Mark Wilkinson

Publications of Mark Wilkinson

• Discovery of a new family of amphibians from northeast India with ancient links to Africa.

  Authors: Rachunliu G Kamei, Diego San Mauro, David J Gower, Ines Van Bocxlaer, Emma Sherratt, Ashish Thomas, Suresh Babu, Franky Bossuyt, Mark Wilkinson, S D Biju

  Proceedings. Biological sciences / The Royal Society. 02/2012;

  The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report theThe limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India-an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

• Experimental Design in Phylogenetics: Testing Predictions from Expected Information.

  Authors: Diego San Mauro, David J Gower, James A Cotton, Rafael Zardoya, Mark Wilkinson, Tim Massingham

  Systematic biology. 02/2012;

  Taxon and character sampling is central to phylogenetic experimental design yet we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based onTaxon and character sampling is central to phylogenetic experimental design yet we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species, and studied how information (both expected and observed) and bootstrap support varies as each new taxon is individually added to our previous dataset. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top three (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the fourth (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: information is related to the ability to estimate branch length accurately, and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well chosen) taxon may increase phylogenetic resolution and support in weakly supported parts of the tree without adding more characters/genes. Altogether our results corroborate that, although still underexplored, Goldman's method offers a powerful tool for experimental design in molecular phylogenetic studies. However, there are still several drawbacks to overcome, and further assessment of the method is needed in order to make it better understood, more accessible, and able to assess the addition of multiple taxa.

• Molecular systematics of caeciliid caecilians (Amphibia: Gymnophiona) of the Western Ghats, India.

  Authors: David J Gower, Diego San Mauro, Varad Giri, Gopalakrishna Bhatta, Venu Govindappa, Ramachandran Kotharambath, Oommen V Oommen, Farrah A Fatih, Jacqueline A Mackenzie-Dodds, Ronald A Nussbaum, S D Biju, Yogesh S Shouche, Mark Wilkinson

  Molecular phylogenetics and evolution. 03/2011; 59(3):698-707.

  Together, Indian plus Seychelles caeciliid caecilian amphibians (Gymnophiona) constitute approximately 10% of the extant species of this order. A molecular phylogenetic analysis of all but one (orTogether, Indian plus Seychelles caeciliid caecilian amphibians (Gymnophiona) constitute approximately 10% of the extant species of this order. A molecular phylogenetic analysis of all but one (or two) nominal species (16, in five genera) is presented based on mitochondrial (12S, 16S, cytb, cox1) and nuclear (RAG1) sequence data. Results strongly support monophyly of both Seychelles and peninsular Indian caeciliids, and their sister-group status. Within the Indian caeciliids, Indotyphlus and Gegeneophis are monophyletic sister genera. The phylogenetic position of Gegeneophis ramaswamii, Gegeneophis seshachari, and Gegeneophis carnosus are not well resolved, but all lie outside a well-supported clade of most northern Western Ghats Gegeneophis (madhavai, mhadeiensis, goaensis, danieli/nadkarnii). Most nominal species of Indian caeciliid are diagnosed by robust haplotype clades, though the systematics of G. carnosus-like forms in northern Kerala and southern Karnataka requires substantial further investigation. For the most part, Indian caeciliid species comprise narrowly distributed, allopatric taxa with low genetic diversity. Much greater geographic genetic diversity exists among populations referred to G. seshachari, such that some populations likely represent undescribed species. This, the first phylogenetic analysis of Indian caeciliids, generally provides additional support for recent increases in described species (eight since 1999), and a framework for ongoing taxonomic revision.

• The impact of conservation on the status of the world's vertebrates.

  Authors: Michael Hoffmann, Craig Hilton-Taylor, Ariadne Angulo, Monika Böhm, Thomas M Brooks, Stuart H M Butchart, Kent E Carpenter, Janice Chanson, Ben Collen, Neil A Cox [......] Susan A Mainka, Jeffery A McNeely, Russell A Mittermeier, Gordon McGregor Reid, Jon Paul Rodriguez, Andrew A Rosenberg, Michael J Samways, Jane Smart, Bruce A Stein, Simon N Stuart

  Science (New York, N.Y.). 10/2010; 330(6010):1503-9.

  Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species areUsing data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

• Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1.

  Authors: Diego San Mauro, David J Gower, Tim Massingham, Mark Wilkinson, Rafael Zardoya, James A Cotton

  Systematic biology. 08/2009; 58(4):425-38.

