Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades

New Insights into the Molecular Evolution of Tapirus pinchaque (Tapiridae, Perissodactyla) and the Rise and Fall of Tapirus kabomani as a Full Species

Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest for many naturalists, the field still lacks critical genetics and systematics information about tapir species. In the current work, we analyzed four molecular datasets (mitogenomes, and three nuclear genes, RAG 1-2, IRBP, and BRCA1) of two South American tapirs: the Andean tapir (Tapirus pinchaque) and the alleged new species of tapir, Tapirus kabomani. We derived four main findings. (1) Our molecular phylogenetic analyses showed T. pinchaque as the youngest tapir branch in Neotropics and a sister species of Tapirus terrestris. This contradicts the traditional morphological observations of renowned zoologists and paleontologists, who considered T. pinchaque as the oldest Neotropical tapir. (2) Our data does not support that the alleged T. kabomani is a full species. Rather, it is a specific group within T. terrestris. (3) T. pinchaque is the Neotropical tapir species which yielded the lowest levels of genetic diversity (both for mitochondrial and nuclear data). (4) The spatial genetic structure for T. pinchaque shows differences depending on the type of molecular marker used. With mitogenomes, the spatial structure is relatively weak, whereas with two nuclear genes (RAG 1-2 and IRBP), the spatial structure is highly significant. Curiously, for the other nuclear gene (BRCA1), the spatial structure is practically nonexistent. In any case, the northernmost population of T. pinchaque we studied (Los Nevados National Park in Colombia) was in a peripatric situation and was the most genetically differentiated. This is important for the adequate conservation of this population. (5) T. pinchaque showed clear evidence of population expansion during the last part of the Pleistocene, a period during which the dryness and glacial cold extinguished many large mammals in the Americas. However, T. pinchaque survived and spread throughout the Northern Andes.

Comparative Phylogeography of Two Specialist Rodents in Forest Fragments in Kenya

The fragmented forests of the Kenya highlands, known for their exceptional species richness and endemism, are among the world's most important biodiversity hotspots. However, detailed studies on the fauna of these ecosystems-especially specialist species that depend on moist forests, which are particularly threatened by habitat fragmentation-are still limited. In this study, we used mitochondrial genes (cytochrome b and the displacement loop) and a nuclear marker (retinol-binding protein 3) to investigate genetic and morphological diversity, phylogenetic associations, historical divergence, population dynamics, and phylogeographic patterns in two rodent species-the soft-furred mouse (Praomys jacksoni) and the African wood mouse (Hylomyscus endorobae)-across Kenya's forest landscapes. We found a complex genetic structure, with P. jacksoni exhibiting greater genetic diversity than H. endorobae. The Mt. Kenya P. jacksoni populations are significantly genetically different from those in southwestern forests (Mau Forest, Kakamega Forest, and Loita Hills). In contrast, H. endorobae presented no observable biogeographic structuring across its range. The genetic diversity and geographic structuring patterns highlighted selectively strong effects of forest fragmentation and differing species' ecological and evolutionary responses to these landscape changes. Our findings further underscore the need for expanded sampling across Kenya's highland forests to better understand species' changing diversity and distribution patterns in response to the impacts of human-mediated habitat changes. These insights are critical for informing conservation strategies to preserve biodiversity better in this globally important region.

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.

Associative colour learning and discrimination in the South African Cape rock sengi Elephantulus edwardii (Macroscelidea, Afrotheria, Mammalia)

Beside insects, sengis also consume plant material such as leaves, fruits, seeds and floral nectar. It is known that they use olfaction for foraging, but little is known about their vision and visual learning capabilities. Colour vision has been tested in two species, showing that they are likely dichromats (green- and blue-sensitive retinal cone-photoreceptors, meaning red-green colour blind). Our aim was to examine the learning and colour discrimination abilities of another species, Elephantulus edwardii. Using training procedures and choice experiments, we tested the hypotheses that the animals can associate a reward with trained colours and that they can discriminate between different colour hues. The sengis preferred the trained colours over the others, indicating associative learning. They could discriminate between all tested colours (blue, red, green, yellow). The sengis’ colour choice behaviour indicates that the animals can use also colour features to find food plant material. Additionally, learning abilities most likely are essential for the sengis’ foraging activities, for instance by associating floral or fruit shape, colour or scent with nectar or ripe fruit, to increase the efficiency to locate food sources.

Lagomorpha as a Model Morphological System

Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.

