Article

Molecular Phylogenetics of Western North American Frogs of the Rana boylii Species Group

May 2001
Molecular Phylogenetics and Evolution 19(1):131-43

May 2001
19(1):131-43

DOI:10.1006/mpev.2000.0908

Source
PubMed

Authors:

Jonathan Macey

Yale University

Jared L Strasburg

Indiana University Bloomington

Vance T Vredenburg

San Francisco State University

Show all 6 authorsHide

Phylogenetic relationships among frogs of the genus Rana from western North America are investigated using 2013 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (O(L)) between the tRNA(Asn) and tRNA(Cys) genes. The aligned sequences contain 401 phylogenetically informative characters. A well-resolved phylogenetic hypothesis in which the Rana boylii species group (R. aurora, R. boylii, R. cascadae, R. muscosa, and R. pretiosa) is monophyletic is obtained. Molecular sequence divergence suggests that the R. boylii species group is approximately 8 million years old. The traditional hypothesis showing monophyly of the yellow-legged frogs (R. boylii and R. muscosa) is statistically rejected in favor of a hypothesis in which R. aurora, R. cascadae, and R. muscosa form a clade. Reanalyses of published nuclear ribosomal DNA restriction-site data and allozymic data support a monophyletic R. boylii group, but do not effectively resolve relationships among species within this group. Eight populations of R. muscosa form two major clades separated by a biogeographic break in the Sierra Nevada of California. This biogeographic break is broadly concordant with breaks found in four other amphibian and reptilian taxa. The two major clades within R. muscosa are estimated to have diverged approximately 2.2 million years before present. Each of these major clades contains two subgroups showing approximately 1.5 million years divergence, implicating climatic effects of Pleistocene glaciation in vicariance. The four distinct subgroups of R. muscosa separated by at least 1.4 million years of evolutionary divergence are suggested as potential units for conservation.

Ghosts of glaciers and the disjunct distribution of a threatened California moth (Euproserpinus euterpe)

Article

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Apr 2015
BIOL CONSERV

Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered Mountain Yellow-legged Frog

Article

Full-text available

Apr 2007

The mountain yellow-legged frog Rana muscosa sensu lato, once abundant in the Sierra Nevada of California and Nevada, and the disjunct Transverse Ranges of southern California, has declined precipitously throughout its range, even though most of its habitat is protected. The species is now extinct in Nevada and reduced to tiny remnants in southern California, where as a distinct population segment, it is classified as Endangered. Introduced predators (trout), air pollution and an infectious disease (chytridiomycosis) threaten remaining populations. A Bayesian analysis of 1901 base pairs of mitochondrial DNA confirms the presence of two deeply divergent clades that come into near contact in the Sierra Nevada. Morphological studies of museum specimens and analysis of acoustic data show that the two major mtDNA clades are readily differentiated phenotypically. Accordingly, we recognize two species, Rana sierrae, in the northern and central Sierra Nevada, and R. muscosa, in the southern Sierra Nevada and southern California. Existing data indicate no range overlap. These results have important implications for the conservation of these two species as they illuminate a profound mismatch between the current delineation of the distinct population segments (southern California vs. Sierra Nevada) and actual species boundaries. For example, our study finds that remnant populations of R. muscosa exist in both the southern Sierra Nevada and the mountains of southern California, which may broaden options for management. In addition, despite the fact that only the southern California populations are listed as Endangered, surveys conducted since 1995 at 225 historic (1899-1994) localities from museum collections show that 93.3% (n=146) of R. sierrae populations and 95.2% (n=79) of R. muscosa populations are extinct. Evidence presented here underscores the need for revision of protected population status to include both species throughout their ranges.

Phylogeography of an endemic California silk moth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity

Article

Jul 2021
MOL PHYLOGENET EVOL

The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from three genes, and reconstructed phylogenetic relationships and estimated divergence times within the lineages. All three species show pronounced evidence of isolation and, in two cases, secondary reconnection. An unexpected monophyletic mtDNA lineage was found in the Central Coast region, in a region thought to represent an intergrade between C. mendocino and C. walterorum. Our genetic data also significantly revise previous hypotheses as to which species occur in which regions, suggesting that historical ecological changes around four Ma ago isolated some lineages, and a secondary isolation event two Ma ago led to isolation of populations both in the Central Coast region and the southern Sierra Nevada. Our results add to a currently under appreciated pattern suggesting that coastal Central California is not a transition zone between Northern and Southern California Floristic Province faunas but rather its own unique, periodically isolated, biogeographic region. They also suggest cryptic diversity may be present in many other currently unrecognized groups. Additional research should focus on this central California region because many species may be highly restricted in range and in need of conservation attention.

ESTUDIO COMPARADO DEL DESARROLLO ESQUELÉTICO Y LAS SECUENCIAS DE OSIFICACIÓN EN ESPECIES DE RANAS COLOMBIANAS ANGÉLICA ARENAS RODRÍGUEZ PONTIFICIA UNIVERSIDAD JAVERIANA

