Luke C. Campillo's research while affiliated with University of Hawaiʻi at Mānoa and other places

The radiation of so-called “great speciators” represents a paradox among the myriad of avian radiations endemic to the southwest Pacific. In such radiations, lineages otherwise capable of dispersing across vast distances of open ocean differentiate rapidly and frequently across relatively short geographic barriers. Here, we evaluate the phylogeography of the Rufous Fantail (Rhipidura rufifrons). Although a presumed “great-speciator”, no formal investigations across its range have been performed. Moreover, delimitation of lineages within R. rufifrons, and the biogeographic implications of those relationships, remain unresolved. To investigate whether R. rufifrons represents a great speciator we identified thousands of single nucleotide polymorphisms for 89 individuals, representing 19 described taxa. Analyses recovered 7 divergent lineages and evidence of gene flow between geographically isolated populations. We also found plumage differences to be a poor proxy for evolutionary relationships. Given the relatively recent divergence dates for the clade (1.35–2.31 mya), rapid phenotypic differentiation, and evidence for multiple independent lineages within the species complex, we determine that R. rufifrons possesses the characteristics of a great speciator.

Clear correlations between human and bird visual assessments of color have been documented, and are often assumed, despite fundamental differences in human and avian visual physiology and morphology. Analyses of plumage colors with avian perceptual models have shown widespread hidden inter-sexual and inter-specific color variation among passerines perceived as monochromatic to humans, highlighting the uncertainty of human vision to predict potentially relevant variation in color. Herein, we use reflectance data from 13 Larus gull species as an exemplar data set to study concordance between human vision and avian visual modeling of feather colors near, or below, the human threshold for discrimination. We found little evidence among gulls for sexual dichromatism hidden from human vision, but did find inter-specific color variation among gulls that is not seen by humans. Neither of these results were predictable a priori, and we reassert that reflectance measurements of actual feather colors, analyzed with avian relevant visual models, represent best practice when studying bird coloration.

Phylogeographical studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation but remains relatively undocumented, perhaps because the current episode of island isolation started in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine whether genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide restriction site associated DNA (RAD) markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographical bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and a sister species, Sarcophanops steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation probably demonstrates an effect of recent geographical isolation (after the Last Glacial Maximum) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated populations is a failure to detect subtle population structure owing to past genetic sampling constraints, rather than the absence of such structure.

A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila . Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

We report the characteristics of the mitochondrial genomes of 22 individuals in the bird genus Piranga, including all currently recognized species in the genus (n = 11). Elements follow the standard avian mitogenome series, including two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein coding genes, and the mitochondrial control region. Excluding tRNA sequences, sequence divergence rate was lowest in rRNA genes and highest in genes encoding NADH (specifically ND1, ND2, ND3) and the control region. Gene trees assembled from 16 elements (non-tRNAs) varied greatly in topological concordance compared to the recognized species tree (based on thousands of nuclear loci), with no one gene tree precisely recovering all relationships in the genus. We also investigated patterns of concordance between the mitogenome tree and the nuclear species tree and found some discrepancies. Across non-tRNA gene trees (n = 16), the species tree topology was recovered by as few as three elements at a particular node and complete concordance (i.e. 16/16 gene trees matched the species tree topology) was recovered at only one node. We found mitochondrial gene regions that are often used in vertebrate systematics (e.g. CytB, ND2) recovered nearly the exact same topology as the nuclear species tree topology.

Phylogeographic studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation, but remains relatively undocumented perhaps because the current episode of island isolation started relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus ( Sarcophanops ) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide RAD markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. steerii , but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

Phylogeographic studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation, but remains relatively undocumented perhaps because the current episode of island isolation started relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus ( Sarcophanops ) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide RAD markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. steerii , but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.