George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.

/pdf/early-bursts-of-body-size-and-shape-evolution-are-rare-in-fnkfb24uyp.pdf

Early bursts of body size and shape evolution are rare in comparative data.

Adaptive radiation refers to diversification from an ancestral species that produces descendants adapted to use a great variety of distinct ecological niches. In this review, I examine two aspects of adaptive radiation: first, that it results from ecological opportunity and, second, that it is deterministic in terms of its outcome and evolutionary trajectory. Ecological opportunity is usually a prerequisite for adaptive radiation, although in some cases, radiation can occur in the absence of preexisting opportunity. Nonetheless, many clades fail to radiate although seemingly in the presence of ecological opportunity; until methods are developed to identify and quantify ecological opportunity, the concept will have little predictive utility in understanding a priori when a clade might be expected to radiate. Although predicted by theory, replicated adaptive radiations occur only rarely, usually in closely related and poorly dispersing taxa found in the same region on islands or in lakes. Continge...

/pdf/adaptive-radiation-ecological-opportunity-and-evolutionary-59u8bnnbz0.pdf

Adaptive Radiation, Ecological Opportunity, and Evolutionary Determinism

Madagascar is one of the world’s hottest biodiversity hot spots due to its diverse, endemic, and highly threatened biota. This biota shows a distinct signature of evolution in isolation, both in the high levels of diversity within lineages and in the imbalance of lineages that are represented. For example, chameleon diversity is the highest of any place on Earth, yet there are no salamanders. These biotic enigmas have inspired centuries of speculation relating to the mechanisms by which Madagascar’s biota came to reside there. The two most probable causal factors are Gondwanan vicariance and/or Cenozoic dispersal. By reviewing a comprehensive sample of phylogenetic studies of Malagasy biota, we find that the predominant pattern is one of sister group relationships to African taxa. For those studies that include divergence time analysis, we find an overwhelming indication of Cenozoic origins for most Malagasy clades. We conclude that most of the present-day biota of Madagascar is comprised of the descendents of Cenozoic dispersers, predominantly with African origins.

http://webpages.icav.up.pt/ptdc/bia-bec/102179/biblio_aulas12e13/annurev.ecolsys.37.091305.pdf

Has Vicariance or Dispersal Been the Predominant Biogeographic Force in Madagascar? Only Time Will Tell

Although the systematic utility of ecological niche modeling is generally well known (e.g., concerning the recognition and discovery of areas of endemism for biogeographic analyses), there has been little discussion of applications concerning species delimitation, and to date, no empirical evaluation has been conducted. However, ecological niche modeling can provide compelling evidence for allopatry between populations, and can also detect divergent ecological niches between candidate species. Here we present results for two taxonomically problematic groups of Phelsuma day geckos from Madagascar, where we integrate ecological niche modeling with mitochondrial DNA and morphological data to evaluate species limits. Despite relatively modest levels of genetic and morphological divergence, for both species groups we find divergent ecological niches between closely related species and parapatric ecological niche models. Niche models based on the new species limits provide a better fit to the known distribution than models based upon the combined (lumped) species limits. Based on these results, we elevate three subspecies of Phelsuma madagascariensis to species rank and describe a new species of Phelsuma from the P. dubia species group. Our phylogeny continues to support a major endemic radiation of Phelsuma in Madagascar, with dispersals to Pemba Island and the Mascarene Islands. We conclude that ecological niche modeling offers great potential for species delimitation, especially for taxonomic groups exhibiting low vagility and localized endemism and for groups with more poorly known distributions. In particular, niche modeling should be especially sensitive for detecting recent parapatric speciation driven by ecological divergence, when the environmental gradients driving speciation are represented within the ecological niche models.

https://www.jstor.org/stable/pdfplus/20143102.pdf

Applications of Ecological Niche Modeling for Species Delimitation: A Review and Empirical Evaluation Using Day Geckos (Phelsuma) from Madagascar

DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.

https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2013.0383

Ancient and modern environmental DNA

Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands.

Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences

C. G. Jones

Papers

Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands.

Interrelationships and history of the slit-eared skinks (Gongylomorphus, Scincidae) of the Mascarene islands, based on mitochondrial DNA and nuclear gene sequences