scholarly journals Mitochondrial genomes and thousands of ultraconserved elements resolve the taxonomy and historical biogeography of the Euphonia and Chlorophonia finches (Passeriformes: Fringillidae)

The Auk ◽  
2020 ◽  
Vol 137 (3) ◽  
Author(s):  
Tyler S Imfeld ◽  
F Keith Barker ◽  
Robb T Brumfield
Keyword(s):  
Divergence Time ◽  
Strong Support ◽  
Species Level ◽  
Mitochondrial Genomes ◽  
South American ◽  
Isthmus Of Panama ◽  
Eastern Hemisphere ◽  
Biogeographic History ◽  
Dispersal Events ◽  
South American Origin

Abstract Relationships of the Neotropical finches in the genera Euphonia and Chlorophonia (Fringillidae: Euphoniinae) have been clarified by recent molecular studies, but species-level relationships within this group have not been thoroughly addressed. In this study, we sampled specimens representing every recognized species of these genera, in addition to 2 outgroup taxa, and used target enrichment to sequence thousands of ultraconserved element (UCE) loci, as well as mitochondrial DNA reconstructed from off-target reads, from each specimen to infer these relationships. We constructed both concatenation and coalescent-based estimates of phylogeny from this dataset using matrices of varying levels of completeness, and we generated a time-scaled ultrametric tree using a recently published fossil-based external calibration. We found uniformly strong support for a monophyletic subfamily Euphoniinae and genus Chlorophonia, but a paraphyletic Euphonia across UCEs and mitochondrial genomes. Otherwise, our inferred relationships were largely concordant with previous studies. Our time-tree indicated a stem divergence time of 13.8 million years ago for this lineage, followed by a relatively young crown age of only 7.1 myr. Reconstructions of biogeographic history based on this tree suggest a South American origin for crown Euphoniinae, possibly resulting from a transoceanic dispersal event from the Eastern Hemisphere, followed by 2 dispersal events into the Caribbean and as many as 6 invasions of North America coinciding with recent estimates of the age at which the Isthmus of Panama had completely formed. We recommend splitting Euphonia and resurrecting the genus Cyanophonia for the 3 blue-hooded species more closely related to Chlorophonia. Based on our results, we suspect that there is undescribed species-level diversity in at least one, possibly many, widespread and phenotypically diverse species.

scholarly journals Early Oligocene chinchilloid caviomorphs from Puerto Rico and the initial rodent colonization of the West Indies

2020 ◽  
Vol 287 (1920) ◽  
pp. 20192806 ◽  
Author(s):  
Laurent Marivaux ◽  
Jorge Vélez-Juarbe ◽  
Gilles Merzeraud ◽  
François Pujos ◽  
Lázaro W. Viñola López ◽  
...  
Keyword(s):  
Puerto Rico ◽  
West Indies ◽  
Distinct Species ◽  
South American ◽  
The West ◽  
Early Oligocene ◽  
Biogeographic History ◽  
Phylogenetic Affinities ◽  
Dispersal Events ◽  
South American Origin

By their past and present diversity, rodents are among the richest components of Caribbean land mammals. Many of these became extinct recently. Causes of their extirpation, their phylogenetic affinities, the timing of their arrival in the West Indies and their biogeographic history are all ongoing debated issues. Here, we report the discovery of dental remains from Lower Oligocene deposits ( ca 29.5 Ma) of Puerto Rico. Their morphology attests to the presence of two distinct species of chinchilloid caviomorphs, closely related to dinomyids in a phylogenetic analysis, and thus of undisputable South American origin. These fossils represent the earliest Caribbean rodents known thus far. They could extend back to 30 Ma the lineages of some recently extinct Caribbean giant rodents ( Elasmodontomys and Amblyrhiza ), which are also retrieved here as chinchilloids. This new find has substantial biogeographic implications because it demonstrates an early dispersal of land mammals from South America to the West Indies, perhaps via the emergence of the Aves Ridge that occurred ca 35–33 Ma (GAARlandia hypothesis). Considering both this new palaeontological evidence and recent molecular divergence estimates, the natural colonization of the West Indies by rodents probably occurred through multiple and time-staggered dispersal events (chinchilloids, then echimyid octodontoids (spiny rats/hutias), caviids and lastly oryzomyin muroids (rice rats)).

Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)

2020 ◽  
Author(s):  
Jeffrey L Weinell ◽  
Anthony J Barley ◽  
Cameron D Siler ◽  
Nikolai L Orlov ◽  
Natalia B Ananjeva ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Oceanic Islands ◽  
Species Level ◽  
Boiga Irregularis ◽  
Brown Tree Snake ◽  
Biogeographic History ◽  
The Pacific ◽  
History Of ◽  
Dispersal Events

Abstract The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.

