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Maximum likelihood tree of the Alcedinidae based on 651 nucleotides of the COI gene and using the GTR+Γ as optimal model. The tree is rooted on motmots (Momotidae) and rollers (Coraciidae) as outgroup taxa. Values on nodes indicate percentage bootstrap support based on ML/NJ/MP analyses; values less than 50% are not shown. Scale bar represents five nucleotide changes for every 100 nucleotides.
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... gene tree ( Figure 2) agrees with the currently established phylogenetic relationships using molecular data (Moyle 2006) with respect to monophyly and lineage sorting. Monophyly of the traditional subfamilies Alcedininae, Daceloninae and Cerylinae as well as monophyly of species were clearly resolved. ...
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The paper presents qualitative and quantitative composition of the nucleotide sequences of the 5'-region of the first subunit of the mitochondrial cytochrome oxidase (COI) gene (decoded in the framework of the International DNA Barcoding Project) and the variability of the corresponding amino acid sequences in the genus Jordanita Verity, 1946. The...
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... The literature reveals a little information about mangrove kingfisher's life history. Researchers have studied a few anatomical, physiological and ecological attributes-the DNA barcoding, hunting method, population status and decline due to alien intruders, cooperative nesting molecular phylogeny niche partitioning-of mangrove kingfisher outside Bangladesh (Luczon et al. 2010, Fitzsimons et al. 2011, Pereira 2013, Beckon 1987, Campbell 2013, Anderson et al. 2015, Borah et al. 2012. No study has been done on the feeding and breeding ecology of mangrove kingfishers in Bangladesh. ...
not available Bangladesh J. Zool. 49 (2): 347-351, 2021
... The final 25-lL PCR reaction mix consists of 12.5 ll GoTaq buffer master mix from Promega (USA), 25 ng of template DNA, 0.2 lM of each amplification primers and up to a final desired volume with deionized distilled water. The PCR thermocycler protocol was achieved as reported previously (Hebert et al., 2004;Luczon et al., 2010;Cawthorn et al., 2012). The specific bands relating to desired genes were excised and cleansed from the gel by Promega kit (Wizard SV Gel and PCR clean up) as designated by the maker's procedure. ...
... Sequence attributes and phylogenetic relationships using three mtDNA barcode genes This study has used three mtDNA barcode genes for molecularly differentiate between two closely related subspecies of Collared Kingfisher, T. c. abyssinicus and T. c. kalbaensis. An earlier molecular study of T. chloris focused on the phylogeny of the species using mtDNA marker (Luczon et al., 2010). It is known that the topologies derived from the results of mtDNA analysis yielded greater resolution than those resulting from the analysis of nuclear introns, therefore, the sequence evolution recovered from mtDNA give a higher rate compared to nuclear DNA (Brown, 1985). ...
The Collared Kingfisher (Todiramphus chloris) is widely distributed across the Indian and western Pacific Oceans and consists of about 50 subspecies. Two different subspecies of T. chloris occur in the Arabian Peninsula: T. c. abyssinicus from the Red Sea coast and T. c. kalbaensis from the Arabian Sea coast in the United Arab Emirates and Oman. The aim of this study was to determine the molecular relationship between the two Arabian subspecies and to establish the first DNA barcodes from the Arabian Peninsula for this species. Three different mitochondrial genes were used: (i) cytochrome c oxidase subunit I (COI), (ii) 12S rRNA (12S) and (iii) NADH dehydrogenase-1 (ND1). The COI gene sequences of the two subspecies were 100% identical, while the 12S and ND1 gene sequences revealed a unique single nucleotide variation between the two subspecies. Thus, this single nucleotide variation can be used as a DNA barcode to discriminate between two subspecies. Furthermore, the genetic profile or fingerprint for both subspecies were compared using ten primers of the highly polymorphic nuclear markers (Inter Simple Sequence Repeat, ISSR). As expected, the DNA analysis of the ISSR markers was able to distinguish between the specimens of the two subspecies. These results suggest that T. c. abyssinicus and T. c. kalbaensis are not identical and thus belong to different subspecies. Besides, the sequences of the COI gene for T. c. abyssinicus and T. c. kalbaensis differs by only 1.28% from T. sanctus suggesting that the Arabian subspecies are closely related to the Sacred Kingfisher (T. sanctus).
... Genomic sequences provide valuable information for tracing the history of gene rearrangements and phylogenetic 1 3 reconstructions (Härlid et al. 1998;Braband et al. 2010;Yang et al. 2010;Cerasale et al. 2012), molecular phylogenetic analyses become popular strategy in nowadays' systematic studies. Some researchers explored the relationships among different genus or families in Coraciiformes with single mitochondrial genes (Overton and Rhoads 2004;Marks and Willard 2005;Kirchman et al. 2001;Luczon et al. 2010), and only limited species were involved in these investigations. In molecular systematic investigations focused on high level phylogeny of birds, only few species of Coraciiformes have been involved, and the evolutionary relationship between Coraciiformes and other orders was still in debate (Chubb 2004;Ericson et al. 2006;Hackett et al. 2008;Pacheco et al. 2011;Jetz et al. 2012;Jarvis et al. 2014). ...
Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.
... base in which barcode sequences can be accessed. In the Philippines, the University of the Philippines Diliman Institute of Biology (UPD IB) established the DNA Barcoding of Life-Philippine Network (DOLPhiN) in 2008 and is an ongoing program that aims to apply DNA barcoding to Philippine biodiversity, particularly to its native and endemic species. Luczon et al. (2010) produced the first set of COI DNA barcodes for DOLPhiN from the White Collared Kingfisher, Todiramphus chloris, from UP Diliman, followed by Ong et al. (2011) for the Philippine accipitrids found in the Philippine Eagle Center in Davao City and Aquilino et al. (2011) for the ichthyofauna of Taal Lake. ...
