Haplotype diversity in the Antarctic springtail Gressittacantha terranova at fine spatial scales - a Holocene twist to a Pliocene tale

2010 ◽  
Vol 22 (6) ◽  
pp. 766-773 ◽  
Author(s):  
T.C. Hawes ◽  
G. Torricelli ◽  
M.I. Stevens
Keyword(s):  
Spatial Scales ◽  
Haplotype Diversity ◽  
Sequence Divergence ◽  
Reference Population ◽  
Landscape Scale ◽  
Coi Gene ◽  
Phylogeographic Structure ◽  
Mitochondrial Coi ◽  
Terra Nova Bay ◽  
The Antarctic

AbstractThe mitochondrial COI gene of the Antarctic springtail, Gressittacantha terranova, was sequenced across a polar coastal landscape at Terra Nova Bay, northern Victoria Land. Samples from two altitudinal transects in the foothills directly south of Campbell Glacier were compared with samples from Springtail Valley (northern foothills) as an external reference population. We found that mtDNA haplotypes clustered into two lineages (clades) with a mean sequence divergence of 10% (uncorrected distance). However, there was no phylogeographic structure found at this spatial (landscape) scale with haplotypes from both divergent clades found sympatric across most populations. At the landscape scale, the considerable genetic divergence revealed within G. terranova is around five times greater than any other continental Antarctic springtail examined to date. These data indicate a Pliocene divergence event in G. terranova around 4–5 million years ago. The unusual distributional profile of haplotypes - occurrence of multiple haplotypes at single sites and genetic contiguity between sites that are not physically contiguous - suggests a subsequent ‘reshuffling’ of haplotypes in the Holocene that has an ecological basis.

Phylogeography of "glacial relict" Gammaracanthus (Crustacea, Amphipoda) from boreal lakes and the Caspian and White seas

2001 ◽  
Vol 58 (11) ◽  
pp. 2247-2257 ◽  
Author(s):  
Risto Väinölä ◽  
Jouni K Vainio ◽  
Jukka U Palo
Keyword(s):  
Caspian Sea ◽  
Sequence Divergence ◽  
Boreal Lakes ◽  
Coi Gene ◽  
Phylogeographic Structure ◽  
Morphological Evidence ◽  
The Caspian Sea ◽  
Mitochondrial Coi ◽  
Glacial Relict ◽  
Allozyme Loci

As with a number of "glacial relict" crustacean genera, species of Gammaracanthus are vicariously distributed in circumarctic coastal waters, in boreal freshwater lakes, and in the Caspian Sea. Various hypotheses have been invoked to explain the origins and diversity of the non-marine taxa. Data on 28 allozyme loci and 558 bp of the mitochondrial COI gene demonstrate a close affinity between G. caspius of the Caspian Sea and G. aestuariorum of the White Sea area (Nei's allozyme distance D = 0.09, COI sequence divergence d = 5%), and a threefold divergence of the two from the Fennoscandian freshwater G. lacustris (D = 0.33, d = 12%). The relative molecular affinities agree with morphological evidence but contradict the idea of a common ancestry of the non-marine taxa, rather they suggest two independent invasions of continental waters. The generally low molecular divergence refutes the recently suggested generic splitting of Gammaracanthus. Previous speculations of an affinity of Gammaracanthus to the Baikalian acanthogammarids or to the Eusiroidea are not substantiated. The interspecific phylogeographic structure of Gammaracanthus is not concordant with that of other "glacial relict" crustacean genera. Phylogeographically, Gammaracanthus seems to match with the genus Monoporeia alone, rather than with Pontoporeia sensu lato.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

scholarly journals Morphological characteristics and mitochondrial COI gene of the green water dragon in Phu Quoc island, Vietnam

2021 ◽  
Vol 63 (3) ◽  
pp. 63-69
Author(s):  
Van Thong Ngo ◽  
◽  
Huu Hanh Tran ◽  
Chi Tao Phan ◽  
◽  
...  
Keyword(s):  
Morphological Characteristics ◽  
Sequence Divergence ◽  
Green Water ◽  
Coi Gene ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Body Weights ◽  
Data Book ◽  
Mitochondrial Cytochrome Oxidase

The green water dragons of Phu Quoc island, Vietnam have been given a VU rating (vulnerable) by the Vietnam red data book and the International Union for conservation of nature and natural resources. A description of the morphological characteristics and sequenced mitochondrial cytochrome oxidase subunit 1 COI gene was completed following a survey of thirty individuals from September 2018 to May 2019. Their body weights ranged from 115 to 850 g and their snout-vent length ranged from 120 to 280 mm. They were identified to have the highest similarity to the species Physignathus cocincinus by the barcode of life data system. Their COI gene sequence was compared to GenBank (KM272197.1) and the following alternations were found: C5483T, A5486C, C5537A, A5564G, A5591G, T5633C, G5684A, A5771G, A5849C, C5927T, T5942C, C5993T, G6002A, and A6020G. The neighbourjoining tree of their COI sequence divergence indicated a distance (compared to the same published species) from 2.3 to 2.8%. Thus, it might be possible that the green water dragons of Phu Quoc island are evolving into a specific subspecies. However, more green water dragon specimens from Phu Quoc should be sequenced to ensure a conclusion and further research into farming should be initiated to protect this vulnerable species.