The phylogeny, biogeography and morphological evolution of Gaultheria (Ericaceae) from Australia and New Zealand

2009 ◽  
Vol 22 (4) ◽  
pp. 229 ◽  
Author(s):  
Catherine M. Bush ◽  
Steven J. Wagstaff ◽  
Peter W. Fritsch ◽  
Kathleen A. Kron
Keyword(s):  
New Zealand ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Morphological Characters ◽  
South American ◽  
South American Species ◽  
Dna Sequence Data ◽  
Biogeographical Analysis ◽  
Dispersal Events ◽  
South American Origin

Phylogenetic relationships within Gaultheria L. from Australia and New Zealand were examined by using DNA sequence data from matK, ndhF, nrITS, waxy and lfy. In the combined parsimony and maximum likelihood analyses, all Australia/New Zealand species form a clade that is sister to a clade of temperate South American species. Optimisation of morphological characters that have been emphasised in classifications of Gaultheria onto the molecular phylogeny revealed that, within the Australia/New Zealand clade, non-fleshy fruiting calyces, berries and solitary-flowered inflorescences each evolved twice, from fleshy fruiting calyces, capsules and multiple-flowered inflorescences, respectively. A historical biogeographical analysis that included the temperate southern hemisphere element in Gaultheria supports a South American origin of the Australia/New Zealand clade, followed by three dispersal events from New Zealand to Australia. Whether the origin is from temperate or tropical South America is ambiguous in our analysis.

scholarly journals Molecular Phylogeny and Historical Biogeography of the Butterfly Tribe Aeromachini Tutt (Lepidoptera: Hesperiidae) from China

Cells ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 294 ◽  
Author(s):  
Yuanyuan Li ◽  
Jianqing Zhu ◽  
Chen Ge ◽  
Ying Wang ◽  
Zimiao Zhao ◽  
...  
Keyword(s):  
Divergence Time ◽  
Strong Support ◽  
Distribution Patterns ◽  
Historical Biogeography ◽  
Central China ◽  
Ancestral Area ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Extant Species ◽  
Dispersal Events

: The butterfly tribe Aeromachini Tutt, 1906 is a large group of skippers. In this study, a total of 10 genera and 45 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2093 bp). The combined dataset was analyzed with maximum likelihood inference using IQtree. We found strong support for monophyly of Aeromachini from China and support for the most recent accepted species in the tribe. Two paraphyletic genera within Aeromachini are presented and discussed. The divergence time estimates with BEAST and ancestral-area reconstructions with RASP provide a detailed description about the historical biogeography of the Aeromachini from China. The tribe very likely originated from the Hengduan Mountains in the late Ecocene and expanded to the Himalaya Mountains and Central China Regions. A dispersal-vicariance analysis suggests that dispersal events have played essential roles in the distribution of extant species, and geological and climatic changes have been important factors driving current distribution patterns.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Amazonia as the Origin and Diversification Area of Didelphidae (Mammalia: Metatheria), and a Review of the Fossil Record of the Clade

2021 ◽  
Author(s):  
Mariela C. Castro ◽  
Murilo J. Dahur ◽  
Gabriel S. Ferreira
Keyword(s):  
South America ◽  
Amazon Basin ◽  
Parametric Models ◽  
Isthmus Of Panama ◽  
Biogeographic History ◽  
Early Diversification ◽  
Northern Portion ◽  
History Of ◽  
Environmental Events ◽  
Fossil Records

AbstractDidelphidae is the largest New World radiation of marsupials, and is mostly represented by arboreal, small- to medium-sized taxa that inhabit tropical and/or subtropical forests. The group originated and remained isolated in South America for millions of years, until the formation of the Isthmus of Panama. In this study, we present the first reconstruction of the biogeographic history of Didelphidae including all major clades, based on parametric models and stratified analyses over time. We also compiled all the pre-Quaternary fossil records of the group, and contrasted these data to our biogeographic inferences, as well as to major environmental events that occurred in the South American Cenozoic. Our results indicate the relevance of Amazonia in the early diversification of Didelphidae, including the divergence of the major clades traditionally ranked as subfamilies and tribes. Cladogeneses in other areas started in the late Miocene, an interval of intense shifts, especially in the northern portion of Andes and Amazon Basin. Occupation of other areas continued through the Pliocene, but few were only colonized in Quaternary times. The comparison between the biogeographic inference and the fossil records highlights some further steps towards better understanding the spatiotemporal evolution of the clade. Finally, our results stress that the early history of didelphids is obscured by the lack of Paleogene fossils, which are still to be unearthed from low-latitude deposits of South America.

scholarly journals Mice as stowaways? Colonization history of Danish striped field mice

