Speciation and phylogeography in Caridina indistincta, a complex of freshwater shrimps from Australian heathland streams

2003 ◽  
Vol 54 (7) ◽  
pp. 807 ◽  
Author(s):  
Stephen F. Chenoweth ◽  
Jane M.Hughes
Keyword(s):  
Sequence Data ◽  
Sequence Divergence ◽  
Population Level ◽  
Specific Rate ◽  
Dna Sequence Data ◽  
Freshwater Streams ◽  
Freshwater Shrimps ◽  
Eastern Australia ◽  
North Eastern ◽  
Mtdna Lineages

The Caridina indistincta complex is a group of closely related atyid shrimps that inhabit coastal freshwater streams throughout north-eastern Australia. Using mitochondrial DNA sequence data (cytochrome oxidase 1, CO1), we (1) inferred the timing of speciation in the C. indistincta group and (2) examined the intraspecific phylogeographic patterns within the group. Assuming a shrimp-specific rate of CO1 evolution, the level of sequence divergence among species suggests that speciation took place during the Miocene epoch. Within one widespread mainland species, phylogeographic patterns suggest strong geographic 'regionalisation' of mtDNA lineages that are most likely of Pleistocene origin. By contrast, another species comprises two highly divergent mtDNA lineages that occur in sympatry. We suggest that although Pleistocene sea-level regressions appear important in generating population-level phylogeographic patterns, these events were largely unimportant in the formation of species in this group.

Bipinnate acacias (Acacia subg. Phyllodineae sect. Botrycephalae) of eastern Australia are polyphyletic based on DNA sequence data

2006 ◽  
Vol 19 (4) ◽  
pp. 315 ◽  
Author(s):  
Gillian K. Brown ◽  
Siti R. Ariati ◽  
Daniel J. Murphy ◽  
Joseph T. H. Miller ◽  
Pauline Y. Ladiges
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Dna Sequence Data ◽  
Main Clade ◽  
Eastern Australia ◽  
Limited Sequence

A phylogenetic analysis of Acacia subg. Phyllodineae sect. Botrycephalae, endemic to eastern Australia, is presented based on a combined dataset of ITS and ETS sequences of nrDNA. A smaller set of species was sequenced also for the cpDNA trnK region. A limited number of morphological characters was also combined with the ITS+ETS dataset for most taxa. Thirty-eight of 41 Botrycephalae species were sequenced, together with a sample of ten uninerved phyllodinous species (sect. Phyllodineae). Although these DNA regions showed limited sequence divergence, bootstrap supported nodes of the consensus ITS+ETS tree indicate that Botrycephalae as currently defined is polyphyletic. Eight bipinnate species fell outside the main clade of Botrycephalae species while seven phyllodinous species were nested within it, near the base. The few derived but homoplasious morphological characters that were discovered included: presence of appressed unicellular hairs, presence of jugary and interjugary glands, number of pinnae > 7 and the funicle half–fully encircling the seed. Section Botrycephalae requires redefinition.

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

Genetics ◽  
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.

A new species of big-headed, fanged dicroglossine frog (Genus Limnonectes) from Thailand

Zootaxa ◽  
2008 ◽  
Vol 1807 (1) ◽  
pp. 26 ◽  
Author(s):  
DAVID S. McLEOD
Keyword(s):  
New Species ◽  
Dna Sequence ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Type Material ◽  
Base Pairs ◽  
Dna Sequence Data ◽  
16S Gene ◽  
A New Species

A new species of the dicroglossine genus Limnonectes from eastern Thailand and its tadpole are described. Analysis of DNA sequence data from 2518 base-pairs of the mitochondrial 12S and 16S gene regions places the species within the complex of frogs currently referred to as Limnonectes kuhlii and demonstrates it to be a separate lineage (>18% sequence divergence from type-material of L. kuhlii from Java). The new species differs from L. kuhlii by having nuptial pads, a greater snout–vent length, and different relative finger lengths than specimens from Java. It has more extensive toe webbing, a different arrangement of nuptial pads, and a greater snout–vent length than Limnonectes laticeps. The new species, which lacks vocal slits, also can be distinguished from the morphologically similar Limnonectes namiyei from Japan, which possesses vocal slits.

