Útdauði tegunda og blinda okkar á hægar breytingar

Arnar Pálsson, 11/03/2019

Útdauði dýra er raunverulegt vandamál og hann getur haft alvarlegar afleiðingar.

Ástæður útdauða eru margvíslegar, ofveiðar, eyðing búsvæða, landnýting, mengun frá t.d. landbúnaði og iðnaði, og vitanlega loftslagsbreytingar.

Í fyrri viku bárust tíðindi af því að fyrsta spendýrið hafi dáið út augljóslega af völdum loftslagsbreytinga.

Tegund sem kallaðist Bramble Cay melomys, var mús sem bjó á lítilli Ástralskri eyju. Hún lifði á litlu rifi milli Ástralíu og Papúa nýju gíneu.

Hækkandi sjávarstaða vegna loftslagbreytinga eyddi búsvæðum á eyjunni. Vitað var um afdrif hennar, vegna þess að hún hafði verið rannsökuð og bjó á lítilli eyju (og vegna þess að hún var sæt mús). Fyrir hverja eina slíka tegund sem við missum, er hætt við að við missum tugi, hundruði, þúsundir annara, ekki jafn vel þekktra eða minna heillandi, vegna loftslagsbreytinga.

Endurfundur skjaldbökunnar

Á svipuðum tíma bárust fréttir af því að skjaldbaka sem talin var útdauð fannst aftur. Skjaldbakan Chelonoidis phantasticus (Kelenædis fantastíkus með íslenskri latínu), býr á Fernandina eyjunni í Galápagoseyjaklasanum. Síðast sást til tegundarinnar fyrir 110 árum, og talið var að hún væri útdauð í kjölfar eldgos. En náttúrufræðingar höfðu fundið margvíslegar vísbendingar um tilvist skjaldböku á eyjunni, m.a. grunsamlegan saur. Með samstilltu stórátaki fannst ein skjaldbaka tegundarinnar. Ljóst er að þó eitt eintak hafi fundist og tegundin ekki formlega útdauð, eru ekki margir einstaklingar eftir.

Blessunarlega eru ennþá óspillt svæði á jörðinni, m.a. á Galapagos eyjum, með stóra þjóðgarða þar sem dýr og aðrar lífverur hafa athvarf. Þau athvörf eru samt of fá, lítil og fer fækkandi.

Hrun skordýra

Nokkrar nýlegar rannsóknir hafa afhjúpað hnignun stofna skordýra. Rannsóknir á skordýrum eru mun erfiðari en á stærri dýrum og gögnin sem fyrir liggja gloppóttari. Samt er augljóst að stofnar skordýra hafa látið á sjá, eins og þekkist e.t.v. best á ástandi býflugnastofna í Evrópu og norður Ameríku. Fréttir um skordýrahrunið voru kannski aðeins of dramatískar, en þær vörpuðu a.m.k. ljósi á vanræktan risa. Skordýr eru ákaflega mikilvæg, í vistkerfum og fyrir landbúnað, en veruleikinn er sá að við þekkjum þau fáranlega illa. Skordýr tilheyra liðdýrum, sem eru 80% af öllum þekktum tegundum dýra. Til að mynda hefur um 900.000 skordýrategundum verið lýst. Talið er að heildarfjöldi tegunda skordýra sé eitthvað í kringum 30 milljónir. Til samanburðar eru bara þekktar um 6500 spendyrategundir. Ólíklegt er að margar tegundir spendýra séu ófundnar.

Spurt var, getur erfðafræðin hjálpað okkur við að bjarga tegundum frá útdauða?

Þrennt hefur verið nefnt. Notkun erfðagreiningar til að skilja fjölbreytileika tegunda og stofna, notun erfðaupplýsinga til að stýra æxlunum tegunda í útrýmingarhættu (til að forðast innæxlun eins og í dýragörðum), eða nota sameindaerfðafræði og frumulíffræði til að klóna tegundir eða erfðabreyta núlifandi tegundum þannig að þær líkist útdauðum (t.d. fíl í loðfíl).

