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PubMed2006

Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae).

We sequenced 15 complete mitochondrial genomes and performed comprehensive molecular phylogenetic analyses to study the origin and phylogeny of the Hynobiidae, an ancient lineage of living salamanders. Our phylogenetic analyses show that the Hynobiidae is a clade with well resolved relationships, and our results contrast with a morphology-based phylogenetic hypothesis. These salamanders have low vagility and are limited in their distribution primarily by deserts, mountains, and oceans. Our analysis suggests that the relationships among living hynobiids have been shaped primarily by geography. We show that four-toed species assigned to Batrachuperus do not form a monophyletic group, and those that occur in Afghanistan and Iran are transferred to the resurrected Paradactylodon. Convergent morphological characters in different hynobiid lineages are likely produced by similar environmental selective pressures. Clock-independent molecular dating suggests that hynobiids originated in the Middle Cretaceous [ approximately 110 million years ago (Mya)]. We propose an "out of North China" hypothesis for hynobiid origins and hypothesize an ancestral stream-adapted form. Given the particular distributional patterns and our molecular dating estimates, we hypothesize that: (i) the interior desertification from Mongolia to Western Asia began approximately 50 Mya; (ii) the Tibetan plateau (at least on the eastern fringe) experienced rapid uplift approximately 40 Mya and reached an altitude of at least 2,500 m; and (iii) the Ailao-Red River shear zone underwent the most intense orogenic movement approximately 24 Mya.

Animals↗
PubMed1971

Interconnected patterns of biogeography and evolution.

Analysis of the fauna of the carabid beetles of New Guinea reveals both a broad dispersal pattern and a local turnover pattern that together fit into a world-wide pattern of successive dispersals and replacements that run from large to small areas and from more to less favorable climates. This pattern coincides broadly with a world-wide pattern of species numbers. Evolution by group selection, proceeding most rapidly and effectively where species are most numerous, connects the patterns and can supply the force that gives direction to the dispersal pattern. Directional change at any level of complexity involves movement that results in the formation of diverse groups of units (which are themselves groups of smaller units) and differential survival. This process-generalized group selection-has been continuous from chemical evolution on the earth's surface, through the origin of life, and into successive interacting levels of organic evolution. A corollary is that evolution should make situations favorable to itself, by group selection, and has probably done so in (for example) tropical rain forest, where new information about group evolution may be sought.

Journal Article↗
PubMed1992

Vicariance biogeography in the Pleistocene and speciation in North American wood warblers: a test of Mengel's model.

It is widely believed that habitat fragmentation during the Pleistocene initiated speciation events in many songbird genera. One such vicariance model for avian speciation in the Pleistocene was developed by R. M. Mengel for North American birds. This model suggests that the first Pleistocene glacial advance reduced the area of an extensive, eastern North American deciduous forest, forcing adaptation by some species to boreal forest. This, in turn, facilitated the development of transcontinental range expansions during interglacials. Subsequent glacial advances repeatedly fragmented the ranges of these species into eastern and western populations; western isolates speciated to form the multispecies groups observed among various North American birds. We used mtDNA restriction site data to reconstruct the phylogeny of the black-throated green warbler complex-the group that Mengel considered the best fit to his model. Contrary to Mengel's model, the phylogeny indicates that not all western endemics were derived from an eastern ancestor. Instead, our results imply a mix, wherein some western endemics were budded off an eastern source, as Mengel posits, while others probably resulted from intermontane isolations in the west.

Journal Article↗
PubMed1992

Caribbean biogeography: molecular evidence for dispersal in West Indian terrestrial vertebrates.

The geological association of the Greater Antilles with North and South America in the late Cretaceous led to the hypothesis that the present Antillean biota reflects those ancient land connections. Molecular data from diverse West Indian amphibians and reptiles and their mainland relatives support a more recent derivation of the Antillean vertebrate fauna by overwater dispersal. The catastrophic bolide impact in the Caribbean region at the close of the Cretaceous provides a proximate cause for the absence of an ancient West Indian biota.

Journal Article↗
PubMed1993

Biogeography of Tongan birds before and after human impact.