Thesis

Full-text available

Sep 2020

Angelica Arenas-Rodríguez

The larval development of the skeleton of Colombian species of frogs of the most diversified families were examined and described: Rhinella marina (Bufonidae), Dendropsophus labialis, D. minutus, Boana xerophylla, Scinax ruber and Trachycephalus typhonius (Hylidae) and Engystomops pustulosus, Leptodactylus insularum and L. colombiensis (Leptodactylidae). These were obtained from biological collections. Differential enzymatic clearing and staining were performed to describe and compare the skeletal structures of craneal and poscraneal regions of the skeleton. Ossification sequences were obtained for analysis of variation of elements and ranks, ossification indexes, and phenotypic divergence. From these sequences and those taken from the literature the heterochronic changes and timing were identified using Parsimov algorithm. It was found that there are differences in the timing of appearance of the first ossified elements among these species, such as the transverse processes of the vertebrae. When considering only the cranium the first ossified elements were the exoccipital, paraesphenoid and frontoparietal, which are common in species of the Hylidae in early stages of development; in Leptodactylidae, was in later stages. The ranks and the number of elements presented ossification variability in all species, being the number smaller in leptodactilids, with respect to the hylids. Taking into account the whole skeleton, it was detected the relevance of the postcraneal elements. In using Parsimov, heterochronic changes in different amphibian groups were identified from the ontogeny of the skeleton, and pedomorphic processes were found in Colombian anurans. https://repository.javeriana.edu.co/handle/10554/50715

Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau

Article

Full-text available

Sep 2017

The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

Estimating synchronous demographic changes across populations using hABC, and its application for a herpetological community from Northeastern Brazil

Article

Full-text available

Jul 2017
MOL ECOL

Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Secondly, we applied the hABC models to a dataset of 7 squamate and 4 amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in Northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the expansion of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest. This article is protected by copyright. All rights reserved.

The invasive guttural toad, Amietophrynus gutturalis

Research

Full-text available

May 2016

Nicolas Telford

MSc thesis investigating the phylogeography of Amietophrynus gutturalis as well as identifying the origin of the invasive populations in Cape Town and Mauritius

Mitochondrial Variation in Sharp-Tailed Snakes (Contia tenuis): Evidence of a Cryptic Species

Article

Full-text available

Dec 2002

We examined genetic variation and structure in mitochondrial DNA sequences of sharp-tailed snakes (Contia tenuis) from California and southern Oregon. Maximum parsimony and maximum likelihood analyses distinguish two mitochondrial lineages: a north coast clade restricted to cool evergreen forest along the Pacific Coast; and an interior/south clade widespread throughout California. The southern limit of the north coast clade is congruent with that of several other vertebrate taxa, a historical pattern consistent with a long-term marine embayment. We interpret additional phylogeographic pattern as resulting from either gene flow or incomplete lineage sorting. Genetic, distributional, ecological, and morphological data suggest that north coast and interior/south mitochondrial lineages of C. tenuis are distinct at the species level.

Systematics and biogeography of Lesser Sunda paddy frogs (Dicroglossidae: Fejervarya)

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May 2024

Systematics and biogeography of Lesser Sunda paddy frogs

Mitogenomics clarifies the position of the Nearctic magpies ( Pica hudsonia and Pica nuttalli ) within the Holarctic magpie radiation

Article

Full-text available

Nov 2023

Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.

Phylogenetic relationships of southern Wallacean ranid frogs (Anura: Ranidae: Hylarana)

Article

Jun 2022
ZOOTAXA

Phylogenetic relationships of southern Wallacean ranid frogs (Anura: Ranidae: Hylarana)

Article

Full-text available

Jun 2022
ZOOTAXA

Frogs in the family Ranidae are diverse in Asia and are thought to have dispersed to the Sahul Shelf approximately 10 million years ago, where they radiated into more than a dozen species. Ranid species in the intervening oceanic islands of Wallacea, such as Hylarana florensis and H. elberti from the Lesser Sundas and H. moluccana from eastern Wallacea, are assumed to belong to the subgenus Papurana, yet this has not been confirmed with molecular data. We analyzed mitochondrial DNA of Hylarana species from five islands spanning the reported ranges of H. florensis and H. elberti and compared them to confirmed Papurana species and closely related subgenera within Hylarana. We find that the Lesser Sunda H. florensis and H. elberti form a clade that is sister to the rest of the Australo-Papuan Papurana assemblage. Species delimitation analyses and divergence time estimates suggest that populations of H. florensis on Lombok may be distinct from those on Flores at the species level. Likewise, populations of H. elberti on Sumba and Timor may be distinct from each other and from those on Wetar, tshe type locality of H. elberti. Samples from Babar Island thought to be members of H. elberti in fact belong to the wide-ranging H. daemeli, which occurs in northern Australia, across New Guinea, and on the neighboring island of Tanimbar. These results suggest that the Lesser Sundas may have served as a stepping-stone for colonization of the Sahul Shelf and that species diversity of Papurana frogs is underestimated in the Lesser Sundas.

Defining relevant conservation targets for the endangered Southern California distinct population segment of the mountain yellow‐legged frog (Rana muscosa)

Article

Full-text available

Mar 2022

The endangered mountain yellow‐legged frog (Rana muscosa) has been reduced to <10 isolated populations in the wild. Due to frequent catastrophic events (floods, droughts, wildfires), the recent dynamics of these populations have been erratic, making the future of the species highly uncertain. In 2018, a recovery plan was developed to improve the species status by reducing the impacts of various threats (predation, disease, habitat destruction), as well as reinforcing wild populations through the reintroduction of captive‐bred frogs. The short‐term goal stated in this plan was to reach a minimum of 20 populations of 50 adults each (hereafter, the 20/50 target), before the species can be considered for downlisting from the U.S. Endangered Species Act. However, there is no guarantee that this 20/50 target will be sufficient to ensure the species persistence in the long run. Using 19 years of mark‐recapture data, we estimated populations' demographic trends and assessed the viability of R. muscosa from a starting state of 20 populations of 50 adults each (i.e., the downlisting criteria). Our results reveal that, from this 20/50 state, the species has high chances of persistence only at a short time horizon (50 years). Moreover, >80% of populations would be extinct 50 years later. Therefore, the species will not be able to persist without implementation of the reintroduction program. We found that it is more important to increase the number of suitable sites occupied by R. muscosa than to simply reinforce or augment existing populations. Expanding the current distribution by establishing new populations at suitable sites, even after the “20 populations” mark has been reached, would increase the likelihood of the species' persistence in the longer term.