Fyrri nálganirnar tvær er auðveldar í framkvæmd og mikið notaðar, hin síðastnefnda er nær því að vera vísindaskáldskapur en veruleiki. Erfðatæknin mun ekki gagnast, þrátt fyrir yfirlýsingar sumra vísindamanna, til að bjarga tegundum frá í útrýmingarhættu. Sannarlega hafa nokkrar tegundir verið klónaðar, svo sem kindur, kýr og skyldar tegundir, en einnig nokkrar aðrar. Heilmikið og kostnaðarsamt þróunarstarf er nauðsynlegt til að geta klónað einstaklinga ákveðinnar tegundar. Þannig að fyrir hverja eina tegund sem við myndum vilja klóna og bjarga á þann hátt yrðum við að leggja í mikinn startkostnað. Og alls er óvíst að klónunin heppnis. Ekki hefur tekist að klóna öll dýr sem reynt hefur verið. Dollý var t.d. afurð tilraunar 277, með klónun á kindum.

Ekki er verjandi að eyða meiri fjármunum í að búa til einn klónaðan nashyrning - en þyrfti til að halda uppi og vernda mörgþúsund ferkílómetra þjóðgarði í langan tíma.

Mikilvægust eru orsakir þess að dýr og aðrar lífverur eru í útrýmingarhættu, þ.e. gjörðir mannana. Eyðing búsvæða vegur þar mest. Ef við klónum fullt af dýrum, en setjum þau síðan í agnarsmáa þjóðgarða eða læsum inni í dýragarði, þá höfum við ekki bjargað málunum. Við höfum í besta falli afvegaleitt sjálf okkur, og frestað því að takast á við rót vandans.

Okkar mesti galli - blinda á hægar breytingar

Við manneskjurnar erum léleg í því að mæla hægfara breytingar, á náttúrunni og öðrum hlutum. Enska hugtakið sem lýsir þessum galla okkar er Shifting baseline syndrome, sem þýða mætti sem viðmiðið hreyfist heilkennið.

Frægt dæmi er af sportveiðum. Hvert einasta ár er haldin sportveiði, og einhver fiskur er stærstur og fólki finnst hann risatór. En ef bornir eru saman stærstu fiskana yfir langt tímabil, t.d. frá 1910 til 2010, sést að þeir fara sífellt minnkandi. Fólk skynjar þetta ekki, því viðmiðið færist á hverju ári.

Það sama á við um allt mat okkar á ástandi náttúrunnar (og mögulega þáttum í samfélaginu). Í Evrópu og Ameríku hefur skordýrum fækkað vegna eyðingu búsvæða, ræktarland kemur í stað villtrar náttúru, og húsahverfi í stað akra, með þeim afleiðingum að yfir ár og áratugi fækkar skordýrunum.

Þetta birtist um alla jörð, í mörgum þáttum umhverfis, og orsakirnar eru yfirleitt mennskar. Breytingar eru á loftslagi, vegna þess að við keyrum bíla, kaupum drasl og fljúgum til útlanda oft á ári! Ef við viljum bjarga sjálfum okkur, börnum okkar og lífinu á jörðinni í leiðinni, þá þurfum við að breyta hegðan okkar. Og þrýsta á stjórnvöld að taka til aðgerða. Við eigum ekki að mótmæla þegar grænir skattar eru settir á eldsneyti til að auðveld orkuskipt, eða flugfargjöld hækka til að draga úr loftslagsbreytingum! Hugsa um langtímahag ekki skammtímavellíðan.

Pistillinn var ritaður eftir samræður við Morgunútvarpsfólk á Rás 2 þann 22. febrúar 2019 (Útrýmingarhætta) og birtist fyrst á apalsson.blog.is (Útdauði tegunda og blinda okkar á hægar breytingar)

Ítarefni:

. CNN 21. febrúar 2019. Australian mammal becomes first to go extinct due to climate change. https://edition.cnn.com/2019/02/20/australia/mammal-climate-change-extinction-intl-trnd/index.html

Giant tortoise believed extinct for 100 years found in Galápagos – The guardian 21. feb 2019.

