Rampant polyphyly indicates cryptic diversity in a clade of Neotropical flycatchers (Aves: Tyrannidae)

Rheindt, Frank E.; Cuervo, Andrés M.; Brumfield, Robb T.

doi:10.1111/j.1095-8312.2012.02036.x

Cited by 23 publications

(14 citation statements)

References 42 publications

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“…Identification of cryptic species has become increasingly prevalent in a variety of environments (e.g. Jackson & Austin, ; Marin et al ., ; Millar & Byrne, ; Rheindt, Cuervo & Brumfield, ; Hammer et al ., ). The criteria and data required to identify morphologically cryptic species genetically remains controversial, however (Sites & Marshall ; DeSalle, Egan & Siddell, ; de Queiroz, ; Whelan, ; Carstens et al ., ; Kvist, ), and often vary among taxa and markers.…”

Section: Discussionmentioning

confidence: 99%

Cryptic speciation along a bathymetric gradient

Glazier

Etter

2014

Biol J Linn Soc Lond

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The deep ocean supports a highly diverse and mostly endemic fauna, yet little is known about how or where new species form in this remote ecosystem. How speciation occurs is especially intriguing in the deep sea because few obvious barriers exist that would disrupt gene flow. Geographic and bathymetric patterns of genetic variation can provide key insights into how and where new species form. We quantified the population genetic structure of a protobranch bivalve, Neilonella salicensis, along a depth gradient (2200-3800 m) in the western North Atlantic using both nuclear (28S and calmodulin intron) and mitochondrial (cytochrome c oxidase subunit I) loci. A sharp genetic break occurred for each locus between populations above 2800 m and below 3200 m, defining two distinct clades with no nuclear or mitochondrial haplotypes shared between depth regimes. Bayesian phylogenetic analyses provided strong support for two clades, separated by depth, within N. salicensis. Although no morphological divergence was apparent, we suggest that the depth-related population genetic and phylogenetic divergence is indicative of a cryptic species. The frequent occurrence of various stages of divergence associated with species formation along bathymetric gradients suggests that depth, and the environmental gradients that attend changes in depth, probably play a fundamental role in the diversification of marine organisms, especially in deep water.

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Section: Discussionmentioning

confidence: 99%

Cryptic speciation along a bathymetric gradient

Glazier

Etter

2014

Biol J Linn Soc Lond

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“…We also required at least 20% of reads within an individual to contain the minor allele in order for that individual to be called heterozygous; individuals with between 0 and 20% minor alleles at a particular site were treated as missing data at that locus. These procedures were similar to the methods and cut-offs used by Rheindt et al [38], although we were more conservative because we had lower overall coverage in our data. More details about our pipeline and the scripts can be found online at: https://github.com/ eacooper400/RAD_Pipeline_Info.…”

Section: (B) Candidate Gene and Next Generation Sequencing Approachesmentioning

confidence: 99%

Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers

Cooper

Cutie

et al. 2016

Proc. R. Soc. B.

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The independent evolution of similar traits across multiple taxa provides some of the most compelling evidence of natural selection. Little is known, however, about the genetic basis of these convergent or parallel traits: are they mediated by identical or different mutations in the same genes, or unique mutations in different genes? Using a combination of candidate gene and reduced representation genomic sequencing approaches, we explore the genetic basis of and the evolutionary processes that mediate similar plumage colour shared by isolated populations of the Monarcha castaneiventris flycatcher of the Solomon Islands. A genome-wide association study (GWAS) that explicitly controlled for population structure revealed that mutations in known pigmentation genes are the best predictors of parallel plumage colour. That is, entirely black or melanic birds from one small island share an amino acid substitution in the melanocortin-1 receptor (MC1R), whereas similarly melanic birds from another small island over 100 km away share an amino acid substitution in a predicted binding site of agouti signalling protein (ASIP). A third larger island, which separates the two melanic populations, is inhabited by birds with chestnut bellies that lack the melanic MC1R and ASIP allelic variants. Formal F ST outlier tests corroborated the results of the GWAS and suggested that strong, directional selection drives the near fixation of the MC1R and ASIP variants across islands. Our results, therefore, suggest that selection acting on different mutations with large phenotypic effects can drive the evolution of parallel melanism, despite the relatively small population size on islands.

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“…All these issues are more relevant when it is considered that IAvH-CT is focused on a megadiverse country, and that the policies of Colombia (e.g., Ministerio de Ambiente y Desarrollo Sostenible, 2013a; Ministerio de Ambiente y Desarrollo Sostenible, 2013b) do not allow the existence of a similar collection in other country. In fact, the bird samples (a large part of them associated to specimen vouchers in Colección de Aves de Colombia del Instituto Humboldt, IAvH-A) positioned IAvH-CT among the most relevant tissue collections of birds in the world (Stoeckle and Winker, 2009), and have allowed to conduct barcoding projects (Gonzalez and Paz, 2013) and have contributed in understanding different evolutionary aspects of the Neotropical species (e.g., Cadena et al, 2007;Puebla-Olivares et al, 2008;Mauck III and Burns, 2009;Parra et al, 2009;Parra, 2010;Sedano and Burns, 2010;Chaves et al, 2011;d'Horta et al, 2012;Gutíerrez-Pinto et al, 2012;Rheindt et al, 2013;Valderrama et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Colombian Frozen Biodiversity: 16 Years of the Tissue Collection of the Humboldt Institute

Arbeláez‐Cortés¹,

Torres²,

López-Álvarez³

et al. 2015

Acta biol. Colomb.

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Collections of tissue samples stand as keystone sources of molecular information to construct biodiversity knowledge, and are particularly useful in megadiverse countries. In 1998 the Humboldt Institute (<em>Instituto de Investigación de Recursos Biológicos Alexander von Humboldt</em>) began a tissue collection of Colombian biodiversity (IAvH-CT) and the aim of this work is to present a diagnostic and an historical narrative for that collection, constructed by compiling information and experiences on its management as well as by organizing and curating the information of each catalogued sample. After 16 years the IAvH-CT harbors 16469 samples, which represent around 2530 species from 1289 genera, and 323 families of the Colombian biodiversity. Samples are biased toward plants and birds (84 %), but also include other animal taxa. Geographically, IAvH-CT includes samples from all Colombian departments, but there is a broad variation in their coverage. When compared with other international collections IAvH-CT fulfills several standards of sample storage and data management, but have a major weakness that is that several tissues seem to lack a vouchered specimen. Tissues housed at IAvH-CT have been included in at least 48 studies published in several scientific journals. IAvH-CT is implementing strategies to improve curatorial standards, fill-up taxonomic gaps, and to explore the potential of its samples to understand the outstanding Colombian biota in a cooperative research frame among institutions.

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Rampant polyphyly indicates cryptic diversity in a clade of Neotropical flycatchers (Aves: Tyrannidae)

Cited by 23 publications

References 42 publications

Cryptic speciation along a bathymetric gradient

Cryptic speciation along a bathymetric gradient

Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers

Colombian Frozen Biodiversity: 16 Years of the Tissue Collection of the Humboldt Institute

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