Multiple molecular markers reinforce the systematic framework of unique Australian cave fishes (Milyeringa : Gobioidei)

Australia was once thought to be a biodiversity desert when considering the subterranean world; however, recent work has revealed a fascinating collection of cave creatures, many with surprising biogeographic histories. This has especially been so in the karstic regions of north-western Australia (Cape Range peninsula, Barrow Island, Pilbara), which is home not only to a diverse collection of subterranean invertebrates, but also to the continent’s only known underworld-adapted vertebrates, which includes the cave fish in the genus Milyeringa. These cave gudgeons have recently been in a state of taxonomic flux, with species being both split and lumped, but this was done with limited data (incomplete geographic sampling and no nuclear DNA sequence data). Therefore, we have revisited the systematic status of Milyeringa in a total-evidence molecular approach by integrating all existing data (mitochondrial, allozymes) with new DNA sequences from nuclear and mitochondrial loci and new multilocus allozyme data. Our conclusion, that there are two species, matches the most recent taxonomic treatment, with Milyeringa veritas present on both the eastern and western sides of the Cape Range peninsula, and Milyeringa justitia on Barrow Island. This has implications for future research in the linked fields of biogeography and conservation.

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A Multifaceted Approach to the Characterization of an Intergeneric Hybrid Manakin (Pipridae) from Brazil

The Auk ◽

10.1093/auk/119.4.1114 ◽

2002 ◽

Vol 119 (4) ◽

pp. 1114-1120 ◽

Cited By ~ 10

Author(s):

Miguel Â Marini ◽

Shannon J. Hackett

Keyword(s):

Dna Sequences ◽

Nuclear Dna ◽

Sequence Data ◽

Female Parent ◽

Intergeneric Hybrid ◽

Morphological Characters ◽

Multifaceted Approach ◽

Dna Sequence Data ◽

Nd2 Gene

Abstract A new intergeneric hybrid manakin is characterized using morphological characters and mitochondrial and nuclear DNA sequences. Many morphological traits suggest the bird is intermediate between Ilicura militaris and Chiroxiphia caudata. Sequences of the maternally inherited mitochondrial ND2 gene demonstrate the female parent to be Chiroxiphia caudata, and the nuclear beta-fibrinogen intron 5 sequences can not eliminate Chiroxiphia and Ilicura as parents. Therefore, DNA sequence data lead to the conclusion that Ilicura is the male parent of this unusual bird. This study is important because it highlights the significance of using multiple character systems in diagnosing unusual bird specimens.

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Ecology and seasonality of Pseudo-nitzschia species (Bacillariophyceae) in the northwestern Adriatic Sea over a 30-years period (1988–2020)

Mediterranean Marine Science ◽

10.12681/mms.26021 ◽

2021 ◽

Vol 22 (3) ◽

pp. 505

Author(s):

