Alfred Roca

Alfred Roca
University of Illinois, Urbana-Champaign | UIUC · Department of Animal Sciences

PhD (Email me for pdf or other requests; I'm not often on this site)
(Email me for pdf or other requests; I'm not often on this site)

About

224
Publications
40,187
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4,189
Citations
Citations since 2016
80 Research Items
2072 Citations
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20162017201820192020202120220100200300400

Publications

Publications (224)
Article
Full-text available
Chronic wasting disease (CWD) is a prion disease of North American cervids. The transmission of CWD to endangered cervid species is of concern for captive breeding programs. Trans-species transmission could occur via direct contact with infected wild deer, or via prion contaminated fomites. Variation in the prion protein gene, PRNP , is associated...
Preprint
Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, and/or dangerous species. Integrating genomic techniques that use non-invasive biological samples with advances in computational approaches can benefit and inform wildlife conservation and management. Here we present a molecular pipeline that uses non-invasi...
Article
Full-text available
Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recre...
Article
Full-text available
Epizootic hemorrhagic disease (EHD) and bluetongue (BT) are vector-borne viral diseases that affect wild and domestic ruminants. Clinical signs of EHD and BT are similar; thus, the syndrome is referred to as hemorrhagic disease (HD). Syndromic surveillance and virus detection in North America reveal a northern expansion of HD. High mortalities at n...
Preprint
Full-text available
Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program NUMT PARSER, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are...
Article
Full-text available
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy caused by prions that has spread across cervid species in North America since the 1960s and has recently been detected in Eurasian cervids. The Association of Zoos and Aquariums (AZA) considers CWD to be of major concern for cervids in AZA-accredited facilities because of th...
Article
Full-text available
In northern Illinois, chronic wasting disease (CWD) was first identified in free-ranging white-tailed deer (Odocoileus virginianus; hereafter referred to as "deer") in 2002. To reduce CWD transmission rates in Illinois, wildlife biologists have conducted locally focussed culling of deer since 2003 in areas where CWD has been detected. We used retro...
Article
Full-text available
Objective The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon si...
Conference Paper
Full-text available
Chronic wasting disease (CWD), a transmissible spongiform encephalopathy, affects captive and free-ranging species of the family Cervidae (moose, deer, and elk). CWD is endemic in North America and has been detected in 26 states in the United States and three Canadian provinces. Disease surveillance is essential to understand the emergence, distrib...
Article
Full-text available
Bluetongue (BT) and epizootic hemorrhagic disease (EHD) cases have increased worldwide, causing significant economic loss to ruminant livestock production and detrimental effects to susceptible wildlife populations. In recent decades, hemorrhagic disease cases have been reported over expanding geographic areas in the United States. Effective BT and...
Preprint
Full-text available
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy caused by prions that has spread across cervid species in North America since the 1960s and recently spread to cervids in Eurasia. The Association of Zoos and Aquariums (AZA) considers CWD to be of major concern for cervids in AZA-accredited facilities because of the indirec...
Article
Full-text available
Repeated retroviral infections of vertebrate germlines have made endogenous retroviruses ubiquitous features of mammalian genomes. However, millions of years of evolution obscure many of the immediate repercussions of retroviral endogenisation on host health. Here we examine retroviral endogenisation during its earliest stages in the koala (Phascol...
Article
DNA has been retrieved from mammoth specimens that are more than one million years old. Comparing the genomes of these animals and their descendants provides insights into the changes that occurred as one species evolved into another. DNA sequences from three ancient mammoth specimens.
Article
The oldest known shipwreck in southern Africa was found in Namibia in 2008. Forty tons of cargo, including gold and silver coins, helped identify the ship as the BomJesus, a Portuguese nau (trading vessel) lost in 1533 while headed to India. The cargo included >100 elephant tusks which we examined using paleogenomic and stable isotope analyses. Nuc...
Article
Full-text available
