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Zhao Z, Conradie W, Pietersen DW, Jordaan A, Nicolau G, Edwards S, Riekert S, Heideman N. Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae). Mol Phylogenet Evol 2023; 182:107747. [PMID: 36849095 DOI: 10.1016/j.ympev.2023.107747] [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: 08/11/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Darren W Pietersen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Gary Nicolau
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Shelley Edwards
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Stephanus Riekert
- Department of Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
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Barrett CF, Santee MV, Fama NM, Freudenstein JV, Simon SJ, Sinn BT. Lineage and role in integrative taxonomy of a heterotrophic orchid complex. Mol Ecol 2022; 31:4762-4781. [PMID: 35837745 PMCID: PMC9452484 DOI: 10.1111/mec.16617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022]
Abstract
Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.
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Affiliation(s)
- Craig F. Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Mathilda V. Santee
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - Nicole M. Fama
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, West Virginia, USA 26506
| | - John V. Freudenstein
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 1315 Kinnear Rd., Columbus, Ohio, USA 43212
| | - Sandra J. Simon
- Department of Biology, West Virginia University Institute of Technology, Beckley, WV, USA
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, USA
- Department of Botany and Ecology, University of Latvia, Jelgavas iela 1, Riga, LV-1004, Latvia
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Minaiyan M, Razzaghi H, Yegdaneh A, Talebi A. Healing effect of hydroalcoholic extract of Humulus lupulus L. (Hops) aerial parts on indomethacin-induced gastric ulcer in rats. JOURNAL OF REPORTS IN PHARMACEUTICAL SCIENCES 2022. [DOI: 10.4103/jrptps.jrptps_115_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Morcol TB, Matthews PD, Kennelly EJ. Differences in Leaf Chemistry and Glandular Trichome Density between Wild Southwestern American Hop ( Humulus neomexicanus) and Commercial Hop Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7798-7814. [PMID: 34181402 DOI: 10.1021/acs.jafc.1c02710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The female flowers ("cones") of the hop plant (Humulus L.) produce compounds that contribute to the flavor and other properties of beer. Hop leaves and cones produce many of the same compounds, which also confer agronomic traits such as insect and disease resistance. Targeted and untargeted ultraperformance liquid chromatography-quadrupole time-of-flight-mass spectrometry with Waters MSE technology (UPLC-QTof-MSE) metabolomics were used to compare leaf phytochemical compositions of greenhouse-grown southwestern American wild Humulus neomexicanus (A. Nelson and Cockerell) Rydb. against a group of commercial hop cultivars consisting of both pure European Humulus lupulus L. and European-North American hybrids. Principal component analysis showed a clear distinction in chemical profiles between the two groups. H. neomexicanus leaves had a significantly higher content of total α acids (p = 4.4 × 10-9), total bitter acids (p = 2.6 × 10-6), cohumulone (p = 1.0 × 10-13), humulone + adhumulone (p = 9.1 × 10-4), and the prenylflavonoids xanthohumol (p = 0.013) and desmethylxanthohumol (p = 0.029) as well as significantly higher densities of glandular trichomes (p = 1.3 × 10-6), the biosynthetic site of those compounds. Most flavonol glycosides measured were also significantly more abundant in H. neomexicanus (p = 1.5 × 10-22 to 0.0027), whereas phenolic acids were consistently, but generally nonsignificantly (p > 0.05), more abundant in the cultivars. The higher bitter acid, prenylflavonoid, and flavonol glycoside content of H. neomexicanus leaves may help to confer more favorable insect and disease-resistance properties.
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Affiliation(s)
- Taylan B Morcol
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States
- Ph.D. Program in Biology, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, United States
| | - Edward J Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, New York 10468, United States
- Ph.D. Program in Biology, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. THE NEW PHYTOLOGIST 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Padgitt-Cobb LK, Kingan SB, Wells J, Elser J, Kronmiller B, Moore D, Concepcion G, Peluso P, Rank D, Jaiswal P, Henning J, Hendrix DA. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. THE PLANT GENOME 2021; 14:e20072. [PMID: 33605092 DOI: 10.1002/tpg2.20072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/03/2020] [Indexed: 05/25/2023]
Abstract
Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Sarah B Kingan
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Jackson Wells
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | | | | | - Paul Peluso
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - David Rank
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | | | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
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7
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Mao X, Wang J, Shrestha N, Ma Y, Liu J. Species Identification in the Rhododendron vernicosum- R. decorum Species Complex (Ericaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:608964. [PMID: 33584768 PMCID: PMC7876077 DOI: 10.3389/fpls.2021.608964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Delimitating species boundaries is the primary aim of biological classification and could be critical for evaluating the evolving process of species and conserving biodiversity. Rhododendron is an iconic group with an extraordinary diversity in southwest China. However, it remains unknown whether the recorded species therein comprise independently evolving lineages or artificially delimitated morphological entities. In this study, we carried out species delimitation of four Rhododendron species in the R. vernicosum-R. decorum species complex based on morphological analyses and population genetic data from nuclear simple sequence repeats (SSR) markers. We randomly selected a total of 105 specimens of different individuals identified as four species across their distributional ranges to examine the statistically distinct phenotypic clusters based on 19 morphological traits. Similarly, we genotyped 55 individuals of four species from 21 populations using 15 SSR markers. The morphological analyses sorted R. decorum and the other three species into two different phenotypic clusters. The genetic clusters were consistent with the morphological clusters. However, we also recovered the third genetic cluster, comprising six R. vernicosum populations and containing the admixed genetic compositions of the other two distinct genetic clusters. This hybrid group was morphologically similar to the typical R. vernicosum (including the samples from its type specimen locality and both R. verruciferum and R. gonggashanense) but with more genetic ancestry from R. decorum. Based on our findings, we identify two distinct species and one putative hybrid group due to introgression in the R. vernicosum-R. decorum species complex. We propose to merge R. verruciferum and R. gonggashanense into R. vernicosum based on genetic compositions and our morphological analyses. The hybrid group inferred from our findings, however, needs further investigations.
