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Items: 16

1.
Evol Lett. 2018 Aug 7;2(4):297-309. doi: 10.1002/evl3.74. eCollection 2018 Aug.

Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow.

Author information

1
Department of Animal and Plant Sciences University of Sheffield UK.
2
Current address: IST Austria Am Campus 1 3400 Klosterneuburg Austria.
3
Department of Marine Sciences University of Gothenburg 40530 Gothenburg Sweden.
4
Department of Physics University of Gothenburg 41296 Gothenburg Sweden.
5
Department of Marine Sciences - Tjärnö University of Gothenburg 45296 Strömstad Sweden.
6
CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo Oslo 0316 Norway.
7
Department of Chemistry and Molecular Biology University of Gothenburg 40530 Gothenburg Sweden.

Abstract

Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.

KEYWORDS:

clines; hybrid zones; inversions; local adaptation; molluscs; speciation

2.
J Chromatogr A. 2018 Aug 17;1563:62-70. doi: 10.1016/j.chroma.2018.05.052. Epub 2018 May 31.

Separation of tartronic and glyceric acids by simulated moving bed chromatography.

Author information

1
Laboratory of Catalytic Process, Chemical Engineering Department, Federal University of Pernambuco, 50670-901 Recife, Brazil; Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Department of Chemical Engineering, Faculty of Engineering of University of Porto, 4200-465 Porto, Portugal.
2
Laboratory of Catalytic Process, Chemical Engineering Department, Federal University of Pernambuco, 50670-901 Recife, Brazil.
3
Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Department of Chemical Engineering, Faculty of Engineering of University of Porto, 4200-465 Porto, Portugal. Electronic address: ruifaria@fe.up.pt.
4
Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Department of Chemical Engineering, Faculty of Engineering of University of Porto, 4200-465 Porto, Portugal.

Abstract

The SMB unit developed by the Laboratory of Separation and Reaction Engineering (FlexSMB-LSRE®) was used to perform tartronic acid (TTA) and glyceric acid (GCA) separation and to validate the mathematical model in order to determine the optimum operating parameters of an industrial unit. The purity of the raffinate and extract streams in the experiments performed were 80% and 100%, respectively. The TTA and GCA productivities were 79 and 115 kg per liter of adsorbent per day, respectively and only 0.50 cubic meters of desorbent were required per kilogram of products. Under the optimum operating conditions, which were determined through an extensive simulation study based on the mathematical model developed to predict the performance of a real SMB unit, it was possible to achieve a productivity of 86 kg of TTA and 176 kg of GCA per cubic meter of adsorbent per day (considering the typical commercial purity value of 97% for both compounds) with an eluent consumption of 0.30 cubic meters per kilogram of products.

KEYWORDS:

Biodiesel valorisation; Continuous chromatographic separation; Fine chemical industry; Glyceric acid; Simulated moving bed; Tartronic acid

PMID:
29908700
DOI:
10.1016/j.chroma.2018.05.052
[Indexed for MEDLINE]
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3.
Mol Biol Evol. 2018 May 1;35(5):1176-1189. doi: 10.1093/molbev/msy030.

Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons.

Author information

1
CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
2
Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
3
Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.

Abstract

Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons. The strongest signature overlapped the CASK gene, a gene implicated in the formation of neuromuscular junctions. However, no diagnostic alleles were found between racing pigeons and other breeds, and only a small proportion of highly differentiated variants were exclusively detected in racing pigeons. We can thus conclude that very few individual genetic changes, if any, are either strictly necessary or sufficient for superior athletics and navigation. Gene expression analysis between racing and nonracing breeds revealed modest differences in muscle (213) and brain (29). These transcripts, however, showed only slightly elevated levels of genetic differentiation between the two groups, suggesting that most differential expression is not causative but likely a consequence of alterations in regulatory networks. Our results show that the unique suite of traits that enable fast flight, long endurance, and accurate navigation in racing pigeons, do not result from few loci acting as master switches but likely from a polygenic architecture that leveraged standing genetic variation available at the onset of the breed formation.

4.
Mar Genomics. 2017 Apr;32:41-47. doi: 10.1016/j.margen.2016.10.006. Epub 2016 Nov 18.

Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis.

