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Heller R, Frandsen P, Lorenzen ED, Siegismund HR. Is diagnosability an indicator of speciation? Response to "Why one century of phenetics is enough". Syst Biol 2014; 63:833-7. [PMID: 24831669 DOI: 10.1093/sysbio/syu034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, DenmarkDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
| | - Eline Deirdre Lorenzen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, DenmarkDepartment of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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102
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Kruckenhauser L, Duda M, Bartel D, Sattmann H, Harl J, Kirchner S, Haring E. Paraphyly and budding speciation in the hairy snail (Pulmonata, Hygromiidae). ZOOL SCR 2014; 43:273-288. [PMID: 25170185 PMCID: PMC4144147 DOI: 10.1111/zsc.12046] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 12/07/2013] [Indexed: 11/29/2022]
Abstract
Delimitation of species is often complicated by discordance of morphological and genetic data. This may be caused by the existence of cryptic or polymorphic species. The latter case is particularly true for certain snail species showing an exceptionally high intraspecific genetic diversity. The present investigation deals with the Trochulus hispidus complex, which has a complicated taxonomy. Our analyses of the COI sequence revealed that individuals showing a T. hispidus phenotype are distributed in nine highly differentiated mitochondrial clades (showing p-distances up to 19%). The results of a parallel morphometric investigation did not reveal any differentiation between these clades, although the overall variability is quite high. The phylogenetic analyses based on 12S, 16S and COI sequences show that the T. hispidus complex is paraphyletic with respect to several other morphologically well-defined Trochulus species (T. clandestinus, T. villosus, T. villosulus and T. striolatus) which form well-supported monophyletic groups. The nc marker sequence (5.8S-ITS2-28S) shows only a clear separation of T. o. oreinos and T. o. scheerpeltzi, and a weakly supported separation of T. clandestinus, whereas all other species and the clades of the T. hispidus complex appear within one homogeneous group. The paraphyly of the T. hispidus complex reflects its complicated history, which was probably driven by geographic isolation in different glacial refugia and budding speciation. At our present state of knowledge, it cannot be excluded that several cryptic species are embedded within the T. hispidus complex. However, the lack of morphological differentiation of the T. hispidus mitochondrial clades does not provide any hints in this direction. Thus, we currently do not recommend any taxonomic changes. The results of the current investigation exemplify the limitations of barcoding attempts in highly diverse species such as T. hispidus.
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Affiliation(s)
- Luise Kruckenhauser
- Natural History Museum Vienna, Central Research LaboratoriesBurgring 7, Vienna, 1010, AustriaAustria. E-mail:
| | - Michael Duda
- 3rd Zoological Department, Natural History Museum ViennaBurgring 7, 1010, Vienna, AustriaE-mail:
| | - Daniela Bartel
- University of Vienna, Department of Integrative ZoologyAlthanstraβe 14, 1090, Vienna, AustriaE-mail:
| | - Helmut Sattmann
- 3rd Zoological Department, Natural History Museum ViennaBurgring 7, 1010, Vienna, AustriaE-mail:
| | - Josef Harl
- Natural History Museum Vienna, Central Research LaboratoriesBurgring 7, Vienna, 1010, AustriaAustria. E-mail:
- University of Vienna, Department of Integrative ZoologyAlthanstraβe 14, 1090, Vienna, AustriaE-mail:
| | - Sandra Kirchner
- Natural History Museum Vienna, Central Research LaboratoriesBurgring 7, Vienna, 1010, AustriaAustria. E-mail:
- University of Vienna, Department of Integrative ZoologyAlthanstraβe 14, 1090, Vienna, AustriaE-mail:
| | - Elisabeth Haring
- Natural History Museum Vienna, Central Research LaboratoriesBurgring 7, Vienna, 1010, AustriaAustria. E-mail:
- University of Vienna, Department of Integrative ZoologyAlthanstraβe 14, 1090, Vienna, AustriaE-mail:
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Abstract
Ernst Mayr (1904-2005) was the twentieth century's most influential writer to wrestle with the species problem. The following draws heavily on his work, albeit without presumptuously claiming to mirror his thinking or present any original ideas. As a personal meditation, I am thinking mostly of platyrrhines. Following Mayr, I adhere to what is commonly called the Biological Species Concept (BSC) as a way of thinking about a species in the real-world biosphere as a taxon. I also hold to the idea that the Linnaean category called species has the same function as other categories: a linguistic tool for organizing and retrieving information about biodiversity while embodying evolutionary hypotheses. In other words, alpha taxonomy, the area of systematics that involves identifying, naming, and classifying species, is not purely an exercise in either biology or inventory because it involves communication as well. The burdensome work of the species category stems partly from tension created by the several purposes associated with the concept: the objective observation and examination of a fundamental biological phenomenon, the collection and interpretation of data in a selective context of relevance, and the intention to deploy scientific decisions as a form of communication within a dynamic but highly structured language system.
