scholarly journals Phylogenetic species delimitation for crayfishes of the genusPacifastacus

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1915 ◽  
Author(s):  
Eric R. Larson ◽  
Magalie Castelin ◽  
Bronwyn W. Williams ◽  
Julian D. Olden ◽  
Cathryn L. Abbott
Keyword(s):  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Taxonomic Diversity ◽  
Pacifastacus Leniusculus ◽  
Phylogenetic Study ◽  
Conservation Priorities ◽  
Species Of Conservation Concern ◽  
Extant Species ◽  
Widely Invasive

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 genusPacifastacus, representing the first comprehensive phylogenetic study of this taxonomic group. Importantly,Pacifastacusincludes both the widely invasive signal crayfishPacifastacus leniusculus,as well as several species of conservation concern like the Shasta crayfishPacifastacus fortis. Our analysis used 83 individuals sampled across the four extantPacifastacusspecies (omitting the extinctPacifastacus 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 genusPacifastacusas 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 leniusculusincluded the majority of PSHs and was not monophyletic relative to the otherPacifastacusspecies considered. Several of these highly distinctP. leniusculusPSHs likely require urgent conservation attention. Our results identify research needs and conservation priorities forPacifastacuscrayfishes in western North America, and may inform better understanding and management ofP. leniusculusin regions where it is invasive, such as Europe and Japan.

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

scholarly journals Genetics, Diagnosis, and Management of Hürthle Cell Thyroid Neoplasms

2021 ◽  
Vol 12 ◽  
Author(s):  
David G. McFadden ◽  
Peter M. Sadow
Keyword(s):  
Molecular Genetic ◽  
Thyroid Neoplasms ◽  
Invasive Disease ◽  
Thyroid Tumor ◽  
Molecular Testing ◽  
Cell Adenoma ◽  
Tumor Subtypes ◽  
Hürthle Cell ◽  
Hürthle Cell Tumors ◽  
Widely Invasive

Hürthle cell lesions have been a diagnostic conundrum in pathology since they were first recognized over a century ago. Controversy as to the name of the cell, the origin of the cell, and even which cells in particular may be designated as such still challenge pathologists and confound those treating patients with a diagnosis of “Hürthle cell” anything within the diagnosis, especially if that anything is a sizable mass lesion. The diagnosis of Hürthle cell adenoma (HCA) or Hürthle cell carcinoma (HCC) has typically relied on a judgement call by pathologists as to the presence or absence of capsular and/or vascular invasion of the adjacent thyroid parenchyma, easy to note in widely invasive disease and a somewhat subjective diagnosis for minimally invasive or borderline invasive disease. Diagnostic specificity, which has incorporated a sharp increase in molecular genetic studies of thyroid tumor subtypes and the integration of molecular testing into preoperative management protocols, continues to be challenged by Hürthle cell neoplasia. Here, we provide the improving yet still murky state of what is known about Hürthle cell tumor genetics, clinical management, and based upon what we are learning about the genetics of other thyroid tumors, how to manage expectations, by pathologists, clinicians, and patients, for more actionable, precise classifications of Hürthle cell tumors of the thyroid.

scholarly journals Using a jumping spider fauna inventory (Araneae, Salticidae) as an indicator of the taxonomic diversity for Misiones, Argentina

2016 ◽  
Vol 64 (2) ◽  
pp. 875 ◽  
Author(s):  
Gonzalo D. Rubio
Keyword(s):  
Reference Data ◽  
Taxonomic Diversity ◽  
Diversity Indices ◽  
Conservation Priorities ◽  
Diversity Analysis ◽  
Jumping Spider ◽  
Future Studies

There is a clear connection between basic taxonomy and biodiversity issues. Faunistic studies with a taxonomically comprehensive inventory of species provide an important source of quantitative compiled information concerning several regions. This information can be used in diversity analysis and have great potential in setting conservation priorities. The salticid spider fauna of Misiones is relatively well known; here this knowledge is used to generate Clarke & Warwick taxonomic diversity indices. Different ecoregional diversities contributing to information about biodiversity levels of salticids in Misiones and providing reference data for future studies are analyzed. Differences between the three ecoregions of the province were found, mainly southern savannas regarding the forests of northern Misiones.