Author information

1
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal. Electronic address: joao.marques@cibio.up.pt.
2
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal. Electronic address: gsotelo.fdz@gmail.com.
3
University of Gothenburg, Department of Marine Sciences, Box 460, SE -405 30 Gothenburg, Sweden. Electronic address: tomas.larsson@marine.gu.se.
4
University of Gothenburg, Department of Marine Sciences, Tjärnö, SE -452 96 Strömstad, Sweden. Electronic address: kerstin.johannesson@marine.gu.se.
5
University of Gothenburg, Department of Marine Sciences, Tjärnö, SE -452 96 Strömstad, Sweden. Electronic address: marina.panova@marine.gu.se.
6
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; IBE, Institute of Evolutionary Biology (CSIC-UPF), Department of Experimental and Health Sciences, Pompeu Fabra University, Doctor Aiguader 88, 08003 Barcelona, Spain. Electronic address: rui.faria@upf.edu.

Abstract

The flat periwinkles, Littorina fabalis and L. obtusata, offer an interesting system for local adaptation and ecological speciation studies. In order to provide genomic resources for these species, we sequenced their mitogenomes together with that of the rough periwinkle L. saxatilis by means of next-generation sequencing technologies. The three mitogenomes present the typical repertoire of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. Although the latter could not be fully recovered in flat periwinkles using short-reads due to a highly repetitive fragment, in L. saxatilis this problem was overcome with additional long-reads and we were able to assemble the complete mitogenome. Both gene order and nucleotide composition are similar between the three species as well as compared to other Littorinimorpha. A large variance in divergence was observed across mitochondrial regions, with six- to ten-fold difference between the highest and the lowest divergence rates. Based on nucleotide changes on the whole molecule and assuming a molecular clock, L. fabalis and L. obtusata started to diverge around 0.8 Mya (0.4-1.1 Mya). The evolution of the mitochondrial protein-coding genes in the three Littorina species appears mainly influenced by purifying selection as revealed by phylogenetic tests based on dN/dS ratios that did not detect any evidence for positive selection, although some caution is required given the limited power of the dataset and the implemented approaches.

KEYWORDS:

Gastropoda; annotation; assembly; mtDNA divergence; selection

PMID:
27867038
DOI:
10.1016/j.margen.2016.10.006
[Indexed for MEDLINE]
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5.
Resuscitation. 2016 Aug;105:188-95. doi: 10.1016/j.resuscitation.2016.06.004. Epub 2016 Jun 16.

EuReCa ONE-27 Nations, ONE Europe, ONE Registry: A prospective one month analysis of out-of-hospital cardiac arrest outcomes in 27 countries in Europe.

Collaborators (310)

