mumtaz baig - Academia.edu (original) (raw)

Papers by mumtaz baig

Nature Precedings, 2010

The present study reports the distribution of ABO and Rh blood groups among the Kunbis (Maratha) ... more The present study reports the distribution of ABO and Rh blood groups among the Kunbis (Maratha) population of Amravati district. The phenotypic frequency of blood group B is observed highest (33.06) percent, O (31.04), A (27.02) and AB is lowest (08.33) percent. The phenotypic frequency of Rh negative is (04.26) percent. TheKunbis (Maratha) population shows close genetic relationship with the Gujratis.

The current study analyzes the Zika virus from Asia from a phylogenomic and phylodynamic perspect... more The current study analyzes the Zika virus from Asia from a phylogenomic and phylodynamic perspective. To perform this study, 68 genomes from Asia were analyzed. A similar dataset was used to perform phylogenomics using Median Joining Network (MJN). MJN reconfirms African origin of Zika virus along with few notable instances of common origin of infection in some Asian countries. We investigated population dynamics using SkyGrid, Exponential Growth, and Constant Coalescence models. According to our phylodynamic analysis, effective population sizes throughout Asia reached higher peaks during the outbreak of 2016-2017. Zika virus population size increased exponentially during 2016-2017. From 1966 to 2021, there was a high and low peak in effective population size except for the outbreak of 2016-2017. To counter the outbreak of Zika Virus in Asian Countries in future, we recommend continuous genomic surveillance.

The Anthropologist, Apr 1, 2011

The origin and spread of agriculture in India is poorly understood. To address this, we analyzed ... more The origin and spread of agriculture in India is poorly understood. To address this, we analyzed mtDNA sequences of some ethnic groups from Eurasia to check for the support for the two most prevalent models of agricultural diffusion that is, "Demic expansion" Vs "Cultural diffusion". Presence of haplogroup T1 in the Madia Gond and Baluch, and its exact identity with population inhabiting in and around Mediterranean region points towards Neolithic linkages between these populations. Further, occurrence of rare haplogroup N1a in one of the Baluch individual and its identity with 7500 old Neolithic farmer sequences from Europe further reinforce dispersal of human from the Fertile Crescent region. Our phylogenetic analysis indicates clustering of Madia Gond and Baluch sequences in the distinct T1 and N1a Neolthic clusters. Application of molecular clock to this cluster yields a time depth of ~10,000 which further reconfirms its Neolithic origin. Though upper Paleolithic origin of majority of Indian population is well established, but presence of T1 and N1a haplogroup in Madia Gond and Baluch respectively supports Neolithic Demic expansion model.

Helminthologia, Nov 1, 2017

"Filariasis free India" is National Health Policy's vision. Currently, India has undertaken Mass ... more "Filariasis free India" is National Health Policy's vision. Currently, India has undertaken Mass Drug Administration drive (MDA) to eliminate the fi lariasis infection. Taking this into account, the emergence of new Wuchereria bancrofti resistant strains against the current choice of drugs cannot be ruled out. In this study, we report the genetic diversity of Wuchereria bancrofti from four districts (Amravati, Nagpur, Chandrapur and Wardha) of Vidarbha, a region in the eastern part of Maharashtra state of India and considered a hot spot of fi lariasis infections. The RAPD profi les were generated for 21 populations using nine random RAPD primers. The RAPD-PCR based distance matrix shows maximum genetic distance of 0.425 between the parasites from Nagpur and Amravati region and minimum genetic distance of 0.210 between the parasites of Wardha and Nagpur. The tree inferred by Neighbour-Joining (NJ) method shows four distinct clusters. With the single exception of isolates from Amravati, all other clusters show the intermingling of isolates with other districts. Further, the representation of isolates from Chandrapur in three out of four clusters revealed to be a founder and indicates towards the entry of the fi larial worm into the Maharashtra state through southern route.

Mitochondrial Dna Part B, May 12, 2016

The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and... more The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

Current Science, 2005

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Journal of Dairy Science, Sep 1, 2008

Annals of Human Genetics, Jul 28, 2004

Genetic relationships among caste-groups are not uniform across the geographical regions of India... more Genetic relationships among caste-groups are not uniform across the geographical regions of India. Many anthropologists have speculated on the tribal origin of some caste groups in Maharashtra and other states of India. To test this hypothesis, we used neutral mtDNA markers to study genetic relatedness among tribal and caste groups from Maharashtra. Descriptive statistics such as nucleotide diversity, gene diversity and average mismatches were found to be of the same magnitude. Phylogenetic network analysis exhibited a star-like expansion that may date back to the peopling of Eurasia, ∼ 50,000 year ago. The reconstruction of mtDNA haplogroups showed that both the caste and tribal populations share similar branches of the tree. Also, the coalescence age estimation of caste and tribal populations suggests the persistence of maternal lineages with their root in early late Pleistocene. Our mtDNA analyses show some preliminary and significant evidence for the origin of prehistoric tribal and hierarchical caste societies of Maharashtra.

