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.

Molecular phylogeny and biogeography of Triplophysa stone loaches in the Central Chinese Mountains

2020 ◽  
Vol 130 (3) ◽  
pp. 563-577
Author(s):  
Huihui Wu ◽  
Qianhong Gu ◽  
Chuanjiang Zhou ◽  
Yongtao Tang ◽  
Martin Husemann ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Yellow River ◽  
Phylogenetic Analyses ◽  
Extreme Environments ◽  
Geological Structure ◽  
Early Pleistocene ◽  
Tibet Plateau ◽  
Biogeographic Patterns ◽  
Low Genetic Diversity ◽  
History Of

Abstract The geological structure and history of mountains often cause highly complex patterns of evolution. The origin and diversity of the genus Triplophysa is considered to be closely associated with the rapid and persistent rise of the Qinghai-Tibet Plateau (QTP). Species of the genus are widely distributed in the QTP and adjacent regions, and are strongly adapted to its extreme environments. However, the Central Chinese Mountains (CCM), which are far apart from the QTP, also have many Triplophysa populations and yet their taxonomy, phylogeny and origin are unknown. We used three mitochondrial genes of 266 individuals from 29 sites in the CCM to shed light on the evolution of these Triplophysa populations. Phylogenetic analyses and species delimitation revealed seven distinct molecular operational taxonomic units (mOTUs) in the CCM, each with low genetic diversity. Molecular clock and biogeographic analyses suggested that vicariance events resulting from the rapid uplifting of the Qinling and Taihang Mountains initialized diversification in the Pliocene. During the early Pleistocene, dispersal events in the central parts of the Yellow River drainage altered genetic diversity and led to the currently observed biogeographic patterns. Our results suggest the presence of at least six species of Triplophysa in the CCM and more are likely to be discovered in the future.

scholarly journals Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: regional discrepancies in farming systems

2013 ◽  
Vol 85 (4) ◽  
pp. 1439-1447 ◽  
Author(s):  
Jonas Aguiar ◽  
Horacio Schneider ◽  
Fatima Gomes ◽  
Jeferson Carneiro ◽  
Simoni Santos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Amazon Basin ◽  
Farming Systems ◽  
Wild Populations ◽  
The West ◽  
Colossoma Macropomum ◽  
Breeding Stock ◽  
History Of

The tambaqui, Colossoma macropomum, is the most popular fish species used for aquaculture in Brazil but there is no study comparing genetic variation among native and farmed populations of this species. In the present study, we analyzed DNA sequences of the mitochondrial DNA to evaluate the genetic diversity among two wild populations, a fry-producing breeding stock, and a sample of fish farm stocks, all from the region of Santarém, in the west of the Brazilian state of Pará. Similar levels of genetic diversity were found in all the samples and surprisingly the breeding stock showed expressive representation of the genetic diversity registered on wild populations. These results contrast considerably with those of the previous study of farmed stocks in the states of Amapá, Pará, Piauí, and Rondônia, which recorded only two haplotypes, indicating a long history of endogamy in the breeding stocks used to produce fry. The results of the two studies show two distinct scenarios of tambaqui farming in the Amazon basin, which must be better evaluated in order to guarantee the successful expansion of this activity in the region, and the rest of Brazil, given that the tambaqui and its hybrids are now farmed throughout the country.

scholarly journals Evolutionary Relationship between Two Firefly Species,Curtos costipennisandC. okinawanus(Coleoptera, Lampyridae), in the Ryukyu Islands of Japan Revealed by the Mitochondrial and Nuclear DNA Sequences

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Masahiko Muraji ◽  
Norio Arakaki ◽  
Shigeo Tanizaki
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Nuclear Dna ◽  
Evolutionary Relationship ◽  
Early Pleistocene ◽  
Ryukyu Islands ◽  
Mtdna Sequences ◽  
Northern Half ◽  
The Ryukyu Islands ◽  
History Of

The phylogenetic relationship, biogeography, and evolutionary history of closely related two firefly species,Curtos costipennisandC. okinawanus, distributed in the Ryukyu Islands of Japan were examined based on nucleotide sequences of mitochondrial (2.2 kb long) and nuclear (1.1-1.2 kb long) DNAs. In these analyses, individuals were divided among three genetically distinct local groups,C. costipennisin the Amami region,C. okinawanusin the Okinawa region, andC. costipennisin the Sakishima region. Their mtDNA sequences suggested that ancestralC. costipennispopulation was first separated between the Central and Southern Ryukyu areas, and the northern half was then subdivided betweenC. costipennisin the Amami andC. okinawanusin the Okinawa. The application of the molecular evolutionary clocks of coleopteran insects indicated that their vicariance occurred 1.0–1.4 million years ago, suggesting the influence of submergence and subdivision of a paleopeninsula extending between the Ryukyu Islands and continental China through Taiwan in the early Pleistocene.

scholarly journals Discovery of a new family of amphibians from northeast India with ancient links to Africa

