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Huang J, Zhang D, Yang S, Liu Y, Ma J, Zhou M, Tan Y, Song Y. Genomic insights and phylogenetics of the mitochondrial genome of Cryptocarya. Genomics 2025; 117:111018. [PMID: 39993545 DOI: 10.1016/j.ygeno.2025.111018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 02/14/2025] [Accepted: 02/19/2025] [Indexed: 02/26/2025]
Abstract
The tropical genus Cryptocarya is known for its valuable timber and the constituents in these trees show potential for medicinal properties. However, the phylogenetic relationships among species in Asia remain unclear. Here, we report the first mitochondrial genome for Cryptocarya kwangtungensis, consisting of 758,020 bp, including 43 protein-coding genes, 23 tRNA genes and three rRNA genes, with 234 simple sequence repeats, and 1275 dispersed repeats, 35 homologous DNA fragments between the mitogenome and the plastome. Comparative genomic analysis indicated frequent recombination events among the sequences of five magnoliids mitogenomes and only five conserved clustered genes. Further phylogenetic analyses based on 91 mitochondrial regions and nuclear ribosomal cistron sequences of 21 species compound three well-resolved congruent groups for the Cryptocarya species in Asia, both of which support the genus divide into three clades, suggesting that the mitogenome sequence can provide strongly supported relationships within the genus in the family Lauraceae.
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Affiliation(s)
- Jiepeng Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Di Zhang
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Shiting Yang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Yanyu Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Jurong Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Maojuan Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, Guangxi 541004, China
| | - Yunhong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China.
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) and University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi Normal University, Guilin, Guangxi 541004, China.
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2
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Probst T, Frandsen PB, Whiting A. Chasing the Rainbow: Decoupled phenotypic and genotypic evolution in New Guinea's rainbow skinks (Squamata: Scincidae). Zootaxa 2025; 5583:309-327. [PMID: 40174111 DOI: 10.11646/zootaxa.5583.2.5] [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: 01/29/2025] [Indexed: 04/04/2025]
Abstract
With the advent of molecular data, the discovery of cryptic species has become commonplace. New Guinea, a region of high vertebrate biodiversity and complex geological history, has been found to contain immense numbers of cryptic skink species. We present the first molecular phylogenetic analysis of Carlia Gray, 1845, and its sister genus Lygisaurus de Vis, 1884, across mainland New Guinea and the Solomon Islands. We find rainbow skinks exhibit significant genetic divergence with minimal morphological variation and our data suggest the existence of many undescribed species. Due to the morphologically cryptic nature of rainbow skinks, we demonstrate the efficacy of the COI gene as a "barcode" for difficult species determinations. Divergence time and biogeographic analyses support four separate dispersal events from Australia to New Guinea for rainbow skinks from ~10-5 mya, with most groups arriving first in the East Papua Composite Terrane (EPCT) and dispersing from there to other terranes and islands. Exceptions to this pattern were observed in Lygisaurus, which dispersed first to the West Papuan portion of the Craton ~8.4mya, and the island clade of the Carlia fusca group, which dispersed to the Vogelkop peninsula ~4.7mya and from there to many islands.
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Affiliation(s)
- Taylor Probst
- Department of Biology and Life Science Museum; Brigham Young University; Provo UT. 84602.
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences; Brigham young University; Provo UT 84602.
| | - Alison Whiting
- Department of Biology and Life Science Museum; Brigham Young University; Provo UT. 84602.
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3
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Tiatragul S, Skeels A, Keogh JS. Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes. Evolution 2024; 78:1854-1868. [PMID: 39283595 DOI: 10.1093/evolut/qpae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 09/05/2024] [Accepted: 09/11/2024] [Indexed: 10/30/2024]
Abstract
Understanding how continental radiations are assembled across space and time is a major question in macroevolutionary biology. Here, we use a phylogenomic-scale phylogeny, a comprehensive morphological dataset, and environmental niche models to evaluate the relationship between trait and environment and assess the role of geography and niche conservatism in the continental radiation of Australian blindsnakes. The Australo-Papuan blindsnake genus, Anilios, comprises 47 described species of which 46 are endemic to and distributed across various biomes on continental Australia. Although we expected blindsnakes to be morphologically conserved, we found considerable interspecific variation in all morphological traits we measured. Absolute body length is negatively correlated with mean annual temperature, and body shape ratios are negatively correlated with soil compactness. We found that morphologically similar species are likely not a result of ecological convergence. Age-overlap correlation tests revealed niche similarity decreased with the relative age of speciation events. We also found low geographical overlap across the phylogeny, suggesting that speciation is largely allopatric with low rates of secondary range overlap. Our study offers insights into the eco-morphological evolution of blindsnakes and the potential for phylogenetic niche conservatism to influence continental scale radiations.
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Affiliation(s)
- Sarin Tiatragul
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Alexander Skeels
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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4
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Heine HLA, Derkarabetian S, Morisawa R, Fu PA, Moyes NHW, Boyer SL. Machine learning approaches delimit cryptic taxa in a previously intractable species complex. Mol Phylogenet Evol 2024; 195:108061. [PMID: 38485107 DOI: 10.1016/j.ympev.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024]
Abstract
Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.
