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Sangster G, Luksenburg JA. The published complete mitochondrial genome of Blue-fronted Redstart ( Phoenicurus frontalis) is a chimera and includes DNA from Pink-rumped Rosefinch Carpodacus waltoni eos (Aves: Passeriformes). Mitochondrial DNA B Resour 2024; 9:861-864. [PMID: 38983844 PMCID: PMC11232634 DOI: 10.1080/23802359.2024.2377170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
The complete mitochondrial genome of Blue-fronted Redstart (Phoenicurus frontalis), GenBank accession number MT360379 (NC_053917), was published by Li and colleages in 2020. Here we show that this mitogenome is actually a chimera containing DNA fragments of both P. frontalis (15,518 bp, 92.5%) and Pink-rumped Rosefinch (Carpodacus waltoni eos, 1258 bp, 7.5%). This mitogenome has been re-used in at least three phylogenies. Our study confirms that mitogenomes are best verified with multiple gene trees, and that any anomalies should be investigated by direct comparison of sequences.
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Affiliation(s)
| | - Jolanda A. Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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2
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Yoğurtçuoğlu B, Kaya C, Atalay MA, Ekmekçi FG, Freyhof J. Two new freshwater blennies from the Eastern Mediterranean basin (Teleostei: Blenniidae). Zootaxa 2023; 5311:85-104. [PMID: 37518654 DOI: 10.11646/zootaxa.5311.1.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Two new species of Salariopsis are described from the Eastern Mediterranean basin. Salariopsis burcuae, new species, from the Bay of Antalya east to the Jordan, is characterised by having a short cirrus, usually not overlapping the 9th circum-orbital sensory pore, and many tiny black dots on the cheek not organised in rows or bands. The new species shows a 4.1% K2P sequence divergence on the cytochrome-c-oxidase subunit 1 (COI) barcoding region from its closest relative, S. fluviatilis. Salariopsis renatorum, new species, from the upper Ceyhan drainage and a coastal stream in Arsuz, is distinguished by having an unbranched supraocular tentacle, black lateral line pores, a short snout, and no black dots on the upper part of the flank and on the cheek. It is also distinguished from its geographically closest congener, S. burcuae, by a molecular distance of 8.8% K2P in its COI barcode region.
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Affiliation(s)
- Baran Yoğurtçuoğlu
- Hacettepe University; Faculty of Science; Biology Department; 06800 Ankara; Türkiye.
| | - Cüneyt Kaya
- Recep Tayyip Erdogan University; Faculty of Fisheries and Aquatic Sciences; 53100 Rize; Türkiye.
| | - Mustafa Altuğ Atalay
- Ministry of Agriculture and Forestry; General Directorate of Fisheries and Aquaculture; 06800; Ankara; Türkiye.
| | - Fitnat Güler Ekmekçi
- Hacettepe University; Faculty of Science; Biology Department; 06800 Ankara; Türkiye.
| | - Jörg Freyhof
- Museum für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; 10115 Berlin; Germany.
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3
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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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Mitochondrial genomes reveal mid-Pleistocene population divergence, and post-glacial expansion, in Australasian snapper (Chrysophrys auratus). Heredity (Edinb) 2023; 130:30-39. [PMID: 36463371 DOI: 10.1038/s41437-022-00579-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Glacial cycles play important roles in determining the phylogeographic structure of terrestrial species, however, relatively little is known about their impacts on the distribution of marine biota. This study utilised modern (n = 350) and ancient (n = 26) mitochondrial genomes from Australasian snapper (Chrysophrys auratus) sampled in New Zealand to assess their demographic and phylogeographic history. We also tested for changes in genetic diversity using the up to 750-year-old mitochondrial genomes from pre-European archaeological sites to assess the potential impacts of human exploitation. Nucleotide diversity and haplotype diversity was high (π = 0.005, h = 0.972). There was no significant change in nucleotide diversity over the last 750 years (p = 0.343), with no detectable loss of diversity as a result of indigenous and industrial-scale fishing activity. While there was no evidence for contemporary population structure (AMOVA, p = 0.764), phylogeographic analyses identified two distinct mitochondrial clades that diverged approximately 650,000 years ago during the mid-Pleistocene, suggesting the species experienced barriers to gene flow when sea levels dropped over 120 m during previous glacial maxima. An exponential population increase was also observed around 8000 years ago consistent with a post-glacial expansion, which was likely facilitated by increased ocean temperatures and rising sea levels. This study demonstrates that glacial cycles likely played an important role in the demographic history of C. auratus and adds to our growing understanding of how dynamic climatic changes have influenced the evolution of coastal marine species.
