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Silva D, Veneza I, Silva RDA, Sampaio I, Evangelista-Gomes G. Molecular delimitation methods validate morphologically similar species of red snappers (Perciformes: Lutjanidae). AN ACAD BRAS CIENC 2023; 95:e20210997. [PMID: 38126517 DOI: 10.1590/0001-3765202320210997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/11/2023] [Indexed: 12/23/2023] Open
Abstract
In this study, we tested the taxonomic validation of red snappers species (Southern red snapper Lutjanus purpureus; Silk snapper L. vivanus; Blackfin snapper L. buccanella; and Pacific red snapper L. peru) based on comparative analysis, using four methods for species delimitation. These methods were based on either genetic similarity or phylogenetic trees inferred from two mitochondrial (Cytochrome b and D-loop) and two nuclear (Myostatin and S7 introns) markers. On one hand, the genetic results corroborated the presence of four red snapper species, confirming their taxonomic validation despite their remarkable morphological similarity. On the other hand, few incongruencies in the species delimitation methods were observed according to the phylogenetic reconstruction method (maximum likelihood or Bayesian inference) when using. Based on the phylogenetic results, L. buccanella should represent a more ancient lineage in relation to the clade that encompasses L. purpureus, L. peru and L. vivanus. The single-locus phylogenetic analysis based on Cytb recovered each the red snapper species as a well-supported clade. Overall, this study provided a DNA-based validation of the traditional morphological taxonomy of red snappers.
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Affiliation(s)
- Danillo Silva
- Universidade Federal do Pará, Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Campus Universitário de Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68000-000 Bragança, PA, Brazil
| | - Ivana Veneza
- Universidade Federal do Oeste do Pará, Campus Universitário de Monte Alegre, Travessa Major Francisco Mariano, s/n, Cidade Alta, 68220-000 Monte Alegre, PA, Brazil
| | - Raimundo DA Silva
- Universidade Federal do Pará, Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Campus Universitário de Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68000-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Universidade Federal do Pará, Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Campus Universitário de Bragança, Alameda Leandro Ribeiro, s/n, Aldeia 68000-000 Bragança, PA, Brazil
| | - Grazielle Evangelista-Gomes
- Universidade Federal do Pará, Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Campus Universitário de Bragança, Alameda Leandro Ribeiro, s/n, Aldeia, 68000-000 Bragança, PA, Brazil
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2
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Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [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: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
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3
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Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns. Mol Phylogenet Evol 2022; 177:107619. [PMID: 36007821 DOI: 10.1016/j.ympev.2022.107619] [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: 11/26/2021] [Revised: 08/01/2022] [Accepted: 08/17/2022] [Indexed: 11/23/2022]
Abstract
The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.
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Wei C, Sangster G, Olsson U, Rasmussen PC, Svensson L, Yao CT, Carey GJ, Leader PJ, Zhang R, Chen G, Song G, Lei F, Wilcove DS, Alström P, Liu Y. Cryptic species in a colorful genus: Integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species. Mol Phylogenet Evol 2022; 175:107580. [PMID: 35810968 DOI: 10.1016/j.ympev.2022.107580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/04/2022] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study, we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic approach by combining multilocus, acoustic, plumage and morphometric analyses. Our results reveal that the isolated north-central Chinese populations of Tarsiger cyanurus, described as the subspecies albocoeruleus but usually considered invalid, is distinctive in genetics and vocalisation, but only marginally differentiated in morphology. We also found the Taiwan endemic T. indicus formosanus to be distinctive in genetics, song and morphology from T. i. indicus and T. i. yunnanensis of the Sino-Himalayan mountains. Moreover, Bayesian species delimitation using BPP suggests that both albocoeruleus and formosanus merit full species status. We propose their treatment as 'Qilian Bluetail' T. albocoeruleus and 'Taiwan Bush Robin' T. formosanus, respectively.
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Affiliation(s)
- Chentao Wei
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China; South China Institute of Environmental Sciences, MEE, Guangzhou 510530, China
| | | | - Urban Olsson
- Biology and Environmental Sciences, Systematics and Biodiversity, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Pamela C Rasmussen
- Department of Integrative Biology and MSU Museum, Michigan State University, East Lansing, MI 48864, USA; Bird Group, The Natural History Museum-UK, Akeman Street, Tring, UK
| | | | - Cheng-Te Yao
- Medium Altitude Experimental Station, Endemic Species Research Institute, Chichi, 15 Nantou 552, Taiwan, China
| | - Geoff J Carey
- AEC Ltd, 127 Commercial Centre, Palm Springs, Hong Kong, China
| | - Paul J Leader
- AEC Ltd, 127 Commercial Centre, Palm Springs, Hong Kong, China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoling Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - David S Wilcove
- Princeton School of Public and International Affairs, Princeton University, NJ 08544, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China.
