Biology subjects

Kerbis Peterhans, J. C.

Publications and source records attributed to Kerbis Peterhans, J. C..

5 recordsLinked to original sources

bioRxiv2026

Incipient speciation, rapid expansion and repeated introgressive hybridization in an African Giant Shrew (Crocidura olivieri)

The African giant shrew (Crocidura olivieri) is one of the most widespread native small mammals in sub-Saharan Africa, occupying habitats ranging from humid tropical forests to arid Savanna. Its broad distribution, ecological diversity, and unresolved evolutionary relationships suggest a history of rapid diversification, yet the roles of hybridization and demographic expansion remain poorly understood. We combined genome-wide ddRAD and mitochondrial data from populations sampled across sub-Saharan Africa to reconstruct the evolutionary history of African giant shrews. We reveal extensive mitonuclear discordance across the clade and show that it reflects a complex history of repeated introgressive hybridization rather than a single evolutionary event. Genomic analyses resolve three major evolutionary lineages and identify four introgression events, including extensive bidirectional genome-wide introgression between the ancestors of the C. olivieri and arid adapted species followed by later unidirectional introgression associated with range expansion. Within the C. olivieri group, we identify five geographically structured lineages connected by ongoing gene flow, representing different stages of incipient speciation. Demographic analyses further reveal repeated population expansion during the Late Pleistocene and Early Holocene, with lineage-specific timing consistent with climatic fluctuations and a possible contribution of increasing human association. Our results identify repeated range expansion and hybridization as major drivers of diversification in African giant shrews and establish this system as a powerful model for studying the genomic processes underlying early speciation.

evolutionary biology↗

bioRxiv2023

Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction

Extinct Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "Black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate extinct Cape lion genome characteristics, population dynamics and genetic distinctiveness prior to their extinction. We generated genomic data from two historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, but rather highlights how alternative knowledge-systems, e.g., Indigenous perspectives, could potentially further inform interpretations of species life histories.

evolutionary biology↗

bioRxiv2022

NUMT PARSER: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera

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 NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW to two other bioinformatic approaches that can be used to account for numt contamination. We found that NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. NO_SCPLOWUMTC_SCPLOW PO_SCPLOWARSERC_SCPLOW therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.

evolutionary biology↗

bioRxiv2019

Small terrestrial mammal distributions in Simien Mountains National Park, Ethiopia: A reassessment after 88 years

Little is known about the distribution and ecology of small mammals inhabiting Simien Mountains National Park despite the presence of mostly endemic species. Prior to this study, the most comprehensive dataset was collected in 1927. This provides a unique opportunity to assess the possible role of climate change over the last 88 years on the elevational distribution of mammals in the Ethiopian highlands. Between September and November 2015, three of us (EWC, WTS, YM) collected non-volant small mammals at four sites (2900, 3250, 3600, and 4000 m a.s.l.) along the western slope of the Simien Mountains using standardized sampling. Over a four-week period we recorded 13 species, comprising 11 rodents and two shrews, all endemic to the Ethiopian Plateau. We found greatest species richness at mid-elevations (3250 m), consistent with a general pattern found on many other mountains worldwide but less so in Africa. We discovered one potentially new species of shrew. No previously unrecorded rodent species were observed. Finally, we compared our species distribution results to the 1927 dataset and found upward elevational shifts in species ranges, suggesting the role and influence of climate change on the small mammal community. Simien Mountains National Park represents an exceptionally valuable core area of endemism and the best protected natural habitat in northern Ethiopia.

ecology↗

bioRxiv2018

Associations between Afrotropical bats, parasites, and microbial symbionts

Bats are among the most diverse animals on the planet and harbor numerous bacterial, viral, and eukaryotic symbionts. The interplay between bacterial community composition and parasitism in bats is not well understood and may have important implications for studies of similar systems. Here we present a comprehensive survey of dipteran and haemosporidian parasites, and characterize the gut, oral, and skin microbiota of Afrotropical bats. We identify significant correlations between bacterial community composition of the skin and dipteran ectoparasite prevalence across four major bat lineages, as well as links between the oral microbiome and malarial parasitism, suggesting a potential mechanism for host selection and vector-borne disease transmission in bats. In contrast to recent studies of host-microbe phylosymbiosis in mammals, we find no correlation between chiropteran phylogenetic distances and bacterial community dissimilarity across the three anatomical sites, suggesting that host environment is more important than shared ancestry in shaping the composition of bat-associated bacterial communities.\n\nSIGNIFICANCEAnimals rely on bacterial symbionts for numerous biological functions, such as digestion and immune system development. Increasing evidence suggests that host-associated microbes may play a role in mediating parasite burden. This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and parasite prevalence. This study provides a framework for future approaches to systems biology of host-symbiont interactions across broad taxonomic scales, emphasizing the interdependence between microbial symbionts and vertebrate health in the study of wild organisms and their natural history.

ecology↗