  In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. Although previous studies have investigated the phylogenetic performance of differentIn molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. Although previous studies have investigated the phylogenetic performance of different genes and the effectiveness of increasing taxon sampling, their conclusions are partly contradictory, probably because they are highly context specific and dependent on the group of organisms used in each study. Goldman introduced a method for experimental design in phylogenetics based on the expected information to be gained that has barely been used in practice. Here we use this method to explore the phylogenetic utility of mitochondrial (mt) genes, mt genomes, and nuclear rag1 for studies of the systematics of caecilian amphibians, as well as the effect of taxon addition on the stabilization of a controversial branch of the tree. Overall phylogenetic information estimates per gene, specific estimates per branch of the tree, estimates for combined (mitogenomic) data sets, and estimates as a hypothetical new taxon is added to different parts of the caecilian tree are calculated and compared. In general, the most informative data sets are those for mt transfer and ribosomal RNA genes. Our results also show at which positions in the caecilian tree the addition of taxa have the greatest potential to increase phylogenetic information with respect to the controversial relationships of Scolecomorphus, Boulengerula, and all other teresomatan caecilians. These positions are, as intuitively expected, mostly (but not all) adjacent to the controversial branch. Generating whole mitogenomic and rag1 data for additional taxa joining the Scolecomorphus branch may be a more efficient strategy than sequencing a similar amount of additional nucleotides spread across the current caecilian taxon sampling. The methodology employed in this study allows an a priori evaluation and testable predictions of the appropriateness of particular experimental designs to solve specific questions at different levels of the caecilian phylogeny.

• Three new species of striped Ichthyophis (Amphibia: Gymnophiona: Ichthyophiidae) from the northeast Indian states of Manipur and Nagaland

  Authors: RACHUNLIU G. KAMEI, MARK WILKINSON, DAVID J. GOWER, S. D. BIJU

  Zootaxa. 01/2009; 2267:26–42.

  Three new ichthyophiid species, Ichthyophis khumhzi sp. nov., Ichthyophis moustakius sp. nov. and Ichthyophis sendenyu sp. nov., from the northeast Indian states of Manipur and Nagaland, areThree new ichthyophiid species, Ichthyophis khumhzi sp. nov., Ichthyophis moustakius sp. nov. and Ichthyophis sendenyu sp. nov., from the northeast Indian states of Manipur and Nagaland, are described on the basis of morphological analysis of new material. The new material (16 specimens) more than doubles the number of northeast Indian caecilian specimens reported in previous literature, and increases the caecilian fauna of the region to seven species. Two of the new species have very distinctive, moustache-like stripes between their tentacles and nares, a feature not reported in other ichthyophiids. Diagnoses, type descriptions, illustrations, data on variation, distribution, and natural history are provided for the new species. Concern for the conservation of northeast Indian caecilians is raised, given the paucity of previous work, evidence of unrecognized diversity, and ongoing habitat destruction.

• Supertrees join the mainstream of phylogenetics.

  Authors: James A Cotton, Mark Wilkinson

  Trends in ecology & evolution (Personal edition). 12/2008;

  Supertree methods are fairly widely used to build comprehensive phylogenies for particular groups, but concerns remain over the adequacy of existing approaches. Steel and Rodrigo recently introducedSupertree methods are fairly widely used to build comprehensive phylogenies for particular groups, but concerns remain over the adequacy of existing approaches. Steel and Rodrigo recently introduced a statistical model of incongruence between trees, allowing maximum-likelihood supertree inference. This approach to supertree construction will enable hypothesis-testing and model-choice methods that are now routine in sequence phylogenetics to be applied in this setting, and might form an important part of future phylogenetic inference from genomic data.

• One hundred million years of skin feeding? Extended parental care in a Neotropical caecilian (Amphibia: Gymnophiona).

  Authors: Mark Wilkinson, Alexander Kupfer, Rafael Marques-Porto, Hilary Jeffkins, Marta M Antoniazzi, Carlos Jared

  Biology letters. 09/2008; 4(4):358-61.

  Maternal dermatophagy, the eating of maternal skin by offspring, is an unusual form of parental investment involving co-evolved specializations of both maternal skin and offspring dentition, whichMaternal dermatophagy, the eating of maternal skin by offspring, is an unusual form of parental investment involving co-evolved specializations of both maternal skin and offspring dentition, which has been recently discovered in an African caecilian amphibian. Here we report the discovery of this form of parental care in a second, distantly related Neotropical species Siphonops annulatus, where it is characterized by the same syndrome of maternal and offspring specializations. The detailed similarities of skin feeding in different caecilian species provide strong evidence of its homology, implying its presence in the last common ancestor of these species. Biogeographic considerations, the separation of Africa and South American land masses and inferred timescales of amphibian diversification all suggest that skin feeding is an ancient form of parental care in caecilians, which has probably persisted in multiple lineages for more than 100Myr. These inferences support the hypotheses that (i) maternal dermatophagy is widespread in oviparous direct-developing caecilians, and (ii) that viviparous caecilians that feed on the hypertrophied maternal oviduct evolved from skin-feeding ancestors. In addition to skin-feeding, young S. annulatus were observed to congregate around, and imbibe liquid exuded from, the maternal cloacal opening.