Diversification rates of the "Old Endemic" murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity

Diversity-dependent cladogenesis occurs when a colonizing lineage exhibits increasing interspecific competition as it ecologically diversifies. Repeated colonization of a region by closely related taxa may cause similar effects as species within each lineage compete with one another. This may be particularly relevant for secondary colonists, which could experience limited diversification due to competition with earlier, incumbent colonists over evolutionary time. We tested the hypothesis that an incumbent lineage may diminish the diversification of secondary colonists in two speciose clades of Philippine "Old Endemic" murine rodents-Phloeomyini and Chrotomyini-on the relatively old oceanic island of Luzon. Although phylogenetic analyses confirm the independent, noncontemporaneous colonization of Luzon by the ancestors of these two clades, we found no support for arrested diversification in either. Rather, it appears that diversification of both clades resulted from constant-rate processes that were either uniform or favored the secondary colonists (Chrotomyini), depending on the method used. Our results suggest that ecological incumbency has not played an important role in determining lineage diversification among Luzon murines, despite sympatric occurrence by constituent species within each lineage, and a substantial head start for the primary colonists.

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla). Individual loci provided weak, but often consistent support for topological hypotheses. Although many gene trees lacked accepted species-tree relationships, summary coalescent topologies were largely consistent with inferences from concatenation. At the root of Eutheria, we identified consistent support for a sister relationship between Xenarthra and Afrotheria (i.e., Atlantogenata). At the other nodes of interest, support was less consistent. We suggest Scandentia is the sister of Primatomorpha (Euarchonta), but we failed to reject a sister relationship between Scandentia and Glires. Similarly, we suggest Perissodactyla is sister to Cetartiodactyla (Euungulata), but a sister relationship between Perissodactyla and Chiroptera remains plausible.

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla). Individual loci provided weak, but often consistent support for topological hypotheses. Although many gene trees lacked accepted species-tree relationships, summary coalescent topologies were largely consistent with inferences from concatenation. At the root of Eutheria, we identified consistent support for a sister relationship between Xenarthra and Afrotheria (i.e., Atlantogenata). At the other nodes of interest, support was less consistent. We suggest Scandentia is the sister of Primatomorpha (Euarchonta), but we failed to reject a sister relationship between Scandentia and Glires. Similarly, we suggest Perissodactyla is sister to Cetartiodactyla (Euungulata), but a sister relationship between Perissodactyla and Chiroptera remains plausible.

Mammal madness: is the mammal tree of life not yet resolved?

Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90-110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain 'hard nodes' such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Multilocus systematics and non-punctuated evolution of Holarctic Myodini (Rodentia: Arvicolinae)

The tribe Myodini consists of five genera of forest and alpine voles (Alticola, Caryomys, Eothenomys, Hyperacrius and Myodes) distributed throughout the Holarctic. Because mitochondrial evidence has revealed paraphyly and polyphyly among genera, we apply the first multilocus tests to clarify taxonomy and phylogenetic relationships. Our analyses of 28 of 36 species within Myodini, including three not previously sequenced (A. montosa, A. albicaudus, and H. fertilis), identify four distinct clades and provide the first molecular evidence that Hyperacrius may not belong in Myodini. Myodes is paraphyletic, while polyphyly of Alticola reflects apparent ancient mitochondrial introgression. Diversification in this tribe was hypothesized to be tightly linked to Late Cenozoic climatic events, however, lineage through time analysis indicates diversification over the last 4 My was gradual and not strongly punctuated.

Independent losses of visual perception genes Gja10 and Rbp3 in echolocating bats (Order: Chiroptera)

A trade-off between the sensory modalities of vision and hearing is likely to have occurred in echolocating bats as the sophisticated mechanism of laryngeal echolocation requires considerable neural processing and has reduced the reliance of echolocating bats on vision for perceiving the environment. If such a trade-off exists, it is reasonable to hypothesize that some genes involved in visual function may have undergone relaxed selection or even functional loss in echolocating bats. The Gap junction protein, alpha 10 (Gja10, encoded by Gja10 gene) is expressed abundantly in mammal retinal horizontal cells and plays an important role in horizontal cell coupling. The interphotoreceptor retinoid-binding protein (Irbp, encoded by the Rbp3 gene) is mainly expressed in interphotoreceptor matrix and is known to be critical for normal functioning of the visual cycle. We sequenced Gja10 and Rbp3 genes in a taxonomically wide range of bats with divergent auditory characteristics (35 and 18 species for Gja10 and Rbp3, respectively). Both genes have became pseudogenes in species from the families Hipposideridae and Rhinolophidae that emit constant frequency echolocation calls with Doppler shift compensation at high-duty-cycles (the most sophisticated form of biosonar known), and in some bat species that emit echolocation calls at low-duty-cycles. Our study thus provides further evidence for the hypothesis that a trade-off occurs at the genetic level between vision and echolocation in bats.

