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1.
Background
Oysters are morphologically plastic and hence difficult subjects for taxonomic and evolutionary studies. It is long been suspected, based on the extraordinary species diversity observed, that Asia Pacific is the epicenter of oyster speciation. To understand the species diversity and its evolutionary history, we collected five Crassostrea species from Asia and sequenced their complete mitochondrial (mt) genomes in addition to two newly released Asian oysters (C. iredalei and Saccostrea mordax) for a comprehensive analysis. 相似文献2.
Background
Broad-scale phylogeographic studies of freshwater organisms provide not only an invaluable framework for understanding the evolutionary history of species, but also a genetic imprint of the paleo-hydrological dynamics stemming from climatic change. Few such studies have been carried out in Siberia, a vast region over which the extent of Pleistocene glaciation is still disputed. Brachymystax lenok is a salmonid fish distributed throughout Siberia, exhibiting two forms hypothesized to have undergone extensive range expansion, genetic exchange, and multiple speciation. A comprehensive phylogeographic investigation should clarify these hypotheses as well as provide insights on Siberia's paleo-hydrological stability. 相似文献3.
African origin and global distribution patterns: Evidence inferred from phylogenetic and biogeographical analyses of ectomycorrhizal fungal genus Strobilomyces
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Li H. Han Bang Feng Gang Wu Roy E. Halling Bart Buyck Nourou S. Yorou Sydney T. N. Ebika Zhu L. Yang 《Journal of Biogeography》2018,45(1):201-212
Aim
The ectomycorrhizal genus Strobilomyces is widely distributed throughout many parts of the world, but its origin, divergence and distribution patterns remain largely unresolved. In this study, we aim to explore the species diversity, distribution and evolutionary patterns of Strobilomyces on a global scale by establishing a general phylogenetic framework with extensive sampling.Location
Africa, Australasia, East Asia, Europe, North America, Central America and Southeast Asia.Methods
The genealogical concordance phylogenetic species recognition method was used to delimit phylogenetic species. Divergence times were estimated using a Bayesian uncorrelated lognormal relaxed molecular clock. The ancestral area and host of Strobilomyces were inferred via the programs rasp and mesquite . The change of diversification rate over time was estimated using Ape, Laser and Bammtools software packages.Results
We recognize a novel African clade and 49 phylogenetic species with morphological evidence, including 18 new phylogenetic species and 23 previously described ones. Strobilomyces probably originated in Africa, in association with Detarioideae/Phyllanthaceae/Monotoideae during the early Eocene. The dispersal to Southeast Asia can be explained by Wolfe's “Boreotropical migration” hypothesis. East Asia, Australasia, Europe and North/Central America are primarily the recipients of immigrant taxa during the Oligocene or later. A rapid radiation implied by one diversification shift was inferred within Strobilomyces during the Miocene.Main conclusions
An unexpected phylogenetic species diversity within Strobilomyces was uncovered. The highest diversity, resulting probably from a rapid radiation, was found in East Asia. Dispersal played an important role in the current distribution pattern of Strobilomyces. The Palaeotropical disjunction is explained by species dispersal from Africa to Southeast Asia through boreotropical forests during the early Eocene. Species from the Northern Hemisphere and Australasia are largely derived from immigrant ancestors from Southeast Asia. 相似文献4.
Stephan Koblmüller Christian Sturmbauer Erik Verheyen Axel Meyer Walter Salzburger 《BMC evolutionary biology》2006,6(1):49-16
Background
Squeaker catfishes (Pisces, Mochokidae, Synodontis) are widely distributed throughout Africa and inhabit a biogeographic range similar to that of the exceptionally diverse cichlid fishes, including the three East African Great Lakes and their surrounding rivers. Since squeaker catfishes also prefer the same types of habitats as many of the cichlid species, we hypothesized that the East African Synodontis species provide an excellent model group for comparative evolutionary and phylogeographic analyses. 相似文献5.
Background
Pleistocene glaciations had considerable impact on phylogeographic patterns within and among closely related species of many vertebrates. Compared to Europe and North America, research on the phylogeography of vertebrates in East Asia, particularly in China, remains limited. The black-spotted frog (Pelophylax nigromaculata) is a widespread species in East Asia. The wide distribution of this species in China makes it an ideal model for the study of palaeoclimatic effects on vertebrates in East Asia. Our previous studies of P. nigromaculata revealed significant subdivisions between the northeast China populations and populations in other regions of the mainland. In the present study, we aim to see whether the deepest splits among lineages and perhaps subsequent genealogical divisions are temporally consistent with a Pleistocene origin and whether clade geographic distributions, with insight into expansion patterns, are similarly spatially consistent with this model. 相似文献6.