Shared response to changes in drainage basin: Phylogeography of the Yunnan small narrow‐mouthed frog, Glyphoglossus yunnanensis (Anura: Microhylidae)

Article

Full-text available

Jan 2020

Aim: With the late Cenozoic uplift of the Qinghai-Tibetan Plateau (QTP), drainage of the southeastern edge of the QTP changed significantly. However, the impact of this dramatic change on the geographical distribution and genetic diversity of endemic organisms is still poorly understood. Here, we examined the geographical patterns of genetic variation in the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Microhylidae), and two alternative hypotheses were tested: That is, the geographical distribution of genetic variation was determined by either the contemporary drainage basin or historical drainage basins. Location: The Mountains of southwest China. Materials and methods: Analyses were based on 417 specimens collected from across the distribution of the species. We reconstructed the genealogy (Bayesian and maximum parsimony methods) and assessed demographic history based on DNA sequencing data from mitochondrial and nuclear markers. We also mapped the genetic diversity and estimated the divergence times by a relaxed clock model. Results: The species has maintained a relatively stable population size without recent population expansion. Four major maternal lineages were identified with good support, one representing a possible cryptic species and the other three showing further subdivision. The distribution of these deeply differentiated lineages/sublineages corresponded well to geographical regions. The secondary contact zones and phylogeographic breaks in distinct lineages of G. yunnanensis were almost concordant with those of Nanorana yunnanensis. Main conclusions: Lineage division conformed to the hypothesis of drainage system evolution, that is, the phylogeographic pattern of G. yunnanensis was shaped by historical drainage patterns. Concordance in phylogeographic patterns may suggest a shared response to common hydrogeological history and also might indicate that there was more contribution of the drainage history than ecological or life-history traits in structuring genetic variation between these two disparate codistributed taxa G. yunnanensis and N. yunnanensis.

Recent colonization and expansion through the Lesser Sundas by seven amphibian and reptile species

Article

Full-text available

Jul 2019

The Lesser Sundas Archipelago is comprised of two parallel chains of islands that extend between the Asian continental shelf (Sundaland) and Australo‐Papuan continental shelf (Sahul). These islands have served as stepping stones for taxa dispersing between the Asian and Australo‐Papuan biogeographical realms. While the oceanic barriers have prevented many species from colonizing the archipelago, a number of terrestrial vertebrate species have colonized the islands either by rafting/swimming or by human introduction. Here, we examine phylogeographic structure within the Lesser Sundas for three snake, two lizard and two frog species that each has a Sunda Shelf origin. These species are suspected to have recently colonized the archipelago, though all have inhabited the Lesser Sundas for over 100 years. We sequenced mtDNA from 231 samples to test whether there is sufficiently deep genetic structure within any of these taxa to reject human‐mediated introduction. Additionally, we tested for genetic signatures of population expansion consistent with recent introduction and estimated the ages of Lesser Sundas clades, if any exist. Our results show little to no genetic structure between populations on different islands in five species and moderate structure in two species. Nucleotide diversity is low for all species, and the ages of the most recent common ancestor for species with monophyletic Lesser Sundas lineages date to the Holocene or late Pleistocene. These results support the hypothesis that these species entered the archipelago relatively recently and either naturally colonized or were introduced by humans to most of the larger islands in the archipelago within a short time span.

Leap-frog dispersal and mitochondrial introgression: Phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea

Article

Full-text available

Feb 2019
J BIOGEOGR

Aim: The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two-way filter for taxa dispersing between the Asian and Australo-Papuan biogeographical realms. Distributional patterns of many terrestrial vertebrates suggest a stepping-stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian-origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping-stone model of island colonization. Location: The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata. Taxon: Limnonectes dammermani and L. kadarsani (Family: Dicroglossidae) Methods: Mitochondrial DNA was sequenced from 153 frogs to identify major lineages and to select samples for an exon-capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analysed using phylogenetic, population genetic and biogeographical model testing methods. Results: The mtDNA phylogeny finds L. kadarsani paraphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping-stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermani mitochondrion into L. kadarsani on Lombok resulting from an isolated ancient hybridization event ~4 Ma. Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping-stone dispersal to be less likely than models involving leapfrog dispersal events. Main conclusions: These results suggest that the currently accepted stepping-stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that L. kadarsani represents five distinct species.

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna

Article

Full-text available

Feb 2019

Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa

Article

Mar 2018

Frogs in the genus Amnirana (family Ranidae) are widely distributed across sub-Saharan Africa and present a model system for exploring the relationship between diversification and geography across the continent. Using multiple loci from the mitochondrial (16S) and nuclear genomes (DISP2, FICD, KIAA2013, REV3L), we generated a strongly supported species-level phylogeny that provides insights into the continental biogeography of African species of Amnirana, which form a monophyletic group within the genus. Species delimitation analyses suggest that there may be as many as seven additional species of Amnirana in Africa. The biogeographic history of Amnirana is marked by several dispersal and vicariance events, including dispersal from the Lower Guinean Forest into the Congo Basin. In addition, phylogeographic patterns within two widespread species, A. albolabris and A. galamensis, reveal undescribed cryptic diversity. Populations assigned to A. albolabris in western Africa are more closely related to A. fonensis and require recognition as a distinct species. Our analyses reveal that the Lower and Upper Guinean Forest regions served as important centers of interspecific and intraspecific diversifications for Amnirana.

