On the monophyly of Porrhothele antipodiana (Porrhothelidae: Mygalomorphae) and a new species of Porrhothele from Banks Peninsula

BackgroundThe last time the phylogenetic relationships among members of the family Hemerobiidae were studied quantitatively was over 12 years ago and based exclusively on morphology. Our study builds upon this morphological evidence by adding sequence data from three gene loci to provide a total evidence phylogeny of brown lacewings (Neuroptera: Hemerobiidae). Thirty-seven species representing nineteen Hemerobiidae genera were compared with outgroups from the families Ithonidae, Psychopsidae and Chrysopidae in Bayesian and parsimony analyses using a single nuclear gene (CAD) and two mitochondrial (16S rDNA and Cytochrome Oxidase I) genes. We compare divergence time estimates of Hemerobiidae cladogenesis under the two most commonly used relaxed clock models and discuss the evolution of wing venation in the family.ResultsWe recovered a phylogeny largely incongruent with previously published morphological studies, although all but two subfamilies (i.e., Notiobiellinae and Drepanacrinae) were recovered as monophyletic. We found the subfamily Drepanacrinae paraphyletic with respect to Psychobiellinae, and Notiobiellinae to be polyphyletic. We thus offer a revised concept of Notiobiellinae, comprising only Notiobiella Banks, and erect a new subfamily Zachobiellinae including the remaining genera previously placed in Notiobiellinae. Psychobiellinae is synonymized with Drepanacrinae. Unlike the previous hypothesis that proposed a remarkably laddered topology, our tree suggests that hemerobiids diverged as three main clades. Moreover, in contrast to the vein proliferation hypothesis, we found that hemerobiids have instead undergone multiple reductions in the number of radial veins, this scenario questions the relevance of this character as diagnostic of various subfamiliesConclusionsOur phylogenetic hypothesis and divergence times analysis suggest that extant hemerobiids originated around the end of the Triassic and evolved as three distinct clades that diverged from one another during the Late Jurassic to Early Cretaceous. Contrary to earlier phylogenetic hypotheses, Carobius Banks (Carobiinae) is sister to the previously unplaced genus Notherobius New in a clade more closely related to Sympherobiinae, Megalominae and Zachobiellinae subfam. nov. The addition of taxa which are not available for DNA sequencing should be the focus of future studies, especially Adelphohemerobius Oswald, which is particularly important to test our inferences regarding the evolution of wing venation in Hemerobiidae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0746-5) contains supplementary material, which is available to authorized users.

Genetic diversity of Culicoides species within the Pulicaris complex (Diptera: Ceratopogonidae) in Turkey inferred from mitochondrial COI gene sequences

Abstract. Roesma DI, Tjong DH, Aidil DR. 2020. Phylogenetic analysis of transparent gobies in three Sumatran lakes, inferred from mitochondrial Cytochrome Oxidase I (COI) gene. Biodiversitas 21: 43-48. The transparent gobies fish found in three lakes in Sumatra island is known as Rinuak fish (in Maninjau Lake and Singkarak Lake, West Sumatra, Indonesia) or Badar fish (in Siais Lake, North Sumatra, Indonesia), and are morphologically very similar to the Gobiopterus brachypterus. The phylogenetic study was carried out by analyzing 619 base pairs of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene in 12 fish individuals from the three lakes. Rinuak and Badar fish in three populations have four haplotypes. The sequence divergences in and between populations are very low (0.0-0.5%). This value indicates that Rinuak and Badar fish are the same species with low genetic diversity. The phylogenetic tree illustrates that this fish belongs to the group of Gobiidae and a sister taxon from G. brachypterus.

A new water mite species, Kongsbergia robisoni, is described from the Interior Highlands of North America based on morphological analysis supported by DNA sequence data. Populations from three ecoregions within the Interior Highlands were found to be morphologically similar to one another and distinct from other known Kongsbergia species. To help to determine whether subtle morphological differences between populations within the Interior Highlands should be interpreted as variability within a single species or were indicative of species endemic to specific ecoregions, mitochondrial cytochrome oxidase I sequences were analyzed. Three primary clades of Kongsbergia were supported by 100% bootstrap values and 1.0 Bayesian posterior probabilities. The phylogenetic hypothesis indicated that specimens from the Interior Highlands, including specimens from the Ozark Highlands, Boston Mountains, and Ouachita Mountains, formed a clade that was differentiated from various species of Kongsbergia from Appalachia (Great Smoky Mountains and Southeast Tennessee).

Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes

Tunas are commercially important fishery worldwide. There are at least 13 species of tuna belonging to three genera, out of which genus Thunnus has maximum eight species. On the basis of their availability, they can be characterised as oceanic such as Thunnus albacares (yellowfin tuna) or coastal such as Thunnus tonggol (longtail tuna). Although these two are different species, morphological differentiation can only be seen in mature individuals, hence misidentification may result in erroneous data set, which ultimately affect conservation strategies. The mitochondrial DNA cytochrome oxidase c subunit 1 (COI) gene is one of the most popular markers for population genetic and phylogeographic studies across the animal kingdom. The present study aims to study the sequence conservation and variation in mitochondrial Cytochrome Oxidase I (COI) between these two species of tuna. COI sequence analysis of yellowfin and longtail revealed the close relationship between them in Thunnus genera. The present study is the first direct comparison of mitochondrial COI sequences of these two tuna species.

