scholarly journals Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11917
Author(s):  
Violeta Cárcamo-Tejer ◽  
Irma Vila ◽  
Francisco Llanquín-Rosas ◽  
Alberto Sáez-Arteaga ◽  
Claudia Guerrero-Jiménez
Keyword(s):  
Evolutionary History ◽  
Andes Mountains ◽  
Endangered Fish ◽  
The Andes ◽  
Genetic Groups ◽  
Biogeographic History ◽  
D Loop ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Genic Diversity

From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.

scholarly journals Genetic differentiation in the genus Characodon: implications for conservation and taxonomy

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11492
Author(s):  
Rosa G. Beltrán-López ◽  
Rodolfo Pérez-Rodríguez ◽  
Ofelia C. Montañez-García ◽  
Juan M. Artigas-Azas ◽  
Michael Köck ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary History ◽  
Genetic Distances ◽  
Genetic Groups ◽  
Evolutionary Significant Units ◽  
Significant Genetic Structure ◽  
D Loop ◽  
History Of ◽  
The Subject ◽  
Phylogeographic Study

The subfamily Goodeinae is a group of fishes endemic to the Mexican highlands. Most of the species are restricted to small and isolated streams or springs. Within this subfamily, the genus Characodon is the earliest diverging lineage of which three species have been described: C. lateralis, C. audax, and C. garmani, with the latter, considered extinct. Characodon lateralis and C. audax are classed as endangered, and have been the subject of taxonomic controversy since their description: previous studies have recognized a genetic differentiation in two groups separated by the El Salto waterfall, but morphological analyses contradict these genetic results. We perform a phylogeographic study using the mitochondrial cytb gene and d-loop region to elucidate the evolutionary history of C. lateralis and C. audax. The results with both markers show the presence of two highly differentiated haplogroups; one distributed north and the other distributed south of the waterfall, with genetic distances of 1.7 and 13.1% with cytb and d-loop respectively, and divergence calculated to have occurred 1.41 Mya. Significant genetic structure was found within each haplogroup and suggests the existence of at least four Evolutionary Significant Units (ESUs) within the examined populations. The possible processes identified as contributing to the formation of differentiated genetic groups are isolation, low population size, recurrent bottlenecks, and the strong sexual selection exhibited by the genus.

scholarly journals Phylogenomics indicates Amazonia as the major source of Neotropical swarm-founding social wasp diversity

2020 ◽  
Vol 287 (1928) ◽  
pp. 20200480 ◽  
Author(s):  
Rodolpho S. T. Menezes ◽  
Michael W. Lloyd ◽  
Seán G. Brady
Keyword(s):  
Evolutionary History ◽  
Empirical Studies ◽  
Social Wasp ◽  
Insect Fauna ◽  
Extinction Rates ◽  
Biogeographic History ◽  
Biotic Diversity ◽  
History Of ◽  
Spatio Temporal ◽  
Amazonian Region

The Neotropical realm harbours unparalleled species richness and hence has challenged biologists to explain the cause of its high biotic diversity. Empirical studies to shed light on the processes underlying biological diversification in the Neotropics are focused mainly on vertebrates and plants, with little attention to the hyperdiverse insect fauna. Here, we use phylogenomic data from ultraconserved element (UCE) loci to reconstruct for the first time the evolutionary history of Neotropical swarm-founding social wasps (Hymenoptera, Vespidae, Epiponini). Using maximum likelihood, Bayesian, and species tree approaches we recovered a highly resolved phylogeny for epiponine wasps. Additionally, we estimated divergence dates, diversification rates, and the biogeographic history for these insects in order to test whether the group followed a ‘museum’ (speciation events occurred gradually over many millions of years) or ‘cradle’ (lineages evolved rapidly over a short time period) model of diversification. The origin of many genera and all sampled extant Epiponini species occurred during the Miocene and Plio-Pleistocene. Moreover, we detected no major shifts in the estimated diversification rate during the evolutionary history of Epiponini, suggesting a relatively gradual accumulation of lineages with low extinction rates. Several lines of evidence suggest that the Amazonian region played a major role in the evolution of Epiponini wasps. This spatio-temporal diversification pattern, most likely concurrent with climatic and landscape changes in the Neotropics during the Miocene and Pliocene, establishes the Amazonian region as the major source of Neotropical swarm-founding social wasp diversity.