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Pourebrahimi S, Mirshamsi O, Ghasempouri SM, Moghaddam FY, Aliabadian M. Phylogeny and evolutionary history of the Sombre Tit, Poecile lugubris in the western Palearctic (Aves, Paridae). Mol Phylogenet Evol 2021; 167:107343. [PMID: 34748874 DOI: 10.1016/j.ympev.2021.107343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 10/01/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022]
Abstract
Few studies have delimited evolutionary entities within the Sombre Tit, Poecile lugubris. Here, we explored its morphological and genetic variability using 24 morphometric variables, two mitochondrial (COX1 and ND2), two nuclear (ODC and MB), and 10 microsatellite loci. Genetic and morphometric characters supported the species status of the Caspian Tit, Poecile hyrcanus with a separation from P. lugubris more than 4.5 MYA. The phylogenetic analyses uncovered three distinct clades within P. lugubris. The subspecies P. l. lugubris, with strong genetic differences from the other subspecies (4.5%), diverged at ∼1.1 MYA. Samples from Iran formed the remaining two clades. Individuals from western and northwestern Iran were placed in a single clade (anatoliae), while those from southern and southwestern Iran were in another independent clade (dubius-kirmanensis). Morphometric analyses also confirmed this pattern. The microsatellite results discriminated Iranian subspecies as discrete clusters with signs of nuclear admixture between dubius and anatoliae in the Zagros Mountains. Signs of population expansion for anatoliae and dubius-kirmanensis coincided with the late LGM. Our results shed new light on the phylogenetic relationships, evolutionary history, and past demographic processes of P. lugubris.
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Affiliation(s)
- Somayeh Pourebrahimi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Omid Mirshamsi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Seyed Mahmoud Ghasempouri
- Environmental Science Department, Natural Resources and Marine Sciences Faculty, Tarbiat Modares University, Noor, Iran
| | - Faezeh Yazdani Moghaddam
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
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6
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Chou MH, Tseng WZ, Sang YD, Morgan B, De Vivo M, Kuan YH, Wang LJ, Chen WY, Huang JP. Incipient speciation and its impact on taxonomic decision: a case study using a sky island sister-species pair of stag beetles (Lucanidae: Lucanus). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis, from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions.
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Affiliation(s)
- Ming-Hsun Chou
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Zhe Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yao-De Sang
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Brett Morgan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsiu Kuan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Liang-Jong Wang
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Wei-Yun Chen
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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7
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Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol 2021; 17:e1008924. [PMID: 33983918 PMCID: PMC8118268 DOI: 10.1371/journal.pcbi.1008924] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/29/2021] [Indexed: 11/22/2022] Open
Abstract
The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.
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Affiliation(s)
- Jeet Sukumaran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation. Mol Phylogenet Evol 2021; 160:107109. [PMID: 33609712 DOI: 10.1016/j.ympev.2021.107109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/20/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022]
Abstract
Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.
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Ortiz D, Pekár S, Bilat J, Alvarez N. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider. Mol Phylogenet Evol 2020; 154:106997. [PMID: 33164854 DOI: 10.1016/j.ympev.2020.106997] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Julia Bilat
- Geneva Natural History Museum, Geneva, Switzerland
| | - Nadir Alvarez
- Geneva Natural History Museum, Geneva, Switzerland; Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
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10
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Dong F, Li SH, Chiu CC, Dong L, Yao CT, Yang XJ. Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Mol Phylogenet Evol 2020; 153:106941. [PMID: 32818596 DOI: 10.1016/j.ympev.2020.106941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chi-Cheng Chiu
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Endemic Species Research Institute, Minsheng East Road, Jiji Township, Nantou County 552, Taiwan.
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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11
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Mays HL, Oehler DA, Morrison KW, Morales AE, Lycans A, Perdue J, Battley PF, Cherel Y, Chilvers BL, Crofts S, Demongin L, Fry WR, Hiscock J, Kusch A, Marin M, Poisbleau M, Quillfeldt P, Raya Rey A, Steinfurth A, Thompson DR, Weakley LA. Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi). J Hered 2020; 110:801-817. [PMID: 31737899 DOI: 10.1093/jhered/esz051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/10/2019] [Indexed: 01/05/2023] Open
Abstract
Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.
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Affiliation(s)
- Herman L Mays
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - David A Oehler
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | | | - Ariadna E Morales
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY
| | - Alyssa Lycans
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Justin Perdue
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Phil F Battley
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| | - B Louise Chilvers
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands
| | | | | | - Jo Hiscock
- Department of Conservation, Invercargill, New Zealand
| | - Alejandro Kusch
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | - Manuel Marin
- Feather Link, Inc., Cincinnati, OH.,Section of Ornithology, Natural History Museum of Los Angeles County, Los Angeles, CA
| | - Maud Poisbleau
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, Antwerp (Wilrijk), Belgium
| | - Petra Quillfeldt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Andrea Raya Rey
- National Scientific and Technical Research Council, Austral Center for Scientific Investigation, Ushuaia, Argentina.,Institute of Polar Science, National University of Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa.,RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Cambridge, UK
| | - David R Thompson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
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12
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Wang X, Wu W, Jian S. Transcriptome analysis of two radiated Cycas species and the subsequent species delimitation of the Cycas taiwaniana complex. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11292. [PMID: 31667020 PMCID: PMC6814181 DOI: 10.1002/aps3.11292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Cycas is an important gymnosperm genus, and the most diverse of all cycad genera. The C. taiwaniana complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources. METHODS We characterized the transcriptomes of two closely related and endangered Cycas species endemic to Hainan, China: C. hainanensis and C. changjiangensis. Three single-copy nuclear genes in the C. taiwaniana complex were sequenced based on these transcriptomes, enabling us to evaluate the species boundaries using the multispecies coalescent method implemented in the Bayesian Phylogenetics and Phylogeography program. RESULTS We obtained 68,184 and 81,561 unigenes for C. changjiangensis and C. hainanensis, respectively. We identified six positively selected genes that are mainly involved in stimulus responses, suggesting that environmental adaptation may have played an important role in the relatively recent divergence of these species. The similar K S distribution peaks at 1.0 observed for the paralogs in the two species indicate a common whole-genome duplication event. Our species delimitation analysis indicated that the C. taiwaniana complex consists of three distinct species, which correspond to the previously reported morphological differences. DISCUSSION Our study provides valuable genetic resources for Cycas species and guidance for the taxonomic treatment of the C. taiwaniana complex, as well as new insights into evolution of species within Cycas.