Evaluating hypotheses of expansion from refugia through comparative phylogeography of south‐eastern Coastal Plain amphibians

Article

Aug 2017
J BIOGEOGR

Aim Early genetic studies in the south‐eastern United States provided the foundation for ideas in the field of comparative phylogeography, but few direct comparisons with consistent sampling across taxa exist for this region. We investigate the influence of historical processes and species‐level characteristics on phylogeographic structure within four anuran species, evaluate previously described biogeographic patterns, and test three hypotheses of expansion from putative glacial refugia. Location South‐eastern United States Coastal Plain. Methods We sampled four anuran species from the same 36 localities, assembled mitochondrial genomes from Illumina sequence data and estimated phylogenetic relationships and divergence times within each species. We used spatially explicit phylogeographic analyses and ecological niche models ( ENM s) to test predictions about expansion from putative glacial refugia and estimate species‐specific parameters including dispersal, migration direction and centre of origin. ENM s for four different time periods were compared within species to assess niche stability. Results Species differ in patterns of mitochondrial divergence, with only one species displaying a pattern consistent with the previously described Alabama suture zone. Few predictions for hypotheses of expansion from putative glacial refugia were met. ENM s suggest that species have responded differently to historical changes in climate, possibly contributing to discordant genetic patterns. Two species with deep mitochondrial divergences (>2.5 Ma) had low niche stability through time and potentially isolated regions of suitable habitat, whereas the two species with relatively stable, continuous niches exhibit less genetic structure. Main conclusions These Coastal Plain anurans appear to have been affected by historical climate change, but were not necessarily isolated in glacial refugia. Different natural history characteristics have likely produced discordant patterns in these species, with more generalist, ephemeral breeders exhibiting greater niche stability and lower phylogeographic structure.

"Karakteristik Parsial Gen Sitokrom-C Oksidase Subunit-I Katak Pohon Suaka Marga Satwa Tanjung Peropa Moramo, Sulawesi Tenggara (CHARACTERISTICS OF PARTIAL CYTOCHROME C OXIDASE SUBUNIT I (COI) GENE OF TREE FROG (Polypedates celebensis) IN TANJUNG PEROPA WILDLIFE RESERVE MORAMO, SOUTHEAST SULAWESI) "

Article

Full-text available

Jan 2017

Tree frog (Polypedates celebensis) is an endemic amphibi found in Southeast Sulawesi. Database ofthis species, in particular genetic databases is still very limited. The purpose of this research was tocharacterize the partial gene cytochrome C oxidase subunit I (COI) of tree frog (P. celebensis). Frog sampleswere collected from Tanjung Peropa Wildlife Reserve, Moramo, Southeast Sulawesi, and extracted theirDNA genome, and amplified using the polymerase chain reaction (PCR) method, with specific primers,and then sequenced. Characterization was done by comparing the COI gene with another COI gene fromother frog (data available on GenBank). The results showed that the COI gene fragment P. celebensisconsisted of 665 base pairs. These fragment gene had 99% conserved nucleotides, and only 1% nucleotidesthat varied. Nine sites of nucleotide varied namely: 65th, 98th, 101th, 358th, 396th, 403th, 405th, 424th, and426th. These sites of nucleotide varied can be used as genetic markers for P. celebensis. Composition ofnitrogenous bases P. celebensis COI gene fragment were 29.9% timine, 28.9% cytocine, 22.0% adenine, and19.2% guanine. Molecular phylogeny of P. celebensis based on 665 bp of their COI gene suggests that thesespecies was monophyletic. It is concluded that the gene fragment of cytochrome C oxidase of tree frog (P.celebensis) the origin of Wildlife Moramo, Southeast Sulawesi, has conserved nucleotides more thannucleotides that varied. These varied nucleotides can be used as genetic markers especially for the treefrog origin of Wildlife Moramo, Southeast Sulawesi. The most nitrogenous bases is thymine, while thefewest is guanine. Molecular phylogeny based on cytochrome C oxidase gene is monophyletic

Intraspecific rearrangement of mitochondrial genome suggests the prevalence of the tandem duplication-random loss (TDLR) mechanism in Quasipaa boulengeri

Article

Full-text available

Nov 2016
BMC GENOMICS

Background: Tandem duplication followed by random loss (TDRL) is the most frequently invoked model to explain the diversity of gene rearrangements in metazoan mitogenomes. The initial stages of gene rearrangement are difficult to observe in nature, which limits our understanding of incipient duplication events and the subsequent process of random loss. Intraspecific gene reorganizations may represent intermediate states, and if so they potentially shed light on the evolutionary dynamics of TDRL. Results: Nucleotide sequences in a hotspot of gene-rearrangement in 28 populations of a single species of frog, Quasipaa boulengeri, provide such predicted intermediate states. Gene order and phylogenetic analyses support a single tandem duplication event and a step-by-step process of random loss. Intraspecific gene rearrangements are not commonly found through comparison of all mitochondrial DNA records of amphibians and squamate reptiles in GenBank. Conclusions: The intraspecific variation in Q. boulengeri provides insights into the rate of partial duplications and deletions within a mitogenome, and reveals that fixation and gene-distribution in mitogenomic reorganization is likely non-adaptive.