Smithsonian, fjöldi skordýra.

Ed Young 19. feb. 2019. The atlantic Is the Insect Apocalypse Really Upon Us?

By Brooke Jarvis, 27. nóv. 2018 The Insect Apocalypse Is Here.

Bioethics of clinical innovation and unproven methods Copenhagen, 9 April 2019

Arnar Pálsson, 07/02/2019
Conference organized by the Nordic Committee on Bioethics in collaboration with Centre for Legal Studies in Welfare and Market at the University of Copenhagen , in Copenhagen, 9 April 2019, 09:00 - 17:00.

How are clinical innovations and unproven methods developed and introduced in western Nordic health-care systems?

What is the legal and regulatory environment concerning unproven methods in medicine?

What ethical principles should guide work on emerging treatments and experimentation in hospitals?

These are questions that will be adressed in the upcoming NCBio-conference in Copenhagen.

You can read more about the upcoming conference here.

Sign up here

I had the great privilege of organizing this event with my colleagues in the Nordic Committee on Bioethics, in collaboration with the Centre for Legal Studies in Welfare and Market at the University of Copenhagen.
Venue: Alf Ross auditorium (room 9A-3-01), Faculty of Law, University of Copenhagen, Karen Blixens Plads 16, 2300 Copenhagen S.Register here

Background: Clinical innovation involves development of new techinques, methods, treatments and diagnostics for detecting, alleviating and curing diseases. By nature novel clinical methods and treatments are unproven when first developed. Through the centuries, medicine has advanced by trials and errors of physicians and researchers experimenting with treatments and methods. The failure of certain methods are inseparable from success of others, because a priori it is hard to know what works and what not. The scientific method is the preferred approach to develop cures and treatments, but many current medical practices were not developed by strict scientific testing or trials. Healthcare professionals may try unproven methods, for instance as a last resort in attempt to safe a life. Such unproven methods for clinics and health care, occur at the intersect of basic research and standard health-care and raise number of bioethical issues. Those include the following issues. Do patients have sufficient and equal access to the experimental methods? Are patients protected from harm when unproven methods are tested? Who should make decisions about when to experiment with a treatment? How can society and the health care system best simultaneously promote clinical innovation and protect patients?

The conference is open to all interested, including medical doctors, clinical researchers, health committees in parliments, civil servants and hospital administrators.

Extensive genetic divergence between recently evolved sympatric Arctic charr morphs

Arnar Pálsson, 09/12/2018
Jóhannes Guđbrandsson, Kalina H. Kapralova, Sigríđur Rut Franzdóttir, Thóra Margrét Bergsveinsdóttir, Völundur Hafstađ, Zophonías O. Jónsson, Sigurđur S. Snorrason, Arnar Pálsson
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus that includes Arctic charr (Salvelinus alpinus), are renowned for both phenotypic diversity and polymorphism. Arctic charr invaded Icelandic streams during the glacial retreat (about 9,000 to 12,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL) and piscivorous (PI) charr differ in many regards, including size, form and life history traits. To investigate relatedness and genomic differentiation between morphs we extracted variants from developmental transcriptome data from three of those morphs, and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. No marker associated fully with morph, suggesting polygenic basis of traits separating them. Furthermore, gene ontology analyses suggest differences in collagen metabolism, odontogenesis and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
One of the preliminary data for the paper, several markers differentiate the four morphs.

Talk in Holar. Evolution of developmental variation, rapid divergence, plasticity and cryptic genetic variation

Arnar Pálsson, 29/11/2018

Couple of weeks back I was lucky enough to visit Holar University College, in the north of Iceland.

There we talked about ongoing work on the Arctic charr system, including genetic variation between sympatric morphs in Lake Þingvallavatn. And some new results on compensatory evolution of gene expression in Drosophila. The discussion was awesome, we got lots of great points and discussed potential new projects.

Then we spent the day processing fishes, phenotyping and taking clippings for DNA extraction. The photo is of charr embryo just past the eying stage.

