Consideration of genetic variation and evolutionary history in future conservation of Indian one-horned rhinoceros (Rhinoceros unicornis)

The extant members of the Eurasian rhino species have experienced severe population and range declines through a combination of natural and anthropogenic factors since the Pleistocene. The one-horned rhino is the only Asian species recovered from such strong population decline but most of their fragmented populations in India and Nepal are reaching carrying capacity. Implementation of any future reintroduction-based conservation efforts would greatly benefit from currently unavailable detailed genetic assessments and the evolutionary history of these populations. We sequenced wild one-horned rhino mitogenomes from all the extant populations (n=16 individuals) for the first time, identified the polymorphic sites and assessed genetic variation (2531bp mtDNA, n=111 individuals) across India. Results showed 30 unique rhino haplotypes distributed as three distinct genetic clades (Fst value 0.68-1) corresponding to the states of Assam (n=28 haplotypes), West Bengal and Uttar Pradesh (both monomorphic). Phylogenetic analyses suggest earlier coalescence of Assam (~0.5 Mya) followed by parallel divergence of West Bengal and Uttar Pradesh/Nepal (~0.06-0.05Mya), supported by the paleobiogeographic history of the Indian subcontinent. Combined together, we propose recognising three Evolutionary Significant Units (ESUs) of the Indian rhino. As recent assessments suggest further genetic isolations of the Indian rhinos at local scales, future management efforts should focus on identifying genetically variable founder animals and consider periodic supplementation events while planning future rhino reintroduction programs in India. Such well-informed, multidisciplinary approach is the only way to ensure evolutionary, ecological and demographic stability of the species across its range.

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Unveiling patterns of genetic variation in parasite–host associations: an example with pinworms and Neotropical primates

Parasitology ◽

10.1017/s0031182018001749 ◽

2018 ◽

Vol 146 (3) ◽

pp. 356-362 ◽

Cited By ~ 2

Author(s):

Brenda Solórzano García ◽

Amanda D. Melin ◽

Filippo Aureli ◽

Gerardo Pérez Ponce de León

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Central America ◽

Genetic Divergence ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Spider Monkey ◽

Neotropical Primates ◽

Genetic Patterns ◽

History Of

AbstractPatterns of genetic variation among populations can reveal the evolutionary history of species. Pinworm parasites are highly host specific and form strong co-evolutionary associations with their primate hosts. Here, we describe the genetic variation observed in four Trypanoxyuris species infecting different howler and spider monkey subspecies in Central America to determine if historical dispersal processes and speciation in the host could explain the genetic patterns observed in the parasites. Mitochondrial (cox1) and ribosomal (28S) DNA were analysed to assess genetic divergence and phylogenetic history of these parasites. Sequences of the 28S gene were identical within pinworms species regardless of host subspecies. However, phylogenetic analyses, haplotype relationships and genetic divergence with cox1 showed differentiation between pinworm populations according to host subspecies in three of the four Trypanoxyuris species analysed. Haplotype separation between host subspecies was not observed in Trypanoxyuris minutus, nor in Trypanoxyuris atelis from Ateles geoffoyi vellerosus and Ateles geoffoyi yucatanensis. Levels of genetic diversity and divergence in these parasites relate with such estimates reported for their hosts. This study shows how genetic patterns uncovered in parasitic organisms can reflect the host phylogenetic and biogeographic histories.

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Genetic variation within African spiny-tailed lizards (Agamidae: Uromastyx) estimated using mitochondrial DNA sequences

Amphibia-Reptilia ◽

10.1163/156853807779799144 ◽

2007 ◽

Vol 28 (1) ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

José Brito ◽

Raquel Vaconcelos ◽

D. James Harris

Keyword(s):

Mitochondrial Dna ◽

Genetic Variation ◽

Dna Sequences ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

North African ◽

History Of ◽

Current Species

AbstractAfrican spiny-tailed lizards (Uromastyx) are large, herbivorous lizards extensively traded locally for food and internationally as pets. Several species have recently been described, although some remain controversial. To determine relationships within North African forms, twenty individuals were analysed for over 1000 bases of mitochondrial DNA sequences. Phylogenetic analyses indicate four deeply divergent lineages that correspond to sampling areas, but not to current species designations. These results indicate that present taxonomy does not reflect the evolutionary history of these species.

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Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

Genome Biology and Evolution ◽

10.1093/gbe/evz155 ◽

2019 ◽

Cited By ~ 4

Author(s):

Sergio A Muñoz-Gómez ◽

Keira Durnin ◽

Laura Eme ◽

Christopher Paight ◽

Christopher E Lane ◽

...

