scholarly journals Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in theOctopus vulgarisspecies complex

2019 ◽  
Author(s):  
Michael D. Amor ◽  
Stephen R. Doyle ◽  
Mark D. Norman ◽  
Alvaro Roura ◽  
Nathan E. Hall ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Octopus Vulgaris ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Mitochondrial Markers ◽  
Species Complexes ◽  
Genome Wide ◽  
Mitochondrial And Nuclear Markers

ABSTRACTMany marine species once considered to be cosmopolitan are now recognised as cryptic species complexes. Mitochondrial markers are ubiquitously used to address phylogeographic questions, and have been used to identify some cryptic species complexes; however, their efficacy in inference of evolutionary processes in the nuclear genome has not been thoroughly investigated. We used double digest restriction site-associated DNA sequencing (ddRADseq) markers to quantify species boundaries in the widely distributed and high value common octopus,Octopus vulgaris, comparing genome-wide phylogenetic signal to that obtained from mitochondrial markers. Phylogenetic analyses, genome-wide concordance and species tree estimation based on 604 genome-wide ddRADseq loci revealed six species within theO. vulgarisgroup. Divergence time estimates suggested modern-day species evolved over the last 2.5 ma, during a period of global cooling. Importantly, our study identified significant phylogenetic discordance between mitochondrial and nuclear markers; genome-wide nuclear loci supportedO. vulgarissensu stricto and Type III (South Africa) as distinct species, which mtDNA failed to recognise. Our finding of conflicting phylogenetic signal between mitochondrial and nuclear markers has broad implications for many taxa. Improved phylogenetic resolution ofO. vulgarishas significant implications for appropriate management of the group and will allow greater accuracy in global fisheries catch statistics.

Cryptic species complexes in manipulative echinostomatid trematodes: when two become six

Parasitology ◽  
2008 ◽  
Vol 136 (2) ◽  
pp. 241-252 ◽  
Author(s):  
T. L. F. LEUNG ◽  
D. B. KEENEY ◽  
R. POULIN
Keyword(s):  
Cryptic Species ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Single Species ◽  
Distinct Species ◽  
Molecular Data ◽  
Spatial Segregation ◽  
Small Scale ◽  
Intermediate Hosts ◽  
Species Complexes

SUMMARYRecent studies have shown that some digenean trematodes previously identified as single species due to the lack of distinguishing morphological characteristics actually consist of a number of genetically distinct cryptic species. We obtained mitochondrial 16S and nuclear ITS1 sequences for the redial stages of Acanthoparyphium sp. and Curtuteria australis collected from snails and whelks at various locations around Otago Peninsula, New Zealand. These two echinostomes are well-known host manipulators whose impact extends to the entire intertidal community. Using phylogenetic analyses, we found that Acanthoparyphium sp. is actually composed of at least 4 genetically distinct species, and that a cryptic species of Curtuteria occurs in addition to C. australis. Molecular data obtained for metacercariae dissected from cockle second intermediate hosts matched sequences obtained for Acanthoparyphium sp. A and C. australis rediae, respectively, but no other species. The various cryptic species of both Acanthoparyphium and Curtuteria also showed an extremely localized pattern of distribution: some species were either absent or very rare in Otago Harbour, but reached far higher prevalence in nearby sheltered inlets. This small-scale spatial segregation is unexpected as shorebird definitive hosts can disperse trematode eggs across wide geographical areas, which should result in a homogeneous mixing of the species on small geographical scales. Possible explanations for this spatial segregation of the species include sampling artefacts, local adaptation by first intermediate hosts, environmental conditions, and site fidelity of the definitive hosts.

Nuclear and mitochondrial markers reveal the existence of several geographically concordant lineages within a Sahelian gecko species, Ptyodactylus ragazzii

2013 ◽  
Vol 34 (1) ◽  
pp. 85-93 ◽  
Author(s):  
Elsa Froufe ◽  
Duarte V. Gonçalves ◽  
José Carlos Brito ◽  
David James Harris
Keyword(s):  
Genetic Diversity ◽  
Intraspecific Variability ◽  
Distinct Species ◽  
12S Rrna ◽  
Nuclear Markers ◽  
Mitochondrial Markers ◽  
Species Complexes ◽  
Mitochondrial 12S Rrna ◽  
Mtdna Lineages ◽  
First Time

