civil and Environmental Engineering (ENAC) Lausanne Switzerland
- Department of Life Science and Biotechnologies University of Ferrara Ferrara Italy
| | - Natalia G. Koronatova
- Laboratory of Biogeocenology, Institute of Soil Science and Agrochemistry Siberian Branch of Russian Academy of Sciences Novosibirsk Russia
| | - Irina Goia
- Department of Taxonomy and Ecology, Faculty of Biology and Geology Babeș‐Bolyai University Cluj‐Napoca Romania
| | - Lorna I. Harris
- School of Geography and Earth Sciences McMaster University Hamilton ON Canada
| | - Katarzyna Kajukało
- Laboratory of Wetland Ecology and Monitoring, Faculty of Geographical and Geological Sciences and Department of Biogeography and Paleoecology Adam Mickiewicz University Poznań Poland
| | - Anush Kosakyan
- Institute of Parasitology, Biology Center Czech Academy of Sciences České Budĕjovice Czech Republic
| | - Mariusz Lamentowicz
- Laboratory of Wetland Ecology and Monitoring, Faculty of Geographical and Geological Sciences and Department of Biogeography and Paleoecology Adam Mickiewicz University Poznań Poland
| | - Natalia P. Kosykh
- Laboratory of Biogeocenology, Institute of Soil Science and Agrochemistry Siberian Branch of Russian Academy of Sciences Novosibirsk Russia
| | - Kai Vellak
- Institute of Ecology and Earth Sciences, Natural History Museum University of Tartu Tartu Estonia
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Real Jardín Botánico CSIC Madrid Spain
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13
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Johns CA, Toussaint EFA, Breinholt JW, Kawahara AY. Origin and macroevolution of micro-moths on sunken Hawaiian Islands. Proc Biol Sci 2018; 285:rspb.2018.1047. [PMID: 30158307 DOI: 10.1098/rspb.2018.1047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/02/2018] [Indexed: 11/12/2022] Open
Abstract
The origins and evolution of Hawaiian biodiversity are a matter of controversy, and the mechanisms of lineage diversification for many organisms on this remote archipelago remain unclear. Here we focus on the poorly known endemic leaf-mining moth genus Philodoria (Lepidoptera, Gracillariidae), whose species feed on a diversity of Hawaiian plant lineages, many of which are critically endangered. We use anchored hybrid enrichment to assemble the first phylogenomic dataset (507 loci) for any Hawaiian animal taxon. To uncover the timing and pattern of diversification of these moths, we apply two frequently used dating calibration strategies, biogeographic calibrations and secondary calibrations. Island calibrations on their own resulted in much younger and unrealistic dates compared to strategies that relied on secondary calibrations. Philodoria probably originated on the now partially sunken islands of Laysan or Lisianski, approximately 21 Ma, and were associated with host plants in the families Ebenaceae, Malvaceae or Primulaceae. Major feeding groups associated with specific host-plant families originated soon after the plants colonized the islands. Allopatric isolation and host shifts, in concert and independently, probably play major roles in the diversification of Philodoria Our dating results indicate that Philodoria is among the oldest known Hawaiian arthropod lineages, and that island calibrations alone can lead to unrealistically young dates.