Editor's evaluation: Competitive interactions between culturable bacteria are highly non-additive

Decision letter: Competitive interactions between culturable bacteria are highly non-additive

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

Effects of changes in dietary protein have been investigated on three mitochondrial enzymes, succinate dehydrogenase, isocitrate dehydrogenase and cytochrome oxidase. Weanling rats (21 days old) were fed for 30 days on (a) a commercially produced diet (CPD) containing 21.0% dietary protein and (b) a low protein-high carbohydrate diet (LPD) containing 3.47% dietary protein. Signs of protein-energy malnutrition developed in the animals having the low protein diet. The mitochondrial enzymes were assayed. Some of the experimental rats were repleted by feeding them on a protein-rich diet for 3 weeks, and the same mitochondrial enzymes were assayed. The activity of mitochondrial cytochrome oxidase, which fell to 24% of the control values during the period of deficiency, rose to 91% of the values for control rats during rehabilitation. The activities of succinate dehydrogenase and NAD+-isocitrate dehydrogenase fell to 75 and 73% of the control values, respectively, during depletion and rose to 83 and 88% during repletion in line with the general rate of recovery of the malnourished rats as reflected by the changes in the body weights during repletion. These results show that mitochondrial cytochrome oxidase is very sensitive to changes in dietary protein. Its activity drops sharply with reduction in dietary protein intake and rises rapidly, outstripping the rate of general recovery on reverting to a protein-rich diet.

Daily acute intermittent hypoxia induced dynamic changes in dendritic mitochondrial ultrastructure and cytochrome oxidase activity in the pre-Bötzinger complex of rats

The correct identification of sand fly vectors of leishmaniasis is important for controlling the disease. Genetic, particularly DNA sequence data, has lately become an important adjunct to the use of morphological criteria for this purpose. A recent DNA sequencing study revealed the presence of two cryptic species in the Sergentomyia bailyi species complex in India. The present study was undertaken to ascertain the presence of cryptic species in the Se. bailyi complex in Sri Lanka using morphological characteristics and DNA sequences from cytochrome c oxidase subunits. Sand flies were collected from leishmaniasis endemic and non-endemic dry zone districts of Sri Lanka. A total of 175 Se. bailyi specimens were initially screened for morphological variations and the identified samples formed two groups, tentatively termed as Se. bailyi species A and B, based on the relative length of the sensilla chaeticum and antennal flagellomere. DNA sequences from the mitochondrial cytochrome c oxidase subunit I (COI) and subunit II (COII) genes of morphologically identified Se. bailyi species A and B were subsequently analyzed. The two species showed differences in the COI and COII gene sequences and were placed in two separate clades by phylogenetic analysis. An allele specific polymerase chain reaction assay based on sequence variation in the COI gene accurately differentiated species A and B. The study therefore describes the first morphological and genetic evidence for the presence of two cryptic species within the Se. bailyi complex in Sri Lanka and a DNA-based laboratory technique for differentiating them.

ABSTRACTMegadromus guerinii, an endemic carabid beetle (Carabidae), is the most common carabid throughout its restricted range on Banks Peninsula, a formation of extinct volcanoes in Canterbury, New Zealand. This study characterises the small-scale phylogeographic patterns of M. guerinii across the formerly volcanically active Banks Peninsula using mitochondrial and ribosomal genes. Between the eastern and western areas of the peninsula, the mitochondrial, but not nuclear, DNA has a well-defined geographic distribution. Specifically, mitochondrial cytochrome c oxidase subunit I (CO1) identifies two distinct groups (> 6% divergence between eastern and western beetles) while ribosomal genes show no discernible pattern. Whether such a pattern represents male-biased dispersal, Wolbachia infection, a recent range expansion of a divergent lineage, or a deeper historic separation is explored. There is potential that male-biased dispersal could have occurred. Wolbachia infection was not detected. We conclude that historical processes have likely separated taxa in the eastern and western peninsula.

The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers

THE importance of studying visceral melanocytes has already been emphasized1–4 and the liver of Amphiuma tridactylum—a rich source of melanocytes—is a suitable material to use. The melanoprotein of the liver of Amphiuma is very similar to that of human liver melanoma5, and the melanin polymer (free from protein) closely resembles that of human substantia nigra pigment and synthetic catecholamine pigment formed by incubating the various amines with a mitochondrial preparation containing monoamine oxidase4. Structural and functional studies of the hepatic melanocytes of Amphiuma may therefore have a bearing on other pigmentary systems. We have reported (refs. 1 and 6 and unpublished work of Prasad) that the melanocytes of Amphiuma constitute about 20 per cent of the liver cell population (hepatocytes and melanocytes). Most of these melanocytes (70–80 per cent of total pigment cell population) are lightly pigmented and have an abundance of melanin-containing organelles which we named polymelanosomes6. The darkly pigmented cells contain closely packed granules lying freely in the cytoplasm, but no polymelanosomes. There is some morphological evidence that melanin-synthesis occurs in the polymelanosomes, and the light melanocytes which have an abundance of these organelles probably represent the younger form6. Polymelanosomes possess three mitochondrial enzymes, monoamine oxidase, cytochrome oxidase and succinic oxidase7.