scholarly journals Taxonomy of Horned Lizards, Genus Phrynosoma (Squamata, Phrynosomatidae)

Taxonomy ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 83-115
Author(s):  
Gunther Köhler
Keyword(s):  
Species Delimitation ◽  
Monophyletic Group ◽  
Separate Species ◽  
Distribution Maps ◽  
Evolutionarily Significant Units ◽  
Horned Lizards ◽  
Mtdna Markers

In this article, I revise the taxonomy of the species and subspecies of the genus Phrynosoma through phylogenetic and species delimitation approaches based on four mtDNA markers (ND1, ND2, ND4, and 12S). The resulting taxonomy recognizes 12 species (P. asio, P. bracconieri, P. cornutum, P. coronatum, P. douglasii, P. hernandesi, P. mcallii, P. modestum, P. orbiculare, P. platyrhinos, P. solare, and P. taurus). Several of these species are divided into subspecies as follows: P. coronatum (P. c. coronatum, P. c. blainvillii, P. c. cerroense, and P. c. frontale), P. cornutum (P. c. cornutum and P. c. bufonium), P. hernandesi (P. h. hernandesi, P. h. ditmarsi, and P. h. ornatum), P. orbiculare (P. o. orbiculare, P. o. bradti, P. o. boucardii, P. o. cortezii, P. o. dugesii, and P. o. durangoensis), P. platyrhinos (P. p. platyrhinos and P. p. goodei), P. taurus (P. t. taurus and P. t. sherbrookei). In this coherent and objective approach, those taxa treated here as subspecies have diverged to a much lesser degree than those that are herein recognized as separate species. Typically, those taxa recognized as subspecies are one another’s closest relatives (i.e., they together form a monophyletic group that represents the species) and are distributed allopatrically. In this approach, all separate evolutionarily significant units are recognized as named taxa—either species or subspecies—thereby reflecting the importance of identifying and naming such units for conservation. I provide a checklist of the recognized species and subspecies of Phrynosoma along with synonymies and distribution maps.

Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

2021 ◽  
Author(s):  
Zaynab Shaik ◽  
Nicola Georgina Bergh ◽  
Bengt Oxelman ◽  
Anthony George Verboom
Keyword(s):  
Species Delimitation ◽  
Bayes Factor ◽  
Cape Floristic Region ◽  
Parametric Models ◽  
Western Cape ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Separate Species ◽  
Multiple Sequence ◽  
Data Set

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

Species delimitation and nematode biodiversity: phylogenies rule

Nematology ◽  
2002 ◽  
Vol 4 (5) ◽  
pp. 615-625 ◽  
Author(s):  
Steven Nadler
Keyword(s):  
Species Delimitation ◽  
Sequence Data ◽  
Molecular Data ◽  
Gene Trees ◽  
California Sea Lions ◽  
Separate Species ◽  
Nucleotide Sequence Data ◽  
Sea Lions ◽  
Multiple Loci ◽  
Fur Seals

AbstractPractitioners of nematode taxonomy have rarely been explicit about what species represent or how data are being used to delimit species prior to their description. This lack of explicitness reflects the broader species problem common to all biology: there is no universally accepted idea of what species are and, as a consequence, scientists disagree on how to go about finding species in nature. However, like other biologists, nematologists seem to agree that species are real and discrete units in nature, and that they result from descent with modification. This evolutionary perspective provides a conceptual framework for nematologists to view species as independent evolutionary lineages, and provides approaches for their delimitation. Specifically, species may be delimited scientifically by methods that can test the hypothesis of lineage independence. For sequence data, such hypothesis testing should be based on sampling many individual organisms for multiple loci to avoid mistaking tokogeny and gene trees as evidence of species. Evolutionary approaches to analysing data and delimiting species avoid the inherent pitfalls in approaches that use all observed sequence differences to define species through calculation of a genetic distance. To illustrate evolutionary species delimitation, molecular data are used to test the hypothesis that hookworms parasitic in northern fur seals and in California sea lions represent separate species. The advantages and potential caveats of employing nucleotide sequence data for species delimitation are discussed, and the merits of evolutionary approaches are contrasted to inherent problems in similarity-based methods.