(Icelandic) Er hægt að endurlífga útdauð dýr?

Arnar Pálsson, 17/08/2018

Sorry, this entry is only available in Icelandic.

(Icelandic) Er hægt að klóna apa?

Arnar Pálsson, 02/05/2018

Sorry, this entry is only available in Icelandic.

(Icelandic) Hversu mörg gen fáum við frá hverjum forföður?

Arnar Pálsson, 03/04/2018

Sorry, this entry is only available in Icelandic.

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Arnar Pálsson, 29/01/2018

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs.

Jóhannes Guðbrandsson, Sigríður Rut Franzdóttir, Bjarni Kristófer Kristjánsson, Ehsan Pashay Ahi, Valerie Helene Maier, Kalina H. Kapralova, Sigurður Sveinn Snorrason, Zophonías Oddur Jónsson, Arnar Pálsson

Published in PeerJ.

Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, leading to altered transcription of genes during development. Comparative developmental studies of closely related species or variable populations within species can help to elucidate the molecular mechanisms related to evolutionary divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10,000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during an important timeframe in early development, i.e., preceding the formation of key trophic structures. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by some form of RNA-degradation even though all samples passed quality control testing, an estimate of 3 0 -bias was the second most common explanatory variable. Importantly, morph, both as an independent variable and as interaction with developmental time, affected the expression of numerous transcripts. Transcripts with morph effect, separated the three morphs at the expression level, with the two benthic morphs being more similar. However, Gene Ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as AT-Rich Interaction Domain 4A (arid4a) and translin (tsn). The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.

Trancriptional co-option, transcriptional decay and the principles of regulatory evolution.

Arnar Pálsson, 19/01/2018

Trancriptional co-option, transcriptional decay and the principles of regulatory evolution.

Arnar Pálsson, Institute of biology, University of Iceland

Marcos A. Antezana, Institute of biology, University of Iceland

PALSSON A. & ANTEZANA M. 2017: Transcriptional co-option, transcriptional decay and the principles of regulatory evolution. Abstract. - In: W ERTH S. & O BERMAYER W. (editors). Lichen Genomics Workshop II. Institute of Plant Sciences, University of Graz, Austria. 2–5 November 2017. - Fritschiana (Graz) 85: 32–34. - ISSN 1024-0306.

Regulatory evolution is important for adaptive evolution and the emergence of novelties, in part because regulatory mutations tend to be less pleiotropic than changes in exons. The functional properties of regulatory elements, e.g. short, degenerate motifs, for multiple activators and repressors, dictate the evolution of regulatory DNA (Wray et al. 2003). Stabilizing selection on transcription may explain the evolutionary turnover of transcription factor binding sites (TFBS) in enhancers (Ludwig et al. 2000). Genes have been recruited for multiple functions during evolution, by a process called transcriptional co-option (TC) (True and Carroll 2002). In TC a mutation in a gene (here called focal gene), not previously expressed in a specific tissue or cell population during development, turns the gene on in that tissue and the responsible allele is fixed in the population. As new TFBS arise easily via mutation, it was proposed that any transcription factor can co-opt (influence the transcription of) any gene in the genome (Prud’homme et al 2007). Here we define the opposite scenario, evolution by transcriptional decay (TD). In TD, a mutation reducing strongly the transcription of a focal gene in tissue or developmentally specific fashion is fixed by positive selection. An example of TC would be the recruitment of various crystallins to the vertebrate lens (Piatigorsky 2006), and of TD the loss of Pitx1 expression in pelvic structures in stickleback (Shapiro et al. 2004). Here we will use transcriptional decay and co-option as a prism to explore the principles of regulatory evolution.

 

TC or TD can arise by mutations in either trans-factors (TF) or cis-elements (figure part A). While we focus on mutations in cis, changes in the structure or tissue specific concentration of a TF can affect expression of a focal gene. Such changes are expected to be pleiotropic, with changes in expression of targets of that TF (if changes are in TF level, then the effects will be more circumscribed). Changes at the level of cis-elements will be less pleiotropic. Disruption of TFBS can for example either increase or decrease expression of the focal gene, depending on whether the TF that binds that TFBS represses or activates transcription. The complementary argument applies for mutations that generate TFBS; TC can occur by gain of an activator binding site affecting the focal gene. And in TD a gain of a binding site for repressor near the focal gene.