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Affiliation(s)
- Xin‐Hui Wang
- Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical GardenChinese Academy of SciencesGuangzhou510650People's Republic of China
- University of Chinese Academy of SciencesBeijing100040People's Republic of China
| | - Wei Wu
- Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical GardenChinese Academy of SciencesGuangzhou510650People's Republic of China
| | - Shu‐Guang Jian
- Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical GardenChinese Academy of SciencesGuangzhou510650People's Republic of China
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13
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Jirapatrasilp P, Backeljau T, Prasankok P, Chanabun R, Panha S. Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus). Mol Phylogenet Evol 2019; 139:106531. [PMID: 31185298 DOI: 10.1016/j.ympev.2019.106531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/19/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022]
Abstract
Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.
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Affiliation(s)
- Parin Jirapatrasilp
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Pongpun Prasankok
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agriculture Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon 47000, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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14
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Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko. Mol Phylogenet Evol 2019; 133:54-66. [DOI: 10.1016/j.ympev.2018.12.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/19/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022]
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15
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Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats. Mol Phylogenet Evol 2019; 132:219-231. [DOI: 10.1016/j.ympev.2018.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 12/09/2018] [Accepted: 12/09/2018] [Indexed: 12/15/2022]
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16
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Taxonomic status of Rhabdochona ictaluri (Nematoda: Rhabdochonidae) based on molecular and morphological evidence. Parasitol Res 2019; 118:441-452. [PMID: 30631928 DOI: 10.1007/s00436-018-6189-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
The genus Rhabdochona includes more than 100 species infecting freshwater fishes in all zoogeographical regions of the world. In Mexico, 12 nominal species of Rhabdochona have been recorded. Of these, Rhabdochona ictaluri was originally described as a parasite of endemic catfishes of the family Ictaluridae; however, the species was later considered on morphological grounds as a junior synonym of Rhabdochona kidderi. In this study, newly sampled specimens of R. ictaluri were obtained from the type host and type locality and were used to perform a detailed morphological analysis and molecular phylogenetic inferences through one mitochondrial and two nuclear genes; data were used in an integrative taxonomy context to test the taxonomic status of R. ictaluri. This approach proved to be very useful to confirm the validity of this species, and robust species limits were established between these two putative species considering morphology, molecular data, host association, and biogeography.
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17
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Zink RM, Vázquez-Miranda H. Species Limits and Phylogenomic Relationships of Darwin’s Finches Remain Unresolved: Potential Consequences of a Volatile Ecological Setting. Syst Biol 2018; 68:347-357. [DOI: 10.1093/sysbio/syy073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Affiliation(s)
- Robert M Zink
- School of Natural Resources
- School of Biological Sciences
- Nebraska State Museum, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Hernán Vázquez-Miranda
- School of Natural Resources
- Nebraska State Museum, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Colección Nacional de Aves (CNAV), Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04500, Mexico
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18
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Massó S, López-Pujol J, Vilatersana R. Reinterpretation of an endangered taxon based on integrative taxonomy: The case of Cynara baetica (Compositae). PLoS One 2018; 13:e0207094. [PMID: 30485285 PMCID: PMC6261557 DOI: 10.1371/journal.pone.0207094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
The Strait of Gibraltar, the gateway between the Atlantic Ocean and the Mediterranean Sea, has a convulsive geological history, with recurring closing and opening events since the late Miocene. As a consequence, this region has played a major role in the evolutionary history of many species. Cynara baetica (Compositae) is a diploid perennial herb distributed in both sides of this strait. It is currently subdivided into two subspecies: C. baetica subsp. baetica for the Spanish populations, and C. baetica subsp. maroccana for the Moroccan ones. Following three different approximations of species delimitation, including phylogenetic and population genetic analyses (based on three AFLP primer combinations and two intergenic spacers of cpDNA), ecological niche modeling (ENM) and morphological studies, this taxon is investigated and reinterpreted. The results obtained showed a clear genetic, morphological and ecological differentiation between the two taxa and the important role played by the Strait of Gibraltar as a geographical barrier. Based on this evidence, the current taxonomic treatment is modified (both taxa should recover their specific rank) and specific conservation guidelines are proposed for the newly delimited taxa.