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Affiliation(s)
- Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ji Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Yazhen Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education and State Key Lab of Hydraulics and Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
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Easterling KA, Pitra NJ, Morcol TB, Aquino JR, Lopes LG, Bussey KC, Matthews PD, Bass HW. Identification of tandem repeat families from long-read sequences of Humulus lupulus. PLoS One 2020; 15:e0233971. [PMID: 32502183 PMCID: PMC7274563 DOI: 10.1371/journal.pone.0233971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/16/2020] [Indexed: 11/28/2022] Open
Abstract
Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. From this we identified 17 new and distinct tandem repeat sequence families, which represent candidates for FISH probe development. For two of these candidates, HuluTR120 and HuluTR225, we produced oligonucleotide FISH probes from conserved regions of and demonstrated their utility by staining meiotic chromosomes from wild hop, var. neomexicanus to address, for example, questions about hop transmission genetics. Collectively, these tandem repeat sequence families represent new resources suitable for development of additional cytogenomic tools for hop research.
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Affiliation(s)
- Katherine A. Easterling
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Nicholi J. Pitra
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Taylan B. Morcol
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, New York, United States America
- The Graduate Center, City University of New York, New York, New York, United States America
| | - Jenna R. Aquino
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Lauren G. Lopes
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Kristin C. Bussey
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
| | - Paul D. Matthews
- Hopsteiner, S.S. Steiner, Inc., New York, New York, United States America
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, United States America
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de Sousa VA, Reeves PA, Reilley A, de Aguiar AV, Stefenon VM, Richards CM. Genetic diversity and biogeographic determinants of population structure in Araucaria angustifolia (Bert.) O. Ktze. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01242-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractAraucaria (Araucaria angustifolia (Bert.) O. Ktze) is a primarily dioecious species threatened with extinction that plays an important social and economic role especially in the southern region of Brazil. The aim of this work is to investigate the diversity and likely determinants of genetic lineages in this species for conservation management. For this, a collection of 30-year-old Araucaria was used. Accessions collected from 12 sites across the species range were analyzed, with ten individuals per site. The SSR genotyping was conducted with 15 loci and the data were analyzed using several complementary approaches. Descriptive statistics among sampling sites were used and diversity was partitioned non-hierarchically to estimate the size and composition of genetic clusters using a Bayesian assignment method. To explore possible biological implications of differences between Niche Models and habitat suitability, a series of statistical procedures were used, and tests were carried out using the software ENM Tools and Maxent. Populations from the southernmost zone showed higher genetic variation and a lower inbreeding coefficient compared to the northernmost zone, which may correlate with their isolation. A positive relation between genetic differentiation and geographic distance was observed. Two genetic groups (southernmost and northernmost zones) were evident. The Niche modelling showed separate ranges for each genetic lineage suggesting that differences in selection pressure may be playing a role in the apparent differentiation and may be adaptive. Finally, an evident correlation was observed between genetic data and habitat suitability. The two distinct groups observed must be considered as independent units for conservation and hybridization in breeding programs.
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Zhao Q, Zhang H, Wei J. Climatic niche comparison across a cryptic species complex. PeerJ 2019; 7:e7042. [PMID: 31183260 PMCID: PMC6546150 DOI: 10.7717/peerj.7042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/30/2019] [Indexed: 12/04/2022] Open
Abstract
According to current molecular evidence, the Chionaspis pinifoliae heterophyllae species complex has been recognized as 10 cryptic species. In this study, we construct potential distribution maps for seven cryptic species based on climatic variables. This was done to assess the main environmental factors that have contributed to the distribution map and test the degree of niche overlap across the seven cryptic species. We used MaxEnt to build the climatic niche models under climatic variables. For these models, the similarities and differences of the niches across the cryptic species were estimated. By comparing the potential distribution model of each cryptic species, our results suggested parapatric, sympatric and allopatry populations for this cryptic species complex. Our results showed high variability in niche overlap, and more often niche conservatism than niche divergence. The current species delimitation of the Chionaspis pinifoliae heterophyllae complex by molecular information and the hypothesis that the niche overlap in the sympatric population is higher than that of the allopatry population were supported based on the findings. This study will provide baseline data and a distribution range to facilitate the further control of these insects and formulate quarantine measures.
