@article{KehlmaierBarlowHastingsetal.2017, author = {Kehlmaier, Christian and Barlow, Axel and Hastings, Alexander K. and Vamberger, Melita and Paijmans, Johanna L. A. and Steadman, David W. and Albury, Nancy A. and Franz, Richard and Hofreiter, Michael and Fritz, Uwe}, title = {Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum}, series = {Proceedings of the Royal Society of London : Series B, Biological sciences}, volume = {284}, journal = {Proceedings of the Royal Society of London : Series B, Biological sciences}, publisher = {The Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2016.2235}, pages = {8}, year = {2017}, abstract = {Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.}, language = {en} } @article{KupferMaxwellReinhardetal.2016, author = {Kupfer, Alexander and Maxwell, Erin and Reinhard, Sandy and Kuehnel, Susanne}, title = {The evolution of parental investment in caecilian amphibians: a comparative approach}, series = {Biological journal of the Linnean Society : a journal of evolution}, volume = {119}, journal = {Biological journal of the Linnean Society : a journal of evolution}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-4066}, doi = {10.1111/bij.12805}, pages = {4 -- 14}, year = {2016}, abstract = {Parental care is widespread among vertebrates and the observed patterns of parental care and investment are extremely diverse. Among amphibians, caecilians (Gymnophiona) exhibit considerable variation in reproductive modes, including both oviparity and viviparity, combined with highly unusual investment strategies (e.g. skin-feeding and intrauterine feeding). In the present study, current knowledge on the reproductive modes is integrated into an analysis of the evolutionary scenario of parental investment of caecilians. Phylogenetically basal caecilians possessing a biphasic life cycle that includes an aquatic larval stage invest in macrolecithal eggs directly corresponding to size at hatching. Some phylogenetically derived caecilians (i.e. the Teresomata) have a smaller clutch size and show a reduction to either medium-yolked (mesolecithal) or small-yolked (microlecithal) eggs. Via alternative pathways of parental investment, such as intrauterine feeding in viviparous taxa and maternal dermatotrophy in oviparous taxa, teresomatan caecilians increase both offspring size and quality. However, more data regarding reproductive biology are needed to obtain a fully resolved understanding of the evolution of reproduction in caecilian amphibians. (C) 2016 The Linnean Society of London}, language = {en} } @article{ValenteEtiennePhillimore2014, author = {Valente, Luis M. and Etienne, Rampal S. and Phillimore, Albert B.}, title = {The effects of island ontogeny on species diversity and phylogeny}, series = {Proceedings of the Royal Society of London : B, Biological sciences}, volume = {281}, journal = {Proceedings of the Royal Society of London : B, Biological sciences}, number = {1784}, publisher = {Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2013.3227}, pages = {9}, year = {2014}, abstract = {A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological time-scales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies.}, language = {en} } @article{FolkertsmaWestburyEccardetal.2018, author = {Folkertsma, Remco and Westbury, Michael V. and Eccard, Jana and Hofreiter, Michael}, title = {The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)}, series = {Mitochondrial DNA Part B}, volume = {3}, journal = {Mitochondrial DNA Part B}, number = {1}, issn = {2380-2359}, doi = {10.1080/23802359.2018.1457994}, pages = {446 -- 447}, year = {2018}, abstract = {The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.}, language = {en} } @misc{FolkertsmaWestburyEccardetal.2018, author = {Folkertsma, Remco and Westbury, Michael V. and Eccard, Jana and Hofreiter, Michael}, title = {The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {481}, issn = {1866-8372}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412994}, pages = {2}, year = {2018}, abstract = {The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.}, language = {en} } @article{ApriyantoTambunan2020, author = {Apriyanto, Ardha and Tambunan, Van Basten}, title = {The complete mitochondrial genome of oil palm pollinating weevil, Elaeidobius kamerunicus Faust}, series = {Mitochondrial DNA: Part B}, volume = {5}, journal = {Mitochondrial DNA: Part B}, number = {3}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {2380-2359}, doi = {10.1080/23802359.2020.1823899}, pages = {3450 -- 3452}, year = {2020}, abstract = {Elaeidobius kamerunicusis the most important insect pollinator in oil palm plantations. In this study, the mitochondrial genome (mitogenome) ofE. kamerunicus(17.729 bp), a member of the Curculionidae family, will be reported. The mitogenome consisted of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a putative control region (CR). Phylogenetic analysis based on 13 protein-coding genes (PCGs) using maximum Likelihood (ML) methods indicated thatE. kamerunicusbelongs to the Curculionidae family. This mitochondrial genome provides essential information for understanding genetic populations, phylogenetics, molecular evolution, and other biological applications in this species.}, language = {en} } @article{HorreoPelaezSuarezetal.2018, author = {Horreo, Jose L. and Pelaez, Maria L. and Suarez, Teresa and Breedveld, Merel Cathelijne and Heulin, Benoit and Surget-Groba, Yann and Oksanen, Tuula A. and Fitze, Patrick S.