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104
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Zimmermann E, Radespiel U. Species concepts, diversity, and evolution in primates: Lessons to be learned from mouse lemurs. Evol Anthropol 2014; 23:11-4. [DOI: 10.1002/evan.21388] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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105
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Kong L, Wang W, Cong H, Son Nguyen T, Yang Q, Wu Y, Li Y. Molecular evidence revealed Lepus hainanus and L. peguensis have a conspecific relationship. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:265-9. [PMID: 24548010 DOI: 10.3109/19401736.2014.888550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Accurate species delimitation in Lepus was often hindered by highly conserved morphology and frequent introgression. In this study, we used rigorous molecular species delimitation methods to evaluate the taxonomic status of Hainan hare (Lepus hainanus) which has been traditionally identified as a distinct species, or a subspecies of Burmese hare (L. peguensis). The genetic distance and phylogenetic network support L. hainanus and L. peguensis are conspecific. However, the phylogenetic species concept and Bayesian species delimitation analysis based on combined mtDNA supported they are different species. The discordance between different methods can be explained by different species criterion. By taking into account our conflict results, we hold the opinion that adoption of the phylogenetic species concept and Bayesian species delimitation analysis would increase the risk of taxonomic inflation of island biota or otherwise spatially isolated population. Conservatively, we suggest that L. hainanus and L. peguensis are conspecific based on the results of our genetic divergence and phylogenetic network exclusively.
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Affiliation(s)
- Lingming Kong
- a Marine College, Shandong University , Weihai , China
| | - Wenquan Wang
- b Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences , Haikou , China
| | - Haiyan Cong
- a Marine College, Shandong University , Weihai , China
| | - Truong Son Nguyen
- c Department of Zoology , Institute of Ecology and Biological Resources , Hanoi , Vietnam
| | - Qisen Yang
- d Institute of Zoology, Chinese Academy of Sciences , Beijing , China , and
| | - Yi Wu
- e College of Life Science, Guangzhou University , Guangzhou , China
| | - Yuchun Li
- a Marine College, Shandong University , Weihai , China
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106
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Cotterill FPD, Taylor PJ, Gippoliti S, Bishop JM, Groves CP. Why One Century of Phenetics is Enough: Response to “Are There Really Twice As Many Bovid Species As We Thought?”. Syst Biol 2014; 63:819-32. [DOI: 10.1093/sysbio/syu003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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108
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Lamb J, Downs S, Eiseb S, John Taylor P. Increased geographic sampling reveals considerable new genetic diversity in the morphologically conservative African Pygmy Mice (Genus Mus; Subgenus Nannomys). Mamm Biol 2014. [DOI: 10.1016/j.mambio.2013.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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109
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Abstract
Since Darwin's time, the question "what a species" has provoked fierce disputes and a tremendous number of publications, from short opinion papers to thick volumes. The debates covered fundamental philosophical questions, such as: Do species exist at all independently of a human observer or are they just a construct of the human mind to categorize nature's organismic diversity and serve as a semantic tool in human communication about biodiversity? or: Are species natural kinds (classes) or individuals that are "born" by speciation, change in course of time, and finally "die" when they go extinct or diverge into new species? Also included was the problem of species as taxa (taxonomic) versus species as products of the speciation process (evolutionary). More pragmatic issues arose, such as: How can we reliably delineate and delimitate species? The great interest in what a species is reflects the importance of "species" as fundamental units in most fields of biology, especially evolutionary biology, ecology, and conservation.
