Biology subjects

Senn, H.

Publications and source records attributed to Senn, H..

7 recordsLinked to original sources

bioRxiv2024

Selection for later flowering time in an orchid through frost damage and pollinator activity

Flowering time is a key trait for plant reproductive success ensuring both overlap with pollinator activity and favorable conditions for fruit development. To quantify selection on flowering time, we individually marked 1250 plants of the Small Spider Orchid, Ophrys araneola RchB., in six populations in Northern Switzerland and surveyed them during three years. We recorded the date of first flowering, frost damage, and fruiting success of individual plants. In addition, we analyzed historical records of the orchid and its only verified pollinator, the solitary bee Andrena combinata in Northern Switzerland, to estimate potential desynchronization due to climate change. We documented strong selection for later flowering driven by frost damage, with all populations showing significant selection for later flowering in at least one year. Selection for later flowering driven by pollination (fruit set) could only be analyzed in one population due to the overall low fruit set, where it was significant in one year. The historical data from between 1970 and 2019 indicated low synchronization between orchid flowering and bee occurrence, with mean flowering three weeks earlier than the mean peak of bee occurrence, corroborating selection for later flowering through fruit set. The data also showed a significant advance of flowering time and bee-occurrence in the last decades, but to a similar degree in orchids and bees, hence without an indication of increasing desynchronization through climate change. Our study shows that selection for later flowering is mostly caused by frost damage, but also by the little synchronized flowering and pollinator activity, which is however unlikely to be a consequence of climate change in this orchid.

evolutionary biology↗

bioRxiv2023

To unscramble an egg: admixed captive breeding populations can be rescued using local ancestry information

This paper asks the question: can genomic information recover a species that is already on the pathway to extinction due to genetic swamping from a related and more numerous population? We show that whole genome sequencing can be used to identify and remove hybrid segments of DNA, when used as part of the breeding policy in a captive breeding program. The proposed policy uses a generalised measure of kinship or heterozygosity accounting for local ancestry, that is, whether a specific genetic location was inherited from from the target of conservation. We then show that optimising these measures would minimise undesired ancestry whilst also controlling undesired kinship or heterozygosity respectively, in a simulated breeding population. The process is applied to real data representing the hybridized Scottish wildcat breeding population, with the result that it should be possible to breed out the domestic cat ancestry. The ability to reverse introgression is a powerful new tool brought about from both sequencing and computational advances in ancestry estimation. Since it works best when applied early in the process, important decisions need to be made about which genetically distinct populations should benefit from it and which should be left to reform into a single population.

genetics↗

bioRxiv2022

Conservation management strategy impacts inbreeding and genetic load in scimitar-horned oryx

In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of inbreeding and mutation load. We address this using whole genome sequence data of scimitar-horned oryx (Oryx dammah), an iconic antelope that has been subject to contrasting management strategies since it was declared extinct in the wild. We show that unmanaged populations are enriched for long runs of homozygosity (ROH) and have significantly higher inbreeding coefficients than managed populations. Additionally, despite the total number of deleterious alleles being similar across management strategies, the burden of homozygous deleterious genotypes was consistently higher in unmanaged groups. These findings emphasise the risks associated with deleterious mutations through multiple generations of inbreeding. As wildlife management strategies continue to diversify, our study reinforces the importance of maintaining genome-wide variation in vulnerable populations and has direct implications for one of the largest reintroduction attempts in the world. Significance statementConservation genetic management is becoming increasingly important for safeguarding and restoring wildlife populations. Understanding how the intensity of intervention influences genomic components of fitness is therefore essential for supporting species viability. We investigate the impact of contrasting management strategies on the genomic landscape of inbreeding and mutation load in captive populations of scimitar-horned oryx. We reveal how several decades of management have prevented the formation of long runs of homozygosity and masked the expression of deleterious mutations. Our findings highlight the dynamics between inbreeding, mutation load and population size and have direct implications for future management of threatened species.

evolutionary biology↗

bioRxiv2020

Locus-specific introgression in young hybrid swarms: drift dominates selection

Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These anthropogenic hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44997 SNPs to identify loci introgressing at excessive rates when compared to the genome wide expectation in an anthropogenic hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centers that were significantly different from the genome wide expectation, and 17.6% had excessive rates of introgression. Based on simulations, we believe that many of these markers have diverged from average due to drift, rather than because of selection. Future work could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are indeed responding to selection in anthropogenic hybrid zones.

evolutionary biology↗

bioRxiv2019

Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management planning. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

genomics↗

bioRxiv2019

Simulating isolated populations to identify emerging genetic structure in the absence of selection

Conservation efforts are often informed by measures of genetic structure within or between isolated populations. We have established a simulation approach to investigate how isolated or captive populations can display misleading (i.e recently acquired) genetic structure as a result of genetic drift. We utilized a combination of softwares to generate isolated population genetic datasets that allow interrogation of emerging genetic structure under a range of conditions. We have developed a new statistic, S, to describe the extent of differentiation due to genetic drift between two isolated populations within the clustering software, STRUCTURE. O_LIA novel method to infer the effects of genetic drift on structure among isolated populations C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/853895v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@19eabc7org.highwire.dtl.DTLVardef@1fc4cforg.highwire.dtl.DTLVardef@1b1f947org.highwire.dtl.DTLVardef@164c916_HPS_FORMAT_FIGEXP M_FIG C_FIG SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@1cdff90org.highwire.dtl.DTLVardef@1455d67org.highwire.dtl.DTLVardef@f74715org.highwire.dtl.DTLVardef@5bbc66org.highwire.dtl.DTLVardef@adfae2_HPS_FORMAT_FIGEXP M_TBL C_TBL

genetics↗

bioRxiv2018

Phylogenomics and species delimitation of mobulid rays reveals cryptic diversity and a new species of manta ray

Practical biodiversity conservation relies on delineation of biologically meaningful units, particularly with respect to global conventions and regulatory frameworks. Traditional approaches have typically relied on morphological observation, resulting in artificially broad delineations and non-optimal species units for conservation. More recently, species delimitation methods have been revolutionised with High-Throughput Sequencing approaches, allowing study of diversity within species radiations using genome-wide data. The highly mobile elasmobranchs, manta and devil rays (Mobula spp.), are threatened globally by targeted and bycatch fishing pressures resulting in recent protection under several global conventions. However, a lack of global data, morphological similarities, a succession of recent taxonomic changes and ineffectual traceability measures combine to impede development and implementation of a coherent and enforceable conservation strategy. Here, we generate genome-wide Single Nucleotide Polymorphism (SNP) data from among the most globally and taxonomically representative set of mobulid tissues. The resulting phylogeny and delimitation of species units represents the most comprehensive assessment of mobulid diversity with molecular data to date. We find a mismatch between current species classifications, and optimal species units for effective conservation. Specifically, we find robust evidence for an undescribed species of manta ray in the Gulf of Mexico and show that species recently synonymised are reproductively isolated. Further resolution is achieved at the population level, where cryptic diversity is detected in geographically distinct populations, and indicates potential for future traceability work determining regional location of catch. We estimate the optimal species tree and uncover substantial incomplete lineage sorting, where standing variation in extinct ancestral populations is identified as a driver of phylogenetic uncertainty, with further conservation implications. Our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

genomics↗