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Affiliation(s)
- Sergi Massó
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
- BioC-GReB, Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
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19
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Zamudio-Beltrán LE, Hernández-Baños BE. Genetic and morphometric divergence in the Garnet-Throated Hummingbird Lamprolaima rhami (Aves: Trochilidae). PeerJ 2018; 6:e5733. [PMID: 30364579 PMCID: PMC6197039 DOI: 10.7717/peerj.5733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/12/2018] [Indexed: 12/28/2022] Open
Abstract
Cloud forests are one of the most endangered ecosystems in the Americas, as well as one of the richest in biological diversity in the world. The species inhabiting these forests are susceptible to environmental changes and characterized by high levels of geographic structure. The Garnet-Throated Hummingbird, Lamprolaima rhami, mainly inhabits cloud forests, but can also be found in other habitats. This species has a highly restricted distribution in Mesoamerica, and five disjunct regions have been delimited within the current geographic distribution of the species from Mexico to Honduras. According to variation in size and color, three subspecies have been described: L. r. rhami restricted to the Mexican highlands and Guatemala, L. r. occidentalis distributed in Guerrero (Mexico), and L. r. saturatior, distributed in the highlands from Honduras and El Salvador. We analyzed the levels of geographic structure in L. rhami and its taxonomic implications. We used mitochondrial and nuclear DNA to analyze genetic variation, demographic history, divergence times, reconstructed a multilocus phylogeny, and performed a species delimitation analyses. We also evaluated morphological variation in 208 specimens. We found high levels of genetic differentiation in three groups, and significant variation in morphological traits corresponding with the disjunct geographic populations. L. rhami presents population stability with the highest genetic variation explained by differences between populations. Divergence time estimates suggest that L. rhami split from its sister group around 10.55 million years ago, and the diversification of the complex was dated ca. 0.207 Mya. The hypotheses tested in the species delimitation analyses validated three independent lineages corresponding to three disjunct populations. This study provides evidence of genetic and/or morphometric differentiation between populations in the L. rhami complex where four separate evolutionary lineages are supported: (1) populations from the Sierra Madre Oriental and the highlands of Oaxaca (rhami), (2) populations from the highlands of Guerrero (occidentalis), (3) populations from the highlands of Chiapas and Guatemala (this is a non-previously proposed potential taxon: tacanensis), and (4) populations from the highlands of Honduras and El Salvador (saturatior). The main promoters of the geographic structure found in the L. rhami complex are likely the Isthmus of Tehuantepec as a geographic barrier, isolation by distance resulting from habitat fragmentation, and climatic conditions during the Pleistocene.
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Affiliation(s)
- Luz E Zamudio-Beltrán
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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20
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Wei C, Dong L, Li SH, Alström P, Liu Y, Xia C, Yao CT, Zhang Y. From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex. Mol Phylogenet Evol 2018; 131:219-227. [PMID: 30316948 DOI: 10.1016/j.ympev.2018.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/06/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.
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Affiliation(s)
- Chentao Wei
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-75007 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Biocontrol and Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Medium Altitude Experimental Station, Endemic Species Research Institute, Chichi, 15, Nantou 552, Taiwan, China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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21
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Martin P, Martinsson S, Wuillot J, Erséus C. Integrative species delimitation and phylogeny of the branchiate wormBranchiodrilus(Clitellata, Naididae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Patrick Martin
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny; Brussels Belgium
| | - Svante Martinsson
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
| | | | - Christer Erséus
- Department of Biological and Environmental Sciences; University of Gothenburg; Göteborg Sweden
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22
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Ramírez-Barrera SM, Hernández-Baños BE, Jaramillo-Correa JP, Klicka J. Deep divergence of Red-crowned Ant Tanager ( Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica. PeerJ 2018; 6:e5496. [PMID: 30225165 PMCID: PMC6139011 DOI: 10.7717/peerj.5496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/31/2018] [Indexed: 11/20/2022] Open
Abstract
Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.
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Affiliation(s)
- Sandra M Ramírez-Barrera
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Blanca E Hernández-Baños
- Departamento de Biología Evolutiva, Facultad de Ciencias, Museo de Zoología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Juan P Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seatle, WA, United States of America
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23
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Wu W, Ng WL, Yang JX, Li WM, Ge XJ. High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China. BMC PLANT BIOLOGY 2018; 18:194. [PMID: 30217175 PMCID: PMC6137913 DOI: 10.1186/s12870-018-1410-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown. RESULTS Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event. CONCLUSION Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Wei-Lun Ng
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jun-Xin Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wei-Ming Li
- Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650 China
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24
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Niu YT, Jabbour F, Barrett RL, Ye JF, Zhang ZZ, Lu KQ, Lu LM, Chen ZD. Combining complete chloroplast genome sequences with target loci data and morphology to resolve species limits in Triplostegia (Caprifoliaceae). Mol Phylogenet Evol 2018; 129:15-26. [PMID: 30026123 DOI: 10.1016/j.ympev.2018.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 02/04/2023]
Abstract
Species represent the most basic unit of taxonomy. As such, species delimitation represents a crucial issue for biodiversity conservation. Taxonomic practices were revolutionized in the last three decades due to the increasing availability of molecular phylogenetic data. The genus Triplostegia (Caprifoliaceae) traditionally consists of two species, T. glandulifera and T. grandiflora, distinguishable mainly based on quantitative morphological features. In this study, we sequenced nine chloroplast loci (i.e., accD, psbK-psbI, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-trnT, trnF-ndhJ, trnH-psbA, trnS-trnG) and one nuclear locus (ITS) of 16 individuals of Triplostegia representing the entire distribution range of both species recognized. Furthermore, we also obtained whole chloroplast sequences for 11 of the 16 individuals for which silica gel-dried leaves were available. Our phylogenetic analyses integrating chloroplast genome sequences and multiple loci data revealed that Triplostegia includes four main clades that largely match geography. Neither T. grandiflora nor T. glandulifera was recovered as monophyletic and no diagnosable differences in leaf, flower, and pollen traits were detected between the two species, indicating the need for a revised species circumscription within Triplostegia. Our study highlights the importance of combining data from different sources while defining species limits.
