Phylogeny of a taxonomically difficult group and evolution of host location mechanism

The parasitic wasps are one of the largest insect groups and their life histories are remarkably variable. Common to all parasitic wasps is that they kill their hosts, which are usually beetles, butterflies and sometimes spiders. Hosts are often at a larval or pupal stage and live in concealed conditions, such as in plant tissue. Parasitic wasps have two main ways of finding their host. 1) They can detect chemical compounds emitted by damaged plant material or released by larvae living in plant tissue, and 2) detect the larvae by sound vibrations. Even though pupae are immobile and silent, and therefore do not cause vibration, parasitoids have, however, adapted to find passive developmental stages by producing vibration themselves by knocking the substrate with their antennae, and then detecting the echoes with their legs. This echolocation allows a parasitoid to locate its potential hosts that are deeply buried in wood. This study focuses on the relationships of the subfamily Cryptinae (Hymenoptera: Ichneumonidae) and related taxa, and the evolution of host location mechanism. There are no earlier studies of the phylogeny of the Cryptinae, and the position of related taxa are unclear. According to the earlier classification, which is entirely intuitional, the Cryptinae is divided into three tribes: Cryptini, Hemigasterini and Phygadeuontini. Further, these tribes are subdiveded into numerous subtribes. This work, based on molecular characters, shows that the cryptine tribes Cryptini, Phygadeuon¬tini and Hemigasterini come out largely as monophyletic groups, thus agreeing with the earlier classification. The earlier subtribal classification had no support. In addition, it is shown that modified antennal structures are associated with host usage of wood-boring coleopteran hosts. The cryptines have a clear modification series on their antennal tips from a simply tip to a hammer-like structure. The species with strongly modified antennae belong mostly to the tribe Cryptini and they utilise wood-boring beetles as hosts. Also, field observations on insect behaviour support this result.

Structure-Based Phylogeny as a Diagnostic for Functional Characterization of Proteins with a Cupin Fold

Background: The members of cupin superfamily exhibit large variations in their sequences, functions, organization of domains, quaternary associations and the nature of bound metal ion, despite having a conserved beta-barrel structural scaffold. Here, an attempt has been made to understand structure-function relationships among the members of this diverse superfamily and identify the principles governing functional diversity. The cupin superfamily also contains proteins for which the structures are available through world-wide structural genomics initiatives but characterized as ``hypothetical''. We have explored the feasibility of obtaining clues to functions of such proteins by means of comparative analysis with cupins of known structure and function. Methodology/Principal Findings: A 3-D structure-based phylogenetic approach was undertaken. Interestingly, a dendrogram generated solely on the basis of structural dissimilarity measure at the level of domain folds was found to cluster functionally similar members. This clustering also reflects an independent evolution of the two domains in bicupins. Close examination of structural superposition of members across various functional clusters reveals structural variations in regions that not only form the active site pocket but are also involved in interaction with another domain in the same polypeptide or in the oligomer. Conclusions/Significance: Structure-based phylogeny of cupins can influence identification of functions of proteins of yet unknown function with cupin fold. This approach can be extended to other proteins with a common fold that show high evolutionary divergence. This approach is expected to have an influence on the function annotation in structural genomics initiatives.

Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae)

The two recently proposed taxonomies of the langurs and leaf monkeys (Subfamily Colobinae) provide different implications to our understanding of the evolution of Nilgiri and purple-faced langurs. Groves (2001) [Groves, C.P., 2001. Primate Taxonomy. Smithsonian Institute Press, Washington], placed Nilgiri and purple-faced langurs in the genus Trachypithecus, thereby suggesting disjunct distribution of the genus Trachypithecus. [Brandon-Jones, D., Eudey, A.A., Geissmann, T., Groves, C.P., Melnick, D.J., Morales, J.C., Shekelle, M., Stewart, C.-B., 2003. Asian primate classification. Int. J. Primatol. 25, 97–162] placed these langurs in the genus Semnopithecus, which suggests convergence of morphological characters in Nilgiri and purple-faced langurs with Trachypithecus. To test these scenarios, we sequenced and analyzed the mitochondrial cytochrome b gene and two nuclear DNA-encoded genes, lysozyme and protamine P1, from a variety of colobine species. All three markers support the clustering of Nilgiri and purple-faced langurs with Hanuman langur (Semnopithecus), while leaf monkeys of Southeast Asian (Trachypithecus) form a distinct clade. The phylogenetic position of capped and golden leaf monkeys is still unresolved. It is likely that this species group might have evolved due to past hybridization between Semnopithecus and Trachypithecus clades.

