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Mallet, James

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Mallet

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James

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Mallet, James
Author's Publications: search.filters.isAuthorOfPublication.62c4cfe7-d6e6-4034-aebd-a03865d9aa34

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    Comments on Petition of Pacific Legal Foundation, et al., for Rule-Making Under the Administrative Procedure Act (Which Aimed to Promulgate New Regulatory Definitions of “Species” and “Subspecies” Under the Endangered Species Act)
    (2018-06-06) Mallet, James; Ehrlich, Paul; Gill, Frank; McCormack, John; Raven, Peter
    Harvard Law School’s Emmett Environmental Law and Policy Clinic submits the following comments on behalf of James Mallet, Paul Ehrlich, Frank Gill, John McCormack, and Peter Raven in response to the Petition of Pacific Legal Foundation, et al. (“PLF”), for Rule- Making under the Administrative Procedure Act (the “Petition”), which was submitted on November 10, 2017 to the United States Department of Interior, the United States Department of Commerce, the United States Fish and Wildlife Service, and the National Marine Fisheries Service (collectively, “the Services”). The Petition asks the Services to promulgate regulatory definitions of “species” and “subspecies” under the Endangered Species Act (“ESA” or “the Act”). We urge the Services to deny the Petition, because PLF’s proposal contains several flaws: (1) The Services should not give “species” a single regulatory definition under the ESA because there is no universally accepted species concept among taxonomists. (2) PLF’s proposed definitions of “species” and “subspecies” are flawed because they are based on erroneously cited authority and they create tension with the statutory definitions in the ESA. (3) Adopting a single regulatory definition of “species” and “subspecies” is impermissible under the ESA because the Services would not be using the best available science (“BAS”), as required by the Act. (4) It is appropriate for the Services to continue to make case-by-case species determinations, using the best available science in each case.
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    Why Was Darwin’s View of Species Rejected by Twentieth Century Biologists?
    (Springer Nature, 2010-05-01) Mallet, James
    Historians and philosophers of science agree that Darwin had an understanding of species which led to a workable theory of their origins. To Darwin species did not differ essentially from 'varieties' within species, but were distinguishable in that they had developed gaps in formerly continuous morphological variation. Similar ideas can be defended today after updating them with modern population genetics. Why then, in the 1930s and 1940s, did Dobzhansky, Mayr and others argue that Darwin failed to understand species and speciation? Mayr and Dobzhansky argued that reproductively isolated species were more distinct and 'real' than Darwin had proposed. Believing species to be inherently cohesive, Mayr inferred that speciation normally required geographic isolation, an argument that he believed, incorrectly, Darwin had failed to appreciate. Also, before the sociobiology revolution of the 1960s and 1970s, biologists often argued that traits beneficial to whole populations would spread. Reproductive isolation was thus seen as an adaptive trait to prevent disintegration of species. Finally, molecular genetic markers did not exist, and so a presumed biological function of species, reproductive isolation, seemed to delimit cryptic species better than character-based criteria like Darwin's. Today, abundant genetic markers are available and widely used to delimit species, for example using assignment tests: genetics has replaced a Darwinian reliance on morphology for detecting gaps between species. In the 150th anniversary of The Origin of Species, we appear to be returning to more Darwinian views on species, and to a fuller appreciation of what Darwin meant.
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    Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies
    (Oxford University Press, 2015) Kozak, Krzysztof M.; Wahlberg, Niklas; Neild, Andrew F. E.; Dasmahapatra, Kanchon K.; Mallet, James; Jiggins, Chris D.
    Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a data set of 22 mitochondrial and nuclear markers from 92% of species in the tribe, obtained by Sanger sequencing and de novo assembly of short read data, to re-examine the phylogeny of Heliconiini with both supermatrix and multispecies coalescent approaches, characterize the patterns of conflicting signal, and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach failed to reflect the underlying variation in the history of individual loci. However, the supermatrix represents a useful approximation where multiple rare species represented by short sequences can be incorporated easily. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Neotropics over the past 23 myr, or changes caused by diversity-dependent effects on the rate of diversification. We find that the rate of diversification has increased on the branch leading to the presently most species-rich genus Heliconius, but the change occurred gradually and cannot be unequivocally attributed to a specific environmental driver. Our study provides comprehensive comparison of philosophically distinct species tree reconstruction methods and provides insights into the diversification of an important insect radiation in the most biodiverse region of the planet.
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    Unraveling the thread of nature’s tapestry: the genetics of diversity and convergence in animal pigmentation
    (Wiley-Blackwell, 2012) Kronforst, Marcus; Barsh, Gregory S.; Kopp, Artyom; Mallet, James; Monteiro, Antónia; Mullen, Sean P.; Protas, Meredith; Rosenblum, Erica B.; Schneider, Christopher; Hoekstra, Hopi
    Animals display incredibly diverse color patterns yet little is known about the underlying genetic basis of these phenotypes. However, emerging results are reshaping our view of how the process of phenotypic evolution occurs. Here, we outline recent research from three particularly active areas of investigation: melanin pigmentation in Drosophila, wing patterning in butterflies, and pigment variation in lizards. For each system, we highlight (i) the function and evolution of color variation, (ii) various approaches that have been used to explore the genetic basis of pigment variation, and (iii) conclusions regarding the genetic basis of convergent evolution which have emerged from comparative analyses. Results from these studies indicate that natural variation in pigmentation is a particularly powerful tool to examine the molecular basis of evolution, especially with regard to convergent or parallel evolution. Comparison of these systems also reveals that the molecular basis of convergent evolution is heterogeneous, sometimes involving conserved mechanisms and sometimes not. In the near future, additional work in other emerging systems will substantially expand the scope of available comparisons.