Revision of Batrachospermum sections Acarposporophytum and Aristata (Batrachospermales, Rhodophyta) with the establishment of the new genera Acarposporophycos and Visia

Phytotaxa ◽  
2019 ◽  
Vol 395 (2) ◽  
pp. 51 ◽  
Author(s):  
ORLANDO NECCHI JR ◽  
AURO GARCIA FILHO ◽  
MONICA O. PAIANO
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Sequence Divergence ◽  
Morphological Evidence ◽  
Similar Species ◽  
Type Specimens ◽  
Generic Level ◽  
Dna Sequence Data ◽  
Cell Layers

Sections of the paraphyletic genus Batrachospermum have been recently investigated using molecular (DNA sequence data) and morphological evidence. Some sections have been recognized as distinct genera in order to resolve paraphyly. Batrachospermum species of sections Acarposporophytum and Aristata are showed to form well-supported clades and, in this study, we propose to raise them to the generic level, Acarposporophycos gen. nov. and Visia gen. nov., respectively. In addition, we re-evaluated the characters used to circumscribe species by reexamining type specimens as well as new collections. Acarposporophycos, with the sole species A. brasiliensis, is characterized by the lack of carposporophytic stage, with the fertilized carpogonia germinating to form directly the filaments of the ‘Chantransia’ stage on the gametophyte. Of the five previously accepted species in the genus Visia, we recognize four species: V. cayennensis—type species (synonym Batrachospermum beraense), V. cylindrocellularis, V. longiarticulata and V. turgida. The species are circumscribed on the basis of morphological characteristics (shape and cell layers of primary fascicles, occurrence of secondary fascicles, post-fertilization development of carpogonia) and DNA sequence data (rbcL and COI-5P). Specimens described as Visia cayennensis from Australia and Brazil had a high sequence divergence in comparison to those from or near the type locality (French Guiana), and are here referred to as Visia spp. Further studies are recommended to better discriminate these morphologically similar species on a broad geographical scale and define their status at the species level. Descriptions, identification key and photomicrographs are presented for each recognized species.

Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

2020 ◽  
Vol 190 (3) ◽  
pp. 1002-1019 ◽  
Author(s):  
Donald L J Quicke ◽  
Sergey A Belokobylskij ◽  
Yves Braet ◽  
Cornelis van Achterberg ◽  
Paul D N Hebert ◽  
...  
Keyword(s):  
Sequence Data ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Sister Group ◽  
Morphological Characters ◽  
Dna Sequence Data ◽  
Elongation Factor 1 Alpha ◽  
Molecular Phylogenetic ◽  
Molecular Dataset ◽  
First Time

Abstract A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

scholarly journals Applying comparative genomics to plant disease epidemiology

2004 ◽  
Vol 85 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Linda M. Kohn
Keyword(s):  
Magnaporthe Grisea ◽  
Sequence Data ◽  
Population Level ◽  
Avirulence Genes ◽  
Genome Database ◽  
Disease Epidemiology ◽  
Dna Sequence Data ◽  
Specific Pathogen ◽  
Pathogen Populations ◽  
Genomic Regions

Astract Phylogenetic or genealogical interpretation of DNA sequence data from multiple genomic regions has become the gold standard for species delimitation and population genetics. Precise species concepts can inform quarantine decisions but are likely to reflect evolutionary events too far in the past to impact disease management. On the other hand, multilocus approaches at the population level can identify patterns of endemism or migration directly associated with episodes of disease, including host shifts and associated changes in determinants of pathogenicity and avirulence. We used the genome database of Magnaporthe grisea to frame a comparative, multilocus genomics approach from which we demonstrate a single origin for rice infecting genotypes with concomitant loss of sex in pandemic clonal lineages, and patterns of gain and loss of avirulence genes. In the Sclerotinia sclerotiorum pathosystem, we identified significant associations of multilocus haplotypes with specific pathogen populations in North America. Following the introduction of a new crop, endemic pathogen genotypes and newly evolved migrant genotypes caused novel, early-season symptoms.

