63 Works

Data from: A multilocus sequencing approach reveals the cryptic phylogeographical history of Phyllodoce nipponica Makino (Ericaceae)

Hajime Ikeda & Hiroaki Setoguchi
Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to re-examine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a...

Data from: Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina)

Charles W. Linkem, Rafe M. Brown, Cameron D. Siler, Ben J. Evans, Christopher C. Austin, Djoko T. Iskandar, Arvin C. Diesmos, Jatna Supriatna, Noviar Andayani, Jimmy A. McGuire & Malte Ebach
Aim: Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dis- persed via mechanisms that were not human-mediated (‘natural’ dispersal) or whether dispersal...

Data from: Himalayan Cambrian brachiopods

Leonid E. Popov, Lars E. Holmer, Nigel C. Hughes, Mansoureh Ghabadi Pour, Paul M. Myrow & Mansoureh Ghobadi Pour
A synoptic analysis of previously published material and new finds reveals that Himalayan Cambrian brachiopods can be referred to 18 genera, of which 17 are considered herein. These contain 20 taxa assigned to species, of which five are new: Eohadrotreta haydeni, Aphelotreta khemangarensis, Hadrotreta timchristiorum, Prototreta? sumnaensis and Amictocracens? brocki. Well-preserved topotype material from the classic Parahio Valley section is described for three species that have not previously been illustrated photographically. A biostratigraphical scheme based...

Data from: Egg morphology fails to identify nests parasitized by conspecifics in common pochard: a test based on protein fingerprinting and including female relatedness

Adéla Petrželková, Hannu Pöysä, Petr Klvaňa, Tomáš Albrecht & David Hořák
Conspecific brood parasites lay eggs in nests of other females of the same species. A variety of methods have been developed and used to detect conspecific brood parasitism (CBP). Traditional methods may be inaccurate in detecting CBP and in revealing its true frequency. On the other hand more accurate molecular methods are expensive and time consuming. Eadie developed a method for revealing CBP based on differences in egg morphology. That method is based on Euclidean...

Data from: Secondary compounds from exotic tree plantations change female mating preferences in the palmate newt (Lissotriton helveticus)

Maider Iglesias-Carrasco, Megan L. Head, Michael D. Jennions & Carlos Cabido
Selection can favor phenotypic plasticity in mate choice in response to environmental factors that alter the costs and benefits of being choosy, or of choosing specific mates. Human-induced environmental change could alter sexual selection by affecting the costs of mate choice, or by impairing the ability of individuals to identify preferred mates. For example, variation in mate choice could be driven by environmentally induced differences in body condition (e.g. health) that change the cost of...

Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Mary E. Prendergast, Michael Buckley, Alison Crowther, Heidi Eager, Laurent Frantz, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eréndira M. Quintana Morales, Verena J. Schuenemann, Ella Reiter, Richard Allen, Evangelos A. Dimopoulos, Richard M. Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark C. Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright … & Mark Horton
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological...

Data from: Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum

Christian Kehlmaier, Axel Barlow, Alexander K. Hastings, Melita Vamberger, Johanna L. A. Paijmans, David W. Steadman, Nancy A. Albury, Richard Franz, Michael Hofreiter & Uwe Fritz
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...

Data from: Nest survival in year-round breeding tropical Red-capped Larks (Calandrella cinerea) increases with higher nest abundance but decreases with higher invertebrate availability and rainfall

Joseph Mwangi, Henry K. Ndithia, Rosemarie Kentie, Muchane Muchai & B. Irene Tieleman
Nest survival is critical to breeding in birds and plays an important role in life-history evolution and population dynamics. Studies evaluating the proximate factors involved in explaining nest survival and the resulting temporal patterns are biased in favor of temperate regions. Yet, such studies are especially pertinent to the tropics, where nest predation rates are typically high and environmental conditions often allow for year-round breeding. To tease apart the effects of calendar month and year,...

Data from: Molecular phylogeny of Terniopsis (Podostemaceae) and contrasting molecular and morphological variations in two species

Satoshi Koi, Hyosig Won, Hùng Trần, La-Aw Ampornpan & Masahiro Kato
Podostemaceae show different patterns of morphological variation relative to molecular ones between genera and between species, but additional material was necessary to make the patterns clearer. Using new material collected from Cambodia, we compared the variations of Terniopsis chanthaburiensis and T. heterostaminata in Cambodia, Laos and Thailand, and conducted matK phylogenetic analysis with many samples and most species of the genus. In contrast to the narrow molecular variation, the morphological variation (e.g., in the length...

