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Amir Afzali Y, Naderloo R, Keikhosravi A, Klaus S. Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species? J Hered 2024; 115:277-291. [PMID: 38501510 DOI: 10.1093/jhered/esae016] [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: 09/30/2023] [Accepted: 03/17/2024] [Indexed: 03/20/2024] Open
Abstract
The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum, utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late Holocene, accompanied by a recent population bottleneck. Species distribution modeling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently, genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance.
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Affiliation(s)
- Yaser Amir Afzali
- Department of Biology, College of Science, University of Tehran, Tehran 1417935840, Iran
| | - Reza Naderloo
- Department of Biology, College of Science, University of Tehran, Tehran 1417935840, Iran
| | - Alireza Keikhosravi
- Department of Biology, Hakim Sabzevari University, Sabzevar 9617976487, Iran
| | - Sebastian Klaus
- Environmental Resources Management, Managing Consultant, ERM GmbH, Siemensstr. 9, Neu-Isenburg 63263, Germany
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2
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Lvarez R, Budaeva N. How complex is the Naineris setosa species complex? First integrative study of a presumed cosmopolitan and invasive annelid (Sedentaria: Orbiniidae). Zootaxa 2023; 5375:349-378. [PMID: 38220815 DOI: 10.11646/zootaxa.5375.3.3] [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: 11/22/2023] [Indexed: 01/16/2024]
Abstract
We performed a comparative study of the specimens from the Naineris setosa complex from the Pacific and the Atlantic Oceans and re-described the syntype of N. setosa, including the selection of the lectotype. Molecular phylogenetic and species delimitation analyses based on two mitochondrial (COI and 16S) and one nuclear (28S) marker revealed the presence of three species. One clade with wide Amphi-Atlantic distribution was attributed as Naineris setosa s. str. The second Atlantic clade restricted to Southern and Southeastern Brazil was described as a new species, Naineris lanai sp. n. The third clade, reported from the Northwestern Pacific, was identified as a new species but was not formally described due to the presence of only juvenile-sized worms in the studied material. Detailed morphological descriptions of several diagnostic characters in the Naineris setosa complex are provided.
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Affiliation(s)
- Ricardo Lvarez
- Graduate program in Oceanic Coastal Systems (PGSISCO); Federal University of Paran; Pontal do Paran; Paran; Brazil.
| | - Nataliya Budaeva
- Department of Natural History; University Museum of Bergen; University of Bergen; Allgaten 41; 5007 Bergen; Norway.
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3
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Haye PA, Segovia NI. Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel. Heredity (Edinb) 2023; 130:402-413. [PMID: 37024547 PMCID: PMC10238476 DOI: 10.1038/s41437-023-00615-8] [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: 11/13/2022] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.
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Affiliation(s)
- Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile
| | - Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
- Instituto Milenio en Socio-Ecología Costera (SECOS), Santiago, Chile.
