1
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Yuan Z, Jiang W, Sha Z. A review of the common crab genus Macromedaeus Ward, 1942 (Brachyura, Xanthidae) from China Seas with description of a new species using integrative taxonomy methods. PeerJ 2022; 10:e12735. [PMID: 35111395 PMCID: PMC8781320 DOI: 10.7717/peerj.12735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/12/2021] [Indexed: 01/07/2023] Open
Abstract
Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and M. orientalis (Takeda & Miyake, 1969) from Hainan Island, South China Sea. M. hainanensis is most related to M. distinguendus (De Haan, 1833-1850) and M. orientalis on the carapace shape and granular appearance, but can be distinguished by unique morphological characteristics especially its front, pereopods and male first gonopod. Taxonomic identities of the six Macromedaeus species recorded from China seas are discussed, and a phylogenetic analyzation is performed on Macromedaeus and related taxa based on three mitochondrial and two nuclear markers (12S, 16S, COI, H3, 18S). Integrated taxonomic evidence is used to support the taxonomic status of each species.
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Affiliation(s)
- Ziming Yuan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Jiang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhongli Sha
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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2
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Mouser JB, Brewer SK, Niemiller ML, Mollenhauer R, Van Den Bussche RA. Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.39.64279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.
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3
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Wood JE, Pugh MW, Harris PM, McGregor SW, Sandel MW. Range Extension of Blackfin Darter and Tennessee Dace, and First Collection of Western Blacknose Dace from Locust Fork of the Black Warrior River in 80 Years. SOUTHEAST NAT 2021. [DOI: 10.1656/058.020.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Julia E. Wood
- Department of Biological and Environmental Sciences, University of West Alabama, 100 US-11 Livingston, AL 35470
| | - M. Worth Pugh
- Department of Biological Sciences, College of Arts and Sciences, University of Alabama, 712 Capstone Drive Tuscaloosa, AL 35401
| | - Phillip M. Harris
- Department of Biological Sciences, College of Arts and Sciences, University of Alabama, 712 Capstone Drive Tuscaloosa, AL 35401
| | | | - Michael W. Sandel
- Department of Biological and Environmental Sciences, University of West Alabama, 100 US-11 Livingston, AL 35470
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4
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Using environmental DNA methods to survey for rare groundwater fauna: Detection of an endangered endemic cave crayfish in northern Alabama. PLoS One 2020; 15:e0242741. [PMID: 33301442 PMCID: PMC7728221 DOI: 10.1371/journal.pone.0242741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/06/2020] [Indexed: 11/25/2022] Open
Abstract
The conservation and management of subterranean biodiversity is hindered by a lack of knowledge on the true distributions for many species, e.g., the Wallacean shortfall. In recent years, several studies have demonstrated the potential of environmental DNA (eDNA) as an effective approach to detect and monitor biodiversity, including rare, threatened, and endangered taxa. However, there are few eDNA studies of groundwater fauna. Here we report the results of the development and implementation of an eDNA assay targeting a short fragment of the mitochondrial CO1 locus of a critically imperiled cave crayfish, the Sweet Home Alabama Cave Crayfish (Cambarus speleocoopi), known from just four cave systems in the Interior Plateau karst region of northern Alabama. We detected C. speleocoopi DNA from water samples collected at 5 of 16 sites sampled (caves and springs), including two historical sites as well as three additional and potentially new sites in Marshall County, Alabama. All three of these sites were within 2 km of historical sites. Our study is the first to detect a groundwater crustacean in the Interior Plateau karst region. Additionally, our study contributes to the growing literature that eDNA is a viable complementary tool for detection and monitoring of a fauna that is difficult to survey and study using traditional approaches.
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5
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Theil EP, Felder DL. Phylogeny of the genus Pinnixa White, 1846 (Crustacea, Brachyura, Pinnotheridae) and allies inferred from mitochondrial and nuclear molecular markers, with generic reassignment of twenty-one species. ZOOSYSTEMA 2020. [DOI: 10.5252/zoosystema2020v42a6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Emma Palacios Theil
- Department of Biology, Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504-2451 (United States)
| | - Darryl L. Felder
- Department of Biology, Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504-2451 (United States)
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6
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Gladstone NS, Niemiller ML, Pieper EB, Dooley K, McKinney ML. Morphometrics and phylogeography of the cave-obligate land snail Helicodiscus barri (Gastropoda, Stylommatophora, Helicodiscidae). SUBTERRANEAN BIOLOGY 2019. [DOI: 10.3897/subtbiol.30.35321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular studies have recently led to the detection of many cryptic species complexes within morphologically ambiguous species formerly undescribed by the scientific community. Organisms such as land snails are at a particularly higher risk of species misidentification and misinterpretation, in that gastropod systematics are based almost entirely on external shell morphology. Subterranean ecosystems are associated with especially high degrees of cryptic speciation, largely owing to the abiotic similarities of these systems. In this study, we attempt to diagnose the potential cryptic diversity in the troglobitic land snail Helicodiscusbarri. Land snails are generally associated with having low vagility, and as such this species’ broad, mosaic distribution indicates the misdiagnosis of this organism as a single species. We analyze both mitochondrial (16S, CO1) and nuclear (28S, H3) genetic data for 23 populations. Phylogeny for H.barri was reconstructed using both maximum-likelihood and Bayesian approaches to assess relationships among populations, and two species delimitation methods (mPTP and ABGD) were used to detect the presence of unique molecular operational taxonomic units (MOTUs). Species delimitation results revealed seven and sixteen MOTUs respectively, suggesting the presence of several cryptic lineages within H.barri. To assess how external shell morphology corresponds with patterns of genetic and environmental variation, two morphometric approaches were used incorporating 115 shells from 31 populations. Both morphometric approaches reveal a significant environmental influence on shell morphology, and one approach showed the significance of MOTU groups. We discuss the delimitation and morphometric results and additionally provide discussion on the taxonomic and conservation implications of this study.
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7
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Nguyen HN, Lu CW, Chu JH, Grismer LL, Hung CM, Lin SM. Historical demography of four gecko species specializing in boulder cave habitat: Implications in the evolutionary dead end hypothesis and conservation. Mol Ecol 2018; 28:772-784. [PMID: 30580492 DOI: 10.1111/mec.14985] [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: 06/20/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022]
Abstract
Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by unsuitable floodplain habitats, these boulder-dwelling geckos are among the most narrowly distributed Squamata in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results reveal long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have greatly impacted population divergence and declines. The habitat specialization of these geckos has led to fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.
