scholarly journals A geography aware reconciliation method to investigate diversification patterns in host/parasite interactions

2017 ◽  
Author(s):  
V. Berry ◽  
F. Chevenet ◽  
J-P. Doyon ◽  
E. Jousselin
Keyword(s):  
Phylogenetic Trees ◽  
Biotic Interactions ◽  
Geographic Information ◽  
Fig Wasp ◽  
Host Shifts ◽  
Host Phylogeny ◽  
Host Parasite ◽  
Reconciliation Method ◽  
Generation Sequencing ◽  
Ancestral Character States

ABSTRACTCospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX in order to visualize ancestral character states on the phylogenetic trees and highlight zones that are geographically inconsistent in reconciliations computed without geographic constraints. We suggest that the comparison of reconciliations obtained with and without constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography and the advent of next-generation sequencing that leads to better-resolved trees, a geography aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.

scholarly journals Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

2021 ◽  
Author(s):  
Marcia Gumiel ◽  
Oscar M Rollano-Penaloza ◽  
Carmelo Peralta-Rivero ◽  
Leslie Tejeda ◽  
Valeria D. Palma Encinas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Next Generation Sequencing ◽  
Theobroma Cacao ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Next Generation ◽  
Center Of Origin ◽  
Chloroplast Genomes ◽  
Geographical Locations ◽  
Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

scholarly journals Loss of top-down biotic interactions changes the relative benefits for obligate mutualists

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182501 ◽  
Author(s):  
Rong Wang ◽  
Xiao-Yong Chen ◽  
Yan Chen ◽  
Gang Wang ◽  
Derek W. Dunn ◽  
...  
Keyword(s):  
Biotic Interactions ◽  
Trophic Levels ◽  
Fig Wasp ◽  
Negative Effects ◽  
Top Down ◽  
Top Predators ◽  
Natural Range ◽  
Obligate Mutualism ◽  
The Stability ◽  
Food Web Complexity

The collapse of mutualisms owing to anthropogenic changes is contributing to losses of biodiversity. Top predators can regulate biotic interactions between species at lower trophic levels and may contribute to the stability of such mutualisms, but they are particularly likely to be lost after disturbance of communities. We focused on the mutualism between the fig tree Ficus microcarpa and its host-specific pollinator fig wasp and compared the benefits accrued by the mutualists in natural and translocated areas of distribution. Parasitoids of the pollinator were rare or absent outside the natural range of the mutualists, where the relative benefits the mutualists gained from their interaction were changed significantly away from the plant's natural range owing to reduced seed production rather than increased numbers of pollinator offspring. Furthermore, in the absence of the negative effects of its parasitoids, we detected an oviposition range expansion by the pollinator, with the use of a wider range of ovules that could otherwise have generated seeds. Loss of top-down control has therefore resulted in a change in the balance of reciprocal benefits that underpins this obligate mutualism, emphasizing the value of maintaining food web complexity in the Anthropocene.

scholarly journals Metagenomic Next-Generation Sequencing Reveal Presence of a Novel Ungulate Bocaparvovirus in Alpacas

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 701 ◽  
Author(s):  
Kumar ◽  
Chaudhary ◽  
Lu ◽  
Duff ◽  
Heffel ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Amino Acid ◽  
Phylogenetic Trees ◽  
Neurological Diseases ◽  
Virus Infectivity ◽  
Whole Genome ◽  
Ns1 Protein ◽  
Next Generation ◽  
Percent Identity ◽  
Generation Sequencing

Viruses belonging to the genus Bocaparvovirus (BoV) are a genetically diverse group of DNA viruses known to cause respiratory, enteric, and neurological diseases in animals, including humans. An intestinal sample from an alpaca (Vicugna pacos) herd with reoccurring diarrhea and respiratory disease was submitted for next-generation sequencing, revealing the presence of a BoV strain. The alpaca BoV strain (AlBoV) had a 58.58% whole genome nucleotide percent identity to a camel BoV from Dubai, belonging to a tentative ungulate BoV 8 species (UBoV8). Recombination events were lacking with other UBoV strains. The AlBoV genome was comprised of the NS1, NP1, and VP1 proteins. The NS1 protein had the highest amino acid percent identity range (57.89–67.85%) to the members of UBoV8, which was below the 85% cut-off set by the International Committee on Taxonomy of Viruses. The low NS1 amino acid identity suggests that AlBoV is a tentative new species. The whole genome, NS1, NP1, and VP1 phylogenetic trees illustrated distinct branching of AlBoV, sharing a common ancestor with UBoV8. Walker loop and Phospholipase A2 (PLA2) motifs that are vital for virus infectivity were identified in NS1 and VP1 proteins, respectively. Our study reports a novel BoV strain in an alpaca intestinal sample and highlights the need for additional BoV research.