The phylogeny and evolutionary timescale of muscoide (Diptera: Brachycera: Calyptratae) inferred from mitochondrial genomes

Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene

Evolution of the Neckeraceae (Bryophyta): resolving the backbone phylogeny

Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.

Taxonomy and phylogeny of white-rot polypores : case studies in Hymenochaetales and Polyporales (Basidiomycota)

Tutkimus käsittelee kääpien sukulaisuussuhteita. Käävät ovat kantasienten (Basidiomycota) muotoryhmä, joiden itiöemien alapinta muodostuu yhteensulautuneista pilleistä. Muotoryhmänä kääpiä voi verrata vaikka puihin siinä mielessä, että käävät kuten puutkaan eivät ole samankaltaisuudestaan huolimatta kaikki sukua toisilleen. DNA:n käyttö sukulaisuussuhteiden selvittämisessä on aloittanut mullistuksen kääpien luokittelussa. Aiemmin käytetty, itiöemien ominaisuuksiin perustunut luokittelu on osoittautunut keinotekoiseksi sukulaisuussuhteiden kannalta. Tutkimuksessani syvennyttiin useamman kääpäsuvun polveutumishistoriaan hyödyntäen DNA:ta ja perinteisiä menetelmiä. Tutkimuksen keskeisimmät tulokset liittyvät sitkokääpien sukuun (Antrodiella). Tämä noin 70 lajia sisältävä suku osoittautui rikkonaiseksi - sitkokääpiin luetut lajit kuuluvat kahteen sienilahkoon ja oikesti vähintään 13 sukuun. Tutkimuksessa löytyi kaksi Suomelle uutta sitkokääpää, leppikääpä (A. ichnusana) ja nipukkakääpä (A. leucoxantha). Uudet suvut kuvattiin Suomessa esiintyville sirppikääville (Sidera) ja talikääville (Obba). Uusi kääpäsuku ja -laji kuvattiin myös Indonesiasta (Sebipora aquosa). Valtaosa sitkokääpiin luetuista lajeista kuuluu orakarakoiden heimoon (Steccherinaceae), joka rajattiin tässä tutkimuksessa uudelleen. Heimoon kuuluvat mm. karakäävät (Junghuhnia) ja orakasmaiset orakarakat (Steccherinum). Sen sisällä selvitettiin kääpien ja orakkaiden sukulaisuussuhteita. Perinteisesti käävät ja orakkaat on viety eri sukuihin riippumatta niiden mikroskooppisesta samankaltaisuudesta. Tulosten valossa orakarakoiden heimossa käävät ja orakkaat pysyvät pääosin erillisissä suvuissa, mutta tästä on myös poikkeuksia (Antrodiella, Metuloidea ja Steccherinum). Lähes kaikki DNA:n perusteella määriteltävissä olevat suvut ovat tunnistettavissa itiöemien ominaisuuksiensa perusteella. Tulokset antavat eväitä kääpien luokitteluun laajemminkin osoittamalla, mitkä ominaisuudet ovat luokittelun kannalta merkityksellisiä. Tarkentunut tieto lajimäärästä ja lajien sukulaisuussuhteista hyödyttää ekologista tutkimusta sekä arvioita lajien uhanalaisuudesta. Tutkimuksen aikana luotua DNA-kirjastoa käytetään lajien tunnistamiseen. Tuloksia voidaan hyödyntää myös etsittäessä bioteknologisia sovelluksia käävistä, sillä sovellusten kannalta kiinnostavat ominaisuudet seuraavat usein sienten sukupuuta.

Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos

Represented by approximately 85 species, Hemidactylus is one of the most diverse and widely distributed genera of reptiles in the world. In the Indian subcontinent, this genus is represented by 28 species out of which at least 13 are endemic to this region. Here, we report the phylogeny of the Indian Hemidactylus geckos based on mitochondrial and nuclear DNA markers sequenced from multiple individuals of widely distributed as well as endemic congeners of India. Results indicate that a majority of the species distributed in India form a distinct clade whose members are largely confined to the Indian subcontinent thus representing a unique Indian radiation. The remaining Hemidactylus geckos of India belong to two other geographical clades representing the Southeast Asian and West-Asian arid zone species. Additionally, the three widely distributed, commensal species (H. brookii, H. frenatus and H. flaviviridis) are nested within the Indian radiation suggesting their Indian origin. Dispersal-vicariance analysis also supports their Indian origin and subsequent dispersal out-of-India into West-Asian arid zone and Southeast Asia. Thus, Indian subcontinent has served as an important arena for diversification amongst the Hemidactylus geckos and in the evolution and spread of its commensal geckos. (C) 2010 Elsevier Inc. All rights reserved.