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Affiliation(s)
- Qing Zhao
- Department of Entomology, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
| | - Hufang Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou, Shanxi, P. R. China
| | - Jiufeng Wei
- Department of Entomology, Shanxi Agricultural University, Taigu, Shanxi, P. R. China
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Easterling KA, Pitra NJ, Jones RJ, Lopes LG, Aquino JR, Zhang D, Matthews PD, Bass HW. 3D Molecular Cytology of Hop ( Humulus lupulus) Meiotic Chromosomes Reveals Non-disomic Pairing and Segregation, Aneuploidy, and Genomic Structural Variation. FRONTIERS IN PLANT SCIENCE 2018; 9:1501. [PMID: 30443259 PMCID: PMC6221928 DOI: 10.3389/fpls.2018.01501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/25/2018] [Indexed: 05/31/2023]
Abstract
Hop (Humulus lupulus L.) is an important crop worldwide, known as the main flavoring ingredient in beer. The diversifying brewing industry demands variation in flavors, superior process properties, and sustainable agronomics, which are the focus of advanced molecular breeding efforts in hops. Hop breeders have been limited in their ability to create strains with desirable traits, however, because of the unusual and unpredictable inheritance patterns and associated non-Mendelian genetic marker segregation. Cytogenetic analysis of meiotic chromosome behavior has also revealed conspicuous and prevalent occurrences of multiple, atypical, non-disomic chromosome complexes, including those involving autosomes in late prophase. To explore the role of meiosis in segregation distortion, we undertook 3D cytogenetic analysis of hop pollen mother cells stained with DAPI and FISH. We used telomere FISH to demonstrate that hop exhibits a normal telomere clustering bouquet. We also identified and characterized a new sub-terminal 180 bp satellite DNA tandem repeat family called HSR0, located proximal to telomeres. Highly variable 5S rDNA FISH patterns within and between plants, together with the detection of anaphase chromosome bridges, reflect extensive departures from normal disomic signal composition and distribution. Subsequent FACS analysis revealed variable DNA content in a cultivated pedigree. Together, these findings implicate multiple phenomena, including aneuploidy, segmental aneuploidy, or chromosome rearrangements, as contributing factors to segregation distortion in hop.
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Affiliation(s)
- Katherine A. Easterling
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
- Hopsteiner, S.S. Steiner, Inc., New York, NY, United States
| | | | | | - Lauren G. Lopes
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Jenna R. Aquino
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Dong Zhang
- Hopsteiner, S.S. Steiner, Inc., New York, NY, United States
| | | | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
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12
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Tomasello S. How many names for a beloved genus? – Coalescent-based species delimitation in Xanthium L. (Ambrosiinae, Asteraceae). Mol Phylogenet Evol 2018; 127:135-145. [DOI: 10.1016/j.ympev.2018.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 11/13/2022]
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Steiner FM, Csősz S, Markó B, Gamisch A, Rinnhofer L, Folterbauer C, Hammerle S, Stauffer C, Arthofer W, Schlick-Steiner BC. Turning one into five: Integrative taxonomy uncovers complex evolution of cryptic species in the harvester ant Messor “structor”. Mol Phylogenet Evol 2018; 127:387-404. [DOI: 10.1016/j.ympev.2018.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/02/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022]
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Posso-Terranova A, Andrés J. Multivariate species boundaries and conservation of harlequin poison frogs. Mol Ecol 2018; 27:3432-3451. [DOI: 10.1111/mec.14803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Andrés Posso-Terranova
- Department of Biology; University of Saskatchewan; Saskatoon SK Canada
- Universidad Nacional de Colombia sede Palmira; Palmira Colombia
| | - Jose Andrés
- Department of Biology; University of Saskatchewan; Saskatoon SK Canada
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Jacobs SJ, Kristofferson C, Uribe‐Convers S, Latvis M, Tank DC. Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult. Mol Ecol 2018; 27:2397-2413. [DOI: 10.1111/mec.14590] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Sarah J. Jacobs
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Casey Kristofferson
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Simon Uribe‐Convers
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - Maribeth Latvis
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
| | - David C. Tank
- Department of Biological Sciences University of Idaho Moscow Idaho
- Stillinger Herbarium University of Idaho Moscow Idaho
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow Idaho
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16
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Padilla-García N, Rojas-Andrés BM, López-González N, Castro M, Castro S, Loureiro J, Albach DC, Machon N, Martínez-Ortega MM. The challenge of species delimitation in the diploid-polyploid complex Veronica subsection Pentasepalae. Mol Phylogenet Evol 2018; 119:196-209. [DOI: 10.1016/j.ympev.2017.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/23/2022]
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17
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Dagnino D, Minuto L, Casazza G. Divergence is not enough: the use of ecological niche models for the validation of taxon boundaries. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:1003-1011. [PMID: 28691341 DOI: 10.1111/plb.12600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 07/04/2017] [Indexed: 06/07/2023]
Abstract
Delimiting taxon boundaries is crucial for any evolutionary research and conservation regulation. In order to avoid mistaken description of species, the approach of integrative taxonomy recommends considering multidisciplinary lines of evidence, including ecology. Unfortunately, ecological data are often difficult to quantify objectively. Here we test and discuss the potential use of ecological niche models for validating taxon boundaries, using three pairs of closely related plant taxa endemic to the south-western Alps as a case study. We also discuss the application of ecological niche models for species delimitation and the implementation of different approaches. Niche overlap, niche equivalency and niche similarity were assessed both in multidimensional environmental space and in geographic space to look for differences in the niche of three pairs of closely related plant taxa. We detected a high degree of niche differentiation between taxa although this result seems not due to differences in habitat selection. The different statistical tests gave contrasting outcomes between environmental and geographic spaces. According to our results, niche divergence does not seem to support taxon boundaries at species level, but may have had important consequences for local adaptation and in generating phenotypic diversity at intraspecific level. Environmental space analysis should be preferred to geographic space as it provides more clear results. Even if the different analyses widely disagree in their conclusions about taxon boundaries, our study suggests that ecological niche models may help taxonomists to reach a decision.