Revision of the Scopula dubernardi species group: how many species? (Lepidoptera: Geometridae, Sterrhinae)

Zootaxa ◽  
2006 ◽  
Vol 1164 (1) ◽  
pp. 35
Author(s):  
PASI SIHVONEN ◽  
DIETER STÜNING
Keyword(s):  
Species Delimitation ◽  
Male Genitalia ◽  
Species Group ◽  
Female Genitalia ◽  
Immature Stages ◽  
Separate Species ◽  
The Common ◽  
Common Situation

The Palaearctic Scopula dubernardi species group (Lepidoptera: Geometridae) is revised on the basis of external and genitalic characters to include Scopula dubernardi (Oberthür, 1923) and Scopula segregata Prout, 1919. Lectotypes are designated for both species, which were described from more than one specimen without holotype designation. The species delimitation is based on small quantitative differences in the female genitalia, i.e., the degree of turn of the ductus bursae along its axis, and on external features. Furthermore, the recognition of the studied taxa as separate species is strengthened by the observation that they occur sympatrically and synchronously in two localities. Unlike the common situation in the genus Scopula, structures of the male genitalia were found uninformative in species delimitation. The length of right ceras on the 8th sternite of S. segregata was found to be polymorphic. Adults and genitalia of S. dubernardi and S. segregata are illustrated, along with the variation in external features and genitalia in both species. The biology and immature stages of both species are unknown.

A revision of the genus Podaena Ordish (Insecta: Coleoptera: Hydraenidae)

Zootaxa ◽  
2010 ◽  
Vol 2678 (1) ◽  
pp. 1
Author(s):  
JUAN A. DELGADO ◽  
RICARDO L. PALMA
Keyword(s):  
New Species ◽  
New Zealand ◽  
West Coast ◽  
Male Genitalia ◽  
Barrier Island ◽  
The West ◽  
Separate Species ◽  
Distribution Maps ◽  
Maxillary Palps ◽  
Eleven Species

The New Zealand endemic genus Podaena Ordish, 1984 is revised. Eleven species are recognized of which four are described as new, and the remainder redescribed. The new species are: Podaena aotea from Great Barrier Island, Podaena hauturu from Little Barrier Island, Podaena mariae from the west coast of the South Island, and Podaena moanaiti from Lake Waikaremoana. The most useful characters to separate species are the shape of the maxillary palps and the shape and chaetotaxy of the foretibiae in males; these characters are illustrated for all the species. Unlike most genera of Hydraenidae, male genitalia in Podaena are not diagnostic for all species. The known geographical distribution of some species is expanded, and the complete collecting data for the type series of all the species described by Ordish (1984) are given, together with distribution maps.

Sorting out the muddle: taxonomy and nomenclature of Thymus ×porcii (Lamiaceae) and related nothotaxa, with comments on parent species delimitation

Phytotaxa ◽  
2021 ◽  
Vol 501 (1) ◽  
pp. 119-139
Author(s):  
VIKTOR O. NACHYCHKO ◽  
YEVHEN V. SOSNOVSKY
Keyword(s):  
Species Delimitation ◽  
Parental Species ◽  
Molecular Data ◽  
Forest Steppe ◽  
Original Material ◽  
Parent Species ◽  
Natural Hybrid ◽  
Separate Species ◽  
Diagnostic Traits

Thymus ×porcii is a natural hybrid between T. pannonicus and T. pulegioides, occurring within the co-occurrence range of its parental species in the forest and forest-steppe zones of Europe. Taxonomy and nomenclature of this hybrid present a longstanding puzzle due to the lack of critical evaluations of the original material as well as conflicting taxonomic interpretations of the parent taxa both at specific and intraspecific levels. The present paper attempts to clarify these issues, arguing against the synonymic treatment and/or consolidation of T. pannonicus and T. pulegioides, which is accepted in modern taxonomies apparently as a result of nomenclatural confusion related to T. pannonicus typification. Based on morphology and reported molecular data, it is proposed to treat T. pannonicus and T. pulegioides as separate species, each containing two varieties being well-distinguished by the presence or absence of leaf indumentum: T. pannonicus var. latifolius (glabrous leaves) and T. pannonicus var. pannonicus (pubescent leaves), and T. pulegioides var. pulegioides (glabrous leaves) and T. pulegioides var. vestitus (pubescent leaves). In view of such treatment, T. ×porcii is divided into three nothovarieties, representing natural crosses between different varieties of the parent species. Namely, in addition to the typical T. ×porcii nothovar. porcii [T. pannonicus var. latifolius × T. pulegioides var. pulegioides] (with T. ×pilisiensis and T. ×goginae as the taxonomic synonyms), we describe a new nothovariety T. ×porcii nothovar. calvariensis [T. pannonicus var. pannonicus × T. pulegioides var. pulegioides], and propose a new nomenclatural combination T. ×porcii nothovar. opizii [T. pannonicus × T. pulegioides var. vestitus] based on the previously published name T. ×opizii. On the basis of original material examination, two collections from BP are designated here as the lectotypes of T. ×porcii (≡ T. ×porcii nothovar. porcii) and T. ×pilisiensis respectively, and one specimen from PR is designated as the lectotype of T. ×opizii (≡ T. ×porcii nothovar. opizii). Main diagnostic traits of T. ×porcii nothovarieties and their parental taxa are compared and discussed.

