Bailey D. McKay

The causes of mitochondrial DNA gene tree paraphyly in birds.

Gene tree paraphyly is a potentially serious problem because many phylogenetic and phylogeographic studies assume species are monophyletic. Funk and Omland (Funk, D.J., Omland, K.E., 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34, 397-423) found that a seemingly high proportion of bird species (16.7%) were paraphyletic in their mtDNA gene trees. This could imply that mtDNA is an unreliable or even misleading marker for delimiting species. We expand on Funk and Omlands survey and identify the causes of species-level paraphyly in birds. We find that in most cases paraphyly is caused by incorrect taxonomy. In such cases, mtDNA serves systematics by exposing and clarifying taxonomic errors. We find the next most common cause of paraphyly to be incomplete lineage sorting due to recent speciation. Here mtDNA gives a consistent picture of evolution, given the timeframe, but it is not useful for delimiting species and other criteria must be employed. There were relatively few clear instances of paraphyly due to hybridization, though there were more cases where incomplete lineage sorting and hybridization could not be distinguished. We ultimately conclude that, far from a hindrance, mtDNA is generally a useful tool that should continue to facilitate delimitation of avian species.

An empirical comparison of character‐based and coalescent‐based approaches to species delimitation in a young avian complex

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 taivanus). Population aggregation analyses of plumage, mitochondrial and 13 nuclear intron character data sets produced conflicting species hypotheses with plumage data suggesting three species, mitochondrial data suggesting two species, and nuclear intron data suggesting one species. Such conflict is expected among recently diverged species, and by integrating all sources of data, we delimited three species verified with independently congruent character evidence as well as a more weakly supported fourth species identified by a single character. Attempts to validate species hypothesis using Bayesian Phylogenetics and Phylogeography (BPP), a coalescent‐based method of species delimitation, revealed several issues that can seemingly affect statistical support for species recognition. We found that θ priors had a dramatic impact on speciation probabilities, with lower values consistently favouring splitting and higher values consistently favouring lumping. More resolved guide trees also resulted in overall higher speciation probabilities. Finally, we found suggestive evidence that BPP is sensitive to the divergent effects of nonrandom mating caused by intraspecific processes such as isolation‐with‐distance, and therefore, BPP may not be a conservative method for delimiting independently evolving population lineages. Based on these concerns, we questioned the reliability of BPP results and based our conclusions about species limits exclusively on character data.

Molecular phylogeny and insular biogeography of the lowland tailorbirds of Southeast Asia (Cisticolidae: Orthotomus)

The lowland tailorbirds of Southeast Asia (Orthotomus) offer an excellent opportunity for comparative biogeography because of their diversity in the Greater Sunda and Philippine islands. We reconstructed the phylogeny of all species in the genus using maximum likelihood, Bayesian, and coalescent methods on DNA sequences of three gene segments: an autosomal intron (TGF), a Z-linked intron (MUSK), and a mitochondrial coding gene (ND2). Although resolution is low in parts of the phylogeny, several well defined clades emerge. When considered in light of distribution, these clades indicate that the Greater Sunda and Philippine islands were occupied early in Orthotomus history by the ancestors of O. sericeus in the Greater Sundas and O. frontalis in the Philippines. Subsequently, tailorbirds diversified further in each island group: O. atrogularis, O. ruficeps, and O. sepium arose in the Greater Sundas, and O. castaneiceps castaneiceps, O. c. chloronotus, O. derbianus, O. samarensis, O. nigriceps, and O. cinereiceps in the Philippines. Among the continental taxa (including Sundaic birds), the older lineages (O. sutorius and O. sericeus) are habitat generalists and the recently evolved taxa are more specialized. In the Philippines, several taxa once considered conspecific with O. atrogularis turn out to be highly divergent species (>9% in ND2). Indeed, all Philippine allospecies are well diverged from one another. This finding supports the recent assertion of higher-than-appreciated bird endemicity in the Philippines.

Incorporating Color into Integrative Taxonomy: Analysis of the Varied Tit (Sittiparus varius) Complex in East Asia

Species designations are critically important scientific hypotheses that serve as the foundational units in a wide range of biological subdisciplines. A growing realization that some classes of data fail to delimit species under certain conditions has led to increasingly more integrative taxonomies, whereby species discovery and hypothesis testing are based on multiple kinds of data (e.g., morphological, molecular, behavioral, ecological, etc.). However, although most taxonomic descriptions have been based on morphology, some key morphological features, such as color, are rarely quantified and incorporated into integrative taxonomic studies. In this article, we applied a new method of ultraviolet digital photography to measure plumage variation in a color-variable avian species complex, the varied tit (Sittiparus varius). Plumage measurements corroborated species limits defined by morphometric, mitochondrial DNA, and nuclear DNA disjunctions and provided the only evidence for distinguishing two recently evolved species. Importantly, color quantification also provided a justification for lumping putative taxa with no evidence of evolutionary independence. Our revised taxonomy thus refines conservation units for listing and management and clarifies the primary units for evolutionary studies. Species tree analyses, which applied the newly delimited species as operational taxonomic units, revealed a robust phylogenetic hypothesis for the group that establishes a foundation for future biogeographic analyses. This study demonstrates how digital photography can be used to incorporate color character variation into integrative taxonomies, which should lead to more informed, more rigorous, and more accurate assessments of biodiversity. [Color, digital photography, integrative taxonomy, Sittiparus varius, species delimitation, varied tit.].

