uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Guschanski, Katerina, Dr.ORCID iD iconorcid.org/0000-0002-8493-5457
Alternative names
Publications (10 of 22) Show all publications
Porter, A., Eckardt, W., Vecellio, V., Guschanski, K., Niehoff, P. P., Ngobobo-As-Ibungu, U., . . . Caillaud, D. (2019). Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.). PeerJ, 7, Article ID e6655.
Open this publication in new window or tab >>Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.)
Show others...
2019 (English)In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6655Article in journal (Refereed) Published
Abstract [en]

Humans were once considered unique in having a concept of death but a growing number of observations of animal responses to dying and dead conspecifics suggests otherwise. Complex arrays of behaviors have been described ranging from corpse removal and burial among social insects to quiet attendance and caregiving among elephants and primates. Less frequently described, however, are behavioral responses of individuals from different age/sex classes or social position toward the death of conspecifics. We describe behavioral responses of mountain gorillas (Gorilla beringei beringei) to the deaths of a dominant silverback and a dominant adult female from the same social group in Volcanoes National Park in Rwanda and the responses of Grauer's gorillas (Gorilla b. graueri) to the corpse of an extra-group silverback in Kahuzi-Biega National Park, Democratic Republic of Congo. In gorillas, interactions between groups or with a lone silverback often result in avoidance or aggression. We predicted that: (i) more individuals should interact with the corpses of same-group members than with the corpse of the extra-group silverback; (ii) adult females with infants should avoid the corpse of the extra-group silverback; and (iii) in the mountain gorilla cases, individuals that shared close social relationships with the dead individual should spend more time with the corpse than other individuals in the group. We used a combination of detailed qualitative reports, photos, and videos to describe all occurrences of affiliative/investigative and agonistic behaviors observed at the corpses. We observed similar responses toward the corpses of group and extra-group individuals. Animals in all three cases showed a variety of affiliative/investigative and agonistic behaviors directed to the corpses. Animals of all age/sex classes interacted with the corpses in affiliative/investigative ways but there was a notable absence of all adult females at the corpse of the extra-group silverback. In all three cases, we observed only silverbacks and blackbacks being agonistic around and/or toward the corpses. In the mountain gorilla cases, the individuals who spent the most time with the corpses were animals who shared close social relationships with the deceased. We emphasize the similarity in the behavioral responses around the corpses of group and extra-group individuals, and suggest that the behavioral responses were influenced in part by close social relationships between the deceased and certain group members and by a general curiosity about death. We further discuss the implications close interactions with corpses have for disease transmission within and between gorilla social groups.

Place, publisher, year, edition, pages
PEERJ INC, 2019
Keywords
Grauer's gorilla, Mountain gorilla, Thanatology, Kahuzi-Biega National Park, Volcanoes National Park, Behavior, Responses to death, Death
National Category
Other Biological Topics
Identifiers
urn:nbn:se:uu:diva-382391 (URN)10.7717/peerj.6655 (DOI)000462981800007 ()30972250 (PubMedID)
Available from: 2019-04-25 Created: 2019-04-25 Last updated: 2019-04-25Bibliographically approved
Robbins, M. M., Akantorana, M., Arinaitwe, J., Kabano, P., Kayijamahe, C., Gray, M., . . . Robbins, A. M. (2019). Dispersal and reproductive careers of male mountain gorillas in Bwindi Impenetrable National Park, Uganda. Primates, 60(2), 133-142
Open this publication in new window or tab >>Dispersal and reproductive careers of male mountain gorillas in Bwindi Impenetrable National Park, Uganda
Show others...
2019 (English)In: Primates, ISSN 0032-8332, E-ISSN 1610-7365, Vol. 60, no 2, p. 133-142Article in journal (Refereed) Published
Abstract [en]

Dispersal is a key event in the life of an animal and it influences individual reproductive success. Male mountain gorillas exhibit both philopatry and dispersal, resulting in a mixed one-male and multimale social organization. However, little is known about the relationship between male dispersal or philopatry and reproductive careers in Bwindi mountain gorillas. Here we analyze data spanning from 1993 to 2017 on social groups in Bwindi Impenetrable National Park, Uganda to examine the proportion of males that disperse, age of dispersal, pathways to attaining alpha status, fate of dispersing males and philopatric males, and male tenure length as well as make comparisons of these variables to the Virunga mountain gorilla population. We report previously undocumented cases of dispersal by immature males and old males and we also observed the only known case of a fully mature male immigrating into a breeding group. We used genetic tracking of known individuals to estimate that a minimum of 25% of males that disperse to become solitary males eventually form new groups. No differences were found between the Bwindi and Virunga population in the age of male dispersal, the proportion of males that disperse, the age of alpha male acquisition, and dominance tenure length. The lack of differences may be due to small sample sizes or because the observed ecological variability does not lead to life history differences between the populations. Males in both populations follow variable strategies to attain alpha status leading to the variable one-male and multimale social organization, including dispersal to become solitary and eventually form a group, via group fissioning, usurping another alpha male, or inheriting the alpha position when a previous group leader dies.