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Affiliation(s)
- Chris A Johns
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA .,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | | | - Jesse W Breinholt
- RAPiD Genomics, 747 SW 2nd Avenue IMB#14, Gainesville, FL 32601, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA .,Department of Biology, University of Florida, Gainesville, FL 32611, USA
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14
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Huang JP, Knowles LL. Testing the impact of oceanic barriers on population subdivision, speciation and zoogeographical community assembly in Xylotrupes beetles across the Indo-Australian Archipelago. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jen-Pan Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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15
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Yuan ML, Zhang QL, Zhang L, Jia CL, Li XP, Yang XZ, Feng RQ. Mitochondrial phylogeny, divergence history and high-altitude adaptation of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) inhabiting the Tibetan Plateau. Mol Phylogenet Evol 2018; 122:116-124. [DOI: 10.1016/j.ympev.2018.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/26/2017] [Accepted: 01/20/2018] [Indexed: 11/16/2022]
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16
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Wang Z, Shi Y, Qiu Z, Che Y, Lo N. Reconstructing the phylogeny of Blattodea: robust support for interfamilial relationships and major clades. Sci Rep 2017; 7:3903. [PMID: 28634362 PMCID: PMC5478607 DOI: 10.1038/s41598-017-04243-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/11/2017] [Indexed: 11/09/2022] Open
Abstract
Cockroaches are among the most recognizable of all insects. In addition to their role as pests, they play a key ecological role as decomposers. Despite numerous studies of cockroach phylogeny in recent decades, relationships among most major lineages are yet to be resolved. Here we examine phylogenetic relationships among cockroaches based on five genes (mitochondrial 12S rRNA, 16S rRNA, COII; nuclear 28S rRNA and histone H3), and infer divergence times on the basis of 8 fossils. We included in our analyses sequences from 52 new species collected in China, representing 7 families. These were combined with data from a recent study that examined these same genes from 49 species, resulting in a significant increase in taxa analysed. Three major lineages, Corydioidea, Blaberoidea, and Blattoidea were recovered, the latter comprising Blattidae, Tryonicidae, Lamproblattidae, Anaplectidae, Cryptocercidae and Isoptera. The estimated age of the split between Mantodea and Blattodea ranged from 204.3 Ma to 289.1 Ma. Corydioidea was estimated to have diverged 209.7 Ma (180.5-244.3 Ma 95% confidence interval [CI]) from the remaining Blattodea. The clade Blattoidea diverged from their sister group, Blaberoidea, around 198.3 Ma (173.1-229.1 Ma). The addition of the extra taxa in this study has resulted in significantly higher levels of support for a number of previously recognized groupings.
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Affiliation(s)
- Zongqing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Yan Shi
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Zhiwei Qiu
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Yanli Che
- College of Plant Protection, Southwest University, Beibei, Chongqing, China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.
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17
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Hash JM, Heraty JM, Brown BV. Phylogeny, host association and biogeographical patterns in the diverse millipede-parasitoid genusMyriophoraBrown (Diptera: Phoridae). Cladistics 2017; 34:93-112. [DOI: 10.1111/cla.12189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Affiliation(s)
- John M. Hash
- Department of Entomology; University of California; Riverside CA 92521 USA
| | - John M. Heraty
- Department of Entomology; University of California; Riverside CA 92521 USA
| | - Brian V. Brown
- Entomology Section; Natural History Museum of Los Angeles County; 900 Exposition Blvd Los Angeles CA 90007 USA
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18
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Ho SYW, Duchêne S, Molak M, Shapiro B. Time-dependent estimates of molecular evolutionary rates: evidence and causes. Mol Ecol 2016; 24:6007-12. [PMID: 26769402 DOI: 10.1111/mec.13450] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/30/2015] [Accepted: 07/17/2015] [Indexed: 12/28/2022]
Abstract
We are writing in response to a recent critique by Emerson & Hickerson (2015), who challenge the evidence of a time-dependent bias in molecular rate estimates. This bias takes the form of a negative relationship between inferred evolutionary rates and the ages of the calibrations on which these estimates are based. Here, we present a summary of the evidence obtained from a broad range of taxa that supports a time-dependent bias in rate estimates, with a consideration of the potential causes of these observed trends. We also describe recent progress in improving the reliability of evolutionary rate estimation and respond to the concerns raised by Emerson & Hickerson (2015) about the validity of rates estimated from time-structured sequence data. In doing so, we hope to dispel some misconceptions and to highlight several research directions that will improve our understanding of time-dependent biases in rate estimates.