Kaufmann M36, Thaler M36, Maier M36, Prause G36, Trimmel H36, de Longueville D37, Preseau T37, Biarent D37, Melot C37, Mpotos N37, Monsieurs K37, Van de Voorde P37, Vanhove M37, Lievens P37, Faniel M37, Keleuva S38, Lazarevic M38, Ujevic RM38, Devcic M38, Bardak B38, Barisic F38, Anticevic SH38, Georgiou M39, Truhlář A40, Knor J40, Smržová E40, Sviták R40, Šín R40, Mokrejš P40, Lippert FK41, Hallikainen J42, Hoikka M42, Iirola T42, Jama T42, Jäntti H42, Jokisalo R42, Jousi M42, Kirves H42, Kuisma M42, Laine J42, Länkimäki S42, Loikas P42, Lund V42, Määttä T42, Nal H42, Niemelä H42, Portaankorva P42, Pylkkänen M42, Sainio M42, Setälä P42, Tervo J42, Väyrynen T42, Jama T42, Murgue D43, Champenois A43, Fournier M43, Meyran D43, Tabary R43, Avondo A43, Gelin G43, Simonnet B43, Joly M43, Megy-Michoux I43, Paringaux X43, Duffait Y43, Vial M43, Segard J43, Narcisse S43, Hamban D43, Hennache J43, Thiriez S43, Doukhan M43, Vanderstraeten C43, Morel JC43, Majour G43, Michenet C43, Tritsch L43, Dubesset M43, Peguet O43, Pinero D43, Guillaumee F43, Fuster P43, Ciacala JF43, Jardel B43, Letarnec JY43, Goes F43, Gosset P43, Vergne M43, Bar C43, Branche F43, Prineau S43, Lagadec S43, Cornaglia C43, Ursat C43, Bertrand P43, Agostinucci JM43, Nadiras P43, de Linares GG43, Jacob L43, Revaux F43, Pernot T43, Roudiak N43, Ricard-Hibon A43, Villain-Coquet L43, Beckers S44, Hanff T44, Strickmann B44, Wiegand N44, Wilke P44, Sues H44, Bogatzki S44, Baumeier W44, Pohl K44, Werner B44, Fischer H44, Zeng T44, Popp E44, Günther A44, Hochberg A44, Lechleuthner A44, Schewe JC44, Lemke H44, Wranze-Bielefeld E44, Bohn A44, Roessler M44, Naujoks F44, Sensen F44, Esser T44, Fischer M44, Messelken M44, Rose C44, Schlüter G44, Lotz W44, Corzilius M44, Muth CM44, Diepenseifen C44, Tauchmann B44, Birkholz T44, Flemming A44, Herrmann S44, Kreimeier U44, Kill C44, Marx F44, Schröder R44, Lenz W44, Botini G45, Grigorios B45, Giannakoudakis N45, Zervopoulos M45, Papangelis D45, Petropoulou-Papanastasiou S45, Liaskos T45, Papanikolaou S45, Karabinis A45, Zentay A46, Þorsteinsson H47, Gilsdóttir A47, Birgisson SA47, Guðmundsson FF47, Hreiðarsson H47, Árnason B47, Hermannsson H47, Björnsson G47, Friðriksson BÞ47, Baldursson G47, Höskuldsson Á47, Valgarðsdottir J47, Ásmundardóttir M47, Guðmundsson G47, Kristjánsson H47, Þórarinsson ER47, Guðlaugsson J47, Skarphéðinsson S47, National Ambulance Service Of The Health Service Executive Dublin Fire Brigade Dublin48, Peratoner A49, Santarelli A49, Sabetta C49, Gordini G49, Sesana G49, Giudici R49, Savastano S49, Pellis T49, Beissel J50, Uhrig J50, Manderscheid T50, Klop M50, Stammet P50, Koch M50, Welter P50, Schuman R50, Bruins W51, Amin H51, Braa N52, Bratland S52, Buanes EA52, Draegni T52, Johnsen KR52, Mathisen WT52, Oedegaarden T52, Oppedal M52, Reksten AS52, Roedsand ME52, Steen-Hansen JE52, Dyrda M53, Frejlich A53, Maciąg S53, Osadnik S53, Weryk I53, Mendonça E54, Freitas C54, Cruz P54, Caldeira C54, Barros J54, Vale L54, Brazão A54, Jardim N54, Rocha F54, Duarte R54, Fernandes N54, Ramos P54, Jardim M54, Reis M54, Ribeiro R54, Zenha S54, Fernandes J54, Francisco J54, Assis D54, Abreu F54, Freitas D54, Ribeiro L54, Azevedo P54, Calafatinho D54, Jardim R54, Pestana A54, Faria R54, Oprita B55, Grasu A55, Nedelea P55, Sovar S55, Agapi F55, Kličković A56, Lazić A56, Nikolić B56, Zivanovic B56, Martinović B56, Milenković D56, Damir H56, Koprivica J56, Jakšić KH56, Pajor M56, Milić S56, Vidović M56, Glamoclija RP56, Andjelic S56, Sladjana V56, Babić Z56, Fišer Z56, Androvic P57, Bajerovska L57, Chabron M57, Dobias V57, Havlikova E57, Horanova B57, Kratochvilova R57, Kubova D57, Murgas J57, Patras J57, Simak L57, Snarskij V57, Zaviaticova Z57, Zuffova M57, Roig FE58, Santos LS58, Sucunza AE58, Cordero Torres JA58, Muñoz GI58, Del Valle MM58, Rozalen IC58, Sánchez EM58, Berlanga MV58, Olalde KI58, Ruiz Azpiazu JI58, García-Ochoa MJ58, López-Navarro RZ58, Adsuar Quesada JM58, Cortés Ramas JA58, Mellado Vergel FJ58, López Messa JB58, Del Valle PF58, The Swedish Association Of Local Authorities And Regions59, Anselmi L60, Federazione Cantonale Ticinese Servizi Ambulanze60, Benvenuti BC60, Batey N61, Ambulance Y61, Booth S61, Bucher P61, Deakin CD61, Duckett J61, Ji C61, Loughlin N61, Lumley-Holmes J61, Lynde J61, Mersom F61, Ramsey C61, Robinson C61, Spaight R61, Dosanjh S61, Virdi G61, Whittington A61.