Out of Borneo, again and again: Biogeography of the Stream Toad genus Ansonia Stoliczka (Anura: Bufonidae) and the discovery of the first limestone cave-dwelling species

Article

Full-text available

Sep 2016
BIOL J LINN SOC

Subsequent to the Miocene (approximately 35 Mya), Borneo has served as an insular refuge and a source of colonization for a broad range of species emigrating to others parts of Sundaland. A phylogeny-based historical biogeographical hypothesis for the Stream Toad genus Ansonia supports multiple instances of an out-of-Borneo scenario. An ancestral range estimation indicates that in situ speciation of Ansonia on the island of Borneo during the Late Miocene and Pliocene (approximately 2–13 Mya) eventually resulted in an invasion of the Philippines, Sumatra, and two independent invasions of the Thai-Malay Peninsula. When collecting material for the biogeographical analysis, a new species of Ansonia, Ansonia khaochangensis sp. nov. was discovered in a limestone cave from the Khao Chang karst tower in Phangnga Province, in southern Thailand. Ansonia khaochangensis sp. nov. can be differentiated from all other species of Ansonia by having a unique combination of morphological and colour pattern characteristics. Phylogenetic evidence based on the mitochondrial genes 12S and 16S indicates that it is nested within a clade of other species distributed north of the Isthmus of Kra. The cave lifestyle of this new species is a unique and a significant departure from lotic environments common to most other species of Ansonia. The reproductive biology of this species is unknown.

Red River barrier and Pleistocene climatic ﬂuctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina

Article

Full-text available

May 2016

South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions.

Evolutionary history of the river frog genus Amietia (Anura: Pyxicephalidae) reveals extensive diversification in Central African highlands

Article

Mar 2016
MOL PHYLOGENET EVOL

The African river frog genus Amietia is found near rivers and other lentic water sources throughout central, eastern, and southern Africa. Because the genus includes multiple morphologically conservative species, taxonomic studies of river frogs have been relatively limited. We sampled 79 individuals of Amietia from multiple localities in and near the Albertine Rift (AR) of Burundi, Democratic Republic of the Congo, and Uganda. We utilized single-gene (16S) and concatenated (12S, 16S, cyt b and RAG1) gene-tree analyses and coalescent species-tree analyses to construct phylogenetic trees. Two divergence dating approaches were used in BEAST, including secondary calibration points with 12S, 16S, cyt b and RAG1, and a molecular clock with the 12S, 16S, and cyt b genes. All analyses recovered Amietia as monophyletic with strong support, and revealed several well-supported cryptic lineages, which is consistent with other recent phylogeography studies of AR amphibians. Dating estimates were similar, and Amietia diversification is coincident with global cooling and aridification events in the Miocene and Pliocene, respectively. Our results suggest additional taxonomic work is needed to describe multiple new species of AR Amietia, some of which have limited geographic distributions that are likely to be of conservation concern.

A peripheral view: Post-glacial history and genetic diversity of an amphibian in northern landscapes

Article

Full-text available

Jul 2015
J BIOGEOGR

Aim Where post‐glacial colonization and founder events are numerous, peripheral populations tend to have reduced genetic diversity as compared to their centrally located counterparts. Such decrease in genetic variability can limit their potential to adapt to changes in their environment. At northern latitudes for instance, populations are often living in conditions close to their physiological limits. Thus, identifying the levels of genetic diversity in peripheral populations is key to estimating the potential for adaptation to ongoing environmental change. In this context, we investigated the distribution of genetic diversity at the northern edge of the wood frog's ( Lithobates sylvaticus ) range by reconstructing its post‐glacial history in an area where phylogeographical data were lacking. Location James Bay area (north‐central Canada). Methods DNA was extracted from 463 wood frog tissue samples from 17 localities. Seven microsatellite loci were used to quantify genetic diversity and evaluate genetic structure through estimates of the fixation index, isolation‐by‐distance analyses and Bayesian clustering algorithms ( tess and structure ). Phylogeographical relationships were investigated using single nucleotide polymorphisms in the ND 2 / tRNA TRP mitochondrial genes. Phylogenetic trees were built using the neighbour‐joining and the maximum likelihood inference methods implemented in mega 5. Results Our analyses identified a contact zone between two colonizing lineages originating from one glacial refugium. Populations in this contact zone present sympatrically distributed haplotypes from both lineages and higher genetic variation than the surrounding populations. Population structure analyses revealed the differentiation of three genetic clusters, each covering large areas around the coast of James Bay. Main conclusions Our study suggests that higher than expected genetic diversity and gene flow may be present in peripheral populations. Such adaptive potential is critical in areas of upcoming development and environmental changes. Thus, our study emphasizes the importance of understanding species post‐glacial history for the prediction of future evolutionary trends and species distributions.

Phylogeography of Nanorana parkeri (Anura: Ranidae) and multiple refugia on the Tibetan Plateau revealed by mitochondrial and nuclear DNA

Article

Full-text available

May 2015

Quaternary climatic changes have been recognized to influence the distribution patterns and evolutionary histories of extant organisms, but their effects on alpine species are not well understood. To investigate the Pleistocene climatic oscillations on the genetic structure of amphibians, we sequenced one mitochondrial and three nuclear DNA fragments in Nanorana parkeri, a frog endemic to the Tibetan Plateau, across its distribution range in the southern plateau. Mitochondrial cytochrome b (Cytb) and three nuclear genes (c-Myc2, Rhod, and Tyr) revealed two distinct lineages (i.e. the lineages East and West), which were strongly geographically structured. The split of the two divergent lineages was dated back earlier than the Middle Pleistocene, probably being associated with climatic and ecological factors. Species distribution modeling, together with the phylogeographic structuring, supported the hypothesis of multiple refugia for N. parkeri on the Tibetan Plateau during the Pleistocene glaciations, and suggested the Yarlung Zangbo valley and the Kyichu catchment to be the potential refugia. Our findings indicate that Pleistocene climatic changes have had a great impact on the evolution and demographic history of N. parkeri. Our study has important implications for conservation of this and other frog species in the Tibetan Plateau.