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Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Sebastián Duchêne
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, USA.,UCSC Genomics Institute, University of California, Santa Cruz, California, USA
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19
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A global molecular phylogeny and timescale of evolution for Cryptocercus woodroaches. Mol Phylogenet Evol 2016; 98:201-9. [DOI: 10.1016/j.ympev.2016.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 01/27/2016] [Accepted: 02/07/2016] [Indexed: 11/21/2022]
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20
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Marshall DC, Hill KBR, Moulds M, Vanderpool D, Cooley JR, Mohagan AB, Simon C. Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini). Syst Biol 2015; 65:16-34. [PMID: 26493828 DOI: 10.1093/sysbio/syv069] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/17/2015] [Indexed: 11/13/2022] Open
Abstract
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
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Affiliation(s)
- David C Marshall
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA;
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA
| | - Max Moulds
- Entomology Department, Australian Museum, 6 College Street, Sydney NSW 2010, Australia
| | - Dan Vanderpool
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA; Division of Biological Sciences, Health Sciences 304, U. Montana, Missoula, MT 59812
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA
| | - Alma B Mohagan
- Central Mindanao University, Sayre Highway, Bukidnon, Philippines
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA
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21
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Dénes AL, Kolcsár LP, Török E, Keresztes L. Phylogeography of the micro-endemicPedicia staryigroup (Insecta: Diptera): evidence of relict biodiversity in the Carpathians. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Avar-Lehel Dénes
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
- Interdisciplinary Research Institute on Bio-Nano-Sciences of Babeş-Bolyai University; Treboniu Laurian 42 400271 Cluj-Napoca Romania
| | - Levente-Péter Kolcsár
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
| | - Edina Török
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
- Romanian Academy, Institute of Biology; Splaiul Independenţei 296 060031 Bucureşti Romania
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
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22
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Yuan ML, Zhang QL, Wang ZF, Guo ZL, Bao GS. Molecular Phylogeny of Grassland Caterpillars (Lepidoptera: Lymantriinae: Gynaephora) Endemic to the Qinghai-Tibetan Plateau. PLoS One 2015; 10:e0127257. [PMID: 26053874 PMCID: PMC4459697 DOI: 10.1371/journal.pone.0127257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
Abstract
Gynaephora (Lepidoptera Erebidae: Lymantriinae) is a small genus, consisting of 15 nominated species, of which eight species are endemic to the Qinghai-Tibetan Plateau (QTP). In this study, we employed both mitochondrial and nuclear loci to infer a molecular phylogeny for the eight QTP Gynaephora spp. We used the phylogeny to estimate divergence dates in a molecular dating analysis and to delimit species. This information allowed us to investigate associations between the diversification history of the eight QTP species and geological and climatic events. Phylogenetic analyses indicated that the eight QTP species formed a monophyletic group with strong supports in both Bayesian and maximum likelihood analyses. The low K2P genetic distances between the eight QTP species suggested that diversification occurred relatively quickly and recently. Out of the eight species, five species were highly supported as monophyletic, which were also recovered by species delimitation analyses. Samples of the remaining three species (G. aureata, G. rouergensis, and G. minora) mixed together, suggesting that further studies using extensive population sampling and comprehensive morphological approaches are necessary to clarify their species status. Divergence time estimation results demonstrated that the diversification and speciation of Gynaephora on the QTP began during the late Miocene/early Pliocene and was potentially affected by the QTP uplift and associated climate changes during this time.
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Affiliation(s)
- Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Qi-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Zhao-Feng Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Zhong-Long Guo
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Gen-Sheng Bao
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
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23
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Molak M, Ho SYW. Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA. PeerJ 2015; 3:e821. [PMID: 25780773 PMCID: PMC4358697 DOI: 10.7717/peerj.821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 02/16/2015] [Indexed: 01/07/2023] Open
Abstract
Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.
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Affiliation(s)
- Martyna Molak
- School of Biological Sciences, University of Sydney , Sydney , Australia ; Museum and Institute of Zoology, Polish Academy of Sciences , Warsaw , Poland
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney , Sydney , Australia
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24
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Santos-Garcia D, Vargas-Chavez C, Moya A, Latorre A, Silva FJ. Genome evolution in the primary endosymbiont of whiteflies sheds light on their divergence. Genome Biol Evol 2015; 7:873-88. [PMID: 25716826 PMCID: PMC5322561 DOI: 10.1093/gbe/evv038] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Whiteflies are important agricultural insect pests, whose evolutionary success is related to a long-term association with a bacterial endosymbiont, Candidatus Portiera aleyrodidarum. To completely characterize this endosymbiont clade, we sequenced the genomes of three new Portiera strains covering the two extant whitefly subfamilies. Using endosymbiont and mitochondrial sequences we estimated the divergence dates in the clade and used these values to understand the molecular evolution of the endosymbiont coding sequences. Portiera genomes were maintained almost completely stable in gene order and gene content during more than 125 Myr of evolution, except in the Bemisia tabaci lineage. The ancestor had already lost the genetic information transfer autonomy but was able to participate in the synthesis of all essential amino acids and carotenoids. The time of divergence of the B. tabaci complex was much more recent than previous estimations. The recent divergence of biotypes B (MEAM1 species) and Q (MED species) suggests that they still could be considered strains of the same species. We have estimated the rates of evolution of Portiera genes, synonymous and nonsynonymous, and have detected significant differences among-lineages, with most Portiera lineages evolving very slowly. Although the nonsynonymous rates were much smaller than the synonymous, the genomic dN/dS ratios were similar, discarding selection as the driver of among-lineage variation. We suggest variation in mutation rate and generation time as the responsible factors. In conclusion, the slow evolutionary rates of Portiera may have contributed to its long-term association with whiteflies, avoiding its replacement by a novel and more efficient endosymbiont.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Carlos Vargas-Chavez
