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Hurtado-Gómez JP, Vargas-Ramírez M, Iverson JB, Joyce WG, McCranie JR, Paetzold C, Fritz U. Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae). Mol Phylogenet Evol 2024; 197:108083. [PMID: 38679303 DOI: 10.1016/j.ympev.2024.108083] [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: 04/16/2023] [Revised: 04/02/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
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Affiliation(s)
| | - Mario Vargas-Ramírez
- Grupo Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia; Estación de Biología Tropical Roberto Franco (EBTRF), Universidad Nacional de Colombia, Villavicencio, Colombia
| | - John B Iverson
- Department of Biology, Earlham College, Richmond, IN 47374, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, 1700 Fribourg, Switzerland
| | - James R McCranie
- Smithsonian Research Associate, 10770 SW 164th Street, Miami, FL 33157, USA
| | - Claudia Paetzold
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany.
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Wei T, Wu Y, Zhang X, Zhang H, Crous P, Jiang Y. A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history. PERSOONIA 2024; 52:119-160. [PMID: 39161634 PMCID: PMC11319840 DOI: 10.3767/persoonia.2024.52.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/12/2024] [Indexed: 08/21/2024]
Abstract
The genera Cephalotrichum and Microascus contain ecologically, morphologically and lifestyle diverse fungi in Microascaceae (Microascales, Sordariomycetes) with a world-wide distribution. Despite previous studies having elucidated that Cephalotrichum and Microascus are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most comprehensive multi-gene (ITS, LSU, tef1 and tub2) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of Microascaceae. Two previously recognised main clades, Cephalotrichum (24 species) and Microascus (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within Microascaceae. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to Cephalotrichum and Microascus, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of Microascaceae was around 210.37 Mya (95 % HPD: 177.18-246.96 Mya) in the Late Triassic, and that Cephalotrichum and Microascus began to diversify approximately 27.07 Mya (95 % HPD: 20.47-34.37 Mya) and 70.46 Mya (95 % HPD: 56.96-86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help elucidate previously unresolved clade relationships. Citation: Wei TP, Wu YM, Zhang X, et al. 2024. A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history. Persoonia 52: 119-160. https://doi.org/10.3767/persoonia.2024.52.05 .
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Affiliation(s)
- T.P. Wei
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Y.M. Wu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
- Shandong Key Laboratory of Agricultural Microbiology, Taian, 271018, China
| | - X. Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550009, Guizhou Province, China
| | - H. Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025, Guizhou Province, China
- Guizhou Academy of Testing and Analysis, Guiyang, 550014, Guizhou Province, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Y.L. Jiang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025, Guizhou Province, China
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Shahzad K, Zhu M, Cao L, Hao Y, Zhou Y, Liu W, Dai J. Phylogenetic conservation in plant phenological traits varies between temperate and subtropical climates in China. FRONTIERS IN PLANT SCIENCE 2024; 15:1367152. [PMID: 38660448 PMCID: PMC11039852 DOI: 10.3389/fpls.2024.1367152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
Phenological traits, such as leaf and flowering dates, are proven to be phylogenetically conserved. The relationship between phylogenetic conservation, plant phenology, and climatic factors remains unknown. Here, we assessed phenological features among flowering plants as evidence for phylogenetic conservatism, the tendency for closely related species to share similar ecological and biological attributes. We use spring phenological traits data from 1968-2018 of 65 trees and 49 shrubs in Xi'an (temperate climate) and Guiyang (subtropical climate) to understand plant phenological traits' relationship with phylogeny. Molecular datasets are employed in evolutionary models to test the phylogenetic conservatism in spring phenological characteristics in response to climate-sensitive phenological features. Significant phylogenetic conservation was found in the Xi'an plant's phenological traits, while there was a non-significant conservation in the Guiyang plant species. Phylogenetic generalized least squares (PGLS) models correlate with phenological features significantly in Xi'an while non-significantly in Guiyang. Based on the findings of molecular dating, it was suggested that the Guiyang species split off from their relatives around 46.0 mya during the middle Eocene of the Tertiary Cenozoic Era, while Xi'an species showed a long evolutionary history and diverged from their relatives around 95 mya during the late Cretaceous Mesozoic Era. First leaf dates (FLD) indicative of spring phenology, show that Xi'an adjourned the case later than Guiyang. Unlike FLD, first flower dates (FFD) yield different results as Guiyang flowers appear later than Xi'an's. Our research revealed that various factors, including phylogeny, growth form, and functional features, influenced the diversity of flowering phenology within species in conjunction with local climate circumstances. These results are conducive to understanding evolutionary conservation mechanisms in plant phenology concerning evolutionary processes in different geographical and climate zones.
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Affiliation(s)
- Khurram Shahzad
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
| | - Mengyao Zhu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
| | - Lijuan Cao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
| | - Yulong Hao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
| | - Yu Zhou
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
| | - Wei Liu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
| | - Junhu Dai
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Acadamy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Hagemann J, Hofreiter M, Bibi F, Holroyd P, Arnold P. Is it inappropriate to ask for your age? Evaluating parameter impact on tree dating in a challenging clade (Macroscelidea). Mol Phylogenet Evol 2023; 183:107756. [PMID: 36906195 DOI: 10.1016/j.ympev.2023.107756] [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: 09/29/2022] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
Sengis (order Macroscelidea) are small mammals endemic to Africa. The taxonomy and phylogeny of sengis has been difficult to resolve due to a lack of clear morphological apomorphies. Molecular phylogenies have already significantly revised sengi systematics, but until now no molecular phylogeny has included all 20 extant species. In addition, the age of origin of the sengi crown clade and the divergence age of its two extant families remain unclear. Two recently published studies based on different datasets and age-calibration parameters (DNA type, outgroup selection, fossil calibration points) proposed highly different divergent age estimates and evolutionary scenarios. We obtained nuclear and mitochondrial DNA from mainly museum specimens using target enrichment of single-stranded DNA libraries to generate the first phylogeny of all extant macroscelidean species. We then explored the effects of different parameters (type of DNA, ratio of ingroup to outgroup sampling, number and type of fossil calibration points) and their resulting impacts on age estimates for the origin and initial diversification of Macroscelidea. We show that, even after correcting for substitution saturation, both using mitochondrial DNA in conjunction with nuclear DNA or alone results in much older ages and different branch lengths than when using nuclear DNA alone. We further show that the former effect can be attributed to insufficient amounts of nuclear data. If multiple calibration points are included, the age of the sengi crown group fossil prior has minimal impact on the estimated time frame of sengi evolution. In contrast, the inclusion or exclusion of outgroup fossil priors has a major effect on the resulting node ages. We also find that a reduced sampling of ingroup species does not significantly affect overall age estimates and that terminal specific substitution rates can serve as a means to evaluate the biological likeliness of the produced temporal estimates. Our study demonstrates how commonly varied parameters in temporal calibration of phylogenies affect age estimates. Dated phylogenies should therefore always be seen in the context of the dataset which was used to produce them.
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Affiliation(s)
- Justus Hagemann
- Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany.
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Faysal Bibi
- Museum Für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Patricia Holroyd
- University of California Museum of Paleontology, 1101 Valley Life Sciences Building, Berkeley, CA 94720 USA
| | - Patrick Arnold
- Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany.