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Affiliation(s)
- Hung N Nguyen
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Zoology, Southern Institute of Ecology, Vietnam Academia of Science and Technology, Ho Chi Minh City, Vietnam.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chia-Wei Lu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jui-Hua Chu
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | | | - Chih-Ming Hung
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Si-Min Lin
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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8
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Dawkins KL, Furse JM, Wild CH, Hughes JM. A novel genus and cryptic species harboured within the monotypic freshwater crayfish genus Tenuibranchiurus Riek, 1951 (Decapoda: Parastacidae). PeerJ 2017; 5:e3310. [PMID: 28560095 PMCID: PMC5445942 DOI: 10.7717/peerj.3310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/13/2017] [Indexed: 11/20/2022] Open
Abstract
Identifying species groups is an important yet difficult task, with there being no single accepted definition as to what constitutes a species, nor a set of criteria by which they should be delineated. Employing the General Lineage Concept somewhat circumvents these issues, as this concept allows multiple concordant lines of evidence to be used as support for species delimitation, where a species is defined as any independently evolving lineage. Genetically diverse groups have previously been identified within the monotypic parastacid genus Tenuibranchiurus Riek, 1951, but no further investigation of this diversity has previously been undertaken. Analysis of two mitochondrial DNA gene regions has previously identified two highly divergent groups within this taxon, representing populations from Queensland (Qld) and New South Wales (NSW), respectively. Additional testing within this study of both mitochondrial and nuclear DNA through species discovery analyses identified genetically diverse groups within these regions, which were further supported by lineage validation methods. The degree of genetic differentiation between Qld and NSW populations supports the recognition of two genera; with Qld retaining the original genus name Tenuibranchiurus, and NSW designated as Gen. nov. until a formal description is completed. Concordance between the species discovery and lineage validation methods supports the presence of six species within Tenuibranchiurus and two within Gen. nov. The recognition of additional species removes the monotypy of the genus, and the methods used can improve species identification within groups of organisms with taxonomic problems and cryptic diversity.
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Affiliation(s)
- Kathryn L Dawkins
- Australian Rivers Institute, Griffith University, Gold Coast, Queensland, Australia
| | - James M Furse
- Environmental Futures Research Institute, Griffith University, Gold Coast, Queensland, Australia.,Miyazaki International College, Miyazaki, Japan
| | - Clyde H Wild
- Environmental Futures Research Institute, Griffith University, Gold Coast, Queensland, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
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9
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Larson ER, Castelin M, Williams BW, Olden JD, Abbott CL. Phylogenetic species delimitation for crayfishes of the genus Pacifastacus. PeerJ 2016; 4:e1915. [PMID: 27114875 PMCID: PMC4841241 DOI: 10.7717/peerj.1915] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 03/18/2016] [Indexed: 12/20/2022] Open
Abstract
Molecular genetic approaches are playing an increasing role in conservation science by identifying biodiversity that may not be evident by morphology-based taxonomy and systematics. So-called cryptic species are particularly prevalent in freshwater environments, where isolation of dispersal-limited species, such as crayfishes, within dendritic river networks often gives rise to high intra- and inter-specific genetic divergence. We apply here a multi-gene molecular approach to investigate relationships among extant species of the crayfish genus Pacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly, Pacifastacus includes both the widely invasive signal crayfish Pacifastacus leniusculus, as well as several species of conservation concern like the Shasta crayfish Pacifastacus fortis. Our analysis used 83 individuals sampled across the four extant Pacifastacus species (omitting the extinct Pacifastacus nigrescens), representing the known taxonomic diversity and geographic distributions within this genus as comprehensively as possible. We reconstructed phylogenetic trees from mitochondrial (16S, COI) and nuclear genes (GAPDH), both separately and using a combined or concatenated dataset, and performed several species delimitation analyses (PTP, ABGD, GMYC) on the COI phylogeny to propose Primary Species Hypotheses (PSHs) within the genus. All phylogenies recovered the genus Pacifastacus as monophyletic, within which we identified a range of six to 21 PSHs; more abundant PSHs delimitations from GMYC and ABGD were always nested within PSHs delimited by the more conservative PTP method. Pacifastacus leniusculus included the majority of PSHs and was not monophyletic relative to the other Pacifastacus species considered. Several of these highly distinct P. leniusculus PSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities for Pacifastacus crayfishes in western North America, and may inform better understanding and management of P. leniusculus in regions where it is invasive, such as Europe and Japan.
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Affiliation(s)
- Eric R Larson
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign , Urbana, Illinois , United States
| | - Magalie Castelin
- Pacific Biological Station, Fisheries and Oceans Canada , Nanaimo, British Columbia , Canada
| | - Bronwyn W Williams
- North Carolina Museum of Natural Sciences , Raleigh, North Carolina , United States
| | - Julian D Olden
- School of Aquatic and Fishery Sciences, University of Washington , Seattle, Washington , United States
| | - Cathryn L Abbott
- Pacific Biological Station, Fisheries and Oceans Canada , Nanaimo, British Columbia , Canada
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10
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Hernández D, Casane D, Chevalier-Monteagudo P, Bernatchez L, García-Machado E. Go West: A One Way Stepping-Stone Dispersion Model for the Cavefish Lucifuga dentata in Western Cuba. PLoS One 2016; 11:e0153545. [PMID: 27082117 PMCID: PMC4833296 DOI: 10.1371/journal.pone.0153545] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 03/31/2016] [Indexed: 11/19/2022] Open
Abstract
Consistent with the limited dispersal capacity of most troglobitic animals, almost all Lucifuga cavefish species have very narrow geographic distribution in Cuba. However, one species, L. dentata, has a wide but disjointed distribution over 300 km in the west of the island. In order to estimate the relative role of vicariance and dispersal in the unexpected L. dentata distribution, we obtained partial sequences of the mitochondrial DNA (mtDNA) cytochrome b (cytb) gene and control region (CR), and then applied Approximate Bayesian Computation (ABC), based on the identification of five genetic and geographic congruent groups of populations. The process that best explains the distribution of genetic diversity in this species is sequential range expansion from east Matanzas to the western Pinar del Río provinces, followed by isolation of groups of populations. We found relative high haplotype diversity and low nucleotide diversity in all but the Havana group, which has high values for both diversity parameters, suggesting that this group has been demographically stable over time. For two groups of populations (Cayuco and Bolondrón), the mismatch distribution analyses suggests past demographic expansion. In the case of the Cayuco region, the star like relationships of haplotypes in the network suggests a recent founding event, congruent with other evidence indicating that this is the most recently colonized region. Over all, the results suggest that a combination of habitat availability, temporal interconnections, and possibly the biological properties of this species, may have enabled its dispersal and range expansion compared to other species of the genus, which are more geographically restricted.