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Affiliation(s)
- Yan-Ting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Florian Jabbour
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National D'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, Paris 75005, France
| | - Russell L Barrett
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, Mrs Macquaries Road, Sydney 2000, New South Wales, Australia
| | - Jian-Fei Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhu-Zhi Zhang
- School of Life Sciences, Shandong University, Jinan 250100, China
| | - Kai-Qing Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Min Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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Noguerales V, Cordero PJ, Ortego J. Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers. Mol Ecol 2018; 27:1229-1244. [DOI: 10.1111/mec.14504] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/16/2017] [Accepted: 01/05/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - Joaquín Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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Freudenstein JV, Broe MB, Folk RA, Sinn BT. Biodiversity and the Species Concept-Lineages are not Enough. Syst Biol 2018; 66:644-656. [PMID: 27798406 DOI: 10.1093/sysbio/syw098] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 10/14/2016] [Indexed: 11/13/2022] Open
Abstract
The nature and definition of species continue to be matters of debate. Current views of species often focus on their nature as lineages-maximal reproductive communities through time. Whereas many authors point to the Evolutionary Species Concept as optimal, in its original form it stressed the ecological role of species as well as their history as lineages, but most recent authors have ignored the role aspect of the concept, making it difficult to apply unambiguously in a time-extended way. This trend has been exacerbated by the application of methods and concepts emphasizing the notion of monophyly, originally applied only at higher levels, to the level of individuals, as well as by the current emphasis on molecular data. Hence, some current authors recognize units that are no more than probable exclusive lineages as species. We argue that biodiversity is inherently a phenotypic concept and that role, as manifested in the organismal extended phenotype, is a necessary component of the species concept. Viewing species as historically connected populations with unique role brings together the temporal and phenotypic natures of species, providing a clear way to view species both in a time-limited and time-extended way. Doing so alleviates perceived issues with "paraphyletic species" and returns the focus of species to units that are most relevant for biodiversity.
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Affiliation(s)
- John V Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA
| | - Michael B Broe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA
| | - Ryan A Folk
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA.,Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Brandon T Sinn
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University Herbarium, 1315 Kinnear Road, Columbus, OH 43212, USA.,New York Botanical Garden, 2900 Southern Blvd., Bronx, NY 10458, USA
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Yu G, Rao D, Matsui M, Yang J. Coalescent-based delimitation outperforms distance-based methods for delineating less divergent species: the case of Kurixalus odontotarsus species group. Sci Rep 2017; 7:16124. [PMID: 29170403 PMCID: PMC5700917 DOI: 10.1038/s41598-017-16309-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/10/2017] [Indexed: 12/30/2022] Open
Abstract
Few empirical studies have compared coalescent-based methods to distance-based methods for delimitation of less divergent species. In this study, we used two coalescent-based (BFD and BPP) and two distance-based barcoding (ABGD and jMOTU) methods to delimit closely related species in the Kurixalus odontotarsus species group. Phylogenetic analyses revealed that the K. odontotarsus species group comprises 11 distinct maternal clades with strong support values. Based on the genetic and morphological evidences, we consider that species diversity in the K. odontotarsus species group was underestimated and the 11 clades represent 11 species, of which six are unnamed. The coalescent-based delimitations decisively supported the scenario of 11-species corresponding to the 11 clades. However, the distance-based ABGD only obtained 3-6 candidate species, which is not consistent with morphological evidence. These results indicate that BFD and BPP are more conservative than ABGD to false negatives (lumping). Method of fixed threshold (jMOTU) may obtain a resolution similar to that inferred by BFD and BPP, but it severely relies on subjective choice of the threshold and lacks statistical support. We consider that coalescent-based BFD and BPP approaches outperform distance-based methods for delineation of less divergent species.
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Affiliation(s)
- Guohua Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China
| | - Dingqi Rao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Kakyo-ku, Kyoto, 606-8501, Japan
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.
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Smith CH, Johnson NA, Pfeiffer JM, Gangloff MM. Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus). Mol Phylogenet Evol 2017; 119:50-62. [PMID: 29074460 DOI: 10.1016/j.ympev.2017.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
Abstract
Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.
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Affiliation(s)
- Chase H Smith
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL 32653, USA
| | - Nathan A Johnson
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - John M Pfeiffer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Michael M Gangloff
- Biology Department, Appalachian State University, Boone, NC 28608-2027, USA
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Hao G, Zhang C, AL-Shehbaz IA, Guo X, Bi H, Wang J, Liu J. Eutrema giganteum (Brassicaceae), a new species from Sichuan, southwest China. PHYTOKEYS 2017; 82:15-26. [PMID: 28794679 PMCID: PMC5546392 DOI: 10.3897/phytokeys.82.12329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
Eutrema giganteum (Brassicaceae), a new species from Hengduan Mountains in Sichuan Province, southwest China, is described, and its relationships to the closely related E. yunnanense is discussed based on morphological, cytological, and molecular data. It is similar morphologically to E. yunnanense but is readily distinguished by having robust (vs. slender), erect (vs. decumbent), and branched (vs. mostly simple), and rather tall stems (60-110 cm vs. 20-60 cm); curved (vs. straight), smooth (vs. torulose), and shorter fruit (5-8 mm vs. 8-15 mm); and fewer ovules per ovary (1-4 vs. 6-10). All examined individuals from different populations of E. giganteum clustered into a single clade sister to E. yunnanense in phylogenetic analyses using the combined nuclear ITS and plastid DNA datasets. Our cytological studies revealed that the chromosome number of E. giganteum is 2n = 44, with a genome size of 1160 (±8) Mb, while that of E. yunnanense is 2n = 28, with a genome size of 718 (±15) Mb. Multiple lines of evidence support the recognition of E. giganteum as a distinct species well differentiated from E. yunnanense.
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Affiliation(s)
- Guoqian Hao
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, P. R. China
| | - Changbing Zhang
- Sichuan Academy of Grassland Sciences, Chengdu 610065, P. R. China
| | | | - Xinyi Guo
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| | - Hao Bi
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| | - Junyin Wang
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, P. R. China
| | - Jianquan Liu
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
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Singh SP, Groeneveld JC, Al-Marzouqi A, Willows-Munro S. A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean. PeerJ 2017; 5:e3356. [PMID: 28560106 PMCID: PMC5446773 DOI: 10.7717/peerj.3356] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.