Lukas Rüber Maurice Kottelat Heok Hui Tan Peter KL Ng Ralf Britz 《BMC evolutionary biology》2007,7(1):38
Background
Paedocypris, a highly developmentally truncated fish from peat swamp forests in Southeast Asia, comprises the world's smallest vertebrate. Although clearly a cyprinid fish, a hypothesis about its phylogenetic position among the subfamilies of this largest teleost family, with over 2400 species, does not exist. Here we present a phylogenetic analyses of 227 cypriniform taxa, including 213 cyprinids, based upon complete mitochondrial DNA cytochrome b nucleotide sequences in order to determine the phylogenetic position of Paedocypris and to study the evolution of miniaturization among cyprinids. 相似文献7.
Background
The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools. 相似文献8.
Priscila Grynberg Cor Jesus F Fontes Austin L Hughes Érika M Braga 《BMC evolutionary biology》2008,8(1):123
Background
In malaria parasites (genus Plasmodium), ama-1 is a highly polymorphic locus encoding the Apical Membrane Protein-1, and there is evidence that the polymorphism at this locus is selectively maintained. We tested the hypothesis that polymorphism at the ama-1 locus reflects population history in Plasmodium vivax, which is believed to have originated in Southeast Asia and is widely geographically distributed. In particular, we tested for a signature of the introduction of P. vivax into the New World at the time of the European conquest and African slave trade and subsequent population expansion. 相似文献9.
Background
In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China. 相似文献10.
Origin of Chinese Goldfish and Sequential Loss of Genetic Diversity Accompanies New Breeds 总被引:1,自引:0,他引:1
Shu-Yan Wang Jing Luo Robert W. Murphy Shi-Fang Wu Chun-Ling Zhu Yun Gao Ya-Ping Zhang 《PloS one》2013,8(3)
Background
Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy–body shape, dorsal fin, eye shape, and tailfin–were selected for hypothesis-testing to identify those that better correspond to evolutionary history.Principal Finding
Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of F ST and Nm revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima’s D and Fu and Li’s D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher’s exact test identified matrilineal constraints on domestication.Conclusions
Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy–Grass-goldfish, Egg-goldfish, and Wen-goldfish–better reflected the history of domestication. 相似文献11.
Claudia Patricia Ornelas-García Omar Domínguez-Domínguez Ignacio Doadrio 《BMC evolutionary biology》2008,8(1):340
Background
Mesoamerica is one of the world's most complex biogeographical regions, mostly due to its complex geological history. This complexity has led to interesting biogeographical processes that have resulted in the current diversity and distribution of fauna in the region. The fish genus Astyanax represents a useful model to assess biogeographical hypotheses due to it being one of the most diverse and widely distributed freshwater fish species in the New World. We used mitochondrial and nuclear DNA to evaluate phylogenetic relationships within the genus in Mesoamerica, and to develop historical biogeographical hypotheses to explain its current distribution. 相似文献12.
Ancient vicariance and climate‐driven extinction explain continental‐wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae)
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Transoceanic distributions have attracted the interest of scientists for centuries. Less attention has been paid to the evolutionary origins of ‘continent‐wide’ disjunctions, in which related taxa are distributed across isolated regions within the same continent. A prime example is the ‘Rand Flora’ pattern, which shows sister taxa disjunctly distributed in the continental margins of Africa. Here, we explore the evolutionary origins of this pattern using the genus Canarina, with three species: C. canariensis, associated with the Canarian laurisilva, and C. eminii and C. abyssinica, endemic to the Afromontane region in East Africa, as case study. We infer phylogenetic relationships, divergence times and the history of migration events within Canarina using Bayesian inference on a large sample of chloroplast and nuclear sequences. Ecological niche modelling was employed to infer the climatic niche of Canarina through time. Dating was performed with a novel nested approach to solve the problem of using deep time calibration points within a molecular dataset comprising both above‐species and population‐level sampling. Results show C. abyssinica as sister to a clade formed by disjunct C. eminii and C. canariensis. Miocene divergences were inferred among species, whereas infraspecific divergences fell within the Pleistocene–Holocene periods. Although C. eminii and C. canariensis showed a strong genetic geographic structure, among‐population divergences were older in the former than in the latter. Our results suggest that Canarina originated in East Africa and later migrated across North Africa, with vicariance and aridification‐driven extinction explaining the 7000 km/7 million year divergence between the Canarian and East African endemics. 相似文献
13.