[Summary of phylogeny in family Felidae of Carnivora]

Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group.

The lemur revolution starts now: the genomic coming of age for a non-model organism

Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman's primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman's career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies - many of which were conducted by Goodman himself - have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates.

Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity

Naked mole-rats (Heterocephalus glaber), the longest-lived rodents, live 7-10 times longer than similarly sized mice and exhibit normal activities for approximately 75% of their lives. Little is known about the mechanisms that allow them to delay the aging process and live so long. Neuregulin-1 (NRG-1) signaling is critical for normal brain function during both development and adulthood. We hypothesized that long-lived species will maintain higher levels of NRG-1 and that this contributes to their sustained brain function and concomitant maintenance of normal activity. We monitored the levels of NRG-1 and its receptor ErbB4 in H. glaber at different ages ranging from 1 day to 26 years and found that levels of NRG-1 and ErbB4 were sustained throughout development and adulthood. In addition, we compared seven rodent species with widely divergent (4-32 year) maximum lifespan potential (MLSP) and found that at a physiologically equivalent age, the longer-lived rodents had higher levels of NRG-1 and ErbB4. Moreover, phylogenetic independent contrast analyses revealed that this significant strong correlation between MLSP and NRG-1 levels was independent of phylogeny. These results suggest that NRG-1 is an important factor contributing to divergent species MLSP through its role in maintaining neuronal integrity.

Alternative PCR protocol using a single primer set for assessing DNA quality in several tissues from a large variety of mammalian species living in areas endemic for leishmaniasis

The aim of this work was to establish a modified pre-diagnostic polymerase chain reaction (PCR) protocol using a single primer set that enables successful amplification of a highly conserved mammalian sequence in order to determine overall sample DNA quality for multiple mammalian species that inhabit areas endemic for leishmaniasis. The gene encoding interphotoreceptor retinoid-binding protein (IRBP), but not other conserved genes, was efficiently amplified in DNA samples from tail skin, ear skin, bone marrow, liver and spleen from all of the species tested. In tissue samples that were PCR-positive for Leishmania, we found that DNA from 100%, 55% and 22% of the samples tested resulted in a positive PCR reaction for the IRBP, beta-actin and beta-globin genes, respectively. Nucleotide sequencing of an IRBP amplicon resolved any questions regarding the taxonomical classification of a rodent, which was previously based simply on the morphological features of the animal. Therefore, PCR amplification and analysis of the IRBP amplicon are suitable for pre-diagnostically assessing DNA quality and identifying mammalian species living in areas endemic to leishmaniasis and other diseases.

Probability Steiner trees and maximum parsimony in phylogenetic analysis

The phylogenetic tree (PT) problem has been studied by a number of researchers as an application of the Steiner tree problem, a well-known network optimisation problem. Of all the methods developed for phylogenies the maximum parsimony (MP) method is a simple and commonly used method because it relies on directly observable changes in the input nucleotide or amino acid sequences. In this paper we show that the non-uniqueness of the evolutionary pathways in the MP method leads us to consider a new model of PTs. In this so-called probability representation model, for each site a node in a PT is modelled by a probability distribution of nucleotide or amino acid states, and hence the PT at a given site is a probability Steiner tree, i.e. a Steiner tree in a high-dimensional vector space. In spite of the generality of the probability representation model, in this paper we restrict our study to constructing probability phylogenetic trees (PPT) using the parsimony criterion, as well as discussing and comparing our approach with the classical MP method. We show that for a given input set although the optimal topology as well as the total tree length of the PPT is the same as the PT constructed by the classical MP method, the inferred ancestral states and branch lengths are different and the results given by our method provide a plausible alternative to the classical ones.