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4
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Maas DL, Prost S, de Leeuw CA, Bi K, Smith LL, Purwanto P, Aji LP, Tapilatu RF, Gillespie RG, Becking LE. Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges. Ecol Evol 2023; 13:e9945. [PMID: 37066063 PMCID: PMC10099488 DOI: 10.1002/ece3.9945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
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Affiliation(s)
- Diede L. Maas
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
| | - Stefan Prost
- LOEWE Centre for Translational Biodiversity GenomicsSenckenberg Natural History MuseumFrankfurt am MainGermany
- South African National Biodiversity InstituteNational Zoological Gardens of South AfricaPretoriaSouth Africa
| | | | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Computational Genomics Resource Laboratory, California Institute for Quantitative BiosciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Lydia L. Smith
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | - Ludi P. Aji
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
- Research Centre for Oceanography, Indonesian Institute of SciencesLembaga Ilmu Pengetahuan IndonesiaJakartaIndonesia
| | - Ricardo F. Tapilatu
- Marine Science and Fisheries Departments and Research Center of Pacific Marine ResourcesState University of PapuaManokwariIndonesia
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Leontine E. Becking
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Aquaculture and Fisheries, Naturalis Biodiversity CenterWageningen University & ResearchWageningenThe Netherlands
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5
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Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00505-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Firneno TJ, O'Neill JR, Portik DM, Emery AH, Townsend JH, Fujita MK. Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads. Mol Ecol 2020; 29:3543-3559. [PMID: 32500624 DOI: 10.1111/mec.15496] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/18/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Mitonuclear discordance is a frequently encountered pattern in phylogeographic studies and occurs when mitochondrial and nuclear DNA display conflicting signals. Discordance among these genetic markers can be caused by several factors including confounded taxonomies, gene flow, and incomplete lineage sorting. In this study, we present a strong case of mitonuclear discordance in a species complex of toads (Bufonidae: Incilius coccifer complex) found in the Chortís Block of Central America. To determine the cause of mitonuclear discordance in this complex, we used spatially explicit genetic data to test species limits and relationships, characterize demographic history, and quantify gene flow. We found extensive mitonuclear discordance among the three recognized species within this group, especially in populations within the Chortís Highlands of Honduras. Our data reveal nuclear introgression within the Chortís Highlands populations that was most probably driven by cyclical range expansions due to climatic fluctuations. Though we determined introgression occurred within the nuclear genome, our data suggest that it is not the key factor in driving mitonuclear discordance in the entire species complex. Rather, due to a lack of discernible geographic pattern between mitochondrial and nuclear DNA, as well as a relatively recent divergence time of this complex, we concluded that mitonuclear discordance has been caused by incomplete lineage sorting. Our study provides a framework to test sources of mitonuclear discordance and highlights the importance of using multiple marker types to test species boundaries in cryptic species.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Justin R O'Neill
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | | | - Alyson H Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Josiah H Townsend
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA.,Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Escuela Agrícola Panamericana Zamorano, Municipalidad de San Antonio de Oriente, Francisco Morazán, Honduras
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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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: 2.8] [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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Kara J, Santos CSG, Macdonald AHH, Simon CA. Resolving the taxonomic identities and genetic structure of two cryptic Platynereis Kinberg species from South Africa. INVERTEBR SYST 2020. [DOI: 10.1071/is19072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The perceived cosmopolitanism of polychaete worms could be an artefact of historical factors such as poor original species descriptions, lack of type material and the European taxonomic bias, to name a few. Thus, it is possible that several cosmopolitan species hide complexes of cryptic and pseudocryptic species. Two putative cosmopolitan species, Platynereis dumerilii and Platynereis australis, collected in South Africa were investigated here (1) to determine whether the South African taxa are conspecific with the morphologically identical taxa from France and New Zealand (the respective type localities of P. dumerilii and P. australis), (2) to compare the South African species morphometrically to determine whether their morphological characters are reliable enough to separate them, and (3) to investigate whether these species have geographically structured populations along the coast of South Africa. Molecular data (COI and ITS1) confirm that P. dumerilii and P. australis do not occur in South Africa. Instead, the South African taxon formerly thought to be Platynereis dumerilii is new and is described here as Platynereis entshonae, sp. nov.; the identity of the other South African species is currently unresolved and is treated here as Platynereis sp. Surprisingly, Platynereis massiliensis (type locality: Marseilles) nested within the South African Platynereissp. clade but, since it is part of a cryptic species complex in the Mediterranean, the name is considered doubtful. Morphological characters traditionally used to define these South African Platynereis species are not reliable as predefined morphological groupings do not match phylogenetic clades and principal component scores revealed no separation in morphological characters that could distinguish between them. Haplotype networks and phylogenetic trees revealed that P. entshonae, sp. nov. and Platynereis sp. have geographically structured populations along the South African coast. http://zoobank.org/urn:lsid:zoobank.org:pub:6E36A210-9E48-430F-8A93-EDC27F0C5631
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9
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Senczuk G, Colangelo P, De Simone E, Aloise G, Castiglia R. A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus. BMC Evol Biol 2017; 17:6. [PMID: 28056768 PMCID: PMC5216540 DOI: 10.1186/s12862-016-0847-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM). RESULTS We identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula. CONCLUSIONS Our population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.