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Chou MH, Chu IH, Lau D, Huang JP. Integrative species delimitation reveals fine-scale allopatric speciation in a good-flying insect: a case study on. INVERTEBR SYST 2022. [DOI: 10.1071/is22011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Alpha taxonomy is fundamental for many biological fields. Delineation of the species boundary, however, can be challenging in a species complex, where different species share a similar morphology and diagnostic characters may not be available. In this context, integrative approaches that incorporate molecular and morphological data sets, and account for speciation history can be helpful to alpha taxonomy. Different approaches to species delimitation based on different assumptions are complementary and by integrating the results from multiple approaches we can generate a more reliable and objective taxonomic decision. In this study, we applied three molecular approaches to species delimitation and inferred the demographic history based on an isolation with migration model to test a morphologically based taxonomic hypothesis for the Cylindera pseudocylindriformis complex. We discuss the association between genetic divergence and microhabitat specialisation, and further corroborate that C. subtilis sp. nov. is a valid new species by integrating the results from model-based species delimitation and the genealogical divergence index. We argue that genetic endemism can occur at a small geographic scale, even in a winged insect like tiger beetles. Our results also indicated that there may still be undocumented species diversity of Taiwanese Cylindera remaining to be discovered. ZooBank LSID: urn:lsid:zoobank.org:pub:9DEC1432-365C-4872-8D06-73B95F30624F
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Park E, Poulin R. Extremely divergent COI sequences within an amphipod species complex: A possible role for endosymbionts? Ecol Evol 2022; 12:e9448. [PMID: 36311398 PMCID: PMC9609454 DOI: 10.1002/ece3.9448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Some heritable endosymbionts can affect host mtDNA evolution in various ways. Amphipods host diverse endosymbionts, but whether their mtDNA has been influenced by these endosymbionts has yet to be considered. Here, we investigated the role of endosymbionts (microsporidians and Rickettsia) in explaining highly divergent COI sequences in Paracalliope fluviatilis species complex, the most common freshwater amphipods in New Zealand. We first contrasted phylogeographic patterns using COI, ITS, and 28S sequences. While molecular species delimitation methods based on 28S sequences supported 3-4 potential species (N, C, SA, and SB) among freshwater lineages, COI sequences supported 17-27 putative species reflecting high inter-population divergence. The deep divergence between NC and S lineages (~20%; 28S) and the substitution saturation on the 3rd codon position of COI detected even within one lineage (SA) indicate a very high level of morphological stasis. Interestingly, individuals infected and uninfected by Rickettsia comprised divergent COI lineages in one of four populations tested, suggesting a potential influence of endosymbionts in mtDNA patterns. We propose several plausible explanations for divergent COI lineages, although they would need further testing with multiple lines of evidence. Lastly, due to common morphological stasis and the presence of endosymbionts, phylogeographic patterns of amphipods based on mtDNA should be interpreted with caution.
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Affiliation(s)
- Eunji Park
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
- Department of BotanyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Robert Poulin
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
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7
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Cowles SA, Witt CC, Bonaccorso E, Grewe F, Uy JAC. Early stages of speciation with gene flow in the Amazilia Hummingbird (
Amazilis amazilia
) subspecies complex of Western South America. Ecol Evol 2022; 12:e8895. [PMID: 35592064 PMCID: PMC9102506 DOI: 10.1002/ece3.8895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/22/2022] [Accepted: 04/14/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Sarah A. Cowles
- Department of Biology University of Miami Coral Gables Florida USA
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico USA
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito Quito Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático Universidad Tecnológica Indoamérica Quito Ecuador
| | - Felix Grewe
- Grainger Bioinformatics Center Field Museum Chicago Illinois USA
| | - J. Albert C. Uy
- Department of Biology University of Miami Coral Gables Florida USA
- Department of Biology University of Rochester Rochester New York USA
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8
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Urfer K, Spasojevic T, Klopfstein S, Baur H, Lasut L, Kropf C. Incongruent molecular and morphological variation in the crab spider Synemaglobosum (Araneae, Thomisidae) in Europe. Zookeys 2021; 1078:107-134. [PMID: 35068955 PMCID: PMC8709837 DOI: 10.3897/zookeys.1078.64116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/29/2021] [Indexed: 11/12/2022] Open
Abstract
Establishing species boundaries is one of the challenges taxonomists around the world have been tackling for centuries. The relation between intraspecific and interspecific variability is still under discussion and in many taxa it remains understudied. Here the hypothesis of single versus multiple species of the crab spider Synemaglobosum (Fabricius) is tested. The wide distribution range as well as its high morphological variability makes this species an interesting candidate for re-evaluation using an integrative approach. This study combines information from barcoding, phylogenetic reconstruction based on mitochondrial CO1 and ITS2 of more than 60 specimens collected over a wide range of European localities, and morphology. The findings show deep clades with up to 6% mean pairwise distance in the CO1 barcode without any biogeographical pattern. The nuclear ITS2 gene did not support the CO1 clades. Morphological assessment of somatic and genital characters in males and females and a morphometric analysis of the male palp uncovered high intraspecific variation that does not match the CO1 or ITS2 phylogenies or biogeography either. Screening for endosymbiotic Wolbachia bacteria was conducted and only a single infected specimen was found. Several scenarios might explain these inconsistent patterns. While the deep divergences in the barcoding marker might suggest cryptic or ongoing speciation or geographical isolation in the past, the lack of congruent variation in the nuclear ITS2 gene or the studied morphological character systems, especially the male palp, indicates that S.globosum might simply be highly polymorphic both in terms of its mtDNA and morphology. Therefore, more data on ecology and behaviour and full genome sequences are necessary to ultimately resolve this taxonomically intriguing case.