Taxonomy and phylogeny of the manna lichens and allied species (Megasporaceae)

This dissertation is focused on the taxonomy, phylogeny, and ecology of the vagrant, erratic and allied terricolous and saxicolous species of the genera Aspicilia A. Massal. and Circinaria Link (Megasporaceae), particularly those traditionally referred to as manna lichens . The group has previously been defined on the basis of few morphological characters. The phylogeny of the family Megasporaceae is inferred from the combined dataset of nuLSU and mtSSU sequences. Five genera Aspicilia, Circinaria, Lobothallia, Megaspora, and Sagedia are recognized. Lobothallia is sister of the four other genera, while Aspicilia and Sagedia form the next clade. All these genera have small asci with eight spores. Circinaria is a sister genus of Megaspora, and these two have in common asci with (1 4) 6 8 large spores. Circinaria forms a monophyletic group and sphaerothallioid species form a monophyletic group within Circinaria. The presence of certain morphological characters such as pseudocyphellae, thickness of cortex and medulla layers, as well as ecological differences in sphaerothallioid species distinguish it from some other crustose species, especially those containing aspicilin and characterised by thin cortex and medulla layers, conidium length c. 6 12 µm and absence of pseudocyphellae. If sphaerothallioid species are accepted as a distinct genus, the rest of the Circinaria species would remain as a paraphyletic assemblage. Currently, the genus Circinaria includes all the sphaerothallioid species and its generic position is confirmed and accepted. Thus, it is proposed as a correct generic name also for the manna lichens described originally in other genera. Phylogeny at the species level was studied using nrITS sequence data. Traditionally, morphological characters have been used for the recognition of species. They were re-evaluated in the light of molecular data. Since characters such as vagrant, erratic and crustose growth forms proved to be misleading for the recognition of some species, a combination of several characters (including molecular data) is recommended. Vagrant growth form seems to have evolved several times among the distantly related lineages and even within a single population. The reasons behind the high plasticity in the external morphology of the sphaerothallioid Circinaria remain, however, unknown. Six new species are recognized: Aspicilia tibetica, Circinaria arida, C. digitata nom provis., C. gyrosa nom. provis., C. rogeri nom. provis., and C. rostamii nom. provis. Based on an analysis of nrITS dataset, three new erratic, vagrant and crustose species were also recognized, but these require additional study. The results also reveal that C. elmorei and C. hispida are not monophyletic as currently understood. In addition, 13 new combinations in the genus Circinaria are proposed.

Molecular Identification and Phylogeny of Bactrocera Species (Diptera: Tephritidae)

Fruit flies that belong to the genus Bactrocera (Diptera: Tephritidae) are major invasive pests of agricultural crops in Asia and Australia. Increased transboundary movement of agricultural produce has resulted in the chance introduction of many invasive species that include Bactrocera mainly as immature stages. Therefore quick and accurate species diagnosis is important at the port of entry, where morphological identification has a limited role, as it requires the presence of adult specimens and the availability of a specialist. Unfortunately when only immature stages are present, a lacunae in their taxonomy impedes accurate species diagnosis. At this juncture, molecular species diagnostics based on COX-I have become handy, because diagnosis is not limited by developmental stages. Yet another method of quick and accurate species diagnosis for Bactrocera spp. is based on the development of species-specific markers. This study evaluated the utility of COX-I for the quick and accurate species diagnosis of eggs, larvae, pupae and adults of B. zonata Saunders, B. tau Walker, and B. dorsalis Hendel. Furthermore the utility of species-specific markers in differentiating B. zonata (500bp) and B. tau (220bp) was shown. Phylogenetic relationships among five subgenera, viz., Austrodacus, Bactrocera, Daculus, Notodacus and Zeugodacus have been resolved employing the 5' region of COX-I (1490-2198); where COX-I sequences for B. dorsalis Hendel, B. tau Walker, B. correcta Bezzi and B. zonata Saunders from India were compared with other NCBI-GenBank accessions. Phylogenetic analysis employing Maximum Parsimony (MP) and Bayesian phylogenetic approach (BP) showed that the subgenus Bactrocera is monophyletic.