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Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy.
| | - Paolo Colangelo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy.,National Research Council, Institute of Ecosystem Study, Largo Tonnoli 50, 28922, Verbania Pallanza, Italy
| | - Emanuela De Simone
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy
| | - Gaetano Aloise
- Museo di Storia Naturale della Calabria e Orto Botanico, Università della Calabria, CAP 87036, Rende, Cosenza, Italy
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy
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10
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Hebert PDN, Hollingsworth PM, Hajibabaei M. From writing to reading the encyclopedia of life. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150321. [PMID: 27481778 PMCID: PMC4971178 DOI: 10.1098/rstb.2015.0321] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 11/12/2022] Open
Abstract
Prologue 'As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life'. J. C. Louden 1829. Magazine of natural history, vol. 1: This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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11
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Becker M, Zielske S, Haase M. Conflict of mitochondrial phylogeny and morphology-based classification in a pair of freshwater gastropods (Caenogastropoda, Truncatelloidea, Tateidae) from New Caledonia. Zookeys 2016:17-32. [PMID: 27551195 PMCID: PMC4977999 DOI: 10.3897/zookeys.603.9144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/17/2016] [Indexed: 11/26/2022] Open
Abstract
Morphological classification and mitochondrial phylogeny of a pair of morphologically defined species of New Caledonian freshwater gastropods, Hemistomiacockerelli and Hemistomiafabrorum, were incongruent. We asked whether these two nominal species can be unambiguously distinguished based on shell morphology or whether the taxonomic discrepancy inferred from these character types was reflected in the variation of shell morphology. Our investigations were based on phylogenetic analyses of a fragment of the mitochondrial cytochrome c oxidase subunit I, geometric morphometric analyses as well as micro computer tomography. The species presorted to morphospecies by eye overlapped in shell shape. However, statistically, all shells were correctly assigned, but not all of them significantly. Qualitatively, both nominal species can be unambiguously distinguished by the presence/absence of a prominent denticle within the shell. In the phylogenetic analyses, individuals from three populations clustered with the “wrong” morphospecies. In the absence of data from multiple loci, it was assumed for the single specimen from one of these populations that its misplacement was due to a recent hybridization event, based on its very shallow position in the tree. For the other two cases of misplacement neither introgression nor incomplete lineage sorting could be ruled out. Further investigations have to show whether the morphological overlap has a genetic basis or is due to phenotypic plasticity. In conclusion, despite their partly unresolved relationships Hemistomiacockerelli and Hemistomiafabrorum may be considered sister species, which are reliably diagnosable by the presence or absence of the denticle, but have not yet fully differentiated in all character complexes investigated.
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Affiliation(s)
- Marlen Becker
- Vogelwarte, Zoologisches Institut und Museum, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstraße 23, D-17489 Greifswald, Germany
| | - Susan Zielske
- Vogelwarte, Zoologisches Institut und Museum, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstraße 23, D-17489 Greifswald, Germany
| | - Martin Haase
- Vogelwarte, Zoologisches Institut und Museum, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstraße 23, D-17489 Greifswald, Germany
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12
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Thomé MTC, Carstens BC. Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs. Proc Natl Acad Sci U S A 2016; 113:8010-7. [PMID: 27432969 PMCID: PMC4961127 DOI: 10.1073/pnas.1601064113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phylogeographic research investigates biodiversity at the interface between populations and species, in a temporal and geographic context. Phylogeography has benefited from analytical approaches that allow empiricists to estimate parameters of interest from the genetic data (e.g., θ = 4Neμ, population divergence, gene flow), and the widespread availability of genomic data allow such parameters to be estimated with greater precision. However, the actual inferences made by phylogeographers remain dependent on qualitative interpretations derived from these parameters' values and as such may be subject to overinterpretation and confirmation bias. Here we argue in favor of using an objective approach to phylogeographic inference that proceeds by calculating the probability of multiple demographic models given the data and the subsequent ranking of these models using information theory. We illustrate this approach by investigating the diversification of two sister species of four-eyed frogs of northeastern Brazil using single nucleotide polymorphisms obtained via restriction-associated digest sequencing. We estimate the composite likelihood of the observed data given nine demographic models and then rank these models using Akaike information criterion. We demonstrate that estimating parameters under a model that is a poor fit to the data is likely to produce values that lead to spurious phylogeographic inferences. Our results strongly imply that identifying which parameters to estimate from a given system is a key step in the process of phylogeographic inference and is at least as important as being able to generate precise estimates of these parameters. They also illustrate that the incorporation of model uncertainty should be a component of phylogeographic hypothesis tests.