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Affiliation(s)
- Karin Urfer
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum St.Gallen, Rorschacher Strasse 263, 9016 St.Gallen, SwitzerlandNatural History Museum BaselBaselSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Tamara Spasojevic
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Seraina Klopfstein
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
- Natural History Museum Basel, Augustinergasse 2, 4051 Basel, SwitzerlandNatural History Museum St.GallenSt.GallenSwitzerland
| | - Hannes Baur
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Liana Lasut
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
| | - Christian Kropf
- Natural History Museum Bern, Bernastrasse 15, 3005 Bern, SwitzerlandNatural History Museum BernBernSwitzerland
- University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3012 Bern, SwitzerlandUniversity of BernBernSwitzerland
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9
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Päckert M. No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference. Ecol Evol 2021; 11:16354-16364. [PMID: 34824832 PMCID: PMC8601899 DOI: 10.1002/ece3.8199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
A recent article in Ecology and Evolution featured the discovery of hybrid snowcocks (Tetraogallus) and speculated on the hybrid origin of an extant species (T. altaicus). Comprehensive re-analyses of original data from the latter paper reliably refute the phylogenetic hypothesis taken as firm evidence of a past hybridization event in these birds. The new re-analyses showed that there is no evidence of hybridization in these snowcocks from the data available so far.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections Museum of Zoology Dresden Germany
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10
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van Riemsdijk I, Arntzen JW, Babik W, Bogaerts S, Franzen M, Kalaentzis K, Litvinchuk SN, Olgun K, Wijnands JWPM, Wielstra B. Next-generation phylogeography of the banded newts (Ommatotriton): A phylogenetic hypothesis for three ancient species with geographically restricted interspecific gene flow and deep intraspecific genetic structure. Mol Phylogenet Evol 2021; 167:107361. [PMID: 34775056 DOI: 10.1016/j.ympev.2021.107361] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022]
Abstract
Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phylogenetic relationships, apparently limited interspecific gene flow and deep intraspecific geographic mtDNA structure. We use parallel tagged amplicon sequencing to obtain 177 nuclear DNA markers for 35 banded newts sampled throughout the range. We determine population structure (with Bayesian clustering and principal component analysis), interspecific gene flow (by determining the distribution of species-diagnostic alleles) and phylogenetic relationships (by maximum likelihood inference of concatenated sequence data and based on a summary-coalescent approach). We confirm that the three proposed species are genetically distinct. A sister relationship between O. nesterovi and O. ophryticus is suggested. We find evidence for introgression between O. nesterovi and O. ophryticus, but this is geographically limited. Intraspecific structuring is extensive, with the only recognized banded newt subspecies, O. vittatus cilicensis, representing the most distinct lineage below the species level. While mtDNA mostly mirrors the pattern observed in nuclear DNA, all banded newt species show mito-nuclear discordance as well.
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Affiliation(s)
- Isolde van Riemsdijk
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands; Institute for Evolution and Ecology, Auf der Morgenstelle 5, D-72076, Tübingen University, Tübingen, Germany
| | - Jan W Arntzen
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | | | - Michael Franzen
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Konstantinos Kalaentzis
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 St. Petersburg, Russia
| | - Kurtuluş Olgun
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, 09010 Aydın, Turkey
| | - Jan Willem P M Wijnands
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands
| | - Ben Wielstra
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, the Netherlands.
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11
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Xu L, Yu R, Lin X, Zhang B, Li N, Lin K, Zhang D, Bai W. Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts. THE NEW PHYTOLOGIST 2021; 232:388-403. [PMID: 34143496 PMCID: PMC8519134 DOI: 10.1111/nph.17564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/13/2021] [Indexed: 05/03/2023]
Abstract
Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.
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Affiliation(s)
- Lin‐Lin Xu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Rui‐Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Xin‐Rui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Bo‐Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
- Centre for Individualised Infection Medicine (CiiM) & TWINCOREJoint ventures between the Helmholtz‐Centre for Infection Research (HZI) and the Hannover Medical School (MHH)Hannover30625Germany
| | - Nan Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Da‐Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Wei‐Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
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12
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Makhov IA, Gorodilova YYU, Lukhtanov VA. Sympatric occurrence of deeply diverged mitochondrial DNA lineages in Siberian geometrid moths (Lepidoptera: Geometridae): cryptic speciation, mitochondrial introgression, secondary admixture or effect of Wolbachia? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The divergent sympatric mitochondrial lineages within traditionally recognized species present a challenge regularly faced by taxonomists and evolutionary biologists. We encountered this problem when studying the Siberian geometrid moths, Alcis deversata and Thalera chlorosaria. Within each of these species we found two deeply diverged mitochondrial lineages that demonstrated a level of genetic differentiation exceeding the standard interspecific DNA barcode threshold. Using analyses of nuclear genes, morphology, ecological preferences and Wolbachia endosymbionts, we tested five hypotheses that might explain the mitochondrial pattern observed: cryptic speciation, ancestral polymorphism, interspecific mitochondrial introgression, secondary admixture of allopatrically evolved populations and an effect of intracellular Wolbachia endosymbionts. We demonstrate that in A. deversata and Th. chlorosaria the mitochondrial differences are not correlated with differences in nuclear genes, morphology, ecology and Wolbachia infection status, thus not supporting the hypothesis of cryptic species and an effect of Wolbachia. Mitochondrial introgression can lead to a situation in which one species has both its own mitochondrial lineage and the lineage obtained from another species. We found this situation in the species pair Alcis repandata and Alcis extinctaria. We conclude that the mitochondrial heterogeneity in A. deversata and Th. chlorosaria is most likely to be attributable to the secondary admixture of allopatrically evolved populations.
