scholarly journals A Molecular Phylogeny of Kingfishers (Alcedinidae) With Insights Into Early Biogeographic History

The Auk ◽  
2006 ◽  
Vol 123 (2) ◽  
pp. 487-499 ◽  
Author(s):  
Robert G. Moyle
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
Nuclear Dna ◽  
Nuclear Data ◽  
Australian Region ◽  
Biogeographic History ◽  
Species Analysis ◽  
The Family ◽  
Dispersal Events ◽  
Natural Groups

Abstract The phylogeny of kingfishers was reconstructed by comparing mitochondrial and nuclear DNA sequences representing 38 ingroup species. Analysis of the combined data and the nuclear data alone recovered the Alcedininae as the basal lineage in the family. This basal arrangement, and support for many relationships within the three subfamilies, allows discussion of biogeographic issues. The Australian region and Pacific islands display the highest diversity of kingfishers, but this diversity is not a reflection of a long history in the region. Rather, high diversity and endemism in the Australian region is inferred to result from relatively recent radiations from southern Asia. The most parsimonious explanation for the origin of New World taxa is two dispersal events from the Old World. Within the large Halcyon radiation, the phylogeny is well resolved and allows evaluation of generic assignments. The phylogeny supports splitting Todiramphus from Halcyon. Todiramphus and Syma are sister taxa, as are Halcyon and Pelargopsis. Thus, merging or retaining those genera is a more subjective decision. Although not fully resolved, relationships within the alcedinines indicate that Ceyx and Alcedo, as currently delimited, are not natural groups. Phylogénie Moléculaire des Alcedinidae avec un Aperçu de l'Histoire Biogéographique Ancienne

Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)

2020 ◽  
Author(s):  
Jeffrey L Weinell ◽  
Anthony J Barley ◽  
Cameron D Siler ◽  
Nikolai L Orlov ◽  
Natalia B Ananjeva ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Oceanic Islands ◽  
Species Level ◽  
Boiga Irregularis ◽  
Brown Tree Snake ◽  
Biogeographic History ◽  
The Pacific ◽  
History Of ◽  
Dispersal Events

Abstract The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.

Molecular phylogenetic studies in the genus Amanita

1998 ◽  
Vol 76 (7) ◽  
pp. 1170-1179 ◽  
Author(s):  
Michael Weiß ◽  
Zhu-Liang Yang ◽  
Franz Oberwinkler
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Large Subunit ◽  
Bootstrap Analysis ◽  
Phylogenetic Studies ◽  
Maximum Likelihood Methods ◽  
Molecular Phylogenetic ◽  
Large Subunit Rdna ◽  
Conditional Clustering ◽  
Natural Groups

A group of 49 Amanita species that had been thoroughly examined morphologically and anatomically was analyzed by DNA sequence comparison to estimate natural groups and phylogenetic relationships within the genus. Nuclear DNA sequences coding for a part of the ribosomal large subunit were determined and evaluated using neighbor-joining with bootstrap analysis, parsimony analysis, conditional clustering, and maximum likelihood methods. Sections Amanita, Caesarea, Vaginatae, Validae, Phalloideae, and Amidella were substantially confirmed as monophyletic groups, while the monophyly of section Lepidella remained unclear. Branching topologies between and within sections could also partially be derived. Subgenera Amanita and Lepidella were not supported. The Mappae group was included in section Validae. Grouping hypotheses obtained by DNA analyses are discussed in relation to the distribution of morphological and anatomical characters in the studied species.Key words: fungi, basidiomycetes phylogeny, Agaricales, Amanita systematics, large subunit rDNA, 28S.

A revision of the Viscaceae of Australia.

