Nicolas Dussex

Nicolas Dussex
Swedish Museum of Natural History · Department of Bioinformatics and Genetics

PhD

About

45
Publications
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Introduction
My research interests lie in field of conservation genomics and evolution. I am particularly interested in the genome-wide effects of population declines and fragmentation on population persistence and in the consequences of translocations on population fitness.

Publications

Publications (45)
Article
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Inferring past demography is a central question in evolutionary and conservation biology. It is however sometimes challenging to infer the processes that shaped the current patterns of genetic variation in endangered species. Population substructuring can occur as a result of survival in several isolated refugia and subsequent recolonization proces...
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The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, w...
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Insect flight-loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci,...
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Species of conservation concern characterized by small and declining populations greatly benefit from proactive management approaches such as population translocations. Because they often show intra-specific genetic and phenotypic variation, which can result from drift or differential selective pressures between habitats, understanding the distribu...
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A species' dispersal capability is difficult to quantify but important for a general understanding of a species' ecology and for applied conservation and management efforts. One approach is to use the information from individual genotypes to estimate recent dispersal rates. These genetic methods differ in the way they use the genotype data, their a...
Article
The biogeographical origins of the endemic birds of New Zealand (Aotearoa) are of great interest, particularly Palaeogene lineages such as Callaeidae, a passerine family characterized by brightly coloured wattles behind the beak and, in some cases, extreme sexual dimorphism in bill size and shape. Ancestral representatives of Callaeidae are thought...
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Understanding how climatic and environmental changes, as well as human activities, induce changes in distribution and population size of avian species refines the ability to predict future impacts on threatened species. Using multilocus genetic data, we show that the population of a threatened New Zealand endemic open‐habitat specialist, the Black‐...
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Background Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling pop...
Chapter
This volume originates in a conference session that took place at the 2018 International Council of Archaeozoology conference in Ankara, Turkey, entitled "Humans and Cattle: Interdisciplinary Perspectives to an Ancient Relationship." The aim of the session was to bring together zooarchaeologists and their colleagues from various other research fiel...
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The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes seq...
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Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptil...
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Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of micro...
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Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identif...
Article
Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary ada...
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Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lago...
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A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.
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Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern geno...
Article
Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life-history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using a...
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Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impac...
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Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic...
Article
Island ecosystems can be severely affected by climate change as they provide limited opportunities for species to track their habitat. Studying the population dynamics of keystone species from these ecosystems can shed a light on climate – ecosystem interactions. Southern beeches are such keystone species in New Zealand with beech forests constitut...
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights i...
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Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across...
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Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44-49 ka BP, an...
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Aim To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black‐fronted tern (Chlidonias albostriatus), a specialist of the spatially and temporally dynamic environments of braided rivers. Location New Zealand. Methods We used a three‐pronged approach based on 17 microsatellites, two...
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Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the st...
Article
Climate shifts are key drivers of ecosystem change. Despite the critical importance of Antarctica and the Southern Ocean for global climate, the extent of climate-driven ecological change in this region remains controversial. In particular, the biological effects of changing sea ice conditions are poorly understood. We hypothesize that rapid postgl...
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Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wi...
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Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss...
Article
Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin...
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Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. He...
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Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal app...
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Taxonomy plays a central role in conservation programs of threatened New Zealand taxa. The role of taxonomy is especially relevant for highly vulnerable taxa, where the identification of distinct lineages is essential to define units of conservation and to appropriately allocate conservation resources. Taxonomy traditionally relied on phenotype,...
Article
While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil...
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Population size and the potential for maintenance of genetic diversity are critical information for the monitoring of species of conservation concern. However, direct estimates of population size are not always feasible, making indirect genetic approaches a valuable alternative. We estimated contemporary effective population size (N e) in the endan...
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h i g h l i g h t s • Conservation practitioners want to use genetics, but do not routinely do so. • This issue is most acute in control of disease and invasive species. • The main barriers to use of genetics in conservation are funding and expertise. • Practitioners want to work with geneticists, but are unsure how to reach them. • Researchers mus...
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Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that...
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Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations and loss of adaptive potential. Otariid pinnipeds have been exploited commercial...
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We describe the isolation and characterization of eight polymorphic microsatellite loci for the endemic New Zealand alpine parrot Kea (Nestor notabilis). The loci were initially tested for eight individuals collected across the range and then for a larger dataset of 410 individuals. The number of alleles per loci ranged from 2 to 11. These new micr...
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The richness of plant species in Swiss alpine-nival summits increased during the climate warming of the 20th century. Thirty-seven summits (2797-3418 m a.s.l.) with both old (∼1900-1920) and recent (∼2000) plant inventories were used to test whether biological species traits can explain the observed rates of summit colonisation. Species were classi...