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Hazzi NA, Hormiga G. Molecular phylogeny of the tropical wandering spiders (Araneae, Ctenidae) and the evolution of eye conformation in the RTA clade. Cladistics 2023; 39:18-42. [PMID: 36200603 DOI: 10.1111/cla.12518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 01/13/2023] Open
Abstract
Tropical wandering spiders (Ctenidae) are a diverse group of cursorial predators with its greatest species richness in the tropics. Traditionally, Ctenidae are diagnosed based on the presence of eight eyes arranged in three rows (a 2-4-2 pattern). We present a molecular phylogeny of Ctenidae, including for the first time representatives of all of its subfamilies. The molecular phylogeny was inferred using five nuclear (histone H3, 28S, 18S, Actin and ITS-2) and four mitochondrial (NADH, COI, 12S and 16S) markers. The final matrix includes 259 terminals, 103 of which belong to Ctenidae and represent 28 of the current 49 described genera. We estimated divergence times by including fossils as calibration points and biogeographic events, and used the phylogenetic hypothesis obtained to reconstruct the evolution of the eye conformation in the retrolateral tibial apophysis (RTA) clade. Ctenidae and its main lineages originated during the Paleocene-Eocene and have diversified in the tropics since then. However, in some analyses Ctenidae was recovered as polyphyletic as the genus Ancylometes Bertkau, 1880 was placed as sister to Oxyopidae. Except for Acantheinae, in which the type genus Acantheis Thorell, 1891 is placed inside Cteninae, the four recognized subfamilies of Ctenidae are monophyletic in most analyses. The ancestral reconstruction of the ocular conformation in the retrolateral tibial apophysis clade suggests that the ocular pattern of Ctenidae has evolved convergently seven times and that it has originated from ocular conformations of two rows of four eyes (4-4) and the ocular pattern of lycosids (4-2-2). We also synonymize the monotypic genus Parabatinga Polotov & Brescovit, 2009 with Centroctenus Mello-Leitão, 1929. We discuss some of the putative morphological synapomorphies of the main ctenid lineages within the phylogenetic framework offered by the molecular phylogenetic results of the study.
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Affiliation(s)
- Nicolas A Hazzi
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Fundación Ecotonos, Cra 72 No. 13ª-56, Cali, Colombia
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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Quintero-Galvis JF, Saenz-Agudelo P, Amico GC, Vazquez S, Shafer ABA, Nespolo RF. Genomic diversity and Demographic History of the Dromiciops genus (Marsupialia: Microbiotheriidae). Mol Phylogenet Evol 2022; 168:107405. [PMID: 35033671 DOI: 10.1016/j.ympev.2022.107405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/28/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022]
Abstract
Three orders represent the South American fauna of marsupials. Of these, Microbiotheria was until recently known as a monotypic genus with the only surviving species Dromiciops gliroides (monito del monte). The recent proposal of a new Dromiciops species (Dromiciops bicinovici), together with new information on the origin and diversification of living microbioterians has changed the prevailing paradigm around the evolutionary history of these emblematic marsupials. Here, we used a RADseq approach to test for evidence of admixture and past or current gene flow among both species of Dromiciops and evaluate the genetic structure within D. gliroides. We analyzed 127 samples of Dromiciops distributed across the known distribution range of both species. We also inferred the joint demographic history of these lineages, thus corroborating the status of D. bozinovici as a distinct species. Demographic history reconstruction indicated that D. bozinovici diverged from D. gliroides around 4my ago and has remained isolated and demographically stable ever since. In contrast, D. gliroides is subdivided into three subclades that experienced recent expansions and moderate gene flow among them (mostly from north to south). Furthermore, genetic distances among populations within D. gliroides were significantly correlated with geographic distances. These results suggest that some of the D. gliroides populations would have survived in glacial refuges, with posterior expansions after ice retreat. Our results have important implications for the systematics of the genus and have profound conservation consequences for the new species, especially considering the fragmentation level of the temperate rainforest.
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Affiliation(s)
- Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia. Chile; Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia. Chile
| | - Guillermo C Amico
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Soledad Vazquez
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Aaron B A Shafer
- Department of Forensic Science & Environmental Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia. Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia. Chile.
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Kazemi E, Nazarizadeh M, Fatemizadeh F, Khani A, Kaboli M. The phylogeny, phylogeography, and diversification history of the westernmost Asian cobra (Serpentes: Elapidae: Naja oxiana) in the Trans-Caspian region. Ecol Evol 2021; 11:2024-2039. [PMID: 33717439 PMCID: PMC7920780 DOI: 10.1002/ece3.7144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 11/21/2022] Open
Abstract
We conducted a comprehensive analysis of the phylogenetic, phylogeographic, and demographic relationships of Caspian cobra (Naja oxiana; Eichwald, 1831) populations based on a concatenated dataset of two mtDNA genes (cyt b and ND4) across the species' range in Iran, Afghanistan, and Turkmenistan, along with other members of Asian cobras (i.e., subgenus Naja Laurenti, 1768). Our results robustly supported that the Asiatic Naja are monophyletic, as previously suggested by other studies. Furthermore, N. kaouthia and N. sagittifera were recovered as sister taxa to each other, and in turn sister clades to N. oxiana. Our results also highlighted the existence of a single major evolutionary lineage for populations of N. oxiana in the Trans-Caspian region, suggesting a rapid expansion of this cobra from eastern to western Asia, coupled with a rapid range expansion from east of Iran toward the northeast. However, across the Iranian range of N. oxiana, subdivision of populations was not supported, and thus, a single evolutionary significant unit is proposed for inclusion in future conservation plans in this region.
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Affiliation(s)
- Elmira Kazemi
- Department of EnvironmentFaculty of Natural Resources and EnvironmentScience and Research BranchIslamic Azad UniversityTehranIran
| | - Masoud Nazarizadeh
- Department of ParasitologyFaculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- Institute of ParasitologyBiology Centre CAS, v.v.i.České BudějoviceCzech Republic
| | - Faezeh Fatemizadeh
- Department of Environmental ScienceFaculty of Natural ResourcesUniversity of TehranKarajIran
| | - Ali Khani
- Department of EnvironmentKhorasan RazaviMashhadIran
| | - Mohammad Kaboli
- Department of Environmental ScienceFaculty of Natural ResourcesUniversity of TehranKarajIran
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Zhao Z, Heideman N, Bester P, Jordaan A, Hofmeyr MD. Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa. BMC Evol Biol 2020; 20:153. [PMID: 33187474 PMCID: PMC7666511 DOI: 10.1186/s12862-020-01717-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world's tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. RESULTS We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63-5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. CONCLUSION Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B-Ptr, Ptt-A and Pv-A.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa.
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Phillip Bester
- Department of Virology, University of the Free State and National Health Laboratory Service (NHLS), Bloemfontein, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Margaretha D Hofmeyr
- Department of Biodiversity and Conservation Biology, Chelonian Biodiversity and Conservation, University of the Western Cape, Bellville, South Africa
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Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12020070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.
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Bos KI, Kühnert D, Herbig A, Esquivel-Gomez LR, Andrades Valtueña A, Barquera R, Giffin K, Kumar Lankapalli A, Nelson EA, Sabin S, Spyrou MA, Krause J. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol 2019; 73:639-666. [PMID: 31283430 DOI: 10.1146/annurev-micro-090817-062436] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.