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Affiliation(s)
- Maria Tereza C Thomé
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Campus Rio Claro, 13506900 Rio Claro, SP, Brazil
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210
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13
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Liu S, Jiang N, Xue D, Cheng R, Qu Y, Li X, Lei F, Han H. Evolutionary history ofApocheima cinerarius(Lepidoptera: Geometridae), a female flightless moth in northern China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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14
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Fang F, Ji Y, Zhao Q, Wang Y, Gao W, Chu K, Sun H. Phylogeography of the Chinese endemic freshwater crabSinopotamon acutum(Brachyura, Potamidae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fang Fang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yongkun Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Qiang Zhao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Yujuan Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Wei Gao
- College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Kelin Chu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology; College of Life Sciences; Nanjing Normal University; Nanjing 210023 China
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15
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Franco FF, Lavagnini TC, Sene FM, Manfrin MH. Mito-nuclear discordance with evidence of shared ancestral polymorphism and selection in cactophilic species ofDrosophila. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12554] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fernando F. Franco
- Depto. Biologia; Centro de Ciências Humanas e Biológicas; Universidade Federal de São Carlos; Sorocaba Brazil
| | - Taís C. Lavagnini
- Programa de Pós-graduação em Biologia Comparada; Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto Brazil
| | - Fabio M. Sene
- Departamento de Biologia - Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto Brazil
- Pós-Graduação; Depto. Genética - Faculdade de Medicina de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto Brazil
| | - Maura H. Manfrin
- Departamento de Biologia - Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto Brazil
- Pós-Graduação; Depto. Genética - Faculdade de Medicina de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto Brazil
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16
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DeBiasse MB, Hellberg ME. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia. Ecol Evol 2015; 5:663-75. [PMID: 25691989 PMCID: PMC4328770 DOI: 10.1002/ece3.1381] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/03/2014] [Indexed: 01/29/2023] Open
Abstract
Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.
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Affiliation(s)
- Melissa B DeBiasse
- Department of Biological Sciences, Louisiana State University202 Life Sciences Building, Baton Rouge, Louisiana, 70803
- Correspondence Melissa B DeBiasse, Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803., Tel: 225 578 4284; Fax: 225 578 2597; E-mail:
| | - Michael E Hellberg
- Department of Biological Sciences, Louisiana State University202 Life Sciences Building, Baton Rouge, Louisiana, 70803
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17
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Dong F, Zou FS, Lei FM, Liang W, Li SH, Yang XJ. Testing hypotheses of mitochondrial gene-tree paraphyly: unravelling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus). Mol Ecol 2014; 23:5855-67. [DOI: 10.1111/mec.12981] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/02/2014] [Accepted: 10/14/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
| | - Fa-Sheng Zou
- South China Institute of Endangered Animals; Guangzhou 510260 China
| | - Fu-Min Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Liang
- Ministry of Education Key Laboratory for Tropical Plant and Animal Ecology; College of Life Sciences; Hainan Normal University; Haikou 571158 China
| | - Shou-Hsien Li
- Department of Life Science; National Taiwan Normal University; Taipei 116 Taiwan
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution; Kunming Institute of Zoology; Chinese Academy of Sciences; Kunming 650223 China
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