Maximum parsimony, substitution model, and probability phylogenetic trees

The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method. In the MP method the optimization criterion is the number of substitutions of the nucleotides computed by the differences in the investigated nucleotide sequences. However, the MP method is often criticized as it only counts the substitutions observable at the current time and all the unobservable substitutions that really occur in the evolutionary history are omitted. In order to take into account the unobservable substitutions, some substitution models have been established and they are now widely used in the DM and ML methods but these substitution models cannot be used within the classical MP method. Recently the authors proposed a probability representation model for phylogenetic trees and the reconstructed trees in this model are called probability phylogenetic trees. One of the advantages of the probability representation model is that it can include a substitution model to infer phylogenetic trees based on the MP principle. In this paper we explain how to use a substitution model in the reconstruction of probability phylogenetic trees and show the advantage of this approach with examples.

Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case study

After the completion of several entire genome projects and a remarkable increase in public genetic databases in the recent years the results of post-genomic analyses can facilitate a better understanding of the genomic evolution underlying the diversity of organisms and the complexity of gene function. This influx of genomic information and resources is also beneficial to the discipline of systematic biology. In this paper, we describe a set of 6 previous and 22 new PCR/sequencing primers for RAG1, Rhodopsin and four novel nuclear markers from IRBP, EGR1, EGR2B and EGR3 that we developed through an approach making use of public genetic/genomic data mining for one of the ongoing tree of life projects aimed at understanding the evolutionary relationships of the planet's largest clade of freshwater fishes--the Cypriniformes. The primers and laboratory protocols presented here were successfully tested in 33 species comprising all cypriniform family and subfamily groups. Phylogenetic performance of each gene, as well as their implications in the investigation of the evolution of cypriniform fishes were assessed and discussed.

Mammalian evolution and biomedicine: new views from phylogeny

Recent progress resolving the phylogenetic relationships of the major lineages of mammals has had a broad impact in evolutionary biology, comparative genomics and the biomedical sciences. Novel insights into the timing and historical biogeography of early mammalian diversification have resulted from a new molecular tree for placental mammals coupled with dating approaches that relax the assumption of the molecular clock. We highlight the numerous applications to come from a well-resolved phylogeny and genomic prospecting in multiple lineages of mammals, from identifying regulatory elements in mammalian genomes to assessing the functional consequences of mutations in human disease loci and those driving adaptive evolution.

The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies

BACKGROUND

Mitochondrial and nuclear genes have generally been employed for different purposes in molecular systematics, the former to resolve relationships within recently evolved groups and the latter to investigate phylogenies at a deeper level. In the case of rapid and recent evolutionary radiations, mitochondrial genes like cytochrome b (CYB) are often inefficient for resolving phylogenetic relationships. One of the best examples is illustrated by Arvicolinae rodents (Rodentia; Muridae), the most impressive mammalian radiation of the Northern Hemisphere which produced voles, lemmings and muskrats. Here, we compare the relative contribution of a nuclear marker--the exon 10 of the growth hormone receptor (GHR) gene--to the one of the mitochondrial CYB for inferring phylogenetic relationships among the major lineages of arvicoline rodents.

RESULTS

The analysis of GHR sequences improves the overall resolution of the Arvicolinae phylogeny. Our results show that the Caucasian long-clawed vole (Prometheomys schaposnikowi) is one of the basalmost arvicolines, and confirm that true lemmings (Lemmus) and collared lemmings (Dicrostonyx) are not closely related as suggested by morphology. Red-backed voles (Myodini) are found as the sister-group of a clade encompassing water vole (Arvicola), snow vole (Chionomys), and meadow voles (Microtus and allies). Within the latter, no support is recovered for the generic recognition of Blanfordimys, Lasiopodomys, Neodon, and Phaiomys as suggested by morphology. Comparisons of parameter estimates for branch lengths, base composition, among sites rate heterogeneity, and GTR relative substitution rates indicate that CYB sequences consistently exhibit more heterogeneity among codon positions than GHR. By analyzing the contribution of each codon position to node resolution, we show that the apparent higher efficiency of GHR is due to their third positions. Although we focus on speciation events spanning the last 10 million years (Myr), CYB sequences display highly saturated codon positions contrary to the nuclear exon. Lastly, variable length bootstrap predicts a significant increase in resolution of arvicoline phylogeny through the sequencing of nuclear data in an order of magnitude three to five times greater than the size of GHR exon 10.

CONCLUSION

Our survey provides a first resolved gene tree for Arvicolinae. The comparison of CYB and GHR phylogenetic efficiency supports recent assertions that nuclear genes are useful for resolving relationships of recently evolved animals. The superiority of nuclear exons may reside both in (i) less heterogeneity among sites, and (ii) the presence of highly informative sites in third codon positions, that evolve rapidly enough to accumulate synapomorphies, but slow enough to avoid substitutional saturation.