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Affiliation(s)
- Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Luis Roger Esquivel-Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; .,Faculty of Biological Sciences, Friedrich Schiller University, 07737 Jena, Germany
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11
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New insights into the phylogeographic distribution of the 3FTx/PLA2 venom dichotomy across genus Micrurus in South America. J Proteomics 2019; 200:90-101. [DOI: 10.1016/j.jprot.2019.03.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 01/01/2023]
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12
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Schedel FDB, Musilova Z, Schliewen UK. East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation. BMC Evol Biol 2019; 19:94. [PMID: 31023223 PMCID: PMC6482553 DOI: 10.1186/s12862-019-1417-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/31/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil †Tugenchromis pickfordi in the cichlid divergence age estimates. RESULTS Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43-33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89-20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88-25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23-18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40-26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93-5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: 'Orthochromis' indermauri and 'Haplochormis' vanheusdeni. CONCLUSIONS Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated "Melting-Pot Tanganyika" hypothesis. The radiation of the 'Lower Congo Lamprologus clade' might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi.
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Affiliation(s)
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44 Prague, Czech Republic
| | - Ulrich Kurt Schliewen
- Department of Ichthyology, SNSB - Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
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13
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Oliver PM, Brown RM, Kraus F, Rittmeyer E, Travers SL, Siler CD. Lizards of the lost arcs: mid-Cenozoic diversification, persistence and ecological marginalization in the West Pacific. Proc Biol Sci 2019; 285:rspb.2017.1760. [PMID: 29343593 DOI: 10.1098/rspb.2017.1760] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/11/2017] [Indexed: 11/12/2022] Open
Abstract
Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the world's most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallace's Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia.
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Affiliation(s)
- Paul M Oliver
- Ecology, Evolution and Genetics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric Rittmeyer
- Ecology, Evolution and Genetics, Australian National University, Canberra, Australian Capital Territory 2601, Australia.,Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA
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14
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de Mazancourt V, Klotz W, Marquet G, Mos B, Rogers DC, Keith P. The complex study of complexes: The first well-supported phylogeny of two species complexes within genus Caridina (Decapoda: Caridea: Atyidae) sheds light on evolution, biogeography, and habitat. Mol Phylogenet Evol 2018; 131:164-180. [PMID: 30423441 DOI: 10.1016/j.ympev.2018.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 02/02/2023]
Abstract
Atyid shrimps, a key component of tropical freshwater ecosystems, face multiple anthropogenic threats and thus need special attention. With more than 300 described species, the genus Caridina is the most speciose of all the Caridea infra-order. Caridina spp. occupy diverse habitats in tropical freshwaters of the Indo-West Pacific region. Several species complexes have been recognized, based on common morphological features, but little is known about how well these morphological characteristics align with phylogenetic characteristics. Furthermore, no phylogeny of the genus Caridina published so far has provided well-resolved and supported relationships among different species, thus impeding the possibility of proposing evolutionary hypotheses. In this study we used next generation sequencing (NGS) to provide new insights into the phylogenetic relationships among the genus Caridina, focusing on two complexes: 'Caridina nilotica' and 'Caridina weberi'. We collected 92 specimens belonging to these two groups from most of their known geographical range, representing 50 species, for which we sequenced seven mitochondrial genes and two nuclear markers using ion torrent NGS. We performed a phylogenetic analysis, which yielded the first well-supported tree for the genus Caridina. On this tree were mapped the geographic ranges and the habitats used by the different species, and a time calibration was tested. We found the driving factors that most likely account for separation of clades are differences in habitat and to a lesser extent geography. This work provides new insights into the taxonomy of this group and identifies opportunities for further studies in order to fill knowledge gaps that currently impede the management and conservation of atyid species.
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Affiliation(s)
- Valentin de Mazancourt
- Muséum national d'Histoire naturelle, Département Adaptations du Vivant, UMR 7208, CP026, 57, rue Cuvier, F-75231 Paris, Cedex 05, France.
| | | | - Gerard Marquet
- Muséum national d'Histoire naturelle, Département Adaptations du Vivant, UMR 7208, CP026, 57, rue Cuvier, F-75231 Paris, Cedex 05, France
| | - Benjamin Mos
- National Marine Science Centre, Southern Cross University, PO Box 4321, Coffs Harbour, NSW 2450, Australia
| | - D Christopher Rogers
- Kansas Biological Survey and the Natural History Museum (Biodiversity Institute), Kansas University, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047-3759, USA
| | - Philippe Keith
- Muséum national d'Histoire naturelle, Département Adaptations du Vivant, UMR 7208, CP026, 57, rue Cuvier, F-75231 Paris, Cedex 05, France
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15
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Durban J, Sasa M, Calvete JJ. Venom gland transcriptomics and microRNA profiling of juvenile and adult yellow-bellied sea snake, Hydrophis platurus, from Playa del Coco (Guanacaste, Costa Rica). Toxicon 2018; 153:96-105. [DOI: 10.1016/j.toxicon.2018.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 08/29/2018] [Indexed: 02/08/2023]
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16
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Ballesteros JA, Hormiga G. Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae). Mol Phylogenet Evol 2018; 121:183-197. [PMID: 29337274 DOI: 10.1016/j.ympev.2018.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States; Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, United States.
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G Street NW, Bell Hall 302, Washington, DC 20052, United States
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17
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Lukoschek V. Congruent phylogeographic patterns in a young radiation of live-bearing marine snakes: Pleistocene vicariance and the conservation implications of cryptic genetic diversity. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vimoksalehi Lukoschek
- ARC Centre of Excellence for Coral Reef Studies; James Cook University; Townsville Qld Australia
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18
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Klimov PB, Mironov SV, OConnor BM. Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds. Evolution 2017; 71:2381-2397. [DOI: 10.1111/evo.13309] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 06/25/2017] [Accepted: 07/07/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Pavel B. Klimov
- Department of Ecology and Evolutionary Biology University of Michigan, Museum of Zoology Ann Arbor Michigan 48109
- Faculty of Biology Tyumen State University Tyumen 625003 Russia
| | - Sergey V. Mironov
- Faculty of Biology Tyumen State University Tyumen 625003 Russia
- Department of Parasitology, Zoological Institute Russian Academy of Sciences 1 Universitetskaya embankment Saint Petersburg 199034 Russia
| | - Barry M. OConnor
- Department of Ecology and Evolutionary Biology University of Michigan, Museum of Zoology Ann Arbor Michigan 48109
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19
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Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger). Sci Rep 2017; 7:3308. [PMID: 28607415 PMCID: PMC5468327 DOI: 10.1038/s41598-017-03395-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/27/2017] [Indexed: 01/02/2023] Open
Abstract
The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the “Tibetan-origin hypothesis” suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a “Tibetan-origin hypothesis”, current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.
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20
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Jurado-Rivera JA, Pons J, Alvarez F, Botello A, Humphreys WF, Page TJ, Iliffe TM, Willassen E, Meland K, Juan C, Jaume D. Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps. Sci Rep 2017; 7:2852. [PMID: 28588246 PMCID: PMC5460120 DOI: 10.1038/s41598-017-03107-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/25/2017] [Indexed: 11/09/2022] Open
Abstract
Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (Atyidae) are restricted to specialised coastal subterranean habitats or nearby freshwaters and have a highly disconnected distribution (Eastern Pacific, Caribbean, Atlantic, Mediterranean, Madagascar, Australia). The combination of a wide distribution and a limited dispersal potential suggests a large-scale process has generated this geographic pattern. Tectonic plates that fragment ancestral ranges (vicariance) has often been assumed to cause this process, with the biota as passive passengers on continental blocks. The ancestors of these cave shrimps are believed to have inhabited the ancient Tethys Sea, with three particular geological events hypothesised to have led to their isolation and divergence; (1) the opening of the Atlantic Ocean, (2) the breakup of Gondwana, and (3) the closure of the Tethys Seaway. We test the relative contribution of vicariance and dispersal in the evolutionary history of this group using mitochondrial genomes to reconstruct phylogenetic and biogeographic scenarios with fossil-based calibrations. Given that the Australia/Madagascar shrimp divergence postdates the Gondwanan breakup, our results suggest both vicariance (the Atlantic opening) and dispersal. The Tethys closure appears not to have been influential, however we hypothesise that changing marine currents had an important early influence on their biogeography.