Phylogeography and species boundaries of Leptopelis (Anura: Arthroleptidae) from the Albertine Rift

Article

Oct 2014

Genetic variability between populations of the critically endangered frog Microbatrachella capensis, Boulenger 1910 (Anura: Ranidae: Cacosterninae)

Article

Lindsey Will

Fregin et al 2012 Genetic distances MPE

Data

Full-text available

Sep 2014

MOUNTAIN YELLOW-LEGGED FROG CONSERVATION ASSESSMENT for the SIERRA NEVADA MOUNTAINS OF CALIFORNIA, USA - A Collaborative Inter-Agency Project

Technical Report

Full-text available

Jul 2014

This report presents a synthesis of scientific literature and expertise regarding the mountain yellow-legged frog complex in the Sierra Nevada, which is now comprised of two species, Rana muscosa and R. sierrae. These species, which inhabit largely higher-elevation (> 1,219 m [> 4,000 ft.]) aquatic habitats of the Sierra Nevada Mountains of California and Nevada, were historically abundant. It is estimated that these frogs have been extirpated over the majority (> 92 percent) of their geographic ranges, with many of the remaining populations depleted. Depletions and extirpations, first recognized during the 1970s, have accelerated markedly since the 1990s. The realization that these patterns would rapidly place these species at risk of extinction led to a multi-agency effort to develop a Conservation Strategy focused on the recovery of mountain yellow-legged frogs in the Sierra Nevada. This Conservation Assessment is the first step toward development of the Conservation Strategy and consists of three integral parts: 1) a description of mountain yellow-legged frog ecology in the Sierra Nevada to determine conditions necessary to provide for viable populations; 2) a review of the distribution and abundance of mountain yellow-legged frogs over their Sierran geographic range to describe the risk; and 3) an evaluation of 17 risk factor categories to identify which of these may constitute the greatest risk to mountain yellow-legged frogs and their habitat in the Sierra Nevada.

Cytonuclear Discordance and Historical Demography of Two Brown Frogs, Rana tagoi and R. sakuraii (Amphibia: Ranidae).

Article

Jun 2014

Population Structure, Historical Biogeography and Demographic History of the Alpine Toad Scutiger ningshanensis in the Tsinling Mountains of Central China

Article

Full-text available

Jun 2014
PLOS ONE

Population genetic structure, historical biogeography and historical demography of the alpine toad Scutiger ningshanensis were studied using the combined data mtDNA cytochrome b (cyt b) and the mtDNA cytochrome c oxidase subunit I (COI) as the molecular markers. This species has high genetic variation. There was a significant genetic differentiation among most populations. Three lineages were detected. The phylogenetic relationship analyses and the SAMOVA (spatial analysis of molecular variance) results showed significant phylogeographic structure. 82.15% genetic variation occurred among populations whereas differentiation within populations only contributed 17.85% to the total. Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (regression coefficient = 0.001286, correlation coefficient = 0.77051, p (rrand≥robs) = 0.0185

The precarious persistence of the Endangered Sierra Madre yellow-legged frog Rana muscosa in southern California, USA

Article

Full-text available

Jan 2013

We conducted surveys for the Endangered Sierra Madre yellow-legged frog Rana muscosa throughout south-ern California to evaluate the current distribution and status of the species. Surveys were conducted during 2000–2009 at 150 unique streams and lakes within the San Gabriel, San Bernardino, San Jacinto, and Palomar mountains of southern California. Only nine small, geographically isolated populations were detected across the four mountain ranges, and all tested positive for the amphibian chytrid fungus Batrachochytrium dendrobatidis. Our data show that when R. muscosa is known to be present it is easily detec-table (89%) in a single visit during the frog's active season. We estimate that only 166 adult frogs remained in the wild in 2009. Our research indicates that R. muscosa populations in southern California are threatened by natural and stochastic events and may become extirpated in the near future unless there is some intervention to save them.

Low levels of genetic diversity among morphologically distinct populations of an enigmatic montane frog from Mexico (Craugastor uno: Craugastoridae)

Article

Jan 2011

Craugastor uno is a direct-developing frog endemic to high-elevation pine-oak forests of the Sierra Madre del Sur in Mexico. The species was described from a single female specimen collected in the state of Guerrero, but otherwise remains poorly known. It is listed as endangered by the IUCN and some authors have considered it extinct. A recent report expanding the range to include montane localities in the state of Oaxaca has been disputed. Herein we describe variation in a group of 7 C. uno specimens that includes males, females, and juveniles collected from 1972 to 2004. We compared individuals from localities in the states of Guerrero and Oaxaca using morphology and several genetic markers. Molecular analyses revealed C. uno exhibits little genetic variation at the loci sampled. Our findings suggest that while the Guerrero and Oaxaca populations have diverged only recently from one another, they appear to be presently isolated and may be distinguished by several distinct quantitative and qualitative morphological traits. We also report multilocus genetic evidence of this putative isolation in the form of regional segregation among haplotypes. However, at this time we refrain from revising the taxonomy owing to our small sample size and limited geographic coverage.

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Article

Jul 2013
MOL ECOL

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28-1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11-18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion-contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.

A genealogical view of geographical variation

Article

Full-text available

Nov 2001

Keywords:coalescent theory;gene genealogy;mtDNA;phylogeography;speciation

Phylogeographic Patterns of mtDNA Variation Revealed Multiple Glacial Refugia for the Frog Species Feirana taihangnica Endemic to the Qinling Mountains

Article

Full-text available

Feb 2013
J MOL EVOL

Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F ct = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.

A new lizard species in the genus Xantusia from Arizona

Book

Jan 2001

Unexpectedly High Levels of Lineage Diversity in Sundaland Puddle Frogs (Dicroglossidae: Occidozyga Kuhl and Van Hasselt, 1822)

Article

Full-text available

May 2021
MOL PHYLOGENET EVOL

One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ∼2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high genetic diversity within Occidozyga based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages defined using the >5% uncorrected p-distance criterion for the 16S rRNA gene, showing that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that the lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether the observed diversity of Puddle frog lineages warrants taxonomic recognition.