Author information

1
University Hospital Schleswig-Holstein, Dep. Anaesthesiology and Intensive Care Medicine, Kiel, Germany; University Hospital Schleswig-Holstein, Institute for Emergency Medicine, Kiel, Germany. Electronic address: jan-thorsten.graesner@uksh.de.
2
University Witten/Herdecke, Cologne, Germany.
3
Academic Medical Center, Amsterdam, The Netherlands.
4
National University of Ireland Galway, Ireland.
5
University Hospital of Cologne, Germany.
6
University of Borås, Sahlgrenska University Hospital, Sweden.
7
University Hospital Schleswig-Holstein, Dep. Anaesthesiology and Intensive Care Medicine, Kiel, Germany; University Hospital Schleswig-Holstein, Institute for Emergency Medicine, Kiel, Germany.
8
Norwegian National Advisory Unit on Prehospital Emergency Medicine (NAKOS), Oslo, Norway.
9
Empresa Pública de Emergencias Sanitarias, Almería, Spain.
10
University Hospital Schleswig-Holstein, Dep. Anaesthesiology and Intensive Care Medicine, Campus Lübeck, Germany.
11
University Hospital Innsbruck, Austria.
12
Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles, Belgium.
13
Medical Faculty Osijek, Josip Juraj Strossmayer University, Osijek, Croatia.
14
Nicosia General Hospital, Cyprus.
15
Emergency Medical Service of the Central Bohemian Region, Kladno, and J.E. Purkinje University, Masaryk Hospital Usti nad Labem, Czech Republic.
16
Emergency Medical Services Copenhagen, University of Copenhagen, Denmark.
17
Emergency Medical Services, Department of Emergency Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
18
University of Lille, France.
19
Konstantopouleio General Hospital, Athens, Greece.
20
Health Care Centers of Csongrad County Hódmezővásárhely - Makó, Hungary.
21
Akureyri Hospital/University of Akureyri, Iceland.
22
Ospedale Maggiore "Carlo Alberto Pizzardi" AUSL Bologna, Italy.
23
Health Service Executive Ballyshannon, Ireland.
24
Luxembourg Resuscitation Council, Luxembourg.
25
Maastricht University, The Netherlands.
26
Jagiellonian University, Kraków, Poland.
27
Serviço de Emergência Médica Regional - SEMER/EMIR, Portugal.
28
University of Medicine and Pharmacy Gr.T. Popa and University County Hospital Sf. Spiridon, Iaşi, Romania.
29
Municipal Institute for Emergency Medicine Novi Sad, Serbia.
30
P.J.Safarik University, Kosice, Slovakia.
31
University Medical Centre Maribor, Maribor, Slovenia.
32
Mälardalens University, Västerås, Sweden.
33
Fondazione Ticino Cuore, Breganzona, Switzerland.
34
University of Warwick and Heart of England NHS Foundation Trust, Coventry, United Kingdom.
35
University of Antwerp, Department of Medicine and Health Sciences, Antwerp, Belgium.
36
Austria.
37
Belgium.
38
Croatia.
39
Cyprus.
40
Czech Republic.
41
Denmark.
42
Finland.
43
France.
44
Germany.
45
Greece.
46
Hungary.
47
Iceland.
48
Ireland.
49
Italy.
50
Luxembourg.
51
The Netherlands.
52
Norway.
53
Poland.
54
Portugal.
55
Romania.
56
Serbia.
57
Slovakia.
58
Spain.
59
Sweden.
60
Switzerland.
61
United Kingdom.

Abstract

INTRODUCTION:

The aim of the EuReCa ONE study was to determine the incidence, process, and outcome for out of hospital cardiac arrest (OHCA) throughout Europe.

METHODS:

This was an international, prospective, multi-centre one-month study. Patients who suffered an OHCA during October 2014 who were attended and/or treated by an Emergency Medical Service (EMS) were eligible for inclusion in the study. Data were extracted from national, regional or local registries.

RESULTS:

Data on 10,682 confirmed OHCAs from 248 regions in 27 countries, covering an estimated population of 174 million. In 7146 (66%) cases, CPR was started by a bystander or by the EMS. The incidence of CPR attempts ranged from 19.0 to 104.0 per 100,000 population per year. 1735 had ROSC on arrival at hospital (25.2%), Overall, 662/6414 (10.3%) in all cases with CPR attempted survived for at least 30 days or to hospital discharge.