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Affiliation(s)
- José A Jurado-Rivera
- Dept. of Biology, Universitat de les Illes Balears. Ctra. Valldemossa km 7'5, Palma, 07122, Balearic Islands, Spain.
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies. C/ Miquel Marquès 21, Esporles, 07190, Balearic Islands, Spain
| | - Fernando Alvarez
- Colección Nacional de Crustáceos, Dpto. de Zoología, Instituto de Biología, UNAM. Tercer circuito s/n, Ciudad Universitaria, Copilco, Coyoacán, A.P. 70-153, México D.F. CP, 04510, Mexico
| | - Alejandro Botello
- Dept. de Ciencias Químico-Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez. Anillo del Pronaf y Estocolmo s/n, Ciudad Juarez, 32300, Chihuahua, Mexico
| | - William F Humphreys
- Western Australian Museum, Collections and Research, Locked Bag 49, Welshpool DC, WA, 6986, Australia
- School of Animal Biology, The University of Western Australia, Crawley, Perth, Western Australia, 6009, Australia
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland, 4111, Australia
- Water Planning Ecology, Queensland Dept. of Science, Information Technology and Innovation, Dutton Park, Queensland, 4102, Australia
| | - Thomas M Iliffe
- Dept. of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, OCSB #251, Galveston, TX, 77553, USA
| | - Endre Willassen
- Dept. of Natural History, University Museum of Bergen, Postboks 7800, N-5020, Bergen, Norway
| | - Kenneth Meland
- University of Bergen, Department of Biology, PO Box 7800, N-5020, Bergen, Norway
| | - Carlos Juan
- Dept. of Biology, Universitat de les Illes Balears. Ctra. Valldemossa km 7'5, Palma, 07122, Balearic Islands, Spain
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies. C/ Miquel Marquès 21, Esporles, 07190, Balearic Islands, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies. C/ Miquel Marquès 21, Esporles, 07190, Balearic Islands, Spain
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21
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Maswanganye KA, Cunningham MJ, Bennett NC, Chimimba CT, Bloomer P. Life on the rocks: Multilocus phylogeography of rock hyrax (Procavia capensis) from southern Africa. Mol Phylogenet Evol 2017; 114:49-62. [PMID: 28411160 DOI: 10.1016/j.ympev.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/31/2017] [Accepted: 04/06/2017] [Indexed: 01/23/2023]
Abstract
Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales. In addition, distribution modelling was used to investigate the current and predicted distribution of the species under different climatic scenarios. Collectively, the data reveal a complex history of isolation followed by secondary contact shaping the current intraspecific diversity. The cyt b sequences confirmed the presence of two previously proposed geographically and genetically distinct lineages distributed across the southern African Great Escarpment and north-western mountain ranges. Molecular dating suggests Miocene divergence of the lineages, yet there are no discernible extrinsic barriers to gene flow. The nuclear markers reveal incomplete lineage sorting or ongoing mixing of the two lineages. Although the microsatellite data lend some support to the presence of two subpopulations, there is weak structuring within and between lineages. These data indicate the presence of gene flow from the northern into the southern parts of the southern African sub-region likely following the secondary contact. The distribution modelling predictably reveal the species' preference for rocky areas, with stable refugia through time in the northern mountain ranges, the Great Escarpment, as well as restricted areas of the Northern Cape Province and the Cape Fold Mountains of South Africa. Different microclimatic variables appear to determine the distributional range of the species. Despite strong habitat preference, the micro-habitat offered by rocky crevices and unique life history traits likely promoted the adaptability of P. capensis, resulting in the widespread distribution and persistence of the species over a long evolutionary period. Spatio-temporal comparison of the evolutionary histories of other co-distributed species across the rocky landscapes of southern Africa will improve our understanding of the regional patterns of biodiversity and local endemism.
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Affiliation(s)
- K Amanda Maswanganye
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa; Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Michael J Cunningham
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Christian T Chimimba
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
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Saladin B, Leslie AB, Wüest RO, Litsios G, Conti E, Salamin N, Zimmermann NE. Fossils matter: improved estimates of divergence times in Pinus reveal older diversification. BMC Evol Biol 2017; 17:95. [PMID: 28376717 PMCID: PMC5381128 DOI: 10.1186/s12862-017-0941-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 03/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods. RESULTS We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of crown Pinus is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines. CONCLUSIONS Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods.
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Affiliation(s)
- Bianca Saladin
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrew B. Leslie
- Department of Ecology and Evolutionary Biology, Brown University, Providence, USA
| | - Rafael O. Wüest
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Glenn Litsios
- Department of Computational Biology, Biophore building, University of Lausanne, Lausanne, Switzerland
- Species, Ecosystems, Landscapes Division, Federal Office for the Environment FOEN, Bern, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany and Botanical Garden, University of Zurich, Zurich, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Biophore building, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, University of Lausanne, Lausanne, Switzerland
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Abstract
Molecular evolution can reveal the relationship between sets of homologous sequences and the patterns of change that occur during their evolution. An important aspect of these studies is the inference of a phylogenetic tree, which explicitly describes evolutionary relationships between homologous sequences. This chapter provides an introduction to evolutionary trees and how to infer them from sequence data using some commonly used inferential methodology. It focuses on statistical methods for inferring trees and how to assess the confidence one should have in any resulting tree, with a particular emphasis on the underlying assumptions of the methods and how they might affect the tree estimate. There is also some discussion of the underlying algorithms used to perform tree search and recommendations regarding the performance of different algorithms. Finally, there are a few practical guidelines, including how to combine multiple software packages to improve inference, and a comparison between Bayesian and Maximum likelihood phylogenetics.
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Affiliation(s)
- Simon Whelan
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
| | - David A Morrison
- Department of Organism Biology, Uppsala University, Uppsala, Sweden
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24
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Kappas I, Vittas S, Pantzartzi CN, Drosopoulou E, Scouras ZG. A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes). PLoS One 2016; 11:e0166988. [PMID: 27907107 PMCID: PMC5132296 DOI: 10.1371/journal.pone.0166988] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.
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Affiliation(s)
- Ilias Kappas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Spiros Vittas
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysoula N. Pantzartzi
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elena Drosopoulou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Zacharias G. Scouras
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
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Phylogeny and diversification of mountain vipers (Montivipera, Nilson et al., 2001) triggered by multiple Plio-Pleistocene refugia and high-mountain topography in the Near and Middle East. Mol Phylogenet Evol 2016; 101:336-351. [PMID: 27165940 DOI: 10.1016/j.ympev.2016.04.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 04/10/2016] [Accepted: 04/20/2016] [Indexed: 11/21/2022]
Abstract
The Near and Middle East is a hotspot of biodiversity, but the region remains underexplored at the level of genetic biodiversity. Here, we present an extensive molecular phylogeny of the viperid snake genus Montivipera, including all known taxa. Based on nuclear and mitochondrial data, we present novel insights into the phylogeny of the genus and review the status of its constituent species. Maximum likelihood methods revealed a montane origin of Montivipera at 12.3Mya. We then analyzed factors of mountain viper diversity. Our data support substantial changes in effective population size through Plio-Pleistocene periods. We conclude that climatic oscillations were drivers of allopatric speciation, and that mountain systems of the Near and Middle East have strongly influenced the evolution and survival of taxa, because climatic and topographical heterogeneities induced by mountains have played a crucial role as filters for dispersal and as multiple refugia. The wide diversity of montane microhabitats enabled mountain vipers to retain their ecological niche during climatic pessima. In consequence the varied geological and topographical conditions between refugia favoured genetic isolation and created patterns of species richness resulting in the formation of neoendemic taxa. Our data support high concordance between geographic distributions of Montivipera haplotypes with putative plant refugia.