Molecular Biology and Evolution, Sep 21, 2009

Animal domestication was a major step forward in human prehistory, contributing to the emergence ... more Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P , 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

Zenodo (CERN European Organization for Nuclear Research), Feb 5, 2023

In the current study, the phylodynamics and phylogenomics of Omicron variants are being examined ... more In the current study, the phylodynamics and phylogenomics of Omicron variants are being examined to provide insight into their evolution. We analyzed 564 genomes deposited to the GISAID database from various states of India. A Pangolin COVID-19 Lineage Assigner tool was used to assign lineages to all retrieved genomes. Maximum likelihood (MLE) tree construction and Reduced Median Joining (RM) network were performed. For phylodynamic analysis, the basic reproduction number (R0) was estimated. A Maximum likelihood tree (MLE) confirms the separation of genomes into two distinct clades, BA. 1. and BA. 2. A very high reproduction number (R0) of 2.445 was estimated for the lineage BA.2. Telangana has the highest R0 value in the country, indicating a high prevalence of the BA.2 lineage. The construction of the Reduced Median (RM) network reveals an evolution of some autochthonous haplogroups and haplotypes, which further supports the rapid evolution of Omicron as opposed to its previous variants. Phylogenomic analyses using maximum likelihood (ML) and RM also reveal the likelihood of the emergence of sub-sublineages and novel haplogroups respectively. Due to the recombinant nature and high transmissibility of the Omicron virus, we suggest continuous and more widespread genome sequencing in all states of India to track the evolution of SARS-CoV-2.

Approaches in Poultry, Dairy & Veterinary Sciences, 2018

Italian Journal of Animal Science, 2010

A screening of casein gene variability was carried out by Polymerase Chain Reaction-Single Strand... more A screening of casein gene variability was carried out by Polymerase Chain Reaction-Single Strand Conformation Polymorphism in 8 goat breeds from Sudan (Nubian goat), Turkey (Angora Goat Lalahan Tiftic, Angora Goat Yerkoy, Hair goat) and India (Jammu, Maharashtra, Rajasthan, South Goat). A total of 16 different alleles or groups of alleles were found, showing conspicuous differences among breeds. The allele frequencies were submitted to cluster analysis in order to highlight differences between breeds, also including data from Red Sokoto, West African Dwarf Nigeria, West African Dwarf Cameroon, and Borno Goat. The tree obtained from the cluster analysis showed two main lineages. The West African goat clustered together, the Indian and Turkish breeds were in the other group. Nubian goat was found in an intermediate position.

Helminthologia, 2017

Summary “Filariasis free India” is National Health Policy’s vision. Currently, India has undertak... more Summary “Filariasis free India” is National Health Policy’s vision. Currently, India has undertaken Mass Drug Administration drive (MDA) to eliminate the filariasis infection. Taking this into account, the emergence of new Wuchereria bancrofti resistant strains against the current choice of drugs cannot be ruled out. In this study, we report the genetic diversity of Wuchereria bancrofti from four districts (Amravati, Nagpur, Chandrapur and Wardha) of Vidarbha, a region in the eastern part of Maharashtra state of India and considered a hot spot of filariasis infections. The RAPD profiles were generated for 21 populations using nine random RAPD primers. The RAPD-PCR based distance matrix shows maximum genetic distance of 0.425 between the parasites from Nagpur and Amravati region and minimum genetic distance of 0.210 between the parasites of Wardha and Nagpur. The tree inferred by Neighbour-Joining (NJ) method shows four distinct clusters. With the single exception of isolates from Am...

Veterinary Microbiology, 2010

Background: Canine distemper virus (CDV) infects a variety of carnivores, including wild and dome... more Background: Canine distemper virus (CDV) infects a variety of carnivores, including wild and domestic Canidae. In this study, we sequenced and phylogenetic analyses of the hemagglutinin (H) genes from eight canine distemper virus (CDV) isolates obtained from seven raccoon dogs (Nyctereutes procyonoides) and a giant panda (Ailuropoda melanoleuca) in China. Results: Phylogenetic analysis of the partial hemagglutinin gene sequences showed close clustering for geographic lineages, clearly distinct from vaccine strains and other wild-type foreign CDV strains, all the CDV strains were characterized as Asia-1 genotype and were highly similar to each other (91.5-99.8% nt and 94.4-99.8% aa). The giant panda and raccoon dogs all were 549Y on the HA protein in this study, irrespective of the host species. Conclusions: These findings enhance our knowledge of the genetic characteristics of Chinese CDV isolates, and may facilitate the development of effective strategies for monitoring and controlling CDV for wild canids and non-cainds in China.

