Local origin and diversification among Lampornis hummingbirds: A Mesoamerican taxon

Sufficient versus optimal climatic stability during the Late Quaternary: using environmental quality to guide phylogeographic inferences in a Neotropical montane system

Quaternary climatic oscillations affected species distributions worldwide, creating cycles of connectivity and isolation that impacted population demography and promoted lineage divergence. These effects have been well studied in temperate regions. Taxa inhabiting mesic montane habitats in tropical ecosystems show high levels of endemism and diversification in the distinct mountain ranges they inhabit; such a pattern has commonly been ascribed to past climatic oscillations, but few phylogeographic studies have tested this hypothesis. Here, we combine ecological niche models of species distributions with molecular data to study phylogeographic patterns in two rodents endemic to the highlands of Costa Rica and western Panama (Reithrodontomys creper and Nephelomys devius). In so doing, we apply a novel approach that incorporates a basic ecological principle: the expected positive relationship between environmental suitability and population abundance. Specifically, we use niche models to predict potential patterns of population connectivity and stability of different suitability levels during climatic extremes of the last glacial–interglacial cycle; we then test these predictions with population genetic analyses of a mitochondrial and a nuclear marker. The detailed predictions arising from the different levels of suitability were moderately to highly congruent with the molecular data depending on the species. Overall, results suggest that in these tropical montane ecosystems, cycles of population connectivity and isolation followed a pattern opposite to that typically described for temperate or lowland tropical ecosystems: namely, higher connectivity during the colder glacials, with isolation in montane refugia during the interglacials, including today. Nevertheless, the individualistic patterns for each species indicate a potentially wide gamut of phylogeographic histories reflecting particularities of their niches. Taken together, this study illustrates how phylogeographic inferences may benefit from niche model outputs that provide more detailed predictions of connectivity and finer characterizations of potential refugia through time.

What drives genetic and phenotypic divergence in the Red-crowned Ant tanager (Habia rubica, Aves: Cardinalidae), a polytypic species?

AIM

The effects of geographic and environmental variables on patterns of genetic and phenotypic differentiation have been thoroughly studied. Ecological speciation involves reproductive isolation due to divergent natural selection that can result in a positive correlation between genetic divergence and adaptive phenotypic divergence (isolation by adaptation, IBA). If the phenotypic target of selection is unknown or not easily measured, environmental variation can be used as a proxy, expecting positive correlation between genetic and environmental distances, independent of geographic distances (isolation by environment, IBE). The null model is that the amount of gene flow between populations decreases as the geographic distance between them increases, and genetic divergence is due simply to the neutral effects of genetic drift (isolation by distance, IBD). However, since phenotypic differentiation in natural populations may be autocorrelated with geographic distance, it is often difficult to distinguish IBA from the neutral expectation of IBD. In this work, we test hypotheses of IBA, IBE, and IBD in the Red-crowned Ant tanager (Habia rubica).

LOCATION

Mesoamerica (Mexico-Central America) and South America.

TAXON

Habia rubica (Aves: Cardinalidae).

METHODS

We compiled genetic data, coloration, and morphometric data from specimens from collections in Mexico and the United States. We used the Multiple Matrix Regression with Randomization (MMRR) approach to evaluate the influence of geographic and environmental distances on genetic and phenotypic differentiation of H. rubica at both phylogroup and population levels.

RESULTS

Our results provide strong evidence that geographic distance is the main driver of genetic variation in H. rubica. We did not find evidence that climate variation is driving population differentiation in this species across a widespread geographic region.

MAIN CONCLUSIONS

Our data point to geographic isolation as the main factor structuring genetic variation within populations of H. rubica and suggest that climate is not playing a major role in genetic differentiation within this species.

Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue‐throated populations (Sierra Madre del Sur); two groups of amethyst‐throated populations (Trans‐Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue‐ and amethyst‐throated populations does not correspond to the 2‐MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest‐interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.

Geographic isolation drives divergence of uncorrelated genetic and song variation in the Ruddy-capped Nightingale-Thrush (Catharus frantzii; Aves: Turdidae)

Montane barriers influence the evolutionary history of lineages by promoting isolation of populations. The effects of these historical processes are evident in patterns of differentiation among extant populations, which are often expressed as genetic and behavioral variation between populations. We investigated the effects of geographic barriers on the evolutionary history of a Mesoamerican bird by studying patterns of genetic and vocal variation in the Ruddy-capped Nightingale-Thrush (Turdidae: Catharus frantzii), a non-migratory oscine bird that inhabits montane forests from central Mexico to Panama. We reconstructed the phylogeographic history and estimated divergence times between populations using Bayesian and maximum likelihood methods. We found strong support for the existence of four mitochondrial lineages of C. frantzii corresponding to isolated mountain ranges: Sierra Madre Oriental; Sierra Madre del Sur; the highlands of Chiapas, Guatemala, and El Salvador; and the Talamanca Cordillera. Vocal features in C. frantzii were highly variable among the four observed clades, but vocal variation and genetic variation were uncorrelated. Song variation in C. frantzii suggests that sexual selection and cultural drift could be important factors driving song differentiation in C. frantzii.