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Affiliation(s)
- Damir Hernández
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 entre 1ra y 3ra, Miramar, Playa, La Habana, 11300, Cuba
| | - Didier Casane
- Laboratoire Evolution, Génomes, Comportement, Ecologie, CNRS, Université Paris-Sud, UMR 9191, IRD UMR 247, Gif-sur-Yvette, France
- Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
| | | | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Erik García-Machado
- Centro de Investigaciones Marinas, Universidad de La Habana, Calle 16, No. 114 entre 1ra y 3ra, Miramar, Playa, La Habana, 11300, Cuba
- * E-mail:
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11
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Palacios Theil E, Cuesta JA, Felder DL. Molecular evidence for non-monophyly of the pinnotheroid crabs (Crustacea : Brachyura : Pinnotheroidea), warranting taxonomic reappraisal. INVERTEBR SYST 2016. [DOI: 10.1071/is15023] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The crabs of the family Pinnotheridae are well known as commensals or parasites, mainly of molluscs and tubeworms. The phylogeny of the group, however, is poorly understood, with preliminary morphological and molecular studies questioning its monophyly. Here we used molecular genetic markers (16S, 12S mitochondrial; histone 3 nuclear) to infer a phylogeny for the family Pinnotheridae De Haan, 1833 to reevaluate the phylogeny and systematics at the level of its subfamilies and genera. Our molecular phylogeny indicated that Parapinnixa cortesi Thoma, Heard, & Vargas, 2005, Parapinnixa hendersoni Rathbun, 1918, Pinnotherelia laevigata H. Milne Edwards & Lucas, 1844, Sakaina yokoyai (Glassell, 1933), Tetrias fischerii (A. Milne-Edwards, 1867) and Tetrias scabripes Rathbun, 1898 should be removed from the family Pinnotheridae, while composition of the present subfamilies, Pinnotherinae De Haan, 1833 and Pinnothereliinae Alcock, 1900, must be revised. At generic level, Clypeasterophilus Campos, 1990, Dissodactylus Smith, 1870, Fabia Dana, 1851, Nepinnotheres Manning, 1993 and Pinnixa White, 1846 were not monophyletic in our analyses. With the exclusion of Pinnotherelia from Pinnotheridae, remaining species of Pinnothereliinae are assigned to Pinnixinae Števčić, 2005, a new subfamily based upon revision and elevation of rank for the tribe Pinnixini Števčić, 2005. In addition, we restructure membership of the subfamily Pinnotherinae and propose Pinnixulalinae, subfam. nov. to accommodate species that were excluded by molecular analyses from the other two subfamilies. These have a firm, wider-than-long carapace with clearly defined regions, strong legs that are usually tuberculate and very setose, and a third maxilliped with an elongate ischiomerus in which the ischium and merus may or may not be indistinguishably fused. Our analyses included 169 pinnotherid exemplars, representing almost half of the genera and about a quarter of the species presently recognised for the family. The relationships within and among some taxa are resolved to greater or lesser extent and the phylogenetic biodiversity of pinnotherid crabs is revealed. However, future publications will most likely result in a further increase in the number of taxa.
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12
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Owen CL, Bracken-Grissom H, Stern D, Crandall KA. A synthetic phylogeny of freshwater crayfish: insights for conservation. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140009. [PMID: 25561670 DOI: 10.1098/rstb.2014.0009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Phylogenetic systematics is heading for a renaissance where we shift from considering our phylogenetic estimates as a static image in a published paper and taxonomies as a hardcopy checklist to treating both the phylogenetic estimate and dynamic taxonomies as metadata for further analyses. The Open Tree of Life project (opentreeoflife.org) is developing synthesis tools for harnessing the power of phylogenetic inference and robust taxonomy to develop a synthetic tree of life. We capitalize on this approach to estimate a synthesis tree for the freshwater crayfish. The crayfish make an exceptional group to demonstrate the utility of the synthesis approach, as there recently have been a number of phylogenetic studies on the crayfishes along with a robust underlying taxonomic framework. Importantly, the crayfish have also been extensively assessed by an IUCN Red List team and therefore have accurate and up-to-date area and conservation status data available for analysis within a phylogenetic context. Here, we develop a synthesis phylogeny for the world's freshwater crayfish and examine the phylogenetic distribution of threat. We also estimate a molecular phylogeny based on all available GenBank crayfish sequences and use this tree to estimate divergence times and test for divergence rate variation. Finally, we conduct EDGE and HEDGE analyses and identify a number of species of freshwater crayfish of highest priority in conservation efforts.
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Affiliation(s)
- Christopher L Owen
- Computational Biology Institute, George Washington University, Ashburn, VA 20132, USA
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - David Stern
- Computational Biology Institute, George Washington University, Ashburn, VA 20132, USA
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA 20132, USA Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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13
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Whelan NV, Strong EE. Morphology, molecules and taxonomy: extreme incongruence in pleurocerids (
G
astropoda,
C
erithioidea,
P
leuroceridae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12139] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathan V. Whelan
- Department of Biological Sciences University of Alabama BOX 870345 Tuscaloosa AL 35487 USA
| | - Ellen E. Strong
- Department of Invertebrate Zoology National Museum of Natural History Smithsonian Institution, PO Box 37012, MRC 163 Washington DC 20013‐7012 USA
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14
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Lasley RM, Klaus S, Ng PKL. Phylogenetic relationships of the ubiquitous coral reef crab subfamily Chlorodiellinae (Decapoda, Brachyura, Xanthidae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Robert M. Lasley
- Department of Biological Sciences; National University of Singapore; Kent Ridge Singapore 119260 Singapore
- Department of Invertebrate Zoology; National Museum of Natural History; Smithsonian Institution; Suitland MD 20746 USA
| | - Sebastian Klaus
- Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu 610041 China
- Department of Ecology and Evolution; J. W. Goethe-Universität; Frankfurt am Main D-60438 Germany
| | - Peter K. L. Ng
- Raffles Museum of Biodiversity Research; National University of Singapore; Kent Ridge Singapore 119260 Singapore
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15
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Wong JM, Pérez-Moreno JL, Chan TY, Frank TM, Bracken-Grissom HD. Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda). Mol Phylogenet Evol 2014; 83:278-92. [PMID: 25482362 DOI: 10.1016/j.ympev.2014.11.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/17/2014] [Accepted: 11/22/2014] [Indexed: 12/17/2022]
Abstract
Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores. Phylogenetic analyses can be useful for tracing the evolution of bioluminescence, however, the few studies that have attempted to reconcile the relationships within Oplophoridae have generated trees with low-resolution. We present the most comprehensive phylogeny of Oplophoridae to date, with 90% genera coverage using seven genes (mitochondrial and nuclear) across 30 oplophorid species. We use our resulting topology to trace the evolution of bioluminescence within Oplophoridae. Previous studies have suggested that oplophorid visual systems may be tuned to differentiate the separate modes of bioluminescence. While all oplophorid shrimp possess a visual pigment sensitive to blue-green light, only those bearing photophores have an additional pigment sensitive to near-ultraviolet light. We attempt to characterize opsins, visual pigment proteins essential to light detection, in two photophore-bearing species (Systellaspis debilis and Oplophorus gracilirostris) and make inferences regarding their function and evolutionary significance.
