scholarly journals Cryptic diversity in Lithobates warszewitschii (Amphibia, Anura, Ranidae)

ZooKeys ◽  
2019 ◽  
Vol 838 ◽  
pp. 49-69
Author(s):  
James Cryer ◽  
Felicity Wynne ◽  
Stephen J. Price ◽  
Robert Puschendorf
Keyword(s):  
Species Complex ◽  
Nucleotide Diversity ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Phylogeographic Structure ◽  
Cryptic Diversity ◽  
Population Declines ◽  
The Status ◽  
Cryptic Species Complex ◽  
Geographic Populations

Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.

scholarly journals First records of the fanged frogs Limnonectes bannaensis Ye, Fei & Jiang, 2007 and L. utara Matsui, Belabut & Ahmad, 2014 (Amphibia: Anura: Dicroglossidae) in Thailand

2021 ◽  
Vol 9 ◽  
Author(s):  
Chatmongkon Suwannapoom ◽  
Ke Jiang ◽  
Yun-He Wu ◽  
Parinya Pawangkhanant ◽  
Sengvilay Lorphengsy ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Species Complex ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Integrative Approach ◽  
Species Identity ◽  
Dna Sequence Data ◽  
Species Complexes ◽  
Cryptic Species Complex

The taxonomic status of the Thai populations belonging to the Limnonectes kuhlii species complex is controversial, due to phenotypic similarity in the cryptic species complex. Recently, some studies on this group in Thailand have discovered four new species: L. taylori, L. megastomias, L. jarujini and L. isanensis. Even so, the diversity of this group is still incomplete. Based on an integrative approach encompassing genetic and morphological analyses, we conclude that the Limnonectes populations from Nan Province (northern) and Yala Province (southern) of Thailand are conspecific with L. bannaensis Ye, Fei & Jiang, 2007 and L. utara Matsui, Belabut & Ahmad, 2014, respectively. These are the first records of these species in Thailand. Our study highlights the importance of using DNA sequence data in combination with morphological data to accurately document species identity and diversity. This is especially important for morphologically cryptic species complexes and sympatrically occurring congeners.

scholarly journals Molecular evidence for cryptic species in the common slug eating snake Duberria lutrix lutrix (Squamata, Lamprophiidae) from South Africa

ZooKeys ◽  
2019 ◽  
Vol 838 ◽  
pp. 133-154 ◽  
Author(s):  
Kyle Kullenkampff ◽  
Francois Van Zyl ◽  
Sebastian Klaus ◽  
Savel R. Daniels
Keyword(s):  
South Africa ◽  
Dna Sequence ◽  
Species Complex ◽  
Sequence Data ◽  
Divergence Time ◽  
Total Evidence ◽  
Phylogeographic Structure ◽  
Climatic Fluctuations ◽  
Dna Sequence Data ◽  
The Common

We examined the impact of climatic fluctuations on the phylogeographic structure of the common slug eating snake (Duberrialutrixlutrix) throughout its distribution in South Africa. The evolutionary history within the taxon was examined using partial DNA sequence data for two mitochondrial genes (ND4 + cytb) in combination with a nuclear locus (SPTBN1). Phylogenetic relationships were investigated for both the combined mtDNA and total evidence DNA sequence data. In addition, population and demographic analyses together with divergence time estimations were conducted on the combined mtDNA data. Topologies derived from the combined mtDNA analyses and the total evidence analyses were congruent and retrieved five statistically well-supported clades, suggesting thatDuberrial.lutrixrepresents a species complex. The five clades were generally allopatric, separated by altitudinal barriers and characterised by the absence of shared mtDNA haplotypes suggesting long term isolation. Divergence time estimations indicate that the diversification within theD.l.lutrixspecies complex occurred during the Plio/Pleistocene as a result of climatic fluctuations and habitat shifts for the species. A taxonomic revision of theD.l.lutrixspecies complex may be required to delineate possible species boundaries.

scholarly journals Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4654 ◽  
Author(s):  
Md Rakeb-Ul Islam ◽  
Daniel J. Schmidt ◽  
David A. Crook ◽  
Jane M. Hughes
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Species Complex ◽  
Gene Tree ◽  
Genetic Connectivity ◽  
Phylogeographic Structure ◽  
Genetic Structuring ◽  
Eastern Australia ◽  
Cryptic Species Complex

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae:Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cytbgene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overallFSTvalues suggested that both groups exhibit very low dispersal among rivers (SEQ-SFST= 0.13; SEQ-NFST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.

Phylogeny of the Crepidula plana (Gastropoda: Calyptraeidae) cryptic species complex in North America

2000 ◽  
Vol 78 (8) ◽  
pp. 1500-1514 ◽  
Author(s):  
Rachel Collin
Keyword(s):  
North Carolina ◽  
North America ◽  
Species Complex ◽  
East Coast ◽  
Sequence Data ◽  
Single Species ◽  
The United States ◽  
Molecular Techniques ◽  
Dna Sequence Data ◽  
Cryptic Species Complex

The taxonomy of Crepidula species with flat white shells is particularly difficult. These animals from the east coast of North America have generally been classified as a single species, Crepidula plana Say, 1822. Based on allozyme and developmental data, however, Hoagland (K.E. Hoagland. 1984. Malacologia, 25: 607-628; K.E. Hoagland. 1986. Am. Malacol. Bull. 4: 173-183) concluded that two species of flat white-shelled Crepidula live along the east coast of the United States, but she did not apply any name to the second species. Herein I use molecular techniques to characterize populations of flat white-shelled Crepidula species from Texas, Florida, Georgia, North Carolina, and |Massachusetts, and describe their morphology and development. DNA-sequence data support the existence of three species. One species is readily distinguished on the basis of morphology and development, but the other two are very similar. To clarify the nomenclature of these species, I designate neotypes for C. plana Say, 1822 and Crepidula depressa Say, 1822, and describe Crepidula atrasolea sp.nov.