Lifeforms as criterion for species delimitation: Are Aristida adscensionis and A. coerulescens (Aristidoideae, Poaceae) two species?

Phytotaxa ◽  
2019 ◽  
Vol 393 (1) ◽  
pp. 67 ◽  
Author(s):  
MIKE THIV ◽  
J. ALFREDO REYES-BETANCORT ◽  
ORI FRAGMAN-SAPIR
Keyword(s):  
Morphometric Analysis ◽  
Species Delimitation ◽  
Phylogenetic Trees ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Life Forms ◽  
Clear Separation ◽  
Taxonomic Treatment ◽  
Molecular Phylogenetic ◽  
The Mediterranean

The distinction of the perennial Aristida coerulescens from the annual A. adscensionis and its taxonomic treatment has been subject of long discussions. We here include accessions from the Mediterranean and Macaronesia for molecular phylogenetic analyses and conducted a morphometric analysis. A lineage of A. adscensionis, A. coerulescens and A. effusa is well supported in phylogenetic trees. Moreover, a group of Mediterranean, Macaronesia and Arabian A. coerulescens and A. adscensionis is revealed where both taxa are intermingled. A morphological analysis of traditionally used spikelet characters did not indicate a clear separation of both taxa. We therefore conclude that A. coerulescens should best be treated as synonym of A. adscensionis. The differential character of annual and perennial life forms seems to be plastic in this taxon indicating rapid shifts between these two strategies. 

New Ordovician marine macroalgae from North America, with observations onButhograptus,Callithamnopsis, andChaetocladus

2018 ◽  
Vol 93 (2) ◽  
pp. 197-214 ◽  
Author(s):  
Steven T. LoDuca
Keyword(s):  
Taxonomic Diversity ◽  
Microscopic Investigation ◽  
Electron Microscopic Investigation ◽  
Marine Macroalgae ◽  
Electron Microscopic ◽  
Green Algal ◽  
Extant Species ◽  
The Family ◽  
New Occurrences ◽  
Northern Michigan

AbstractOrdovician material from the Platteville Formation (Sandbian) of southern Wisconsin and Big Hill Formation (Katian) of northern Michigan is described that provides novel information about the phylogenetic affinity, taxonomic diversity, and stratigraphic range of the nonbiomineralized taxaButhograptus,Callithamnopsis, andChaetocladus. Two new species ofButhograptus, a previously monotypic genus, are erected on the basis of the Platteville Formation material,Buthograptus gundersonin. sp. andB.meyerin. sp., and new occurrences ofB.laxusare recorded from several localities and two distinct stratigraphic levels within this unit. On the basis of scanning electron microscopic investigation of the material and the fact that each of the threeButhograptusspecies has a close counterpart in the frond morphology of an extant species ofCaulerpa,Buthograptusis interpreted as a member of the green algal order Bryopsidales. New specimens from the Platteville Formation assigned toCallithamnopsisreveal new morphological details for the type species,C.fruticosa(Hall, 1865), aspects of which indicate that the genus belongs to the family Triploporellaceae rather than Seletonellaceae within the green algal order Dasycladales, andChaetocladusmaterial from the Big Hill Formation includes specimens that are formally assigned toChaetocladus dubius(Spencer, 1884), a species of dasycladalean alga known previously only from the mid-Silurian of Ontario.

scholarly journals Check-list of Vertebrates in the “Tenuta dei Massimi” nature reserve (Rome, central Italy) with some remarks on local conservation priorities

2014 ◽  
Vol 1 (1) ◽  
pp. 25 ◽  
Author(s):  
Corrado Battisti
Keyword(s):  
Nature Reserve ◽  
Central Italy ◽  
Conservation Priorities ◽  
Check List ◽  
Local Conservation ◽  
Mosaic Landscape ◽  
Data Set ◽  
Species Of Conservation Concern ◽  
Bibliographic Data ◽  
Conservation Concern

We reported a complete check-list of Vertebrates for the “Tenuta dei Massimi” nature reserve, a protected area well representing a remnant agro-forest heterogeneous mosaic landscape of the “Campagna Romana”. Data were obtained from a large original and bibliographic data-set on a large time-span (1991-2012). This reserve represents an area with a high value of species richness when compared to the surrounding metropolitan areas, also including a large number of species of conservation concern at different scales. We obtained evidences for the occurrence of 141 species (one fish, six amphibians, 12 reptiles, 101 birds, 21 mammals). Among them, some species are of conservation concern at European, regional or local scale. Further research should be focused on a set of fragmentation-sensitive species to verify the long-term viability of their local small populations [<em>e.g. Hyla intermedia</em> Boulenger, 1882, <em>Bufo lineatus</em> Ninni, 1879, <em>Muscardinus avellanarius</em> (Linnaeus, 1758), <em>Sorex samniticus</em> Altobello, 1926)].