Phylogeny of the Asian Eutropis (Squamata: Scincidae) reveals an `into India' endemic Indian radiation

Recent generic rearrangement of the circumtropical distributed skink genus `Mabuya' has raised a lot of debate. According to this molecular phylogeny based rearrangement, the tropical Asian members of this genus have been assigned to Eutropis. However, in these studies the Asian members of `Mabuya' were largely sampled from Southeast (SE) Asia with very few species from Indian subcontinent. To test the validity of this assignment and to determine the evolutionary origin of Indian members of this group we sequenced one nuclear and two mitochondrial genes from most of the species from the Indian subregion. The nuclear and mitochondrial trees generated from these sequences confirmed the monophyly of the tropical Asian Eutropis. Furthermore, in the tree based on the combined mitochondrial and nuclear dataset an endemic Indian radiation was revealed that was nested within a larger Asian clade. Results of dispersal-vicariance analysis and molecular dating suggested an initial dispersal of Eutropis from SE Asia into India around 5.5-17 million years ago, giving rise to the extant members of the endemic Indian radiation. This initial dispersal was followed by two back dispersals from India into SE Asia. We also discuss the relationships within the endemic Indian radiation and its taxonomic implications. (c) 2012 Elsevier Inc. All rights reserved.

Insights into Himalayan biogeography from geckos: A molecular phylogeny of Cyrtodactylus (Squamata: Gekkonidae)

The India-Asia collision profoundly influenced the climate, topography and biodiversity of Asia, causing the formation of the biodiverse Himalayas. The species-rich gekkonid genus Cyrtodactylus is an ideal clade for exploring the biological impacts of the India-Asia collision, as previous phylogenetic hypotheses suggest basal divergences occurred within the Himalayas and Indo-Burma during the Eocene. To this end, we sampled for Cyrtodactylus across Indian areas of the Himalayas and Indo-Burma Hotspots and used three genes to reconstruct relationships and estimate divergence times. Basal divergences in Cyrtodactylus, Hemidactylus and the Palaearctic naked-toed geckos were simultaneous with or just preceded the start of the India-Asia collision. Diversification within Cyrtodactylus tracks the India-Asia collision and subsequent geological events. A number of geographically concordant clades are resolved within Indo-Burmese Cyrtodactylus. Our study reveals 17 divergent lineages that may represent undescribed species, underscoring the previously undocumented diversity of the region. The importance of rocky habitats for Cyrtodactylus indicates the Indo-Gangetic flood plains and the Garo-Rajmahal Gap are likely to have been important historical barriers for this group. (C) 2014 Elsevier Inc. All rights reserved.

Phylogeny of the freshwater crabs of the Western Ghats (Brachyura, Gecarcinucidae)

The Western Ghats mountain range in India is a biodiversity hotspot for a variety of organisms including a large number of endemic freshwater crab species and genera of the family Gecarcinucidae. The phylogenetic relationships of these taxa, however, have remained poorly understood. Here, we present a phylogeny that includes 90% of peninsular Indian genera based on mitochondrial 16S rRNA and nuclear histone H3 gene sequences. The subfamily Gecarcinucinae was found to be paraphyletic with members of two other subfamilies, Liotelphusinae and Parathelphusinae, nesting within. We identify a well-supported clade consisting of north Indian species and one clade comprising mostly south Indian species that inhabit the southern sky islands' of the Western Ghats. Relationships of early diverging genera, however, were resolved with low support. This study also includes newly sampled material from an isolated mountain plateau in the northern part of the Western Ghats, representing a new species of Gubernatoriana, which we describe here as Gubernatoriana basalticola sp. n. The new species is immediately distinguished from its congeners and the related genera Ghatiana and Inglethelphusa by its carapace and cheliped morphology, which are unique among Indian freshwater crabs. This study highlights the urgent need for continued faunistic studies to assess the true diversity of gecarcinucid crabs on the Indian subcontinent, to fully understand the basal phylogenetic relationships within the freshwater crab family Gecarcinucidae, and to evaluate the conservation threat status and biogeography of the montane freshwater crabs of the Western Ghats.