Comparative phylogeography has proved useful for investigating biological responses to past climate change and is strongest when combined with extrinsic hypotheses derived from the fossil record or geology. However, the rarity of species with sufficient, spatially explicit fossil evidence restricts the application of this method. Here, we develop an alternative approach in which spatial models of predicted species distributions under serial paleoclimates are compared with a molecular phylogeography, in this case for a snail endemic to the rainforests of North Queensland, Australia. We also compare the phylogeography of the snail to those from several endemic vertebrates and use consilience across all of these approaches to enhance biogeographical inference for this rainforest fauna. The snail mtDNA phylogeography is consistent with predictions from paleoclimate modeling in relation to the location and size of climatic refugia through the late Pleistocene-Holocene and broad patterns of extinction and recolonization. There is general agreement between quantitative estimates of population expansion from sequence data (using likelihood and coalescent methods) vs. distributional modeling. The snail phylogeography represents a composite of both common and idiosyncratic patterns seen among vertebrates, reflecting the geographically finer scale of persistence and subdivision in the snail. In general, this multifaceted approach, combining spatially explicit paleoclimatological models and comparative phylogeography, provides a powerful approach to locating historical refugia and understanding species' responses to them. P hylogeography seeks to reveal biogeographical history of species and the habitats they occupy via (i) qualitative spatial association of divisions between monophyletic clusters of alleles with biogeographic barriers, and (ii) quantitative estimates of historical population size (1-4). Much of this work has focused on mitochondrial DNA; however, stochastic variance limits our confidence in reconstructions of history from a single gene. One approach solving this limitation is to sample more genes (5). A more common approach is comparative phylogeography (6) in which sequence variation is surveyed at a single gene for multiple species across the same landscape. A limitation here is that histories of local extinction and recolonization may vary among species despite a common history of habitat fluctuation.To improve inference of historical biogeography, we need to incorporate spatially explicit evidence from paleoecology into interpretation of species' phylogeography. Some recent studies have promoted the use of fossil evidence along with phylogeography to estimate historical distributions (7) or have examined sequence variation in the fossils themselves (e.g., refs. 8 and 9) However, appropriate fossils are sparse or nonexistent for most taxa. We explore a novel and more widely applicable approach that uses paleoclimatological models of species' distributions in conjunction with phylogeography.

A phylogeny of tetrapods is inferred from nearly complete sequences of the nuclear RAG-1 gene sampled across 88 taxa encompassing all major clades, analyzed via parsimony and Bayesian methods. The phylogeny provides support for Lissamphibia, Theria, Lepidosauria, a turtle-archosaur clade, as well as most traditionally accepted groupings. This tree allows simultaneous molecular clock dating for all tetrapod groups using a set of well-corroborated calibrations. Relaxed clock (PLRS) methods, using the amniote = 315 Mya (million years ago) calibration or a set of consistent calibrations, recovers reasonable divergence dates for most groups. However, the analysis systematically underestimates divergence dates within archosaurs. The bird-crocodile split, robustly documented in the fossil record as being around approximately 245 Mya, is estimated at only approximately 190 Mya, and dates for other divergences within archosaurs are similarly underestimated. Archosaurs, and particulary turtles have slow apparent rates possibly confounding rate modeling, and inclusion of calibrations within archosaurs (despite their high deviances) not only improves divergence estimates within archosaurs, but also across other groups. Notably, the monotreme-therian split ( approximately 210 Mya) matches the fossil record; the squamate radiation ( approximately 190 Mya) is younger than suggested by some recent molecular studies and inconsistent with identification of approximately 220 and approximately 165 Myo (million-year-old) fossils as acrodont iguanians and approximately 95 Myo fossils colubroid snakes; the bird-lizard (reptile) split is considerably older than fossil estimates (< or = 285 Mya); and Sphenodon is a remarkable phylogenetic relic, being the sole survivor of a lineage more than a quarter of a billion years old. Comparison with other molecular clock studies of tetrapod divergences suggests that the common practice of enforcing most calibrations as minima, with a single liberal maximal constraint, will systematically overestimate divergence dates. Similarly, saturation of mitochondrial DNA sequences, and the resultant greater compression of basal branches means that using only external deep calibrations will also lead to inflated age estimates within the focal ingroup.

Our understanding of the origin, evolution, and biogeography of seafloor fauna is limited because we have insufficient spatial and temporal data to resolve underlying processes. The abundance and wide distribution of modern and disarticulated fossil Ophiuroidea, including brittle stars and basket stars, make them an ideal model system for global marine biogeography if we have the phylogenetic framework necessary to link extant and fossil morphology in an evolutionary context. Here we construct a phylogeny from a highly complete 425-gene, 61-taxa transcriptome-based data set covering 15 of the 18 ophiuroid families and representatives of all extant echinoderm classes. We calibrate our phylogeny with a series of novel fossil discoveries from the early Mesozoic. We confirm the traditional paleontological view that ophiuroids are sister to the asteroids and date the crown group Ophiuroidea to the mid-Permian (270 ± 30 mega-annum). We refute all historical classification schemes of the Ophiuroidea based on gross structural characters but find strong congruence with schemes based on lateral arm plate microstructure and the temporal appearance of various plate morphologies in the fossil record. The verification that these microfossils contain phylogenetically informative characters unlocks their potential to advance our understanding of marine biogeographical processes.