Morphological and molecular identification of some species of nematode of the family Protostrongylidae Leiper, 1926

2016 ◽  
Vol 3 (4) ◽  
pp. 454-461
Author(s):  
Салахутдинов ◽  
I. Salakhutdinov ◽  
Рузиев ◽  
B. Ruziev ◽  
Каримова ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Digital Camera ◽  
Molecular Genetic Analysis ◽  
Nucleotide Sequences ◽  
Genetic Identification ◽  
Mountain Area ◽  
Phylogenetic Relations ◽  
The Family

Objective of research: conducting morphological and molecular-genetic identification and studying phylogenetic relations between protostrongylids. Materials and methods: helminthological material was collected from wild (Capra sibirica, C. falconeri, Ovis vignei and O. ammon) and domestic hollow horned ruminants (C. hircus and O. aries), and land mollusks of the family Xeropicta in the piedmont and mountain area of Uzbekisan. The morphology of protostrongylids was studied using the methods of Boev (1975) and Anderson (1978). To identify the nematode type we used temporary preparations treated with glycerol. The first-stage larvae were investigated by examination of fecal samples from animals taking into account the length, tail form and body size. To study the morphology of the third-stage protostrongylid larvae the feet of infected mollusks Xeropicta candaсharica were separated and placed into the artificial gastric juice where the cap was destroyed and the infected larvae were eliminated. After determination of species belonging of mature and larval nematodes the material was stored in separate test-tubes with distilled water under the low temperature (- 20 ºС) or in 70 % Ethanol for the molecular analysis. We used microscopes ML 2000 with a digital camera and Olympus CX3. DNA extraction, amplification and sequencing were performed with an automated sequencer. Phylogenetic analysis was conducted using the software Clustal X 2.0. Phylogenetic trees were created by the Neighbor–Joining method. Nucleotide sequences ITS-2 regions of species Protostrongylus rufescens (EU018485), P. shiozawai (AB478249), Ortostrongylus macrotis (EU018483), Cystocaulus ocreatus (EU018481) and Umingmakstrongylus pallikuukensis (AY648409) received from the NCBI GenBank were used in phylogenetic analysis. Results and discussion: Four species of adult protostrongylid nematodes: Protostrongylus rufescens, P. hobmaieri, Spiculocaulus leuckarti and Cystocaulus ocreatus were determined. DNA from four species of mature protostrongylids and larvae was amplified by using ITS-2 regions. Amplificate dimension of nematodes P. rufescens and P. hobmaieri was 380 base pairs (b.p.), S. leuckarti – 388, C. ocreatus – 399 b.p. According to the results of phylogenetic analysis and comparison of nucleotide sequences, five protostrongylid species were found in animals of the Caprinae subfamily: P. rufescens, P. hobmaieri, Protostrongylus sp., S. leuckarti and C. ocreatus. The morphological and molecular-genetic analysis of detected nematodes enables the precise identification.

scholarly journals A new Middle Miocene tarsier from Thailand and the reconstruction of its orbital morphology using a geometric–morphometric method

2010 ◽  
Vol 278 (1714) ◽  
pp. 1956-1963 ◽  
Author(s):  
Yaowalak Chaimanee ◽  
Renaud Lebrun ◽  
Chotima Yamee ◽  
Jean-Jacques Jaeger
Keyword(s):  
New Species ◽  
Southeast Asia ◽  
Middle Miocene ◽  
Taxonomic Diversity ◽  
Geometric Morphometric ◽  
Morphometric Method ◽  
Extant Species ◽  
Degree Of Convergence ◽  
High Degree ◽  
Geometric Morphometric Method