Brunonia ◽  
1983 ◽  
Vol 6 (1) ◽  
pp. 25 ◽  
Author(s):  
BA Barlow
Keyword(s):  
New Combinations ◽  
Australian Region ◽  
Biogeographic History ◽  
The Family ◽  
History Of

The Australian Viscaceae comprise 3 genera, Viscum, Notothixos and Korthalsella, and 14 species. A further 2 species of Korthalsella are endemic to Norfolk and Lord Howe Islands respectively. None of the genera and only 7 of the species are endemic to Australia. Three species are described as new, viz. Korthalsella emersa, K. grayi and K. leucothrix. One subspecies is described as new, viz. K. rubra subsp. geijericola. There are 2 new combinations, viz. K. japonica subsp. brassiana (K. brassiana Blakely) and Viscum whitei subsp. flexicaule (V. flexicaule Barlow). The biogeographic history of the family in the Australian region is briefly discussed.

Bernieridae (Aves: Passeriformes): a family-group name for the Malagasy sylvioid radiation

Zootaxa ◽  
2010 ◽  
Vol 2554 (1) ◽  
pp. 65 ◽  
Author(s):  
ALICE CIBOIS ◽  
NORMAND DAVID ◽  
STEVEN M. S. GREGORY ◽  
ERIC PASQUET
Keyword(s):  
Dna Sequences ◽  
Morphological Diversity ◽  
Family Group ◽  
Zoological Nomenclature ◽  
International Code ◽  
Large Size ◽  
The Family ◽  
History Of ◽  
Adaptive Radiations ◽  
Dispersal Events

The island of Madagascar is a renowned hotspot for adaptive radiations. Madagascar has been separated from mainland Africa since the end of the Jurassic, and from India since the Late Cretaceous. This long isolation, combined with the island’s large size and relatively few dispersal events has resulted in an avifauna characterized by a low species count and high endemism: for instance, 80% of the breeding Malagasy songbirds (Passeriformes) are endemic (Hawkins & Goodman 2003). A first series of papers (Cibois et al. 1999, 2001; Fjeldsa et al. 1999) on the phylogeny of the Malagasy taxa traditionally classified as Timaliidae, Sylviidae and Pycnonotidae (all families included in the large sylvioid clade) showed that several of these passerines form an original radiation endemic to the island. Because these results were based solely on a single kind of molecular marker (mitochondrial DNA sequences), the authors refrained at that time from giving a name to this clade. More recently, other studies using nuclear markers as well (Beresford et al. 2005; Johansson et al. 2008a, 2008b) confirm the existence of this Malagasy sylvioid radiation. The species that comprise this group exhibit a great variety of bill shapes, wing and tail proportions, and tarsus lengths. This diversity in morphology is linked to varieties of habitat and prey favoured by these insectivorous forest dwellers (Schulenberg 2003). Thus the endemic Malagasy sylvioid clade rivals other island radiations, including the vangas of Madagascar and the finches of the Galapagos, in ecological and morphological diversity. Several authors were inclined to consider this group at the family level, using the name ‘Bernieridae’. To our knowledge the first study using this name was the book “The natural history of Madagascar”, edited by S. M. Goodman and J. Benstead in 2003, where the name ‘Bernieridae’ appeared in two chapters (in Tingle et al. (2003: p. 522) and Hawkins & Goodman (2003: p. 1036), although Schulenberg (2003: p. 1131) referred to the Malagasy "warblers" in his chapter on the radiations of passerine birds on Madagascar). An alternative spelling for the family-group name, ‘Bernieriidae’, can be found in several personal pages on the internet, but we have not found an occurrence of this in any publication, as defined in the International Code of Zoological Nomenclature (4th edition, 1999). The name ‘Bernieridae’ was later used in several journal articles (Chouteau & Fenosoa 2008; Fuchs et al. 2008; Johansson et al. 2008a, 2008b), however, none of these have introduced the family-group name ‘Bernieridae’ according to the provisions of the International Code of Zoological Nomenclature, i.e. the nominal taxon was not explicitly indicated as intentionally new (Article 16.1) and the type genus was not cited (Article 16.2). In the present paper, we therefore propose to rectify this situation by correctly introducing the family-group name for the Malagasy sylvioid radiation.