}, title = {Phylogeography, evolutionary history and effects of glaciations in a species (Zootoca vivipara) inhabiting multiple biogeographic regions}, series = {Journal of biogeography}, volume = {45}, journal = {Journal of biogeography}, number = {7}, publisher = {Wiley}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.13349}, pages = {1616 -- 1627}, year = {2018}, abstract = {Location Eurasia. Methods We generated the largest molecular dataset to date of Z. vivipara, ran phylogenetic analyses, reconstructed its evolutionary history, determined the location of glacial refuges and reconstructed ancestral biogeographic regions. Results The phylogenetic analyses revealed a complex evolutionary history, driven by expansions and contractions of the distribution due to glacials and interglacials, and the colonization of new biogeographic regions by all lineages of Z. vivipara. Many glacial refugia were detected, most were located close to the southern limit of the Last Glacial Maximum. Two subclades recolonized large areas covered by permafrost during the last glaciation: namely, Western and Northern Europe and North-Eastern Europe and Asia.}, language = {en} } @misc{RainfordHofreiterMayhew2016, author = {Rainford, James L. and Hofreiter, Michael and Mayhew, Peter J.}, title = {Phylogenetic analyses suggest that diversification and body size evolution are independent in insects}, series = {BMC evolutionary biology}, journal = {BMC evolutionary biology}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-407328}, pages = {17}, year = {2016}, abstract = {Background: Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. Results: The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Conclusions: Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.}, language = {en} } @article{PyšekPerglEssletal.2017, author = {Pyšek, Petr and Pergl, Jan and Essl, Franz and Lenzner, Bernd and Dawson, Wayne and Kreft, Holger and Weigelt, Patrick and Winter, Marten and Kartesz, John and Nishino, Misako and Antonova, Liubov A. and Barcelona, Julie F. and Cabezas, Francisco Jos{\´e} and C{\´a}rdenas L{\´o}pez, Dairon and C{\´a}rdenas-Toro, Juliana and Castańo, Nicol{\´a}s and Chac{\´o}n, Eduardo and Chatelain, Cyrille and Dullinger, Stefan and Ebel, Aleksandr L. and Figueiredo, Estrela and Fuentes, Nicol and Genovesi, Piero and Groom, Quentin J. and Henderson, Lesley and Inderjit, and Kupriyanov, Andrey and Masciadri, Silvana and Maurel, No{\"e}lie and Meerman, Jan and Morozova, Olʹga V. and Moser, Dietmar and Nickrent, Daniel and Nowak, Pauline M. and Pagad, Shyama and Patzelt, Annette and Pelser, Pieter B. and Seebens, Hanno and Shu, Wen-sheng and Thomas, Jacob and Velayos, Mauricio and Weber, Ewald and Wieringa, Jan J. and Baptiste, Maria P. and Kleunen, Mark van}, title = {Naturalized alien flora of the world}, series = {Preslia : the journal of the Czech Botanical Society}, volume = {89}, journal = {Preslia : the journal of the Czech Botanical Society}, number = {3}, publisher = {Czech Botanical Soc.}, address = {Praha}, issn = {0032-7786}, doi = {10.23855/preslia.2017.203}, pages = {203 -- 274}, year = {2017}, abstract = {Using the recently built Global Naturalized Alien Flora (GloNAF) database, containing data on the distribution of naturalized alien plants in 483 mainland and 361 island regions of the world, we describe patterns in diversity and geographic distribution of naturalized and invasive plant species, taxonomic, phylogenetic and life-history structure of the global naturalized flora as well as levels of naturalization and their determinants. The mainland regions with the highest numbers of naturalized aliens are some Australian states (with New South Wales being the richest on this continent) and several North American regions (of which California with 1753 naturalized plant species represents the world’s richest region in terms of naturalized alien vascular plants). England, Japan, New Zealand and the Hawaiian archipelago harbour most naturalized plants among islands or island groups. These regions also form the main hotspots of the regional levels of naturalization, measured as the percentage of naturalized aliens in the total flora of the region. Such hotspots of relative naturalized species richness appear on both the western and eastern coasts of North America, in north-western Europe, South Africa, south-eastern Australia, New Zealand, and India. High levels of island invasions by naturalized plants are concentrated in the Pacific, but also occur on individual islands across all oceans. The numbers of naturalized species are closely correlated with those of native species, with a stronger correlation and steeper increase for islands than mainland regions, indicating a greater vulnerability of islands to invasion by species that become successfully naturalized. South Africa, India, California, Cuba, Florida, Queensland and Japan have the highest numbers of invasive species. Regions in temperate and tropical zonobiomes harbour in total 9036 and 6774 naturalized species, respectively, followed by 3280 species naturalized in the Mediterranean zonobiome, 3057 in the subtropical zonobiome and 321 in the Arctic. The New World is richer in naturalized alien plants, with 9905 species compared to 7923 recorded in the Old World. While isolation is the key factor driving the level of naturalization on islands, zonobiomes differing in climatic regimes, and socioeconomy represented by per capita GDP, are central for mainland regions. The 11 most widely distributed species each occur in regions covering about one third of the globe or more in terms of the number of regions where they are naturalized and at least 35\% of the Earth’s land surface in terms of those regions’ areas, with