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Affiliation(s)
- Juliet M Wong
- Florida International University, Department of Biological Sciences, 3000 NE 151st St, North Miami, FL 33181, United States.
| | - Jorge L Pérez-Moreno
- Florida International University, Department of Biological Sciences, 3000 NE 151st St, North Miami, FL 33181, United States.
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan, ROC.
| | - Tamara M Frank
- Nova Southeastern University, Oceanographic Center, 8000 North Ocean Drive, Dania Beach, FL 33004, United States.
| | - Heather D Bracken-Grissom
- Florida International University, Department of Biological Sciences, 3000 NE 151st St, North Miami, FL 33181, United States.
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16
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Marchiori AB, Fornel R, Santos S. Morphometric variation in allopatric populations of Aegla platensis (Crustacea: Decapoda: Anomura): possible evidence for cryptic speciation. ZOOMORPHOLOGY 2014. [DOI: 10.1007/s00435-014-0242-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Perrotta I, Aquila S, Mazzulla S. Expression profile and subcellular localization of GAPDH in the smooth muscle cells of human atherosclerotic plaque: an immunohistochemical and ultrastructural study with biological therapeutic perspectives. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:1145-1157. [PMID: 24851941 DOI: 10.1017/s1431927614001020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has long been considered a classical glycolytic enzyme involved exclusively in cytosolic energy production. Several recent studies, however, have demonstrated that GAPDH is a multifunctional protein whose presence and activity can be regulated by disease states and/or experimental manipulation. Expression levels of GAPDH have been shown to be altered in certain tumors as well as in proliferating and differentiating cells. Since dedifferentiation and proliferation of smooth muscle cells (SMCs) are important features of human atherosclerosis, we have characterized the expression profile of GAPDH in the SMCs of atherosclerotic plaques and its putative interrelationship with the synthetic/proliferative status of these cells utilizing the proliferating cell nuclear antigen (PCNA) antibody, a valuable marker of cell proliferation. Western blot data revealed that GAPDH was significantly upregulated in atherosclerotic plaque specimens. Immunohistochemical stains demonstrated that GAPDH accumulated in the nucleus of dedifferentiated SMCs that also showed positive immunoreactivity for PCNA, but remained cytoplasmatic in the contractile SMCs (PCNA-negative), thus reflecting the proliferative, structural and synthetic differences between them. We suggest that, in human atherosclerotic plaque, GAPDH might exert additional functions that are independent of its well-documented glycolytic activity and might play key roles in development of the disease.
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Affiliation(s)
- Ida Perrotta
- 1Department of Biology,Ecology and Earth Science (Di.B.E.S.T.),University of Calabria - Arcavacata,Rende 87036,Cosenza,Italy
| | - Saveria Aquila
- 2Centro Sanitario - Department of Pharmacy and Sciences of Health and Nutrition,University of Calabria - Arcavacata,Rende 87036,Cosenza,Italy
| | - Sergio Mazzulla
- 1Department of Biology,Ecology and Earth Science (Di.B.E.S.T.),University of Calabria - Arcavacata,Rende 87036,Cosenza,Italy
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18
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Bracken-Grissom HD, Ahyong ST, Wilkinson RD, Feldmann RM, Schweitzer CE, Breinholt JW, Bendall M, Palero F, Chan TY, Felder DL, Robles R, Chu KH, Tsang LM, Kim D, Martin JW, Crandall KA. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida). Syst Biol 2014; 63:457-79. [PMID: 24562813 DOI: 10.1093/sysbio/syu008] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A rich fossil history coupled with dense taxon coverage allowed us to estimate and compare divergence times and origins of major lineages using two drastically different approaches. Age priors were constructed and/or included based on fossil age information or fossil discovery, age, and extant species count data. Results from the two approaches were largely congruent across deep to shallow taxonomic divergences across major lineages. The origin of the first lobster-like decapod (Polychelida) was estimated in the Devonian (∼409-372 Ma) with all infraorders present in the Carboniferous (∼353-318 Ma). Fossil calibration subsampling studies examined the influence of sampling density (number of fossils) and placement (deep, middle, and shallow) on divergence time estimates. Results from our study suggest including at least 1 fossil per 10 operational taxonomic units (OTUs) in divergence dating analyses. [Dating; decapods; divergence; lobsters; molecular; morphology; phylogenetics.].