Phylogenetics and population structure of the steppe species Hycleus polymorphus (Coleoptera: Meloidae: Mylabrini) reveal multiple refugia in Mediterranean mountain ranges

2020 ◽  
Vol 130 (3) ◽  
pp. 507-519
Author(s):  
Alessandra Riccieri ◽  
Emiliano Mancini ◽  
Mattia Iannella ◽  
Daniele Salvi ◽  
Marco A Bologna
Keyword(s):  
Dna Sequences ◽  
Western Europe ◽  
Nuclear Dna ◽  
Mediterranean Area ◽  
Species Group ◽  
Last Interglacial ◽  
Steppe Species ◽  
Quaternary Climate ◽  
Biogeographic History ◽  
Allopatric Divergence

Abstract Many continental species distributed in the Eurasian steppe occur as relict populations in the mountains of Western Europe. Their biogeographical responses to Quaternary climate changes have been poorly studied; however, they could have responded as cold-adapted species. We investigated the biogeographic history of a steppe beetle, Hycleus polymorphus, using mitochondrial and nuclear DNA sequences (COI, CAD, ITS2), and species distribution modelling (SDM) under present and past bioclimatic envelopes. We first performed a phylogenetic assessment to define species boundaries within the H. polymorphus species group. Specimens previously treated as Hycleus humerosus on morphological grounds are assigned to H. polymorphus, and those identified as Hycleus zebraeus assigned to Hycleus atratus. ITS2 data analyses revealed a strong phylogeographical structure of H. polymorphus populations, with four haplogroups corresponding to the (i) Italian Alps, (ii) French Alps and Pyrenees, (iii) South Balkan and Pontic mountains, and (iv) North Dinaric Alps. Based on these analyses and the SDM, we propose that during a glacial period, following the spread of steppic habitat, H. polymorphus underwent a range expansion from Asia to South-West Europe. Within the Mediterranean area, during the last interglacial the climatic suitability for the species was limited to mountains that acted as refugia and prompted allopatric divergence into four main lineages.

scholarly journals Heaven and hell: Spotlights on some DNA barcodes for species identification and delimitation in ground beetles

2019 ◽  
Vol 2 ◽  
Author(s):  
Thorsten Assmann ◽  
Estève Boutaud ◽  
Jörn Buse ◽  
Claudia Drees ◽  
Ariel-Leib-Leonid Friedman ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Intraspecific Variability ◽  
Cost Effective ◽  
Nuclear Data ◽  
Ground Beetles ◽  
Western Alps ◽  
Barcoding Gap

In the face of the decline of many insects, there is an increasing demand for contemporary, fast and cost-effective approaches to monitor the development of populations and species. Numerous scientists favor molecular methods, especially those involving barcoding of the CO1 gene, as an alternative to classical, morphology-based species identification. Moreover, DNA barcoding is also discussed as a suitable method to support species delimitations in complexes of closely related taxa. We used the available sequences of ground beetles from North and Central Europe with additional ones we generated from Southern Europe and the Middle East to draw conclusion about the practicability of such approach for ground beetles. In general, while strong intraspecific differentiations within the CO1 fragment seem to characterize some wingless species (e.g. Graphipterus serrator, Siagona longula, Carabus problematicus, some Platycarabus species), others do not display much intraspecific variability (e.g. Graphipterus multiguttatus and G. sharonae within the “G. serrator clade”). These results certainly complicate the application of a metabarcoding approach without a larger database to delimitate these ground beetles. Furthermore, these results limit the applicability of the well-known barcoding gap, in ecological studies. With regards to taxonomic problems, mitochondrial and nuclear DNA sequences can provide support for taxonomic decisions. For example, the two taxa Carabus variolosus and nodulosus are characterized predominantely by K2P values lower than the barcoding gap. In view of the otherwise strong intraspecific differentiation within the genus Carabus, these two taxa should be regarded as subspecies. In contrast, DNA barcoding can also help to identify "good" species. Mitochondrial and nuclear data suggest, for example, that an Oreonebria taxon and a Platycarabus taxon from the South-western Alps represent "good species", although they were usually considered as synonyms or subspecies. In another case, two tiger beetle taxa, which until a few months ago were considered to belong to the same species, show such strong differentiation that only two species can be postulated (Calomera aulicoides and C. littoralis winkleri). In summary, we can state that DNA sequences and the barcoding gap can help to define species delimitations in ground beetles. However, several species, including widespread sister species, cannot be identified by DNA barcoding for various reasons (e.g. young species or horizontal gene flow). Consequently, until an automated, fast, and reliable method to identify species from samples emerges, ecological investigations have to rely on classical, morphology-based identifications.

