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Yuan Z, Wu D, Wen Y, Xu W, Gao W, Dahn HA, Liu X, Jin J, Yu C, Xiao H, Che J. Historical mitochondrial genome introgression confounds species delimitation: Evidence from phylogenetic inference in the odorrana grahami species complex. Curr Zool 2022; 69:82-90. [PMID: 36974146 PMCID: PMC10039181 DOI: 10.1093/cz/zoac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/11/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated two clades, with O. grahami and O. junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.
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Affiliation(s)
- Zhiyong Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Dongyi Wu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Yang Wen
- School of Life Sciences, Yunnan University, Kunming, 650091, China
- School of Ecology and Environment Sciences, Yunnan University, Kunming, 650091, China
| | - Wei Xu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Xiaolong Liu
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming, 650224, China
| | - Jieqiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Chuanxin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Heng Xiao
- School of Ecology and Environment Sciences, Yunnan University, Kunming, 650091, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
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2
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Lu B, Jin H, Fu J. Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region. BMC Genomics 2020; 21:839. [PMID: 33246413 PMCID: PMC7694343 DOI: 10.1186/s12864-020-07269-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. RESULTS Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar's test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3-32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. CONCLUSIONS There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hong Jin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China. .,Department of Integrative Biology, University of Guelph, Guelph, Canada.
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3
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Mao X, Rossiter SJ. Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis). Mol Phylogenet Evol 2020; 150:106886. [PMID: 32534185 DOI: 10.1016/j.ympev.2020.106886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.
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Affiliation(s)
- Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, China.
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
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McEntee JP, Burleigh JG, Singhal S. Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation. Am Nat 2020; 196:9-28. [PMID: 32552108 DOI: 10.1086/709109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.
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5
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Beugin M, Salvador O, Leblanc G, Queney G, Natoli E, Pontier D. Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France. Ecol Evol 2020; 10:263-276. [PMID: 31988727 PMCID: PMC6972816 DOI: 10.1002/ece3.5892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 11/30/2022] Open
Abstract
European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the subspecies and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization remain largely unknown. In France, wildcats are mainly present in the northeast and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the northeastern wildcat population. The two wildcat populations were significantly differentiated (F ST = 0.072) to an extent close to what has been reported (F ST = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.
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Affiliation(s)
- Marie‐Pauline Beugin
- Laboratoire de Biométrie et Biologie Evolutive UMR5558CNRSUniv LyonUniversité Lyon 1VilleurbanneFrance
- Animal Genomics LaboratoryANTAGENELa tour de SalvagnyFrance
| | - Olivier Salvador
- Réserve naturelle nationale de Jujols et de NohèdesRéserves Naturelles CatalanesPradesFrance
| | | | | | | | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive UMR5558CNRSUniv LyonUniversité Lyon 1VilleurbanneFrance
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6
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Gene Introgression among Closely Related Species in Sympatric Populations: A Case Study of Three Walnut (Juglans) Species. FORESTS 2019. [DOI: 10.3390/f10110965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Gene introgression usually results from natural hybridization occurring among closely related species in sympatric populations. In this study, we discussed two rare and frequent gene flow phenomena between three species of Juglans plants and analyzed the possible causes for the difference. We collected 656 individuals from 40 populations of Persian walnut (Juglans regia L.), Chinese walnut (J. cathayensis Dode), and Iron walnut (J. sigillata Dode) that were genotyped at 17 expressed sequence tag simple sequence repeat (EST-SSR) loci to analyze the introgressions between J. regia and J. cathayensis, and J. regia and J. sigillata. Our study compared the spatial patterns of expected heterozygosity (HE), allelic richness (Rs), and private allele richness (PAR) so as to vividly infer the biogeographic history of related species of Juglans in the two regions. The results of the PCoA, UPGMA, and STRUCTURE analyses showed that all J. regia and J. sigillata populations clustered into one group, and the J. cathayensis populations clustered into the other group. The results of the historical gene flow analysis indicated that J. regia and J. sigillata have no genetic barriers, and the directional gene flow is mainly from J. regia to J. sigillata. For the three species of Juglans, all the above results indicated that gene flow was common among the same group of Juglans, and only rare and low-level gene flow appeared in distinct groups. Therefore, our study revealed multiple phenomena of gene flow and introgression among closely related species in sympatric populations, thereby providing a theoretical basis for the genetic evolution of the genus Juglans.