the most widely distributed species Sonchus oleraceus occuring in 48\% of the regions that cover 42\% of the world area. Other widely distributed species are Ricinus communis, Oxalis corniculata, Portulaca oleracea, Eleusine indica, Chenopodium album, Capsella bursa-pastoris, Stellaria media, Bidens pilosa, Datura stramonium and Echinochloa crus-galli. Using the occurrence as invasive rather than only naturalized yields a different ranking, with Lantana camara (120 regions out of 349 for which data on invasive status are known), Calotropis procera (118), Eichhornia crassipes (113), Sonchus oleraceus (108) and Leucaena leucocephala (103) on top. As to the life-history spectra, islands harbour more naturalized woody species (34.4\%) thanmainland regions (29.5\%), and fewer annual herbs (18.7\% compared to 22.3\%). Ranking families by their absolute numbers of naturalized species reveals that Compositae (1343 species), Poaceae (1267) and Leguminosae (1189) contribute most to the global naturalized alien flora. Some families are disproportionally represented by naturalized aliens on islands (Arecaceae, Araceae, Acanthaceae, Amaryllidaceae, Asparagaceae, Convolvulaceae, Rubiaceae, Malvaceae), and much fewer so on mainland (e.g. Brassicaceae, Caryophyllaceae, Boraginaceae). Relating the numbers of naturalized species in a family to its total global richness shows that some of the large species-rich families are over-represented among naturalized aliens (e.g. Poaceae, Leguminosae, Rosaceae, Amaranthaceae, Pinaceae), some under-represented (e.g. Euphorbiaceae, Rubiaceae), whereas the one richest in naturalized species, Compositae, reaches a value expected from its global species richness. Significant phylogenetic signal indicates that families with an increased potential of their species to naturalize are not distributed randomly on the evolutionary tree. Solanum (112 species), Euphorbia (108) and Carex (106) are the genera richest in terms of naturalized species; over-represented on islands are Cotoneaster, Juncus, Eucalyptus, Salix, Hypericum, Geranium and Persicaria, while those relatively richer in naturalized species on the mainland are Atriplex, Opuntia, Oenothera, Artemisia, Vicia, Galium and Rosa. The data presented in this paper also point to where information is lacking and set priorities for future data collection. The GloNAF database has potential for designing concerted action to fill such data gaps, and provide a basis for allocating resources most efficiently towards better understanding and management of plant invasions worldwide.}, language = {en} } @phdthesis{Treplin2006, author = {Treplin, Simone}, title = {Inference of phylogenetic relationships in passerine birds (Aves: Passeriformes) using new molecular markers}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-11230}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {The aim of this study was to provide deeper insights in passerine phylogenetic relationships using new molecular markers. The monophyly of the largest avian order Passeriformes (~59\% of all living birds) and the division into its suborders suboscines and oscines are well established. Phylogenetic relationships within the group have been extremely puzzling, as most of the evolutionary lineages originated through rapid radiation. Numerous studies have hypothesised conflicting passerine phylogenies and have repeatedly stimulated further research with new markers. In the present study, I used three different approaches to contribute to the ongoing phylogenetic debate in Passeriformes. I investigated the recently introduced gene ZENK for its phylogenetic utility for passerine systematics in combination and comparison to three already established nuclear markers. My phylogenetic analyses of a comprehensive data set yielded highly resolved, consistent and strongly supported trees. I was able to show the high utility of ZENK for elucidating phylogenetic relationships within Passeriformes. For the second and third approach, I used chicken repeat 1 (CR1) retrotransposons as phylogenetic markers. I presented two specific CR1 insertions as apomorphic characters, whose presence/absence pattern significantly contributed to the resolution of a particular phylogenetic uncertainty, namely the position of the rockfowl species Picathartes spp. in the passerine tree. Based on my results, I suggest a closer relationship of these birds to crows, ravens, jays, and allies. For the third approach, I showed that CR1 sequences contain phylogenetic signal and investigated their applicability in more detail. In this context, I screened for CR1 elements in different passerine birds, used sequences of several loci to construct phylogenetic trees, and evaluated their reliability. I was able to corroborate existing hypotheses and provide strong evidence for some new hypotheses, e.g. I suggest a revision of the taxa Corvidae and Corvinae as vireos are closer related to crows, ravens, and allies. The subdivision of the Passerida into three superfamilies, Sylvioidea, Passeroidea, and Muscicapoidea was strongly supported. I found evidence for a split within Sylvioidea into two clades, one consisting of tits and the other comprising warblers, bulbuls, laughingthrushes, whitethroats, and allies. Whereas Passeridae appear to be paraphyletic, monophyly of weavers and estrild finches as a separate clade was strongly supported. The sister taxon relationships of dippers and the thrushes/flycatcher/chat assemblage was corroborated and I suggest a closer relationship of waxwings and kinglets to wrens, tree-creepers, and nuthatches.}, language = {en} }