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Affiliation(s)
- Haley L A Heine
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Rina Morisawa
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Phoebe A Fu
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Nathaniel H W Moyes
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Sarah L Boyer
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
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5
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Lin H, Li W, Zhao Y. A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data. PLANTS (BASEL, SWITZERLAND) 2024; 13:1296. [PMID: 38794366 PMCID: PMC11124813 DOI: 10.3390/plants13101296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an Fst of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an Fst value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.
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Affiliation(s)
- Hanyang Lin
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China;
| | - Wenhao Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yunpeng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
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6
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Meneses CG, Pitogo KME, Supsup CE, Brown RM. Philippine herpetology (Amphibia, Reptilia), 20 years on: two decades of progress towards an increasingly collaborative, equitable, and inclusive approach to the study of the archipelago's amphibians and reptiles. Zookeys 2024; 1190:213-257. [PMID: 38327266 PMCID: PMC10848817 DOI: 10.3897/zookeys.1190.109586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024] Open
Abstract
A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized the diverse topics studied and highlighted the development and achievements in research up to the year 2000. This study revisits and re-assesses what Philippine herpetology has accomplished, both as a discipline and a community, during the last two decades (2002-2022). A total of 423 herpetological publications was collated, revealing a substantial increase in annual publications, rising from approximately four per year during 2002-2008 to around 28 per year in 2009-2022. Half of the published studies focused on squamate reptiles (lizards 30.5%, snakes 21%) and 28.4% on amphibians, 5.9% on turtles, and 2.6% on crocodiles. The remaining 11.6% of studies focused simultaneously on multiple taxa (i.e., faunal inventories). Diversity and distribution (35.2%) and ecological (26.5%) studies remained popular, while studies on taxonomy (14.9%), phylogenetics and biogeography (11.8%), and conservation (11.6%) all increased. However, geographical gaps persist urging immediate surveys in many understudied regions of the country. Finally, we found a balanced representation between Filipino and foreign first authors (1.0:1.1), yet a substantial gender gap exists between male and female first authors (7.1:1.0). Nonetheless, the steep increase in publications and the diversity of people engaged in Philippine herpetology is a remarkable positive finding compared to the 20 years preceding the last review (1980-2000). Our hope is that the next decades will bring increasingly equitable, internationally collaborative, and broadly inclusive engagement in the study of amphibians and reptiles in the Philippines.
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Affiliation(s)
- Camila G. Meneses
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Kier Mitchel E. Pitogo
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Christian E. Supsup
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USAUniversity of KansasLawrenceUnited States of America
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7
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Khan M, Joshi M, Espeland M, Huemer P, Lopez-Vaamonde C, Mutanen M. Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture. Mol Ecol 2024; 33:e17194. [PMID: 37933590 DOI: 10.1111/mec.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.
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Affiliation(s)
- Maria Khan
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mukta Joshi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Hall, Austria
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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8
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Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
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Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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Ador K, Gobilik J, Benedick S. Phylogenetic and Morphological Characteristics Reveal Cryptic Speciation in Stingless Bee, Tetragonula laeviceps s.l. Smith 1857 (Hymenoptera; Meliponinae). INSECTS 2023; 14:insects14050438. [PMID: 37233066 DOI: 10.3390/insects14050438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/27/2023]
Abstract
Tetragonula laeviceps sensu lato (s.l.) Smith 1857 has the most complicated nomenclatural history among the Tetragonula genera. The objective of this study was to investigate whether T. laeviceps s.l. individuals with worker bees are grouped in the same or nearly the same morphological characteristics and have similar COI haplotype cluster groups. A total of 147 worker bees of T. laeviceps s.l. were collected from six sampling sites in Sabah (RDC, Tuaran, Kota Marudu, Putatan, Kinarut and Faculty of Sustainable Agriculture (FSA)), but only 36 were selected for further studies. These specimens were first classified according to the most obvious morphological characteristics, i.e., hind tibia color, hind basitarsus color and body size. Group identification was based on morphological characteristics important for distinguishing the four groups within T. laeviceps s.l. The four groups of T. laeviceps s.l. had significantly different body trait measurements for the TL (total length), HW (head width), HL (head length), CEL (compound eye length), CEW (compound eye width), FWLT (forewing length, including tegula), FWW (forewing width), FWL (forewing length), ML (mesoscutum length), MW (mesoscutum width), SW (mesoscutellum width), SL (mesoscutellum length), HTL = (hind tibia length), HTW (hind tibia width), HBL (hind basitarsus length) and HBW (hind basitarsus width) (p < 0.001). Body color included HC (head color), CC (clypeus color), ASC (antennae scape color), CFPP (Clypeus and frons plumose pubescence), HTC (hind tibia color), BSC (basitarsus color), SP (leg setae pubescence), SP (Thorax mesoscutellum pubescence), SPL (thorax mesoscutellum pubescence length) and TC (thorax color) (p < 0.05). The most distinctive features of the morphological and morphometric characteristics measured by PCA and LDA biplot that distinguish Group 1 (TL6-1, TL6-2 and TL6-3) from the other groups were the yellowish-brown ASC and the dark brown TC. Group 2 (haplotypes TL2-1, TL2-2 and TL2-3 and TL4-1, TL4-2 and TL4-3) had a dark brown ASC and a black TC, while Group 3 (haplotypes TL11-1, TL11-2 and TL11-3) had a blackish-brown ASC, a black TC and the largest TL, FWW and FWL. As for phylogenetic relationships, 12 out of 36 haplotypes showed clear separation with good bootstrap values (97-100%). The rest of the haplotypes did not show clear differentiation between subclades that belonged together, regardless of their morphology and morphometric characteristics. This suggests that the combination of DNA barcoding for species identification and phylogenetic analysis, as well as traditional methods based on morphological grouping by body size and body color, can be reliably used to determine intraspecific variations within T. laeviceps s.l.