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7
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Atlas JE, Fu J. Isolation by resistance analysis reveals major barrier effect imposed by the Tsinling Mountains on the Chinese wood frog. J Zool (1987) 2019. [DOI: 10.1111/jzo.12702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. E. Atlas
- Department of Integrative Biology University of Guelph Guelph Ontario Canada
| | - J. Fu
- Department of Integrative Biology University of Guelph Guelph Ontario Canada
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8
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Traditional Uses, Bioactive Constituents, Biological Functions, and Safety Properties of Oviductus ranae as Functional Foods in China. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:4739450. [PMID: 31281578 PMCID: PMC6589215 DOI: 10.1155/2019/4739450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/16/2019] [Indexed: 11/23/2022]
Abstract
Oviductus ranae is an animal-based traditional Chinese material widely used as tonics in China for hundreds of years. Various bioactive components are present in OR including proteins, amino acids, steroids, fatty acids, phospholipids, nucleosides, vitamins, hydantoins, and mineral elements. These constituents exert a myriad of biological functions such as immunomodulatory, antioxidant, antifatigue, antiaging, estrogen-like, hepatoprotective, hypolipidemic, antiosteoporotic, antidepressant, antitumor, antitussive, expectorant, anti-inflammatory, and antiasthmatic activities. Unlike other traditional Chinese crude drugs recorded in Chinese Pharmacopoeia, OR is seldom prescribed as medicine but often consumed as nutraceuticals to optimize health. In this review, the traditional uses, bioactive constituents, biological functions, and safety properties of OR as functional foods in China were summarized and discussed. It is expected that this review will provide useful information for anyone who is interested in OR.
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9
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Acute Toxicity, Antioxidant, and Antifatigue Activities of Protein-Rich Extract from Oviductus ranae. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:9021371. [PMID: 29991975 PMCID: PMC5845489 DOI: 10.1155/2018/9021371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/09/2018] [Accepted: 01/16/2018] [Indexed: 12/16/2022]
Abstract
The paper investigated the preparation, amino acid composition, acute toxicity, and in vitro and in vivo antioxidant, coupled with in vivo antifatigue activities of protein-rich extract of Oviductus ranae (PEOR). The results indicated that PEOR possesses high-safety property with maximum tolerated dose (MTD) higher than 20 g/kg in mice, shows weak scavenging capacities against hydroxyl, superoxide anion, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals, as well as ferric-reducing antioxidant power in vitro, but exerts strong antioxidant effect in ethanol-induced oxidative stress mice model; it can decrease malonaldehyde (MDA) and protein carbonyl (PCO) formation and increase total superoxide dismutase (T-SOD) activity and glutathione (GSH) synthesis. Besides the strong in vivo antioxidant activity, PEOR in a dose of 400 mg/kg also has antifatigue effect in mice, and it can prolong the exhaustive swimming time, reduce the elevated blood urea nitrogen (BUN) and blood lactic acid (BLA) caused by intense exercise. The in vivo activity of PEOR may be contributed by its absorbed amino acids, due to the fact that eight antioxidant amino acids and twelve glucogenic ones were found in it. This study will provide an evidence for the clinical use of PEOR as a dietary supplement for antioxidant and antifatigue in the same oral dose (400 mg/kg).
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10
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A novel multilocus phylogenetic estimation reveals unrecognized diversity in Asian horned toads, genus Megophrys sensu lato (Anura: Megophryidae). Mol Phylogenet Evol 2017; 106:28-43. [DOI: 10.1016/j.ympev.2016.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/18/2022]
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11
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Zhou H, Jiang Y, Nie L, Yin H, Li H, Dong X, Zhao F, Zhang H, Pu Y, Huang Z, Song J, Sun E. The Historical Speciation of Mauremys Sensu Lato: Ancestral Area Reconstruction and Interspecific Gene Flow Level Assessment Provide New Insights. PLoS One 2015; 10:e0144711. [PMID: 26657158 PMCID: PMC4678219 DOI: 10.1371/journal.pone.0144711] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022] Open
Abstract
Mauremys sensu lato was divided into Mauremys, Chinemys, Ocadia, and Annamemys based on earlier research on morphology. Phylogenetic research on this group has been controversial because of disagreements regarding taxonomy, and the historical speciation is still poorly understood. In this study, 32 individuals of eight species that are widely distributed in Eurasia were collected. The complete mitochondrial (mt) sequences of 14 individuals of eight species were sequenced. Phylogenetic relationships, interspecific divergence times, and ancestral area reconstructions were explored using mt genome data (10,854 bp). Subsequent interspecific gene flow level assessment was performed using five unlinked polymorphic microsatellite loci. The Bayesian and maximum likelihood analyses revealed a paraphyletic relationship among four old genera (Mauremys, Annamemys, Chinemys, and Ocadia) and suggested the four old genera should be merged into the genus (Mauremys). Ancestral area reconstruction and divergence time estimation suggested Southeast Asia may be the area of origin for the common ancestral species of this genus and genetic drift may have played a decisive role in species divergence due to the isolated event of a glacial age. However, M. japonica may have been speciated due to the creation of the island of Japan. The detection of extensive gene flow suggested no vicariance occurred between Asia and Southeast Asia. Inconsistent results between gene flow assessment and phylogenetic analysis revealed the hybrid origin of M. mutica (Southeast Asian). Here ancestral area reconstruction and interspecific gene flow level assessment were first used to explore species origins and evolution of Mauremys sensu lato, which provided new insights on this genus.