This is the first study on omicron genomes from India to focus on phylodynamics and phylogenomics... more This is the first study on omicron genomes from India to focus on phylodynamics and phylogenomics trait to provide an insight into the evolution of omicron variants. We analyzed 564 genomes deposited to GISAID database from various states of India. Pangolin COVID-19 Lineage Assigner tool was used to determine lineage assignment of all retrieved genomes. A Maximum likelihood (MLE) tree construction further confirms the separation of genomes into two distinct clades, BA. 1. and BA. 2. A very high reproduction number (R0) of 2.445 was estimated for the lineage BA.2. The highest R0 value in Telangana confirms the prevalence of lineage BA.2 in the state. Construction of the Reduced Median (RM) network shows evolution of some autochthonous haplogroups and haplotypes, which further supports the rapid evolution of omicron as compared to its previous variants. Phylogenomic analyses using maximum likelihood (ML) and RM show the potential for the emergence of sub-sublineages and novel haplogro...

Bos gaurus gaurus commonly called as gaur is a wild bovid species inhabiting S... more Bos gaurus gaurus commonly called as gaur is a wild bovid species inhabiting South and Southeast Asia and attained vulnerable status in India. In this study, we typed 62 extant free-ranging wild gaur individuals for mitochondrial partial displacement loop (D-loop) and cytochrome b gene (Cyt b) from the Melghat Tiger Reserve (MTR). Two historical DNA samples originating from museums and two Tectona grandis bark fibers samples browsed by wild gaur were also used as a source of environmental DNA. Both D-loop and Cyt b loci show the occurrence of a single haplotype in the contemporary wild gaur population. While D-loop fragment sequencing of two historical museum samples reveals two unique haplotypes, virtually absent in the present wild gaur population of MTR. Amplifications of the similar haplotypes in gaur DNA samples obtained through chewed T. grandis bark fibers have proved the efficacy of eDNA. Bayesian Skyline Plot (BSP) analysis using extant and historical D-loop sequences illustrate population decline starting from upper Mesolithic. Also, the BSP graph indicates accelerated effective population size decline (Ne), a time period coinciding with the different phases of the ∼5000 years old Indus civilization. The plot shows an overall declining trend in the wild gaur population, a probable outcome of ever-shrinking habitat in the central Indian landscape caused by prehistoric, medieval and colonial hunting practices.

Journal of the Bombay Natural History Society (JBNHS), 2020

Mammalian Biology, 2021

The Indian bison, commonly called gaur (Bos gaurus gaurus), is native to South and Southeast Asia... more The Indian bison, commonly called gaur (Bos gaurus gaurus), is native to South and Southeast Asia. In all its distribution ranges, the conservation status of the gaur lies between “vulnerable” and “endangered”. In this study, we genotyped 70 free-ranging wild gaurs from the Melghat Tiger Reserve (MTR), one of the first nine tiger reserves created in 1972 for tiger conservation in India. Fourteen microsatellite loci were genotyped in DNA extracted from the dung samples. An observed average heterozygosity of 0.726, evidence of gene flow was observed in the wild gaur population sampled from 11 locations in MTR. The effective population size (Ne) was 52.7. Approximate Bayesian computation analysis revealed population decline in the wild gaur population with the rise of mature Indus civilization ~ 2880 years ago. The population decline intensified during the reign of the medieval Monarch, extending further with the arrival of the British ~ 250 years ago. Our analyses detect population recovery in the free-ranging gaur population of MTR around 66 years ago, a time period coinciding with the independence of India followed by the implementation of the Indian wildlife protection act in the year 1972. The genetic data were discussed in the background of anthropology, archaeology and history of the Indian subcontinent.

Future Virology, 2020

Background: This is the first phylodynamic study attempted on SARS-CoV-2 genomes from India to in... more Background: This is the first phylodynamic study attempted on SARS-CoV-2 genomes from India to infer the current state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution using phylogenetic network and growth trends. Materials & Methods: Out of 286 retrieved whole genomes from India, 138 haplotypes were used to build a phylogenetic network. The birth–death serial model (BDSIR) package of BEAST2 was used to calculate the reproduction number of SARS-CoV-2. Population dynamics were investigated using the stamp date method as implemented in BEAST2 and BEAST 1.10.4. Results: A median-joining network revealed two ancestral clusters. A high basic reproduction number of SARS-CoV-2 was found. An exponential rise in the effective population size of Indian isolates was detected. Conclusion: The phylogenetic network reveals dual ancestry and possibility of community transmission of SARS-CoV-2 in India.