scholarly journals A western representative of an eastern clade: phylogeographic history of the gypsophilous plant Nepeta hispanica

2022 ◽  
Author(s):  
Ignacio Ramos-Gutierrez ◽  
Juan Carlos Moreno Saiz ◽  
Mario Fernandez-Mazuecos
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Western Mediterranean ◽  
Niche Modelling ◽  
Biogeographic Patterns ◽  
Biogeographic History ◽  
History Of

The preference of certain plant species for gypsum soils leads to disjunct population structures that are thought to generate island-like dynamics potentially influencing biogeographic patterns at multiple evolutionary scales. Here, we study the evolutionary and biogeographic history of Nepeta hispanica, a western Mediterranean plant associated with gypsum soils and displaying a patchy distribution with populations very distant from each other. Three approaches were used: (a) interspecific phylogenetic analyses based on nuclear DNA sequences of the ITS region to unveil the relationships and times of divergence between N. hispanica and its closest relatives; (b) phylogeographic analyses using plastid DNA regions trnS-trnG and psbJ-petA to evaluate the degree of genetic isolation between populations of N. hispanica, their relationships and their genetic diversity; and (c) ecological niche modelling to evaluate historical distributional changes. Results reveal that N. hispanica belongs to an eastern Mediterranean and Asian clade diversified in arid environments since the Miocene-Pliocene. This species represents the only extant lineage of this clade that colonized the western Mediterranean, probably through the northern Mediterranean coast (southern Europe). Present Iberian populations display a high plastid genetic diversity and, even if geographically distant from each other, they are highly connected according to the distribution of plastid haplotypes and lineages. This can be explained by a scenario involving a complex history of back-and-forth colonisation events, facilitated by a relative stability of suitable conditions for the species across the Iberian Peninsula throughout the Quaternary.

Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)

2019 ◽  
Vol 104 (1) ◽  
pp. 33-48 ◽  
Author(s):  
Alejandro Zuluaga ◽  
Martin Llano ◽  
Ken Cameron
Keyword(s):  
Dna Sequences ◽  
Pacific Islands ◽  
R Package ◽  
Morphological Characters ◽  
Ancestral State ◽  
Seed Shape ◽  
Long Distance ◽  
The Pacific ◽  
And Migration ◽  
The Tropics

The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of the genera within Monsteroideae. However, we found low rates of variation in the DNA sequences used and a lack of molecular markers suitable for species-level phylogenies in the group. We also performed ancestral state reconstruction of some morphological characters traditionally used for genera delimitation. Only seed shape and size, number of seeds, number of locules, and presence of endosperm showed utility in the classification of genera in Monsteroideae. We estimated ancestral ranges using a dispersal-extinction-cladogenesis model as implemented in the R package BioGeoBEARS and found evidence for a Gondwanan origin of the clade. One tropical disjunction (Monstera Adans. sister to Amydrium Schott–Epipremnum Schott) was found to be the product of a previous Boreotropical distribution. Two other disjunctions are more recent and likely due to long-distance dispersal: Spathiphyllum Schott (with Holochlamys Engl. nested within) represents a dispersal from South America to the Pacific Islands in Southeast Asia, and Rhaphidophora represents a dispersal from Asia to Africa. Future studies based on stronger phylogenetic reconstructions and complete morphological datasets are needed to explore the details of speciation and migration within and among areas in Asia.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

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