The evolutionary and biogeographic history of the armoured harvestmen – Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)

2011 ◽  
Vol 25 (2) ◽  
pp. 106 ◽  
Author(s):  
Prashant P. Sharma ◽  
Gonzalo Giribet
Keyword(s):  
Sequence Data ◽  
Elongation Factor ◽  
Molecular Dating ◽  
12S Rrna ◽  
28S Rrna ◽  
Biogeographic History ◽  
Ancestral Area Reconstruction ◽  
Tree Estimation ◽  
Taxonomic Changes ◽  
Permian Mass Extinction

We investigated the internal phylogeny of Laniatores, the most diverse suborder of Opiliones, using sequence data from 10 molecular loci: 12S rRNA, 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I (COI), cytochrome b, elongation factor-1α, histones H3 and H4, and U2 snRNA. Exemplars of all previously described families of Laniatores were included, in addition to two families – Petrobunidae, fam. nov. and Tithaeidae, fam. nov. – that we erect herein. Data analyses were based on maximum likelihood and Bayesian approaches on static alignments, and included phylogenetic tree estimation, molecular dating, and biogeographic analysis of ancestral area reconstruction. The results obtained include the monophyly of Laniatores and the infraorder Grassatores – the focus of this study – as well as support for numerous interfamilial relationships. The two new families described cluster with other South-east Asian families (Podoctidae and Epedanidae). Diversification of Laniatores is estimated at ~348 Mya, and origin of most Grassatores superfamilies occurs in a ~25 million year span of time immediately after the end-Permian mass extinction (254 Mya). Ancestral range reconstruction of the clade (Samooidea + Zalmoxoidea) suggests that the ancestral range of Samooidea comprises West Tropical Gondwana (West Africa + Neotropics), whereas that of Zalmoxoidea is exclusively Neotropical. The following additional taxonomic changes are proposed: (1) Remyus is transferred to Phalangodidae, and (2) Escadabiidae and Kimulidae are transferred to Zalmoxoidea.

Molecular phylogeny of Australasian anopsobiine centipedes (Chilopoda : Lithobiomorpha)

2004 ◽  
Vol 18 (3) ◽  
pp. 235 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
South Africa ◽  
New Species ◽  
New Zealand ◽  
New Caledonia ◽  
Sequence Data ◽  
Mitochondrial Protein ◽  
Molecular Data ◽  
12S Rrna ◽  
28S Rrna ◽  
16S Rna

Species assigned to the anopsobiine centipede genera Anopsobius Silvestri, 1899, and Dichelobius Attems, 1911, are widely distributed on fragments of the Gondwanan supercontinent, including temperate and tropical Australia, New Zealand, New Caledonia, the Cape region of South Africa, and southern South America. Phylogenetic relationships between Australasian and other Gondwanan Anopsobiinae are inferred based on parsimony and maximum likelihood analyses (via direct optimisation) of sequence data for five markers: nuclear ribosomal 18S rRNA and 28S rRNA, mitochondrial ribosomal 12S rRNA and 16S RNA, and the mitochondrial protein-coding cytochrome c oxidase subunit I. New molecular data are added for Anopsobius from South Africa and New Zealand, Dichelobius from New Caledonia, and a new species from Queensland, Australia, Dichelobius etnaensis, sp. nov. The new species is based on distinctive morphological and molecular data. The molecular phylogenies indicate that antennal segmentation in the Anopsobiinae is a more reliable taxonomic character than is spiracle distribution. The former character divides the Gondwanan clade into a 17-segmented group (Dichelobius) and a 15-segmented group (Anopsobius). Confinement of the spiracles to segments 3, 10 and 12 has at least two origins in the Gondwanan clade. The area cladogram for Dichelobius (Queensland (Western Australia + New Caledonia)) suggests a relictual distribution pruned by extinction.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2019 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Time Estimation ◽  
Geographic Range ◽  
Molecular Dating ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background: Distichodus, the type genus of the endemic African characiform family Distichodontidae, is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group.Conclusions: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment ever conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies might be a consequence of deep coalescence and recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting acomplex scenario for the assemblage of Africa’s continental ichthyofaunal communities. Keywords: Distichodontidae, Distichodus, Congo Basin, molecular phylogeny, African fishes, geographic range evolution, molecular dating.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

scholarly journals Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia

2017 ◽  
Author(s):  
Vuong Tan Tu ◽  
Gábor Csorba ◽  
Manuel Ruedi ◽  
Neil M. Furey ◽  
Nguyen Truong Son ◽  
...  
Keyword(s):  
New Species ◽  
Southeast Asia ◽  
Molecular Dating ◽  
Bamboo Forest ◽  
Sea Level Changes ◽  
Climatic Oscillations ◽  
Biogeographic History ◽  
Species Complexes ◽  
Taxonomic Changes ◽  
A New Species

