Molecular Taxonomy and Phylogenetic Analysis of Dove and Pigeon Species (Aves: Columbidae) of Pakistan, Based on COI Region of Mitochondrial DNA

Doves and Pigeons are the members of living family Columbidae (Order: Columbiformes) having a wide range of taxonomic diversity and geographic distribution. Seven species with one sample each of family Columbidae were collected via random sampling from different districts of Pakistan to carry out this study. The targeted gene region was sequenced and identified by using BLAST tool at National Center for Biotechnology Information (NCBI). CLUSTALW was used for sequence alignment and MEGA6 for reconstruction of phylogenetic trees to predict the effective ancestry of different Columbidae species. The following phylogenetic trees were obtained i.e. Maximum Likelihood tree, Neighborhood joining tree, Maximum parsimony tree and UPGMA tree. In the current study, COI gene barcoding and phylogenetic analysis of family Columbidae gave results of multiple alignment which showed that Columba livia livia and Columba eversmanni, closely resembled as well as Spilopelia senegalensis and Streptopelia decaocta. While Streptopelia tranquebarica and Spilopelia chinensis have great affinity due to small clade difference and Treron phoenicoptera was distinctly related to other species due to large clade difference.

Phylogeny of Tacca (Taccaceae) and traits in reproductive structures, with description of a new Bornean species

Wong SY, Chua KS. 2019. Phylogeny of Tacca (Taccaceae) and traits in reproductive structures, with description of a new Bornean species. Biodiversitas 20: 3096-3118. A phylogenetic study of 16 of the c. 20 Tacca species is presented using nuclear ITS and plastid matK gene regions. Tacca leontopetaloides and T. maculata are a sister clade to the rest of the Tacca species. Tacca palmata and T. palmatifida are strongly supported together in a clade with this clade sister to T. bibracteata and T. plantaginea. All endemic Bornean taxa except T. bibracteata formed a derived clade together with non-Bornean T. cristata and T. sumatrana. The Bornean taxa are separated into three clades with T. borneensis sister to the other two clades. Twelve morphological characteristics are coded and mapped onto the Maximum Parsimony tree to elucidate potential evolutionary patterns. Results indicated shifts from a geophytic (irregularly-) seasonally dormant to an evergreen mesophytic habit, a decompound to a simple leaf blade, a long to a short peduncle, green to dark-colored inflorescences, numerous to few inner bracts, bracteoles, and flowers, and a low to an increased number of ovules. Within the Bornean taxa, there is a reversal from showy bracts and elaborate inflorescences to less showy bracts and simplified inflorescences. Tacca cristata Jack is resurrected from within T. integrifolia Ker Gawl. sensu Drenth. A new species, Tacca havilandii S.Y.Wong & K.S.Chua from Borneo is described.

Chemosystematics Using Cuticular Compounds: A Powerful Tool to Separate Species in Mediterranean Dung Beetles (Coleoptera: Geotrupidae)

The use of chemical characters to infer a phylogeny is known to be promising to ascertain phylogenetic relationships in controversial groups. Dung beetle classifications containing the Geotrupidae family, based on morphological characters and genes, are debated with respect to the subfamilies, such as the Bolboceratids. In our study, we used different approaches to generate and compare the Geotrupidae phylogenies based on genetics and chemotaxonomy. Cuticular compounds were analyzed for 12 species of Mediterranean dung beetles to build a chemical phylogeny. In addition, mitochondrial and nuclear marker concatenation have been used to elaborate the molecular phylogeny. Using the cuticular compound continuous data, our results showed that each species was associated with a specific chemical pattern and that all individuals belonging to the same species displayed a similar chemical blend. The most distant species was Bolbelasmus gallicus, with an evident distinction from the other species due to several compounds. The maximum parsimony tree showed that all genera belonging to a Geotrupidae subfamily were grouped in the same clade, with B. gallicus species isolated in another clade, similar to the chemotaxonomy grouping. A strong positive correlation between chemotaxonomy and genetic phylogeny has been demonstrated, underlying a genetic basis for cuticular hydrocarbon variations. Our results are congruent with previous studies using morphological or genetic data. Our results also showed that only 10 compounds can be used to distinguish at least six species of dung beetle and that chemotaxonomy could become a useful and affordable tool to determine phylogenetic relationships in insects.