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Affiliation(s)
- Ilia A Makhov
- Department of Entomology, Saint Petersburg State University, Universitetskaya Embankment 7/9, 199034 Saint Petersburg, Russia
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, 199034 Saint Petersburg, Russia
| | - Yelizaveta Y U Gorodilova
- Biological Faculty, Saint Petersburg State University, Botanicheskaya Street 17, Stary Peterhof, Saint Petersburg 198504, Russia
| | - Vladimir A Lukhtanov
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, 199034 Saint Petersburg, Russia
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13
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Pârâu LG, Wink M. Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review. JOURNAL OF ORNITHOLOGY 2021; 162:937-959. [PMID: 34007780 PMCID: PMC8118378 DOI: 10.1007/s10336-021-01893-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10336-021-01893-x.
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Affiliation(s)
- Liviu G. Pârâu
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
- Present Address: SARS-CoV-2 Data Evaluation Office, Eurofins Genomics Europe Applied Genomics GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Department Biology, Heidelberg University, Im Neuenheimer Feld 364, 4 OG, Heidelberg, Germany
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14
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Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon. DIVERSITY 2020. [DOI: 10.3390/d12110428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.
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15
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Wielstra B, Salvi D, Canestrelli D. Genetic Divergence Across Glacial Refugia Despite Interglacial Gene Flow in a Crested Newt. Evol Biol 2020. [DOI: 10.1007/s11692-020-09519-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractMtDNA-based phylogeography has illuminated the impact of the Pleistocene Ice Age on species distribution dynamics and the build-up of genetic divergence. The well-known shortcomings of mtDNA in biogeographical inference can be compensated by integrating multilocus data and species distribution modelling into phylogeography. We re-visit the phylogeography of the Italian crested newt (Triturus carnifex), a species distributed in two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas. While a new 51 nuclear DNA marker dataset supports the existence of three lineages previously suggested by mtDNA (Balkan, northern Italy and southern Italy), the nuclear DNA dataset also provides improved resolution where these lineages have obtained secondary contact. We observe geographically restricted admixture at the contact between the Balkan and northern Italy gene pools and identify a potential mtDNA ghost lineage here. At the contact between the northern and southern Italy gene pools we find admixture over a broader area, as well as asymmetric mtDNA introgression. Our species distribution model is in agreement with a distribution restricted to distinct refugia during Pleistocene glacial cycles and postglacial expansion with secondary contact. Our study supports: (1) the relevance of the north-western Balkan Peninsula as a discrete glacial refugium; (2) the importance of north-eastern Italy and the northern Apennine as suture zones; and (3) the applicability of a refugia-within-refugia scenario within the Italian Peninsula.
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16
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Medolago CAB, Costa MC, Silveira LF, Francisco MR. Hybridization between two recently diverged Neotropical passerines: The Pearly-bellied Seedeater Sporophila pileata, and the Copper Seedeater S. bouvreuil (Aves, Passeriformes, Thraupidae). PLoS One 2020; 15:e0229714. [PMID: 32218563 PMCID: PMC7100935 DOI: 10.1371/journal.pone.0229714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/13/2020] [Indexed: 12/30/2022] Open
Abstract
The small Neotropical finches called capuchinos are outstanding because they have experienced one of the most recent and explosive avian radiations ever documented for birds. Despite very low morphological and niche divergence among species, many of them are reproductively isolated when in sympatry due to strong sexual selection in plumage traits. However, a specific pair of mostly parapatric species, the Pearly-bellied, Sporophila pileata, and the Copper Seedeaters, S. bouvreuil, has confounded taxonomists because individuals with intermediate color patterns can be found. By analyzing diagnostic COI mtDNA sequences and adult male plumage we provide evidence for hybridization. Paternity tests using microsatellites also indicated that representatives with intermediate plumage pattern can be fertile. Our findings are consistent with the classification of S. bouvreuil and S. pileata as distinct taxa, but we demonstrate that the sexual selection mechanisms involved in the isolation of other reproductively sympatric capuchinos are not applicable to this pair of species, likely because of reduced barriers to mate recognition.