CONCLUSION:

The results of EuReCa ONE highlight that OHCA is still a major public health problem accounting for a substantial number of deaths in Europe. EuReCa ONE very clearly demonstrates marked differences in the processes for data collection and reported outcomes following OHCA all over Europe. Using these data and analyses, different countries, regions, systems, and concepts can benchmark themselves and may learn from each other to further improve survival following one of our major health care events.

KEYWORDS:

Cardiac arrest; Emergency medicine, Europe; Epidemiology; Resuscitation; Resuscitation registry

[Indexed for MEDLINE]
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6.
Mol Ecol. 2016 Apr;25(7):1420-2. doi: 10.1111/mec.13598.

Magadi tilapia ecological specialization: filling the early gap in the speciation continuum.

Author information

1
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
2
Department of Experimental and Health Sciences, IBE, Institute of Evolutionary Biology (CSIC-UPF), Pompeu Fabra University, Doctor Aiguader 88, 08003, Barcelona, Spain.

Abstract

Cichlid fish are well known for their high speciation rates, which are usually accompanied by spectacular and rapid diversification in eco-morphological and secondary sexual traits. This is best illustrated by the famous repeated explosive radiations in the African Great Lakes Tanganyika, Malawi and Victoria, each lake harbouring several hundreds of mostly endemic species. Correspondingly, cichlids diversified very rapidly in many other lakes across their range. Although the larger radiations, unparalleled in vertebrates, are certainly the most intriguing, they are also the most intricate and difficult to address because of their complex nature. This is where smaller, simpler systems may prove to be the most useful. In this issue of Molecular Ecology, Kavembe et al. (2016) report very recent genetic diversification accompanied by ecological specialization in cichlids of the small and ecologically extreme Lake Magadi, in Kenya. Combining geometric morphometrics, stable isotope analysis, population genomics using RADSeq data and coalescent-based modelling techniques, the authors characterize the eco-morphological differences between genetically distinct populations of Magadi tilapia (Alcolapia grahami), which are consistent with the different environmental conditions they experience, and infer their history of divergence. The simplicity of the focal system and the use of a multidisciplinary approach make this work particularly important for our understanding of the early stages of speciation, in both cichlids and other organisms.

KEYWORDS:

cichlids; diversification; ecological specialization; history of divergence; interdisciplinary; model-based inference; radiations

PMID:
27012820
DOI:
10.1111/mec.13598
[Indexed for MEDLINE]
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7.
Mitochondrial DNA A DNA Mapp Seq Anal. 2017 Jan;28(1):116-118. doi: 10.3109/19401736.2015.1111349. Epub 2015 Dec 28.

The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis.

Kolora SR1,2,3, Faria R4,5, Weigert A2,6, Schaffer S2, Grimm A7, Henle K7, Sahyoun AH3, Stadler PF3,8,9,10,11,12,13, Nowick K3,8,14, Bleidorn C1,2, Schlegel M1,2.

Author information

1
a German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Leipzig , Germany.
2
b Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig , Leipzig , Germany.
3
c Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig , Leipzig , Germany.
4
d CIBIO, Centro De Investigacßao Em Biodiversidade E Recursos Geneticos, InBio, Laboratorio Associado, Universidade Do Porto , Campus Agrário De Vairão , Vairão , Portugal.
5
e Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC) , PRBB, Barcelona , Catalonia , Spain.
6
f Max Planck Institute for Evolutionary Anthropology , Deutscher Platz 6 , Leipzig , Germany.
7
g Department of Conservation Biology , UFZ - Helmholtz Center for Environmental Research , Leipzig , Germany.
8
h Paul-Flechsig-Institute for Brain Research, University of Leipzig , Leipzig , Germany.
9
i Max-Planck-Institute for Mathematics in the Sciences , Leipzig , Germany.
10
j Fraunhofer Institut Für Zelltherapie Und Immunologie , Leipzig , Germany.
11
k Department of Theoretical Chemistry , University of Vienna , Wien , Austria.
12
l Center for non-Coding RNA In Technology and Health, University of Copenhagen , Frederiksberg , Denmark.
13
m Santa Fe Institute , Santa Fe , NM , USA , and.
14
n TFome Research Group, Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig , Leipzig , Germany.

