On the species identities of a complex Liolaemus fauna from the Altiplano and Atacama Desert: insights on Liolaemus stolzmanni, L. reichei, L. jamesi pachecoi, and L. poconchilensis (Squamata: Liolaemidae)

Zootaxa ◽  
2011 ◽  
Vol 2809 (1) ◽  
pp. 20 ◽  
Author(s):  
ROBERTO LANGSTROTH P.
Keyword(s):  
Adaptive Radiation ◽  
Atacama Desert ◽  
Sequence Divergence ◽  
South American ◽  
Morphometric Data ◽  
Mtdna Sequence ◽  
Complex Adaptive ◽  
Chilean Altiplano ◽  
Taxonomic Confusion ◽  
Intense Research

The South American lizard genus Liolaemus has undergone a complex adaptive radiation that has resulted in the evolution of more than 200 species widely spread in an extraordinary diversity of environments, and forming a complex array of assemblages. This evolutionary complexity has puzzled systematists and taxonomists since the first species were described more than 150 years ago. Within this lineage, the Andean Liolaemus faunas have proven to be a major challenge for herpetologists. Therefore, intense research is needed in this area to clarify long-standing problems. After more than a century of taxonomic confusion, the identity of Liolaemus stolzmanni (Steindachner, 1891) is here restored as the name that must be applied to the lizards widely known as Phrynosaura (= Liolaemus) reichei Werner, 1907 from the low to midelevation deserts of Tarapacá, Chile. Since 1966, the name L. stolzmanni has been erroneously assigned to populations of Liolaemus from the high Andes of the Chile-Bolivia borderlands which, according to observations presented in this study, correspond to Liolaemus pachecoi Laurent, 1995. A lectotype and allotype for L. stolzmanni are designated and the type locality for L. stolzmanni (= L. reichei) is emended to “Deserts of Iquique, Tarapacá Region, Chile”. Furthermore, the recognition of L. pachecoi as a species distinct from L. jamesi is supported by mtDNA sequence divergence data despite the inconclusive meristic and morphometric data. In summary, I conclude that (i) the Chilean L. reichei is a synonym of L. stolzmanni, and hence, that L. stolzmanni is a species endemic to Chile, not an element of the fauna of present-day Peru and that (ii) the Chilean Altiplano populations currently recognized as L. stolzmanni are L. pachecoi, a species hitherto known only from Bolivia. Also, I report the first confirmed specimens of L. poconchilensis from Peru, a species previously known only from Chile and confused with L. reichei.

scholarly journals Human mitochondrial DNA diversity is compatible with the multiregional continuity theory of the origin of Homo sapiens

2021 ◽  
Vol 84 (4) ◽  
pp. 487-502
Author(s):  
Robert B. Eckhardt
Keyword(s):  
Homo Sapiens ◽  
Sequence Divergence ◽  
Homo Erectus ◽  
Gradual Transition ◽  
Complete Replacement ◽  
Human Mitochondrial Dna ◽  
Coalescence Time ◽  
Dna Diversity ◽  
Mtdna Sequence ◽  
Out Of Africa

Abstract Confidence intervals for estimates of human mtDNA sequence diversity, chimpanzee-human mtDNA sequence divergence, and the time of splitting of the pongid-hominid lineages are presented. Consistent with all the data used in estimating the coalescence time for human mitochondrial lineages to a common ancestral mitochondrion is a range of dates from less than 79,000 years ago to more than 1,139,000 years ago. Consequently, the hypothesis that a migration of modern humans (Homo sapiens) out of Africa in the range of 140,000 to 280,000 years ago resulted in the complete replacement, without genetic interchange, of earlier Eurasian hominid populations (Homo erectus) is but one of several possible interpretations of the mtDNA data. The data are also compatible with the hypothesis, suggested earlier and supported by fossil evidence, of a single, more ancient expansion of the range of Homo erectus from Africa, followed by a gradual transition to Homo sapiens in Europe, Asia, and Africa.