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Affiliation(s)
- D Dagnino
- Dipartimento di Scienze della Terra, Ambiente e Vita, Università degli Studi di Genova, Genova, Italy
| | - L Minuto
- Dipartimento di Scienze della Terra, Ambiente e Vita, Università degli Studi di Genova, Genova, Italy
| | - G Casazza
- Dipartimento di Scienze della Terra, Ambiente e Vita, Università degli Studi di Genova, Genova, Italy
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18
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Zhang D, Easterling KA, Pitra NJ, Coles MC, Buckler ES, Bass HW, Matthews PD. Non-Mendelian Single-Nucleotide Polymorphism Inheritance and Atypical Meiotic Configurations are Prevalent in Hop. THE PLANT GENOME 2017; 10. [PMID: 29293819 DOI: 10.3835/plantgenome2017.04.0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Hop ( L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female-biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using a genotyping-by-sequencing (GBS) approach. From the resulting ∼1.2 million single-nucleotide polymorphisms (SNPs), prequalified GBS markers were validated by inferences in population structures and phylogeny. Analysis of pseudo-testcross (Pt) mapping data from F families revealed mixed patterns of Mendelian and non-Mendelian segregation. Three-dimensional (3D) cytogenetic analysis of late meiotic prophase nuclei from two wild and two cultivated hop revealed conspicuous and prevalent occurrences of multiple, atypical, nondisomic chromosome complexes including autosomes. We used genome-wide association studies (GWAS) and fixation index (F) analysis to demonstrate selection mapping of genetic loci for key traits including sex, bitter acids, and drought tolerance. Among the possible mechanisms underlying the observed segregation distortion from the genomic data analysis, the cytogenetic analysis points to meiotic chromosome behavior as one of the contributing factors. The findings shed light on long-standing questions on the unusual transmission genetics and phenotypic variation in hop, with major implications for breeding, cultivation, and the natural history of .
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Chan KO, Alexander AM, Grismer LL, Su YC, Grismer JL, Quah ESH, Brown RM. Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs. Mol Ecol 2017; 26:5435-5450. [DOI: 10.1111/mec.14296] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Kin Onn Chan
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - Alana M. Alexander
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
| | - L. Lee Grismer
- Department of Biology; La Sierra University; Riverside CA USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology; Kaohsiung Medical University; Kaohsiung City Taiwan
| | - Jesse L. Grismer
- Department of Biological Sciences; Auburn University; Auburn AL USA
- La Kretz Center for Californian Conservation Science; Institute of the Environment and Sustainability; University of California Los Angeles; Los Angeles CA USA
| | - Evan S. H. Quah
- School of Biological Sciences; Universiti Sains Malaysia; Penang Malaysia
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS USA
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20
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Otálora MAG, Martínez I, Aragón G, Wedin M. Species delimitation and phylogeography of the Pectenia species-complex: A misunderstood case of species-pairs in lichenized fungi, where reproduction mode does not delimit lineages. Fungal Biol 2017; 121:222-233. [PMID: 28215350 DOI: 10.1016/j.funbio.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 11/02/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups. Our results suggest that the production of asexual propagules and sexual structures are not characterizing monophyletic groups. The genus includes two morphologically well-characterized main lineages, where one lineage is composed by two sub-lineages that are with a case of cryptic speciation explained by a biogeographic pattern. We suggest treating the two lineages as two species, which are characterized by lobe structure: Pectenia plumbea and P. atlantica. Both of these species include samples with asexual propagules and apothecia, and thus do not correspond to any of the earlier morphologically defined species. The results of the biogeographic analysis indicate that the Mediterranean basin is the most likely ancestral distribution area of P. plumbea, whereas P. atlantica probably originated in Macaronesia.