Keyword(s):

Life Style ◽

Metabolic Pathways ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Biosynthetic Pathways ◽

History Of ◽

Sea Squirts ◽

Shed Light ◽

Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

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The Evolutionary History of Genetic Variation: An Emerging Issue in the Behavioral Genetic Study of Personality

Personality Psychology ◽

10.1007/978-1-4684-0634-4_25 ◽

1989 ◽

pp. 320-332 ◽

Cited By ~ 1

Author(s):

Steven W. Gangestad

Keyword(s):

Genetic Variation ◽

Genetic Study ◽

Evolutionary History ◽

Behavioral Genetic ◽

History Of ◽

Behavioral Genetic Study

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A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

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Characteristics of children with leprosy: Factors associated with delay in disease diagnosis

Indian Journal of Dermatology Venereology and Leprology ◽

10.25259/ijdvl_1382_20 ◽

2021 ◽

Vol 0 ◽

pp. 1-5

Author(s):

Joydeepa Darlong ◽

Karthikeyan Govindasamy ◽

Amrita Daniel

Keyword(s):

West Bengal ◽

Economic Status ◽

Uttar Pradesh ◽

Disease Diagnosis ◽

The Body ◽

Delayed Presentation ◽

Newly Diagnosed ◽

Factors Associated ◽

History Of ◽

History Of Migration

Objectives: The objectives of the study were to characterize the clinical profile of childhood leprosy presenting at tertiary leprosy care hospitals in the states of Bihar, West Bengal and Uttar Pradesh in India, and to determine the possible risk factors associated with disabilities at presentation. Methods: Subjects were children with newly diagnosed leprosy registered for treatment at tertiary Leprosy Mission Hospitals in Muzaffarpur (Bihar), Purulia (West Bengal) and Faizabad (Uttar Pradesh), India, between June and December 2019. Demographic and leprosy characteristics were collected at the time of diagnosis. Parents/guardians were interviewed on reasons for delay in presenting at the hospital. Associations between various factors and delay in diagnosis were assessed. Results: Among the 84 children, the mean (SD) age was 10 (3) years with a range of 4–14 years. There were more boys (58%) and most children were currently in school (93%), resident in rural areas (90%) and belonged to a lower socioeconomic status (68%). More children were diagnosed with multibacillary leprosy (69%), one-third of them being skin smear positive for Mycobacterium leprae. On presentation, 17% had deformity (5% grade 1 deformity and 12% grade 2), 29% had nerve involvement and skin lesions were spread across the body in half of the children. Mean (SD) duration of delay was 10.5 (9.8) months. Delayed presentation was more in boys (43% vs. 17%; P = 0.01), those without a history of migration for work compared to those who had a history of migration (40% vs. 9%; P = 0.008) and in those children who were from a poor economic status compared with those that came from a better economic status (44% vs. 7%; P = 0.001) Limitations: Because our study was conducted at tertiary care hospitals, the findings are not representative of the situation in the field. Furthermore, a comparison group of newly diagnosed adult leprosy patients with disability could have been included in the study. Conclusion: Childhood leprosy continues to occur in endemic pockets in India and a substantial number present with skin smear positivity and deformity. Guardians of these children cite many reasons for the delay in presentation.

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Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

10.1101/2021.09.11.459886 ◽

2021 ◽

Author(s):

Keerthic Aswin ◽

Srinivasan Ramachandran ◽

Vivek T Natarajan

Keyword(s):

Convergent Evolution ◽

Genome Stability ◽

Evolutionary History ◽

Rna Binding ◽

Phylogenetic Analyses ◽

Comparative Genome Analysis ◽

The Family ◽

History Of ◽

Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

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Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.2929 ◽

2019 ◽

Vol 286 (1897) ◽

pp. 20182929 ◽

Cited By ~ 2

Author(s):

Elena A. Ritschard ◽

Robert R. Fitak ◽

Oleg Simakov ◽

Sönke Johnsen

Keyword(s):

Signal Transduction ◽

Positive Selection ◽

G Protein ◽

Evolutionary History ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Genomic Signatures ◽

History Of ◽

G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

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Evolutionary relationships of the Sparidae (Teleostei: Percoidei): integrating fossil and Recent data

Transactions of the Royal Society of Edinburgh Earth Sciences ◽

10.1017/s0263593300000468 ◽

2002 ◽

Vol 93 (4) ◽

pp. 333-353 ◽

Cited By ~ 3

Author(s):

Julia J. Day

Keyword(s):

Evolutionary History ◽

Phylogenetic Analyses ◽

Successive Approximations ◽

Feeding Strategies ◽

New Genera ◽

Minimum Age ◽

Character Weighting ◽

History Of ◽

London Clay ◽

Fossil Data

ABSTRACTThe Eocene sparid fauna (Teleostei: Percoidei) from Monte Bolca, Italy and from the London Clay, U.K. is revised based on re-examination of the type material and phylogenetic analyses of primarily osteological data. Two phylogenetic analyses, one of the Eocene taxa and a combined analysis of fossil and extant taxa, were performed. The addition of fossils to the extant data greatly increased numbers of most parsimonious trees, destabilising and obscuring basal relationships within the Sparidae. Combination of the data from fossil and extant data also affected relationships among the fossil taxa, changing some from those recovered using fossil data alone and destabilising others. Successive approximations character weighting supported the inclusion of the Eocene taxa within a monophyletic Sparidae. The genus Sparnodus, as previously conceived, is paraphyletic and is partitioned to remove the paraphyly. Five monotypic genera are recognised, including three new genera, Abromasta, Ellaserrata and Pseudosparnodus. Inclusion of the fossils in the phylogenetic analysis implies a minimum age of origin for the Sparidae of 55 Ma with most Recent sparid fauna in place no later than the Miocene, and provides further evidence that the diversification of feeding strategies occurred early on in the evolutionary history of the group.

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