The genetic diversity within Ptyodactylus ragazzii was analysed for the first time across the Western part of its range. We have used two mitochondrial (12s rRNA and 16s rRNA) and one nuclear (Cmos) marker to compare results directly with other related Ptyodactylus species, P. oudrii and P. hasselquistii. Results show high levels of intraspecific variability, with at least three divergent mtDNA lineages that have different haplotypes for Cmos and that are geographically concordant. P. ragazzii from Mauritania is probably a distinct species and possibly other lineages too, such as those from the Aïr Mountains in Niger, although more nuclear markers are needed to confirm this. All analysed Ptyodactylus species appear to be cryptic species complexes containing multiple deeply divergent forms, highlighting the need for a careful reassessment of the taxonomy of the whole genus.

scholarly journals Mammomonogamus nematodes in felid carnivores: a minireview and the first molecular characterization

Parasitology ◽  
2018 ◽  
Vol 145 (14) ◽  
pp. 1959-1968 ◽  
Author(s):  
Barbora Červená ◽  
Kristýna Hrazdilová ◽  
Peter Vallo ◽  
Jennifer Ketzis ◽  
Pompei Bolfa ◽  
...  
Keyword(s):  
Life Cycle ◽  
Dna Markers ◽  
Phylogenetic Analyses ◽  
Geographic Origin ◽  
Review Of The Literature ◽  
Domestic Cats ◽  
Nuclear Markers ◽  
The Family ◽  
Wild Felids ◽  
Mitochondrial And Nuclear Markers

AbstractFive of the 13 known species of Mammomonogamus have been described in members of the family Felidae, including domestic cats, making felids the most frequent hosts of Mammomonogamus. The occurrence of Mammomonogamus in felids is geographically scattered and information on the life cycle and other aspects of infections is lacking. The paucity of data opens the questions on possible conspecificity of some of the described species of Mammomonogamus and on the existence of possible reservoirs for infections in domestic cats in geographically isolated endemic foci of infection. To test such hypotheses, we compared sequences of mitochondrial and nuclear markers obtained from Mammomonogamus adults or eggs collected from domestic cats in three geographically distant localities. Based on morphology, geographic origin and site of infection, the worms examined can be referred to as Mammomonogamus ierei and Mammomonogamus auris. Phylogenetic analyses of both mitochondrial and ribosomal DNA markers showed monophyly of the genus Mammomonogamus and suggested the existence of at least two species in cats. Review of the literature, the existence of several species and the discontinuous geographic distribution of Mammomonogamus infections in domestic cats suggest an historical spillover of infection from wild reservoirs, presumably wild felids.

scholarly journals Local adaptation fuels cryptic speciation in terrestrial annelids

2019 ◽  
Author(s):  
Daniel Fernández Marchán ◽  
Marta Novo ◽  
Nuria Sánchez ◽  
Jorge Domínguez ◽  
Darío J. Díaz Cosín ◽  
...  
Keyword(s):  
Geometric Morphometrics ◽  
Cryptic Species ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Phylogenetic Signal ◽  
Regulation Of Transcription ◽  
Cryptic Speciation ◽  
Evolutionary Forces ◽  
Genome Wide

AbstractUncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

scholarly journals Cryptic intermediate snail host of the liver fluke Fasciola hepatica in Africa

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Anna Mahulu ◽  
Catharina Clewing ◽  
Björn Stelbrink ◽  
Fred D. Chibwana ◽  
Immaculate Tumwebaze ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Fasciola Hepatica ◽  
Phylogenetic Analyses ◽  
Public Health Problem ◽  
Distinct Species ◽  
Sub Saharan Africa ◽  
Major Public Health Problem ◽  
Galba Truncatula ◽  
Divergence Time Estimates ◽  
Sub Saharan