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Florida International University, 3000 NE 151st Street, North Miami, FL 33181, USA;
| | - Shane T Ahyong
- Australian Museum, 6 College Street, Sydney, NSW 2010, Australia;University of New South Wales, Kensington, NSW 2052, Australia
| | | | | | - Carrie E Schweitzer
- Kent State University at Stark, 6000 Frank Avenue NW, North Canton, OH 44720, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Ferran Palero
- Unitat Mixta Genòmica i Salut CSISP-UV, Institut Cavanilles Universitat de Valencia, C/Catedrático Jose Beltran 2,46980 Paterna, Spain
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan, R.O.C
| | - Darryl L Felder
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Rafael Robles
- Laboratory of Bioecology and Crustacean Systematics, Department of Biology, FFCLRP, University of São Paulo (USP), Ave. Bandeirantes 3900, CEP 14040 - 901, Ribeirão Preto, SP Brazil
| | - Ka-Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ling-Ming Tsang
- Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan, R.O.C.;School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Dohyup Kim
- Brigham Young University, 401 WIDB, Provo, UT 84606, USA
| | - Joel W Martin
- Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Keith A Crandall
- George Washington University, Computational Biology Institute, Ashburn, VA 20147, USA
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19
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Windsor AM, Felder DL. Molecular phylogenetics and taxonomic reanalysis of the family Mithracidae MacLeay (Decapoda : Brachyura : Majoidea). INVERTEBR SYST 2014. [DOI: 10.1071/is13011] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mithracid crabs comprise a primarily subtidal reef- and rubble-dwelling group inhabiting both tropical and subtropical seas. Despite their relative ubiquity in many hard-substrate environments, there has been little consensus about their phylogenetic relationships or whether their group rank should be that of subfamily or family. We have used a combined molecular dataset of two nuclear (18S, H3) and three mitochondrial (12S, 16S, COI) genes to build a preliminary molecular phylogeny of Majoidea in order to examine the membership of Mithracidae. We then built a second molecular phylogeny based on three mitochondrial genes to assess the internal composition of the family, and conducted comparative morphological examinations of genera and species that resolved in unexpected positions on the phylogram. Four genera are designated under new or resurrected names on the basis of molecular and morphological characters, while memberships of several other existing genera are modified. Following review of molecular and morphological characters, the genera Coelocerus, Cyclocoeloma, Cyphocarcinus, Leptopisa, Micippa, Picrocerodes, Stenocionops and Tiarinia are provisionally excluded from Mithracidae s.s., while Hemus and Pitho are included in it. A key to genera of Mithracidae is provided.
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20
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Thoma BP, Guinot D, Felder DL. Evolutionary relationships among American mud crabs (Crustacea: Decapoda: Brachyura: Xanthoidea) inferred from nuclear and mitochondrial markers, with comments on adult morphology. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brent P. Thoma
- Department of Biology and Laboratory for Crustacean Research; University of Louisiana at Lafayette; Lafayette LA 70504 USA
| | - Danièle Guinot
- Muséum national d'Histoire naturelle; Département milieux et peuplements aquatiques; 61 rue Buffon Paris 75005 France
| | - Darryl L. Felder
- Department of Biology and Laboratory for Crustacean Research; University of Louisiana at Lafayette; Lafayette LA 70504 USA
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21
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Capderrey C, Kaufmann B, Jean P, Malard F, Konecny-Dupré L, Lefébure T, Douady CJ. Microsatellite development and first population size estimates for the groundwater isopod Proasellus walteri. PLoS One 2013; 8:e76213. [PMID: 24086709 PMCID: PMC3785429 DOI: 10.1371/journal.pone.0076213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/17/2013] [Indexed: 11/18/2022] Open
Abstract
Effective population size (N e) is one of the most important parameters in, ecology, evolutionary and conservation biology; however, few studies of N e in surface freshwater organisms have been published to date. Even fewer studies have been carried out in groundwater organisms, although their evolution has long been considered to be particularly constrained by small N e. In this study, we estimated the contemporary effective population size of the obligate groundwater isopod: Proaselluswalteri (Chappuis, 1948). To this end, a genomic library was enriched for microsatellite motifs and sequenced using 454 GS-FLX technology. A total of 54,593 reads were assembled in 10,346 contigs or singlets, of which 245 contained candidate microsatellite sequences with suitable priming sites. Ninety-six loci were tested for amplification, polymorphism and multiplexing properties, of which seven were finally selected for N e estimation. Linkage disequilibrium and approximate Bayesian computation methods revealed that N e in this small interstitial groundwater isopod could reach large sizes (> 585 individuals). Our results suggest that environmental conditions in groundwater, while often referred to as extreme, are not necessarily associated with small N e.
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Affiliation(s)
- Cécile Capderrey
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Bernard Kaufmann
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Pauline Jean
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Florian Malard
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Lara Konecny-Dupré
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Tristan Lefébure
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Christophe J. Douady
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
- Institut Universitaire de France, Paris, France
- * E-mail:
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22
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Bracken-Grissom HD, Cannon ME, Cabezas P, Feldmann RM, Schweitzer CE, Ahyong ST, Felder DL, Lemaitre R, Crandall KA. A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda). BMC Evol Biol 2013; 13:128. [PMID: 23786343 PMCID: PMC3708748 DOI: 10.1186/1471-2148-13-128] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 05/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history-phylogeny, divergence times, character evolution and diversification-of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses. RESULTS Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224-296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae. CONCLUSIONS Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights into the origins of major lineages and events and the timing of morphological (body form) and ecological (habitat) transitions. Living anomuran biodiversity is the product of 2 major changes in the tempo of diversification; our initial insights suggest that the acquisition of a crab-like form did not act as a key innovation.
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Florida International University-Biscayne Bay Campus, North Miami, FL 33181, USA.
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Niemiller ML, Zigler KS. Patterns of cave biodiversity and endemism in the Appalachians and Interior Plateau of Tennessee, USA. PLoS One 2013; 8:e64177. [PMID: 23717562 PMCID: PMC3661478 DOI: 10.1371/journal.pone.0064177] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 04/13/2013] [Indexed: 11/19/2022] Open
Abstract
Using species distribution data, we developed a georeferenced database of troglobionts (cave-obligate species) in Tennessee to examine spatial patterns of species richness and endemism, including >2000 records for 200 described species. Forty aquatic troglobionts (stygobionts) and 160 terrestrial troglobionts are known from caves in Tennessee, the latter having the greatest diversity of any state in the United States. Endemism was high, with 25% of terrestrial troglobionts (40 species) and 20% of stygobionts (eight species) known from just a single cave and nearly two-thirds of all troglobionts (130 species) known from five or fewer caves. Species richness and endemism were greatest in the Interior Plateau (IP) and Southwestern Appalachians (SWA) ecoregions, which were twice as diverse as the Ridge and Valley (RV). Troglobiont species assemblages were most similar between the IP and SWA, which shared 59 species, whereas the RV cave fauna was largely distinct. We identified a hotspot of cave biodiversity with a center along the escarpment of the Cumberland Plateau in south-central Tennessee defined by both species richness and endemism that is contiguous with a previously defined hotspot in northeastern Alabama. Nearly half (91 species) of Tennessee’s troglobiont diversity occurs in this region where several cave systems contain ten or more troglobionts, including one with 23 species. In addition, we identified distinct troglobiont communities across the state. These communities corresponded to hydrological boundaries and likely reflect past or current connectivity between subterranean habitats within and barriers between hydrological basins. Although diverse, Tennessee’s subterranean fauna remains poorly studied and many additional species await discovery and description. We identified several undersampled regions and outlined conservation and management priorities to improve our knowledge and aid in protection of the subterranean biodiversity in Tennessee.