Data from: Distinguishing the victim from the threat: SNP‐based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration

Helen V. Senn, Muhammad Ghazali, Jennifer Kaden, David Barcaly, Ben Harrower, Ruairidh D. Campbell, David W. MacDonald, Andrew C. Kitchener & David Barclay
The degree of introgressive hybridisation between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here we use a 35-SNP-marker test, designed to assess hybridisation between wildcat and domestic cat populations in Scotland, to assess a database of 265 wild-living and captive cat samples, and test the assumptions of the test using 3097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic...

Data from: Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate

Rafe M. Brown, Jennifer A. Weghorst, Karen V. Olson, Mariano R. M. Duya, Anthony J. Barley, Melizar V. Duya, Myron Shekelle, Irene Neri-Arboleda, Jacob A. Esselstyn, Nathaniel J. Dominy, Perry S. Ong, Gillian L. Moritz, Adrian Luczon, Mae Lowe L. Diesmos, Arvin C. Diesmos & Cameron D. Siler
Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies,...

Data from: Systematics of spiny-backed treefrogs (Hylidae: Osteocephalus): an Amazonian puzzle

Karl-Heinz Jungfer, Julián Faivovich, José M. Padial, Santiago Castroviejo-Fisher, Mariana M. Lyra, Bianca Von Muller Berneck, Patricia P. Iglesias, Philippe J. R. Kok, Ross T. Macculloch, Miguel Trefaut Rodrigues, Vanessa K. Verdade, Claudia P. Torres Gastello, Juan Carlos Chaparro, Paula H. Valdujo, Steffen Reichle, Jiří Moravec, Václav Gvoždík, Giussepe Gagliardi-Urrutia, Raffael Ernst, Ignacio De La Riva, Donald Bruce Means, Albertina P. Lima, J. Celsa Señaris, Ward C. Wheeler & Célio F. B. Haddad
Spiny-backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134 bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight countries and 218 localities, representing 89% of the 28 currently recognized nominal species. Our phylogenetic analyses reveal (i) the paraphyly...

Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

Data from: Enemy at the gates: rapid defensive trait diversification in an adaptive radiation of lizards

Chris Broeckhoven, Genevieve Diedericks, Cang Hui, Buyisile G. Makhubo & Pieter Le Fras Nortier Mouton
Adaptive radiation, the product of rapid diversification of an ancestral species into novel adaptive zones, has become pivotal in our understanding of biodiversity. While it has widely been accepted that predators may drive the process of adaptive radiation by creating ecological opportunity (e.g. enemy-free space), the role of predators as selective agents in defensive trait diversification remains controversial. Using phylogenetic comparative methods, we provide evidence for an ‘early burst’ in the diversification of antipredator phenotypes...

Data from: Population-specific responses to an invasive species

Martin Reichard, Karel Douda, Mirosław Przybyłski, Oana P. Popa, Eva Karbanová, Klára Matasová, Kateřina Rylková, Matej Polačik, Radim Blažek & Carl Smith
Predicting the impacts of non-native species remains a challenge. As populations of a species are genetically and phenotypically variable, the impact of non-native species on local taxa could crucially depend on population-specific traits and adaptations of both native and non-native species. Bitterling fishes are brood parasites of unionid mussels and unionid mussels produce larvae that parasitize fishes. We used common garden experiments to measure three key elements in the bitterling–mussel association among two populations of...

Data from: Dark pigmentation limits thermal niche position in birds

Ismael Galván, Sol Rodríguez-Martínez & Luis M. Carrascal
1. Animal pigmentation has evolved because of several adaptive functions. In the case of pigmentation produced by melanins, the most common pigments in animals, the main function is protection against UV radiation. However, pigmentation also affects animal surface's ability to absorb solar radiation and gain heat, which may represent a thermal constraint for endotherms due to their relatively high and constant body temperatures. 2. As darker colours absorb more radiation than lighter colours, dark-pigmented endotherm...

Data from: Effects of experimental night lighting on the daily timing of winter foraging in common European songbirds

Arnaud Da Silva, David Diez-Méndez & Bart Kempenaers
The ecological effects of light pollution are becoming better understood, especially in birds. Recent studies have shown that several bird species can use street lighting to extend activity into the night during the breeding season. However, most of these studies are correlational and little is known about the effects of artificial night lighting on the timing of activities outside the breeding season. During winter, low temperatures and short days may limit foraging opportunities and can...