Keywords
Dispersal, Philopatry, Solitary male, Dominance transitions, Alpha status
National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-381834 (URN)10.1007/s10329-019-00718-z (DOI)000462209600006 ()30847670 (PubMedID)
Funder
Max Planck Society
Available from: 2019-04-16 Created: 2019-04-16 Last updated: 2019-04-16Bibliographically approved
van der Valk, T., Díez-Del-Molino, D., Marques-Bonet, T., Guschanski, K. & Dalén, L. (2019). Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas. Current Biology, 29(1), 165-170.e6, Article ID S0960-9822(18)31554-9.
Open this publication in new window or tab >>Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas
Show others...
2019 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. 165-170.e6, article id S0960-9822(18)31554-9Article in journal (Refereed) Published
Abstract [en]

Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.

Keywords
conservation genomics, critically endangered, genetic load, genome erosion, inbreeding, museum collections
National Category
Other Biological Topics Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-374204 (URN)10.1016/j.cub.2018.11.055 (DOI)30595519 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Research Council Formas, 2016-00835; 2015-676
Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-12-09Bibliographically approved
Hooper, R., Brealey, J. C., van der Valk, T., Alberdi, A., Durban, J. W., Fearnbach, H., . . . Guschanski, K. (2019). Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. Molecular Ecology, 28(2), 484-502
Open this publication in new window or tab >>Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Show others...
2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 2, p. 484-502Article in journal (Refereed) Published
Abstract [en]

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
Orcinus orca, Cetacea, contamination, metagenomics, microbiota
National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-374203 (URN)10.1111/mec.14860 (DOI)000459345000024 ()30187987 (PubMedID)
Funder
EU, European Research Council, ERCStG‐336536EU, Horizon 2020, 663830Swedish Research Council Formas, 2016-00835
Note

These authors contributed equally to this work: Rebecca Hooper, Jaelle C. Brealey, Katerina Guschanski, Andrew D. Foote

Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-08-01Bibliographically approved
Baas, P., van der Valk, T., Vigilant, L., Ngobobo, U., Binyinyi, E., Nishuli, R., . . . Guschanski, K. (2018). Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas. American Journal of Physical Anthropology, 165(3), 565-575
Open this publication in new window or tab >>Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas
Show others...
2018 (English)In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 165, no 3, p. 565-575Article in journal (Refereed) Published
Abstract [en]

Objectives: The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range.

Materials and Methods: We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population.

Results: In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments.

Discussion: Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.

National Category
Other Biological Topics
Identifiers
urn:nbn:se:uu:diva-348947 (URN)10.1002/ajpa.23393 (DOI)000425728300012 ()29313894 (PubMedID)
Available from: 2018-04-19 Created: 2018-04-19 Last updated: 2019-06-04Bibliographically approved
van der Valk, T., Sandoval-Castellanos, E., Caillaud, D., Ngobobo, U., Binyinyi, E., Nishuli, R., . . . Guschanski, K. (2018). Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas. Scientific Reports, 8, Article ID 6551.
Open this publication in new window or tab >>Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
Show others...
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 6551Article in journal (Refereed) Published
Abstract [en]

Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.

National Category
Biochemistry and Molecular Biology Genetics
Identifiers
urn:nbn:se:uu:diva-354951 (URN)10.1038/s41598-018-24497-7 (DOI)000430795000050 ()29695730 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationSwedish Research Council Formas, 2015-676
Available from: 2018-06-25 Created: 2018-06-25 Last updated: 2019-06-04Bibliographically approved
Malukiewicz, J., Guschanski, K., Grativol, A. D., Oliveira, M. A., Ruiz-Miranda, C. R. & Stone, A. C. (2017). Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchus and C-penicillata). American Journal of Primatology, 79(2), Article ID UNSP e22587.
Open this publication in new window or tab >>Application of PE-RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchus and C-penicillata)
Show others...
2017 (English)In: American Journal of Primatology, ISSN 0275-2565, E-ISSN 1098-2345, Vol. 79, no 2, article id UNSP e22587Article in journal (Refereed) Published
Abstract [en]

Callithrix jacchus and C. penicillata are among the smallest anthropoid primates, are highly specialized tree gougers, and largely occupy Brazil's most extreme, semi-arid biomes. However, the underlying genomic factors that underpin the evolution of these species and their unique traits are under-investigated. Additionally, exotic populations of these two species are widely established throughout Brazil and hybridize with threatened native congers. Thus, both genomic and conservation factors call for a better understanding of C. jacchus and C. penicillata evolution. Here, we applied PE-RADseq to characterize genomic variation in these two species, using six C. jacchus and seven C. penicillata individuals. We identified an average of 7,463 and 5,180 SNPs/individual in C. penicillata and C. jacchus, respectively, and also found 1,395 variable sites that were represented in both species. C. penicillata showed overall higher levels of genetic diversity than C. jacchus at the variable sites present in both species. Additionally, among these variable sites, 106 showed relative interspecific divergence levels that were significantly higher than the genome-wide average. We further compared relative and absolute divergence for C. penicillata and C. jacchus between RAD loci associated with the 106 significantly diverged variable sites and all other RAD loci present in both species. The former RAD loci set showed significantly elevated relative and absolute divergence measures in comparison to the latter set. This convergence suggests that C. jacchus and C. penicillata may have diverged under a scenario of gene flow under secondary contact. Here, we demonstrate that RADseq is an efficient method to simultaneously discover and genotype a large number of markers and validate the utility of RADseq for examining Callithrix evolution.