Bones deposited in caves show that, before the arrival of humans, at least 27 species of land birds lived on the Tongan island of 'Eua, where 13 indigenous species live today. Six of these 13 species were recorded from pre-human strata; three others probably occurred on 'Eua in pre-human times but were not in the fossil sample; and four others probably colonized 'Eua since the arrival of humans approximately 3000 years ago. Of the 23 species of extinct or extirpated land birds recorded from 'Eua, the nearest geographic occurrences of conspecifics or most closely related congeners are from the Solomon Islands (1 species), New Caledonia (2 species), Fiji and/or Samoa (9 species), elsewhere in Tonga (8 species), or unknown (3 species). The avifauna of West Polynesia (Fiji-Tonga-Samoa) is more closely related to that of Melanesia than that of East Polynesia. There was little pre-human turnover in Tongan land birds. The arrival of humans has influenced the Tongan avifauna more than any climatic, tectonic, or biological event of the past approximately 100,000 years.

Journal Article↗
PubMed1995

Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution.

The internal transcribed spacers (ITS) of nuclear ribosomal DNA of 33 species of genus Paeonia (Paeoniaceae) were sequenced. In section Paeonia, different patterns of nucleotide additivity were detected in 14 diploid and tetraploid species at sites that are variable in the other 12 species of the section, suggesting that reticulate evolution has occurred. Phylogenetic relationships of species that do not show additivity, and thus ostensibly were not derived through hybridization, were reconstructed by parsimony analysis. The taxa presumably derived through reticulate evolution were then added to the phylogenetic tree according to additivity from putative parents. The study provides an example of successfully using ITS sequences to reconstruct reticulate evolution in plants and further demonstrates that the sequence data could be highly informative and accurate for detecting hybridization. Maintenance of parental sequences in the species of hybrid origin is likely due to slowing of concerted evolution caused by the long generation time of peonies. The partial and uneven homogenization of parental sequences displayed in nine species of putative hybrid origin may have resulted from gradients of gene conversion. The documented hybridizations may have occurred since the Pleistocene glaciations. The species of hybrid origin and their putative parents are now distantly allopatric. Reconstruction of reticulate evolution with sequence data, therefore, provides gene records for distributional histories of some of the parental species.

Asia↗
PubMed1999

Early hominid biogeography.

We examined the biogeographic patterns implied by early hominid phylogenies and compared them to the known dispersal patterns of Plio-Pleistocene African mammals. All recent published phylogenies require between four and seven hominid dispersal events between southern Africa, eastern Africa, and the Malawi Rift, a greater number of dispersals than has previously been supposed. Most hominid species dispersed at the same time and in the same direction as other African mammals. However, depending on the ages of critical hominid specimens, many phylogenies identify at least one hominid species that dispersed in the direction opposite that of contemporaneous mammals. This suggests that those hominids may have possessed adaptations that allowed them to depart from continental patterns of mammalian dispersal.

Africa↗
PubMed1999

Macroevolution of insect-plant associations: the relevance of host biogeography to host affiliation.

Identifying the factors that have promoted host shifts by phytophagous insects at a macroevolutionary scale is critical to understanding the associations between plants and insects. We used molecular phylogenies of the beetle genus Blepharida and its host genus Bursera to test whether these insects have been using hosts with widely overlapping ranges over evolutionary time. We also quantified the importance of host range coincidence relative to host chemistry and host phylogenetic relatedness. Overall, the evolution of host use of these insects has not been among hosts that are geographically similar. Host chemistry is the factor that best explains their macroevolutionary patterns of host use. Interestingly, one exceptional polyphagous species has shifted among geographically close chemically dissimilar plants.

Journal Article↗
PubMed2004

Phylogeny and biogeography of the "Australian" trichostomes (Ciliophora: Litostomata).