Data from: Ecology, biofacies, biogeography and systematics of micromorphic lingulate brachiopods from the Ordovician (Darriwilian–Sandbian) of south-central China

Lars E. Holmer, Mansoureh Ghobadi Pour, Leonid E. Popov, Zhiliang Zhang & Zhifei Zhang
Ordovician (Darriwilian to Sandbian) micromorphic linguliform lingulate brachiopods are described from the Guniutan Formation at the Fenxiang section in Hubei province, and the Maocaopu and Cili sections in Hunan province of south-central China, situated on the Yangtze Platform. A total of 7560 specimens from 155 limestone samples (within the interval of Lenodus variabilis – Pygodus anserinus biozones) are assigned to 22 species, representing a low taxonomic diversity and low abundance fauna. The fauna is dominated...

Data from: Global mtDNA genetic structure and hypothesized invasion history of a major pest of citrus, Diaphorina citri (Hemiptera: Liviidae)

Yufa Luo & Ingi Agnarsson
The Asian citrus psyllid Diaphorina citri Kuwayama, is a key pest of citrus as the vector of the bacterium causing the ‘huanglongbing’ disease (HLB). To assess the global mtDNA population genetic structure, and possible dispersal history of the pest, we investigated genetic variation at the COI gene collating newly collected samples with all previously published data. Our dataset consists of 356 colonies from 106 geographic sites worldwide. High haplotype diversity (H-mean = 0.702 ± 0.017),...

Data from: Morphology of the petrosal and stapes of Borealestes (Mammaliaformes, Docodonta) from the Middle Jurassic of Skye, Scotland

Elsa Panciroli, Julia A. Schultz & Zhe-Xi Luo
\We describe, in unprecedented detail, the petrosals and stapes of the docodont Borealestes from the Middle Jurassic of Scotland, using high resolution μCT and phase‐contrast synchrotron imaging. We describe the inner ear endocast and the vascularized interior structure of the petrosal, and provide the first endocranial view of a docodontan petrosal. Our study confirms some similarities in petrosal and stapedial morphology with the better known Haldanodon of the Late Jurassic of Portugal, including: (1) the...

Whence came these plants most foul? Phylogenomics and biogeography of Lowiaceae (Zingiberales)

Matti Niissalo, Elliot Gardner, Gillian Khew, Otakar Šída, Axel Poulsen & Jana Leong-Škornicková
Lowiaceae (order Zingiberales) is a small family of forest herbs in Southeast Asia. All species belong to the genus Orchidantha. They are known for possessing orchid-like flowers that are smelly, apparently mimicking dead animals, feces, or mushrooms. Little is known of the biogeographic patterns or character evolution of the family. We sampled the family extensively, including many recently discovered species, and reconstructed the phylogeny of the family using HybSeq with Lowiaceae-specific RNA baits. Our phylogenetic...

Data from: An empirical comparison of a character-based and a coalescent-based approach to species delimitation in a young avian complex

Bailey D. McKay, , Yuchun Wu, Hui Li, Cheng-Te Yao, Isao Nishiumi, Fasheng Zou & Herman L. Mays
The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus...

Data from: The evolution of canaliculate rudists in the light of a new canaliculate polyconitid rudist from the Albian of the Central Pacific

Shin-Ichi Sano, Yasuhiro Iba, Peter W. Skelton, Jean-Pierre Masse, Yolanda M. Aguilar & Tomoki Kase
A new polyconitid rudist, Magallanesia canaliculata gen. et sp. nov., of probably late Albian age, is described from the Pulangbato area, central Cebu Island, the Philippines in the western Central Pacific and Takuyo Daini Seamount, now located in the Northwest Pacific. It is similar to Praecaprotina Yabe and Nagao, 1926, a Japanese – Central Pacific endemic genus of late Aptian – early Albian age, but differs in having canals that developed by partitioning of the...

Data from: Dragons in our midst: phyloforensics of illegally traded Southeast Asian monitor lizards

Welton J. Luke, Cameron D. Siler, Charles W. Linkem, Arvin C. Diesmos, Mae L. Diesmos, Emerson Sy, Rafe M. Brown & Luke J. Welton
We provide a phylogenetic and population genetic evaluation of the illegal pet and bush meat trade of monitor lizards in the Philippines. We use a molecular dataset assembled from vouchered samples with known localities throughout the country, as a reference for statistical phylogenetic, population genetic, and DNA barcoding analyses of genetic material obtained during a three year survey of the Manila pet trade. Our results provide the first genetic evaluation of a major Southeast Asian...

Data from: An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

Dahiana Arcila, R. Alexander Pyron, James C. Tyler, Guillermo Ortí & Ricardo Betancur-R.
Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new...

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