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Affiliation(s)
- Sohana P. Singh
- Oceanographic Research Institute, Durban, KwaZulu-Natal, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal, South Africa
| | - Johan C. Groeneveld
- Oceanographic Research Institute, Durban, KwaZulu-Natal, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal, South Africa
| | - Abdulaziz Al-Marzouqi
- Marine Science and Fisheries Centre, Ministry of Agriculture and Fisheries, Muscat, Oman
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal, South Africa
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31
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Willis SC. One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes. PLoS One 2017; 12:e0172349. [PMID: 28235096 PMCID: PMC5325279 DOI: 10.1371/journal.pone.0172349] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/03/2017] [Indexed: 11/18/2022] Open
Abstract
Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.
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Affiliation(s)
- Stuart C. Willis
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, United States of America
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32
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Barrowclough GF, Cracraft J, Klicka J, Zink RM. How Many Kinds of Birds Are There and Why Does It Matter? PLoS One 2016; 11:e0166307. [PMID: 27880775 PMCID: PMC5120813 DOI: 10.1371/journal.pone.0166307] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/23/2016] [Indexed: 12/30/2022] Open
Abstract
Estimates of global species diversity have varied widely, primarily based on variation in the numbers derived from different inventory methods of arthropods and other small invertebrates. Within vertebrates, current diversity metrics for fishes, amphibians, and reptiles are known to be poor estimators, whereas those for birds and mammals are often assumed to be relatively well established. We show that avian evolutionary diversity is significantly underestimated due to a taxonomic tradition not found in most other taxonomic groups. Using a sample of 200 species taken from a list of 9159 biological species determined primarily by morphological criteria, we applied a diagnostic, evolutionary species concept to a morphological and distributional data set that resulted in an estimate of 18,043 species of birds worldwide, with a 95% confidence interval of 15,845 to 20,470. In a second, independent analysis, we examined intraspecific genetic data from 437 traditional avian species, finding an average of 2.4 evolutionary units per species, which can be considered proxies for phylogenetic species. Comparing recent lists of species to that used in this study (based primarily on morphology) revealed that taxonomic changes in the past 25 years have led to an increase of only 9%, well below what our results predict. Therefore, our molecular and morphological results suggest that the current taxonomy of birds understimates avian species diversity by at least a factor of two. We suggest that a revised taxonomy that better captures avian species diversity will enhance the quantification and analysis of global patterns of diversity and distribution, as well as provide a more appropriate framework for understanding the evolutionary history of birds.
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Affiliation(s)
- George F. Barrowclough
- Department of Ornithology, American Museum of Natural History, New York, New York United States of America
- * E-mail:
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, New York United States of America
| | - John Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, United States of America
| | - Robert M. Zink
- School of Natural Resources, Nebraska State Museum, and School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
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Wang N, Liang B, Wang J, Yeh CF, Liu Y, Liu Y, Liang W, Yao CT, Li SH. Incipient speciation with gene flow on a continental island: Species delimitation of the Hainan Hwamei (Leucodioptron canorum owstoni, Passeriformes, Aves). Mol Phylogenet Evol 2016; 102:62-73. [PMID: 27233437 DOI: 10.1016/j.ympev.2016.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 04/26/2016] [Accepted: 05/20/2016] [Indexed: 01/11/2023]
Abstract
Because of their isolation, continental islands (e.g., Madagascar) are often thought of as ideal systems to study allopatric speciation. However, many such islands have been connected intermittently to their neighboring continent during recent periods of glaciation, which may cause frequent contact between the diverging populations on the island and continent. As a result, the speciation processes on continental islands may not meet the prerequisites for strictly allopatric speciation. We used multiple lines of evidence to re-evaluate the taxonomic status of the Hainan Hwamei (Leucodioptron canorum owstoni), which is endemic to Hainan, the largest continental island in the South China Sea. Our analysis of mitochondrial DNA and twelve nuclear loci suggests that the Hainan Hwamei can be regarded as an independent species (L. owstoni); the morphological traits of the Hainan Hwamei also showed significant divergence from those of their mainland sister taxon, the Chinese Hwamei (L. canorum). We also inferred the divergence history of the Hainan and Chinese Hwamei to see whether their divergence was consistent with a strictly allopatric model. Our results suggest that the two Hwameis split only 0.2 million years ago with limited asymmetrical post-divergence gene flow. This implies that the Hainan Hwamei is an incipient species and that speciation occurred through ecologically divergent selection and/or assortative mating rather than a strictly allopatric process.
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Affiliation(s)
- Ning Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bin Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jichao Wang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Chia-Fen Yeh
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Yang Liu
- State Key Laboratory of BioControl, College of Ecology and Evolution/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanlin Liu
- Institute of Forestry Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Cheng-Te Yao
- High-Altitude Experimental Station, Taiwan Endemic Species Research Institute, Chi-chi 55244, Taiwan
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan.
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Feng X, Liu J, Gong X. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data. FRONTIERS IN PLANT SCIENCE 2016; 7:134. [PMID: 26913044 PMCID: PMC4753401 DOI: 10.3389/fpls.2016.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 06/02/2023]
Abstract
The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective.
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Affiliation(s)
- Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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Huang JP, Knowles LL. The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles. Syst Biol 2015; 65:685-99. [PMID: 26681696 DOI: 10.1093/sysbio/syv119] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/10/2015] [Indexed: 11/13/2022] Open
Abstract
With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status.