In Southeast Asia, bats of the genus Tylonycteris Peters, 1872 have traditionally been classified into two wide-ranging species, T. pachypus (Temminck, 1840) and T. robustula Thomas, 1915. Our comparative phylogeographic analyses based on two mitochondrial and seven nuclear genes, combined with our multivariate morphological analyses, show that these species actually represent cryptic species complexes that share a similar biogeographic history in three major regions, i.e., Sundaland, southern Indochina, and northern Indochina. Our molecular dating estimates suggest that Pleistocene climatic oscillations and sea level changes have repeatedly isolated ancestral populations of Tylonycteris spp. in distant bamboo forest refugia. The analyses indicate, however, that populations of the T. pachypus complex were less affected by forest fragmentation in mainland Southeast Asia than those of the T. robustula complex. Accordingly, we propose several taxonomic changes within the genus Tylonycteris: the species T. fulvida and T. malayana are revalidated, and a new species, T. tonkinensis Tu, Csorba, Ruedi & Hassanin sp. nov., endemic to northern Indochina, is described.

Blind scolopendrid centipedes of the genus Cormocephalus from subterranean habitats in Western Australia (Myriapoda: Scolopendromorpha: Scolopendridae)

2019 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Joel A. Huey ◽  
William F. Humphreys ◽  
Mia Hillyer ◽  
Mieke A. Burger ◽  
...  
Keyword(s):  
Western Australia ◽  
Sequence Data ◽  
Arid Zone ◽  
Morphological Characters ◽  
Species Group ◽  
Bootstrap Support ◽  
12S Rrna ◽  
28S Rrna ◽  
South West ◽  
Single Blind

Only a single blind species is known in the centipede family Scolopendridae, representing the monotypic genus Tonkinodentus Schileyko, 1992, from Vietnam. All of more than 400 other species have four ocelli on each side of the cephalic plate. A complex of three new blind species of the genus Cormocephalus Newport, 1844, is described from the subterranean fauna of the central Pilbara region of Western Australia. Phylogenies based on sequence data for the barcode region of COI and a concatenated matrix that also includes 12S rRNA, 28S rRNA and ITS2 unite the blind Pilbara species as a monophyletic group, albeit with moderate bootstrap support, informally named the C. sagmus species group. Cormocephalus sagmus, C. pyropygus and C. delta spp. nov. supplement 17 epigean congeners previously described from Australia. The new species are all morphologically similar, but can be distinguished using the shape and spinulation of the ultimate leg prefemur. Two additional genetically distinct lineages were recovered that are not described, owing to the specimens being immature or lacking diagnostic morphological characters. The subterranean radiation in the Pilbara is more closely related to species from forests in the south-west of Western Australia than to congeners from the arid zone. http://zoobank.org/urn:lsid:zoobank.org:pub:6F67FD31-A373-4DC5-A5FD-374D32DEE02C

scholarly journals Phylogeny, Historical Biogeography and the Evolution of Migration in Accipitrid Birds of Prey (Aves: Accipitriformes)

2014 ◽  
Vol 22 (1) ◽  
pp. 15-35 ◽  
Author(s):  
Jenő Nagy ◽  
Jácint Tökölyi
Keyword(s):  
Large Scale ◽  
Bird Species ◽  
Ecological Factors ◽  
Molecular Dating ◽  
Birds Of Prey ◽  
Tropical Species ◽  
Ancestral State ◽  
Biogeographic History ◽  
Ancestral Area Reconstruction ◽  
Evolution Of Migration

Abstract Migration plays a fundamental part in the life of most temperate bird species. The regular, large-scale seasonal movements that characterize temperate migration systems appear to have originated in parallel with the postglacial northern expansion of tropical species. Migratoriness is also influenced by a number of ecological factors, such as the ability to survive harsh winters. Hence, understanding the origins and evolution of migration requires integration of the biogeographic history and ecology of birds in a phylogenetic context. We used molecular dating and ancestral state reconstruction to infer the origins and evolutionary changes in migratory behavior and ancestral area reconstruction to investigate historical patterns of range evolution in accipitrid birds of prey (Accipitriformes). Migration evolved multiple times in birds of prey, the earliest of which occurred in true hawks (Accipitrinae), during the middle Miocene period, according to our analyses. In most cases, a tropical ancestral distribution was inferred for the non-migratory ancestors of migratory lineages. Results from directional evolutionary tests indicate that migration evolved in the tropics and then increased the rate of colonization of temperate habitats, suggesting that temperate species might be descendants of tropical ones that dispersed into these seasonal habitats. Finally, we found that diet generalization predicts migratoriness in this group.