The phylogenetic relationships of members of the ciliate class Litostomatea were determined by a molecular phylogeny using the small subunit of the ribosomal RNA (ssu-rRNA) gene and a morphological phylogeny based on ultrastructural analyses of the group. Molecular analyses consistently supported the monophyly of Trichostomatia, Entodiniomorphida and the "Australian" trichostomes but provided limited support for a monophyletic Vestibuliferida and Haptoria. The results of the morphological analyses depended on the way in which the dataset was treated: "unordered" and "ordered" recovered a monophyletic Trichostomatia, Haptoria and the "Australian" trichostomes but challenged the monophyly of Entodinimorphida and Vestibuliferida; "dollo" recovered a monophyletic Trichostomatia and Entodiniomorphida but at the cost of a greatly longer tree than either "unordered" or "ordered" datasets. The monophyly of each "Australian" trichostome family was supported in all analyses and by both approaches. These results suggest that the trichostome ciliates may have become associated with mammals in Gondwana with the "Australian" trichostome ciliates entering Australia with primitive herbivorous marsupials. Subsequent diversification of the "Australian" families was probably a result of dietary specialization and oral and cortical synapomorphies define each family. We decline at this time to erect a formal taxon name for the "Australian" trichostomes due to the instability of other superfamilial taxa within the Litosomatea and concerns about the stability of tree topology until a better taxon sample of litostome ciliates is available.

Animals↗
PubMed2000

Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides.

The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the Southern Hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as several relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, we examine several hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias. Although most workers consider Lepidogalaxias to be an unusual scaled member of the Southern Hemisphere galaxioids, it has also been suggested that this species is related to the Northern Hemisphere esocoids. Our data strongly suggest that this species is not a galaxiid, and the alternative hypothesized esocoid relationship cannot be rejected. The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships. Juvenile saltwater-tolerance is phylogenetically distributed throughout the Galaxiinae, and the loss of this migratory phase may be a major cause of speciation.

Animals↗
PubMed2003

Phylogenetic relationships among calyptraeid gastropods and their implications for the biogeography of marine speciation.

Although calyptraeid gastropods are not well understood taxonomically, in part because their simple plastic shells are the primary taxonomic character, they provide an ideal system to examine questions about evolution in the marine environment. I conducted a phylogenetic analysis of calyptraeid gastropods using DNA sequence data from mitochondrial cytochrome oxidase I (COI) and 16S genes and the nuclear 28S gene. The resultant phylogeny was used to examine the biogeographic patterns of speciation in the Calyptraeidae. Parsimony and Bayesian analyses of the combined data sets for 94 calyptraeid operational taxonomic units and 24 outgroups produced well-resolved phylogenies. Both approaches resulted in identical sister-species relationships, and the few differences in deeper topology did not affect biogeographic inferences. The geographic distribution of the species included here demonstrate numerous dispersal events both between the Pacific and Atlantic oceans and across the equator. When parsimony is used to reconstruct the movement from the Pacific to the Atlantic oceans on the phylogeny, there are 12 transitions between oceans, primarily from the Pacific to the Atlantic. When the latitude is coded as north versus south of the equator, the most-parsimonious reconstruction gives the origin of calyptraeids in the north followed by 15 dispersal events to regions south of the equator and no returns to the north. Many clades of the most closely related species are either sympatric or occur along a single coastline. Closely related species can, however, occur in such divergent regions as Southern California and South Africa. There is little evidence for sister-species pairs or larger clades having been split by the Isthmus of Panama or the Benguela upwelling, but the East Pacific Barrier appears to separate the most basal taxa from the rest of the family.

Animals↗
PubMed2003

Biotic element analysis in biogeography.

Biotic element analysis is an alternative to the areas-of-endemism approach for recognizing the presence or absence of vicariance events in a given region. If an ancestral biota was fragmented by vicariance events, biotic elements or clusters of distribution areas should emerge. We propose a statistical test for clustering of distribution areas based on a Monte Carlo simulation with a null model that considers the spatial autocorrelation in the data. The hypothesis tested is that the observed degree of clustering of ranges can be explained by the range size distribution, the varying number of taxa per cell, and the spatial autocorrelation of the occurrences of a taxon alone. A method for the delimitation of biotic elements which uses model-based Gaussian clustering is introduced. We demonstrate our methods and show the importance of grid size by means of a case study, an analysis of the distribution patterns of southern African species of the weevil genus Scobius. The example highlights the difficulties in delimiting areas of endemism if dispersal has occurred and illustrates the advantages of the biotic element approach.