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    Estimation of the Spontaneous Mutation Rate in Heliconius melpomene
    (Oxford University Press, 2014) Keightley, Peter D.; Pinharanda, Ana; Ness, Rob W.; Simpson, Fraser; Dasmahapatra, Kanchon K.; Mallet, James; Davey, John W.; Jiggins, Chris D.
    We estimated the spontaneous mutation rate in Heliconius melpomene by genome sequencing of a pair of parents and 30 of their offspring, based on the ratio of number of de novo heterozygotes to the number of callable site-individuals. We detected nine new mutations, each one affecting a single site in a single offspring. This yields an estimated mutation rate of 2.9 × 10−9 (95% confidence interval, 1.3 × 10−9–5.5 × 10−9), which is similar to recent estimates in Drosophila melanogaster, the only other insect species in which the mutation rate has been directly estimated. We infer that recent effective population size of H. melpomene is about 2 million, a substantially lower value than its census size, suggesting a role for natural selection reducing diversity. We estimate that H. melpomene diverged from its Müllerian comimic H. erato about 6 Ma, a somewhat later date than estimates based on a local molecular clock.
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    Speciation: Frog Mimics Prefer Their Own
    (Elsevier BV, 2014) Mallet, James
    Ranitomeya poison frogs in the Peruvian Amazon mimic one another, a rare example of Müllerian mimicry in vertebrates. In Ranitomeya imitator, courtship is more likely between same-coloured mimics than between differently coloured mimics. Divergence in mimicry may therefore play a role in the origin of new species.
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    Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?
    (BioMed Central, 2015) Rosser, Neil; Kozak, Krzysztof M.; Phillimore, Albert B.; Mallet, James
    Background: Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Results: Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32 %–95 % of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Conclusions: Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on “strict and ” “relaxed” biological species concepts (BSC), as well as on a surrogate for the widely-used “diagnostic” version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0420-3) contains supplementary material, which is available to authorized users.
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    Genome-wide introgression among distantly related Heliconius butterfly species
    (BioMed Central, 2016) Zhang, Wei; Dasmahapatra, Kanchon K.; Mallet, James; Moreira, Gilson R. P.; Kronforst, Marcus R.
    Background: Although hybridization is thought to be relatively rare in animals, the raw genetic material introduced via introgression may play an important role in fueling adaptation and adaptive radiation. The butterfly genus Heliconius is an excellent system to study hybridization and introgression but most studies have focused on closely related species such as H. cydno and H. melpomene. Here we characterize genome-wide patterns of introgression between H. besckei, the only species with a red and yellow banded ‘postman’ wing pattern in the tiger-striped silvaniform clade, and co-mimetic H. melpomene nanna. Results: We find a pronounced signature of putative introgression from H. melpomene into H. besckei in the genomic region upstream of the gene optix, known to control red wing patterning, suggesting adaptive introgression of wing pattern mimicry between these two distantly related species. At least 39 additional genomic regions show signals of introgression as strong or stronger than this mimicry locus. Gene flow has been on-going, with evidence of gene exchange at multiple time points, and bidirectional, moving from the melpomene to the silvaniform clade and vice versa. The history of gene exchange has also been complex, with contributions from multiple silvaniform species in addition to H. besckei. We also detect a signature of ancient introgression of the entire Z chromosome between the silvaniform and melpomene/cydno clades. Conclusions: Our study provides a genome-wide portrait of introgression between distantly related butterfly species. We further propose a comprehensive and efficient workflow for gene flow identification in genomic data sets. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0889-0) contains supplementary material, which is available to authorized users.
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    Diversification of clearwing butterflies with the rise of the Andes
    (John Wiley and Sons Inc., 2015) De‐Silva, Donna Lisa; Elias, Marianne; Willmott, Keith; Mallet, James; Day, Julia J.
    Abstract Aim Despite the greatest butterfly diversity on Earth occurring in the Neotropical Andes and Amazonia, there is still keen debate about the origins of this exceptional biota. A densely sampled calibrated phylogeny for a widespread butterfly subtribe, Oleriina (Nymphalidae: Ithomiini) was used to estimate the origin, colonization history and diversification of this species‐rich group. Location Neotropics. Methods: Ancestral elevation and biogeographical ranges were reconstructed using data generated from detailed range maps and applying the dispersal‐extinction‐cladogenesis model using stratified palaeogeographical time slice matrices. The pattern of diversification through time was examined by comparing constant and variable rate models. We also tested the hypothesis that a change in elevation is associated with speciation. Results: The Oleriina likely originated in the Andes in the Early to Middle Miocene and rapidly diversified to include four genera all of which also originated in the Andes. These clades, together with four species groups, experienced varying spatial and temporal patterns of diversification. An overall early burst and decreasing diversification rate is identified, and this pattern is reflected for most subclades. Main conclusions Changes in the palaeogeological landscape, particularly the prolonged uplift of the Andes, had a profound impact on the diversification of the subtribe. The Oleriina mostly remained within the Andes and vicariant speciation resulted in some instances. Dynamic dispersal occurred with the disappearance of geological barriers such as the Acre System and the subtribe exploited newly available habitats. Our results confirm the role of the Andean uplift in the evolution of Neotropical biodiversity.
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    How reticulated are species?
    (John Wiley and Sons Inc., 2015) Mallet, James; Besansky, Nora; Hahn, Matthew W.
    Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.