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Affiliation(s)
- Matthew L. Niemiller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Kirk S. Zigler
- Department of Biology, University of the South, Sewanee, Tennessee, United States of America
- * E-mail:
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24
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Ainscough BJ, Breinholt JW, Robison HW, Crandall KA. Molecular phylogenetics of the burrowing crayfish genusFallicambarus(Decapoda: Cambaridae). ZOOL SCR 2013. [DOI: 10.1111/zsc.12006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Breinholt JW, Porter ML, Crandall KA. Testing phylogenetic hypotheses of the subgenera of the freshwater crayfish genus Cambarus (Decapoda: Cambaridae). PLoS One 2012; 7:e46105. [PMID: 23049950 PMCID: PMC3458831 DOI: 10.1371/journal.pone.0046105] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression. Methodology/Principal Findings We use three mitochondrial and one nuclear gene regions to estimate the phylogenetic relationships for species within the genus Cambarus and test evolutionary hypotheses of relationships and associated morphological and biogeographical hypotheses. Our resulting phylogeny indicates that the genus Cambarus is polyphyletic, however we fail to reject the monophyly of Cambarus with a topology test. The majority of the Cambarus subgenera are rejected as monophyletic, suggesting the morphological characters used to define those taxa are subject to convergent evolution. While we found incongruence between taxonomy and estimated phylogenetic relationships, a multiple model regression analysis indicates that taxonomy had more explanatory power of genetic relationships than either habitat or geographic distance. Conclusions We find convergent evolution has impacted the morphological features used to delimit Cambarus subgenera. Studies of the crayfish genus Orconectes have shown gonopod morphology used to delimit subgenera is also affected by convergent evolution. This suggests that morphological diagnoses based on traditional crayfish taxonomy might be confounded by convergent evolution across the cambarids and has little utility in diagnosing relationships or defining natural groups. We further suggest that convergent morphological evolution appears to be a common occurrence in invertebrates suggesting the need for careful phylogenetically based interpretations of morphological evolution in invertebrate systematics.
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26
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Bracken-Grissom HD, Felder DL, Vollmer NL, Martin JW, Crandall KA. Phylogenetics links monster larva to deep-sea shrimp. Ecol Evol 2012; 2:2367-73. [PMID: 23145324 PMCID: PMC3492765 DOI: 10.1002/ece3.347] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/10/2012] [Accepted: 07/14/2012] [Indexed: 11/07/2022] Open
Abstract
Mid-water plankton collections commonly include bizarre and mysterious developmental stages that differ conspicuously from their adult counterparts in morphology and habitat. Unaware of the existence of planktonic larval stages, early zoologists often misidentified these unique morphologies as independent adult lineages. Many such mistakes have since been corrected by collecting larvae, raising them in the lab, and identifying the adult forms. However, challenges arise when the larva is remarkably rare in nature and relatively inaccessible due to its changing habitats over the course of ontogeny. The mid-water marine species Cerataspis monstrosa (Gray 1828) is an armored crustacean larva whose adult identity has remained a mystery for over 180 years. Our phylogenetic analyses, based in part on recent collections from the Gulf of Mexico, provide definitive evidence that the rare, yet broadly distributed larva, C. monstrosa, is an early developmental stage of the globally distributed deepwater aristeid shrimp, Plesiopenaeus armatus. Divergence estimates and phylogenetic relationships across five genes confirm the larva and adult are the same species. Our work demonstrates the diagnostic power of molecular systematics in instances where larval rearing seldom succeeds and morphology and habitat are not indicative of identity. Larval-adult linkages not only aid in our understanding of biodiversity, they provide insights into the life history, distribution, and ecology of an organism.
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Brigham Young University Provo, Utah, 84602 ; Department of Biology, Florida International University-Biscayne Bay Campus North Miami, Florida, 33181
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27
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Loss of genetic diversity means loss of geological information: the endangered Japanese crayfish exhibits remarkable historical footprints. PLoS One 2012; 7:e33986. [PMID: 22470505 PMCID: PMC3314697 DOI: 10.1371/journal.pone.0033986] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 02/24/2012] [Indexed: 11/19/2022] Open
Abstract
Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall FST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events.
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SCHILTHUIZEN MENNO, RUTTEN ELISEMJ, HAASE MARTIN. Small-scale genetic structuring in a tropical cave snail and admixture with its above-ground sister species†. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2011.01835.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biol Evol 2011; 3:1312-23. [PMID: 22002916 PMCID: PMC3236605 DOI: 10.1093/gbe/evr106] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2011] [Indexed: 12/03/2022] Open
Abstract
Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.
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Affiliation(s)
- Seth M Bybee
- Department of Biology, Brigham Young University, USA.
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30
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Yang CH, Bracken-Grissom H, Kim D, Crandall KA, Chan TY. Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae). Mol Phylogenet Evol 2011; 62:237-50. [PMID: 22008407 DOI: 10.1016/j.ympev.2011.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/23/2011] [Accepted: 09/26/2011] [Indexed: 10/17/2022]
Abstract
The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.
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Affiliation(s)
- Chien-Hui Yang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan, ROC
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Bybee SM, Bracken-Grissom HD, Hermansen RA, Clement MJ, Crandall KA, Felder DL. Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea). ZOOL ANZ 2011. [DOI: 10.1016/j.jcz.2011.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Dixon GB, Zigler KS. Cave-Obligate Biodiversity on the Campus of Sewanee: The University of the South, Franklin County, Tennessee. SOUTHEAST NAT 2011. [DOI: 10.1656/058.010.0206] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Evidence for population fragmentation within a subterranean aquatic habitat in the Western Australian desert. Heredity (Edinb) 2011; 107:215-30. [PMID: 21343944 DOI: 10.1038/hdy.2011.6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The evolution of subterranean animals following multiple colonisation events from the surface has been well documented, but few studies have investigated the potential for species diversification within cavernicolous habitats. Isolated calcrete (carbonate) aquifers in central Western Australia have been shown to contain diverse assemblages of aquatic subterranean invertebrate species (stygofauna) and to offer a unique model system for exploring the mechanisms of speciation in subterranean ecosystems. In this paper, we investigated the hypothesis that microallopatric speciation processes (fragmentation and isolation by distance (IBD)) occur within calcretes using a comparative phylogeographic study of three stygobiontic diving beetle species, one amphipod species and a lineage of isopods. Specimens were sequenced for the mitochondrial cytochrome c oxidase 1 gene from three main sites: Quandong Well, Shady Well (SW) and Mt. Windarra (MW), spanning a 15 km region of the Laverton Downs Calcrete. Phylogenetic and haplotype network analyses revealed that each species possessed a single divergent clade of haplotypes that were present only at the southern MW site, despite the existence of other haplotypes at MW that were shared with SW. IBD between MW and SW was evident, but the common phylogeographic pattern most likely resulted from fragmentation, possibly by a salt lake adjacent to MW. These findings suggest that microallopatric speciation within calcretes may be a significant diversifying force, although the proportion of stygofauna species that may have resulted from in situ speciation in this system remains to be determined.