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Affiliation(s)
- Jen-Pan Huang
- Department of Ecology and Evolutionary Biology, 1109 Geddes Avenue, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, 1109 Geddes Avenue, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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Pfeiffer III JM, Johnson NA, Randklev CR, Howells RG, Williams JD. Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896). CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0780-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Su X, Wu G, Li L, Liu J. Species delimitation in plants using the Qinghai-Tibet Plateau endemic Orinus (Poaceae: Tridentinae) as an example. ANNALS OF BOTANY 2015; 116:35-48. [PMID: 25987712 PMCID: PMC4479750 DOI: 10.1093/aob/mcv062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/27/2014] [Accepted: 03/31/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Accurate identification of species is essential for the majority of biological studies. However, defining species objectively and consistently remains a challenge, especially for plants distributed in remote regions where there is often a lack of sufficient previous specimens. In this study, multiple approaches and lines of evidence were used to determine species boundaries for plants occurring in the Qinghai-Tibet Plateau, using the genus Orinus (Poaceae) as a model system for an integrative approach to delimiting species. METHODS A total of 786 individuals from 102 populations of six previously recognized species were collected for niche, morphological and genetic analyses. Three plastid DNA regions (matK, rbcL and trnH-psbA) and one nuclear DNA region [internal transcribed space (ITS)] were sequenced. KEY RESULTS Whereas six species had been previously recognized, statistical analyses based on character variation, molecular data and niche differentiation identified only two well-delimited clusters, together with a third possibly originating from relatively recent hybridization between, or historical introgression from, the other two. CONCLUSIONS Based on a principle of integrative species delimitation to reconcile different sources of data, the results provide compelling evidence that the six previously recognized species of the genus Orinus that were examined should be reduced to two, with new circumscriptions, and a third, identified in this study, should be described as a new species. This empirical study highlights the value of applying genetic differentiation, morphometric statistics and ecological niche modelling in an integrative approach to re-circumscribing species boundaries. The results produce relatively objective, operational and unbiased taxonomic classifications of plants occurring in remote regions.
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Affiliation(s)
- Xu Su
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Guili Wu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Lili Li
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
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38
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Hedin M, Carlson D, Coyle F. Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia. Mol Ecol 2015; 24:3467-84. [PMID: 26011071 DOI: 10.1111/mec.13248] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 01/31/2023]
Abstract
Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic-scale data sets are gathered for taxa found in naturally fragmented habitats.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Dave Carlson
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
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39
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Zamudio-Beltrán LE, Hernández-Baños BE. A multilocus analysis provides evidence for more than one species within Eugenes fulgens (Aves: Trochilidae). Mol Phylogenet Evol 2015; 90:80-4. [PMID: 25982690 DOI: 10.1016/j.ympev.2015.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/19/2022]
Abstract
The status of subspecies in systematic zoology is the focus of controversy. Recent studies use DNA sequences to evaluate the status of subspecies within species complexes and to recognize and delimit species. Here, we assessed the phylogenetic relationships, the taxonomic status of the proposed subspecies, and the species limits of the monotypic hummingbird genus Eugenes (E. fulgens with traditionally recognized subspecies E. f. fulgens, E. f. viridiceps, and E. f. spectabilis), using nuclear (Beta Fibrinogen BFib, Ornithine Decarboxylase ODC, and Muscle Skeletal Receptor Tyrosine Kinase MUSK) and mitochondrial (NADH dehydrogenase subunit 2 ND2, NADH dehydrogenase subunit 4 ND4, and Control Region CR) markers. We performed Bayesian and Bayesian Phylogenetics and Phylogeography analyses and found genetic differences between the three groups, suggesting the existence of two cryptic species (E. fulgens and E. viridiceps) and one phenotypically differentiated species (E. spectabilis). Our analyses show that the E. viridiceps and E. fulgens groups are more closely related with one another than with E. spectabilis.
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Affiliation(s)
- Luz E Zamudio-Beltrán
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, México, D.F., Mexico.
| | - Blanca E Hernández-Baños
- Museo de Zoología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, México, D.F., Mexico.
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40
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Solís-Lemus C, Knowles LL, Ané C. Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution 2015; 69:492-507. [DOI: 10.1111/evo.12582] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 11/17/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Claudia Solís-Lemus
- Department of Statistics; University of Wisconsin; 1300 University Avenue Madison Wisconsin 53706
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology; University of Michigan; 1109 Geddes Ave Ann Arbor Michigan 48109
| | - Cécile Ané
- Department of Statistics; University of Wisconsin; 1300 University Avenue Madison Wisconsin 53706
- Department of Botany; University of Wisconsin; 430 Lincoln Drive Madison Wisconsin 53706
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41
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Pedraza-Lara C, Barrientos-Lozano L, Rocha-Sánchez AY, Zaldívar-Riverón A. Montane and coastal species diversification in the economically important Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae). Mol Phylogenet Evol 2015; 84:220-31. [PMID: 25593084 DOI: 10.1016/j.ympev.2015.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 12/31/2014] [Accepted: 01/02/2015] [Indexed: 01/31/2023]
Abstract
The genus Sphenarium (Pyrgomorphidae) is a small group of grasshoppers endemic to México and Guatemala that are economically and culturally important both as a food source and as agricultural pests. However, its taxonomy has been largely neglected mainly due to its conserved interspecific external morphology and the considerable intraspecific variation in colour pattern of some taxa. Here we examined morphological as well as mitochondrial and nuclear DNA sequence data to assess the species boundaries and evolutionary history in Sphenarium. Our morphological identification and DNA sequence-based species delimitation, carried out with three different approaches (DNA barcoding, general mixed Yule-coalescent model, Bayesian species delimitation), all recovered a higher number of putative species of Sphenarium than previously recognised. We unambiguously delimit seven species, and between five and ten additional species depending on the data/method analysed. Phylogenetic relationships within the genus strongly support two main clades, one exclusively montane, the other coastal. Divergence time estimates suggest late Miocene to Pliocene ages for the origin and most of the early diversification events in the genus, which were probably influenced by the formation of the Trans-Mexican Volcanic Belt. A series of Pleistocene events could have led to the current species diversification in both montane and coastal regions. This study not only reveals an overlooked species richness for the most popular edible insect in Mexico, but also highlights the influence of the dynamic geological and climatic history of the region in shaping its current diversity.