SONIA GIULIETTI ◽

TIZIANA ROMAGNOLI ◽

ALESSANDRA CAMPANELLI ◽

CECILIA TOTTI ◽

STEFANO ACCORONI

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Species Complex ◽

Adriatic Sea ◽

Sequence Data ◽

Coastal Station ◽

Dna Sequence Data ◽

The Mean ◽

First Time ◽

North Western

The ecology and seasonality of Pseudo-nitzschia species and their contribution to phytoplankton community were analysed for the first time at the coastal station of the LTER-Senigallia-Susak transect (north-western Adriatic Sea) from 1988 to 2020. Species composition was addressed using DNA sequence data obtained from 106 monoclonal strains isolated from January 2018 to January 2020. The mean annual cycle of total phytoplankton in the study period (Feb 1988–Jan 2020) showed maximum abundances in winter followed by other peaks in spring and autumn. Diatoms were the main contributors in terms of abundance during the winter and the spring blooms. The autumn peak was due to phytoflagellates and diatoms. In summer phytoflagellates dominated the community, followed by diatoms and dinoflagellates, which in this season reached their annual maximum. Pseudo-nitzschia spp. represented on average 0.4–17.6% of diatom community, but during their blooms they could reach up to up to 90% of the total diatom abundances with 106 cells l-1. By LM, six different taxa were recognized: Pseudo-nitzschia cf. delicatissima and P. cf. pseudodelicatissima were the most abundant, followed by P. cf. fraudulenta, P. pungens, P. multistriata and P. cf. galaxiae. P. cf. fraudulenta and P. pungens were indicator taxa of winter. P. cf. delicatissima and P. cf. pseudodelicatissima were spring and summer taxa, respectively. P. galaxiae showed maximum abundances in autumn. DNA sequences revealed the presence of two species belonging to the ’P. seriata group’ (i.e. P. fraudulenta and P. pungens) and four species belonging to the ‘P. delicatissima group’ (P. calliantha and P. mannii within the P. pseudodelicatissima species complex, and P. delicatissima and P. cf. arenysensis within the P. delicatissima species complex). The presence of several cryptic and pseudo-cryptic species highlights the need to combine LM observations with DNA sequence data when the ecology of Pseudo-nitzschia is investigated.

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Nuclear and mitochondrial DNA sequences from two Denisovan individuals

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1519905112 ◽

2015 ◽

Vol 112 (51) ◽

pp. 15696-15700 ◽

Cited By ~ 75

Author(s):

Susanna Sawyer ◽

Gabriel Renaud ◽

Bence Viola ◽

Jean-Jacques Hublin ◽

Marie-Theres Gansauge ◽

...

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Nuclear Dna ◽

Sequence Data ◽

Nuclear Genome ◽

Extended Period ◽

Sister Group ◽

Morphological Description ◽

Dna Sequence Data ◽

Mtdna Sequence

Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.

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Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽

10.1093/genetics/134.4.1195 ◽

1993 ◽

Vol 134 (4) ◽

pp. 1195-1204

Author(s):

S Tarès ◽

J M Cornuet ◽

P Abad

Keyword(s):

Apis Mellifera ◽

Dna Sequence ◽

Dna Sequences ◽

Sequence Data ◽

Sequence Divergence ◽

Repeated Sequence ◽

Consensus Sequences ◽

Dna Sequence Data ◽

Repeat Class ◽

Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

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A review of the fern genus Pellaea (Pteridaceae) in Australasia

Australian Systematic Botany ◽

10.1071/sb20006 ◽

2020 ◽

Author(s):

Patrick J. Brownsey ◽

Daniel J. Ohlsen ◽

Lara D. Shepherd ◽

Whitney L. M. Bouma ◽

Erin L. May ◽

...

Keyword(s):

New Zealand ◽

Chloroplast Dna ◽

Dna Sequences ◽

Sequence Data ◽

Indigenous Species ◽

Ploidy Levels ◽

Dna Sequence Data ◽

Australian Species ◽

The Status ◽

Chloroplast Dna Sequences

Five indigenous species of Pellaea in Australasia belong to section Platyloma. Their taxonomic history is outlined, morphological, cytological and genetic evidence for their recognition reviewed, and new morphological and chloroplast DNA-sequence data provided. Australian plants of P. falcata (R.Br.) Fée are diploid and have longer, narrower pinnae than do New Zealand plants previously referred to P. falcata, which are tetraploid. Evidence indicates that P. falcata does not occur in New Zealand, and that collections so-named are P. rotundifolia (G.Forst.) Hook. Chloroplast DNA sequences are uninformative in distinguishing Australian P. falcata from New Zealand P. rotundifolia, but show that Australian P. nana is distinct from both. Sequence data also show that Australian and New Zealand populations of P. calidirupium Brownsey & Lovis are closely related, and that Australian P. paradoxa (R.Br.) Hook. is distinct from other Australian species. Although P. falcata is diploid and P. rotundifolia tetraploid, P. calidirupium, P. nana (Hook.) Bostock and P. paradoxa each contain multiple ploidy levels. Diploid populations of Pellaea species are confined to Australia, and only tetraploids are known in New Zealand. Evolution of the group probably involved hybridisation, autoploidy, alloploidy, and possibly apomixis. Further investigation is required to resolve the status of populations from Mount Maroon, Queensland and the Kermadec Islands.