scholarly journals Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot

2017 ◽  
Author(s):  
Christine D. Bacon ◽  
Francisco Velásquez-Puentes ◽  
Luis Felipe Hinojosa ◽  
Thomas Schwartz ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Biodiversity Hotspot ◽  
Tropical Andes ◽  
Quaternary Climate ◽  
Biogeographic History ◽  
Plant Groups ◽  
History Of ◽  
Rapid Diversification ◽  
High Degree ◽  
Evolutionary Persistence

Several studies have demonstrated the contribution of northern immigrants to the flora of the tropical Andes – the world’s “hottest” biodiversity hotspot. However, much less is known about the biogeographic history and diversification of Andean groups with southern origins, although it has been suggested that northern and southern groups have contributed roughly equally to the high Andean (i.e. páramo) flora. Here we infer the evolutionary history of the southern hemisphere plant genus Gunnera, a lineage with a rich fossil history and an important ecological role as an early colonising species characteristic of wet, montane environments. Our results show striking contrasts in species diversification, where some species may have persisted for some 90 million years, whereas others date to less than 2 Ma since origination. The outstanding longevity of the group is likely linked to a high degree of niche conservatism across its highly disjunct range, whereby Gunnera tracks damp and boggy soils in cool habitats. Colonisation of the northern Andes is related to Quaternary climate change, with subsequent rapid diversification appearing to be driven by their ability to take advantage of environmental opportunities. This study demonstrates the composite origin of a mega-diverse biota.

scholarly journals A new cryptic species of Pithecopus (Anura, Phyllomedusidae) in north-eastern Brazil

2020 ◽  
Vol 723 ◽  
pp. 108-134
Author(s):  
Felipe Silva De Andrade ◽  
Isabelle Aquemi Haga ◽  
Johnny Sousa Ferreira ◽  
Shirlei Maria Recco-Pimentel ◽  
Luís Felipe Toledo ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Evolutionary History ◽  
Small Body ◽  
Head Width ◽  
The Andes ◽  
Eastern Brazil ◽  
Sister Clade ◽  
North Eastern ◽  
Geographical Barrier ◽  
History Of

The genus of Neotropical frogs Pithecopus includes 11 species occurring east of the Andes from southern Venezuela to northern Argentina. Recent genetic approaches pointed out an unusual genetic diversity among populations from localities in north-eastern Brazil recognized as P. nordestinus. In fact, one of these studies confirmed the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus, resulting in two principal, highly divergent clades. Herein we formally describe this divergent clade as a new cryptic species of Pithecopus from north-eastern Brazil, the sister clade of P. nordestinus. It differs from other species of Pithecopus, except for P. azureus and P. nordestinus, by its small body size, lack of the reticulate pattern on flanks, smaller head width, and advertisement calls generally composed of a three-pulsed core.

Hypseocharis reveals early history of physical dormancy in Geraniaceae

2016 ◽  
Vol 27 (1) ◽  
pp. 39-42
Author(s):  
Filip Vandelook ◽  
Ann Van de Vyver ◽  
Edgar E. Gareca
Keyword(s):  
Early History ◽  
Early Evolution ◽  
Andes Mountains ◽  
Disjunct Distribution ◽  
Physical Dormancy ◽  
Germination Ecology ◽  
The Andes ◽  
History Of ◽  
The Cross ◽  
Basal Position

AbstractHypseocharis is a genus endemic to the high Andes and sister to all other Geraniaceae genera. Regarding its basal position in Geraniaceae evolution, its germination ecology can provide important insights into the early evolution of physical dormancy. Imbibition tests performed on seeds of two Hypseocharis populations from Bolivia indicate that their seeds indeed have physical dormancy like all other Geraniaceae. These results indicate that physical dormancy in Geraniaceae evolved during the Eocene before the uplift of the Andes mountains and before the events that led to the cross-Atlantic disjunct distribution of Geraniacae.

scholarly journals Population subdivision and hybridization in a species complex of Gentiana in the Qinghai-Tibetan Plateau

2020 ◽  
Vol 125 (4) ◽  
pp. 677-690
Author(s):  
Peng-Cheng Fu ◽  
Shan-Shan Sun ◽  
Gulzar Khan ◽  
Xiao-Xia Dong ◽  
Jin-Zhou Tan ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Evolutionary History ◽  
Distinct Species ◽  
Population Subdivision ◽  
Last Interglacial ◽  
Niche Modelling ◽  
Climatic Fluctuations ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Approximate Bayesian