Abstract

We sequenced the mitochondrial genome of the Western green lizard (Lacerta bilineata) using Illumina technology and additional Sanger sequencing. The assembled 17 086 bp mitogenome had a GC content of 40.32% and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (CR), with a gene order identical to the chordate consensus. In addition, we re-sequenced the mitogenome of the closely related Eastern green lizard L. viridis using the same techniques as for L. bilineata. The mitogenomes of L. bilineata and L. viridis showed a sequence identity of 94.4% and 99.9%, respectively, relative to the previously published L. viridis mitogenome. The phylogenetic reconstruction based on 17 Lacertinae mitogenomes using Anolis carolinensis as the outgroup supported L. bilineata and its sister species L. viridis as distinct lineages.

KEYWORDS:

Complete mitochondrial genome; Illumina sequencing; Lacerta bilineata; Lacerta viridis; Lacertinae; phylogeny

PMID:
26709540
DOI:
10.3109/19401736.2015.1111349
[Indexed for MEDLINE]
8.
J Chromatogr A. 2015 Nov 20;1421:82-102. doi: 10.1016/j.chroma.2015.08.045. Epub 2015 Aug 28.

Instrumental aspects of Simulated Moving Bed chromatography.

Author information

1
Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering, Faculty of Engineering of University of Porto, 4200-465 Porto, Portugal.
2
Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering, Faculty of Engineering of University of Porto, 4200-465 Porto, Portugal. Electronic address: arodrig@fe.up.pt.

Abstract

The Simulated Moving Bed (SMB) is one of the greatest illustrations of the potential of continuous multicolumn counter-current chromatographic processes. Although it was initially developed for the purification of petrochemicals, the advances that this technology has experienced during more than 50 years of existence were at the basis of its successful expansion into the food and pharmaceuticals industries. In this context, the present work provides an overview of the evolution of SMB focused on the most relevant instrumental aspects related with this technology. For that purpose, the details of the design and construction of this equipment will be reviewed, with special attention to the valves design. Due to its increasing interest, the technical requirements imposed by unconventional operating modes will be addressed together with the design adaptations that allow the operation of SMB units with compressible fluids and the implementation of Hybrid-SMB processes. Finally, as SMB technology has been unable to meet all the process specifications within the growing biopharmaceuticals industry, the development of alternative multicolumn counter-current units has intensified over the last few years. Hence, examples of the design and application of these new units will be provided.

KEYWORDS:

Chromatographic separation; Equipment design; Multicolumn counter-current chromatographic processes; Simulated Moving Bed

PMID:
26341597
DOI:
10.1016/j.chroma.2015.08.045
[Indexed for MEDLINE]
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9.
Mol Ecol. 2014 Apr;23(7):1653-5. doi: 10.1111/mec.12685.

Pool and conquer: new tricks for (c)old problems.

Author information

1
Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader 88, Barcelona, 08003, Catalonia, Spain; Centre de Regulació Genòmica (CRG), Barcelona, Spain; National Institute for Bioinformatics (INB), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

Abstract

The early period of genetics is closely associated with the study of chromosomal inversions. For almost a century, evolutionary biologists found evidence for the role of inversions in central processes such as adaptation and speciation. In spite of huge efforts, many questions remain about the evolutionary forces underlying the distribution and dynamics of inversions in natural populations. Fortunately, old problems can be solved with new tools. In this issue, Kapun et al. (2014) present a remarkable combination of resources and techniques, including publicly available data, karyotyping, statistical estimation of haplotypes, Pool-Seq data and experimental evolution, setting the ground for exciting developments in the field.

KEYWORDS:

Drosophila; Pool-Seq; clines; experimental evolution; inversion; natural selection

PMID:
24667009
DOI:
10.1111/mec.12685
[Indexed for MEDLINE]
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10.
Mol Ecol. 2014 Feb;23(3):513-21. doi: 10.1111/mec.12616.

Advances in Ecological Speciation: an integrative approach.

Author information

1
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio, Laboratório Associado, Universidade do Porto. Campus Agrário de Vairão, 4485-661, Vairão, Portugal; IBE, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra. PRBB, Av. Doctor Aiguader N88, 08003, Barcelona, Spain.

Abstract

The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunity to study the mechanisms involved in ecological speciation. Genome scans provide significant insights but have some important limitations; efforts are needed to integrate them with other approaches to make full use of the sequencing data deluge. An international conference 'Advances in Ecological Speciation' organized by the University of Porto (Portugal) aimed to review current progress in ecological speciation. Using some of the examples presented at the conference, we highlight the benefits of integrating ecological and genomic data and discuss different mechanisms of parallel evolution. Finally, future avenues of research are suggested to advance our knowledge concerning the role of natural selection in the establishment of reproductive isolation during ecological speciation.