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110
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Casacci LP, Barbero F, Balletto E. The “Evolutionarily Significant Unit” concept and its applicability in biological conservation. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/11250003.2013.870240] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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111
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Phylogeny and vicariant speciation of the Grey Rhebok, Pelea capreolus. Heredity (Edinb) 2013; 112:325-32. [PMID: 24281547 DOI: 10.1038/hdy.2013.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/18/2013] [Accepted: 09/24/2013] [Indexed: 12/31/2022] Open
Abstract
A South African endemic antelope, the Grey Rhebok (Pelea capreolus), has long been an evolutionary enigma in bovid systematics-its phylogenetic intractability attributed to its curious combination of derived and primitive morphological attributes and the consequences of a rapid radiation. By using a combination of DNA sequences, chromosomal characteristics and quantitative and qualitative morphological features we show that the species is a sister taxon to a clade that comprises the waterbuck, reedbuck and allies. Our finding of few unambiguous synapomorphies reinforces suggestions of a rapid radiation and highlights the effects of incomplete lineage sorting, including the hemiplasic nature of several chromosomal rearrangements. We investigate these data to address the general question of what may have led to Pelea being both genetically and ecologically distinct from the Reduncini. We argue that its adaptation to exposed habitats, free of standing water, arose by vicariance prompted by increasing aridity of the extreme south/southwestern region of the African continent in the Miocene. Ancestral lineages leading to the extant Redunca and Kobus, on the other hand, retreated to water-abundant refugia in the north during these mostly globally cool phases. The mosaic of water-rich environments provided by the Okavango and the drainage systems in the southwestern extension of the East African Rift system are considered to have facilitated speciation and chromosomal evolution within these antelope.
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112
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John L, Philip S, Dahanukar N, Anvar Ali PH, Tharian J, Raghavan R, Antunes A. Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited red lined torpedo barbs endemic to the Western Ghats of India. PLoS One 2013; 8:e69741. [PMID: 23894533 PMCID: PMC3718778 DOI: 10.1371/journal.pone.0069741] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 06/16/2013] [Indexed: 11/19/2022] Open
Abstract
Red lined torpedo barbs (RLTBS) (Cyprinidae: Puntius) endemic to the Western Ghats Hotspot of India, are popular and highly priced freshwater aquarium fishes. Two decades of indiscriminate exploitation for the pet trade, restricted range, fragmented populations and continuing decline in quality of habitats has resulted in their 'Endangered' listing. Here, we tested whether the isolated RLTB populations demonstrated considerable variation qualifying to be considered as distinct conservation targets. Multivariate morphometric analysis using 24 size-adjusted characters delineated all allopatric populations. Similarly, the species-tree highlighted a phylogeny with 12 distinct RLTB lineages corresponding to each of the different riverine populations. However, coalescence-based methods using mitochondrial DNA markers identified only eight evolutionarily distinct lineages. Divergence time analysis points to recent separation of the populations, owing to the geographical isolation, more than 5 million years ago, after the lineages were split into two ancestral stocks in the Paleocene, on north and south of a major geographical gap in the Western Ghats. Our results revealing the existence of eight evolutionarily distinct RLTB lineages calls for the re-determination of conservation targets for these cryptic and endangered taxa.
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Affiliation(s)
- Lijo John
- Marine Biotechnology Division, Central Marine Fisheries Research Institute (CMFRI), Kochi, India
- Export Inspection Agency (EIA), Kochi, India
| | - Siby Philip
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
- Conservation Research Group (CRG), St. Albert’s College, Kochi, India
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER), Pune, India
- Zoo Outreach Organization (ZOO), Coimbatore, India
| | | | - Josin Tharian
- Department of Zoology, St. John’s College, Anchal, Kerala, India
| | - Rajeev Raghavan
- Conservation Research Group (CRG), St. Albert’s College, Kochi, India
- Zoo Outreach Organization (ZOO), Coimbatore, India
- Durrell Institute of Conservation and Ecology (DICE), University of Kent, Canterbury, United Kingdom
- Research Group Zoology: Biodiversity & Toxicology, Center for Environmental Sciences, University of Hasselt, Diepenbeek, Belgium
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Rua dos Bragas, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
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113
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Heller R, Frandsen P, Lorenzen ED, Siegismund HR. Are There Really Twice as Many Bovid Species as We Thought? Syst Biol 2013; 62:490-3. [DOI: 10.1093/sysbio/syt004] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; 2Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; 3Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and 4Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; 2Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; 3Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and 4Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark
| | - Peter Frandsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; 2Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; 3Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and 4Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark
| | - Eline D. Lorenzen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; 2Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; 3Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and 4Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; 2Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; 3Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and 4Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark
| | - Hans R. Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; 2Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal; 3Department of Integrative Biology, University of California Berkeley, 1005 Valley Life Sciences Building, Berkeley, CA 94720, USA; and 4Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen K, Denmark
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