Sisyphean evolution in Darwin's finches

The trajectory of speciation involves geographic isolation of ancestral populations followed by divergence by natural selection, genetic drift or sexual selection. Once started, the process may experience fits and starts, as sometimes diverging populations intermittently reconnect. In theory populations might cycle between stages of differentiation and never attain species status, a process we refer to as Sisyphean evolution. We argue that the six putative ground finch species (genus Geospiza) of the Galápagos Islands represent a dramatic example of Sisyphean evolution that has been confused with the standard model of speciation. The dynamic environment of the Galápagos, closely spaced islands, and frequent dispersal and introgression have prevented the completion of the speciation process. We suggest that morphological clusters represent locally adapted ecomorphs, which might mimic, and have been confused with, species, but these ecomorphs do not form separate gene pools and are ephemeral in space and time. Thus the pattern of morphological, behavioural and genetic variation supports recognition of a single species of Geospiza, which we suggest should be recognized as Darwins ground finch (Geospiza magnirostris). We argue that instead of providing an icon of insular speciation and adaptive radiation, which is featured in nearly every textbook on evolutionary biology, Darwins ground finch represents a potentially more interesting phenomenon, one of transient morphs trapped in an unpredictable cycle of Sisyphean evolution. Instead of revealing details of the origin of species, the mechanisms underlying the transient occurrence of ecomorphs provide one of the best illustrations of the antagonistic effects of natural selection and introgression.

Evidence for the Species Status of the Bahama Yellow-Throated Warbler (Dendroica “Dominica” Flavescens)

ABSTRACT. The Bahama subspecies of the Yellow-throated Warbler (Dendroica dominica flavescens) was originally described as a species. However, it was later reclassified as a subspecies, in part because the trinomial was considered useful for demonstrating relationships. Although flavescens has been widely reported as diagnostic in plumage and distinctive in ecology, it has remained a subspecies of D. dominica, perhaps because of the notion that its song is similar to that of continental dominica. We investigated the taxonomic status of flavescens by examining morphological, song, and genetic data. We found statistically significant differences between flavescens and continental dominica in wing chord and in bill, tarsus, and tail lengths. Discriminant function analysis correctly predicted 100% of flavescens individuals using morphological characters. Contrary to earlier accounts, we also found the ascending song of flavescens to be diagnosable from the descending song of continental dominica. Mitochondrial control-region sequence data revealed fixed differences and a 1.0% divergence between flavescens and continental dominica. Phylogenetic analysis indicated that flavescens samples form a monophyletic group and that continental dominica is paraphyletic with respect to flavescens. This is consistent with a scenario of peripatric speciation: complete lineage sorting in the flavescens population but incomplete lineage sorting in the much larger continental dominica population. We conclude that flavescens satisfies the requirements of both the biological and phylogenetic species concepts, and we therefore recommend that flavescens be reclassified as a separate species, the Bahama Warbler (Dendroica flavescens).

Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii)

BackgroundThe subtropical island of Taiwan is an area of high endemism and a complex topographic environment. Phylogeographic studies indicate that vicariance caused by Taiwans mountains has subdivided many taxa into genetic phylogroups. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the evolutionary history of an endemic montane bird, Steeres Liocichla (Liocichla steerii), fit the general vicariant paradigm for a montane organism.ResultsWe found that while mountains appear to channel gene flow they are not a significant barrier for Steeres Liocichla. Recent demographic expansion was evident, and genetic diversity was relatively high across the island, suggesting expansion from multiple areas rather than a few isolated refugia. Ecological niche modeling corroborated the molecular results and suggested that populations of Steeres Liocichla are connected by climatically suitable habitat and that there was less suitable habitat during the Last Glacial Maximum.ConclusionsGenetic and ecological niche modeling data corroborate a single history--Steeres Liocichla was at lower density during the Last Glacial Maximum and has subsequently expanded in population density. We suggest that such a range-wide density expansion might be an overlooked cause for the genetic patterns of demographic expansion that are regularly reported. We find significant differences among some populations in FSTindices and an admixture analysis. Though both of these results are often used to suggest conservation action, we affirm that statistically significant results are not necessarily biologically meaningful and we urge caution when interpreting highly polymorphic data such as microsatellites.

Phenotypic Variation is Clinal in the Yellow-Throated Warbler

Abstract Subspecies are assumed to have unique evolutionary histories, but molecular data sometimes contradict subspecies designations based on morphology. A recent genetic survey of the Yellow-throated Warbler (Dendroica dominica) found that none of its three continental subspecies qualified as evolutionarily significant units. I performed a range-wide morphological assessment of the continental Yellow-throated Warbler subspecies in an effort to quantify their differences and examine if and how subspecific differences related to geography. Results indicated much overlap in the morphological characters most important in diagnosing Yellow-throated Warbler subspecies (bill length and the proportion of yellow in the lores), and discriminant function analysis failed to correctly assign most individuals, especially those collected near a subspecies border. There was a strong west-to-east clinal change in bill length and the proportion of yellow in the lores and no evidence of discrete morphological groups. I recommend eliminating the subspecies D. d. albilora and D. d. stoddardi because they cannot be reliably diagnosed by morphology or mtDNA.