A new feather mite species of the genus Neumannella Trouessart, 1916 (Analgoidea, Dermoglyphidae) from the Red-winged Tinamou Rhynchotus rufescens (Temminck, 1815) (Aves, Tinamiformes) with remarks to the evolution of host-parasite associations of the genus

2014 ◽  
Vol 59 (2) ◽  
Author(s):  
Jacek Dabert
Keyword(s):  
New Species ◽  
Evolutionary History ◽  
Morphological Characters ◽  
Mite Species ◽  
Feather Mite ◽  
History Of ◽  
Host Parasite ◽  
Reconciliation Method ◽  
A New Species ◽  
Mite Family

AbstractNeumannella skorackii, a new species of the feather mite family Dermoglyphidae (Acari, Astigmata) is described from the Red-winged Tinamou Rhynchotus rufescens (Temminck, 1815) (Aves, Tinamiformes) from Paraguay and a key to all known species of the genus is provided. The phylogenetic relationships (MP analysis of 25 morphological characters) between Neumannella species along with the evolutionary history of host-parasite associations revealed by Jungle reconciliation method are reconstructed. Relatively low cospeciation contribution to the recent host-parasite associations is discovered.

scholarly journals A geography-aware reconciliation method to investigate diversification patterns in host/parasite interactions

2018 ◽  
Vol 18 (5) ◽  
pp. 1173-1184 ◽  
Author(s):  
Vincent Berry ◽  
François Chevenet ◽  
Jean-Philippe Doyon ◽  
Emmanuelle Jousselin
Keyword(s):  
Host Parasite Interactions ◽  
Host Parasite ◽  
Reconciliation Method

scholarly journals Microsporidian infections in the species complex Gammarus roeselii (Amphipoda) over its geographical range: evidence for both host–parasite co-diversification and recent host shifts

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Adrien Quiles ◽  
Karolina Bacela-Spychalska ◽  
Maria Teixeira ◽  
Nicolas Lambin ◽  
Michal Grabowski ◽  
...  
Keyword(s):  
Species Complex ◽  
Geographical Range ◽  
Host Shifts ◽  
Host Parasite

scholarly journals Analysis of large new South African dataset using two host-specificity indices shows generalism in both adult and larval ticks of mammals

Parasitology ◽  
2015 ◽  
Vol 143 (3) ◽  
pp. 366-373 ◽  
Author(s):  
MARCELA P. A. ESPINAZE ◽  
ELÉONORE HELLARD ◽  
IVAN G. HORAK ◽  
GRAEME S. CUMMING
Keyword(s):  
Host Specificity ◽  
South African ◽  
New South ◽  
Life Stage ◽  
Host Preferences ◽  
Infestation Intensity ◽  
Host Parasite Interactions ◽  
Host Phylogeny ◽  
Pathogen Control ◽  
Host Parasite

SUMMARYTicks and tick-borne pathogens can have considerable impacts on the health of livestock, wildlife and people. Knowledge of tick–host preferences is necessary for both tick and pathogen control. Ticks were historically considered as specialist parasites, but the range of sampled host species has been limited, infestation intensity has not been included in prior analyses, and phylogenetic distances between hosts have not been previously considered. We used a large dataset of 35 604 individual collections and two host-specificity indices to assess the specificity of 61 South African tick species, as well as distinctions between adult and juvenile ticks, for 95 mammalian hosts. When accounting for host phylogeny, most adult and juvenile ticks behaved as generalists, with juveniles being significantly more generalist than adults. When we included the intensity of tick infestation, ticks exhibited a wider diversity of specificity in all life stages. Our results show that ticks of mammals in South Africa tend to behave largely as generalists and that adult ticks are more host-specific. More generally, our analysis shows that the incorporation of life-stage differences, infestation intensity and phylogenetic distances between hosts, as well as the use of more than one specificity index, can all contribute to a deeper understanding of host–parasite interactions.

scholarly journals Similarities among ectoparasite fauna of sigmodontine rodents: phylogenetic and geographical influences

Parasitology ◽  
2012 ◽  
Vol 139 (13) ◽  
pp. 1749-1756 ◽  
Author(s):  
LEONARDO DOMINICI CRUZ ◽  
FERNANDA RODRIGUES FERNANDES ◽  
ARÍCIO XAVIER LINHARES
Keyword(s):  
Geographical Distribution ◽  
Host Species ◽  
Divergence Time ◽  
Mite Species ◽  
Mantel Test ◽  
Partial Mantel Test ◽  
Parasitic Species ◽  
Host Phylogeny ◽  
Host Parasite ◽  
Ectoparasite Fauna

SUMMARYPhylogenetic and geographical overlaps in host distributions influence the compositional similarity of ectoparasite fauna in a host–parasite system. In these systems, hosts that are more closely related (phylogenetically) are expected to share more parasitic species than more distantly related hosts. Similarly, hosts sharing a larger geographical distribution overlap are expected to have similar ectoparasites. This study investigated the influence of phylogeny (divergence time) and geographical overlap of some neotropical sigmodontine rodent species on the similarities among their ectoparasite fauna (Mesostigmata and Siphonaptera), using a partial Mantel test. Divergence time was the only significant factor that influenced the similarity among the ectoparasites, when mites and fleas were analysed together. Host species that had diverged more recently displayed ectoparasite fauna that were similar. The similarities of the flea species showed similar results in both separate and joint analyses, but neither phylogenetic nor geographical overlap influenced the similarity in mite species. Fleas were shown to be more host-specific than were mesostigmate mites, probably because of the increased influence of host phylogeny.

scholarly journals 60 million years of co-divergence in the fig–wasp symbiosis

2005 ◽  
Vol 272 (1581) ◽  
pp. 2593-2599 ◽  
Author(s):  
Nina Rønsted ◽  
George D Weiblen ◽  
James M Cook ◽  
Nicolas Salamin ◽  
Carlos A Machado ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Time Frame ◽  
Molecular Dating ◽  
Fig Wasp ◽  
Geological Time ◽  
Molecular Phylogenetic ◽  
Pollinator Specialization ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Plant Pollinator

Figs ( Ficus ; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant–pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant–insect co-divergence over a geological time frame spanning at least 60 million years.

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