Morphological and genetic concordance of cutthroat trout diversification from western North America

2021 ◽  
Author(s):  
Ernest R Keeley ◽  
Janet L Loxterman ◽  
Sammy L Matsaw ◽  
Zacharia M Njoroge ◽  
Meredith B Seiler ◽  
...  
Keyword(s):  
North America ◽  
Phenotypic Variability ◽  
Sequence Divergence ◽  
Cutthroat Trout ◽  
Distance Measures ◽  
Western North America ◽  
Morphological Comparison ◽  
Oncorhynchus Clarkii ◽  
Diverse Range ◽  
Mtdna Sequence

The cutthroat trout, Oncorhynchus clarkii (Richardson, 1836), is one of the most widely distributed species of freshwater fish in western North America. Occupying a diverse range of habitats, they exhibit significant phenotypic variability that is often recognized by intraspecific taxonomy. Recent molecular phylogenies have described phylogenetic diversification across cutthroat trout populations, but no study has provided a range-wide morphological comparison of taxonomic divisions. In this study, we used linear and geometric-based morphometrics to determine if phylogenetic and subspecies divisions correspond to morphological variation in cutthroat trout, using replicate populations from throughout the geographic range of the species. Our data indicate significant morphological divergence of intraspecific categories in some, but not all, cutthroat trout subspecies. We also compare morphological distance measures with distance measures of mtDNA sequence divergence. DNA sequence divergence was positively correlated with morphological distance measures, indicating that morphologically more similar subspecies have lower sequence divergence in comparison to morphologically distant subspecies. Given these results, integrating both approaches to describing intraspecific variation may be necessary for developing a comprehensive conservation plan in wide-ranging species.

scholarly journals Genetic Variability and Taxonomic Status of the Nihoa and Laysan Millerbirds

The Condor ◽  
2007 ◽  
Vol 109 (4) ◽  
pp. 954-962
Author(s):  
Robert C. Fleischer ◽  
Beth Slikas ◽  
Jon Beadell ◽  
Colm Atkins ◽  
Carl E. McINTOSH ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Microsatellite Loci ◽  
Sequence Divergence ◽  
Taxonomic Status ◽  
Small Population ◽  
Base Pairs ◽  
Stochastic Effects ◽  
Mtdna Sequence ◽  
Species Pairs ◽  
Two Populations

Abstract The Millerbird (Acrocephalus familiaris) is an endemic Northwestern Hawaiian Islands reed warbler that existed until about 1923 on Laysan Island (A. f. familiaris) and currently occurs in a small population on Nihoa Island (A. f. kingi). The two populations are described as separate subspecies or species on the basis of size and plumage differences. We assessed genetic variation in blood samples from 15 individuals in the modern Nihoa population using approximately 3000 base pairs (bp) of mitochondrial DNA (mtDNA) sequence and 14 microsatellite loci. We also obtained up to 1028 bp of mtDNA sequence from the fragmented DNA of museum specimens of three birds collected on Nihoa in 1923 and five birds collected on Laysan in 1902 and 1911 (ancient samples). Genetic variation in both marker types was extremely low in the modern Nihoa population (nucleotide diversity [π]  =  0.00005 for mtDNA sequences; observed heterozygosity was 7.2% for the microsatellite loci). In contrast, we found three mtDNA haplotypes among the five Laysan individuals (π  =  0.0023), indicating substantially greater genetic variation. The Nihoa and Laysan taxa differed by 1.7% uncorrected mtDNA sequence divergence, a magnitude that would support designation at the subspecies, and perhaps species, level relative to other closely related Acrocephalus species pairs. However, in light of strong ecological similarity between the two taxa, and a need to have additional populations to prevent extinction from stochastic effects and catastrophes, we believe these genetic differences should not deter a potential translocation of individuals from Nihoa to Laysan.

Mitochondrial lineages or discrete species? Assessing diversity within Timon tangitanus (Lacertidae) using mitochondrial and nuclear DNA sequences

2020 ◽  
Vol 41 (1) ◽  
pp. 123-132
Author(s):  
João M. Abreu ◽  
Daniele Salvi ◽  
Ana Perera ◽  
D. James Harris
Keyword(s):  
North Africa ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Divergence ◽  
Lineage Sorting ◽  
Lizard Species ◽  
Nuclear Markers ◽  
Species Complexes ◽  
Mtdna Sequence ◽  
Mtdna Lineages

Abstract Identification of extremely high levels of mitochondrial DNA (mtDNA) sequence divergence within reptiles from North Africa is commonplace. This high divergence often compares with interspecific levels among widely accepted species, leading to the hypothesis of the occurrence of species complexes. Indeed, in many examples, data from nuclear markers support such taxonomic recognition. Such is the case of two recently recognized ocellated lizard species of the genus Timon, T. nevadensis, from Spain, and T. kurdistanicus, from the Middle East, which both showed notable genetic differentiation from their sister taxa. In North Africa, highly divergent mtDNA lineages of Timon tangitanus were previously identified but not corroborated with nuclear markers. Here we expand geographic sampling across the range of Timon tangitanus and complement mtDNA sequences with data from nuclear markers (MC1R and ACM4). We identify four divergent mtDNA lineages, at a level similar to some reptile species. However, the nuclear markers show limited differentiation and lack of lineage sorting. This and some other recent assessments within reptiles discourage the use of mtDNA data alone as a proxy for taxonomic units, demonstrating once more the need for integrative taxonomic approaches.