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Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics. Genome Biol Evol 2011. [DOI: 10.evr106[pii]10.1093/gbe/evr106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | | | | | - Russell A. Hermansen
- Department of Biology, Brigham Young University
- Department of Molecular Biology, University of Wyoming
| | - Robert L. Byers
- Department of Plant and Wildlife Sciences, Brigham Young University
| | | | - Joshua A. Udall
- Department of Plant and Wildlife Sciences, Brigham Young University
| | - Edward R. Wilcox
- Department of Biology, Brigham Young University
- DNA Sequencing Center, Brigham Young University
| | - Keith A. Crandall
- Department of Biology, Brigham Young University
- Monte L. Bean Life Science Museum, Brigham Young University
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Baibai T, Oukhattar L, Mountassif D, Assobhei O, Serrano A, Soukri A. Comparative molecular analysis of evolutionarily distant glyceraldehyde-3-phosphate dehydrogenase from Sardina pilchardus and Octopus vulgaris. Acta Biochim Biophys Sin (Shanghai) 2010; 42:863-72. [PMID: 21106768 DOI: 10.1093/abbs/gmq103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The NAD(+)-dependent cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12), which is recognized as a key to central carbon metabolism in glycolysis and gluconeogenesis and as an important allozymic polymorphic biomarker, was purified from muscles of two marine species: the skeletal muscle of Sardina pilchardus Walbaum (Teleost, Clupeida) and the incompressible arm muscle of Octopus vulgaris (Mollusca, Cephalopoda). Comparative biochemical studies have revealed that they differ in their subunit molecular masses and in pI values. Partial cDNA sequences corresponding to an internal region of the GapC genes from Sardina and Octopus were obtained by polymerase chain reaction using degenerate primers designed from highly conserved protein motifs. Alignments of the deduced amino acid sequences were used to establish the 3D structures of the active site of two enzymes as well as the phylogenetic relationships of the sardine and octopus enzymes. These two enzymes are the first two GAPDHs characterized so far from teleost fish and cephalopod, respectively. Interestingly, phylogenetic analyses indicated that the sardina GAPDH is in a cluster with the archetypical enzymes from other vertebrates, while the octopus GAPDH comes together with other molluscan sequences in a distant basal assembly closer to bacterial and fungal orthologs, thus suggesting their different evolutionary scenarios.
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Affiliation(s)
- Tarik Baibai
- Université Hassan II, Casablanca B.P., Morrocco.
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Juan C, Guzik MT, Jaume D, Cooper SJB. Evolution in caves: Darwin’s ‘wrecks of ancient life’ in the molecular era. Mol Ecol 2010; 19:3865-80. [PMID: 20637049 DOI: 10.1111/j.1365-294x.2010.04759.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Carlos Juan
- Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, (Balearic Islands) Spain.
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BOTELLO ALEJANDRO, ALVAREZ FERNANDO. Genetic variation in the stygobitic shrimp Creaseria morleyi (Decapoda: Palaemonidae), evidence of bottlenecks and re-invasions in the Yucatan Peninsula. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2009.01355.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Guzik MT, Austin AD, Cooper SJB, Harvey MS, Humphreys WF, Bradford T, Eberhard SM, King RA, Leys R, Muirhead KA, Tomlinson M. VIEWPOINT. Is the Australian subterranean fauna uniquely diverse? INVERTEBR SYST 2010. [DOI: 10.1071/is10038] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Australia was historically considered a poor prospect for subterranean fauna but, in reality, the continent holds a great variety of subterranean habitats, with associated faunas, found both in karst and non-karst environments. This paper critically examines the diversity of subterranean fauna in several key regions for the mostly arid western half of Australia. We aimed to document levels of species richness for major taxon groups and examine the degree of uniqueness of the fauna. We also wanted to compare the composition of these ecosystems, and their origins, with other regions of subterranean diversity world-wide. Using information on the number of ‘described’ and ‘known’ invertebrate species (recognised based on morphological and/or molecular data), we predict that the total subterranean fauna for the western half of the continent is 4140 species, of which ~10% is described and 9% is ‘known’ but not yet described. The stygofauna, water beetles, ostracods and copepods have the largest number of described species, while arachnids dominate the described troglofauna. Conversely, copepods, water beetles and isopods are the poorest known groups with less than 20% described species, while hexapods (comprising mostly Collembola, Coleoptera, Blattodea and Hemiptera) are the least known of the troglofauna. Compared with other regions of the world, we consider the Australian subterranean fauna to be unique in its diversity compared with the northern hemisphere for three key reasons: the range and diversity of subterranean habitats is both extensive and novel; direct faunal links to ancient Pangaea and Gondwana are evident, emphasising their early biogeographic history; and Miocene aridification, rather than Pleistocene post-ice age driven diversification events (as is predicted in the northern hemisphere), are likely to have dominated Australia’s subterranean speciation explosion. Finally, we predict that the geologically younger, although more poorly studied, eastern half of the Australian continent is unlikely to be as diverse as the western half, except for stygofauna in porous media. Furthermore, based on similar geology, palaeogeography and tectonic history to that seen in the western parts of Australia, southern Africa, parts of South America and India may also yield similar subterranean biodiversity to that described here.
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Affiliation(s)
- Christopher E. Skelton
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061; .