Evolução em Cycloramphidae (Anura): diversidade e especiação na Mata Atlântica brasileira

Thesis

Nov 2019

Fábio P. de Sá

Natural and sexual selection forces act on individuals and may lead to reproductive isolation. The increase in evolutionary modifications may lead to the emergence of new entities. Species is the basal unity in biology; thus, with its exuberant biodiversity, the Atlantic rainforest is a fundamental Neotropical forest for studies of evolutionary processes in anuran amphibians. Comprising the genera Cycloramphus, Thoropa, and Zachaenus, the family Cycloramphidae gathers saxicolous and terrestrial anuran species, all endemic to the Brazilian Atlantic rainforest. Because of their specialized life and reproductive habits, cycloramphids are an attractive group for evolutionary studies. In the present thesis we show four chapters that address three distinct scales of evolution: the diversification among species, populations, and individuals. We goaled: (1) the multilocus molecular phylogeny of Cycloramphus- Zachaenus, demonstrating that the evolution of terrestriality in the clade is correlated with the sexual size dimorphism; (2) the phenotypic diversification associated with the genetic diversifications in populations of C. boraceiensis and C. dubius, demonstrating that these two saxicolous sister species show a contact zone and hybridization; (3) the promiscuous mating system and the social relations in C. boraceiensis, demonstrating that female and male sizes, and mate relatedness influence pair formation; and (4) the polygynic mating system with fidelity in the saxicolous species Thoropa taophora, extending the haremic system for all tetrapods.

Male‐male competition and repeated evolution of terrestrial breeding in Atlantic Coastal Forest frogs

Article

Nov 2019
EVOLUTION

Terrestrial breeding is a derived condition in frogs, with multiple transitions from an aquatic ancestor. Shifts in reproductive mode often involve changes in habitat use, and these are typically associated with diversification in body plans, with repeated transitions imposing similar selective pressures. We examine the diversification of reproductive modes, male and female body sizes, and sexual size dimorphism (SSD) in the Neotropical frog genera Cycloramphus and Zachaenus , both endemic to the Atlantic rainforest of Brazil. Species in this clade either breed in rocky streams (saxicolous) or in terrestrial environments, allowing us to investigate reproductive habitat shifts. We constructed a multilocus molecular phylogeny and inferred evolutionary histories of reproductive habitats, body sizes, and SSD. The common ancestor was small, saxicolous, and had low SSD. Terrestrial breeding evolved independently three times and we found a significant association between reproductive habitat and SSD, with shifts to terrestrial breeding evolving in correlation with decreases in male body size, but not female body size. Terrestrial breeding increases the availability of breeding sites and results in concealment of amplexus, egg‐laying, and parental care, therefore reducing male‐male competition at all stages of reproduction. We conclude that correlated evolution of terrestrial reproduction and small males is due to release from intense male‐male competition that is typical of exposed saxicolous breeding.

Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA

Article

Sep 2019

Contact zones between species provide a unique opportunity to test whether taxa can hybridize or not. Cross‐breeding or hybridization between closely related taxa can promote gene flow (introgression) between species, adaptation, or even speciation. Though hybridization events may be short‐lived and difficult to detect in the field, genetic data can provide information about the level of introgression between closely related taxa. Hybridization can promote introgression between species, which may be an important evolutionary mechanism for either homogenization (reversing initial divergence between species) or reproductive isolation (potentially leading to speciation). Here, we used thousands of genetic markers from nuclear DNA to detect hybridization between two parapatric frog species (Rana boylii and Rana sierrae) in the Sierra Nevada of California. Based on principal components analysis, admixture, and analysis of heterozygosity at species diagnostic SNPs, we detected two F1 hybrid individuals in the Feather River basin, as well as a weak signal of introgression and gene flow between the frog species compared with frog populations from two other adjacent watersheds. This study provides the first documentation of hybridization and introgression between these two species, which are of conservation concern.

Genetic Diversity of Rana catesbeiana in Korea based on Mitochondrial ND1/tRNA Sequence Analysis

Article

Dec 2005

The American bullfrog, Rana catesbeiana was imported from Japan for farming for the human consumption in 1970`s and introduced populations were a great threat to native habitats in the pond and lake ecosystem. However, it is thought that the population of bullfrog has rapidly declined for past years in Korea. In this study, we investigated the intra-genetic diversity of R. catesbeiana habitated in Korea. The nucleotide sequences of 1,215bp mitochondrial ND1/tRNA region in bullfrogs sampled from 5 sites in Jeollanamdo were analyzed and compared to the original sequence of R. catesbeiara reported in Genbank. The nucleotide similarity between Korean and North American bullfrog was ranged from 98.7% to 100% based on kimura-2-parameter distance. In addition, bullfrogs analyzed in this study were clustered into two groups with one including Jangheung and the other including Gwangju populations in the neighbor-joining tree. North American R. catesbeiana was grouped in Jangheung cluster, indicating that there is the very low genetic difference between Korean and North American populations. The maximum parsimony tree in which North American R. catesbeiana was set as an outgroup suggests that Jangheung group represents the introduced population to Korea. Taken together, the results indicate that the population of R. catesbeiana in Korea has not segregated geographically yet, after the introduction.