• Care and parentage in a skin-feeding caecilian amphibian.

  Authors: Alexander Kupfer, Mark Wilkinson, David J Gower, Hendrik Müller, Robert Jehle

  Journal of experimental zoology. Part A, Ecological genetics and physiology. 08/2008;

  An exceptional form of parental care has recently been discovered in a poorly known caecilian amphibian. Mothers of the Taita Hills (Kenya) endemic Boulengerula taitanus provide their own skin as aAn exceptional form of parental care has recently been discovered in a poorly known caecilian amphibian. Mothers of the Taita Hills (Kenya) endemic Boulengerula taitanus provide their own skin as a food source for their offspring. Field data suggest that nursing is costly. Females found attending young had a lower body condition and fat body volume than nonbrooding and egg-incubating females, and the female condition decreased substantially during parental care. Most mothers and their eggs or offspring were found in close proximity to other nesting females, in high-density nest sites that enhance the potential for social interactions and highlighting the possibility of communal breeding. Parentage was investigated using Amplified Fragment Length Polymorphism (AFLP) genetic markers in 29 offspring from six litters guarded by putative mothers. Our data provide the first evidence of multiple paternity in a caecilian, implying that two fathers sired one litter. Some young from two litters had genotypes not matching the guarding female suggesting that not all offspring are cared for by their biological mothers. This study provides evidence for alloparenting in an amphibian with cost-intensive parental care. J. Exp. Zool. 309A, 2008. (c) 2008 Wiley-Liss, Inc.

• Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians.

  Authors: Simon P Loader, Davide Pisani, James A Cotton, David J Gower, Julia J Day, Mark Wilkinson

  Biology letters. 11/2007; 3(5):505-8.

  Parallel patterns of distribution in different lineages suggest a common cause. Explanations in terms of a single biogeographic event often imply contemporaneous diversifications. Phylogenies withParallel patterns of distribution in different lineages suggest a common cause. Explanations in terms of a single biogeographic event often imply contemporaneous diversifications. Phylogenies with absolute time scales provide the most obvious means of testing temporal components of biogeographic hypotheses but, in their absence, the sequence of diversification events and whether any could have been contemporaneous can be tested with relative date estimates. Tests using relative time scales have been largely overlooked, but because they do not require the calibration upon which absolute time scales depend, they make a large amount of existing molecular data of use to historical biogeography and may also be helpful when calibration is possible but uncertain. We illustrate the use of relative dating by testing the hypothesis that parallel, disjunct east/west distributions in three independent lineages of African caecilians have a common cause. We demonstrate that at least two biogeographic events are implied by molecular data. Relative dating analysis reveals the potential complexity of causes of parallel distributions and cautions against inferring common cause from common spatial patterns without considering the temporal dimension.

• Majority-rule supertrees.

  Authors: James A Cotton, Mark Wilkinson

  Systematic biology. 07/2007; 56(3):445-52.

  Most supertree methods proposed to date are essentially ad hoc, rather than designed with particular properties in mind. Although the supertree problem remains difficult, one promising avenue is toMost supertree methods proposed to date are essentially ad hoc, rather than designed with particular properties in mind. Although the supertree problem remains difficult, one promising avenue is to develop from better understood consensus methods to the more general supertree setting. Here, we generalize the widely used majority-rule consensus method to the supertree setting. The majority-rule consensus tree is the strict consensus of the median trees under the symmetric-difference metric, so we can generalize the consensus method by generalizing this metric to trees with differing leaf sets. There are two different natural generalizations, based on pruning or grafting leaves to produce comparable trees, and these two generalizations produce two different, but related, majority-rule supertree methods.

• Properties of supertree methods in the consensus setting.

  Authors: Mark Wilkinson, James A Cotton, François-Joseph Lapointe, Davide Pisani

  Systematic biology. 05/2007; 56(2):330-7.

• Of clades and clans: terms for phylogenetic relationships in unrooted trees.

  Authors: Mark Wilkinson, James O McInerney, Robert P Hirt, Peter G Foster, T Martin Embley

  Trends in ecology & evolution (Personal edition). 04/2007; 22(3):114-5.

• Investigating stagnation in morphological phylogenetics using consensus data.

  Authors: Simon R Harris, Davide Pisani, David J Gower, Mark Wilkinson

  Systematic biology. 03/2007; 56(1):125-9.

• Congruence of morphological and molecular phylogenies.

  Authors: Davide Pisani, Michael J Benton, Mark Wilkinson

  Acta biotheoretica. 02/2007; 55(3):269-81.

  When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular resultsWhen phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori.

• On the origin of the Synodontis catfish species flock from Lake Tanganyika.

  Authors: Julia J Day, Mark Wilkinson

  Biology letters. 01/2007; 2(4):548-52.