The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences

The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].

Preliminary genetic characterization of two lineages of black rats (Rattus rattus sensu lato) in Japan, with evidence for introgression at several localities

We conducted a pilot survey of genetic diversity among 37 karyotyped individuals of the black rat Rattus rattus (sensu lato) from six localities on the Japanese Islands, using complete gene sequences of mitochondrial cytochrome b (cyt b) and nuclear interphotoreceptor retinoid binding protein (IRBP). Our sampling included two previously documented karyotypic groups: 'Oceanian' with 2n = 38 and 'Asian' with 2n = 42. Cyt b sequences for most individuals clustered according to their karyotypic groups, with an average between-group divergence of 3.8%. One exception was that individuals from Kagoshima (Kyushu Island) showed 'Asian' karyotypes combined with a cyt b haplotype that differed by a single nucleotide substitution from the haplotype of the 'Oceanian' karyotypic group. Six IRBP haplotypes were identified. They belonged to three distinct IRBP lineages (I-III), with an average inter-lineage divergence of 1%. Among homozygous individuals, these lineages showed good association with the karyotypic groups: IRBP lineage I occurred only with 'Oceanian' karyotypes, while IRBP lineages II and III both occurred with 'Asian' karyotypes. Individuals from Kagoshima all possessed IRBP of 'Asian' lineages, despite the presence of an 'Oceanian' mitochondrial type. The Chichijima population (Ogasawara Islands) featured exclusively 'Asian' karyotypes and cyt b sequences, but various combinations of all three IRBP lineages. The Kagoshima and Chichijima populations thus provide strong evidence of viable hybridization and genetic introgression between the two karyotypic groups, but with variable genetic outcomes. Our results demonstrate the potential of combined analysis of karyotypes and mitochondrial and nuclear gene sequences to elucidate the complex dispersal and population history of the black rat.

A retroposon analysis of Afrotherian phylogeny

Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.

Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP

The first third (ca. 1200 bp) of exon 1 of the nuclear gene encoding the interstitial retinoid-binding protein (IRBP) has been sequenced for 12 representative primates belonging to Lemuriformes, Lorisiformes, Tarsiiformes, Platyrrhini, and Catarrhini, and combined with available data (13 other primates, 11 nonprimate placentals, and 2 marsupials). Phylogenetic analyses using maximum likelihood on nucleotides and amino acids robustly support the monophyly of primates, Strepsirrhini, Lemuriformes, Lorisiformes, Anthropoidea, Catarrhini, and Platyrrhini. It is interesting to note that 1) Tarsiidae grouped with Anthropoidea, and the support for this node depends on the molecular characters considered; 2) Cheirogaleidae grouped within Lemuriformes; and 3) Daubentonia was the sister group of all other Lemuriformes. Study of the IRBP evolutionary rate shows a high heterogeneity within placentals and also within primates. Maximum likelihood local molecular clocks were assigned to three clades displaying significantly contrasted evolutionary rates. Paenungulata were shown to evolve 2.5-3 times faster than Perissodactyla and Lemuriformes. Six independent calibration points were used to estimate splitting ages of the main primate clades, and their compatibility was evaluated. Divergence ages were obtained for the following crown groups: 13.8-14.2 MY for Lorisiformes, 26.5-27.2 MY for Lemuroidea, 39.6-40.7 MY for Lemuriformes, 45.4-46.7 MY for Strepsirrhini, and 56.7-58.4 MY for Haplorrhini. The incompatibility between some paleontological and molecular estimates may reflect the incompleteness of the placental fossil record, and/or indicate that the variable IRBP evolutionary rates are not fully accommodated by local molecular clocks.

The phylogenetic history of New World monkey beta globin reveals a platyrrhine beta to delta gene conversion in the atelid ancestry

Orthologues of the beta globin gene locus from 10 New World monkey species were sequenced and aligned against available beta and delta globin sequences from rabbit and other primates. Where needed, additional primate sequencing was performed. Phylogenetic analysis identified a beta to delta conversion in the stem of the Anthropoidea, stretching from the 3' part of the proximal promotor to the 5' start of intron 2, consistent with earlier findings. No further conversion appeared to have occurred in the descent of the catarrhines. Within the New World monkey lineage that led to spider monkey and other atelids, another shorter gene conversion was found, spanning adjacent parts of exon 1 and intron 1. The analysis also confirmed that galago beta had replaced galago delta, that an earlier loriform-specific gene conversion extended over intron 2, and that gene conversion throughout the main gene conversion region occurred in the tarsiiform lineage. Platyrrhine phylogenetic relationships were investigated with beta sequences restricted to those that were not involved in gene conversions. This phylogeny generally agreed with results from other nuclear genes. The one exception was that the beta sequences did not place the callitrichine clade within the Cebidae but weakly joined the callitrichine and atelid clades.

Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences

We sequenced mitochondrial (cytochrome b, 12S rRNA) and nuclear (IRBP, RAG1) genes for 17 species of the Old World murine genus Mus, drawn primarily from the Eurasian subgenus Mus. Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus (Mus, Coelomys, Nannomys, and Pyromys), with an unresolved basal polytomy. Our data further indicate that the subgenus Mus contains three distinct 'species groups': (1) a Mus booduga Species Group, also including Mus terricolor and Mus fragilicauda (probably also Mus famulus); (2) a Mus cervicolor Species Group, also including Mus caroli and Mus cookii; and (3) a Mus musculus Species Group, also including Mus macedonicus, Mus spicilegus, and Mus spretus. Species diversity in Eurasian Mus is probably explicable in terms of several phases of range expansion and vicariance, and by a propensity within the group to undergo biotope transitions. IRBP and RAG1 molecular clocks for Mus date the origin of subgenera to around 5-6 mya and the origin of Species Groups within subgenus Mus to around 2-3 mya. The temporal pattern of evolution among Eurasian Mus is more complex than that within the Eurasian temperate genus Apodemus.

Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes

The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ two nuclear single-copy gene segments, the partial exon 1 from gene encoding interphotoreceptor retinoid binding protein (IRBP) and the complete intron 1 from transthyretin (TTR) gene, in conjunction with previously published mt data, to clarify these enigmatic problems. The combined analyses of nuclear IRBP and TTR datasets not only corroborated prior hypotheses, positioning the spectacled bear most basally and grouping the brown and polar bear together but also provided new insights into the bear phylogeny, suggesting the sister-taxa association of sloth bear and sun bear with strong support. Analyses based on combination of nuclear and mt genes differed from nuclear analysis in recognizing the sloth bears as the earliest diverging species among the subfamily ursine representatives while the exact placement of the sun bear did not resolved. Asiatic and American black bears clustered as sister group in all analyses with moderate levels of bootstrap support and high posterior probabilities. Comparisons between the nuclear and mtDNA findings suggested that our combined nuclear dataset have the resolving power comparable to mtDNA dataset for the phylogenetic interpretation of the bear family. As can be seen from present study, the unanimous phylogeny for this recently derived family was still not produced and additional independent genetic markers were in need.

Phylogenetic relationships and divergence times of the genusTokudaiawithin Murinae (Muridae; Rodentia) inferred from the nucleotide sequences encoding the Cytbgene, RAG 1, and IRBP

The phylogenetic relationships of six genera of Murinae (Apodemus, Diplothrix, Micromys, Mus, Rattus, and Tokudaia) were examined using the nucleotide sequences for the mitochondrial cytochrome b (Cytb), as well as the nuclear recombination activating gene 1 (RAG1) and interphotoreceptor retinoid-binding protein (IRBP), with special emphasis on the position of the genus Tokudaia, which is endemic to the Ryukyu Islands. Compared with Cytb at all codon positions, the first and second codon positions of Cytb, RAG1 (1002 base pairs (bp)), and IRBP (1586 bp) sequences were less prone to saturation. Close affinity between the genera Tokudaia and Apodemus was observed in the analyses using the IRBP (1586 bp) and combined nuclear (2588 bp; RAG1 + IRBP) sequences. The divergence time for the Tokudaia–Apodemus clade was estimated at approximately 6.5–8.0 Ma, which is more recent than previously reported, thereby indicating the recent colonization of the Ryukyu Islands by the genus Tokudaia. The other relationships among the main genera were highly ambiguous, owing either to saturation or insufficient phylogenetic information. The radiation of the main genera within a relatively short period of evolutionary time may explain the unresolved topologies, although molecular sources that are less subject to saturation are required to resolve the outstanding issues.