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Affiliation(s)
- Cesar A. B. Medolago
- Programa de Pós Graduação em Ecologia e Recursos Naturais, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Mariellen C. Costa
- Programa de Pós Graduação em Ecologia e Recursos Naturais, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Luis F. Silveira
- Seção de Aves, Museu de Zoologia da Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Mercival R Francisco
- Programa de Pós Graduação em Ecologia e Recursos Naturais, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Departamento de Ciências Ambientais, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
- * E-mail:
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17
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Wilcox CL, Motomura H, Matsunuma M, Bowen BW. Phylogeography of Lionfishes (Pterois) Indicate Taxonomic Over Splitting and Hybrid Origin of the Invasive Pterois volitans. J Hered 2019. [PMID: 28637254 DOI: 10.1093/jhered/esx056] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The lionfish is an iconic marine fish, and recently renowned for a disastrous introduction into the West Atlantic. Genetic surveys of the putative invaders (Pterois volitans and Pterois miles) in their natural Indo-Pacific range can illuminate both topics. Previous research indicated that P. volitans and P. miles are sister species that hybridize in the invasive range, but hybridization in the native range is unknown. Here, we apply mtDNA COI and 2 nuclear introns (S7 RP1 and Gpd2) from 229 lionfish including the 2 invaders and 2 closely-related taxa (44 P. miles, 91 P. volitans, 31 Pterois lunulata, and 63 Pterois russelii) from 10 locations in their native ranges. Genetic data are supplemented with key morphological characters: dorsal, anal, and pectoral fin ray counts. We observed 2 lineages (d = 4.07%, 0.89%, and 2.75% at COI, S7 RP1, and Gpd2, respectively) among the 4 putative species: an Indian Ocean lineage represented by P. miles, and a Pacific Ocean lineage represented by P. lunulata and P. russelii. All specimens of the invasive P. volitans appear to be hybrids between the Indian Ocean P. miles and a Pacific lineage encompassing P. lunulata/russelii, a conclusion supported by both genetics and morphology. The divergences between Indian and Pacific forms are within the range of species-level partitions in fishes, and we recommend retention of the names P. miles and P. russelii for Indian and Pacific forms. The hybrid origin of the Atlantic invasion invokes the possibility of heterosis as a contributing factor to invasion success.
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Affiliation(s)
- Christie L Wilcox
- Hawai'i Institute of Marine Biology, Kane'ohe, HI.,Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI
| | | | - Mizuki Matsunuma
- Laboratory of Marine Biology, Faculty of Science, Kochi University, Kochi, Japan
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18
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Zhang D, Tang L, Cheng Y, Hao Y, Xiong Y, Song G, Qu Y, Rheindt FE, Alström P, Jia C, Lei F. 'Ghost introgression' as a cause of deep mitochondrial divergence in a bird species complex. Mol Biol Evol 2019; 36:2375-2386. [PMID: 31364717 DOI: 10.1093/molbev/msz170] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/19/2022] Open
Abstract
In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by 'speciation reversal' or by mitochondrial capture through genetic introgression. Here we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of 'ghost introgression' as the cause of DMD, and we suggest that 'ghost introgression' may be a widely overlooked phenomenon in nature.
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Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfang Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, Sweden.,Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, Uppsala, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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19
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Benham PM, Cheviron ZA. Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah sparrow (Passerculus sandwichensis). Mol Ecol 2019; 28:1765-1783. [PMID: 30770598 DOI: 10.1111/mec.15049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 12/24/2022]
Abstract
Unusual patterns of mtDNA diversity can reveal interesting aspects of a species' biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next-generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA-based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus-specific patterns.
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Affiliation(s)
- Phred M Benham
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana
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20
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Tritsch C, Stuckas H, Martens J, Pentzold S, Kvist L, Lo Valvo M, Giacalone G, Tietze DT, Nazarenko AA, PÄckert M. Gene flow in the European coal tit, Periparus ater (Aves: Passeriformes): low among Mediterranean populations but high in a continental contact zone. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christian Tritsch
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Pentzold
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie biologiche, chimiche e farmaceutiche, Via Archirafi, Palermo, Italy
| | | | | | - Alexander A Nazarenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Martin PÄckert
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
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21
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Affiliation(s)
- Werner Kunz
- Institut für Genetik; Heinrich-Heine-Universität; Universitätsstr. 1 D-40225 Düsseldorf
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22
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Marlétaz F, Le Parco Y, Liu S, Peijnenburg KTCA. Extreme Mitogenomic Variation in Natural Populations of Chaetognaths. Genome Biol Evol 2018; 9:1374-1384. [PMID: 28854623 PMCID: PMC5470650 DOI: 10.1093/gbe/evx090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2017] [Indexed: 12/15/2022] Open
Abstract
The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.
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Affiliation(s)
- Ferdinand Marlétaz
- Department of Zoology, University of Oxford, United Kingdom.,Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Yannick Le Parco
- Institut Méditerranéen d'Océanologie (CNRS UMR 7294), Aix-Marseille Université, Campus de Luminy, Marseille, France
| | - Shenglin Liu
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, The Netherlands
| | - Katja T C A Peijnenburg
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, The Netherlands.,Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands
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23
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Dai C, Hao Y, He Y, Lei F. The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone. BMC Evol Biol 2017; 17:266. [PMID: 29262786 PMCID: PMC5738821 DOI: 10.1186/s12862-017-1114-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses. RESULTS ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids. CONCLUSIONS Isolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.