Paleowetlands and regional climate change in the central Atacama Desert, northern chile

2008 ◽  
Vol 69 (03) ◽  
pp. 343-360 ◽  
Author(s):  
Jay Quade ◽  
Jason A. Rech ◽  
Julio L. Betancourt ◽  
Claudio Latorre ◽  
Barbra Quade ◽  
...  
Keyword(s):  
Regional Climate ◽  
Atacama Desert ◽  
Regional Climate Change ◽  
Western Slope ◽  
South American ◽  
Groundwater Levels ◽  
The Andes ◽  
Water Tables ◽  
Lithic Artifacts ◽  
North And South

Widespread, organic-rich diatomaceous deposits are evidence for formerly wetter times along the margins of the central Atacama Desert, one of the driest places on Earth today. We mapped and dated these paleowetland deposits at three presently waterless locations near Salar de Punta Negra (24.5°S) on the western slope of the Andes. Elevated groundwater levels supported phreatic discharge into wetlands during two periods: 15,900 to ~ 13,800 and 12,700 to ~ 9700 cal yr BP. Dense concentrations of lithic artifacts testify to the presence of paleoindians around the wetlands late in the second wet phase (11,000?–9700 cal yr BP). Water tables dropped below the surface before 15,900 and since 8100 cal yr BP, and briefly between ~ 13,800 and 12,700 cal yr BP. This temporal pattern is repeated, with some slight differences, in rodent middens from the study area, in both paleowetland and rodent midden deposits north and south of the study area, and in lake level fluctuations on the adjacent Bolivian Altiplano. The regional synchroneity of these changes points to a strengthening of the South American Monsoon — which we term the "Central Andean Pluvial Event" — in two distinct intervals (15,900–13,800 and 12,700–9700 cal yr BP), probably induced by steepened SST gradients across the tropical Pacific (i.e., La Niña-like conditions).

A new Reed Frog (Hyperoliidae: Hyperolius) from coastal northeastern Mozambique

Zootaxa ◽  
2018 ◽  
Vol 4379 (2) ◽  
pp. 177 ◽  
Author(s):  
WERNER CONRADIE ◽  
LUKE VERBURGT ◽  
DANIEL M. PORTIK ◽  
ANNEMARIE OHLER ◽  
BERYL A. BWONG ◽  
...  
Keyword(s):  
New Species ◽  
Genetic Divergence ◽  
Sequence Divergence ◽  
Biodiversity Hotspot ◽  
Eastern Africa ◽  
Sister Taxon ◽  
Coastal Forests ◽  
Phylogenetic Reconstructions ◽  
Mtdna Sequence ◽  
A New Species

A new species of African reed frog (genus Hyperolius Rapp, 1842) is described from the Coastal Forests of the Eastern Africa Biodiversity Hotspot in northeastern Mozambique. It is currently only known from less than ten localities associated with the Mozambican coastal pans system, but may also occur in the southeastern corner of Tanzania. Phylogenetic reconstructions using the mitochondrial 16S marker revealed that it is the sister taxon of Hyperolius mitchelli (>5.6% 16S mtDNA sequence divergence) and forms part of a larger H. mitchelli complex with H. mitchelli and H. rubrovermiculatus. The new species is distinguished from other closely related Hyperolius species by genetic divergence, morphology, vocalisation, and dorsal colouration. 

scholarly journals A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4422 ◽  
Author(s):  
Chatmongkon Suwannapoom ◽  
Montri Sumontha ◽  
Jitthep Tunprasert ◽  
Thiti Ruangsuwan ◽  
Parinya Pawangkhanant ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
12S Rrna ◽  
New Taxon ◽  
Ecological Specialization ◽  
Limestone Cave ◽  
Mtdna Sequence

We report on a discovery ofSiamophryne troglodytesGen. et sp. nov.,a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA–16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genusGastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates thatS. troglodytesGen. et sp. nov.represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the “out of Indo-Eurasia” biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such,S. troglodytesGen. et sp. nov.is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it.