Abstract Background and Aims Hosting several global biodiversity hotspots, the region of the Qinghai-Tibetan Plateau (QTP) is exceptionally species-rich and harbours a remarkable level of endemism. Yet, despite a growing number of studies, factors fostering divergence, speciation and ultimately diversity remain poorly understood for QTP alpine plants. This is particularly the case for the role of hybridization. Here, we explored the evolutionary history of three closely related Gentiana endemic species, and tested whether our results supported the mountain geo-biodiversity hypothesis (MGH). Methods We genotyped 69 populations across the QTP with one chloroplast marker and 12 nuclear microsatellite loci. We performed phylogeographical analysis, Bayesian clustering, approximate Bayesian computation and principal components analysis to explore their genetic relationship and evolutionary history. In addition, we modelled their distribution under different climates. Key Results Each species was composed of two geographically distinct clades, corresponding to the south-eastern and north-western parts of their distribution. Thus Gentiana veitchiorum and G. lawrencei var. farreri, which diverged recently, appear to have shared at least refugia in the past, from which their range expanded later on. Indeed, climatic niche modelling showed that both species went through continuous expansion from the Last Interglacial Maximum to the present day. Moreover, we have evidence of hybridization in the northwest clade of G. lawrencei var. farreri, which probably occurred in the refugium located on the plateau platform. Furthermore, phylogenetic and population genetic analyses suggested that G. dolichocalyx should be a geographically limited distinct species with low genetic differentiation from G. lawrencei var. farreri. Conclusions Climatic fluctuations in the region of the QTP have played an important role in shaping the current genetic structure of G. lawrencei var. farreri and G. veitchiorum. We argue that a species pump effect did occur prior to the Last Interglacial Maximum, thus lending support to the MGH. However, our results do depart from expectations as suggested in the MGH for more recent distribution range and hybridization dynamics.

scholarly journals Geographic variation and evolutionary history of Dipodomys nitratoides (Rodentia: Heteromyidae), a species in severe decline

2019 ◽  
Vol 100 (5) ◽  
pp. 1546-1563
Author(s):  
James L Patton ◽  
Daniel F Williams ◽  
Patrick A Kelly ◽  
Brian L Cypher ◽  
Scott E Phillips
Keyword(s):  
Evolutionary History ◽  
Molecular Level ◽  
Haplotype Network ◽  
Single Step ◽  
San Joaquin Valley ◽  
Central California ◽  
Biogeographic History ◽  
Geographic Patterns ◽  
Kangaroo Rat ◽  
History Of

Abstract We examined geographic patterns of diversification in the highly impacted San Joaquin kangaroo rat, Dipodomys nitratoides, throughout its range in the San Joaquin Valley and adjacent basins in central California. The currently recognized subspecies were distinct by the original set of mensural and color variables used in their formal diagnoses, although the Fresno kangaroo rat (D. n. exilis) is the most strongly differentiated with sharp steps in character clines relative to the adjacent Tipton (D. n. nitratoides) and short-nosed (D. n. brevinasus) races. The latter two grade more smoothly into one another but still exhibit independent, and different, character clines within themselves. At the molecular level, as delineated by mtDNA cytochrome b sequences, most population samples retain high levels of diversity despite significant retraction in the species range and severe fragmentation of local populations in recent decades due primarily to landscape conversion for agriculture and secondarily to increased urbanization. Haplotype apportionment bears no relationship to morphologically defined subspecies boundaries. Rather, a haplotype network is shallow, most haplotypes are single-step variants, and the time to coalescence is substantially more recent than the time of species split between D. nitratoides and its sister taxon, D. merriami. The biogeographic history of the species within the San Joaquin Valley appears tied to mid-late Pleistocene expansion following significant drying of the valley resulting from the rain shadow produced by uplift of the Central Coastal Ranges.

scholarly journals The evolutionary history of manatees told by their mitogenomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Érica Martinha Silva de Souza ◽  
Lucas Freitas ◽  
Elisa Karen da Silva Ramos ◽  
Giovanna Selleghin-Veiga ◽  
Michelle Carneiro Rachid-Ribeiro ◽  
...  
Keyword(s):  
Late Miocene ◽  
Evolutionary History ◽  
Amazon Basin ◽  
Sister Group ◽  
Protein Coding ◽  
Posterior Mean ◽  
D Loop ◽  
History Of ◽  
West Indian Manatee ◽  
Rna Genes