Phylogeny of Neotropical oryzomyine rodents (Muridae: Sigmodontinae) based on the nuclear IRBP exon

Sigmodontine rodents are the most diverse family-level mammalian clade in the Neotropical region, with about 70 genera and 320 recognized species. Partial sequences (1266 bp) from the first exon of the nuclear gene encoding the Interphotoreceptor Retinoid Binding Protein (IRBP) were used to infer the phylogenetic relationships among 44 species representing all 16 currently recognized genera of the largest sigmodontine tribe, the Oryzomyini. Monophyly of the tribe was assessed relative to 15 non-oryzomyine sigmodontine taxa representing all major sigmodontine lineages. Twelve taxa from seven muroid subfamilies were used as outgroups. The resulting matrix included 71 taxa and 386 parsimony-informative characters. Phylogenetic analysis of this matrix resulted in 16 equally parsimonious cladograms, which contained the following well-supported groups: (i). a monophyletic Oryzomyini, (ii). a clade containing all oryzomyines except Scolomys and Zygodontomys, (iii). a clade containing Oecomys, Handleyomys, and several species of forest-dwelling Oryzomys, and (iv). a clade containing the remaining oryzomyine taxa. The last clade is composed of two large subclades, each with lower nodal support, containing the following taxa: (i). Microryzomys, Oligoryzomys, Neacomys, and Oryzomys balneator; (ii). Holochilus, Lundomys, Pseudoryzomys, Nectomys, Amphinectomys, Sigmodontomys, and several species of open-vegetation or semiaquatic Oryzomys. Regarding relationships among non-oryzomyine taxa, sigmodontines, neotomines, and tylomyines do not form a monophyletic group; a clade containing Rheomys and Sigmodon is basal relative to all other sigmodontines; and the remaining sigmodontines are grouped in three clades: the first containing Thomasomyini, Akodontini, and Reithrodon; the second containing Abrothrichini, and Phyllotini, plus Wiedomys, Juliomys, Irenomys, and Delomys; and the third containing the oryzomyines. No conflict is observed between IRBP results and previous robust hypotheses from mitochondrial data, while a single case of incongruence is present between the IRBP topology and robust hypothesis from morphological studies.

Daily torpor in free-ranging rock elephant shrews, Elephantulus myurus: a year-long study

Under laboratory conditions, rock elephant shrews, Elephantulus myurus, use daily torpor under both short and long photoperiod acclimation. However, use of heterothermy often differs under field and laboratory conditions. We investigated the use of torpor in free-ranging elephant shrews from May 2001 to May 2002. The elephant shrews were capable of daily torpor throughout the year, with torpor most prevalent during winter. We recorded two torpor bouts during early summer (November). We recorded a total of 467 torpor bouts during the year. The mean torpor minimum body temperature (Tbmin) for the whole year was 15.3 degrees +/-4.4 degrees C, and the mean bout length was 8.6+/-3.5 h. These values were in the range expected for daily heterotherms. However, there was some marginal overlap with hibernation characteristics; a few torpor bouts were longer than 24 h in duration, and Tbmin decreased below 10 degrees C. Torpor was highly correlated with low ambient temperature and photoperiod. Torpor was also correlated with invertebrate abundance after controlling for photoperiod effects. During the year in which this study was conducted, the rainfall was 14% below long-term average. Historical rainfall records show that summer rainfall during strong El Nino years is up to 40% below the long-term average. During these drought years, the frequency of summer torpor may be higher, highlighting the need for long-term physiological data in free-ranging animals.

Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences

The rodent family Muridae is the single most diverse family of mammals with over 1300 recognized species. We used DNA sequences from the first exon ( approximately 1200bp) of the IRBP gene to infer phylogenetic relationships within and among the major lineages of muroid rodents. We included sequences from every recognized muroid subfamily except Platacanthomyinae and from all genera within the endemic Malagasy subfamily Nesomyinae, all recognized tribes of Sigmodontinae, and a broad sample of genera in Murinae. Phylogenetic analysis of the IRBP data suggest that muroid rodents can be sorted into five major lineages: (1) a basal clade containing the fossorial rodents in the subfamilies Spalacinae, Myospalacinae, and Rhizomyinae, (2) a clade of African and Malagasy genera comprising the subfamilies Petromyscinae, Mystromyinae, Cricetomyinae, Nesomyinae, and core dendromurines, (3) a clade of Old World taxa belonging to Murinae, Otomyinae, Gerbillinae, Acomyinae, and Lophiomyinae, (4) a clade uniting the subfamilies Sigmodontinae, Arvicolinae, and Cricetinae, and (5) a unique lineage containing the monotypic Calomyscinae. Although relationships among the latter four clades cannot be resolved, several well-supported supergeneric groupings within each are identified. A preliminary examination of molar tooth morphology on the resulting phylogeny suggests the triserial murid molar pattern as conceived by evolved at least three times during the course of muroid evolution.