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Lee MSY, Sanders KL, King B, Palci A. Diversification rates and phenotypic evolution in venomous snakes (Elapidae). ROYAL SOCIETY OPEN SCIENCE 2016; 3:150277. [PMID: 26909162 PMCID: PMC4736917 DOI: 10.1098/rsos.150277] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/08/2015] [Indexed: 05/19/2023]
Abstract
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high rates of diversification within Elapidae, yet exhibit rates of body size evolution almost identical to the general elapid 'background' rate. Although correlations between speciation rates and rates of body size change exist in certain groups (e.g. ray-finned fishes, passerine birds), the two processes appear to be uncoupled in elapid snakes. There is also no detectable shift in diversification dynamics associated with the colonization of Australasia, which is surprising given that elapids appear to be the first clade of venomous snakes to reach the continent.
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Affiliation(s)
- Michael S. Y. Lee
- Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, SA 5001, Australia
- Author for correspondence: Michael S. Y. Lee e-mail:
| | - Kate L. Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Benedict King
- School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, SA 5001, Australia
| | - Alessandro Palci
- Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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Hortal J, de Bello F, Diniz-Filho JAF, Lewinsohn TM, Lobo JM, Ladle RJ. Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054400] [Citation(s) in RCA: 544] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joaquín Hortal
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain; ,
- Department of Ecology, Instituto de Ciências Biologicas, Universidade Federal de Goiás, 74001-970 Goiânia, Brazil;
- Center for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Francesco de Bello
- Institute of Botany, Czech Academy of Sciences, CZ-379 82 Třeboň, Czech Republic;
- Department of Botany, Faculty of Sciences, University of South Bohemia, 370 05 Budějovice, Czech Republic
| | | | - Thomas M. Lewinsohn
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862 Campinas, Brazil;
| | - Jorge M. Lobo
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), 28006 Madrid, Spain; ,
| | - Richard J. Ladle
- Instituto de Ciências Biológicas e da Saúde (ICBS), Universidade Federal de Alagoas, 57072-900 Maceió, Brazil
- School of Geography and the Environment, University of Oxford, OX1 3QY Oxford, United Kingdom;
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Toussaint EFA, Condamine FL. To what extent do new fossil discoveries change our understanding of clade evolution? A cautionary tale from burying beetles (Coleoptera:Nicrophorus). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12710] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Emmanuel F. A. Toussaint
- Department of Ecology & Evolutionary Biology & Division of Entomology; Biodiversity Institute; University of Kansas; Lawrence KS 66045 USA
| | - Fabien L. Condamine
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G 2E9 Canada
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Laustsen AH, Gutiérrez JM, Rasmussen AR, Engmark M, Gravlund P, Sanders KL, Lohse B, Lomonte B. Danger in the reef: Proteome, toxicity, and neutralization of the venom of the olive sea snake, Aipysurus laevis. Toxicon 2015; 107:187-96. [PMID: 26169672 DOI: 10.1016/j.toxicon.2015.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/03/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
Four specimens of the olive sea snake, Aipysurus laevis, were collected off the coast of Western Australia, and the venom proteome was characterized and quantitatively estimated by RP-HPLC, SDS-PAGE, and MALDI-TOF-TOF analyses. A. laevis venom is remarkably simple and consists of phospholipases A2 (71.2%), three-finger toxins (3FTx; 25.3%), cysteine-rich secretory proteins (CRISP; 2.5%), and traces of a complement control module protein (CCM; 0.2%). Using a Toxicity Score, the most lethal components were determined to be short neurotoxins. Whole venom had an intravenous LD50 of 0.07 mg/kg in mice and showed a high phospholipase A2 activity, but no proteinase activity in vitro. Preclinical assessment of neutralization and ELISA immunoprofiling showed that BioCSL Sea Snake Antivenom was effective in cross-neutralizing A. laevis venom with an ED50 of 821 μg venom per mL antivenom, with a binding preference towards short neurotoxins, due to the high degree of conservation between short neurotoxins from A. laevis and Enhydrina schistosa venom. Our results point towards the possibility of developing recombinant antibodies or synthetic inhibitors against A. laevis venom due to its simplicity.
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Affiliation(s)
- Andreas H Laustsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Arne R Rasmussen
- Royal Danish Academy of Fine Arts, Schools of Architecture, Design and Conservation, Denmark
| | - Mikael Engmark
- Department of Systems Biology, Technical University of Denmark, Denmark
| | | | - Kate L Sanders
- School of Earth & Environmental Sciences, University of Adelaide, Australia
| | - Brian Lohse
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
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van Tuinen M, Torres CR. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families. Front Genet 2015; 6:203. [PMID: 26106406 PMCID: PMC4459087 DOI: 10.3389/fgene.2015.00203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 05/25/2015] [Indexed: 11/13/2022] Open
Abstract
Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree of Life.
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Affiliation(s)
- Marcel van Tuinen
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- Centre of Evolutionary and Ecological Studies, Marine Evolution and Conservation Group, University of GroningenGroningen, Netherlands
| | - Christopher R. Torres
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- National Evolutionary Synthesis CenterDurham, NC, USA
- Department of Integrative Biology, University of Texas at AustinAustin, TX, USA
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Alectorioid Morphologies in Paleogene Lichens: New Evidence and Re-Evaluation of the Fossil Alectoria succini Mägdefrau. PLoS One 2015; 10:e0129526. [PMID: 26053106 PMCID: PMC4460037 DOI: 10.1371/journal.pone.0129526] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/11/2015] [Indexed: 11/19/2022] Open
Abstract
One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon.
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Lillywhite HB, Heatwole H, Sheehy CM. Dehydration and drinking behavior in true sea snakes (Elapidae: Hydrophiinae: Hydrophiini). J Zool (1987) 2015. [DOI: 10.1111/jzo.12239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. B. Lillywhite
- Earth and Environmental Sciences; James Cook University; Townsville Qld Australia
- Department of Biology; University of Florida; Gainesville FL USA
| | - H. Heatwole
- Earth and Environmental Sciences; James Cook University; Townsville Qld Australia
- Department of Biology; North Carolina State University; Raleigh NC USA
- Department of Zoology; The University of New England; Armidale NSW Australia
| | - C. M. Sheehy
- Earth and Environmental Sciences; James Cook University; Townsville Qld Australia
- Department of Biology; University of Florida; Gainesville FL USA
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Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach. Genetics 2015; 200:295-308. [PMID: 25769979 DOI: 10.1534/genetics.115.174425] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/04/2015] [Indexed: 12/30/2022] Open
Abstract
Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10(-9)/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.