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Phylogeographic structure in the threatened Yarra pygmy perch Nannoperca obscura (Teleostei: Percichthyidae) has major implications for declining populations. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0024-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau. Mol Phylogenet Evol 2009; 53:1025-31. [DOI: 10.1016/j.ympev.2009.03.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 03/11/2009] [Indexed: 11/15/2022]
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42
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Timpe EK, Graham SP, Bonett RM. Phylogeography of the Brownback Salamander reveals patterns of local endemism in Southern Appalachian springs. Mol Phylogenet Evol 2009; 52:368-76. [DOI: 10.1016/j.ympev.2009.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 02/26/2009] [Accepted: 03/29/2009] [Indexed: 11/26/2022]
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Vaezi J, Brouillet L. Phylogenetic relationships among diploid species of Symphyotrichum (Asteraceae: Astereae) based on two nuclear markers, ITS and GAPDH. Mol Phylogenet Evol 2009; 51:540-53. [PMID: 19289175 DOI: 10.1016/j.ympev.2009.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 02/15/2009] [Accepted: 03/06/2009] [Indexed: 10/21/2022]
Abstract
The mostly North American subtribe Symphyotrichinae (Asteraceae: Astereae) comprises Canadanthus, Ampelaster, Psilactis, Almutaster, and Symphyotrichum. Intergeneric and interspecific relationships within the subtribe have been investigated in the past, particularly by Nesom [Nesom, G.L., 1994. Review of the taxonomy of Aster sensu lato (Asteraceae: Astereae), emphasizing the new world species, Phytologia 77, 141-297] and Semple [Semple, J.C., 2005. Classification of Symphyotrichum. Available from: <http://www.jcsemple.uwaterloo.ca/Symphyotrichumclassification.htm/>], using morphological and cytological approaches. Symphyotrichum is the largest and most complex genus within the subtribe and includes four subgenera: Symphyotrichum (x=7, 8), Virgulus (x=4, 5), Astropolium (x=5), and Chapmaniani (x=7). In this study we used two nuclear markers, the nrDNA internal transcribed spacer (ITS) and the low-copy nuclear gene glyceraldehyde 3-phosphate dehydrogenase (GAPDH), to resolve intergeneric and interspecific relationships within the subtribe at the diploid level, and to determine whether our phylogenies validate the classifications of Nesom or Semple. Our results confirm the distinct generic status of Canadanthus and Ampelaster, whereas Psilactis and Almutaster form a polytomy with Symphyotrichum. Within Symphyotrichum, subg. Virgulus is monophyletic based on ITS and appears polyphyletic based on GAPDH. Neither the ITS nor the GAPDH analyses support a distinct status for subg. Astropolium, which groups within subg. Symphyotrichum. In general, interspecific relationships within Symphyotrichum are unresolved. Lack of resolution may be interpreted as a case of recent and rapid evolutionary radiation.
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Affiliation(s)
- Jamil Vaezi
- Dép Sciences Biologiques, Herbier Marie-Victorin, Institut de recherche en Biologie Végétale Université de Montréal, Montréal, Que, Canada.
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Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson. Mol Phylogenet Evol 2009; 50:580-98. [DOI: 10.1016/j.ympev.2008.11.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 11/26/2008] [Accepted: 11/28/2008] [Indexed: 11/21/2022]
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SCHULTZ MARKB, IERODIACONOU DANIELA, SMITH SARAHA, HORWITZ PIERRE, RICHARDSON ALASTAIRMM, CRANDALL KEITHA, AUSTIN CHRISTOPHERM. Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfishEngaeus sericatusClark (Decapoda: Parastacidae). Mol Ecol 2008; 17:5291-314. [DOI: 10.1111/j.1365-294x.2008.03996.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Schuster GA, Taylor CA, Johansen J. An Annotated Checklist and Preliminary Designation of Drainage Distributions of the Crayfishes of Alabama. SOUTHEAST NAT 2008. [DOI: 10.1656/1528-7092-7.3.493] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Tsang L, Ma K, Ahyong S, Chan TY, Chu K. Phylogeny of Decapoda using two nuclear protein-coding genes: Origin and evolution of the Reptantia. Mol Phylogenet Evol 2008; 48:359-68. [DOI: 10.1016/j.ympev.2008.04.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 04/01/2008] [Accepted: 04/06/2008] [Indexed: 12/01/2022]
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48
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Venarsky MP, Anderson FE, Wilhelm FM. Population genetic study of the U.S. federally listed Illinois cave amphipod, Gammarus acherondytes. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9579-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Crandall KA, Robison HW, Buhay JE. Avoidance of extinction through nonexistence: the use of museum specimens and molecular genetics to determine the taxonomic status of an endangered freshwater crayfish. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9546-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Mathews LM, Adams L, Anderson E, Basile M, Gottardi E, Buckholt MA. Genetic and morphological evidence for substantial hidden biodiversity in a freshwater crayfish species complex. Mol Phylogenet Evol 2008; 48:126-35. [PMID: 18346914 DOI: 10.1016/j.ympev.2008.02.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 02/05/2008] [Accepted: 02/06/2008] [Indexed: 11/15/2022]
Abstract
North America is a center of biodiversity for freshwater crayfish, with >300 described species, mostly in the family Cambaridae. However, the phylogenetic and phylogeographic relationships among these taxa are poorly understood, despite their ubiquitous occurrence in North American freshwater habitats. Here, we target the geographically widespread Orconectesvirilis and its sister taxa for genetic and morphological investigation. We used sequence data from two mitochondrial genes (16S rRNA and cytochrome oxidase I) and from one nuclear gene (glyceraldehyde-3-phosphate dehydrogenase), as well as morphological data from the male gonopod, to gain insights into phylogenetic relationships among individuals collected in the northeastern United States, where this taxon is considered to be invasive, and from Kansas. Our data reveal evidence for three cryptic species in our collections, in addition to O.virilis sensu stricto; all four clades are separated by both mitochondrial and nuclear sequence data. In addition, two of the newly discovered species, O.sp. nov. A and O.sp. nov. B, are distinguishable from O.virilis by significant differences in gonopod morphology (no data on gonopod morphology were available for O.sp. nov. C). O.sp. nov. A was collected at numerous sites in Massachusetts; additional sampling is required to determine if this species is native to New England. Two other taxa, O.sp. nov. B and O.sp. nov. C, were both collected from sites in eastern Kansas, and historically have probably been considered to be O.nais. In summary, this investigation indicates that this species complex may harbor a great deal of unknown biodiversity over the rest of its described range, and suggests that further attention to the phylogenetics and phylogeography of North American crayfishes may yield interesting insights into the evolution of biodiversity.
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Affiliation(s)
- Lauren M Mathews
- Department of Biology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA.
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