2017 ◽  
Vol 13 (7) ◽  
pp. 20170064 ◽  
Author(s):  
Liselotte Wesley Andersen ◽  
Magnus Jacobsen ◽  
Christina Vedel-Smith ◽  
Thomas Secher Jensen
Keyword(s):  
Eastern Europe ◽  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Field Mouse ◽  
Colonization History ◽  
Striped Field Mouse ◽  
Steppe Region ◽  
History Of ◽  
Field Mice ◽  
Human Introduction

Species from the steppe region of Eastern Europe likely colonized northwestern Europe in connection with agriculture after 6500 BP. The striped field mouse ( Apodemus agrarius Pallas, 1783), is a steppe-derived species often found in human crops. It is common on the southern Danish islands of Lolland and Falster, which have been isolated from mainland Europe since approximately 10 300–8000 BP. Thus, this species could have been brought in with humans in connection with agriculture, or it could be an earlier natural invader. We sequenced 86 full mitochondrial genomes from the northwestern range of the striped field mouse, analysed phylogenetic relationships and estimated divergence time. The results supported human-induced colonization of Denmark in the Subatlantic or Subboreal period. A newly discovered population from Central Jutland in Denmark diverged from Falster approximately 100–670 years ago, again favouring human introduction. One individual from Sweden turned out to be a recent introduction from Central Jutland.

Taxonomic status of Andersen’s fruit-eating bat (Artibeus jamaicensis aequatorialis) and revised classification of Artibeus (Chiroptera: Phyllostomidae)

Zootaxa ◽  
2010 ◽  
Vol 2648 (1) ◽  
pp. 45 ◽  
Author(s):  
PETER A. LARSEN ◽  
MARÍA R. MARCHÁN-RIVADENEIRA ◽  
ROBERT J. BAKER
Keyword(s):  
Taxonomic Status ◽  
Morphological Characters ◽  
Species Level ◽  
South American ◽  
Reciprocal Monophyly ◽  
Dna Variation ◽  
The Andes ◽  
Artibeus Jamaicensis ◽  
Phylogenetic Studies

Fruit-eating bats of the genus Artibeus are widely distributed across the Neotropics and are one of the most recently evolved assemblages of the family Phyllostomidae. Although the taxonomy and systematics of species of Artibeus has been the subject of an intense historical debate, the most current taxonomic arrangements recognize approximately eleven species within the genus. However, recent phylogenetic studies indicate that species diversity within South and Middle American populations of Artibeus is underestimated. South American populations referable to A. jamaicensis aequatorialis are of considerable interest because previous studies of mitochondrial DNA variation identified potential species level variation west of the Andes Mountains. In this study we use morphometric and genetic data (nuclear AFLPs) to investigate the taxonomic status of A. j. aequatorialis. Our results indicate that elevating aequatorialis to species level is appropriate based on statistically supported reciprocal monophyly in mitochondrial and nuclear datasets and diagnostic morphological characters. In light of our results, and of those presented elsewhere, we provide a revised classification of the genus.

scholarly journals Global Sourcing of Low-Inorganic Arsenic Rice Grain

2019 ◽  
Vol 12 (4) ◽  
pp. 711-719 ◽  
Author(s):  
Manus Carey ◽  
Caroline Meharg ◽  
Paul Williams ◽  
Ernest Marwa ◽  
Xiao Jiujin ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Arsenic Speciation ◽  
Inorganic Arsenic ◽  
Rice Grain ◽  
Dimethylarsinic Acid ◽  
South American ◽  
Global Sourcing ◽  
Human Diet ◽  
Tropical Regions ◽  
Eastern Hemisphere

AbstractArsenic in rice grain is dominated by two species: the carcinogen inorganic arsenic (the sum of arsenate and arsenite) and dimethylarsinic acid (DMA). Rice is the dominant source of inorganic arsenic into the human diet. As such, there is a need to identify sources of low-inorganic arsenic rice globally. Here we surveyed polished (white) rice across representative regions of rice production globally for arsenic speciation. In total 1180 samples were analysed from 29 distinct sampling zones, across 6 continents. For inorganic arsenic the global $$\tilde{x}$$ x ~ was 66 μg/kg, and for DMA this figure was 21 μg/kg. DMA was more variable, ranging from < 2 to 690 μg/kg, while inorganic arsenic ranged from < 2 to 399 μg/kg. It was found that inorganic arsenic dominated when grain sum of species was < 100 μg/kg, with DMA dominating at higher concentrations. There was considerable regional variance in grain arsenic speciation, particularly in DMA where temperate production regions had higher concentrations. Inorganic arsenic concentrations were relatively consistent across temperate, subtropical and northern hemisphere tropical regions. It was only in southern hemisphere tropical regions, in the eastern hemisphere that low-grain inorganic arsenic is found, namely East Africa ($$\tilde{x}$$ x ~  < 10 μg/kg) and the Southern Indonesian islands ($$\tilde{x}$$ x ~  < 20 μg/kg). Southern hemisphere South American rice was universally high in inorganic arsenic, the reason for which needs further exploration.

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