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Affiliation(s)
- Kimberly Ador
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Locked Bag No. 3, Sandakan 90509, Malaysia
| | - Januarius Gobilik
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Locked Bag No. 3, Sandakan 90509, Malaysia
| | - Suzan Benedick
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, Locked Bag No. 3, Sandakan 90509, Malaysia
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10
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Gene drive in species complexes: defining target organisms. Trends Biotechnol 2023; 41:154-164. [PMID: 35868886 DOI: 10.1016/j.tibtech.2022.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 01/24/2023]
Abstract
Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.
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11
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Camelo-Júnior AE, Ferreira AWC, Andrade IM, Mayo SJ, Nollet F, Silva JL, Barros MC, Fraga E, Pessoa EM. Species delimitation in the Trichocentrum cepula (Oncidiinae, Orchidaceae) complex: a multidisciplinary approach. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2099478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Antonio E. Camelo-Júnior
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
| | | | - Ivanilza M. Andrade
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, Biotec, Campus de Parnaíba, Universidade Federal do Delta do Piauí, Parnaíba, Piauí, Brazil
| | - Simon J. Mayo
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, Surrey, UK
| | - Felipe Nollet
- Departamento de Biologia, Programa de Pós-Graduação em Botânica, Universidade Federal Rural de Pernambuco, Dois Irmãos, Recife, 52171–900, Pernambuco, Brazil
| | - José L. Silva
- Departamento de Ciências Biológicas, Universidade Federal da Paraíba Centro de Ciências Agrárias, Campus II, Areia, 58397-000, Paraíba, Brazil
| | - Maria C. Barros
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
| | - Elmary Fraga
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
| | - Edlley M. Pessoa
- Programa de Pós-Graduação em Biodiversidade, Ambiente e Saúde, Universidade Estadual do Maranhão, Campus Caxias, 65.604-380, Caxias, Maranhão, Brazil
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, 78060-900, Mato Grosso, Brazil
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12
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Reilly SB, Karin BR, Stubbs AL, Arida E, Arifin U, Kaiser H, Bi K, Hamidy A, Iskandar DT, McGuire JA. Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago. Evolution 2022; 76:2281-2301. [PMID: 35932243 DOI: 10.1111/evo.14592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Zoology Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Hinrich Kaiser
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, California, 92395, USA.,Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djoko T Iskandar
- Basic Sciences Commission, Indonesian Academy of Sciences, 11, Jl. Medan Merdeka, Selatan Jakarta, 10110, Indonesia.,School of Life Sciences and Technology, Institut Teknologi Bandung, 10 Jalan Ganesha, Bandung, 40132, Indonesia
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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13
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Luan YX, Cui Y, Chen WJ, Jin JF, Liu AM, Huang CW, Potapov M, Bu Y, Zhan S, Zhang F, Li S. High-quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (Collembola). Mol Ecol Resour 2022; 23:273-293. [PMID: 35962787 PMCID: PMC10087712 DOI: 10.1111/1755-0998.13699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
The collembolan Folsomia candida Willem, 1902, is widely distributed throughout the world and has been frequently used as a test organism in soil ecology and ecotoxicology studies. However, it is questioned as an ideal "standard" because of differences in reproductive modes and cryptic genetic diversity between strains from various geographical origins. In this study, we obtained two high-quality chromosome-level genomes of F. candida, for a parthenogenetic strain (named as FCDK, 219.08 Mb, 25,139 protein-coding genes) and a sexual strain (named as FCSH, 153.09 Mb, 21,609 protein-coding genes), reannotated the genome of the parthenogenetic strain reported by Faddeeva-Vakhrusheva et al. in 2017 (named as FCBL, 221.7 Mb, 25,980 protein-coding genes), and conducted comparative genomic analyses of three strains. High genome similarities between FCDK and FCBL on synteny, genome architecture, mitochondrial and nuclear gene sequences support they are conspecific. The seven chromosomes of FCDK are each 25-54% larger than the corresponding chromosomes of FCSH, showing obvious repetitive element expansions and large-scale inversions and translocations but no whole-genome duplication. The strain-specific genes, expanded gene families and genes in nonsyntenic chromosomal regions identified in FCDK are highly related to the broader environmental adaptation of parthenogenetic strains. In addition, FCDK has fewer strain-specific microRNAs than FCSH, and their mitochondrial and nuclear genes have diverged greatly. In conclusion, FCDK/FCBL and FCSH have accumulated independent genetic changes and evolved into distinct species since 10 Mya. Our work provides important genomic resources for studying the mechanisms of rapidly cryptic speciation and soil arthropod adaptation to soil ecosystems.