Description of a new eelpout Pachycara angeloi sp. nov. (Perciformes: Zoarcidae) from deep-sea hydrothermal vent fields in the Indian Ocean

Zootaxa ◽  
2021 ◽  
Vol 4980 (1) ◽  
pp. 99-112
Author(s):  
RALF THIEL ◽  
THOMAS KNEBELSBERGER ◽  
TERUE KIHARA ◽  
KLAAS GERDES
Keyword(s):  
New Species ◽  
Indian Ocean ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Dorsal Fin ◽  
Fin Rays ◽  
Specific Variation ◽  
The Indian Ocean

A new species of eelpout genus Pachycara Zugmayer, 1911 is described based on five specimens caught at a depth of 2419–3275 m along the Central and Southeast Indian Ridges in the Indian Ocean. The specimens were collected during the INDEX cruises in 2016, 2018 and 2019, respectively. The new species is distinguished from its congeners by the following combination of characters: scales and pelvic fins absent; lateral line configuration mediolateral; dorsal fin origin associated with vertebrae 7–9 with no free predorsal pterygiophores; vertebrae 27–28 + 57–59 = 85–87; dorsal-fin rays 78–80, anal-fin rays 58–62; pectoral fin rays 13–15. DNA sequences of a mitochondrial COI gene fragment showed low intra-specific variation ranging from 0–0.3 % sequence divergence and do not reflect different vent sites. This is the 29th species of Pachycara, which is the fifth to be described from specimens collected only from chemosynthetic environments and the sixth known from the Indian Ocean. 

scholarly journals Deep Phylogenetic Divergence and Lack of Taxonomic Concordance in Species of Astronotus (Cichlidae)

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Olavo Pinhatti Colatreli ◽  
Natasha Verdasca Meliciano ◽  
Daniel Toffoli ◽  
Izeni Pires Farias ◽  
Tomas Hrbek
Keyword(s):  
Amazon Basin ◽  
Color Pattern ◽  
Diagnostic Character ◽  
Coi Gene ◽  
Valid Species ◽  
Phylogeographic Structure ◽  
Mitochondrial Coi ◽  
Meristic Counts ◽  
Historical Processes ◽  
Phylogenetic Divergence

The neotropical cichlid genus Astronotus currently comprises two valid species: A. ocellatus Agassiz, 1831 and A. crassipinnis Heckel, 1840. The diagnosis is based on color pattern and meristics counts. However, body color pattern is highly variable between regions and the meristic counts show a considerable overlap between populations differing in color patterning. They do not represent true synapomorphies that diagnose species. Purportedly the only truly diagnostic character is the presence or absence of one or more ocelli at the base of the dorsal fin, diagnosing A. ocellatus and A. crassipinnis, respectively. Using the 5′ portion of the mitochondrial COI gene and EPIC nuclear markers, the validity of the dorsal ocelli as diagnostic character was tested in individuals sampled from ten localities in the Amazon basin. Analyses rejected the hypothesis that dorsal ocelli are diagnostic at the species level. However, they revealed the existence of five hypothetical, largely allopatrically distributed morphologically cryptic species. The phylogeographic structure is not necessarily surprising, since species of the genus Astronotus have sedentary and territorial habits with low dispersal potential. The distribution of these hypothetical species is coincident with patterns observed in other Amazonian aquatic fauna, suggesting the role of common historical processes in generating current biodiversity patterns.

Combining Nuclear and Mitochondrial Loci Provides Phylogenetic Information in the Philopterus Complex of Lice (Psocodea: Ischnocera: Philopteridae)

2020 ◽  
Author(s):  
Tomas Najer ◽  
Ivo Papousek ◽  
Oldrich Sychra ◽  
Andrew D Sweet ◽  
Kevin P Johnson
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Nuclear Genes ◽  
Morphological Data ◽  
Coi Gene ◽  
Phylogenetic Information ◽  
Mitochondrial Coi ◽  
Putative Species ◽  
Mitochondrial Loci