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Affiliation(s)
- Chuanyin Dai
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yong He
- School of Chemistry and Life Sciences, Guizhou Normal College, Gaoxin Road 115, Guiyang, Guizhou 550018 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beichen Xi Road 1, Beijing, 100101 China
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24
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Soltani GG, Bénon D, Alvarez N, Praz CJ. When different contact zones tell different stories: putative ring species in the Megachile concinna species complex (Hymenoptera: Megachilidae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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25
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Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0317-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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26
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Martinsson S, Erséus C. Cryptic speciation and limited hybridization within Lumbricus earthworms (Clitellata: Lumbricidae). Mol Phylogenet Evol 2017; 106:18-27. [DOI: 10.1016/j.ympev.2016.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 12/16/2022]
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27
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Campbell KK, Braile T, Winker K. Integration of Genetic and Phenotypic Data in 48 Lineages of Philippine Birds Shows Heterogeneous Divergence Processes and Numerous Cryptic Species. PLoS One 2016; 11:e0159325. [PMID: 27442510 PMCID: PMC4956044 DOI: 10.1371/journal.pone.0159325] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/30/2016] [Indexed: 12/19/2022] Open
Abstract
The Philippine Islands are one of the most biologically diverse archipelagoes in the world. Current taxonomy, however, may underestimate levels of avian diversity and endemism in these islands. Although species limits can be difficult to determine among allopatric populations, quantitative methods for comparing phenotypic and genotypic data can provide useful metrics of divergence among populations and identify those that merit consideration for elevation to full species status. Using a conceptual approach that integrates genetic and phenotypic data, we compared populations among 48 species, estimating genetic divergence (p-distance) using the mtDNA marker ND2 and comparing plumage and morphometrics of museum study skins. Using conservative speciation thresholds, pairwise comparisons of genetic and phenotypic divergence suggested possible species-level divergences in more than half of the species studied (25 out of 48). In speciation process space, divergence routes were heterogeneous among taxa. Nearly all populations that surpassed high genotypic divergence thresholds were Passeriformes, and non-Passeriformes populations surpassed high phenotypic divergence thresholds more commonly than expected by chance. Overall, there was an apparent logarithmic increase in phenotypic divergence with respect to genetic divergence, suggesting the possibility that divergence among these lineages may initially be driven by divergent selection in this allopatric system. Also, genetic endemism was high among sampled islands. Higher taxonomy affected divergence in genotype and phenotype. Although broader lineage, genetic, phenotypic, and numeric sampling is needed to further explore heterogeneity among divergence processes and to accurately assess species-level diversity in these taxa, our results support the need for substantial taxonomic revisions among Philippine birds. The conservation implications are profound.
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Affiliation(s)
- Kyle K. Campbell
- University of Alaska Museum and Department of Biology and Wildlife, Fairbanks, Alaska, United States of America
| | - Thomas Braile
- University of Alaska Museum and Department of Biology and Wildlife, Fairbanks, Alaska, United States of America
| | - Kevin Winker
- University of Alaska Museum and Department of Biology and Wildlife, Fairbanks, Alaska, United States of America
- * E-mail:
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28
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Mutanen M, Kivelä SM, Vos RA, Doorenweerd C, Ratnasingham S, Hausmann A, Huemer P, Dincă V, van Nieukerken EJ, Lopez-Vaamonde C, Vila R, Aarvik L, Decaëns T, Efetov KA, Hebert PDN, Johnsen A, Karsholt O, Pentinsaari M, Rougerie R, Segerer A, Tarmann G, Zahiri R, Godfray HCJ. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Syst Biol 2016; 65:1024-1040. [PMID: 27288478 PMCID: PMC5066064 DOI: 10.1093/sysbio/syw044] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/14/2022] Open
Abstract
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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Affiliation(s)
- Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Finland;
| | | | - Rutger A Vos
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | - Axel Hausmann
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Peter Huemer
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Vlad Dincă
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Carlos Lopez-Vaamonde
- INRA, UR633 Zoologie Forestière, 45075 Orléans, France.,Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leif Aarvik
- Natural History Museum University of Oslo, Norway
| | - Thibaud Decaëns
- Centre d'Écologie Fonctionnelle et Évolutive, UMR 5175 CNRS / University of Montpellier / University of Montpellier 3 / EPHE / SupAgro Montpellier / INRA / IRD, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | | | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
| | | | - Ole Karsholt
- Zoologisk Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | | | - Rodolphe Rougerie
- Département Systématique et Evolution, Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France
| | - Andreas Segerer
- SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | - Gerhard Tarmann
- Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
| | - Reza Zahiri
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada.,Ottawa Plant Laboratory, Canadian Food Inspection Agency, Canada
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Klinth MJ, Martinsson S, Erséus C. Phylogeny and species delimitation of North EuropeanLumbricillus(Clitellata, Enchytraeidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mårten J. Klinth
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