"Same-same, but different": an unusual new species of the Limnonectes kuhlii Complex from West Sumatra (Anura: Dicroglossidae)

Zootaxa ◽  
2011 ◽  
Vol 2883 (1) ◽  
pp. 52 ◽  
Author(s):  
DAVID S. MCLEOD ◽  
STEPHANI J. HORNER ◽  
COLIN HUSTED ◽  
ANTHONY BARLEY ◽  
DJOKO ISKANDAR
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Sensu Stricto ◽  
Morphological Data ◽  
Sister Taxon ◽  
Dna Sequence Data ◽  
16S Gene ◽  
West Sumatra ◽  
A New Species

A new species in the dicroglossine genus Limnonectes from West Sumatra, Indonesia, is described. Analysis of DNA sequence data from the mitochondrial 12S and 16S gene regions places the species within the Limnonectes kuhlii Complex and demonstrates it to be the sister taxon of Limnonectes kuhlii sensu stricto from Java. Both molecular and morphological data support the recognition of this lineage as a new species. Notably, the presence of a spinule-covered mental plate distinguishes Limnonectes sisikdagu sp. nov. from all other members of the L. kuhlii Complex. Additionally, pair-wise sequence divergence greater than 10% separate the new species from its sister taxon, L. kuhlii from Java.

Systematic revision of the Indo-West Pacific mangrove-associated snails of the genus Bakawan (Cephalaspidea: Haminoeidae)

2020 ◽  
Vol 86 (4) ◽  
pp. 323-341 ◽  
Author(s):  
Trond R Oskars ◽  
Manuel António E Malaquias
Keyword(s):  
Sequence Data ◽  
Distinct Species ◽  
Morphological Characters ◽  
The Philippines ◽  
Systematic Revision ◽  
West Pacific ◽  
Dna Sequence Data ◽  
Eastern Australia ◽  
Discovery Method ◽  
The Western Pacific

ABSTRACT The genus Bakawan includes species of haminoeid snails associated with mangrove habitats and mud flats in the Indo-West Pacific. Here, we revise the diversity and systematics of the genus Bakawan based on our recent molecular phylogeny (Oskars & Malaquias, 2019) and detailed analysis of morphological characters. We examined a range of morphological characters (the shells, external morphology of the animal, jaw, radula, gizzard plate and male reproductive system) using light and scanning electron microscopy. We also carried out a species delimitation analysis (we used the automatic barcode gap discovery method) based on cytochrome c oxidase subunit I DNA sequence data. Four distinct species were recognized: Bakawan rotundata (A. Adams, 1850), which is the type species of the genus and ranges from the eastern Indian Ocean to the western Pacific; B. fusca (A. Adams, 1850), currently known only from the Philippines; and two species new to science, B. puti n. sp., known only from the Philippines, and B. hedleyi n. sp., restricted to tropical eastern Australia.

Discovery of the second European Amalopis species: an integrative survey of the widespread Pedicia (Amalopis) occulta (Meigen, 1830) (Insecta, Diptera, Pediciidae)

Zootaxa ◽  
2012 ◽  
Vol 3189 (1) ◽  
pp. 1 ◽  
Author(s):  
LUJZA UJVÁROSI ◽  
MIKLÓS BÁLINT
Keyword(s):  
Sequence Data ◽  
Far East ◽  
Sequence Divergence ◽  
Integrative Taxonomy ◽  
Type Specimens ◽  
Species Discovery ◽  
Dna Sequence Data ◽  
Close Relationship ◽  
Male Genital ◽  
Comprehensive Study

Integrative taxonomy enhances species discovery and facilitates species delimitation by combining DNA sequence data,morphology, and distributional and ecological information. In this paper we use complementary methods of morphologyand DNA barcoding to delineate species boundaries in a widespread European spring-dwelling crane-fly, Pedicia (Amalo-pis) occulta (Meigen). We describe a previously overlooked large cryptic dipteran as Pedicia (Amalopis) fusca n. sp. Wealso designate the lectotype of P. occulta of the basis of a comprehensive study of relevant type specimens. Morphologicaldifferences between the two species are delicate but detectable, and comprise mostly male genital structures. However,the sequence divergence of 13.1% reflects an ancient divergence, which plausibly pre-dates the Pleistocene. The EuropeanAmalopis species differ significantly from all the rest of Amalopis species with Far East distributions, but share a numberof similarities with a species identified from the Himalayas, India and described as Pedicia (Tricyphona) ericarum Alexander, 1966. We also discuss a possible close relationship between P. ericarum and the European Amalopis species.

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