  Species flocks within Great Lakes provide unique insights into the factors affecting diversification. Lake Tanganyika (LT) is of particular interest because it contains many endemic groups for whichSpecies flocks within Great Lakes provide unique insights into the factors affecting diversification. Lake Tanganyika (LT) is of particular interest because it contains many endemic groups for which general factors affecting diversification can be discerned. Here, we present the first phylogenetic study of the LT Synodontis (Siluriformes, Mochokidae) species flock using mtDNA sequence data. Our data reveal some previously unrecognized species diversity and indicate that the LT species flock is not monophyletic, and that two closely related clades of endemics may have independently colonized LT. Other comparable small species flocks are characterized by a single colonization event. Molecular date estimates of the timing of the initial within-lake diversification of the LT endemics, based on a fossil calibration, are comparable to those reported for other groups, suggesting that extrinsic factors maybe important common causes of clade diversification. The basal divergence in the sampled Synodontis reveals an East-West African faunal split seen in many terrestrial, but few aquatic groups, the timing of which coincides with East African rifting events.

• Global patterns of diversification in the history of modern amphibians.

  Authors: Kim Roelants, David J Gower, Mark Wilkinson, Simon P Loader, S D Biju, Karen Guillaume, Linde Moriau, Franky Bossuyt

  Proceedings of the National Academy of Sciences of the United States of America. 01/2007; 104(3):887-92.

  The fossil record of modern amphibians (frogs, salamanders, and caecilians) provides no evidence for major extinction or radiation episodes throughout most of the Mesozoic and early Tertiary.The fossil record of modern amphibians (frogs, salamanders, and caecilians) provides no evidence for major extinction or radiation episodes throughout most of the Mesozoic and early Tertiary. However, long-term gradual diversification is difficult to reconcile with the sensitivity of present-day amphibian faunas to rapid ecological changes and the incidence of similar environmental perturbations in the past that have been associated with high turnover rates in other land vertebrates. To provide a comprehensive overview of the history of amphibian diversification, we constructed a phylogenetic timetree based on a multigene data set of 3.75 kb for 171 species. Our analyses reveal several episodes of accelerated amphibian diversification, which do not fit models of gradual lineage accumulation. Global turning points in the phylogenetic and ecological diversification occurred after the end-Permian mass extinction and in the late Cretaceous. Fluctuations in amphibian diversification show strong temporal correlation with turnover rates in amniotes and the rise of angiosperm-dominated forests. Approximately 86% of modern frog species and >81% of salamander species descended from only five ancestral lineages that produced major radiations in the late Cretaceous and early Tertiary. This proportionally late accumulation of extant lineage diversity contrasts with the long evolutionary history of amphibians but is in line with the Tertiary increase in fossil abundance toward the present.

• Molecular evidence for dim-light vision in the last common ancestor of the vertebrates.

  Authors: Davide Pisani, Samantha M Mohun, Simon R Harris, James O McInerney, Mark Wilkinson

  Current biology : CB. 06/2006; 16(9):R318-9; author reply R320.

• Discriminating supported and unsupported relationships in supertrees using triplets.

  Authors: James A Cotton, Claire S C Slater, Mark Wilkinson

  Systematic biology. 05/2006; 55(2):345-50.

• Parental investment by skin feeding in a caecilian amphibian.

  Authors: Alexander Kupfer, Hendrik Müller, Marta M Antoniazzi, Carlos Jared, Hartmut Greven, Ronald A Nussbaum, Mark Wilkinson

  Nature. 05/2006; 440(7086):926-9.

  Although the initial growth and development of most multicellular animals depends on the provision of yolk, there are many varied contrivances by which animals provide additional or alternativeAlthough the initial growth and development of most multicellular animals depends on the provision of yolk, there are many varied contrivances by which animals provide additional or alternative investment in their offspring. Providing offspring with additional nutrition should be favoured by natural selection when the consequent increased fitness of the young offsets any corresponding reduction in fecundity. Alternative forms of nutrition may allow parents to delay and potentially redirect their investment. Here we report a remarkable form of parental care and mechanism of parent-offspring nutrient transfer in a caecilian amphibian. Boulengerula taitanus is a direct-developing, oviparous caecilian, the skin of which is transformed in brooding females to provide a rich supply of nutrients for the developing offspring. Young animals are equipped with a specialized dentition, which they use to peel and eat the outer layer of their mother's modified skin. This new form of parental care provides a plausible intermediate stage in the evolution of viviparity in caecilians. At independence, offspring of viviparous and of oviparous dermatotrophic caecilians are relatively large despite being provided with relatively little yolk. The specialized dentition of skin-feeding (dermatophagous) caecilians may constitute a preadaptation to the fetal feeding on the oviduct lining of viviparous caecilians.