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Affiliation(s)
- Yun-Xia Luan
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yingying Cui
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | | | - Jian-Feng Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ai-Min Liu
- Department of Pomology, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Cheng-Wang Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai, China
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, China
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14
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Derkarabetian S, Starrett J, Hedin M. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Front Zool 2022; 19:8. [PMID: 35193622 PMCID: PMC8862334 DOI: 10.1186/s12983-022-00453-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA, 95616-5270, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
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15
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Abstract
Even if a species' phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways causes a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism's internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size ( Ne$N_e$ ). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of Ne$N_e$ generations. This model also naturally predicts Haldane's rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.
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Affiliation(s)
- Joshua S. Schiffman
- New York Genome CenterNew YorkNew York 10013,Weill Cornell MedicineNew YorkNew York 10065,Department of Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesCalifornia 90089
| | - Peter L. Ralph
- Department of Molecular and Computational BiologyUniversity of Southern CaliforniaLos AngelesCalifornia 90089,Department of Mathematics, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon 97403,Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregon 97403
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16
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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17
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Gowri Shankar P, Swamy P, Williams RC, Ganesh SR, Moss M, Höglund J, Das I, Sahoo G, Vijayakumar SP, Shanker K, Wüster W, Dutta SK. King or royal family? Testing for species boundaries in the King Cobra, Ophiophagus hannah (Cantor, 1836), using morphology and multilocus DNA analyses. Mol Phylogenet Evol 2021; 165:107300. [PMID: 34474153 DOI: 10.1016/j.ympev.2021.107300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 01/15/2023]
Abstract
In widespread species, the diverse ecological conditions in which the populations occur, and the presence of many potential geographical barriers through their range are expected to have created ample opportunities for the evolution of distinct, often cryptic lineages. In this work, we tested for species boundaries in one such widespread species, the king cobra, Ophiophagus hannah (Cantor, 1836), a largely tropical elapid snake distributed across the Oriental realm. Based on extensive geographical sampling across most of the range of the species, we initially tested for candidate species (CS) using Maximum-Likelihood analysis of mitochondrial genes. We then tested the resulting CS using both morphological data and sequences of three single-copy nuclear genes. We used snapclust to determine the optimal number of clusters in the nuclear dataset, and Bayesian Phylogenetics and Phylogeography (BPP) to test for likely species status. We used non-metric multidimensional scaling (nMDS) analysis for discerning morphological separation. We recovered four independently evolving, geographically separated lineages that we consider Confirmed Candidate Species: (1) Western Ghats lineage; (2) Indo-Chinese lineage (3) Indo-Malayan lineage; (4) Luzon Island lineage, in the Philippine Archipelago. We discuss patterns of lineage divergence, particularly in the context of low morphological divergence, and the conservation implications of recognizing several endemic king cobra lineages.
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Affiliation(s)
- P Gowri Shankar
- Maharaja Shrirama Chandra Bhanja Deo University, Baripada, Takatpur, Odisha, India; CES, Indian Institute of Science, Bangalore, India; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden; Kālinga Foundation, Agumbe, Karnataka, India.
| | | | - Rhiannon C Williams
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - S R Ganesh
- Chennai Snake Park, Raj Bhavan Post, Chennai, India
| | - Matt Moss
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Jacob Höglund
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Malaysia
| | | | | | | | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Bangor LL57 2UW, Wales, UK
| | - Sushil K Dutta
- Maharaja Shrirama Chandra Bhanja Deo University, Baripada, Takatpur, Odisha, India; Department of Zoology, Assam Don Bosco University, Tapesia, Assam, India
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18
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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19
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Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, Scheidt U, Iskandar DT, Jankowski A, Hertwig ST. Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822). Mol Phylogenet Evol 2021; 163:107210. [PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 01/04/2023]
Abstract
One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.
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Affiliation(s)
- Jana M Flury
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
| | - Alexander Haas
- Centrum für Naturkunde, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Dyche Hall, Lawrence, KS 66045, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Yong Min Pui
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Kueh Boon-Hee
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Ulrich Scheidt
- Naturkundemuseum Erfurt, Große Arche 14, 99084 Erfurt, Germany
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesa 10, Bandung 40132, Indonesia
| | - André Jankowski
- Centrum für Naturkunde, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland; University of Bern, Institute of Ecology and Evolution, Baltzerstrasse 6, 3006 Bern, Switzerland.