Colour polymorphism exemplifies extreme morphological diversity within populations. It is taxonomically widespread but generally rare. Theory suggests that where colour polymorphism does occur, processes generating and maintaining it can promote speciation but the generality of this claim is unclear. Here we confirm, using species-level molecular phylogenies for five families of non-passerine birds, that colour polymorphism is associated with accelerated speciation rates in the three groups in which polymorphism is most prevalent. In all five groups, colour polymorphism is lost at a significantly greater rate than it is gained. Thus, the general rarity and phylogenetic dispersion of colour polymorphism is accounted for by a combination of higher speciation rate and higher transition rate from polymorphism to monomorphism, consistent with theoretical models where speciation is driven by fixation of one or more morphs. This is corroborated by evidence from a species-level molecular phylogeny of passerines, incorporating 4,128 (66.5%) extant species, that polymorphic species tend to be younger than monomorphic species. Our results provide empirical support for the general proposition, dating from classical evolutionary theory, that colour polymorphism can increase speciation rates.

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A new classification of Ophiuroidea, considering family rank and above, is presented. The new family and superfamily taxa in O’Hara et al. (2017) were proposed to ensure a better readability of the new phylogeny but are unavailable under the provisions of the ICZN. Here, the morphological diagnoses to all 33 families and five superfamilies are provided. Ten new families, Ophiosphalmidae fam. nov., Ophiomusaidae fam. nov., Ophiocamacidae fam. nov., Ophiopteridae fam. nov., Clarkcomidae fam. nov., Ophiopezidae fam. nov., Ophiernidae fam. nov., Amphilimnidae fam. nov., Ophiothamnidae fam. nov. and Ophiopholidae fam. nov., are described. The family Ophiobyrsidae Matsumoto, 1915, not yet discovered in the previous publication, is added, based on new molecular data. A new phylogenetic reconstruction is presented. Definitions of difficult-to-apply morphological characters are given.

Among root knot nematodes of the genus Meloidogyne, the polyploid obligate mitotic parthenogens M. arenaria, M. javanica, and M. incognita are widespread and common agricultural pests. Although these named forms are distinguishable by closely related mitochondrial DNA (mtDNA) haplotypes, detailed sequence analyses of internal transcribed spacers (ITSs) of nuclear ribosomal genes reveal extremely high diversity, even within individual nematodes. This ITS diversity is broadly structured into two very different groups that are 12%-18% divergent: one with low diversity (< 1.0%) and one with high diversity (6%-7%). In both of these groups, identical sequences can be found within individual nematodes of different mtDNA haplotypes (i.e., among species). Analysis of genetic variance indicates that more than 90% of ITS diversity can be found within an individual nematode, with small but statistically significant (5%-10%; P < 0.05) variance distributed among mtDNA lineages. The evolutionarily distinct parthenogen M. hapla shows a similar pattern of ITS diversity, with two divergent groups of ITSs within each individual. In contrast, two diploid amphimictic species have only one lineage of ITSs with low diversity (< 0.2%). The presence of divergent lineages of rDNA in the apomictic taxa is unlikely to be due to differences among pseudogenes. Instead, we suggest that the diversity of ITSs in M. arenaria, M. javanica, and M. incognita is due to hybrid origins from closely related females (as inferred from mtDNA) and combinations of more diverse paternal lineages.

Recent mtDNA phylogenies of Australasian agamid lizards are highly incongruent with existing morphological views. To resolve this discrepancy we sequenced two nuclear gene regions, c-mos and brain-derived neurotrophic factor (BDNF). These were highly concordant with each other and the mtDNA phylogeny, but not the morphology. A combined molecular analysis reveals substantial hidden support (additional phylogenetic signal that emerges only when the data sets interact in a combined analysis). Bayesian posteriors, and a partitioned bootstrap procedure introduced here, indicate strong support for most nodes. The resultant tree implies extensive morphological homoplasy, with many genera emerging as non-monophyletic (Amphibolurus, Rankinia, Ctenophorus, Physignathus, Diporiphora). The water and forest dragons (Physignathus and Hypsilurus) form a paraphyletic basal assemblage to the more derived Australian forms such as Amphibolurus and Ctenophorus, which include almost all the xeric taxa. However, the thorny devil Moloch horridus is a basal lineage and not closely related to the other arid forms. Tree topology, inferred divergence dates, palaeogeographical and palaeoclimatic data are all consistent with Miocene immigration into Australia from the north by mesic forest ecomorphs, followed by initial diversification in mesic habitats before radiation into xeric habitats facilitated by increasing aridity.