Abstract The Philopterus Complex includes several lineages of lice that occur on birds. The complex includes the genera Philopterus (Nitzsch, 1818; Psocodea: Philopteridae), Philopteroides (Mey, 2004; Psocodea: Philopteridae), and many other lineages that have sometimes been regarded as separate genera. Only a few studies have investigated the phylogeny of this complex, all of which are based on morphological data. Here we evaluate the utility of nuclear and mitochondrial loci for recovering the phylogeny within this group. We obtained phylogenetic trees from 39 samples of the Philopterus Complex (Psocodea: Philopteridae), using sequences of two nuclear (hyp and TMEDE6) and one mitochondrial (COI) marker. We evaluated trees derived from these genes individually as well as from concatenated sequences. All trees show 20 clearly demarcated taxa (i.e., putative species) divided into five well-supported clades. Percent sequence divergence between putative species (~5–30%) for the COI gene tended to be much higher than those for the nuclear genes (~1–15%), as expected. In cases where species are described, the lineages identified based on molecular divergence correspond to morphologically defined species. In some cases, species that are host generalists exhibit additional underlying genetic variation and such cases need to be explored by further future taxonomic revisions of the Philopterus Complex.

scholarly journals Weak Population Structure of Perna Viridis in Indo-Pacific Region based on Nuclear and Mitochondrial DNA Marker

2021 ◽  
Author(s):  
Yingying Ye ◽  
Chengrui Yan ◽  
Ferruccio Maltagliati ◽  
Zeqin Fu ◽  
Baoying Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Haplotype Diversity ◽  
Its Region ◽  
Coi Gene ◽  
Perna Viridis ◽  
Thai Population ◽  
Mitochondrial Coi ◽  
Loop Region ◽  
D Loop

Abstract Perna viridis is a mussel commonly distributed along the Asian Indo-Pacific coasts. It is one of the main cultured species of that region. Previous studies focused mostly on the native populations within single countries; with the present study we analyzed the genetic diversity of P. viridis in a large study area, spanning from Oman to southern China. Three molecular markers were used, namely portions of the nuclear ITS region, and the mitochondrial COI gene and D-Loop region. The nuclear marker showed moderate levels of genetic diversity (haplotype diversity h = 0.543 to 0.897) and nucleotide diversity π = 0.0022 to 0.0064); whereas mitochondrial markers exhibited higher levels of genetic variability (h = 0.858 to 0.964 and π = 0.0012 to 0.0079). The estimates of inter-sample genetic divergence (FST) and the analysis of molecular variance highlighted that the Thai population is genetically divergent from the others. Our results showed the genetic variation of P. viridis at the rim of South China Sea and obtained the genetic basic information of P. viridis.

scholarly journals The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

2020 ◽  
Author(s):  
Gunilla Ståhls ◽  
Rudolf Meier ◽  
Christoph Sandrock ◽  
Martin Hauser ◽  
Ljiljana Šašić Zorić ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
28S Rdna ◽  
Coi Gene ◽  
Invasion History ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Mitochondrial Coi ◽  
Western Palearctic ◽  
Biogeographic Regions

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens ) is renowned for bioconversion ability of organic waste, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens . We here use genetic data of 424 rearing culture and wild caught fly samples from 38 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA). Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial COI gene (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear ITS2 and 28S rDNA markers are invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (54 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely explained by many independent acquisitions of cultures via sharing and/or establishing new colonies from wild-caught flies. However, explaining the observed high diversity in most biogeographic regions is difficult. The origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. But distinct, private haplotypes are also known from the Australasian (N=2), Oriental (N=4), and the Palearctic (N=5) populations. We review museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and the Afrotropical regions which lack distinct, private haplotypes. Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and to share this data in research publications and when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

2020 ◽  
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea ◽  
Mitochondrial Coi Gene

Ophiura sarsii is a common brittle star species across Arctic and subarctic regions of Atlantic and Pacific oceans. In the Barents Sea O. sarsii is among the dominant echinoderms. We studied genetic diversity of O. sarsii by sequencing the 548 bp fragment of mitochondrial COI gene. O.sarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, as well as other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes, being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of Ophiura sarsii in the Barents Sea most plausibly has started during the Bølling–Allerød interstadial, during the deglaciation of the western margin of the Barents Sea.

scholarly journals The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species

2020 ◽  
Author(s):  
Gunilla Ståhls ◽  
Rudolf Meier ◽  
Christoph Sandrock ◽  
Martin Hauser ◽  
Ljiljana Šašić Zorić ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
28S Rdna ◽  
Coi Gene ◽  
Invasion History ◽  
Black Soldier Fly ◽  
Hermetia Illucens ◽  
Mitochondrial Coi ◽  
Western Palearctic ◽  
Biogeographic Regions

Abstract Background The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for bioconversion ability of organic waste, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here use genetic data of 424 rearing culture and wild caught fly samples from 38 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA). Results Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial COI gene (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear ITS2 and 28S rDNA markers are invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (54 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely explained by many independent acquisitions of cultures via sharing and/or establishing new colonies from wild-caught flies. However, explaining the observed high diversity in most biogeographic regions is difficult. The origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. But distinct, private haplotypes are also known from the Australasian (N=2), Oriental (N=4), and the Palearctic (N=5) populations. We review museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and the Afrotropical regions which lack distinct, private haplotypes. Conclusions Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and to share this data in research publications and when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.

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