Revisiting the Glires concept--phylogenetic analysis of nuclear sequences

The so-called Glires hypothesis postulates a sister-group relationship between Rodentia (e.g., rat and mouse) and Lagomorpha (e.g., rabbit). Recent molecular phylogenetic analyses have yielded incongruent results, and either supported or refuted the Glires grouping. In order to study this inconsistency we have reconstructed phylogenetic trees based on data sets of 20 orthologous nuclear protein coding genes (6441 aa, sites) and 12 mitochondrial protein coding genes (3559 aa sites). The size of the nuclear data set is considerably larger than any comparable data set hitherto used to study the Glires concept. Analysis of the nuclear data strongly supported the phylogenetic tree (frog, chicken, ((rat, mouse), (rabbit, (human, (cattle, dog))))), while the mt data could not conclusively resolve the position of rabbit relative to that of human. This result was supported by all methods. Thus, the Glires hypothesis was rejected by this study.

Molecular estimation of eulipotyphlan divergence times and the evolution of "Insectivora"

"Insectivores" are one of the key groups in understanding mammalian origins. For years, systematics of "Lipotyphla" taxa remained extremely unstable and challenged. Today, with the application of molecular techniques, "Lipotyphla" appears to be a paraphyletic assemblage that encompasses hedgehogs, shrews, and moles (i.e., Eulipotyphla-a member of Laurasiatheria), and golden moles and tenrecs (i.e., Afrosoricida-a member of Afrotheria). Based on nuclear genes and on this well-established phylogenetic framework, we estimated Bayesian relaxed molecular clock divergence times among major lineages of "Lipotyphla." Crown placental mammals are shown to diversify 102+/-6 million years ago (Mya; mean+/-one standard-deviation), followed by Boreoeutheria (94+/-6 Mya), Laurasiatheria (85+/-5 Mya), and Eulipotyphla (73+/-5), with moles separating from hedgehogs+shrews just at the K/T boundary (65+/-5 Mya). During the Early and Middle Eocene, all extant eulipotyphlan subfamilies originated: Uropsilinae (52+/-5 Mya), and Desmaninae, Talpinae, Erinaceinae, Hylomyinae, Soricinae, and Crocidurinae (38-42+/-5 Mya). Afrosoricida separated from Macroscelidae 69+/-5 Mya, golden moles from tenrecs 63+/-5 Mya, and the diversification within tenrecs occurred 43+/-5 Mya. Divergence times are shown to be in reasonably good agreement with the fossil record of eulipotyphlans, but not with the one of afrosoricid "insectivores." Eulipotyphlans diversification might have been sculpted by variations in paleoclimates of the cenozoic era.

Phylogenetic relationships and divergence times among mustelids (Mammalia: Carnivora) based on nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein and mitochondrial cytochrome b genes

Phylogenetic relationships among 20 species-group taxa of Mustelidae, representing Mustelinae (Mustela, Martes, Gulo), Lutrinae (Enhydra), and Melinae (Meles), were examined using nucleotide sequences of the nuclear interphotoreceptor retinoid binding protein (IRBP) and mitochondrial cytochrome b genes. Neighbor-joining and maximum-parsimony phylogenetic analyses on these genes separately and combined were conducted. While IRBP performed better than cytochrome b in recovering more-inclusive clades, cytochrome b demonstrated more resolving power in recovering less-inclusive clades. Strong support was found for a close affinity of Enhydra with Mustela to the exclusion of Martes and Gulo (causing Mustelinae to be paraphyletic); the most-basal position of Mustela vison within Mustela, followed by Mustela erminea; an association of Mustela lutreola, Mustela itatsi, Mustela sibirica, and the subgenus Putorius (including Mustela putorius and Mustela eversmanii), to the exclusion of Mustela nivalis and Mustela altaica; and a basal position of Mustela itatsi to a clade containing Mustela sibirica and Putorius. Whereas cytochrome b strongly supported Mustela lutreola as the sister species to Putorius, IRBP strongly supported its basal placement to the Mustela itatsi-Mustela sibirica-Putorius clade. The low level of sequence divergence in cytochrome b between Mustela lutreola and Putorius is therefore a result of interspecific mitochondrial introgression between these taxa, rather than a recent origin of Mustela lutreola in a close relationship to Putorius. Time estimates inferred from IRBP and cytochrome b for mustelid divergence events are mostly in agreement with the fossil record.