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34
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Emerson BC, Hickerson MJ. Lack of support for the time-dependent molecular evolution hypothesis. Mol Ecol 2015; 24:702-9. [DOI: 10.1111/mec.13070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/17/2014] [Accepted: 12/30/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife, Canary Islands 38206 Spain
| | - Michael J. Hickerson
- Biology Department; City College of New York; New York NY 10031 USA
- The Graduate Center; City University of New York; New York NY 10016 USA
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A species-level phylogeny of all extant and late Quaternary extinct mammals using a novel heuristic-hierarchical Bayesian approach. Mol Phylogenet Evol 2014; 84:14-26. [PMID: 25542649 DOI: 10.1016/j.ympev.2014.11.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 10/30/2014] [Accepted: 11/02/2014] [Indexed: 11/20/2022]
Abstract
Across large clades, two problems are generally encountered in the estimation of species-level phylogenies: (a) the number of taxa involved is generally so high that computation-intensive approaches cannot readily be utilized and (b) even for clades that have received intense study (e.g., mammals), attention has been centered on relatively few selected species, and most taxa must therefore be positioned on the basis of very limited genetic data. Here, we describe a new heuristic-hierarchical Bayesian approach and use it to construct a species-level phylogeny for all extant and late Quaternary extinct mammals. In this approach, species with large quantities of genetic data are placed nearly freely in the mammalian phylogeny according to these data, whereas the placement of species with lower quantities of data is performed with steadily stricter restrictions for decreasing data quantities. The advantages of the proposed method include (a) an improved ability to incorporate phylogenetic uncertainty in downstream analyses based on the resulting phylogeny, (b) a reduced potential for long-branch attraction or other types of errors that place low-data taxa far from their true position, while maintaining minimal restrictions for better-studied taxa, and (c) likely improved placement of low-data taxa due to the use of closer outgroups.
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36
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Ho SYW, Duchêne S. Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol 2014; 23:5947-65. [DOI: 10.1111/mec.12953] [Citation(s) in RCA: 225] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Y. W. Ho
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Sebastián Duchêne
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
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Arcila D, Alexander Pyron R, Tyler JC, Ortí G, Betancur-R R. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol 2014; 82 Pt A:131-45. [PMID: 25462998 DOI: 10.1016/j.ympev.2014.10.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new fossilized birth-death process model for node dating (implemented in the program DPPDiv), and the other using a total-evidence or tip-dating method (implemented in MrBayes and BEAST). These methods are applied herein to tetraodontiform fishes, a diverse group of living and extinct taxa that features one of the most extensive fossil records among teleosts. Previous estimates of time-calibrated phylogenies of tetraodontiforms using node-dating methods reported disparate estimates for their age of origin, ranging from the late Jurassic to the early Paleocene (ca. 150-59Ma). We analyzed a comprehensive dataset with 16 loci and 210 morphological characters, including 131 taxa (95 extant and 36 fossil species) representing all families of fossil and extant tetraodontiforms, under different molecular clock calibration approaches. Results from node-dating methods produced consistently younger ages than the tip-dating approaches. The older ages inferred by tip dating imply an unlikely early-late Jurassic (ca. 185-119Ma) origin for this order and the existence of extended ghost lineages in their fossil record. Node-based methods, by contrast, produce time estimates that are more consistent with the stratigraphic record, suggesting a late Cretaceous (ca. 86-96Ma) origin. We show that the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under assessment. This study suggests that current implementations of tip dating may overestimate ages of divergence in calibrated phylogenies. It also provides a comprehensive phylogenetic framework for tetraodontiform systematics and future comparative studies.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States.
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - James C Tyler
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States; Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan 00931, Puerto Rico
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Prates I, Rodrigues MT, Melo-Sampaio PR, Carnaval AC. Phylogenetic relationships of Amazonian anole lizards (Dactyloa): taxonomic implications, new insights about phenotypic evolution and the timing of diversification. Mol Phylogenet Evol 2014; 82 Pt A:258-68. [PMID: 25451806 DOI: 10.1016/j.ympev.2014.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/24/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
The ecology and evolution of Caribbean anoles are well described, yet little is known about mainland anole species. Lack of phylogenetic information limits our knowledge about species boundaries, morphological evolution, and the biogeography of anoles in South America. To help fill this gap, we provide an updated molecular phylogeny of the Dactyloa (Dactyloidae), with emphasis on the punctata species group. By sampling understudied Amazonian taxa, we (i) assess the phylogenetic placement of the 'odd anole', D. dissimilis; (ii) infer the relationships of the proboscis-bearing D. phyllorhina, testing the hypothesis of independent nasal appendage evolution within the anole radiation; and (iii) examine genetic and dewlap color variation in D. punctata and D. philopunctata. Combining multiple nuclear loci with a review of the fossil record, we also (iv) estimate divergence times within the pleurodont iguanian clade of lizards, including Amazonian representatives of Dactyloa and Norops (Dactyloidae) and of Polychrus (Polychrotidae). We recover the five Dactyloa clades previously referred to as the aequatorialis, heteroderma, latifrons, punctata and roquet species groups, as well as a sixth clade composed of D. dissimilis and the non-Amazonian D. neblinina and D. calimae. We find D. phyllorhina to be nested within the punctata group, suggesting independent evolution of the anole proboscis. We consistently recover D. philopunctata nested within D. punctata, and report limited genetic divergence between distinct dewlap phenotypes. The most recent common ancestor of Dactyloa, Anolis and Norops dates back to the Eocene. Most Amazonian taxa within both Dactyloa and Norops diverged in the Miocene, but some diversification events were as old as the late Eocene and late Oligocene. Amazonian Polychrus diverged in the Pliocene. Our findings have broad implications for anole biogeography, disputing recent suggestions that modern dactyloid genera were present in the Caribbean region during the Cretaceous.
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Affiliation(s)
- Ivan Prates
- Department of Biology, City College of New York, New York, NY, USA; Graduate Center, City University of New York, New York, NY, USA.
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Paulo Roberto Melo-Sampaio
- Programa de Pós-graduação em Ecologia e Manejo de Recursos Naturais and Laboratório de Herpetologia, Universidade Federal do Acre, Rio Branco, AC, Brazil; União Educacional do Norte, Rio Branco, AC, Brazil.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, NY, USA; Graduate Center, City University of New York, New York, NY, USA.
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Clarke JA, Boyd CA. Methods for the quantitative comparison of molecular estimates of clade age and the fossil record. Syst Biol 2014; 64:25-41. [PMID: 25281846 DOI: 10.1093/sysbio/syu068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Approaches quantifying the relative congruence, or incongruence, of molecular divergence estimates and the fossil record have been limited. Previously proposed methods are largely node specific, assessing incongruence at particular nodes for which both fossil data and molecular divergence estimates are available. These existing metrics, and other methods that quantify incongruence across topologies including entirely extinct clades, have so far not taken into account uncertainty surrounding both the divergence estimates and the ages of fossils. They have also treated molecular divergence estimates younger than previously assessed fossil minimum estimates of clade age as if they were the same as cases in which they were older. However, these cases are not the same. Recovered divergence dates younger than compared oldest known occurrences require prior hypotheses regarding the phylogenetic position of the compared fossil record and standard assumptions about the relative timing of morphological and molecular change to be incorrect. Older molecular dates, by contrast, are consistent with an incomplete fossil record and do not require prior assessments of the fossil record to be unreliable in some way. Here, we compare previous approaches and introduce two new descriptive metrics. Both metrics explicitly incorporate information on uncertainty by utilizing the 95% confidence intervals on estimated divergence dates and data on stratigraphic uncertainty concerning the age of the compared fossils. Metric scores are maximized when these ranges are overlapping. MDI (minimum divergence incongruence) discriminates between situations where molecular estimates are younger or older than known fossils reporting both absolute fit values and a number score for incompatible nodes. DIG range (divergence implied gap range) allows quantification of the minimum increase in implied missing fossil record induced by enforcing a given set of molecular-based estimates. These metrics are used together to describe the relationship between time trees and a set of fossil data, which we recommend be phylogenetically vetted and referred on the basis of apomorphy. Differences from previously proposed metrics and the utility of MDI and DIG range are illustrated in three empirical case studies from angiosperms, ostracods, and birds. These case studies also illustrate the ways in which MDI and DIG range may be used to assess time trees resultant from analyses varying in calibration regime, divergence dating approach or molecular sequence data analyzed.