| | - Svante Martinsson
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
| | - Christer Erséus
- Department of Biological & Environmental Sciences; University of Gothenburg; P.O. Box 463 SE-405 30 Gothenburg Sweden
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Ruskey JA, Taylor EB. Morphological and genetic analysis of sympatric dace within the Rhinichthys cataractaespecies complex: a case of isolation lost. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer A. Ruskey
- Department of Zoology; Biodiversity Research Centre and Beaty Biodiversity Museum; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Eric B. Taylor
- Department of Zoology; Biodiversity Research Centre and Beaty Biodiversity Museum; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
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Majhi RK, Kumar A, Yadav M, Kumar P, Maity A, Giri SC, Goswami C. Light and electron microscopic study of mature spermatozoa from White Pekin duck (Anas platyrhynchos): an ultrastructural and molecular analysis. Andrology 2016; 4:232-44. [DOI: 10.1111/andr.12130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 07/30/2015] [Accepted: 10/12/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Rakesh Kumar Majhi
- School of Biological Sciences; National Institute of Science Education and Research; Bhubaneswar India
| | - Ashutosh Kumar
- School of Biological Sciences; National Institute of Science Education and Research; Bhubaneswar India
| | - Manoj Yadav
- School of Biological Sciences; National Institute of Science Education and Research; Bhubaneswar India
| | | | - Apratim Maity
- Department of Biochemistry; OVC; Orissa University of Agriculture and Technology; Bhubaneswar India
| | | | - Chandan Goswami
- School of Biological Sciences; National Institute of Science Education and Research; Bhubaneswar India
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Martinsson S, Rhodén C, Erséus C. Barcoding gap, but no support for cryptic speciation in the earthworm Aporrectodea longa (Clitellata: Lumbricidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:147-155. [PMID: 26709635 DOI: 10.3109/19401736.2015.1115487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA-barcoding, using the mitochondrial marker COI, has been found successful for the identification of specimens in many animal groups, but may not be suited for species discovery and delimitation if used alone. In this study, we investigate whether two observed COI haplogroups in the earthworm Aporrectodea longa correspond to two cryptic species or if the variation is intraspecific. This is done by complementing COI with two nuclear markers, ITS2 and Histone 3. The variation is studied using distance methods, parsimony networks and Bayesian coalescent trees, and the statistical distinctness of the groups is tested on gene trees using the genealogical sorting index, Rosenberg's PAB and Rodrigo et al.'s P(RD). We also applied multilocus species delimitation based on the multispecies coalescence model. The two haplogroups were found in COI, and all tests except P(RD) found them to be significantly distinct. However, in ITS2, the same groups were not recovered in any analyses or tests. H3 was invariable in A. longa, and was, therefore, included only in the multilocus analysis, which preferred a model treating A. longa as one species over a model splitting it into two. We also compared two measurements of size, body length, and no. of segments between the groups. No difference in body length was found, and although a significant difference in no. of segments was noted the haplogroup with the lower mean showed both the highest and the lowest value. When combined, these results led us to the conclusion that there is no support for the separation of A. longa into two cryptic species. This study again highlights the importance of complementing mitochondrial barcodes with more data when establishing species boundaries.
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Affiliation(s)
- Svante Martinsson
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Caroline Rhodén
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
| | - Christer Erséus
- a Division of Systematics and Biodiversity, Department of Biological and Environmental Sciences , University of Gothenburg , Göteborg , Sweden
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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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Block NL, Goodman SM, Hackett SJ, Bates JM, Raherilalao MJ. Potential merger of ancient lineages in a passerine bird discovered based on evidence from host-specific ectoparasites. Ecol Evol 2015; 5:3743-55. [PMID: 26380702 PMCID: PMC4567877 DOI: 10.1002/ece3.1639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 07/10/2015] [Accepted: 07/13/2015] [Indexed: 01/08/2023] Open
Abstract
The merger of formerly isolated lineages is hypothesized to occur in vertebrates under certain conditions. However, despite many demonstrated instances of introgression between taxa in secondary contact, examples of lineage mergers are rare. Preliminary mtDNA sequencing of a Malagasy passerine, Xanthomixis zosterops (Passeriformes: Bernieridae), indicated a possible instance of merging lineages. We tested the hypothesis that X. zosterops lineages are merging by comparing mtDNA sequence and microsatellite data, as well as mtDNA sequence data from host-specific feather lice in the genus Myrsidea (Phthiraptera: Menoponidae). Xanthomixis zosterops comprises four deeply divergent, broadly sympatric, cryptic mtDNA clades that likely began diverging approximately 3.6 million years ago. Despite this level of divergence, the microsatellite data indicate that the X. zosterops mtDNA clades are virtually panmictic. Three major phylogroups of Myrsidea were found, supporting previous allopatry of the X. zosterops clades. In combination, the datasets from X. zosterops and its Myrsidea document a potential merger of previously allopatric lineages that likely date to the Pliocene. This represents the first report of sympatric apparent hybridization among more than two terrestrial vertebrate lineages. Further, the mtDNA phylogeographic pattern of X. zosterops, namely the syntopy of more than two deeply divergent cryptic clades, appears to be a novel scenario among vertebrates. We highlight the value of gathering multiple types of data in phylogeographic studies to contribute to the study of vertebrate speciation.