A multilocus analysis provides evidence for more than one species within Eugenes fulgens (Aves: Trochilidae)

The status of subspecies in systematic zoology is the focus of controversy. Recent studies use DNA sequences to evaluate the status of subspecies within species complexes and to recognize and delimit species. Here, we assessed the phylogenetic relationships, the taxonomic status of the proposed subspecies, and the species limits of the monotypic hummingbird genus Eugenes (E. fulgens with traditionally recognized subspecies E. f. fulgens, E. f. viridiceps, and E. f. spectabilis), using nuclear (Beta Fibrinogen BFib, Ornithine Decarboxylase ODC, and Muscle Skeletal Receptor Tyrosine Kinase MUSK) and mitochondrial (NADH dehydrogenase subunit 2 ND2, NADH dehydrogenase subunit 4 ND4, and Control Region CR) markers. We performed Bayesian and Bayesian Phylogenetics and Phylogeography analyses and found genetic differences between the three groups, suggesting the existence of two cryptic species (E. fulgens and E. viridiceps) and one phenotypically differentiated species (E. spectabilis). Our analyses show that the E. viridiceps and E. fulgens groups are more closely related with one another than with E. spectabilis.

Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA

Evolutionary timescales can be estimated from genetic data using the molecular clock, often calibrated by fossil or geological evidence. However, estimates of molecular rates in mitochondrial DNA appear to scale negatively with the age of the clock calibration. Although such a pattern has been observed in a limited range of data sets, it has not been studied on a large scale in metazoans. In addition, there is uncertainty over the temporal extent of the time-dependent pattern in rate estimates. Here we present a meta-analysis of 239 rate estimates from metazoans, representing a range of timescales and taxonomic groups. We found evidence of time-dependent rates in both coding and non-coding mitochondrial markers, in every group of animals that we studied. The negative relationship between the estimated rate and time persisted across a much wider range of calibration times than previously suggested. This indicates that, over long time frames, purifying selection gives way to mutational saturation as the main driver of time-dependent biases in rate estimates. The results of our study stress the importance of accounting for time-dependent biases in estimating mitochondrial rates regardless of the timescale over which they are inferred.

Geographical patterns of genetic divergence in the widespread Mesoamerican bumble bee Bombus ephippiatus (Hymenoptera: Apidae)

Bumble bees (Bombus Latreille) are an important group of social insects, well recognized throughout northern temperate regions as important pollinators of wild and agricultural plants. Little is known about the biology of this group in southern portions of the Americas, especially in Mesoamerica, a region of geological and ecological complexity from Mexico through Central America. One ubiquitous Mesoamerican species, Bombus ephippiatus, is enigmatic. Like many other Bombus, this species is homogeneous in body structure yet exhibits striking intraspecific color pattern polymorphism across its range, leading to uncertainty about its genealogical boundaries. It has been grouped taxonomically with B. wilmattae, a species narrowly restricted to southern Mexico and northern Guatamala. Furthermore, the relationships between these two taxa and a third species, B. impatiens, found only in America north of Mexico, have been controversial. Our phylogenetic analysis of DNA sequences from mitochondrial COI and nuclear PEPCK and CAD resolves the phylogeny of these three taxa as (B. impatiens, (B. ephippiatus, B. wilmattae)). Additional data from eight nuclear microsatellite markers reveal complex patterns of genetic divergence and isolation among populations of B. ephippiatus across its extensive geographic range, providing evidence for multiple independent evolutionary lineages. These lineages correspond not only to geographic and habitat variation across their range, but also to distinct color pattern groups present in the species. Knowledge of the phylogeny and genetic divergence of the B. ephippiatus group will provide a framework for understanding evolutionary and ecological origins of color pattern polymorphism in bumble bees, as well as providing insight into geographical factors enhancing speciation in Mesoamerica.

A dated phylogeny of the palm tribe Chamaedoreeae supports Eocene dispersal between Africa, North and South America

The palm tribe Chamaedoreeae reaches its higher diversity in Central America, however, its distribution ranges from the north eastern part of Mexico to Bolivia with a disjunction to the Mascarene Islands in the Indian Ocean. The disjunct distribution of Chamaedoreeae is generally considered a result of Gondwana vicariance and extinction from Africa and/or Madagascar. However, latitudinal migrations and their role in shaping the distribution of this tribe in the Americas have been largely overlooked. In this study we used seven plastid and two nuclear DNA regions to investigate the phylogenetic relationships and biogeography of the Chamaedoreeae. The resulting phylogeny fully resolved the generic relationships within the tribe. The exact area of origin of the tribe remains uncertain, but dating analyses indicated an initial diversification of the Chamaedoreeae during the Early Eocene, followed by long distance dispersion to the Mascarene Islands in the late Miocene. The radiation of Hyophorbe could have taking place on islands in the Indian Ocean now submerged, but its former presence in Africa or Madagascar cannot be ruled out. At least two independent migrations between North and South America predating the rise of the Panama isthmus need to be postulated to explain the distribution of Chamaedoreeae, one during the Middle Eocene and a second during the Miocene. Whereas the traditional interpretation of distribution of Chamaedoreeae species assumes a west Gondwana origin of the group, the findings presented in this paper make it equally possible to interpret the group as a primarily boreotropical element.

Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands

The arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) are among the most poorly known Neotropical rodents. We investigated species-level phylogenetic relationships among the seven described Habromys species using 1331 aligned bases from the mitochondrial ND3 and ND4 regions. Sequences were obtained from 30 specimens of the seven known species of Habromys and we performed maximum parsimony, maximum likelihood, and Bayesian probabilities analyses. The monophyly of the genus Habromys within the Neotomines was verified. The northernmost H. simulatus is sister to the remaining species of the group; within the latter, the southernmost clade (Oaxaca to Central America) is sister to the Transmexican Volcanic Belt clade. Four major clades are clearly distinguished: H. simulatus from the Sierra Madre Oriental and the closely associated Sierra Mazateca; H. delicatulus and H. schmidlyi from the Transmexican Volcanic Belt; H. lepturus, H. chinanteco, and H. ixtlani from the northern Oaxacan highlands; and H. lophurus from Nuclear Central America. Within species, the analyses suggest that H. simulatus and H. lophurus are each composed by two different taxa.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.