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20
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Onn Chan K, Hutter CR, Wood PL, Su YC, Brown RM. Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis). Syst Biol 2021; 71:40-57. [PMID: 33964168 DOI: 10.1093/sysbio/syab034] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022] Open
Abstract
In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, Alabama 36849, USA
| | - Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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21
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Diversity and distribution of amphibians and reptiles in the Caramoan Island Group, Maqueda Channel, Southern Luzon, Philippines. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2021. [DOI: 10.1016/j.japb.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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22
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Amador L, Victoriano PF, D’Elía G. Molecular species delimitation reveals hidden specific diversity within a freshwater burrowing crayfish (Decapoda: Parastacidae) from southern Chile. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2020.1865471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luis Amador
- Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
- Universidad Laica Vicente Rocafuerte, Guayaquil, 090514, Ecuador
| | - Pedro F. Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, 4030000, Chile
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, 5090000, Chile
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Rutherford S, Wan JSH, Cohen JM, Benson D, Rossetto M. Looks can be deceiving: speciation dynamics of co-distributed Angophora (Myrtaceae) species in a varying landscape. Evolution 2020; 75:310-329. [PMID: 33325041 DOI: 10.1111/evo.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome-wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome-wide analyses of related species in a diverse landscape can provide insights into speciation.
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Affiliation(s)
- Susan Rutherford
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Justin S H Wan
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Joel M Cohen
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Doug Benson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
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Magalhães FDM, Lyra ML, de Carvalho TR, Baldo D, Brusquetti F, Burella P, Colli GR, Gehara MC, Giaretta AA, Haddad CF, Langone JA, López JA, Napoli MF, Santana DJ, de Sá RO, Garda AA. Taxonomic Review of South American Butter Frogs: Phylogeny, Geographic Patterns, and Species Delimitation in the Leptodactylus latrans Species Group (Anura: Leptodactylidae). HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/0733-1347-31.4.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Felipe de M. Magalhães
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
| | - Mariana L. Lyra
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Thiago R. de Carvalho
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - Diego Baldo
- Instituto de Biología Subtropical (IBS, CONICET-UNaM), Laboratorio de Genética Evolutiva, Facultad de Ciencias Exactas, Universidad Nacional de Misiones, CP N3300LQF, Posadas, Misiones, Argentina
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay (IIBP), Del Escudo 1607, CP 1425 Asunción, Paraguay
| | - Pamela Burella
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Guarino R. Colli
- Departamento de Zoologia, Universidade de Brasília (UNB), CEP 70910-900, Brasília, Distrito Federal, Brazil
| | - Marcelo C. Gehara
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, 07102, USA
| | - Ariovaldo A. Giaretta
- Laboratório de Taxonomia e Sistemática de Anuros Neotropicais (LTSAN), Instituto de Ciências Exatas e Naturais do Pontal (ICENP), Universidade Federal de Uberlândia (UFU), Ituiutaba, Minas Gerais, Brazil
| | - Célio F.B. Haddad
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Campus Rio Claro, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), CEP 13506-900, Rio Claro, São Paulo, Brazil
| | - José A. Langone
- Departamento de Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, CP 11.000, Montevideo, Uruguay
| | - Javier A. López
- Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, Universidad Nacional del Litoral. Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - Marcelo F. Napoli
- Laboratório de Taxonomia e História Natural de Anfíbios (AMPHIBIA), Museu de História Natural, Instituto de Biologia, Universidade Federal da Bahia (UFBA), CEP 40170–115, Salvador, Bahia, Brazil
| | - Diego J. Santana
- Mapinguari – Laboratório de Biogeografia e Sistemática de Anfíbios e Répteis, Universidade Federal de Mato Grosso do Sul (UFMS), CEP 79002-970 Campo Grande, Mato Grosso, Brazil
| | - Rafael O. de Sá
- Department of Biology, University of Richmond, Richmond, Virginia, 23173, USA
| | - Adrian A. Garda
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba (UFPB), Centro de Ciências Exatas e da Natureza, Cidade Universitária, CEP 58000-000, João Pessoa, Paraíba, Brazil
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Firneno TJ, Itgen MW, Jacobs JL, Mcdaniels CX, Luque-Montes IR, Wilson LD, Townsend JH. Integrating phylogenetics, morphology, and osteology to delimit a new species of endemic montane sheep frog (Microhylidae: Hypopachus) from the Lenca Highlands of Honduras. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1841325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Thomas J. Firneno
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Michael W. Itgen
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA
| | - Justin L. Jacobs
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Chris X. Mcdaniels
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Ileana R. Luque-Montes
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA 15705–1081, USA
- Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
| | - Larry David Wilson
- Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
- 1350 Pelican Court, Homestead, FL 33035-1031, USA
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA 15705–1081, USA
- Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
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The Leafless Vanilla Species-Complex from the South-West Indian Ocean Region: A Taxonomic Puzzle and a Model for Orchid Evolution and Conservation Research. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12120443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The pantropical genus Vanilla is a member of the Orchidaceae family, one of the largest and most diverse families of angiosperms in the world. It originated in America and differentiated in America, Africa, and Asia. About 132 species of Vanilla have now been accepted since the discovery of the genus. Within the Vanilla genus, leaflessness has appeared at least three independent times, in Africa, Asia, and America as an adaptation to drought conditions. The South-West Indian Ocean (SWIO) region, a biodiversity hotspot for orchids, is home to seven leafless species. Chloroplast markers failed to differentiate species within this recent SWIO clade. Morphological traits used for description are very similar between species and do not provide reliable identification. Moreover, some of the species have overlapping flowering periods and geographic distribution in Madagascar, increasing the probability of finding some sympatric species and, therefore, hybrids. Leafless Vanilla species from the SWIO islands are thus an excellent model for understanding the evolution of orchids. For their conservation, and to confirm the identity of these leafless species, an integrated approach with classical taxonomy using a large number of samples, intense fieldwork on biology and ecology, and molecular studies using variable markers is necessary.