Place, publisher, year, edition, pages
WILEY, 2017
Keywords
Callithrix, divergence, diversity, genomics, RADseq, speciation
National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-320694 (URN)10.1002/ajp.22587 (DOI)000394659000007 ()
Available from: 2017-04-24 Created: 2017-04-24 Last updated: 2018-04-20
Malukiewicz, J., Hepp, C. M., Guschanski, K. & Stone, A. C. (2017). Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes. American Journal of Physical Anthropology, 162(1), 157-169
Open this publication in new window or tab >>Phylogeny of the jacchus group of Callithrix marmosets based on complete mitochondrial genomes
2017 (English)In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no 1, p. 157-169Article in journal (Refereed) Published
Abstract [en]

ObjectivesTwo subgroups make up the marmoset genus Callithrix. The "aurita" group is composed of two species, whereas evolutionary relationships among the four species of the "jacchus" group remain unclear. To uncover these relationships, we first sequenced mitochondrial genomes for C. kuhlii and C. penicillata to complement data available for congeners. We then constructed a phylogenetic tree based on mtDNA heavy chain protein coding genes from several primates to untangle species relationships and estimate divergence times of the jacchus group. Materials and MethodsMtDNA genomes of C. kuhlii and C. penicillata were Sanger sequenced. These Callithrix mitogenomes were combined with other publically available primate mtDNA genomes. Phylogenies were produced using maximum likelihood and Bayesian inference. Finally, divergence times within the jacchus group of marmosets were estimated with Bayesian inference. ResultsIn our phylogenetic tree, C. geoffroyi was the sister to all other jacchus group species, followed by C. kuhlii, while C. jacchus and C. penicillata diverged most recently. Bayesian inference showed that C. jacchus and C. penicillata diverged approximately 0.70 MYA and that the jacchus group radiated approximately 1.30 MYA. DiscussionCallithrix nuclear and mtDNA phylogenies frequently result in polytomies and paraphyly. Here, we present a well-supported phylogenetic tree based on mitochondrial genome sequences, which facilitates the understanding of the divergence of the jacchus marmosets. Our results demonstrate how mitochondrial genomes can enrich Callithrix phylogenetic studies by alleviating some of the difficulties faced by previous mtDNA studies and allow formulation of hypotheses to test further under larger genomic-scale analyses.

Place, publisher, year, edition, pages
WILEY-BLACKWELL, 2017
Keywords
phylogenetics, divergence, Callitrichidae, New World primates
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-318607 (URN)10.1002/ajpa.23105 (DOI)000393780600010 ()27762445 (PubMedID)
Available from: 2017-03-31 Created: 2017-03-31 Last updated: 2018-04-20
Guschanski, K., Warnefors, M. & Kaessmann, H. (2017). The evolution of duplicate gene expression in mammalian organs. Genome Research, 27(9), 1461-1474
Open this publication in new window or tab >>The evolution of duplicate gene expression in mammalian organs
2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 9, p. 1461-1474Article in journal (Refereed) Published
Abstract [en]

Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis-and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.

National Category
Biochemistry and Molecular Biology Agricultural Biotechnology Microbiology Genetics and Breeding in Agricultural Sciences
Identifiers
urn:nbn:se:uu:diva-334918 (URN)10.1101/gr.215566.116 (DOI)000408790600001 ()
Funder
EU, European Research Council, 242597
Available from: 2017-11-29 Created: 2017-11-29 Last updated: 2017-11-29Bibliographically approved
van der Valk, T., Durazo, F. L., Dalen, L. & Guschanski, K. (2017). Whole mitochondrial genome capture from faecal samples and museum-preserved specimens. Molecular Ecology Resources, 17(6), e111-e121
Open this publication in new window or tab >>Whole mitochondrial genome capture from faecal samples and museum-preserved specimens
2017 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e111-e121Article in journal (Refereed) Published
Abstract [en]

Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.

Keywords
great apes, mtDNA, natural history collections, noninvasive samples, target enrichment
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-342910 (URN)10.1111/1755-0998.12699 (DOI)000415921900010 ()28675688 (PubMedID)
Funder
Swedish Research Council Formas, 2015-676
Available from: 2018-03-02 Created: 2018-03-02 Last updated: 2019-06-04
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-8493-5457

Search in DiVA

Show all publications