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Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae)

Zootaxa ◽

10.11646/zootaxa.2989.1.1 ◽

2011 ◽

Vol 2989 (1) ◽

pp. 1 ◽

Cited By ~ 26

Author(s):

HERBERT RÖSLER ◽

AARON M. BAUER ◽

MATTHEW P. HEINICKE ◽

ELI GREENBAUM ◽

TODD JACKMAN ◽

...

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Nuclear Dna ◽

Sequence Data ◽

Identification Key ◽

Dna Sequence Data ◽

Preliminary Identification ◽

Specific Rank ◽

Species Groups

A review of the taxonomy, phylogeny, and zoogeography of all currently recognized Gekko species is provided based on morphology (including size, scalation, color, and pattern) and mitochondrial and nuclear DNA sequence data. We distinguish six morphological (phenotypic) species groups within the gekkonid genus Gekko: the G. gecko, G. japonicus, G. monarchus, G. petricolus, G. porosus, and G. vittatus groups, all of which receive support from molecular phylogenetics. The taxon G. reevesii, formerly evaluated as a synonym of G. gekko, is revalidated herein at specific rank. Furthermore, a preliminary identification key of all currently recognized Gekko taxa is provided.

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New genetic lineages within Moroccan day geckos Quedenfeldtia (Sphaerodactylidae) revealed by mitochondrial and nuclear DNA sequence data

Amphibia-Reptilia ◽

10.1163/15685381-00003088 ◽

2017 ◽

Vol 38 (1) ◽

pp. 97-101 ◽

Cited By ~ 1

Author(s):

David James Harris ◽

Daniela Rosado ◽

Raquel Xavier ◽

Daniele Salvi

Keyword(s):

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Reconstruction ◽

Taxonomic Revision ◽

Substantial Portion ◽

Genetic Lineages ◽

Mountainous Regions ◽

Dna Sequence Data ◽

Atlas Mountains ◽

Morphological Assessment

The genus Quedenfeldtia is composed of two species, Q. moerens and Q. trachyblepharus, both endemic to the Atlas Mountains region of Morocco. Previous studies recovered two main genetic lineages within each Quedenfeldtia species, although sampling did not cover a substantial portion of their known distribution. In this study we collected individuals from previously unsampled localities of Quedenfeldtia and carried out genetic analyses in order to assess the range of previously identified lineages and the occurrence of additional lineages. Phylogenetic reconstruction based on both mitochondrial (12S and ND4 + tRNA) and nuclear (MC1R) markers revealed that while the new individuals of Q. moerens belong to previously described lineages, two new lineages of Q. trachyblepharus were uncovered from the northern and southern parts of the range. Genetic divergence of these new lineages (8-9% ND4 + tRNA p-distance) was higher than values observed between other lizard sister species. In the future a thorough morphological assessment is needed to complement this study and allow a taxonomic revision of these taxa. The results of this study highlight the importance of biodiversity assessments in mountainous regions characterized by high endemicity but which are difficult to access.

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Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

Zootaxa ◽

10.11646/zootaxa.3608.1.4 ◽

2013 ◽

Vol 3608 (1) ◽

pp. 67-74 ◽

Cited By ~ 1

Author(s):

Chris J. LAW ◽

KELLY M. DORGAN ◽

GREG W. ROUSE

Keyword(s):