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Affiliation(s)
- Mónica A G Otálora
- Department of Botany, The Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden; Department of Biology, Geology, Physic and Inorganic Chemical, Rey Juan Carlos University, Móstoles, 28932, Spain.
| | - Isabel Martínez
- Department of Biology, Geology, Physic and Inorganic Chemical, Rey Juan Carlos University, Móstoles, 28932, Spain
| | - Gregorio Aragón
- Department of Biology, Geology, Physic and Inorganic Chemical, Rey Juan Carlos University, Móstoles, 28932, Spain
| | - Mats Wedin
- Department of Botany, The Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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21
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Methods for verifying the authenticity of hops - an effective tool against falsification. KVASNY PRUMYSL 2016. [DOI: 10.18832/kp2016030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Nava S, Gerardi M, Szabó MP, Mastropaolo M, Martins TF, Labruna MB, Beati L, Estrada-Peña A, Guglielmone AA. Different lines of evidence used to delimit species in ticks: A study of the South American populations of Amblyomma parvum (Acari: Ixodidae). Ticks Tick Borne Dis 2016; 7:1168-1179. [DOI: 10.1016/j.ttbdis.2016.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 11/29/2022]
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23
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Allmon WD. Species, lineages, splitting, and divergence: why we still need ‘anagenesis’ and ‘cladogenesis’. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Warren D. Allmon
- Paleontological Research Institution; Department of Earth and Atmospheric Sciences; Cornell University; 1259 Trumansburg Road Ithaca NY 14850 USA
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25
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Mrinalini, Thorpe RS, Creer S, Lallias D, Dawnay L, Stuart BL, Malhotra A. Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers. Mol Phylogenet Evol 2015; 92:266-79. [DOI: 10.1016/j.ympev.2015.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 04/24/2015] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
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Giska I, Sechi P, Babik W. Deeply divergent sympatric mitochondrial lineages of the earthworm Lumbricus rubellus are not reproductively isolated. BMC Evol Biol 2015; 15:217. [PMID: 26438011 PMCID: PMC4595309 DOI: 10.1186/s12862-015-0488-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/14/2015] [Indexed: 11/10/2022] Open
Abstract
Background The accurate delimitation of species is essential to numerous areas of biological research. An unbiased assessment of the diversity, including the cryptic diversity, is of particular importance for the below ground fauna, a major component of global biodiversity. On the British Isles, the epigeic earthworm Lumbricus rubellus, which is a sentinel species in soil ecotoxicology, consists of two cryptic taxa that are differentiated in both the nuclear and the mitochondrial (mtDNA) genomes. Recently, several deeply divergent mtDNA lineages were detected in mainland Europe, but whether these earthworms also constitute cryptic species remains unclear. This information is important from an evolutionary perspective, but it is also essential for the interpretation and the design of ecotoxicological projects. In this study, we used genome-wide RADseq data to assess the reproductive isolation of the divergent mitochondrial lineages of L. rubellus that occur in sympatry in multiple localities in Central Europe. Results We identified five divergent (up to 16 % net p-distance) mitochondrial lineages of L. rubellus in sympatry. Because the clustering of the RADseq data was according to the population of origin and not the mtDNA lineage, reproductive isolation among the mtDNA lineages was not likely. Although each population contained multiple mtDNA lineages, subdivisions within the populations were not observed for the nuclear genome. The lack of fixed differences and sharing of the overwhelming majority of nuclear polymorphisms between localities, indicated that the populations did not constitute allopatric species. The nucleotide diversity within the populations was high, 0.7–0.8 %. Conclusions The deeply divergent mtDNA sympatric lineages of L. rubellus in Central Europe were not reproductively isolated groups. The earthworm L. rubellus, which is represented by several mtDNA lineages in continental Europe, apparently is a single highly polymorphic species rather than a complex of several cryptic species. This study demonstrated the critical importance of the use of multilocus nuclear data for the unbiased assessment of cryptic diversity and for the delimitation of species in soil invertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0488-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iwona Giska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
| | - Pierfrancesco Sechi
- Institute of Ecosystem Study, Sassari, National Research Council, Traversa La Crucca 3, Regione Baldinca, 07100, Sassari, Italy.
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
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Meik JM, Streicher JW, Lawing AM, Flores-Villela O, Fujita MK. Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes. PLoS One 2015; 10:e0131435. [PMID: 26107178 PMCID: PMC4479545 DOI: 10.1371/journal.pone.0131435] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/02/2015] [Indexed: 01/05/2023] Open
Abstract
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus.