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Myers TC, de Mello PLH, Glor RE. A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractCryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.
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Affiliation(s)
- Tanner C Myers
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - Pietro L H de Mello
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Herpetology Division, Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Herpetology Division, Biodiversity Institute, University of Kansas, Lawrence, KS, USA
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28
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Barley AJ, Diesmos AC, Siler CD, Martinez CM, Brown RM. Taxonomic Revision of Philippine Sun Skinks (Reptilia: Squamata: Scincidae: Eutropis), and Descriptions of Eight New Species. HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/herpmonographs-d-19-00009.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Biology, University of Hawai‘i, Honolulu, HI 96822, USA
| | | | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA
| | | | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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29
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Balao F, Lorenzo MT, Sánchez-Robles JM, Paun O, García-Castaño JL, Terrab A. Early diversification and permeable species boundaries in the Mediterranean firs. ANNALS OF BOTANY 2020; 125:495-507. [PMID: 31730195 PMCID: PMC7061173 DOI: 10.1093/aob/mcz186] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/14/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. METHODS We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. KEY RESULTS Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene-Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. CONCLUSIONS Our phylogenomic results contribute to shed light on conifers' diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.
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Affiliation(s)
- Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
- For correspondence. E-mail
| | - María Teresa Lorenzo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - José Manuel Sánchez-Robles
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Juan Luis García-Castaño
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
| | - Anass Terrab
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Apdo. 1095, 41080 Sevilla, Spain
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Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns. Mol Phylogenet Evol 2020; 147:106785. [PMID: 32135306 DOI: 10.1016/j.ympev.2020.106785] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/03/2020] [Accepted: 02/27/2020] [Indexed: 11/24/2022]
Abstract
The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of cryptic diversity and revealed numerous taxonomic complications, especially within the C. consobrinus, C. malayanus, and C. pubisulcus groups. Comparisons of pairwise genetic distances and a preliminary species delimitation analysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-ranging species on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricted distributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneo into the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derived from multiple separate invasions into the geopolitical areas comprising the Philippines. Although our investigation of Bornean Cyrtodactylus is the most comprehensive to-date, it highlights the need for expanded taxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeography of Bornean Cyrtodactylus is far from complete.
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Chen Z, Li H, Zhai X, Zhu Y, He Y, Wang Q, Li Z, Jiang J, Xiong R, Chen X. Phylogeography, speciation and demographic history: Contrasting evidence from mitochondrial and nuclear markers of the Odorrana graminea sensu lato (Anura, Ranidae) in China. Mol Phylogenet Evol 2020; 144:106701. [DOI: 10.1016/j.ympev.2019.106701] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
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Freitas ES, Miller AH, Reynolds RG, Siler CD. A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar. Mol Phylogenet Evol 2020; 146:106754. [PMID: 32028030 DOI: 10.1016/j.ympev.2020.106754] [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: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 10/25/2022]
Abstract
Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, species delimitation analyses, and morphological data, we examine lineage diversification in a cryptic radiation of Riopa skinks in Myanmar. Four species of Riopa skinks are currently recognized from Myanmar based on morphological traits, but the boundaries between three of these species, R. anguina, R. lineolata, and R. popae, are not well-defined. We find high levels of genetic diversity within these three species. Our analyses suggest that they may comprise as many as 12 independently evolving lineages, highlighting the extent to which species diversity in the region is underestimated. However, quantitative trait data suggest that these lineages have not differentiated morphologically, possibly indicating that this cryptic radiation represents non-adaptive evolution, although additional data is needed to corroborate this.
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Affiliation(s)
- Elyse S Freitas
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA.