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Affiliation(s)
- Nicholas L Block
- Biology Department, Stonehill College 320 Washington Street, Easton, Massachusetts, 02357 ; Field Museum of Natural History 1400 S. Lake Shore Dr., Chicago, Illinois, 60605
| | - Steven M Goodman
- Field Museum of Natural History 1400 S. Lake Shore Dr., Chicago, Illinois, 60605 ; Association Vahatra BP 3972, Antananarivo (101), Madagascar
| | - Shannon J Hackett
- Field Museum of Natural History 1400 S. Lake Shore Dr., Chicago, Illinois, 60605
| | - John M Bates
- Field Museum of Natural History 1400 S. Lake Shore Dr., Chicago, Illinois, 60605
| | - Marie J Raherilalao
- Association Vahatra BP 3972, Antananarivo (101), Madagascar ; Département de Biologie Animale, Université d'Antananarivo BP 906, Antananarivo (101), Madagascar
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35
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Voelker G, Semenov G, Fadeev IV, Blick A, Drovetski SV. The biogeographic history ofPhoenicurusredstarts reveals an allopatric mode of speciation and an out-of-Himalayas colonization pattern. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2014.992380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Sánchez-González LA, Navarro-Sigüenza AG, Krabbe NK, Fjeldså J, García-Moreno J. Diversification in the Andes: theAtlapetesbrush-finches. ZOOL SCR 2014. [DOI: 10.1111/zsc.12088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luis A. Sánchez-González
- Museo de Zoología “Alfonso L. Herrera”; Depto. de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México; Apdo. Postal 70-399 México DF 04510 México
| | - Adolfo G. Navarro-Sigüenza
- Museo de Zoología “Alfonso L. Herrera”; Depto. de Biología Evolutiva; Facultad de Ciencias; Universidad Nacional Autónoma de México; Apdo. Postal 70-399 México DF 04510 México
| | - Niels K. Krabbe
- Center of Macroecology, Evolution and Climate; Natural History Museum of Denmark; Universitetsparken 15 Copenhagen DK-2100 Denmark
| | - Jon Fjeldså
- Center of Macroecology, Evolution and Climate; Natural History Museum of Denmark; Universitetsparken 15 Copenhagen DK-2100 Denmark
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Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). THE NEW PHYTOLOGIST 2014; 204:693-703. [PMID: 25078531 DOI: 10.1111/nph.12956] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/16/2014] [Indexed: 05/03/2023]
Abstract
As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance - the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees - are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6-7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a 'ghost lineage' of a now-extinct North American poplar.
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Affiliation(s)
- Daisie I Huang
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Charles A Hefer
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Natalia Kolosova
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Carl J Douglas
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
- Beaty Biodiversity Research Centre, University of British Columbia, Main Mall, Vancouver, BC, V6T 1Z4, Canada
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Pavan SE, Jansa SA, Voss RS. Molecular phylogeny of short-tailed opossums (Didelphidae: Monodelphis ): Taxonomic implications and tests of evolutionary hypotheses. Mol Phylogenet Evol 2014; 79:199-214. [DOI: 10.1016/j.ympev.2014.05.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/23/2014] [Accepted: 05/26/2014] [Indexed: 02/01/2023]
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Saitoh T, Sugita N, Someya S, Iwami Y, Kobayashi S, Kamigaichi H, Higuchi A, Asai S, Yamamoto Y, Nishiumi I. DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago. Mol Ecol Resour 2014; 15:177-86. [PMID: 24835119 DOI: 10.1111/1755-0998.12282] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/29/2022]
Abstract
DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese-breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.
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Affiliation(s)
- Takema Saitoh
- Division of Natural History, Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
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Martinsson S, Achurra A, Svensson M, Erséus C. Integrative taxonomy of the freshwater wormRhyacodrilus falciformiss.l. (Clitellata: Naididae), with the description of a new species. ZOOL SCR 2013. [DOI: 10.1111/zsc.12032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Svante Martinsson
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 463; SE-405 30; Göteborg; Sweden
| | | | - Marcus Svensson
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 463; SE-405 30; Göteborg; Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 463; SE-405 30; Göteborg; Sweden
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Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA, Sunnucks P. PERCHED AT THE MITO-NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD. Evolution 2013; 67:3412-28. [DOI: 10.1111/evo.12107] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 03/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - J. Nevil Amos
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO Ecosystem Sciences; GPO Box 1700 Canberra Australian Capital Territory 2601 Australia
| | - Kate Loynes
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA (ACAD); School of Earth & Environmental Sciences, The University of Adelaide; Darling Building North Terrace Campus South Australia 5005 Australia
- Sciences Department; Museum Victoria; Carlton Gardens Melbourne Victoria 3001 Australia
| | - J. Scott Keogh
- Division of Evolution; Ecology and Genetics, Building 116, Daley Road, Research School of Biology, The Australian National University; Canberra Australian Capital Territory 0200 Australia
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - James A. Nicholls
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road Edinburgh EH9 3JT Scotland
| | - Paul Sunnucks
- School of Biological Sciences and Australian Centre for Biodiversity; Clayton Campus, Monash University; Wellington Road Clayton Victoria 3800 Australia
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Kvie KS, Hogner S, Aarvik L, Lifjeld JT, Johnsen A. Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata). Ecol Evol 2012; 3:126-44. [PMID: 23404314 PMCID: PMC3568849 DOI: 10.1002/ece3.434] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 02/01/2023] Open
Abstract
Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.
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Affiliation(s)
- Kjersti S Kvie
- Natural History Museum, University of Oslo P.O. Box 1172, Blindern, N-0318, Oslo, Norway ; Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science P.O. Box 8146 Dep, N-0033, Oslo, Norway
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