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Affiliation(s)
- Jesse M. Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, United States of America
| | - Jeffrey W. Streicher
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - A. Michelle Lawing
- Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas, United States of America
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Distrito Federal, México
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
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Zhang Y, Li S. A spider species complex revealed high cryptic diversity in South China caves. Mol Phylogenet Evol 2014; 79:353-8. [DOI: 10.1016/j.ympev.2014.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
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Talve T, Mürk M, Lindell T, Oja T. Rhinanthus plants found in calcareous fens on Gotland (Sweden): Are they related to Rhinanthus osiliensis from Saaremaa (Estonia)? BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chetan N, Praveen KK, Vasudeva GK. Delineating ecological boundaries of Hanuman langur species complex in peninsular India using MaxEnt modeling approach. PLoS One 2014; 9:e87804. [PMID: 24498377 PMCID: PMC3912124 DOI: 10.1371/journal.pone.0087804] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 12/31/2013] [Indexed: 11/19/2022] Open
Abstract
Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.
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Affiliation(s)
- Nag Chetan
- Department of Biology, Undergraduate Program, Indian Institute of Science, Bangalore, Karnataka, India
| | - Karanth K. Praveen
- Center for ecological sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Gururaja Kotambylu Vasudeva
- Centre for infrastructure, Sustainable Transportation and Urban Planning (CiSTUP), Indian Institute of Science, Bangalore, Karnataka, India
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Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species. PLoS One 2013; 8:e78228. [PMID: 24205167 PMCID: PMC3812143 DOI: 10.1371/journal.pone.0078228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 09/10/2013] [Indexed: 11/19/2022] Open
Abstract
Background and Aims Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.
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32
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Miralles A, Vences M. New metrics for comparison of taxonomies reveal striking discrepancies among species delimitation methods in Madascincus lizards. PLoS One 2013; 8:e68242. [PMID: 23874561 PMCID: PMC3710018 DOI: 10.1371/journal.pone.0068242] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/24/2013] [Indexed: 01/17/2023] Open
Abstract
Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence C tax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index R tax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist approaches). Quantifying excessive splitting is more difficult than quantifying excessive lumping, suggesting a priority for conservative taxonomies in which errors are more liable to be detected and corrected by subsequent studies.
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Affiliation(s)
- Aurélien Miralles
- Division of Evolutionary Biology, Zoological Institute, Technical University of Braunschweig, Braunschweig, Germany.
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Fior S, Li M, Oxelman B, Viola R, Hodges SA, Ometto L, Varotto C. Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions. THE NEW PHYTOLOGIST 2013; 198:579-592. [PMID: 23379348 DOI: 10.1111/nph.12163] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/20/2012] [Indexed: 05/02/2023]
Abstract
Aquilegia is a well-known model system in the field of evolutionary biology, but obtaining a resolved and well-supported phylogenetic reconstruction for the genus has been hindered by its recent and rapid diversification. Here, we applied 454 next-generation sequencing to PCR amplicons of 21 of the most rapidly evolving regions of the plastome to generate c. 24 kb of sequences from each of 84 individuals from throughout the genus. The resulting phylogeny has well-supported resolution of the main lineages of the genus, although recent diversification such as in the European taxa remains unresolved. By producing a chronogram of the whole Ranunculaceae family based on published data, we inferred calibration points for dating the Aquilegia radiation. The genus originated in the upper Miocene c. 6.9 million yr ago (Ma) in Eastern Asia, and diversification occurred c. 4.8 Ma with the split of two main clades, one colonizing North America, and the other Western Eurasia through the mountains of Central Asia. This was followed by a back-to-Asia migration, originating from the European stock using a North Asian route. These results provide the first backbone phylogeny and spatiotemporal reconstruction of the Aquilegia radiation, and constitute a robust framework to address the adaptative nature of speciation within the group.
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Affiliation(s)
- Simone Fior
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Mingai Li
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Bengt Oxelman
- Department of Biology and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30, Gothenburg, Sweden
| | - Roberto Viola
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Scott A Hodges
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Lino Ometto
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
| | - Claudio Varotto
- Biodiversity and Molecular Ecology Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy
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Thomé MTC, Zamudio KR, Haddad CFB, Alexandrino J. Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization. BMC Evol Biol 2012; 12:242. [PMID: 23228224 PMCID: PMC3574056 DOI: 10.1186/1471-2148-12-242] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/04/2012] [Indexed: 11/29/2022] Open
Abstract
Background Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification. The six species within the Rhinella crucifer group of toads were defined under morphological criteria alone. Previous data suggest limited correspondence of these species to mitochondrial lineages, and morphological intergradation at transitions between forms suggests hybridization. Here we extensively sampled populations throughout the geographic distribution of the group and analyzed mitochondrial and nuclear sequence data to delimit genetic units using tree–based and allele frequency–based approaches. Results These approaches yielded complementary results, with allele frequency-based methods performing unexpectedly well given the limited number of loci examined. Both mitochondrial and nuclear markers supported a genetic structure of five units within the group, with three of the inferred units distributed within its main range, while two other units occur in separate isolates. The inferred units are mostly discordant with currently described forms: unequivocal association exists for only two of the six species in the group. Genetic evidence for hybridization exists for two pairs of units, with clear cyto–nuclear allele mixing observed in one case. Conclusions Our results confirmed that current taxonomy does not represent evolutionary units in the Rhinella crucifer group. Correspondence between genetically distinguishable units and the currently recognized species is only possible for Rhinella henseli and R. inopina. The recognition of other species relies on the reassessment of the geographic range of R. crucifer, the examination of the type series of R. ornata for hybrids, and on the use of additional markers to verify the genetic distinctiveness of R. abei. We state that R. pombali should not remain a valid species since its description appears to be based on hybrids, and that the name R. pombali should be considered a synonym of both R. crucifer and R. ornata. The fifth inferred but undescribed genetic unit may represent a new species. Our results underscore the potential of the R. crucifer species group to contribute to a better understanding of diversification processes and hybridization patterns in the Neotropics, and provide the basis for future evolutionary and taxonomic studies.