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Affiliation(s)
- Julia A Clarke
- Jackson School of Geosciences, The University of Texas at Austin, 1 University Station C1100, Austin, TX 78712; Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, 501 East Saint Joseph Street, Rapid City, SD 57701, USA
| | - Clint A Boyd
- Jackson School of Geosciences, The University of Texas at Austin, 1 University Station C1100, Austin, TX 78712; Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, 501 East Saint Joseph Street, Rapid City, SD 57701, USA
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Toussaint EF, Condamine FL, Hawlitschek O, Watts CH, Porch N, Hendrich L, Balke M. Unveiling the Diversification Dynamics of Australasian Predaceous Diving Beetles in the Cenozoic. Syst Biol 2014; 64:3-24. [DOI: 10.1093/sysbio/syu067] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Emmanuel F.A. Toussaint
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Fabien L. Condamine
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Oliver Hawlitschek
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Chris H. Watts
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Nick Porch
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Lars Hendrich
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
| | - Michael Balke
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
- SNSB-Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247 Munich, Germany; 2CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique), Route de Saclay, 91128 Palaiseau cedex, France; 3South Australian Museum, Adelaide, South Australia, Australia; 4Centre for Integrated Ecology & School of Life and Environmental Sciences, Deakin University, 221 Burwood Highway, Burwood, Victoria 3125, Australia; and 5GeoBioCenter, Ludwig-Maximilians University, Munich, Germany
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Duchêne S, Lanfear R, Ho SYW. The impact of calibration and clock-model choice on molecular estimates of divergence times. Mol Phylogenet Evol 2014; 78:277-89. [PMID: 24910154 DOI: 10.1016/j.ympev.2014.05.032] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/16/2014] [Accepted: 05/28/2014] [Indexed: 11/26/2022]
Abstract
Phylogenetic estimates of evolutionary timescales can be obtained from nucleotide sequence data using the molecular clock. These estimates are important for our understanding of evolutionary processes across all taxonomic levels. The molecular clock needs to be calibrated with an independent source of information, such as fossil evidence, to allow absolute ages to be inferred. Calibration typically involves fixing or constraining the age of at least one node in the phylogeny, enabling the ages of the remaining nodes to be estimated. We conducted an extensive simulation study to investigate the effects of the position and number of calibrations on the resulting estimate of the timescale. Our analyses focused on Bayesian estimates obtained using relaxed molecular clocks. Our findings suggest that an effective strategy is to include multiple calibrations and to prefer those that are close to the root of the phylogeny. Under these conditions, we found that evolutionary timescales could be estimated accurately even when the relaxed-clock model was misspecified and when the sequence data were relatively uninformative. We tested these findings in a case study of simian foamy virus, where we found that shallow calibrations caused the overall timescale to be underestimated by up to three orders of magnitude. Finally, we provide some recommendations for improving the practice of molecular-clock calibration.
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Affiliation(s)
- Sebastián Duchêne
- School of Biological Sciences, University of Sydney, NSW 2006, Australia.
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, NSW 2006, Australia
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Mello B, Schrago CG. Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates. Evol Bioinform Online 2014; 10:79-85. [PMID: 24855333 PMCID: PMC4022701 DOI: 10.4137/ebo.s13908] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 03/25/2014] [Accepted: 04/03/2014] [Indexed: 11/25/2022] Open
Abstract
Divergence time estimation has become an essential tool for understanding macroevolutionary events. Molecular dating aims to obtain reliable inferences, which, within a statistical framework, means jointly increasing the accuracy and precision of estimates. Bayesian dating methods exhibit the propriety of a linear relationship between uncertainty and estimated divergence dates. This relationship occurs even if the number of sites approaches infinity and places a limit on the maximum precision of node ages. However, how the placement of calibration information may affect the precision of divergence time estimates remains an open question. In this study, relying on simulated and empirical data, we investigated how the location of calibration within a phylogeny affects the accuracy and precision of time estimates. We found that calibration priors set at median and deep phylogenetic nodes were associated with higher precision values compared to analyses involving calibration at the shallowest node. The results were independent of the tree symmetry. An empirical mammalian dataset produced results that were consistent with those generated by the simulated sequences. Assigning time information to the deeper nodes of a tree is crucial to guarantee the accuracy and precision of divergence times. This finding highlights the importance of the appropriate choice of outgroups in molecular dating.
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Affiliation(s)
- Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G Schrago
- Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Beimforde C, Feldberg K, Nylinder S, Rikkinen J, Tuovila H, Dörfelt H, Gube M, Jackson DJ, Reitner J, Seyfullah LJ, Schmidt AR. Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data. Mol Phylogenet Evol 2014; 78:386-98. [PMID: 24792086 DOI: 10.1016/j.ympev.2014.04.024] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 12/12/2013] [Accepted: 04/21/2014] [Indexed: 12/18/2022]
Abstract
The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered.
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Affiliation(s)
- Christina Beimforde
- Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany.
| | - Kathrin Feldberg
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
| | - Stephan Nylinder
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden
| | - Jouko Rikkinen
- Department of Biosciences, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland
| | - Hanna Tuovila
- Department of Biosciences, University of Helsinki, P.O. Box 65, FIN-00014 Helsinki, Finland
| | - Heinrich Dörfelt
- Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany
| | - Matthias Gube
- Microbial Communication, Friedrich Schiller University Jena, Neugasse 25, 07743 Jena, Germany; Department of Soil Science of Temperate Ecosystems, Büsgen Institute, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Daniel J Jackson
- Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
| | - Joachim Reitner
- Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
| | - Leyla J Seyfullah
- Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
| | - Alexander R Schmidt
- Courant Research Centre Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
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Peart CR, Bills R, Wilkinson M, Day JJ. Nocturnal claroteine catfishes reveal dual colonisation but a single radiation in Lake Tanganyika. Mol Phylogenet Evol 2014; 73:119-28. [DOI: 10.1016/j.ympev.2014.01.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 12/03/2013] [Accepted: 01/17/2014] [Indexed: 11/28/2022]
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Bracken-Grissom HD, Ahyong ST, Wilkinson RD, Feldmann RM, Schweitzer CE, Breinholt JW, Bendall M, Palero F, Chan TY, Felder DL, Robles R, Chu KH, Tsang LM, Kim D, Martin JW, Crandall KA. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida). Syst Biol 2014; 63:457-79. [PMID: 24562813 DOI: 10.1093/sysbio/syu008] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A rich fossil history coupled with dense taxon coverage allowed us to estimate and compare divergence times and origins of major lineages using two drastically different approaches. Age priors were constructed and/or included based on fossil age information or fossil discovery, age, and extant species count data. Results from the two approaches were largely congruent across deep to shallow taxonomic divergences across major lineages. The origin of the first lobster-like decapod (Polychelida) was estimated in the Devonian (∼409-372 Ma) with all infraorders present in the Carboniferous (∼353-318 Ma). Fossil calibration subsampling studies examined the influence of sampling density (number of fossils) and placement (deep, middle, and shallow) on divergence time estimates. Results from our study suggest including at least 1 fossil per 10 operational taxonomic units (OTUs) in divergence dating analyses. [Dating; decapods; divergence; lobsters; molecular; morphology; phylogenetics.].