KEYWORDS:

adaptive evolution; ecology; genome scan; natural selection; parallel evolution; reproductive isolation

PMID:
24354648
DOI:
10.1111/mec.12616
[Indexed for MEDLINE]
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11.
Trends Genet. 2013 Mar;29(3):130-9. doi: 10.1016/j.tig.2012.11.007. Epub 2012 Dec 17.

A prominent role of KRAB-ZNF transcription factors in mammalian speciation?

Author information

1
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. nowick@bioinf.uni-leipzig.de

Abstract

The mechanisms of speciation have been one of the most debated topics in evolutionary biology. Among all reproductive barriers, postzygotic reproductive isolation is perhaps the one that has attracted the most attention from geneticists. Despite remarkable advances in the identification of loci involved in Drosophila speciation, little is known about the genes, functions, and biochemical interactions of the molecules underlying hybrid sterility and inviability in mammals. Here, we discuss the main evolutionary and molecular features that make transcription factors (TFs), especially the family of zinc finger proteins with a Krüppel-associated box domain (KRAB-ZNF), strong candidates to play an important role in postzygotic reproductive isolation. Motivated by the recent identification of the gene encoding PR domain zinc finger protein 9 (Prdm9; a KRAB-ZNF gene) as the first hybrid sterility gene identified in mammals, we further propose integrative approaches to study KRAB-ZNF genes with the main goal of characterizing the molecular pathways and interactions involved in hybrid incompatibilities.

PMID:
23253430
DOI:
10.1016/j.tig.2012.11.007
[Indexed for MEDLINE]
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12.
BMC Evol Biol. 2012 Sep 30;12:194. doi: 10.1186/1471-2148-12-194.

Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA.

Author information

1
CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Campus Agrário de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal. ruifaria@cibio.up.pt

Abstract

BACKGROUND:

Comparative broad-scale phylogeographic studies of aquatic organisms provide insights on biotic responses to the paleohydrological dynamics associated with climatic oscillations. These insights can be used to formulate a framework for understanding the evolutionary history of a species or closely related taxa as well as aid in predictive modeling of further responses to climate change. Anadromous fishes constitute interesting models for understanding the relative importance of environmental versus biological factors in shaping intraspecific genetic substructure on the interface between marine and freshwater realms. European shads, Alosa alosa and A. fallax are anadromous species that have persisted through historical large-scale environmental perturbations and now additionally face an array of anthropogenic challenges. A comprehensive phylogeographic investigation of these species is needed to provide insights on both the historical processes that have shaped their extant genetic structure and diversity, and the prospects for their future management and conservation.

RESULTS:

Despite introgressive hybridization, A. alosa and A. fallax are genetically divergent, congruent with previous studies. Three similarly divergent mtDNA clades were recognized within both A. fallax and A. alosa, most likely originating during common periods of isolation during the Pleistocene among the studied oceanographic regions. Periods of basin isolation apparently extended to the Black Sea as additional Alosa clades occur there. The present day geographic distribution of genetic diversity within European Alosa sp. suggests the existence of a strong but permeable barrier between the Atlantic and Mediterranean seas, as shown for a number of other aquatic species. Overall mtDNA diversity is considerably lower for A. alosa compared to A. fallax, suggesting that the former species is more sensitive to climatic as well as anthropogenic changes. For A. fallax, migration from the Mediterranean to the Atlantic was detected but not in the opposite direction, with colonization of the North Atlantic probably occurring after last glacial maximum.

CONCLUSION:

The similar haplotype network topologies between the two species support a common intraspecific history of isolation. Despite these similarities, A. alosa and A. fallax have clearly responded differently to the hydrological dynamics of the Pleistocene, as reflected in their distinct demographic histories. As the species additionally occupy different ecological niches it should not be surprising that they differ in resilience to natural or human-mediated climatic changes. For A. fallax, it is further clear that its demographic response to large-scale hydrological events is not synchronized between the Atlantic and Mediterranean basins. These regional and species-specific differences should be incorporated into future predictive modeling of biological response to climate change as well as current management concepts.

PMID:
23020523
PMCID:
PMC3523006
DOI:
10.1186/1471-2148-12-194
[Indexed for MEDLINE]
Free PMC Article
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13.
Nature. 2011 Jan 27;469(7331):529-33. doi: 10.1038/nature09687.

Comparative and demographic analysis of orang-utan genomes.