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Affiliation(s)
- Maria Tereza C Thomé
- Departamento de Zoologia, Instituto de Biociências, UNESP - Univ Estadual Paulista, Campus Rio Claro, Caixa Postal 19913506-900, Rio Claro, SP, Brazil.
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Beck JB, Allison JR, Pryer KM, Windham MD. Identifying multiple origins of polyploid taxa: a multilocus study of the hybrid cloak fern (Astrolepis integerrima; Pteridaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:1857-1865. [PMID: 23108464 DOI: 10.3732/ajb.1200199] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Molecular studies have shown that multiple origins of polyploid taxa are the rule rather than the exception. To understand the distribution and ecology of polyploid species and the evolutionary significance of polyploidy in general, it is important to delineate these independently derived lineages as accurately as possible. Although gene flow among polyploid lineages and backcrossing to their diploid parents often confound this process, such post origin gene flow is very infrequent in asexual polyploids. In this study, we estimate the number of independent origins of the apomictic allopolyploid fern Astrolepis integerrima, a morphologically heterogeneous species most common in the southwestern United States and Mexico, with outlying populations in the southeastern United States and the Caribbean. METHODS Plastid DNA sequence and AFLP data were obtained from 33 A. integerrima individuals. Phylogenetic analysis of the sequence data and multidimensional clustering of the AFLP data were used to identify independently derived lineages. KEY RESULTS Analysis of the two datasets identified 10 genetic groups within the 33 analyzed samples. These groups suggest a minimum of 10 origins of A. integerrima in the northern portion of its range, with both putative parents functioning as maternal donors, both supplying unreduced gametes, and both contributing a significant portion of their genetic diversity to the hybrids. CONCLUSIONS Our results highlight the extreme cryptic genetic diversity and systematic complexity that can underlie a single polyploid taxon.
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MESH Headings
- Amplified Fragment Length Polymorphism Analysis
- DNA, Intergenic/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Evolution, Molecular
- Genes, Plant/genetics
- Geography
- Mexico
- Molecular Sequence Data
- Phylogeny
- Polyploidy
- Pteridaceae/classification
- Pteridaceae/genetics
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Gly/genetics
- Sequence Analysis, DNA
- United States
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Affiliation(s)
- James B Beck
- Department of Biological Sciences, Wichita State University, 537 Hubbard Hall, Wichita, Kansas 67260, USA.
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Rosero DA, Jaramillo LM, Gutiérrez LA, Conn JE, Correa MM. Genetic diversity of Anopheles triannulatus s.l. (Diptera: Culicidae) from northwestern and southeastern Colombia. Am J Trop Med Hyg 2012; 87:910-20. [PMID: 22949519 DOI: 10.4269/ajtmh.2012.12-0285] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Anopheles triannulatus s.l. is a species complex, however in Colombia its taxonomic status is unclear. This study was conducted to understand the level of genetic differentiation or population structure of specimens of An. triannulatus s.l. from northwestern and southeastern Colombia. Cytochrome oxidase subunit I (COI) and internal transcribed spacer (ITS2) sequence analyses suggested high genetic differentiation between the NW and SE populations. A TCS network and Bayesian inference analysis based on 814 bp of COI showed two main groups: group I included samples from the NW and group II samples from the SE. Two main ITS2-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns were found. Pattern I is present in both the NW and SE, and pattern II is found in the SE specimens. To further elucidate the taxonomic status of An. triannulatus s.l. in Colombia and how these COI lineages are related to the Triannulatus Complex species, the evaluation of immature stages, male genitalia, and additional mitochondrial and nuclear markers will be needed.
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Affiliation(s)
- Doris A Rosero
- Grupo de Microbiología Molecular, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia.