AbstractThe manatee family encompasses three extant congeneric species: Trichechus senegalensis (African manatee), T. inunguis (Amazonian manatee), and T. manatus (West Indian manatee). The fossil record for manatees is scant, and few phylogenetic studies have focused on their evolutionary history. We use full mitogenomes of all extant manatee species to infer the divergence dates and biogeographical histories of these species and the effect of natural selection on their mitogenomes. The complete mitochondrial genomes of T. inunguis (16,851 bp), T. senegalensis (16,882 bp), and T. manatus (16,882 bp), comprise 13 protein-coding genes, 2 ribosomal RNA genes (rRNA - 12S and 16S), and 22 transfer RNA genes (tRNA), and (D-loop/CR). Our analyses show that the first split within Trichechus occurred during the Late Miocene (posterior mean 6.56 Ma and 95% HPD 3.81–10.66 Ma), followed by a diversification event in the Plio-Pleistocene (posterior mean 1.34 Ma, 95% HPD 0.1–4.23) in the clade composed by T. inunguis and T. manatus; T. senegalensis is the sister group of this clade with higher support values (pp > 0.90). The branch-site test identified positive selection on T. inunguis in the 181st position of the ND4 amino acid gene (LRT = 6.06, p = 0.0069, BEB posterior probability = 0.96). The ND4 gene encodes one subunit of the NADH dehydrogenase complex, part of the oxidative phosphorylation machinery. In conclusion, our results provide novel insight into the evolutionary history of the Trichechidae during the Late Miocene, which was influenced by geological events, such as Amazon Basin formation.

scholarly journals A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241231
Author(s):  
Joel H. Nitta ◽  
Atsushi Ebihara ◽  
Alan R. Smith
Keyword(s):  
Costa Rica ◽  
Evolutionary History ◽  
Cloud Forest ◽  
Dna Barcode ◽  
Hybrid Origin ◽  
Forest Reserve ◽  
Biogeographic History ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Ferns And Lycophytes

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

scholarly journals Phylogenetic relationships and biogeographical history of the large extinct European testudinids

2015 ◽  
Author(s):  
Evangelos Vlachos ◽  
Adán Pérez-García ◽  
Márton Rabi
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
General Scheme ◽  
Morphological Characters ◽  
Limited Attention ◽  
Biogeographic History ◽  
Early Diversification ◽  
Open Questions ◽  
History Of ◽  
In The Beginning

Background. Large-sized testudinids had a long evolutionary history in Europe during the last 50 million years before becoming extinct in the beginning of the Pleistocene. Despite a 150-year long history in research and a decent fossil record, the European large testudinids have received limited attention so far. Methods. New excavations, descriptions of new specimens from Greece, Spain and Germany, revisions of previously published European taxa and comparative studies with extant testudinids now provide a major advancement in understanding the anatomy and evolutionary history of these turtles. This contribution aims to provide an updated summary of the accumulated knowledge on European large tortoises and to explore in detail their phylogenetic relationships in a global context (including small-sized extinct and extant taxa). The phylogenetic analysis is based on a new character/taxon matrix of morphological characters. Parsimony analysis was performed both with and without molecular backbone constraints. Results. We describe new material of large testudinids from Greece, Spain and Germany and revise most of the available material that has been previously published. Our morphology-based results are promising since they are consistent with recent molecular studies in identifying large testudinids traditionally referred to the Geochelone complex as polyphyletic. Furthermore, we were able to reproduce the molecular phylogeny of Mediterranean tortoises (Testudona). Discussion. The phylogenetic framework presented here allows addressing several open questions of the history of testudinids. First of all, it hints to a more complex biogeographic history of European testudinids than previously recognized. Although the early Paleogene history of testudinids cannot be accurately traced at the moment it seems probable that, besides Asia and North America, Europe also played a major role in the early diversification of Testudinidae. We demonstrate that large European testudinids do not form a monophyletic lineage. The widely recognized genus Cheirogaster should only include the Eocene type species, and exclude other large Paleogene or giant Neogene taxa so far known. Our analysis reveals that large size evolved independently in several clades and in several continents during warmer parts of the Cenozoic. Besides this general scheme other factors might have played a role regionally (e.g. changes in vegetation, island isolation).

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