... Alström et al. (2011) later changed Megaluridae to Locustellidae as the name Locustellinae (Bonaparte, 1854) has priority over Megalurinae (Blyth, 1875) (Bock, 1994). This study, which is a continuation of that of Luczon et al. (2010), aims to produce a barcode profile for Philippine birds found within the UP Diliman campus. Vallejo et al. (2008) identified 36 species, of which 14% are endemic, interspersed in various habitats in UP Diliman such as the campus's green spaces and buildings. ...
... All species are native and resident species in the Philippines, with the exception of the Eurasian Tree Sparrow Passer montanus, which is an introduced species. Another species, the White-collared Kingfisher Todiramphus chloris, was already sequenced and analyzed by Luczon et al. (2010). All sequences were checked for gaps by comparing the translated amino acid sequences with Gallus gallus complete cytochrome c oxidase subunit 1 gene (GenBank AP003580). ...
DNA barcoding is increasingly being used by researchers across the globe to aid in the identification of species. Using this taxonomic tool on bird species in an urban green space within Manila, i.e. the University of the Philippines Diliman campus, Luzon, Philippines, DNA barcodes of eleven species were generated. Different haplotypes for some of the species were observed. Using BLAST, the cytochrome oxidase subunit 1 (COI) sequence of every species from this study was correctly matched with the corresponding species having a COI record in Genbank, with the exception of the Striated Grassbird Megalurus palustris, which is a new COI record. The three distinct haplotypes for M. palustris were then compared with COI sequences from other members of the sylviid " Old World Warblers " to determine the effectiveness of the DNA barcode in discriminating it with other species. Results show that COI was successful in placing M. palustris as a distinct taxon.
As biodiversity loss reaches critical levels, greater knowledge of its distribution is needed to concentrate conservation efforts. Biodiversity can be measured at several levels, with the species typically the unit used in conservation planning. Attempts to set accurate conservation priorities face a number of prominent challenges; 1. species distributions are often poorly known, particularly in the tropics where the rate of biodiversity loss is highest, 2. the number of currently described species is known to be a huge underestimate, with many cryptic species awaiting formal description, and 3. much remains unknown about the drivers of speciation, particularly what adaptations are associated with population divergence in the early stages of the process. In this thesis I explore each of these main topics in a study system in South-east Sulawesi, in the biodiversity hotspot of the Wallacea region. I focus on the avifauna of the region, contributing to characterising the community composition of unstudied islands, assess the species status of island populations which have diverged from the mainland and provide insight into how adaptations to island life may drive population divergence.
In Chapters 2 and 3 we filled in some of the gaps in the knowledge of the avifaunal distribution in South-east Sulawesi on the previously unsurveyed islands of Kabaena, Muna and Wawonii, identifying potentially important populations, particularly for the Endangered Milky Stork Mycteria cinerea. Chapters 4 and 5 evaluated the diversification of the ‘great speciator’ taxa of South-east Sulawesi, Zosterops white-eyes and Todiramphus kingfishers, lineages renowned for their wide range and propensity for speciation. We propose two new white-eye species, an isolated population descended from the widespread island coloniser the Lemon-bellied White-eye Zosterops chloris, and a single island endemic the ‘Wangi-wangi White-eye’. The ‘Wangi-wangi White-eye’ is a particularly intriguing new species, as its closest relatives are found >3000 km away in the Solomon Islands. Chapters 4 and 5 also flag up other populations for further taxonomic refinement, the Wakatobi Islands Collared Kingfisher Todiramphus chloris population and Runduma Island Lemon-bellied White-eye populations may represent endemic subspecies for South-east Sulawesi.
Chapters 4-7 investigated different morphological adaptations that are associated with island colonisation and the early stages of speciation. Chapter 5 suggested that a reduced dispersal ability, in comparison to source populations, may be a feature of populations of widespread island colonisers which become isolated. In Chapter 4 we discussed how potential differences in habitat, and associated increases in interspecific competition, may have driven a niche shift in Collared Kingfishers on the Wakatobi Islands. Chapter 6 outlined how Lemon-bellied White-eyes had a larger morphological niche volume and greater population density in allopatry from the Pale-bellied White-eye Zosterops consobrinorum, on both a small island and in urban areas. Reduced interspecific competition, and greater intraspecific competition in high density populations, likely led to the increase in niche volume seen in the Lemon-bellied White-eye populations. This chapter highlights the potential for urban areas to act as ecological islands for island colonising edge species in the Indo-Pacific. Chapter 7 looked at some of the effects of island colonisation on sexual dimorphism. Showed that Olive-backed Sunbirds Cinnyris jugularis on the small oceanic Wakatobi Islands showed greater sexual dimorphism and higher population density than those on the mainland and continental islands. There was no difference in the niche volume of males from Wakatobi and mainland populations, but females from the Wakatobi Islands had a smaller niche volume than those from the mainland. Potentially their niche volume has contracted to reduce intersexual competition in the high density populations of the Wakatobi Islands.
This thesis illustrates how studying the populations of Indo-Pacific island colonisers, particularly the ‘great speciator’ lineages, provides the opportunity to contribute both taxonomic revision and insight into the early stages of speciation. Their rapid speed of evolutionary change, ability to colonise islands and the frequency with which they are found in secondary sympatry makes ‘great speciators’ ideal groups in which to study speciation. This work is given impetus by the looming biodiversity crisis that threatens not just Southeast Asia, but the whole world. Much biodiversity, and the evolutionary lessons it can teach us, faces extinction before being formally recognised.