Author information

1
The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA. dlocke@wustl.edu

Abstract

'Orang-utan' is derived from a Malay term meaning 'man of the forest' and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N(e)) expanded exponentially relative to the ancestral N(e) after the split, while Bornean N(e) declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

PMID:
21270892
PMCID:
PMC3060778
DOI:
10.1038/nature09687
[Indexed for MEDLINE]
Free PMC Article
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14.
BMC Genomics. 2011 Jan 24;12:55. doi: 10.1186/1471-2164-12-55.

Recent human evolution has shaped geographical differences in susceptibility to disease.

Author information

1
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.

Abstract

BACKGROUND:

Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies.

RESULTS:

We report three main findings. First, contrary to previous results, genes associated to complex diseases present lower degrees of genetic differentiation among human populations than average genome-wide levels. Second, also contrary to previous results, the differences in replicability of disease associated-loci between Europeans and East Asians are highly correlated with genetic differentiation between these populations. Finally, highly replicated genes present increased levels of high-frequency derived alleles in European and Asian populations when compared to African populations.

CONCLUSIONS:

Our findings highlight the heterogeneous nature of the genetic etiology of complex disease, confirm the importance of the recent evolutionary history of our species in current patterns of disease susceptibility and could cast doubts on the status as false positives of some associations that have failed to replicate across populations.

PMID:
21261943
PMCID:
PMC3039608
DOI:
10.1186/1471-2164-12-55
[Indexed for MEDLINE]
Free PMC Article
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15.
Trends Ecol Evol. 2010 Nov;25(11):660-9. doi: 10.1016/j.tree.2010.07.008. Epub 2010 Oct 1.

Chromosomal speciation revisited: rearranging theory with pieces of evidence.

Author information

1
Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. rui.faria@upf.edu

Abstract

The suggestion that chromosomal rearrangements play a role in speciation resulted from the observation that heterokaryotypes are often infertile. However, the first chromosomal speciation models were unsatisfactory and data available to test them was scarce. Recently, large amounts of data have become available and new theoretical models have been developed explaining how rearrangements facilitate speciation in the face of gene flow. Here, we re-examine theoretical predictions and revisit different sources of data. Although rearrangements are often associated with increased levels of divergence, unequivocal demonstration that their role in suppressing recombination results in speciation is often lacking. Finally, we question some previous predictions and suggest new empirical and theoretical approaches to understanding the relevance of rearrangements in the origin of species.

PMID:
20817305
DOI:
10.1016/j.tree.2010.07.008
[Indexed for MEDLINE]
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16.
J Hered. 2006 May-Jun;97(3):193-205. Epub 2006 Feb 17.

Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits.

Author information

1
CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal. aantunes@ncifcrf.gov

Abstract

The Atlantic Iberian brown trout is at the southwestern limit of its distribution. At this ecological edge, which was once a glacial refugia, anadromy becomes less common as increased water temperatures restricted populations closer to the headwaters. We examined 847 individuals from 20 populations from throughout this region and assessed spatial genetic structure using 11 protein and four microsatellite loci. The higher levels of heterozygosity and allelic diversity north of the southernmost limit of anadromy (SLA), as well as an isolation-by-distance model of population structure, likely influenced by the anadromous forms, suggest that more stable demographic conditions existed over time in this region. Populations south of the SLA were highly differentiated given the restricted size of the area (protein F(ST) = 0.16 in the north and 0.63 in the south of the SLA; microsatellite F(ST) = 0.18 in the north and 0.70 in the south of the SLA). The low levels of heterozygosity and the pattern of southward allele depletion in resident populations is indicative of fragmentation, caused by stressful ecological conditions that reduced the anadromy (restricting gene flow) and the effective population sizes (higher genetic drift), which, in combination, dramatically decreased within-population genetic variation and increased among-population genetic variation. The higher gene diversity north of the SLA does not reflect ancestry but rather the signature of a population size expansion, as evidence suggest the persistence of older populations (with several private alleles) south of the SLA. These data support a scenario that demonstrates how contemporary events (critical ecological conditions) can moderate historical influences, suggesting that careful interpretation of the evolutionary history of glacial refugia is necessary, especially where populations persisted for a long time but not always with optimal ecological conditions. These peripheral populations are of high conservation value and should be preserved to help conserve the future potential of the species.

PMID:
16489148
DOI:
10.1093/jhered/esj014
[Indexed for MEDLINE]
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