Classic problems in historical biogeography are where did penguins originate, and why are such mobile birds restricted to the Southern Hemisphere? Competing hypotheses posit they arose in tropical-warm temperate waters, species-diverse cool temperate regions, or in Gondwanaland approximately 100 mya when it was further north. To test these hypotheses we constructed a strongly supported phylogeny of extant penguins from 5851 bp of mitochondrial and nuclear DNA. Using Bayesian inference of ancestral areas we show that an Antarctic origin of extant taxa is highly likely, and that more derived taxa occur in lower latitudes. Molecular dating estimated penguins originated about 71 million years ago in Gondwanaland when it was further south and cooler. Moreover, extant taxa are inferred to have originated in the Eocene, coincident with the extinction of the larger-bodied fossil taxa as global climate cooled. We hypothesize that, as Antarctica became ice-encrusted, modern penguins expanded via the circumpolar current to oceanic islands within the Antarctic Convergence, and later to the southern continents. Thus, global cooling has had a major impact on penguin evolution, as it has on vertebrates generally. Penguins only reached cooler tropical waters in the Galapagos about 4 mya, and have not crossed the equatorial thermal barrier.

The ratites have stimulated much debate as to how such large £ightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of £ight. Hypotheses regarding the relationships among taxa di¡er for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of ¢ve extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary) and two tinamous from di¡erent genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and nonhomogeneous maximum likelihood, the ratites are found to be monophyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor^descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages ¢t the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.

Molecular dating largely overturned the paradigm that global cooling during recent Pleistocene glacial cycles resulted in a burst of species diversification although some evidence exists that speciation was commonly promoted in habitats near the expanding and retracting ice sheets. Here, we used a genome-wide dataset of more than half a million base pairs of DNA to test for a glacially induced burst of diversification in kiwi, an avian family distributed within several hundred kilometers of the expanding and retracting glaciers of the Southern Alps of New Zealand. By sampling across the geographic range of the five kiwi species, we discovered many cryptic lineages, bringing the total number of kiwi taxa that currently exist to 11 and the number that existed just before human arrival to 16 or 17. We found that 80% of kiwi diversification events date to the major glacial advances of the Middle and Late Pleistocene. During this period, New Zealand was repeatedly fragmented by glaciers into a series of refugia, with the tiny geographic ranges of many kiwi lineages currently distributed in areas adjacent to these refugia. Estimates of effective population size through time show a dramatic bottleneck during the last glacial cycle in all but one kiwi lineage, as expected if kiwi were isolated in glacially induced refugia. Our results support a fivefold increase in diversification rates during key glacial periods, comparable with levels observed in classic adaptive radiations, and confirm that at least some lineages distributed near glaciated regions underwent rapid ice age diversification.kiwi | Apteryx | New Zealand | glaciation | diversification P leistocene climate cycles resulted in glaciation and the buildup of extensive ice sheets at temperate latitudes during periods of global cooling, followed by recession of ice sheets during brief interglacial periods. These cycles were originally proposed to have fragmented populations, resulting in speciation and the formation of much of today's species richness (1-5).

To test the hypothesis put forward by Feduccia of the origin of modern birds from transitional birds, we sequenced the first two complete mitochondrial genomes of shorebirds (ruddy turnstone and blackish oystercatcher) and compared their sequences with those of already published avian genomes. When corrected for rate heterogeneity across sites and non-homogeneous nucleotide compositions among lineages in maximum likelihood (ML), the optimal tree places palaeognath birds as sister to the neognaths including shorebirds. This optimal topology is a re-rooting of recently published ordinal-level avian trees derived from mitochondrial sequences. Using a penalized likelihood (PL) rate-smoothing process in conjunction with dates estimated from fossils, we show that the basal splits in the bird tree are much older than the Cretaceous-Tertiary (K-T) boundary, reinforcing previous molecular studies that rejected the derivation of modern birds from transitional shorebirds. Our mean estimate for the origin of modern birds at about 123 million years ago (Myr ago) is quite close to recent estimates using both nuclear and mitochondrial genes, and supports theories of continental break-up as a driving force in avian diversification. Not only did many modern orders of birds originate well before the K-T boundary, but the radiation of major clades occurred over an extended period of at least 40 Myr ago, thus also falsifying Feduccia's rapid radiation scenario following a K-T bottleneck.