| | - Aryeh H Miller
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - R Graham Reynolds
- Department of Biology, University of North Carolina, Asheville, Asheville, NC 28804, USA
| | - Cameron D Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA
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Rivera D, Prates I, Rodrigues MT, Carnaval AC. Effects of climate and geography on spatial patterns of genetic structure in tropical skinks. Mol Phylogenet Evol 2020; 143:106661. [DOI: 10.1016/j.ympev.2019.106661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022]
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Chambers EA, Hillis DM. The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa. Syst Biol 2020; 69:184-193. [PMID: 31180508 DOI: 10.1093/sysbio/syz042] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/14/2022] Open
Abstract
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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Ochoa LE, Melo BF, García-Melo JE, Maldonado-Ocampo JA, Souza CS, Albornoz-Garzón JG, Conde-Saldaña CC, Villa-Navarro F, Ortega-Lara A, Oliveira C. Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes). NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2020-0048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT Catfishes of the family Astroblepidae form a group composed by 82 valid species of the genus Astroblepus inhabiting high-gradient streams and rivers throughout tropical portions of the Andean Cordillera. Little has been advanced in the systematics and biodiversity of astroblepids other than an unpublished thesis, a single regional multilocus study and isolated species descriptions. Here, we examined 208 specimens of Astroblepus that apparently belong to 16 valid species from several piedmont rivers from northern Colombia to southern Peru. Using three single-locus approaches for species delimitation in combination with a species tree analysis estimated from three mitochondrial genes, we identified a total of 25 well-delimited lineages including eight valid and 17 potential undescribed species distributed in two monophyletic groups: the Central Andes Clade, which contains 14 lineages from piedmont rivers of the Peruvian Amazon, and the Northern Andes Clade with 11 lineages from trans- and cis-Andean rivers of Colombia and Ecuador, including the Orinoco, Amazon, and Magdalena-Cauca basins and Pacific coastal drainages. Results of species delimitation methods highlight several taxonomical incongruences in recently described species denoting potential synonymies.
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Affiliation(s)
- Luz E. Ochoa
- Universidade de São Paulo, Brazil; Universidade Estadual Paulista, Brazil
| | | | | | | | | | - Juan G. Albornoz-Garzón
- Universidad del Tolima, Colombia; Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Colombia
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Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M. A demonstration of unsupervised machine learning in species delimitation. Mol Phylogenet Evol 2019; 139:106562. [PMID: 31323334 PMCID: PMC6880864 DOI: 10.1016/j.ympev.2019.106562] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 01/13/2023]
Abstract
One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, United States; Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, United States.
| | - Stephanie Castillo
- Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Entomology, University of California, Riverside, Riverside, CA 92521, United States
| | - Peter K Koo
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, United States
| | - Sergey Ovchinnikov
- Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA 92182, United States
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37
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Jin Y, Brown RP. Morphological species and discordant mtDNA: A genomic analysis of Phrynocephalus lizard lineages on the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2019; 139:106523. [DOI: 10.1016/j.ympev.2019.106523] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/27/2022]
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38
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Jacobs SJ, Herzog S, Tank DC. Quantifying morphological variation in the Castilleja pilosa species complex (Orobanchaceae). PeerJ 2019; 7:e7090. [PMID: 31259097 PMCID: PMC6589334 DOI: 10.7717/peerj.7090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/06/2019] [Indexed: 11/20/2022] Open
Abstract
Robustly delimited species are of paramount importance, the identification of which relies on our ability to discern boundaries between one species and the next. This is not difficult to do when species are very distinct from one another. However, in recently evolved lineages where putative species may have relatively few diagnostic features (e.g., species complexes composed of very similar species, the boundaries between which are often unclear), defining species boundaries can be more challenging. Hence, the field of species delimitation has widely advocated the use of multiple lines of evidence to delimit species, particularly in species complexes. Excessive taxonomic confusion, often the result of species descriptions that shift through time (e.g., during revisionary work and regional treatments), can further complicate the search for diagnostic features in species complexes. Here, as a first step in robustly delimiting species boundaries, we quantify and describe morphological variation in the Castilleja pilosa species complex. We first infer the morphospace of the species complex and use fuzzy-clustering techniques to explore the morphological variation in the system. Next, we hypothesize the position of type specimens within that morphospace. In so doing, we aim to visualize the impact that regional treatments have had on the conceptualization of taxa through time. We find that there is limited morphological variation among members of this complex, and we determine that the morphological concept of these species have shifted through time and are no longer accurately represented by species descriptions.
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Affiliation(s)
- Sarah J Jacobs
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA.,Biological Sciences, University of Idaho, Moscow, ID, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
| | - Sarah Herzog
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA.,Biological Sciences, University of Idaho, Moscow, ID, USA
| | - David C Tank
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA.,Biological Sciences, University of Idaho, Moscow, ID, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
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39
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Firneno TJ, Townsend JH. Evaluation of species boundaries in sympatric and parapatric populations of Mesoamerican toads. ZOOL SCR 2019. [DOI: 10.1111/zsc.12354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Thomas J. Firneno
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
| | - Josiah H. Townsend
- Department of Biology Indiana University of Pennsylvania Indiana Pennsylvania
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40
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Czekanski-Moir JE, Rundell RJ. The Ecology of Nonecological Speciation and Nonadaptive Radiations. Trends Ecol Evol 2019; 34:400-415. [DOI: 10.1016/j.tree.2019.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/08/2023]
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41
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Chan KO, Grismer LL. To split or not to split? Multilocus phylogeny and molecular species delimitation of southeast Asian toads (family: Bufonidae). BMC Evol Biol 2019; 19:95. [PMID: 31023232 PMCID: PMC6485082 DOI: 10.1186/s12862-019-1422-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index (gdi) was shown to be a viable alternative, especially for delimiting allopatric populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes. RESULTS Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (< 3%) and consistent with intraspecific divergences of other closely related taxa. The BPP analysis produced variable results depending on prior settings and priors estimated from empirical data produced the best results that were also congruent with the gdi analysis. CONCLUSIONS This study showed that the evolutionary history of Southeast Asian toads is difficult to resolve and numerous relationships remain ambiguous. Although some results from the species delimitation analyses were inconclusive, they were nevertheless efficacious at identifying potential new species and taxonomic incompatibilities for future in-depth investigation. We also demonstrated the sensitivity of BPP to different priors and that careful selection priors based on empirical data can greatly improve the analysis. Finally, the gdi can be a robust tool to complement other species delimitation methods.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore, 117377 Singapore
| | - L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92515 USA
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42
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Strong EE, Whelan NV. Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda). Mol Phylogenet Evol 2019; 136:87-103. [PMID: 30974201 DOI: 10.1016/j.ympev.2019.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 04/06/2019] [Accepted: 04/07/2019] [Indexed: 01/24/2023]
Abstract
Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.