Abstract Background Snails such as Galba truncatula are hosts for trematode flukes causing fascioliasis, a zoonosis that is a major public health problem. Galba truncatula has recently been shown to be a cryptic species complex. African populations of Galba spp. are not yet studied using molecular assessments and is imperative to do so and reconstruct the centre of origin of Galba and to understand when and by what means it may have colonized the highlands of Africa and to what extent humans might have been involved in that process. Methods Samples from all known sub-ranges throughout Africa and new samples from Europe and Asia were obtained. We used a combination of two mitochondrial (cox1 and 16S) and one nuclear (ITS2) markers and phylogenetic, divergence time estimates and phylogeographical methods to determine the identity and biogeographical affinities. We also reconstructed the colonization history including the likely mode of dispersal and tested for the presence of cryptic Galba species in Africa. Results Galba truncatula is restricted to the Palaearctic region of the continent, namely Morocco. All sub-Saharan populations proved to be a distinct species according to the phylogenetic analyses and genetic distance. We propose to use the existing name Galba mweruensis (Connolly, 1929) for this species which is morphologically indistinguishable from the other two species hitherto known to occur in northern Africa, i.e. G. truncatula and G. schirazensis. Sub-tropical Africa has been colonized only once in either the Pliocene and possibly Miocene. Diversification within G. mweruensis is dated to the Plio-Pleistocene and thus human-mediated dispersal can be ruled out for the initial colonization of the isolated mountain ranges. There are potentially even more cryptic species in high altitude areas of Africa as outlined by the distinctness of the population found at the top of Mt. Elgon, Uganda. Conclusions From a novel genetic inspection of available African material, a hitherto neglected distinct species, G. mweruensis, now appears a major host of F. hepatica throughout sub-Saharan Africa. A closer examination of trematode parasites hosted by this species is needed in order to understand transmission patterns in highlands throughout eastern and southern Africa. We encourage future studies to inspect other high altitudes areas in Africa in light of parasites of either veterinary or medical importance.

scholarly journals A morphological and molecular review of the genus Goniurosaurus, including an identification key

2021 ◽  
Vol 751 ◽  
Author(s):  
Hai Ngoc Ngo ◽  
Huy Quoc Nguyen ◽  
Hieu Minh Tran ◽  
Hanh Thi Ngo ◽  
Minh Duc Le ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Species Identification ◽  
Phylogenetic Analyses ◽  
Field Work ◽  
Identification Key ◽  
Morphological Description ◽  
Northern Vietnam ◽  
Taxonomic Review ◽  
Species Complexes

The genus Goniurosaurus (tiger geckos) currently consists of 23 species distributed in China, Japan and Vietnam. Several species complexes and recent discoveries of cryptic species pose challenges to the species identification, which is crucial to effectively implement the recent listing of the species from China and Vietnam in CITES Appendix II and the species from Japan in CITES Appendix III. Based on the results of our field work in northern Vietnam and data compiled from literature, we herein provide a taxonomic review of the genus Goniurosaurus. Our phylogenetic analyses showed that all recorded populations of tiger geckos from Vietnam, which were found to be monophyletic with low intra-specific genetic divergences, are assigned to one of the four species: G. catbaensis, G. huuliensis, G. lichtenfelderi or G. luii. Both genetic and morphological analyses confirm that the species from China and Vietnam can be split into three major groups. Based on the newly collected data, we provide an extended morphological description of the Vietnamese species. In addition, we provide an identification key for all Goniurosaurus species from China, Japan and Vietnam in order to assist authorities in the enforcement of the recent CITES listing.

scholarly journals Different behaviour of mitochondrial and nuclear markers: introgression and the evolutionary history of Chrysocarabus (Coleoptera: Carabidae)

2006 ◽  
Vol 17 (3) ◽  
Author(s):  
Andreas Düring ◽  
Martina Brückner ◽  
Dietrich Mossakowski
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Gene Tree ◽  
Gene Trees ◽  
Nuclear Markers ◽  
Mitochondrial Haplotypes ◽  
History Of ◽  
Mitochondrial And Nuclear Markers

Phylogenetic analyses of Chrysocarabus taxa using different markers result in different phylogenetic trees. In particular, the mitochondrial gene tree contradicts the results of morphological and inbreeding studies. Two very different haplotypes of Carabus splendens Olivier, 1790 do not form a clade within this phylogenetic tree. We have earlier proposed that contradictory results are due to introgression. To verify our hypothesis, we analysed the internal transcribed spacer 2. No substitutions were observed in these nuclear sequences between the individuals of Carabus splendens, which contain the different mitochondrial haplotypes in question. The differences in the gene trees based on mitochondrial and nuclear sequences can be explained with at least two introgression events.

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