Tarsius is an extant genus of primates endemic to the islands of Southeast Asia that is characterized by enormously enlarged orbits reflecting its nocturnal activity pattern. Tarsiers play a pivotal role in reconstructing primate phylogeny, because they appear to comprise, along with Anthropoidea, one of only two extant haplorhine clades. Their fossils are extremely rare. Here, we describe a new species of Tarsius from the Middle Miocene of Thailand. We reconstructed aspects of its orbital morphology using a geometric–morphometric method. The result shows that the new species of Tarsius had a very large orbit (falling within the range of variation of modern Tarsius ) with a high degree of frontation and a low degree of convergence. Its relatively divergent lower premolar roots suggest a longer mesial tooth row and therefore a longer muzzle than in extant species. The new species documents a previous unknown Miocene group of Tarsius , indicating greater taxonomic diversity and morphological complexity during tarsier evolution. The current restriction of tarsiers to offshore islands in Southeast Asia appears to be a relatively recent phenomenon.

Molecular genetic evidence for allotetraploid hybrid speciation in the genus Crocus L. (Iridaceae)

Phytotaxa ◽  
2016 ◽  
Vol 258 (2) ◽  
pp. 121 ◽  
Author(s):  
ÁGNES MOSOLYGÓ-L ◽  
GÁBOR SRAMKÓ ◽  
SÁNDOR BARABÁS ◽  
LEVENTE CZEGLÉDI ◽  
ANDRÁS JÁVOR ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Parental Species ◽  
Molecular Genetic ◽  
Parallel Evolution ◽  
Carpathian Basin ◽  
Hybrid Origin ◽  
F1 Hybrids ◽  
Aflp Data ◽  
F1 Hybrid

Although dysploidy and polyploidisation events are known to be important drivers in the evolutionary history of the genus Crocus, only a few examples of natural hybrid origins have so far been documented. Here, we describe the phylogenetic affinities of five taxa in the Crocus vernus species complex from the Carpathian Basin in Central Europe. Genetic variability was evaluated using chloroplast DNA sequences of the accD-psaI intergenic spacer and amplified fragment length polymorphism (AFLP) in combination with karyological observations. Genetic diversity and differentiation of the seven investigated Crocus species were also evaluated using AFLP data. We created a phylogenetic hypothesis using both sequences and AFLP fingerprinting data under maximum parsimony (MP). AFLPs were also analysed by means of multivariate statistics using principal coordinate (PCoA) analysis and Bayesian clustering (BC) to test for hybridity. Both the AFLP and plastid phylogenetic trees separated the taxa into two groups: (1) a ‘Balkan’ clade, and; (2) an ‘Adriatic’ clade. The Balkan clade contained Crocus heuffelianus samples and one Crocus vittatus from Croatia as well as Crocus tommasinianus samples from Hungary; the Adriatic clade included Crocus vittatus and Crocus vernus samples from Hungary and Croatia as well as Crocus neapolitanus from Italy. A hard incongruence was found in the placement of the Slovakian Crocus scepusiensis which clustered inside the Balkan clade on our plastid tree, while it fell in the Adriatic clade on the AFLP tree. The same populations occupied intermediate position on the PCoA plot. The BC analysis assigned all Crocus scepusiensis specimens as F1 hybrids, while Crocus vernus and Crocus heuffelianus were assigned as parental species. Together with our cytological investigation that determined a 2n=18 chromosome number of Crocus scepusiensis, we conclude an allopolyploid hybrid origin for this Northern Carpathian taxon as the result of a cross between members of the 2n=10 Balkan clade (e.g., Crocus heuffelianus from Transylvania) and the 2n=8 Adriatic clade (Crocus vernus). A similar origin is postulated for the North Balkan Crocus vittatus (2n=18), which was clustered as an F1 hybrid in the BC analysis; thus, parallel evolution may have taken place in the northern and southern part of the Carpathian Basin beginning from the same parental species but leading to different allopolyploid derivatives.

Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

2017 ◽  
Vol 33 (S1) ◽  
pp. 132-155 ◽  
Author(s):  
Barbara L. Taylor ◽  
Frederick I. Archer ◽  
Karen K. Martien ◽  
Patricia E. Rosel ◽  
Brittany L. Hancock-Hanser ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Molecular Genetic ◽  
Genetic Data ◽  
Molecular Genetic Data
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