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Affiliation(s)
- Huaxing Zhou
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Yuan Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liuwang Nie
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Huazong Yin
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Haifeng Li
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Xianmei Dong
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Feifei Zhao
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Huanhuan Zhang
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China.,Life Science College, Anhui Normal University, Wuhu, China
| | - Youguang Pu
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Zhenfeng Huang
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Jiaolian Song
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui, China
| | - Entao Sun
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
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12
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Langone JA, Camargo A, de Sá RO. High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America. Mol Phylogenet Evol 2015; 95:137-51. [PMID: 26639101 DOI: 10.1016/j.ympev.2015.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 11/03/2015] [Accepted: 11/07/2015] [Indexed: 11/16/2022]
Abstract
Relative to South America's ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is a small-size species (<20mm) with extensive coloration and morphological variation, we suspected that it might represent a complex of cryptic species. In addition, we expected strong genetic and geographic structuring within Pseudopaludicola falcipes due to its large geographic distribution, potentially short dispersal distances, and multiple riverine barriers. We found that P. falcipes is a single evolutionary lineage with poor geographic structuring. Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow. We conclude that the demographic history of P. falcipes, combined with its ecological attributes and the landscape features of the Pampas, favored a unique combination among anurans of small body size, large population size, high genetic variability, but high cohesiveness of populations over a wide geographic distribution.
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Affiliation(s)
- José A Langone
- Sección Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, Código Postal 11.000, Montevideo, Uruguay.
| | - Arley Camargo
- Programa de Desarrollo Universitario, Centro Universitario de Rivera, Universidad de la República. Ituzaingó 667, Código Postal 40.000, Rivera, Uruguay.
| | - Rafael O de Sá
- Sección Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, Código Postal 11.000, Montevideo, Uruguay; Department of Biology, University of Richmond, Richmond, VA 23173, USA.
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13
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Cimmaruta R, Lucente D, Nascetti G. Persistence, isolation and diversification of a naturally fragmented species in local refugia: the case of Hydromantes strinatii. PLoS One 2015; 10:e0131298. [PMID: 26107249 PMCID: PMC4479377 DOI: 10.1371/journal.pone.0131298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 06/01/2015] [Indexed: 11/19/2022] Open
Abstract
The study of the European plethodontid salamander Hydromantes strinatii using allozyme and mitochondrial markers showed a strong geographical genetic structure. This was likely the outcome of different evolutionary mechanisms leaving their signature despite the effects of the genetic drift due to the low population size typical of this species. Two highly divergent clades were identified in the eastern and central-western part of the range, with further geographic sub-structure. Nuclear and mitochondrial markers substantially recovered the same population groups but were conflicting in reconstructing their relationships. This apparent incongruence highlighted the action of different mechanisms such as secondary contacts and incomplete lineage sorting in originating the observed genetic variation. The troglophilic habit of this species provided the opportunity to show the importance of caves as local refugia in maintaining the genetic diversity through the persistence of local populations. Accordingly, high nucleotide and haplotype diversity, strong geographic genetic structuring and lack of expansion were evidenced. This signature was found in the populations from the Ligurian and Maritime Alps, in agreement with the complex orography and paleoclimatic history of this Mediterranean hotspot.
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Affiliation(s)
- Roberta Cimmaruta
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
- * E-mail:
| | - Daniela Lucente
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
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14
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Liu Q, Zhu F, Zhong G, Wang Y, Fang M, Xiao R, Cai Y, Guo P. COI-based barcoding of Chinese vipers (Reptilia: Squamata: Viperidae). AMPHIBIA-REPTILIA 2015. [DOI: 10.1163/15685381-00003012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
DNA barcoding seeks to assemble a standardized reference library for rapid and unambiguous identification of species, and can be used to screen for potentially cryptic species. The 5′ region of cytochrome oxidase subunit I (COI), which is a mitochondrial DNA (mtDNA) gene fragment, has been proposed as a universal marker for this purpose among animals. However, DNA barcoding of reptiles is still supported only by few datasets compared with other groups. We investigated the utilization of COI to discriminate 34 putative species of vipers, representing almost 92% of the recorded species in China. Based on a total of 241 sequences, our results indicated that the average degree of intraspecific variability (0.0198) tends to be one-sixth the average of interspecific divergence (0.0931), but no barcoding gap was detected between them. The threshold method, BLOG analyses and tree-based methods all can identify species with a high success rate. These results consistently suggested the usefulness and reliability of the DNA barcoding approach in Chinese vipers.
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Affiliation(s)
- Qin Liu
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Fei Zhu
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Guanghui Zhong
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
- College of Tourism and Urban-Rural Planning, Chengdu University of Technology, Chengdu 610059, China
| | - Yunyu Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Min Fang
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
| | - Rong Xiao
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
| | - Yansen Cai
- Department of Medical Biology and Genetics, Luzhou Medical College, Luzhou, 646000, China
| | - Peng Guo
- College of Life Sciences and Food Engineering, Yibin University, Yibin 644007, China
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