Phylogenetic analysis reveals high local endemism and clear biogeographic breaks in southern African stoneflies (Notonemouridae, Plecoptera)

The low vagility of the southern African Notonemouridae (stoneflies, Plecoptera), and their restriction to temperate montane refugia, make them a useful model for examining the evolution and biogeography of the rich palaeogenic fauna of the region. Here we use maximum parsimony tree reconstruction based on morphological characters and a partial COI mtDNA sequence to explore the evolutionary history and biogeography of the family in southern Africa. Morphological and molecular parsimony cladograms were largely in agreement, and supported monophyly of all six genera in the region. Previously undocumented morphological features in Plecoptera are identified: the first record of paraproct glands, and the presence of paired spermathecae in Aphanicercopsis Barnard females (all other Plecoptera have a single or a divided spermatheca). Some phylogenetically useful characters were the degree of fusion of the ventral abdominal nerve cord ganglia, male paraproct glands (presence and shape), and accessory glands of the male seminal vesicle. Two main biogeographic zones were defined: Eastern Highlands and the Cape Fold Mountains, with an additional outlying zone, the Namaqualand Highlands. Almost 41% of species were endemic to a single mountain range group. The most species-rich region was the intersection of the Southern and Western Cape Fold Mountains. It is hypothesized that, after the separation of Gondwanaland, the common ancestor of the region’s six genera dispersed from a Cape Fold Mountain origin to the Amatola and Drakensberg montane areas of the southern tip of the African continent. The high number of species within the Cape Fold Mountains compared to other mountain ranges in the region is likely a reflection of the topographic complexity of this mountain system and its influence on vicariant events.

Morphological phylogeny of the Australian genera of the bee fly subfamily Bombyliinae (Diptera : Bombyliidae) with description of four new genera

Bombyliinae, one of the largest subfamilies of Bombyliidae, including 78 genera assigned to four tribes, is distributed on all continents except Antarctica. Their larvae are parasitoids, and adults are important pollinators. The Australian Bombyliinae currently has 17 described genera and 87 described species. The purpose of this study is to establish the phylogeny of the Australian members of the subfamily Bombyliinae, including the boundaries and relationships of the genera, using morphological characters. One maximum parsimony tree was generated from 83 morphological characters scored for 50 species, representing all recognised genera and some unplaced species that we considered may represent new genera. Phylogenetic analysis recovered the relationships between the recognised Australian genera of Bombyliinae and clarified generic limits. The group comprises five main clades, with the genus Pilosia being sister to the remaining Bombyliinae. On the basis of this analysis, four new genera are described: Lambkinomyia Li & Yeates, gen. nov., Dissodesma Bowden & Li, gen. nov., Nigromyia Li & Yeates, gen. nov. and Robertsmyia Li & Yeates, gen. nov. Ten new species are described: Dissodesma immaculata Li & Yeates, sp. nov., Dissodesma flava Li & Yeates, sp. nov., Dissodesma smarti Li & Yeates, sp. nov., Nigromyia collessi Li & Yeates, sp. nov., Nigromyia crocea Li & Yeates, sp. nov., Nigromyia flavimana Li & Yeates, sp. nov., Nigromyia longistriata Li & Yeates, sp. nov., Nigromyia pantherina Li & Yeates, sp. nov., Nigromyia parva Li & Yeates, sp. nov. and Nigromyia tomentosa Li & Yeates, sp. nov. Two new junior synonyms are identified: Apiformyia is a junior synonym of Eristalopsis and Brychosoma is a junior synonym of Staurostichus. The following new combinations are proposed: from Apiformyia: Eristalopsis australis (Yeates), comb. nov.; from Bombylius: Dissodesma primogenita (Walker) comb. nov.; from Brychosoma: Staurostichus aureolatus (Walker), comb. nov., Staurostichus hilaris (Walker), comb. nov. and Staurostichus pictipennis (Macquart), comb. nov.; from Laurella: Robertsmyia pallidoventris (Roberts), comb. nov.; from Mandella: Lambkinomyia cinctiventris (Roberts), comb. nov., Lambkinomyia flavovillosa (Roberts), comb. nov., Lambkinomyia pallida (Roberts), comb. nov. and Lambkinomyia rubida (Roberts), comb. nov.; and from Meomyia: Mandella australis (Guérin-Méneville), comb. nov. http://zoobank.org/urn:lsid:zoobank.org:pub:E4A86A19-4AC3-498C-8BDF-B8B501E5A248

Corrigendum to: Morphological phylogeny of the Australian genera of the bee fly subfamily Bombyliinae (Diptera : Bombyliidae) with description of four new genera