Regulatory mutations can be pleiotropic. In one scenario, a mutation alters the expression of two or more genes in the same chromosome region. If the fitness increase of the increased expression of the focal gene outweighs the fitness reduction of its chromosome neighbors (figure, part B), then TC can occur. The stronger the selection, the more serious the regulatory side effects can be. After fixation of such a mutation, we anticipate rounds of refinement where the deleterious expression of nearby genes will be alleviated, e.g. by loss of activator sites or gain of repressor sites (figure, part B). Other regulatory changes (miRNA binding sites, RNA degradation etc) may play a role, and the complementary case when reduced expression of two or more genes is favored will adhere to the same principles. Similar mechanistic and evolutionary logic will also be apply if adaptive expression increase of a focal gene in a tissue, leads to increased expression of the gene in other tissues.

The central principles discussed here are, i) mutations disrupting TFBS can lead to beneficial changes in gene expression, ii) cis-regulatory mutations can be pleiotropic, affecting multiple genes and potentially tissues, iii) the likelihood of fixation of such pleiotropic mutations depends on the strength of selection, iv) natural selection is likely to alleviate such side-effects by favoring modifiers (e.g. in cis or trans). Finally, these principles are likely to apply more generally, to gain and decay of associations between trans-regulators and regulatory motifs in DNA, RNA and proteins. For instance regulatory systems like those controlling mRNA splicing, export, stability and localization, translation, protein maturation and modifications and other cellular regulatory cascades.

Acknowledgements. We thank Silke Werth and other organizers of the Lichen Genomics Workshop.

References

Wray G.A., Hahn M.W., Abouheif E., Balhoff J.P., Pizer M., Rockman M.V., Romano L.A. 2003: The evolution of transcriptional regulation in eukaryotes. Molecular Biology and Evolution.20: 1377-1419.

Ludwig M.Z., Bergman C., Patel N.H., Kreitman M. 2000: Evidence for stabilizing selection in a eukaryotic enhancer element. Nature. 403: 564-567.

True J.R., Carroll S.B. 2002 Gene co-option in physiological and morphological evolution. Annual Review Cellular and Developmental Biology. 18: 53-80.

Prud'homme B., Gompel N., Carroll S.B. 2007 Emerging principles of regulatory evolution. Proceedings of the National Academy of Sciences U S A. 15: 8605-8612.

Piatigorsky J. 2006 Evolutionary genetics: seeing the light: the role of inherited developmental cascades in the origins of vertebrate lenses and their crystallins. Heredity. 96: 275-277.

Shapiro M.D., Marks M.E., Peichel C.L., Blackman B.K., Nereng K.S., Jónsson B., Schluter D., Kingsley D.M. 2004 Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature. 428: 717-723

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Arnar Pálsson, 29/09/2017

Sent to a PeerJ near you.

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Jóhannes Guðbrandsson, Sigríður Rut Franzdóttir, Bjarni Kristófer Kristjánsson, Ehsan Pashay Ahi, Valerie Helene Maier, Sigurður Sveinn Snorrason, Zophonías Oddur Jónsson, Arnar Pálsson

Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, in both cases leading to altered transcription of genes during the structural and functional development of the body. Comparative developmental studies of closely related species or variable populations of the same species can help to elucidate the molecular mechanisms related to population divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ~10.000 year old Lake Thingvallavatn, which differ in numerous morphologicaland life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during a timeframe in early development.

Expectedly, developmental time was the predominant explanatory variable. As the data were affected by RNA-degradation, an estimate of 3’-bias was the second most common explanatory variable. Morph, both as a independent variable and as interaction with developmental time, affected the expression of numerous transcripts. The majority of transcripts with significant morph effects separated the limnetic and the benthic morphs. However, gene ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as Arid4a and Tsn. The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.