scholarly journals Phylogeography and population genetics of the endemic Malagasy bat,Macronycteris commersonis.s. (Chiroptera: Hipposideridae)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e5866
Author(s):  
Andrinajoro R. Rakotoarivelo ◽  
Steven M. Goodman ◽  
M. Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Phylogeographic Structure ◽  
Climate Conditions ◽  
Climate Fluctuations ◽  
Pleistocene Climate ◽  
Clade B ◽  
Clade C ◽  
Forested Areas ◽  
Open Woodland ◽  
Western Half

Macronycteris commersoni(Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence thatM. commersoniexhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages withinM. commersoni.Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events ofM.commersoniwere probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

scholarly journals Phylogeography and population genetics of Macronycteris commersonii s.s. (Chiroptera: Hipposideridae), an endemic Malagasy bat

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Steven M Goodman ◽  
M Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Recent Common Ancestor ◽  
Climate Conditions ◽  
Most Recent Common Ancestor ◽  
Pleistocene Climate ◽  
Clade C ◽  
Distance Model ◽  
Forested Areas

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

scholarly journals Phylogeography and population genetics of Macronycteris commersonii s.s. (Chiroptera: Hipposideridae), an endemic Malagasy bat

2018 ◽  
Author(s):  
Andrinajoro R Rakotoarivelo ◽  
Steven M Goodman ◽  
M Corrie Schoeman ◽  
Sandi Willows-Munro
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Recent Common Ancestor ◽  
Climate Conditions ◽  
Most Recent Common Ancestor ◽  
Pleistocene Climate ◽  
Clade C ◽  
Distance Model ◽  
Forested Areas

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

scholarly journals The flickering connectivity system of the north Andean páramos

2019 ◽  
Author(s):  
Suzette G.A. Flantua ◽  
Aaron O’Dea ◽  
Renske E. Onstein ◽  
Henry Hooghiemstra
Keyword(s):  
Lower Boundary ◽  
Habitat Connectivity ◽  
Pollen Record ◽  
Climate Conditions ◽  
Northern Andes ◽  
Climate Fluctuations ◽  
Mountain Ranges ◽  
Biogeographic Patterns ◽  
The North ◽  
Pleistocene Climate

ABSTRACT AND KEYWORDSAimTo quantify the effect of Pleistocene climate fluctuations on habitat connectivity across páramos in the Neotropics.LocationThe Northern AndesMethodsThe unique páramos habitat underwent dynamic shifts in elevation in response to changing climate conditions during the Pleistocene. The lower boundary of the páramos is defined by the upper forest line, which is known to be highly responsive to temperature. Here we reconstruct the extent and connectivity of páramos over the last 1 million years (Myr) by reconstructing the UFL from the long fossil pollen record of Funza09, Colombia, and applying it to spatial mapping on modern topographies across the Northern Andes for 752 time slices. Data provide an estimate of how often and for how long different elevations were occupied by páramos and estimates their connectivity to provide insights into the role of topography in biogeographic patterns of páramos.ResultsOur findings show that connectivity amongst páramos of the Northern Andes was highly dynamic, both within and across mountain ranges. Connectivity amongst páramos peaked during extreme glacial periods but intermediate cool stadials and mild interstadials dominated the climate system. These variable degrees of connectivity through time result in what we term the ‘flickering connectivity system’. We provide a visualization (video) to showcase this phenomenon. Patterns of connectivity in the Northern Andes contradict patterns observed in other mountain ranges of differing topographies.Main conclusionsPleistocene climate change was the driver of significant elevational and spatial shifts in páramos causing dynamic changes in habitat connectivity across and within all mountain ranges. Some generalities emerge, including the fact that connectivity was greatest during the most ephemeral of times. However, the timing, duration and degree of connectivity varied substantially among mountain ranges depending on their topographic configuration. The flickering connectivity system of the páramos uncovers the dynamic settings in which evolutionary radiations shaped the most diverse alpine biome on Earth.

scholarly journals Mitochondrial sequence data indicate “Vicariance by Erosion” as a mechanism of species diversification in North American Ptomaphagus (Coleoptera, Leiodidae, Cholevinae) cave beetles

2019 ◽  
Vol 29 ◽  
pp. 35-57 ◽  
Author(s):  
Vincent L. Leray ◽  
Jason Caravas ◽  
Markus Friedrich ◽  
Kirk S. Zigler
Keyword(s):  
Molecular Phylogeny ◽  
Sequence Data ◽  
Single Species ◽  
The South ◽  
Cumberland Plateau ◽  
Climate Fluctuations ◽  
The Past ◽  
Pleistocene Climate ◽  
Group 2 ◽  
Carrion Beetles