Animals↗
PubMed2004

Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae).

Swallowtail butterflies are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. We inferred phylogenetic relationships for 51 of about 205 species of the genus Papilio (sensu lato) from 3.3-Kilobase (kb) sequences of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidases I and II and 1.0 kb of elongation factor 1 alpha). Congruent phylogenetic trees were recovered within Papilio from analyses of combined data using maximum likelihood, Bayesian analysis, and maximum parsimony bootstrap consensus. Several disagreements with the traditional classification of Papilio were found. Five major previously hypothesized subdivisions within Papilio were well supported: Heraclides, Pterourus, Chilasa, Papilio (sensu stricto), and Eleppone. Further studies are required to clarify relationships within traditional "Princeps," which was paraphyletic. Several biologically interesting characteristics of Papilio appear to have polyphyletic origins, including mimetic adults, larval host associations, and larval morphology. Early diversification within Papilio is estimated at 55-65 million years ago based on a combination of biogeographic time constraints rather than fossils. This divergence time suggests that Papilio has slower apparent substitution rates than do Drosophila and fig-pollinating wasps and/or divergences corrected using best-fit substitution models are still being consistently underestimated. The amount of sequence divergence between Papilio subdivisions is equivalent to divergences between genera in other tribes of the Papilionidae, and between genera of moths of the noctuid subfamily Heliothinae.

Animals↗
PubMed2004

Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns.

The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. We examined the relative roles played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1,393 terminals). Parsimony-based tree fitting in conjunction with permutation tests was used to examine to what extent Southern Hemisphere biogeographic patterns fit the breakup sequence of Gondwana and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana breakup: (Africa(New Zealand(southern South America, Australia))). Trans-Antarctic dispersal (Australia <--> southern South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (southern South America(Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.

Africa↗
PubMed2004

Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference.

Pistia stratiotes (water lettuce) and Lemna (duckweeds) are the only free-floating aquatic Araceae. The geographic origin and phylogenetic placement of these unrelated aroids present long-standing problems because of their highly modified reproductive structures and wide geographical distributions. We sampled chloroplast (trnL-trnF and rpl20-rps12 spacers, trnL intron) and mitochondrial sequences (nad1 b/c intron) for all genera implicated as close relatives of Pistia by morphological, restriction site, and sequencing data, and present a hypothesis about its geographic origin based on the consensus of trees obtained from the combined data, using Bayesian, maximum likelihood, parsimony, and distance analyses. Of the 14 genera closest to Pistia, only Alocasia, Arisaema, and Typhonium are species-rich, and the latter two were studied previously, facilitating the choice of representatives that span the roots of these genera. Results indicate that Pistia and the Seychelles endemic Protarum sechellarum are the basalmost branches in a grade comprising the tribes Colocasieae (Ariopsis, Steudnera, Remusatia, Alocasia, Colocasia), Arisaemateae (Arisaema, Pinellia), and Areae (Arum, Biarum, Dracunculus, Eminium, Helicodiceros, Theriophonum, Typhonium). Unexpectedly, all Areae genera are embedded in Typhonium, which throws new light on the geographic history of Areae. A Bayesian analysis of divergence times that explores the effects of multiple fossil and geological calibration points indicates that the Pistia lineage is 90 to 76 million years (my) old. The oldest fossils of the Pistia clade, though not Pistia itself, are 45-my-old leaves from Germany; the closest outgroup, Peltandreae (comprising a few species in Florida, the Mediterranean, and Madagascar), is known from 60-my-old leaves from Europe, Kazakhstan, North Dakota, and Tennessee. Based on the geographic ranges of close relatives, Pistia likely originated in the Tethys region, with Protarum then surviving on the Seychelles, which became isolated from Madagascar and India in the Late Cretaceous (85 my ago). Pistia and Protarum provide striking examples of ancient lineages that appear to have survived in unique or isolated habitats.

Araceae↗