Chronic wasting disease (CWD) is caused by prions, infectious proteinaceous particles, PrPCWD. We sequenced the PRNP gene of 2,899 white-tailed deer (WTD) from Illinois and southern Wisconsin, finding 38 haplotypes. Haplotypes A, B, D, E, G and 9 others encoded Q95G96S100N103A123Q226, designated ‘PrP variant A.’ Haplotype C and 4 other haplotypes e...
Preprint
Spatial analysis of chronic wasting disease in free-ranging white-tailed deer (Odocoileus virginianus) in Illinois, 2008-2019 RH: Space-time cluster analysis of CWD in Illinois Abstract Understanding the geographic distribution and clustering of chronic wasting disease (CWD) among free-ranging white-tailed deer (Odocoileus virginianus) populations...
Article
Full-text available
Understanding the geographic distribution and clustering of chronic wasting disease (CWD) among free-ranging white-tailed deer (Odocoileus virginianus) populations can inform disease management practices. We used a retrospective analysis of surveillance data to evaluate CWD's spatial and temporal dynamics within 16 CWD-infected northern Illinois co...
Article
The woolly rhinoceros was a charismatic inhabitant of the frigid steppes of Pleistocene Eurasia. Now, the genome of an 18,500-year-old woolly rhino has been sequenced. It points to a thriving population less than 5000 years before the species disappeared.
Article
Chronic wasting disease (CWD) is a fatal, highly transmissible spongiform encephalopathy caused by an infectious prion protein. CWD is spreading across North American cervids. Studies of the prion protein gene (PRNP) in white-tailed deer (WTD; Odocoileus virginianus) have identified non-synonymous substitutions associated with reduced CWD frequency...
Article
Full-text available
Sex identification of ancient animal biological remains can benefit our understanding of historical population structure, demography and social behavior. Traditional methods for sex identification (e.g. osteological and morphometric comparisons) may be ineffective when animal remains are not well preserved, when sex distinguishing characteristics h...
Article
Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins...
Article
During the last two decades, our understanding of the genetics of African elephant populations has greatly increased. Strong evidence, both morphological and genetic, supports recognition of two African elephant species: the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis). Among elephantids, phylogeographic patterns for...
Article
Full-text available
Endogenous retroviruses (ERVs) are proviral sequences that result from host germ-line invasion by exogenous retroviruses. The majority of ERVs are degraded. Using the koala retrovirus (KoRV) as a model system, we demonstrate that recombination with an ancient koala retroelement disables KoRV, and that recombination occurs frequently and early in th...
Article
Full-text available
Managing and controlling the spread of diseases in wild animal populations is challenging, especially for social and mobile species. Effective management benefits from information about disease susceptibility, allowing limited resources to be focused on areas or populations with a higher risk of infection. Chronic wasting disease (CWD), a transmiss...
Article
The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samp...
Article
Full-text available
Solenodons are insectivores living in Hispaniola and Cuba that form an isolated branch in the tree of placental mammals highly divergent from other eulipothyplan insectivores The history, unique biology and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data, but a whole genome assembly for soleno...
Article
Full-text available
Significance Elephantids were once among the most widespread megafaunal families. However, only three species of this family exist today. To reconstruct their evolutionary history, we generated 14 genomes from living and extinct elephantids and from the American mastodon. While previous studies examined only simple bifurcating relationships, we fou...
Article
Full-text available
African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in...
Article
The mammalian order Eulipotyphla includes four extant families of insectivorans: Solenodontidae (solenodons); Talpidae (moles); Soricidae (shrews); and Erinaceidae (hedgehogs). Of these, Solenodontidae includes only two extant species, which are endemic to the largest islands of the Greater Antilles: Cuba and Hispaniola. Most molecular studies sugg...
Article
Full-text available
Seven fish vertebrae were chosen for analysis from the 49-KEN-147 archaeological site in the Kenai Peninsula, Alaska. Mitochondrial DNA analysis of the ancient fish bones revealed that they were from sockeye and coho salmon. Here, we report the ancient mitochondrial genomes for three sockeye salmon and one coho salmon fish bone.
Article
Full-text available
Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrov...
Article