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, FISABIO-Salud Pública and Universitat de València, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, FISABIO-Salud Pública and Universitat de València, Spain
| | - Francisco J Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, FISABIO-Salud Pública and Universitat de València, Spain
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25
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Seal JN, Brown L, Ontiveros C, Thiebaud J, Mueller UG. Gone to Texas: phylogeography of twoTrachymyrmex(Hymenoptera: Formicidae) species along the southeastern coastal plain of North America. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12426] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jon N. Seal
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Larrimy Brown
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Cynthia Ontiveros
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Jeffrey Thiebaud
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
| | - Ulrich G. Mueller
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
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26
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Hipsley CA, Müller J. Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology. Front Genet 2014; 5:138. [PMID: 24904638 PMCID: PMC4033271 DOI: 10.3389/fgene.2014.00138] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/27/2014] [Indexed: 01/22/2023] Open
Abstract
Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types. In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from previous analyses. To illustrate the breadth and frequency of calibration types currently employed, we conducted a literature survey of over 600 articles published from 2007 to 2013. Over half of all analyses implemented one or more fossil dates as constraints, followed by geological events and secondary calibrations (15% each). Vertebrate taxa were subjects in nearly half of all studies, while invertebrates and plants together accounted for 43%, followed by viruses, protists and fungi (3% each). Current patterns in calibration practices were disproportionate to the number of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected in methodological evaluations. Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each. This critique should serve as a call to action for researchers across multiple communities, particularly those working on clades for which fossil records are poor, to develop their own guidelines regarding selection and implementation of alternative calibration types. This issue is particularly relevant now, as time-calibrated phylogenies are used for more than dating evolutionary origins, but often serve as the backbone of investigations into biogeography, diversity dynamics and rates of phenotypic evolution.
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Affiliation(s)
- Christy A. Hipsley
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany
| | - Johannes Müller
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und BiodiversitätsforschungBerlin, Germany
- Berlin-Brandenburg Institute of Avanced Biodiversity ResearchBerlin, Germany
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27
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Zhang F, Yu D, Luo Y, Ho SYW, Wang B, Zhu C. Cryptic diversity, diversification and vicariance in two species complexes ofTomocerus(Collembola, Tomoceridae) from China. ZOOL SCR 2014. [DOI: 10.1111/zsc.12056] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Feng Zhang
- Department of Entomology; College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Daoyuan Yu
- School of Life Sciences; Nanjing University; Nanjing China
| | - Yongzheng Luo
- Jinling College; Nanjing University; Nanjing 100101 China
| | - Simon Y. W. Ho
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Beixing Wang
- Department of Entomology; College of Plant Protection; Nanjing Agricultural University; Nanjing 210095 China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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Boykin LM, Bell CD, Evans G, Small I, De Barro PJ. Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed. BMC Evol Biol 2013; 13:228. [PMID: 24138220 PMCID: PMC3853546 DOI: 10.1186/1471-2148-13-228] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 10/01/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and has been driven in part by human-assisted dispersal supported through rapid global trade and low-cost air passenger transport. One of these pests, is the whitefly, Bemisia tabaci, a cryptic species complex that contains some of the world's most damaging pests of agriculture. The complex shows considerable genetic diversity and strong phylogeographic relationships. One consequence of the considerable impact that members of the B. tabaci complex have on agriculture, is the view that human activity, particularly in relation to agricultural practices, such as use of insecticides, has driven the diversification found within the species complex. This has been particularly so in the case of two members of the complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), which have become globally distributed invasive species. An alternative hypothesis is that diversification is due to paleogeographic and paleoclimatological changes. RESULTS The idea that human activity is driving speciation within the B. tabaci complex has never been tested, but the increased interest in fossil whiteflies and the growth in molecular data have enabled us to apply a relaxed molecular clock and so estimate divergence dates for the major lineages within the B. tabaci species complex. The divergence estimates do not support the view that human activity has been a major driver of diversification. CONCLUSIONS Our analysis suggests that the major lineages within the complex arose approximately 60-30 mya and the highly invasive MED and MEAM1 split from the rest of the species complex around 12 mya well before the evolution of Homo sapiens and agriculture. Furthermore, the divergence dates coincide with a period of global diversification that occurred broadly across the plant and animal kingdoms and was most likely associated with major climatic and tectonic events.
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Affiliation(s)
- Laura M Boykin
- ARC Centre of Excellence in Plant Energy Biology, M315, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
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