2012 ◽  
Vol 279 (1737) ◽  
pp. 2396-2401 ◽  
Author(s):  
Rachunliu G. Kamei ◽  
Diego San Mauro ◽  
David J. Gower ◽  
Ines Van Bocxlaer ◽  
Emma Sherratt ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Northeast India ◽  
Sister Group Relationship ◽  
New Family ◽  
Ancient Lineage ◽  
Molecular Phylogenetic ◽  
Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

Genetic diversity patterns in an endangered desert shrub from north-western China: implications for conservation

2019 ◽  
Vol 67 (7) ◽  
pp. 571
Author(s):  
Zhihao Su ◽  
Liuqiang Wang ◽  
Li Zhuo ◽  
Xiaolong Jiang ◽  
Wenjun Li
Keyword(s):  
Genetic Diversity ◽  
Tarim Basin ◽  
Dna Sequences ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
In Situ Conservation ◽  
Western China ◽  
Niche Modelling ◽  
Diversity Patterns ◽  
North Western

Tamarix taklamakanensis is an endangered shrub endemic to the Tarim Basin and adjacent Kumtag Desert in north-western China. Here, we used two chloroplast DNA sequences, namely, psbA-trnH and trnS-trnG, to examine the genetic diversity patterns of this species across its entire covered range. A total of nineteen haplotypes were detected. The total gene diversity within the species is high. Genetic variation mainly occurred among populations, SAMOVA groups, and geographic regions. The test for isolation-by-distance showed a significant correlation between genetic and geographical distances, and the genetic landscape shape analysis showed a significant genetic divergence between the Tarim Basin and Kumtag Desert. T. taklamakanensis likely had a potential geographic range during the Last Glacial Maximum period that was much smaller than the present range predicted by ecological niche modelling. The cold and dry climate during the glacial periods of the Quaternary might be a driver of the genetic isolation and divergence detected within T. taklamakanensis, and climatic oscillations might account for the habitat fragmentation of the species. Within the inner of the basin, populations have a higher level of genetic diversity and harbor most of this genetic diversity, thus a nature reserves should be set up in this area for the in situ conservation. In addition, five genetically distinct groups within T. taklamakanensis should be treated as different management units (MUs) when implementing conservation activities.

scholarly journals Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

2012 ◽  
Vol 58 (6) ◽  
pp. 837-850 ◽  
Author(s):  
Lanping Zheng ◽  
Junxing Yang ◽  
Xiaoyong Chen
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Morphological Characters ◽  
Character Evolution ◽  
Lower Lip ◽  
Molecular Phylogenetic Tree ◽  
Systematic Exploration ◽  
Molecular Phylogenetic ◽  
History Of

Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals (representing 24 genera and 73 species) of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oroman-dibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine , a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.

scholarly journals Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

2015 ◽  
Vol 2 (8) ◽  
pp. 140255 ◽  
Author(s):  
Claire C. Keely ◽  
Joshua M. Hale ◽  
Geoffrey W. Heard ◽  
Kirsten M. Parris ◽  
Joanna Sumner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Urban Expansion ◽  
Nuclear Gene ◽  
Management Approach ◽  
Natural Habitats ◽  
High Genetic Diversity ◽  
Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

scholarly journals Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability

Botany ◽  
2016 ◽  
Vol 94 (9) ◽  
pp. 863-884 ◽  
Author(s):  
David S. Gernandt ◽  
Garth Holman ◽  
Christopher Campbell ◽  
Matthew Parks ◽  
Sarah Mathews ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Consensus Methods ◽  
Topological Stability ◽  
Branch Support ◽  
Tree Topologies ◽  
Cone Scale

Relationships of living and fossil Pinaceae were inferred using parsimony and Bayesian inference of morphological characters and plastid and nuclear DNA sequences. When considering extant taxa only, adding molecular to morphological characters resulted in markedly increased resolution and branch support compared with analysis of morphology alone. Including 45 fossil taxa resulted in drastically decreased resolution in morphology-based consensus trees. We evaluated the effect on branch support and resolution of including DNA sequences, deleting fossils lacking information for cone scale apices and seeds, using reduced consensus methods, and using implied weighting, and found that the greatest improvements were found by including DNA sequences and using implied weighting. The tree topologies from parsimony and Bayesian inference confirm previous findings that the fossil genus Pseudoaraucaria and a few species of Pityostrobus from the Lower Cretaceous are related to abietoid genera, and that other species of Pityostrobus are pinoid and closely related to Pinus. Focusing phylogenetic analyses on the most complete fossil cones, specifically those that are anatomically preserved and include both cone scale apices and seeds, and taking into account homoplasy, resulted in the clearest hypotheses for the timing and sequence of diversification in the family.

scholarly journals Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

2006 ◽  
Vol 2 (3) ◽  
pp. 451-454 ◽  
Author(s):  
Nikos Poulakakis ◽  
Aris Parmakelis ◽  
Petros Lymberakis ◽  
Moysis Mylonas ◽  
Eleftherios Zouros ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Ancient Dna ◽  
Evolutionary History ◽  
Eastern Mediterranean ◽  
Multiple Displacement Amplification ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Mediterranean Islands ◽  
Amplification Method ◽  
History Of

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10 000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cyt b ) DNA fragments from 4200 to 800 000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800 000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas , suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus , seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas .

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