scholarly journals Synopsis of Schizanthus Ruiz & Pav. (Solanaceae), a genus endemic to the southern Andes

PhytoKeys ◽  
2020 ◽  
Vol 154 ◽  
pp. 57-102
Author(s):  
Vanezza Morales-Fierro ◽  
Mélica Muñoz-Schick ◽  
Andrés Moreira-Muñoz
Keyword(s):  
New Taxa ◽  
Atacama Desert ◽  
New Combination ◽  
Herbarium Specimens ◽  
South American ◽  
Habitat Distribution ◽  
Type Specimens ◽  
Private Protected Areas ◽  
Infraspecific Taxa ◽  
Key Characters

We present a taxonomic synopsis of the South American genus Schizanthus Ruiz & Pav. (Solanaceae), within which we recognise seventeen taxa (14 species with three infraspecific taxa). The genus is mainly distributed in Chile between the coast of the Atacama Desert and the southern temperate forests, while two species occur in the Argentinian Provinces of Mendoza and Neuquén. This taxonomic treatment is based on the analysis of herbarium specimens from 30 different herbaria. For each accepted species we provide details of type specimens and synonymy, key characters, habitat, distribution information and presence in public or private protected areas. We also incorporate a list of representative localities from examined material. We here described three new taxa: Schizanthus porrigens Graham ex Hook. subsp. borealis V.Morales & Muñoz-Schick, subsp. nov., Schizanthus carlomunozii V.Morales & Muñoz-Schick, sp. nov. and its variety Schizanthus carlomunozii var. dilutimaculatus V.Morales & Muñoz-Schick, var. nov., all of them from the coast of Coquimbo Region. We also recognise Schizanthus litoralis Phil. var. humilis (Lindl.) V.Morales & Muñoz-Schick, comb. nov., as a new combination.

scholarly journals Molecular Phylogenetic Relationships Among the Geositta Miners (Furnariidae) and Biogeographic Implications for Avian Speciation in Fuego-Patagonia

The Auk ◽  
2005 ◽  
Vol 122 (1) ◽  
pp. 158-174
Author(s):  
Z. A. Cheviron ◽  
Angelo P. Capparella ◽  
François Vuilleumier
Keyword(s):  
Sequence Data ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Glacial Refugia ◽  
Tierra Del Fuego ◽  
Allopatric Speciation ◽  
South American ◽  
Glacial Cycles ◽  
Sister Relationship ◽  
Wide Range

Abstract Pleistocene glacial cycles have often been hypothesized to provide vicariant mechanisms leading to allopatric speciation in a wide range of southern South American (Fuegian and Patagonian) avian taxa. Few of those biogeographic hypotheses, however, have been rigorously tested using phylogenetic analysis. We examined sequence variation in three mitochondrial gene fragments (cytochrome b, ND2, and ND3) to construct a molecular phylogeny for the South American genus Geositta (Furnariidae) and to test the interrelated hypotheses that Geositta cunicularia and G. antarctica are sister species that originated from a common ancestor while isolated in glacial refugia during Pleistocene glacial events in Fuego-Patagonia. Sequence data were obtained for all 10 currently recognized species of Geositta as well as Geobates poecilopterus and two outgroup taxa (Upucerthia ruficauda and Aphrastura spinicauda). We found levels of sequence divergence among Geositta species to be high, ranging from 7.4% to 16.3%. Our phylogenetic reconstructions clearly indicate relationships among Geositta species that differ considerably from those of traditional Geositta phylogeny. These data also strongly suggest that Geositta, as currently defined, is paraphyletic, with Geobates being embedded within Geositta. Our data do not support the hypothesized sister relationship between G. antarctica and G. cunicularia. Instead, they suggest that Geositta consists of two distinct clades, with antarctica and cunicularia falling into different clades. The high levels of sequence divergence among Geositta species, lack of a sister relationship between cunicularia and antarctica, and placement of Fuego-Patagonian antarctica into a clade consisting of two high-Andean (saxicolina and isabellina) and one coastal-west-slope (maritima) species demonstrate that the evolutionary history of Geositta is much older and far more complex than a simple model of allopatric speciation in glacial refugia would suggest. Filogenia Molecular del Género Geositta (Furnariidae) e Implicaciones Biogeográficas para la Especiación de la Aves en Tierra del Fuego y Patagonia

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