Small carrion beetles (Coleoptera: Leiodidae: Cholevinae) are members of cave communities around the world and important models for understanding the colonization of caves, adaptation to cave life, and the diversification of cave-adapted lineages. We developed a molecular phylogeny to examine the diversification of the hirtus-group of the small carrion beetle genus Ptomaphagus. The hirtus-group has no surface-dwelling members; it consists of 19 short-range endemic cave- and soil-dwelling species in the central and southeastern United States of America. Taxonomic, phylogenetic and biogeographic data were previously interpreted to suggest the hirtus-group diversified within the past 350,000 years through a series of cave colonization and speciation events related to Pleistocene climate fluctuations. However, our time-calibrated molecular phylogeny resulting from the analysis of 2,300 nucleotides from five genes across three mitochondrial regions (cox1, cytb, rrnL-trnL-nad1) for all members of the clade paints a different picture. We identify three stages of diversification in the hirtus-group: (1) ~10 million years ago (mya), the lineage that develops into P.shapardi, a soil-dwelling species from the Ozarks, diverged from the lineage that gives rise to the 18 cave-obligate members of the group; (2) between 8.5 mya and 6 mya, seven geographically distinct lineages diverged across Kentucky, Tennessee, Alabama and Georgia; six of these lineages represent a single species today, whereas (3) the ‘South Cumberlands’ lineage in Tennessee and Alabama diversified into 12 species over the past ~6 my. While the events triggering diversification during the first two stages remain to be determined, the distributions, phylogenetic relationships and divergence times in the South Cumberlands lineage are consistent with populations being isolated by vicariant events as the southern Cumberland Plateau eroded and fragmented over millions of years.

scholarly journals Modelling the Antarctic Ice Sheet across the mid-Pleistocene transition – implications for Oldest Ice

2019 ◽  
Vol 13 (7) ◽  
pp. 2023-2041 ◽  
Author(s):  
Johannes Sutter ◽  
Hubertus Fischer ◽  
Klaus Grosfeld ◽  
Nanna B. Karlsson ◽  
Thomas Kleiner ◽  
...  
Keyword(s):  
Ice Core ◽  
Ice Sheet ◽  
Middle Pleistocene ◽  
Climate Modelling ◽  
Geothermal Heat ◽  
Antarctic Ice Sheet ◽  
West Antarctic Ice Sheet ◽  
Climate Conditions ◽  
West Antarctic ◽  
Pleistocene Climate

Abstract. The international endeavour to retrieve a continuous ice core, which spans the middle Pleistocene climate transition ca. 1.2–0.9 Myr ago, encompasses a multitude of field and model-based pre-site surveys. We expand on the current efforts to locate a suitable drilling site for the oldest Antarctic ice core by means of 3-D continental ice-sheet modelling. To this end, we present an ensemble of ice-sheet simulations spanning the last 2 Myr, employing transient boundary conditions derived from climate modelling and climate proxy records. We discuss the imprint of changing climate conditions, sea level and geothermal heat flux on the ice thickness, and basal conditions around previously identified sites with continuous records of old ice. Our modelling results show a range of configurational ice-sheet changes across the middle Pleistocene transition, suggesting a potential shift of the West Antarctic Ice Sheet to a marine-based configuration. Despite the middle Pleistocene climate reorganisation and associated ice-dynamic changes, we identify several regions conducive to conditions maintaining 1.5 Myr (million years) old ice, particularly around Dome Fuji, Dome C and Ridge B, which is in agreement with previous studies. This finding strengthens the notion that continuous records with such old ice do exist in previously identified regions, while we are also providing a dynamic continental ice-sheet context.

A new species of forest-dwelling Cyrtodactylus Gray (Squamata: Gekkonidae) from the Indawgyi Wildlife Sanctuary, Kachin State, Myanmar

Zootaxa ◽  
2019 ◽  
Vol 4623 (1) ◽  
pp. 1-25 ◽  
Author(s):  
L. LEE GRISMER ◽  
PERRY L. JR. WOOD ◽  
EVAN S. H. QUAH ◽  
MYINT KYAW THURA ◽  
MARK W. HERR ◽  
...  
Keyword(s):  
New Species ◽  
Color Pattern ◽  
Phylogeographic Structure ◽  
Undescribed Species ◽  
Wildlife Sanctuary ◽  
Taxonomic Analysis ◽  
Forested Areas ◽  
A New Species ◽  
Nd2 Gene ◽  
Mitochondrial Clade