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FERNÁNDEZ MARIAJIMENAGÓMEZ, GAGGIOTTI OSCARE, MIROL PATRICIA. The evolution of a highly speciose group in a changing environment: are we witnessing speciation in the Iberá wetlands? Mol Ecol 2012; 21:3266-82. [DOI: 10.1111/j.1365-294x.2012.05598.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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LEGA MARGHERITA, FIOR SIMONE, PROSSER FILIPPO, BERTOLLI ALESSIO, LI MINGAI, VAROTTO CLAUDIO. Application of the unified species concept reveals distinct lineages for disjunct endemics of the Brassica repanda (Brassicaceae) complex. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01887.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Puillandre N, Modica MV, Zhang Y, Sirovich L, Boisselier MC, Cruaud C, Holford M, Samadi S. Large-scale species delimitation method for hyperdiverse groups. Mol Ecol 2012; 21:2671-91. [PMID: 22494453 DOI: 10.1111/j.1365-294x.2012.05559.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accelerating the description of biodiversity is a major challenge as extinction rates increase. Integrative taxonomy combining molecular, morphological, ecological and geographical data is seen as the best route to reliably identify species. Classic molluscan taxonomic methodology proposes primary species hypotheses (PSHs) based on shell morphology. However, in hyperdiverse groups, such as the molluscan family Turridae, where most of the species remain unknown and for which homoplasy and plasticity of morphological characters is common, shell-based PSHs can be arduous. A four-pronged approach was employed to generate robust species hypotheses of a 1000 specimen South-West Pacific Turridae data set in which: (i) analysis of COI DNA Barcode gene is coupled with (ii) species delimitation tools GMYC (General Mixed Yule Coalescence Method) and ABGD (Automatic Barcode Gap Discovery) to propose PSHs that are then (iii) visualized using Klee diagrams and (iv) evaluated with additional evidence, such as nuclear gene rRNA 28S, morphological characters, geographical and bathymetrical distribution to determine conclusive secondary species hypotheses (SSHs). The integrative taxonomy approach applied identified 87 Turridae species, more than doubling the amount previously known in the Gemmula genus. In contrast to a predominantly shell-based morphological approach, which over the last 30 years proposed only 13 new species names for the Turridae genus Gemmula, the integrative approach described here identified 27 novel species hypotheses not linked to available species names in the literature. The formalized strategy applied here outlines an effective and reproducible protocol for large-scale species delimitation of hyperdiverse groups.
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Affiliation(s)
- N Puillandre
- 'Systématique, Adaptation et Evolution', UMR 7138 UPMC-IRD-MNHN-CNRS-UR IRD 148, Muséum National d'Histoire Naturelle, Département Systématique et Evolution, CP 26, 57 Rue Cuvier, F-75231 Paris Cedex 05, France.
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Baird HP, Miller KJ, Stark JS. Genetic population structure in the Antarctic benthos: insights from the widespread amphipod, Orchomenella franklini. PLoS One 2012; 7:e34363. [PMID: 22479613 PMCID: PMC3313966 DOI: 10.1371/journal.pone.0034363] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 03/01/2012] [Indexed: 11/24/2022] Open
Abstract
Currently there is very limited understanding of genetic population structure in the Antarctic benthos. We conducted one of the first studies of microsatellite variation in an Antarctic benthic invertebrate, using the ubiquitous amphipod Orchomenella franklini (Walker, 1903). Seven microsatellite loci were used to assess genetic structure on three spatial scales: sites (100 s of metres), locations (1-10 kilometres) and regions (1000 s of kilometres) sampled in East Antarctica at Casey and Davis stations. Considerable genetic diversity was revealed, which varied between the two regions and also between polluted and unpolluted sites. Genetic differentiation among all populations was highly significant (F(ST) = 0.086, R(ST) = 0.139, p<0.001) consistent with the brooding mode of development in O. franklini. Hierarchical AMOVA revealed that the majority of the genetic subdivision occurred across the largest geographical scale, with N(e)m≈1 suggesting insufficient gene flow to prevent independent evolution of the two regions, i.e., Casey and Davis are effectively isolated. Isolation by distance was detected at smaller scales and indicates that gene flow in O. franklini occurs primarily through stepping-stone dispersal. Three of the microsatellite loci showed signs of selection, providing evidence that localised adaptation may occur within the Antarctic benthos. These results provide insights into processes of speciation in Antarctic brooders, and will help inform the design of spatial management initiatives recently endorsed for the Antarctic benthos.
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Affiliation(s)
- Helena Phoenix Baird
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia.
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Bacon CD, McKenna MJ, Simmons MP, Wagner WL. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). BMC Evol Biol 2012; 12:23. [PMID: 22353848 PMCID: PMC3356231 DOI: 10.1186/1471-2148-12-23] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages. RESULTS Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups. CONCLUSIONS Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.
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Affiliation(s)
- Christine D Bacon
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
- Smithsonian Tropical Research, Box 0843-03092, Balboa, Ancón, Republic of Panamá
| | - Miles J McKenna
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Warren L Wagner
- Department of Botany, Smithsonian Institution, MRC-166, P.O. Box 37012, Washington, D.C. 20013-7012, USA
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WOOTEN JA, GIBBS HL. Niche divergence and lineage diversification among closely related Sistrurus rattlesnakes. J Evol Biol 2011; 25:317-28. [DOI: 10.1111/j.1420-9101.2011.02426.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Maggs CA, Fletcher HL, Fewer D, Loade L, Mineur F, Johnson MP. Speciation in Red Algae: Members of the Ceramiales as Model Organisms. Integr Comp Biol 2011; 51:492-504. [DOI: 10.1093/icb/icr075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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