The phylogeography of Asian Schistosoma (Trematoda: Schistosomatidae)

Parasitology ◽  
2002 ◽  
Vol 125 (2) ◽  
pp. 99-112 ◽  
Author(s):  
S. W. ATTWOOD ◽  
E. S. UPATHAM ◽  
X. H. MENG ◽  
D.-C. QIU ◽  
V. R. SOUTHGATE
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Rrna Genes ◽  
12S Rrna ◽  
28S Rrna ◽  
Asian Origin ◽  
Dna Sequence Data ◽  
African Group ◽  
Mitochondrial 12S Rrna ◽  
Central Thailand

Partial (DNA) sequences are presented for 2 nuclear (18S and 28S rRNA genes) and 2 mitochondrial (12S rRNA and ND1 genes) loci for 5 species belonging to the Schistosoma japonicum, S. sinensium and S. indicum groups of Asian Schistosoma. Fresh field isolates were collected and cultured for the following taxa: S. incognitum (S. indicum group, central Thailand), S. mekongi (S. japonicum group, southern Laos), S. ovuncatum (S. sinensium group, northern Thailand), S. spindale (S. indicum group, northeast Thailand and central Thailand isolates) and S. sinensium (S. sinensium group, Sichuan Province, China). This represents the first published DNA sequence data for S. ovuncatum and for S. sinensiums.s. from the type locality in China. The paper also presents the first sequence data at the above loci for S. incognitum (except for the 28S sequences) and S. sinensium. Congruence was observed between the phylogenies estimated for each locus, although the relationships of S. incognitum were not so well resolved. Fitch–Margoliash, maximum likelihood (ML) and maximum parsimony methods were used to estimate the phylogenies and the agreement between them was similar to that observed between loci. The ML tree was considered to best represent the data and additional 28S sequences (taken from the GenBank), for S. haematobium, S. japonicum, S. mansoni and Orientobilharzia turkestanicum, were used to construct an overall phylogeny. The S. indicum group taxa showed considerable divergence from the other Asian species and closest affinity with the African group. S. ovuncatum and S. sinensium appeared as sister taxa but their status as sibling species remained supported. The findings are discussed in the context of phylogeographical hypotheses for the origin of Schistosoma. An Asian origin for Schistosoma is also considered.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. To our knowledge, this is the first study to use nuclear rRNA at this taxonomic level, presumably because this marker is assumed to evolve so slowly that it is only suitable for phylogenetics.   Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolves effectively clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

The millipede genus Antichiropus (Diplopoda: Polydesmida: Paradoxosomatidae), part 3: species of the Pilbara bioregion of Western Australia

Zootaxa ◽  
2019 ◽  
Vol 4617 (1) ◽  
pp. 1-71
Author(s):  
CATHERINE A. CAR ◽  
MARK S. HARVEY ◽  
MIA J. HILLYER ◽  
JOEL A. HUEY
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Western Australia ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Diagnostic Feature ◽  
12S Rrna ◽  
28S Rrna ◽  
Oxidase Subunit

The species of the millipede genus Antichiropus Attems, 1911 found in the Pilbara region of Western Australia are reviewed, and 33 new species are described. The new species are: A. anguinus Car, n. sp., A. antius Car, n. sp., A. apricus Car, n. sp., A. cirratus Car, n. sp., A. confragus Car, n. sp., A. cristatus Car, n. sp., A. cucumeraceous Car, n. sp., A. cunicularis Car, n. sp, A. echinus Car, n. sp., A. filiolus Car, n. sp., A. forcipatus Car, n. sp., A. georginae Car, n. sp., A. gibbus Car, n. sp., A. hystricosus Car, n. sp., A. julianneae Car, n. sp., A. literulus Car, n. sp., A. lucyae Car, n. sp., A. nicholasi Car, n. sp., A. nimbus Car, n. sp., A. patriciae Car, n. sp., A. pendiculus Car, n. sp., A. picus Car, n. sp., A. procerus Car, n. sp., A. quaestionis Car, n. sp., A. rupinus Car, n. sp., A. salutus Car, n. sp., A. servulus Car, n. sp., A. simmonsi Car, n. sp., A. sloanae Car, n. sp., A. spathion Car, n. sp., A. uvulus Car, n. sp., A. verutus Car, n. sp. and A. vindicatus Car, n. sp.. The number of described Antichiropus species now stands at 72. Two species (A. julianneae Car, n. sp. and A. pendiculus Car, n. sp.) lack one diagnostic feature of the genus, namely a solenomere process, but are included here because they conform to the genus definition in all other characters. We also obtained sequence data from four mitochondrial genes (cytochrome c oxidase subunit 1 [COI], cytochrome c oxidase subunit 3 [COIII], cytochrome B [CytB], and 12S rRNA [12S]), and one nuclear gene (28S rRNA [28S]) for 19 species. Three main clades were recovered: one in the northern Pilbara, one in the southern Pilbara, and one just outside the south-western margin of the Pilbara. 

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