Full-text available
The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cycloti...
Preprint
Full-text available
Solenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly f...
Data
This spreadsheet contains summary statistics of all sequence data generated in this study, the sequences of PCR primers used for reconstructing mtDNA sequences of extant elephants, as well as amino acid racemization data on opercula of Bithynia tentaculata from Amersfoort.DOI: http://dx.doi.org/10.7554/eLife.25413.005
Article
Full-text available
The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants ( Elephas maximus ), and many paleontologists place Palaeoloxodon within Elephas . Here, we report the recovery of full mitochondrial genomes from four...
Article
Background: Innate immune responses induced by in vitro stimulation of primary mammary epithelial cells (MEC) using Gram-negative lipopolysaccharide (LPS) and Gram-positive lipoteichoic acid (LTA) bacterial cell wall components are well- characterized in bovine species. The objective of the current study was to characterize the downstream regulat...
Article
Full-text available
The Toll-like receptor (TLR) signaling pathway constitutes an essential component of the innate immune system. Highly conserved proteins, indicative of their critical roles in host survival, characterize this pathway. Selective constraints could vary depending on the gene’s position within the pathway as TLR signaling is a sequential process and th...
Article
Toll-like receptor 2 (TLR2) plays an important role in recognition by the innate immune system of Gram-positive bacteria. As Gram-positive bacteria cause mastitis, we examined variations in the region of the TLR2 gene that codes for the extracellular domain. Samples of forty goats from a single dairy herd were collected, half with low SCC (≤200,000...
Article
Full-text available
The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges and Stony Rises by translocating individuals from a population on French Island descended from a small number of founders. To e...
Data
Table S1. Samples used in this study. Table S2. Characterization of microsatellite loci genotyped in Namibian elephants. Table S3. Haplotypes identified in Namibian elephants using 4258 bp mitochondrial DNA sequences. Table S4. Haplotypes identified in Namibian elephants using 316 bp mitochondrial DNA sequences. Figure S1. Spatial autocorrelati...
Article
Full-text available
Locally isolated populations in marginal habitats may be genetically distinctive and of heightened conservation concern. Elephants inhabiting the Namib Desert have been reported to show distinctive behavioral and phenotypic adaptations in that severely arid environment. The genetic distinctiveness of Namibian desert elephants relative to other Afri...
Article
Full-text available
Background African elephants comprise two species, the savanna elephant (Loxodonta africana) and the forest elephant (L. cyclotis), which are distinct morphologically and genetically. Forest elephants are seriously threatened by poaching for meat and ivory, and by habitat destruction. However, microsatellite markers have thus far been developed onl...
Article
Full-text available
Importance: Gibbon ape leukemia virus (GALV) and the koala retrovirus (KoRV) are very closely related, yet their hosts are neither closely related nor overlap geographically. Direct cross-species infection between koalas and gibbons is unlikely. Therefore, GALV and KoRV may have arisen via a cross-species transfer from an intermediate host that ov...
Article
Full-text available
Solenodons are insectivores found only in Hispaniola and Cuba, with a Mesozoic divergence date versus extant mainland mammals. Solenodons are the oldest lineage of living eutherian mammal for which a mitogenome sequence has not been reported. We determined complete mitogenome sequences for six Hispaniolan solenodons (Solenodon paradoxus) using next...
Article
Full-text available
Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas de...
Data
Primers used in our experiments for PEC, SPEX and to generate bait for hybridization capture
Data
KoRV5′ integration sites shared among at least two koalas
Data
Matched 5-3 integration site from different koalas The sequences shown are the concatenation of matched 5′ and 3′ integration sites from different koala individuals.
Data
Novel scripts used in study Novel scripts developed for the study are provided for review.
Data
The proportion of KoRV integration sites that are shared among koalas may be increasing over time Plotted results of a Generalised Mixed effect Model analysis against the shared integration sites by year.
Data
Indexing primers for Illumina library construction
Data
Information on all koala samples compared in this study
Data
Length distribution of raw sequence reads R plot of sequence length distributions from PEC (red), SPEX (blue) and hybridization capture (HC) (green) reads.