Description of Poecilia (Acanthophacelus) obscura n. sp., (Teleostei: Poeciliidae), a new guppy species from western Trinidad, with remarks on P. wingei and the status of the “Endler’s guppy”

Zootaxa ◽  
2009 ◽  
Vol 2266 (1) ◽  
pp. 35-50 ◽  
Author(s):  
SUSANNE SCHORIES ◽  
MANFRED K. MEYER ◽  
MANFRED SCHARTL
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
New Species ◽  
Species Complex ◽  
Valid Species ◽  
The Status ◽  
Molecular Phylogenetic ◽  
Cryptic Species Complex ◽  
The Common ◽  
Definition Of

Poecilia obscura, new species, is described from the Oropuche system, Trinidad. A mitochondrial DNA-sequence based molecular phylogenetic analysis revealed the status of the new species as a separate taxon. It is most closely related to the Common guppy, P. reticulata and to the recently described species, P. wingei. It can also be distinguished by morphometrics and gonopodial characteristics from these two species, although the ranges for all values overlap. A definition of the new species on morphology criteria alone is thus impossible. Therefore, P. obscura forms a cryptic species complex with the two other species. P. wingei is now unequivocally defined by the molecular phylogeny as a valid species. The three guppy species are included in the subgenus Acanthophacelus Eigenmann (1907), which is considered as generically different from all other taxa of the Poeciliinae sensu Parenti (1981).

scholarly journals Patterns of Cryptic Diversity and Phylogeography in Four Freshwater Copepod Crustaceans in European Lakes

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 448
Author(s):  
Elena Kochanova ◽  
Abhilash Nair ◽  
Natalia Sukhikh ◽  
Risto Väinölä ◽  
Arild Husby
Keyword(s):  
Sequence Data ◽  
Rrna Genes ◽  
Phylogeographic Structure ◽  
Cryptic Diversity ◽  
Widespread Species ◽  
Geographical Patterns ◽  
Mtdna Coi ◽  
Nuclear Its ◽  
Freshwater Copepods ◽  
18S Rrna Genes

Comparative phylogeography has become a powerful approach in exploring hidden or cryptic diversity within widespread species and understanding how historical and biogeographical factors shape the modern patterns of their distribution. Most comparative phylogeographic studies so far focus on terrestrial and vertebrate taxa, while aquatic invertebrates (and especially freshwater invertebrates) remain unstudied. In this article, we explore and compare the patterns of molecular diversity and phylogeographic structure of four widespread freshwater copepod crustaceans in European water bodies: the harpacticoids Attheyella crassa, Canthocamptus staphylinus and Nitokra hibernica, and the cyclopoid Eucyclops serrulatus, using sequence data from mtDNA COI and nuclear ITS/18S rRNA genes. The three taxa A. crassa, C. staphylinus and E. serrulatus each consist of deeply diverged clusters and are deemed to represent complexes of species with largely (but not completely) non-overlapping distributions, while in N. hibernica only little differentiation was found, which may however reflect the geographically more restricted sampling. However, the geographical patterns of subdivision differ. The divisions in A. crassa and E. serrulatus follow an east–west pattern in Northern Europe whereas that in C. staphylinus has more of a north–south pattern, with a distinct Fennoscandian clade. The deep mitochondrial splits among populations of A. crassa, C. staphylinus and E. serrulatus (model-corrected distances 26–36%) suggest that divergence of the lineages predate the Pleistocene glaciations. This study provides an insight into cryptic diversity and biogeographic distribution of freshwater copepods.

Transoceanic dispersal and cryptic diversity in a cosmopolitan rafting nudibranch

2016 ◽  
Vol 30 (3) ◽  
pp. 290 ◽  
Author(s):  
Jennifer S. Trickey ◽  
Martin Thiel ◽  
Jonathan M. Waters
Keyword(s):  
Species Complex ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Cryptic Diversity ◽  
Its1 Region ◽  
Dna Sequence Data ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Mtdna Lineages ◽  
Transoceanic Dispersal

The aeolid nudibranch Fiona pinnata (Eschscholtz, 1831) is an obligate rafter that occurs exclusively on macroalgal rafts and other floating substrata, and has a seemingly cosmopolitan marine distribution. Mitochondrial (mtDNA) and nuclear DNA sequence data were generated from specimens collected worldwide to test for global connectivity in this species. Phylogeographic analyses revealed three divergent mtDNA lineages, two of which were abundant and widespread. One of these lineages has an apparent circumequatorial distribution, whereas the other may have an antitropical distribution within the Pacific Ocean. Low genetic divergences within each lineage suggest that rafting can mediate dispersal across transoceanic scales. A third, highly divergent, lineage was detected in a single Indonesian specimen. Broadly concordant phylogeographic relationships were detected for the nuclear ITS1 region, with distinct tropical versus antitropical lineages observed. The substantial genetic divergences and largely allopatric distributions observed among the F. pinnata lineages suggest that they represent a species complex.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

scholarly journals Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark ( Alaudala rufescens ) — Sand Lark ( A. raytal ) species complex (Aves, Passeriformes) reveal cryptic diversity

2020 ◽  
Vol 49 (4) ◽  
pp. 427-439 ◽  
Author(s):  
Fatemeh Ghorbani ◽  
Mansour Aliabadian ◽  
Ruiying Zhang ◽  
Martin Irestedt ◽  
Yan Hao ◽  
...  
Keyword(s):  
Species Complex ◽  
Phylogenetic Analyses ◽  
Cryptic Diversity
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