L. Masson D. Almeida A. S. Tarkan B. Önsoy R. Miranda M. J. Godard G. H. Copp 《Zeitschrift fur angewandte Ichthyologie》2011,27(5):1286-1290
The identification of fish species from head bone remains is employed in various sciences, including archaeology, paleontology and field ecology, with the estimation of fish size from biometric relationships being useful in the assessment of predation pressure exerted by increasing numbers of piscivorous species (e.g. Eurasian otter Lutra lutra and great cormorant Phalacrocorax carbo). This is particularly relevant for crucian carp, Carassius carassius, which is in decline in Europe due to changes in land use and to increasing numbers of non‐native Carassius species (i.e. goldfish C. auratus, gibel carp C. gibelio), which hybridize with C. carassius. However, diagnostic keys and biometric relationships are lacking for C. carassius and its most common hybrids, crosses with C. auratus. The present paper addresses this gap in knowledge, providing diagnostic keys and biometric relationships for the head bones of all Carassius species found in Europe as well as for C. carassius × C. auratus hybrids. All bone size to body length relationships were statistically significant. Similarly, all bone size to body weight relationships were significant for C. carassius, C. auratus, and C. gibelio, but none were significant for C. carassius × C. auratus hybrids. Diagnostic structures were found to distinguish easily between the Carassius species and hybrids, which will assist in determining the identity and sizes of prey found in faecal and archaeological remains. 相似文献
14.
15.
Pierre-Yves Le Bail Alexandra Depince Nathalie Chenais Sophie Mahe Gerard Maisse Catherine Labbe 《BMC developmental biology》2010,10(1):64
Background
Nuclear transfer has the potential to become one strategy for fish genetic resources management, by allowing fish reconstruction from cryopreserved somatic cells. Survival rates after nuclear transfer are still low however. The part played by unsuitable handling conditions is often questioned, but the different steps in the procedure are difficult to address separately. In this work led on goldfish (Carassius auratus), the step of somatic cells injection was explored. Non-enucleated metaphase II oocytes were used as a template to explore the toxicity of the injection medium, to estimate the best location where the cell should be injected, and to assess the delay necessary between cell injection and oocyte activation. 相似文献16.
Fernando Rodríguez Trinidad Pérez Sabine E Hammer Jesús Albornoz Ana Domínguez 《BMC evolutionary biology》2010,10(1):222
Background
The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range. 相似文献17.
Background
Phylogenetic studies of wild Canis species have relied heavily on the mitochondrial DNA control region (mtDNA CR) to infer species relationships and evolutionary lineages. Previous analyses of the CR provided evidence for a North American evolved eastern wolf (C. lycaon), that is more closely related to red wolves (C. rufus) and coyotes (C. latrans) than grey wolves (C. lupus). Eastern wolf origins, however, continue to be questioned. Therefore, we analyzed mtDNA from 89 wolves and coyotes across North America and Eurasia at 347 base pairs (bp) of the CR and 1067 bp that included the ATPase6 and ATPase8 genes. Phylogenies and divergence estimates were used to clarify the evolutionary history of eastern wolves, and regional comparisons of nonsynonomous to synonomous substitutions (dN/dS) at the ATPase6 and ATPase8 genes were used to elucidate the potential role of selection in shaping mtDNA geographic distribution. 相似文献18.
Capsicum
Use in Cambodia: The Continental Region of Southeast Asia Is Not Related to the Dispersal Route of
C. frutescens
in the Ryukyu Islands. The local nomenclature and use of Capsicum by Khmer and other ethnic groups in Cambodia and the distribution of the diagnostic ShDH-B isozyme pattern of C. frutescens were studied. People in Cambodia use Capsicum in various ways, not only as a condiment but also as a vegetable, a medicine, and a colorant, and in popular beliefs, agricultural
rituals, taboos, and rice malt. The findings showed that the ShDH-B phenotype may not have occurred as a mutation in Asia
but in the Americas and then was introduced to Asia. Also, the ShDH-B phenotype is distributed in the insular regions of Southeast
and East Asia and Oceania, but seems not to be distributed in the continental region of Southeast Asia. One possible hypothesis
is that C. frutescens possessing the ShDH-B phenotype was introduced directly from the Americas via Oceania to the Philippines, and it thereafter
dispersed into the insular regions. 相似文献
19.
Background
Studied since the early 1940's, chromosomal polymorphisms in the deciduous woods species Drosophila robusta have been characterized by well-defined latitudinal, longitudinal, and elevational clines, but – until at least ten years ago – stable, local population frequencies. Recent biogeographical analyses indicate that D. robusta invaded North America from southeast Asia and has persisted in eastern temperate forests for at least 20–25 my without speciating. The abundant chromosome polymorphisms found across the range of D. robusta are thus likely to be relatively ancient, having accumulated over many well known climatic cycles in North America. Sufficient long-term data are now available such that we can now gauge the rate of these evolutionary changes in natural populations due to environmental change. 相似文献20.
Liliana Milani Fabrizio Ghiselli Marco Pellecchia Valerio Scali Marco Passamonti 《BMC evolutionary biology》2010,10(1):258