Dna Sequence ◽

Nuclear Dna ◽

Sequence Data ◽

Hemoglobin Concentration ◽

Sympatric Species ◽

Sandy Beaches ◽

Additional Species ◽

Dna Sequence Data ◽

C Subunit ◽

Coi Sequences

Thoracophelia (Annelida, Opheliidae) are burrowing deposit feeders generally found in the mid- to upper intertidal areas of sandy beaches. Thoracophelia mucronata (Treadwell, 1914) is found along the west coast of North America, including at Dillon Beach, CA. Two additional species, Thoracophelia dillonensis (Hartman, 1938) and T. williamsi (Hartman, 1938) were also described from this beach. These three sympatric species have been primarily distinguished by branchial morphology, and efforts to determine the validity of the species have been based on morphological, reproductive and ecological studies. Here we demonstrate using mitochondrial and nuclear DNA sequence data that these three species are valid. Mitochondrial Cytochrome c subunit 1 (COI) sequences show uncorrected interspecific distances of ~9–13%. We found no inter—specific differences in body color or in hemoglobin concentration, but found that reproductive males were pinkish-red in color and had lower hemoglobin concentrations than purplish—red reproductive females.

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Cymbidium jiangchengense (Orchidaceae; Epidendroideae; Cymbidiinae), a new species from China: evidence from morphology and DNA sequences

Phytotaxa ◽

10.11646/phytotaxa.408.1.6 ◽

2019 ◽

Vol 408 (1) ◽

pp. 77-84

Author(s):

YING-LI PENG ◽

ZHUANG ZHOU ◽

SI-REN LAN ◽

ZHONG-JIAN LIU

Keyword(s):

Dna Sequences ◽

Yunnan Province ◽

Sequence Data ◽

Detailed Comparison ◽

Distinct Species ◽

Molecular Study ◽

Orchid Species ◽

Dna Sequence Data ◽

Pink Flower ◽

A New Species

A new orchid species, Cymbidium jiangchengense, from Yunnan Province, China, is described and illustrated. Its distinctiveness is evaluated with morphology and molecular analyses. A detailed comparison between the newly discovered orchid and other members of Cymbidium was performed. The new plant was characterized by stem-like pseudobulbs, narrowly oblong leaves, coriaceous leaves with an acute apex, a 2-flowered inflorescence, a purplish pink flower, narrowly elliptic sepals, petals, a obovate-lanceolate lip with a cordate midlobe, a yellow central callus, and a disc with a trough shape longitudinal lamella from the base extending to the base of the midlobe and a lamellae apex inflated to form two calluses that are not confluent apically. These features distinguish this new orchid from all other known species of Cymbidium. A molecular study based on nuclear ribosomal ITS and plastid matK and rbcL DNA sequence data indicates that C. jiangchengense is a distinct species that sister to C. wadae and a member of section Eburnea, subgenus Cyperorchis.

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Strelitziana sarbhoyi sp. nov. (Strelitzianaceae, Chaetothyriales), from North-Western Himalayas, India, described based on morphology and molecular phylogeny

Phytotaxa ◽

10.11646/phytotaxa.427.1.6 ◽

2019 ◽

Vol 427 (1) ◽

pp. 51-59

Author(s):

SHIWALI RANA ◽

SANJAY KUMAR SINGH ◽

PARAS NATH SINGH

Keyword(s):

Phylogenetic Tree ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Culture Collection ◽

Fungal Culture ◽

Western Himalayas ◽

Holotype Specimen ◽

North Western

Strelitziana sarbhoyi is established as a new species to accommodate a phylloplane fungus isolated from Mallotus philippensis collected from Kangra region of North-Western Himalayas, Himachal Pradesh. The identity of the fungus is confirmed based on the asexual-morphs, cultural characteristics and phylogenetic analyses of the internal transcribed spacer (ITS) rDNA and partial nuclear ribosomal 28S large subunit (LSU) sequence data. The placement of S. sarbhoyi in the phylogenetic tree was determined based on DNA sequences from authenticated isolates of Strelitziana. Strelitziana sarbhoyi shows nearly 94% similarity with other known species of Strelitziana. Area description is provided for the proposed taxon along with microscopic images, and a phylogenetic tree. This is probably the first report of Strelitziana from India. Holotype specimen (dried voucher culture) is deposited in the Ajrekar Mycological Herbarium (AMH), and an ex-type culture is deposited in National Fungal Culture Collection of India (NFCCI).

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