Bombyliinae, one of the largest subfamilies of Bombyliidae, including 78 genera assigned to four tribes, is distributed on all continents except Antarctica. Their larvae are parasitoids, and adults are important pollinators. The Australian Bombyliinae currently has 17 described genera and 87 described species. The purpose of this study is to establish the phylogeny of the Australian members of the subfamily Bombyliinae, including the boundaries and relationships of the genera, using morphological characters. One maximum parsimony tree was generated from 83 morphological characters scored for 50 species, representing all recognised genera and some unplaced species that we considered may represent new genera. Phylogenetic analysis recovered the relationships between the recognised Australian genera of Bombyliinae and clarified generic limits. The group comprises five main clades, with the genus Pilosia being sister to the remaining Bombyliinae. On the basis of this analysis, four new genera are described: Lambkinomyia Li & Yeates, gen. nov., Dissodesma Bowden & Li, gen. nov., Nigromyia Li & Yeates, gen. nov. and Robertsmyia Li & Yeates, gen. nov. Ten new species are described: Dissodesma immaculata Li & Yeates, sp. nov., Dissodesma flava Li & Yeates, sp. nov., Dissodesma smarti Li & Yeates, sp. nov., Nigromyia collessi Li & Yeates, sp. nov., Nigromyia crocea Li & Yeates, sp. nov., Nigromyia flavimana Li & Yeates, sp. nov., Nigromyia longistriata Li & Yeates, sp. nov., Nigromyia pantherina Li & Yeates, sp. nov., Nigromyia parva Li & Yeates, sp. nov. and Nigromyia tomentosa Li & Yeates, sp. nov. Two new junior synonyms are identified: Apiformyia is a junior synonym of Eristalopsis and Brychosoma is a junior synonym of Staurostichus. The following new combinations are proposed: from Apiformyia: Eristalopsis australis (Yeates), comb. nov.; from Bombylius: Dissodesma primogenita (Walker) comb. nov.; from Brychosoma: Staurostichus aureolatus (Walker), comb. nov., Staurostichus hilaris (Walker), comb. nov. and Staurostichus pictipennis (Macquart), comb. nov.; from Laurella: Robertsmyia pallidoventris (Roberts), comb. nov.; from Mandella: Lambkinomyia cinctiventris (Roberts), comb. nov., Lambkinomyia flavovillosa (Roberts), comb. nov., Lambkinomyia pallida (Roberts), comb. nov. and Lambkinomyia rubida (Roberts), comb. nov.; and from Meomyia: Mandella australis (Guérin-Méneville), comb. nov. <a ext-link-type=

Molecular phylogeny of Barbin fishes of North - East Indiabased on mitochondrial 16SrRNA gene sequences

The Barbin fishes (Cypriniformes: Barbinae) have achieved great diversity in the world and cosmopolitan in distribution but their phyletic classification is ambiguous. Molecular phylogeny of barbin fishes of North-East India was studied by using mitochondrial 16S rRNA sequences. Partial sequences (540-615 bp) of mit. 16S rRNA genes of four species of barbin fishes – Pethia atra, Puntius chola, P. javanicus, and P. sophore were generated and sequences of 7 species were downloaded from GenBank for present study. The aim of our present study is to resolve the taxonomic relationship and to establish the molecular phylogeny of Barbin fishes of North-East India based on mitochondrial 16S rRNA genes sequences. The Maximum Parsimony Tree shows three clusters with high bootstrap value and present data indicates that all fishes in this group had a common ancestor but now they have separated into distinct evolutionary lineages.

Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution

Anchors are important attachment appendages that prevent the physical dislodging of a monogenean parasite from fish host gills. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies. We used a geometric morphometric approach to explore anchor shape variation in 13 Ligophorus (Monogenea:Ancyrocephalidae) species infecting two marine mugilid (Teleostei: Mugilidae) fish hosts (Moolgarda buchanani and Liza subviridis) in the waters off West Peninsular Malaysia. Molecular sequence data from three nuclear markers: 28S rRNA, 18S rRNA and ITS1, were used to infer a maximum likelihood phylogeny to enable visualization of shape evolution in phylomorphospace. For inferring patterns of size evolution in the phylogeny, we used a size measure based on the first principal component of all pairwise Euclidean distances between landmarks. Cluster heat map and principal component analysis showed that anchor shape variation had sufficient systematic information for delimiting 12 of the 13 species. Adams' multivariate K test indicated significant correlation between anchor shape and phylogeny (p-value = 0.0001). We also discovered that characters based on anchor shaft shape, the length between inner and outer root tips and the length between inner root tip and the dent point were more phylogenetically informative than inner and outer lengths, as indicated by a maximum parsimony tree that was better resolved and had major clades congruent with those of the molecular phylogenetic tree. Continuous character mapping of size onto the inferred molecular phylogeny and Rayleigh’s test for departure from directional uniformity in each species’s landmark relative to the ancestor indicated that species infecting M. buchanani generally evolved larger and more robust anchors, while those infecting L. subviridis generally evolved smaller and more delicate anchors. Nevertheless, phylogenetic regression of anchor shape against body size and anchor size showed significant correlation (p-value = 0.02) between anchor shape and size, suggesting morphometric constraints in anchor evolution. Finally, morphological integration analysis revealed tight integration between the root and point compartments within anchors, confirming that the anchor functions as a single, fully integrated module. The present work is supported by the development of integrative analytical tools in the form of a new R package – monogeneaGM. By lowering barriers to data integration and analysis , we aim to encourage the scientific community to collect and contribute morphometric and genetic data from other Ligophorus species, which are essential for developing Ligophorus as a model system for understanding association between patterns of anchor shape size evolution and biodiversity in the Monogenea.