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Affiliation(s)
- Ellen E Strong
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, 10th and Constitution Ave NW, Washington DC 20560, USA.
| | - Nathan V Whelan
- United States Fish and Wildlife Service, Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, Auburn, AL 36849, USA; School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
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43
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Freitas ES, Datta-Roy A, Karanth P, Grismer LL, Siler CD. Multilocus phylogeny and a new classification for African, Asian and Indian supple and writhing skinks (Scincidae: Lygosominae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.
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Affiliation(s)
- Elyse S Freitas
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Aniruddha Datta-Roy
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, California, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
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44
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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: 4.8] [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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45
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Costa CLN, Lemos-Costa P, Marquitti FMD, Fernandes LD, Ramos MF, Schneider DM, Martins AB, de Aguiar MAM. Signatures of Microevolutionary Processes in Phylogenetic Patterns. Syst Biol 2018; 68:131-144. [PMID: 29939352 DOI: 10.1093/sysbio/syy049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.
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Affiliation(s)
- Carolina L N Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Paula Lemos-Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Flavia M D Marquitti
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Marlon F Ramos
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Department of Fish Ecology & Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
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46
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Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae). Mol Phylogenet Evol 2018; 129:242-257. [DOI: 10.1016/j.ympev.2018.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 08/01/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022]
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47
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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: 0.7] [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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48
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Comprehensive multi-locus phylogeny of Old World tree frogs (Anura: Rhacophoridae) reveals taxonomic uncertainties and potential cases of over- and underestimation of species diversity. Mol Phylogenet Evol 2018; 127:1010-1019. [DOI: 10.1016/j.ympev.2018.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 11/19/2022]
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49
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Hidden diversity within the depauperate genera of the snake tribe Lampropeltini (Serpentes, Colubridae). Mol Phylogenet Evol 2018; 129:214-225. [PMID: 30189319 DOI: 10.1016/j.ympev.2018.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022]
Abstract
Accurate representation of lineage diversity through complete taxon sampling is crucial to understanding the evolution of biodiversity, particularly when using molecular phylogenetics to estimate evolutionary relationships. In this interest, taxonomic diversity is often used as a proxy for lineage diversity even though the two concepts are not synonymous. We explore this within the snake tribe Lampropeltini which includes some of the most conspicuous and heavily studied snakes in North America. Both the taxonomy and hypothesized relationships within this tribe have been in flux. The number of species has increased from 23 to 51 over the last thirty years, predominately within three of the nine genera (Lampropeltis, Pantherophis, Pituophis). The remaining six depauperate genera (Arizona, Bogertophis, Cemophora, Pseudelaphe, Rhinocheilus, and Senticolis) have been poorly represented in phylogenetic studies. To estimate evolutionary relationships and determine if the dichotomy in depauperate and speciose genera within Lampropeltini is a function of taxon sampling or truly represents the lineage diversity, we estimated the phylogeny of this group using nuclear and mitochondrial loci in a concatenated and coalescent framework with the largest sampling of the six depauperate genera to date. In addition, we estimated the divergence dates among the genera to assess whether the instability of Lampropeltini phylogenetic relationships is due to an adaptive radiation. While some nodes still remain unresolved, the generic-level relationships we recovered agree with those of a recent next-generation study that used a much larger set of loci for fewer individuals. We also tested two putative species, Arizona pacata and Pseudelaphe phaescens, for the first time phylogenetically and find evidence that they are distinct lineages. Overall, we find that the taxonomic and genetic diversity are not correlated in Lampropeltini and that representing putative diversity in phylogenies will lead to a better estimate of evolutionary histories, especially in groups with complex radiations.
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50
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Posso-Terranova A, Andrés J. Multivariate species boundaries and conservation of harlequin poison frogs. Mol Ecol 2018; 27:3432-3451. [DOI: 10.1111/mec.14803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/15/2018] [Accepted: 06/28/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Andrés Posso-Terranova
- Department of Biology; University of Saskatchewan; Saskatoon SK Canada
- Universidad Nacional de Colombia sede Palmira; Palmira Colombia
| | - Jose Andrés
- Department of Biology; University of Saskatchewan; Saskatoon SK Canada
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