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Affiliation(s)
- Carlos Pedraza-Lara
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito exterior s/n Cd. Universitaria, Copilco, Coyoacán, A.P. 70-233, C.P. 04510, D.F., México, Mexico
| | - Ludivina Barrientos-Lozano
- Instituto Tecnológico de Cd. Victoria, Blvd. Emilio Portes Gil No. 1301, C.P. 87010, Ciudad Victoria, Tamaulipas, Mexico
| | - Aurora Y Rocha-Sánchez
- Instituto Tecnológico de Cd. Victoria, Blvd. Emilio Portes Gil No. 1301, C.P. 87010, Ciudad Victoria, Tamaulipas, Mexico
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. Circuito exterior s/n Cd. Universitaria, Copilco, Coyoacán, A.P. 70-233, C.P. 04510, D.F., México, Mexico.
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42
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Hedin M. High-stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas. Mol Ecol 2015; 24:346-61. [PMID: 25492722 DOI: 10.1111/mec.13036] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 01/26/2023]
Abstract
A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is 'high-stakes'- it is imperative that species hypotheses are data rich, objective, and robust. This study focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial and nuclear DNA sequence data evidence, analysed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
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43
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Reddy S, Sharief S, Yohe LR, Witkowski J, Hosner PA, Nyári ÁS, Moyle RG. Untangling taxonomic confusion and diversification patterns of the Streak-breasted Scimitar Babblers (Timaliidae: Pomatorhinus ruficollis complex) in southern Asia. Mol Phylogenet Evol 2014; 82 Pt A:183-92. [PMID: 25450499 DOI: 10.1016/j.ympev.2014.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/07/2014] [Accepted: 10/17/2014] [Indexed: 11/18/2022]
Abstract
Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa - P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a 'suture' zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The 'suture' zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.
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Affiliation(s)
- Sushma Reddy
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Sarah Sharief
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Laurel R Yohe
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA; Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Julie Witkowski
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA.
| | - Peter A Hosner
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
| | - Árpád S Nyári
- Biology Department, Loyola University Chicago, 1050 W Sheridan Road, Chicago, IL 60660, USA; Department of Zoology, Oklahoma State University, 501 Life Sciences West, Stillwater, OK 74078, USA.
| | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA.
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Hung CM, Hung HY, Yeh CF, Fu YQ, Chen D, Lei F, Yao CT, Yao CJ, Yang XJ, Lai YT, Li SH. Species delimitation in the Chinese bamboo partridgeBambusicola thoracica(Phasianidae; Aves). ZOOL SCR 2014. [DOI: 10.1111/zsc.12071] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chih-Ming Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Hsin-Yi Hung
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Chia-Fen Yeh
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Yi-Qiang Fu
- College of Life Science; Leshan Normal University; Leshan 614000 China
| | - De Chen
- Department of Life Science; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng-Te Yao
- Division of Zoology; Endemic Species Research Institute; Chi-chi Nantou 55244 Taiwan
| | - Chiou-Ju Yao
- Department of Biology; National Museum of Natural Science; Taichung 40453 Taiwan
| | - Xiao-Jun Yang
- Kunming Institute Zoology; Chinese Academy of Sciences; Kunming Yunnan China
| | - Yu-Ting Lai
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 11677 Taiwan
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45
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Ren Q, Yuan J, Zhu X, Wang P, Zhang L, Jiang L, Kan X. Complete mitochondrial genome of a Light-vented Bulbul subspecies,Pycnonotus sinensis hainanus(Passeriformes: Pycnonotidae). ACTA ACUST UNITED AC 2014; 27:375-7. [DOI: 10.3109/19401736.2014.895993] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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46
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McKay BD, Mays HL, Yao CT, Wan D, Higuchi H, Nishiumi I. Incorporating Color into Integrative Taxonomy: Analysis of the Varied Tit (Sittiparus varius) Complex in East Asia. Syst Biol 2014; 63:505-17. [DOI: 10.1093/sysbio/syu016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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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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48
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Li Q, Liu Z. New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): genome description and phylogenetic performance. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:163-4. [PMID: 24450717 DOI: 10.3109/19401736.2013.878925] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A new complete sequence of mitochondrial genome of Odontobutis potamophila has been reported. It was 16,843 bp and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Except for 8 tRNA and ND6 genes, all other mitochondrial genes were encoded on the heavy strand. Phylogenetic comparison proved that ND4, ND5 and ND6 genes might be dependable "leading" indicators of lineage divergence in Odontobutis obscurus. Also, COII, ND5 and cytb genes are useful in examining intraspecific population genetic diversity.
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Affiliation(s)
- Qiang Li
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai 201306 , P.R. China
| | - Zhizhi Liu
- a Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Shanghai Ocean University, Ministry of Education , Shanghai 201306 , P.R. China
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