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Florida International University, 3000 NE 151st Street, North Miami, FL 33181, USA;
| | - Shane T Ahyong
- Australian Museum, 6 College Street, Sydney, NSW 2010, Australia;University of New South Wales, Kensington, NSW 2052, Australia
| | | | | | - Carrie E Schweitzer
- Kent State University at Stark, 6000 Frank Avenue NW, North Canton, OH 44720, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Ferran Palero
- Unitat Mixta Genòmica i Salut CSISP-UV, Institut Cavanilles Universitat de Valencia, C/Catedrático Jose Beltran 2,46980 Paterna, Spain
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan, R.O.C
| | - Darryl L Felder
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Rafael Robles
- Laboratory of Bioecology and Crustacean Systematics, Department of Biology, FFCLRP, University of São Paulo (USP), Ave. Bandeirantes 3900, CEP 14040 - 901, Ribeirão Preto, SP Brazil
| | - Ka-Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ling-Ming Tsang
- Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan, R.O.C.;School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Dohyup Kim
- Brigham Young University, 401 WIDB, Provo, UT 84606, USA
| | - Joel W Martin
- Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Keith A Crandall
- George Washington University, Computational Biology Institute, Ashburn, VA 20147, USA
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Christin PA, Spriggs E, Osborne CP, Stromberg CAE, Salamin N, Edwards EJ. Molecular Dating, Evolutionary Rates, and the Age of the Grasses. Syst Biol 2013; 63:153-65. [DOI: 10.1093/sysbio/syt072] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Diniz-Filho JAF, Loyola RD, Raia P, Mooers AO, Bini LM. Darwinian shortfalls in biodiversity conservation. Trends Ecol Evol 2013; 28:689-95. [PMID: 24091208 DOI: 10.1016/j.tree.2013.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 11/25/2022]
Abstract
If we were to describe all the species on Earth and determine their distributions, we would solve the popularly termed 'Linnean' and 'Wallacean' shortfalls in biodiversity conservation. Even so, we would still be hindered by a 'Darwinian shortfall', that is, the lack of relevant phylogenetic information for most organisms. Overall, there are too few comprehensive phylogenies, large uncertainties in the estimation of divergence times, and, most critically, unknown evolutionary models linking phylogenies to relevant ecological traits and life history variation. Here, we discuss these issues and offer suggestions for further research to support evolutionary-based conservation planning.
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Aoki S, Ito M, Iwasaki W. From β- to α-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ. Mol Biol Evol 2013; 30:2494-508. [PMID: 24030554 DOI: 10.1093/molbev/mst153] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Although many α- and some β-proteobacterial species are symbiotic with legumes, the evolutionary origin of nitrogen-fixing nodulation remains unclear. We examined α- and β-proteobacteria whose genomes were sequenced using large-scale phylogenetic profiling and revealed the evolutionary origin of two nodulation genes. These genes, nodI and nodJ (nodIJ), play key roles in the secretion of Nod factors, which are recognized by legumes during nodulation. We found that only the nodulating β-proteobacteria, including the novel strains isolated in this study, possess both nodIJ and their paralogous genes (DRA-ATPase/permease genes). Contrary to the widely accepted scenario of the α-proteobacterial origin of rhizobia, our exhaustive phylogenetic analysis showed that the entire nodIJ clade is included in the clade of Burkholderiaceae DRA-ATPase/permease genes, that is, the nodIJ genes originated from gene duplication in a lineage of the β-proteobacterial family. After duplication, the evolutionary rates of nodIJ were significantly accelerated relative to those of homologous genes, which is consistent with their novel function in nodulation. The likelihood analyses suggest that this accelerated evolution is not associated with changes in either nonsynonymous/synonymous substitution rates or transition/transversion rates, but rather, in the GC content. Although the low GC content of the nodulation genes has been assumed to reflect past horizontal transfer events from donor rhizobial genomes with low GC content, no rhizobial genome with such low GC content has yet been found. Our results encourage a reconsideration of the origin of nodulation and suggest new perspectives on the role of the GC content of bacterial genes in functional adaptation.
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Affiliation(s)
- Seishiro Aoki
- Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo, Japan
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49
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Bibi F. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evol Biol 2013; 13:166. [PMID: 23927069 PMCID: PMC3751017 DOI: 10.1186/1471-2148-13-166] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species. RESULTS The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record. CONCLUSIONS The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.
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Affiliation(s)
- Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Invalidenstrasse 43, Berlin 10115, Germany
- Current address: Department of Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
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50
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Santini F, Kong X, Sorenson L, Carnevale G, Mehta RS, Alfaro ME. A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes). Mol Phylogenet Evol 2013; 69:884-94. [PMID: 23831455 DOI: 10.1016/j.ympev.2013.06.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 05/21/2013] [Accepted: 06/24/2013] [Indexed: 11/25/2022]
Abstract
Anguilliformes are an ecologically diverse group of predominantly marine fishes whose members are easily recognized by their extremely elongate bodies, and universal lack of pelvic fins. Recent studies based on mitochondrial loci, including full mitogenomes, have called into question the monophyly of both the Anguilliformes, which appear to be paraphyletic without the inclusion of the Saccopharyngiformes (gulper eels and allies), as well as other more commonly known eel families (e.g., Congridae, Serrivomeridae). However, no study to date has investigated anguilliform interrelationships using nuclear loci. Here we present a new phylogenetic hypothesis for the Anguilliformes based on five markers (the nuclear loci Early Growth Hormone 3, Myosin Heavy Polypeptide 6 and Recombinase Activating Gene 1, as well as the mitochondrial genes Cytochrome b and Cytochrome Oxidase I). Our sampling spans 148 species and includes 19 of the 20 extant families of anguilliforms and saccopharyngiforms. Maximum likelihood analysis reveals that saccopharyngiform eels are deeply nested within the anguilliforms, and supports the non-monophyly of Congridae and Nettastomatidae, as well as that of Derichthyidae and Chlopsidae. Our analyses suggest that Protanguilla may be the sister group of the Synaphobranchidae, though the recent hypothesis that this species is the sister group to all other anguilliforms cannot be rejected. The molecular phylogeny, time-calibrated using a Bayesian relaxed clock approach and seven fossil calibration points, reveals a Late Cretaceous origin of this expanded anguilliform clade (stem age ~116 Ma, crown age ~99 Ma). Most major (family level) lineages originated between the end of the Cretaceous and Early Eocene, suggesting that anguilliform radiation may have been facilitated by the recovery of marine ecosystems following the KP extinction.
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Affiliation(s)
- Francesco Santini
- University of California Los Angeles, Department of Ecology and Evolutionary Biology, 610 Charles E Young Drive South, Los Angeles, CA 90095, USA; Università degli Studi di Torino, Dipartimento di Scienze della Terra, Via Valperga Caluso 35, 10125 Torino, Italy.
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