scholarly journals Testing species hypotheses for Fridericia magna, an enchytraeid worm (Annelida: Clitellata) with great mitochondrial variation

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Svante Martinsson ◽  
Mårten Klinth ◽  
Christer Erséus
Keyword(s):  
Species Delimitation ◽  
Single Species ◽  
The Other ◽  
Cryptic Speciation ◽  
Incipient Speciation ◽  
Nuclear Markers ◽  
Separate Species ◽  
Mitochondrial Markers ◽  
Morphological Differences ◽  
Barcode Gap

Abstract Background Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. Results A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. Conclusion We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.

A taxonomic revision of Caloplaca herbidella and C. furfuracea

2009 ◽  
Vol 41 (5) ◽  
pp. 465-480 ◽  
Author(s):  
Ulf ARUP ◽  
Elin ÅKELIUS
Keyword(s):  
North America ◽  
Molecular Analysis ◽  
Taxonomic Revision ◽  
Strict Sense ◽  
Separate Species ◽  
Distribution Maps ◽  
Morphometric Methods ◽  
Large Genus ◽  
Grey Colour ◽  
New Distribution

AbstractCaloplaca herbidella (Hue) H. Magn. and C. furfuracea H. Magn. are two isidiate, epiphytic species in the large genus Caloplaca. Caloplaca herbidella in a strict sense is normally grey and fertile with thick, somewhat coralloid isidia, but orange, sterile forms with thin isidia also occur. Caloplaca furfuracea is superficially similar morphologically to C. herbidella s. str. but has thinner, more granular isidia and generally a darker grey colour. Doubts have been raised as to whether C. furfuracea should be acknowledged as a proper species or incorporated in C. herbidella. Using morphometric methods and molecular analysis of the nrITS DNA gene we show that C. herbidella and C. furfuracea are two clearly separated species. Furthermore, the mainly sterile, orange form of C. herbidella can be regarded as a separate species that is here described as C. coralliza Arup & Åkelius. All three species are described in detail, including photographs and notes on their ecology. Finally, new distribution maps for Europe show that C. herbidella and C. coralliza are widespread in Europe, but the latter is probably less common than the former. Caloplaca furfuracea is clearly very rare in Europe with only few collections from Switzerland and Sweden, but seems to be more common in North America.

A taxonomic study of the large-glumed species of Stipa (Gramineae) occurring in Canada

1978 ◽  
Vol 56 (6) ◽  
pp. 606-625 ◽  
Author(s):  
Mary E. Barkworth
Keyword(s):  
Numerical Analysis ◽  
Cross Sections ◽  
Morphological Characters ◽  
Leaf Margin ◽  
Taxonomic Study ◽  
Separate Species ◽  
Distribution Maps ◽  
Quantitative Characters ◽  
Infraspecific Taxa ◽  
Stipa Comata

The morphology and awn anatomy of the large-glumed species of Stipa occurring in Canada were examined. Numerical analysis of the data indicates that S. spartea var. spartea and S. spartea var. curtiseta are very distinct taxa differing not only in many of their quantitative characters but also in nodal pubescence, ligule shape, and pubescence of the leaf margin. It is proposed that they be treated as separate species, S. spartea and S. curtiseta. Some evidence was found for differentiation within S. spartea s.s. but it was deemed insufficient for the recognition of infraspecific taxa. Stipa comata var. comata and S. comata var. intermedia are very similar in all morphological characters examined. Cross sections of their distal awn segments do, however, show consistent distinguishing characters; those of var. intermedia are more heavily lignified and tend to be square in outline compared with those of var. comata. Although similar to each other, cross sections of the varieties of S. comata are distinct from those of S. spartea and S. curtiseta. The possibility that certain specimens were hybrids between S. comata var. comata and S. curtiseta was explored and rejected. Distribution maps and a key to the accepted taxa are given.

scholarly journals A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3356 ◽  
Author(s):  
Sohana P. Singh ◽  
Johan C. Groeneveld ◽  
Abdulaziz Al-Marzouqi ◽  
Sandi Willows-Munro
Keyword(s):  
Indian Ocean ◽  
Species Delimitation ◽  
Statistical Power ◽  
Life Stage ◽  
Larval Settlement ◽  
Spiny Lobster ◽  
Separate Species ◽  
Southwest Indian Ocean ◽  
Mitochondrial Data ◽  
Divergence Dating

Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.

Sign in / Sign up

Export Citation Format

Share Document