A herpetological survey of the Indawgyi Wildlife Sanctuary in Kachin State, Myanmar resulted in the discovery of a new species of Cyrtodactylus Gray along the eastern watershed of the Mokso Mountains. An integrative taxonomic analysis based on the mitochondrial ND2 gene, morphology, and color pattern recovered this new species, Cyrtodactylus mombergi sp. nov., as the sister taxon to an undescribed species from Miao, Arunachal Pradesh, India. Bayesian and maximum likelihood analyses recovered notable genetically divergent (4.7%) phylogeographic structure between northern and southern populations of C. mombergi sp. nov. across only 14 km of continuous habitat. Conversely, genetic divergence did not exceed 9.2% between C. mombergi sp. nov. and the undescribed species from Miao from across 355 km of habitat. Cyrtodactylus mombergi sp. nov. belongs to a well-supported, mitochondrial clade of 18 other species which now compose an expanded and redefined C. gansi group. Cyrtodactylus mombergi sp. nov. is only the third species of Bent-toed Gecko reported from Kachin State and indicates that additional herpetological surveys are needed in unexplored forested areas. 

scholarly journals Griffithsin Retains Anti-HIV-1 Potency with Changes in gp120 Glycosylation and Complements Broadly Neutralizing Antibodies PGT121 and PGT126

2019 ◽  
Vol 64 (1) ◽  
Author(s):  
Kathryn Fischer ◽  
Kimberly Nguyen ◽  
Patricia J. LiWang
Keyword(s):  
Neutralizing Antibodies ◽  
Glycosylation Site ◽  
Significant Loss ◽  
Broadly Neutralizing Antibodies ◽  
Clade B ◽  
Key Factor ◽  
Clade C ◽  
Cd4 Binding Site ◽  
Gp120 Glycosylation ◽  
Hiv 1

ABSTRACT Griffithsin (Grft) is an antiviral lectin that has been shown to potently inhibit HIV-1 by binding high-mannose N-linked glycosylation sites on HIV-1 gp120. A key factor for Grft potency is glycosylation at N295 of gp120, which is directly adjacent to N332, a target glycan for an entire class of broadly neutralizing antibodies (bNAbs). Here, we unify previous work on the importance of other glycans to Grft potency against HIV-1 and Grft’s role in mediating the conformational change of gp120 by mutating nearly every glycosylation site in gp120. In addition to a significant loss of Grft activity by the removal of glycosylation at N295, glycan absence at N332 or N448 was found to have moderate effects on Grft potency. Interestingly, in the absence of N295, Grft effectiveness could be improved by a mutation that results in the glycan at N448 shifting to N446, indicating that the importance of individual glycans may be related to their effect on glycosylation density. Grft’s ability to alter the structure of gp120, exposing the CD4 binding site, correlated with the presence of glycosylation at N295 only in clade B strains, not clade C strains. We further demonstrate that Grft can rescue the activity of the bNAbs PGT121 and PGT126 in the event of a loss or a shift of glycosylation at N332, where the bNAbs suffer a drastic loss of potency. Despite targeting the same region, Grft in combination with PGT121 and PGT126 produced additive effects. This indicates that Grft could be an important combinational therapeutic.

scholarly journals New insights from molecular characterization of the tick Rhipicephalus (Boophilus) microplus in Brazil

2016 ◽  
Vol 25 (3) ◽  
pp. 317-326 ◽  
Author(s):  
Bárbara Guimarães Csordas ◽  
Marcos Valério Garcia ◽  
Rodrigo Casquero Cunha ◽  
Poliana Fernanda Giachetto ◽  
Isabella Maiumi Zaidan Blecha ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Strong Support ◽  
Boophilus Microplus ◽  
The Other ◽  
Clade B ◽  
Clade C ◽  
Taxonomic Problem ◽  
Cox 1 ◽  
Brazilian Populations

Abstract The Rhipicephalus (Boophilus) microplus complex currently consists of five taxa, namely R. australis, R. annulatus, R. (B.) microplus clade A sensu, R. microplus clade B sensu, and R. (B.) microplus clade C sensu. Mitochondrial DNA-based methods help taxonomists when they are facing the morpho-taxonomic problem of distinguishing members of the R. (B.) microplus complex. The purpose of this study was to perform molecular characterization of ticks in all five regions of Brazil and infer their phylogenetic relationships. Molecular analysis characterized 10 haplotypes of the COX-1 gene. Molecular network analysis revealed that haplotype H-2 was the most dispersed of the studied populations (n = 11). Haplotype H-3 (n = 2) had the greatest genetic differentiation when compared to other Brazilian populations. A Bayesian phylogenetic tree of the COX-1 gene obtained strong support. In addition, it was observed that the population of R. (B.) microplus haplotype H-3 exhibited diverging branches among the other Brazilian populations in the study. The study concludes that the different regions of Brazil have R. (B.) microplus tick populations with distinct haplotypes.

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