An annotated check list of the amphibians and reptiles of California and adjacent waters

Article

Sep 2004
CALIF FISH GAME

M.R. Jennings

This represents a comprehensive check list of the present status of all known marine, freshwater, and terrestrial amphibians and reptiles that have been reliably reported as part of the California fauna. Included is a main list of native and established introduced species and four supplementary lists: (1) native species extinct in California, (2) distributionally or taxonomically invalid species, (3) established introduced species, and (4) introduced species unsuccessfully established or of questionable status. The main list is composed of 159 species, comprising 144 native freshwater and terrestrial species (includes 2 species which have subspecies or populations from Introductions originating outside the state), 5 native marine species, and 12 introduced species. The 159 species comprise 33 families and 69 genera.

Zoogeography of the Northern Hemisphere and amphibians: the Palearctic and the Nearctic vs. the Holarctic?

Article

Full-text available

Dec 2014

Various schemes, proposed by zoologists and botanists of the second half of the 19th century and the first third of the 20th century, to unite temperate parts of the Northern Hemisphere (the Palearctic and Nearctic realms) in a single biogeographic region under the names "the Boreal Region" or Realm, "the Arctogaean Region", "the Triarctic" or "the Holarctic", and "Periarctic region" are briefly outlined. The history of the concept of the Holarctic (A. Heilprin 1883, 1887) and of its critics by Alfred Wallace and Theodore Gill are described. Based on the list of amphibian families and their zoogeographic distribution provided by A. Wallace (1876b), our re-evaluation by means of the Czekanovsky–Sørensen Coefficient confirmed Heilprin's conclusion about larger similarity between the Palearctic and the Nearctic in comparison with their neighbouring zoogeographic regions. However, the same quantitative analysis of the distribution of amphibians (at the level of families, genera as well as species) in these five regions, based on modern taxonomy evidenced for significant distinctness of amphibian faunas of the Palearctic realm and the Nearctic realm and, thus, did not support the reality of the Holarctic for amphibians.

Ossification sequence heterochrony among amphibians

Article

Sep 2013
EVOL DEV

Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

Nesting Behavior of a Gladiator Frog Hyla boans in Peru

Article

Dec 2002

The temporal pattern, basin construction and egg-laying of the Neotropical gladiator frog Hyla boans were studied along a small stream that enters the Manu River in Peru in August 2000. Initially we located 60 basins which were all destroyed by flood waters; subsequently 89 basins were constructed in the same area. In basins where eggs were deposited, oviposition usually occurred on the night the basin was constructed (60%) or during the following night (30%). Of the breached basins that were initially unused the first night, but were subsequently used, 91% were repaired before oviposition. Significantly more basins were located on the top of sand islands than in the center or along the other edges. Basins with eggs had significantly higher rims than those without eggs, and new basins and those with eggs had deeper water than basins with tadpoles or old basins that were disintegrating. Of the basins constructed following the flood, 55% ultimately had eggs, 89% of the eggs hatched in these basins, and 91% of the tadpoles reached maturity or left the basin when the rims were breached. Of the eggs that hatched, 89% of the clutches hatched on the second day after egg-laying, and 11% hatched on the third day. Of the total 146 basins we located, tadpoles reached maturity in five of the original 60 and in 38 of the 86 basins constructed after the flood, for an overall success rate of 29%. However, considering only those basins with eggs, 43 of 81 clutches were successful (53%).

Analysis of Spotted Salamander (Ambystoma maculatum) Growth Rates Based on Long-Bone Growth Rings

Article

Full-text available

Sep 2003

Amphibians experience indeterminate growth, but although factors affecting larval growth are relatively well studied, less is known about correlates of postmetamorphic growth. We measured areas between lines of arrested growth (inter-LAG) to determine yearly growth rates to test whether the post- metamorphic growth of 32 Spotted Salamanders (Ambystoma maculatum) was related to age, sex, or year of emergence. Growth decreased with age and was not associated with sex or year of emergence. Using interLAG area as a metric of growth provides growth information in the years before first capture and can be done using the toe-clips commonly taken for marking individuals.

Falling apart and merging: diversification of slender salamanders (Plethodontidae : Batrachoseps) in the American West

Article

Jul 2002

The plethodontid genus Batrachoseps, the slender salamanders, is the most diverse clade of salamanders in western North America, but it has posed taxonomic difficulties because it contains many morphologically cryptic species. A segment of the mitochondrial DNA gene cytochrome b was studied for 278 individuals densely sampled from throughout the range of all 18 described species and several undescribed species. Phylogenetic analyses of the mtDNA data identify six major clades, one corresponding to the subgenus Plethopsis and five within a monophyletic subgenus Batrachoseps. All major clades and most species within these clades display strong phylogeographic structuring. Comparisons of mtDNA and allozyme data show that several allozymically cohesive groups are not monophyletic with respect to mtDNA. We suggest that this phenomenon results from fragmentation of populations, divergence in allopatry, and then recontact and gradual merging of units caused predominantly by male-mediated gene flow. The mtDNA offers evidence that populations were once more isolated than they are now, while the patterns of allozyme variation reflect recent and current interactions among populations. The complex patterns of morphological, allozymic and mtDNA variation associated with the constantly changing geological landscape give insight into the nature of processes responsible for species formation in Batrachoseps. (C) 2002 The Linnean Society of London. Biological Journal of the Linnean Society, 2002, 76, 361-391.

A new lizard species in the genus Xantusia from Arizona

Article

Full-text available

Sep 2001

No abstract prepared.

Immunological Distance and the Phylogenetic Relationships of the Rana Boylii Species Group

Article

Full-text available

Dec 1982
Syst Zool

Cryptic Species of Spotted Frogs, Rana pretiosa Complex, In Western North America

Article

Full-text available

Feb 1997

Two species of spotted frogs (Rana pretiosa complex) are discernable on the basis of allozymes Adh, Fha, Iddh, Ldh-l, Mdh-l, and Mdhp. Frogs from the vicinity of the type locality of R. pretiosa were found to be conspecific with the species residing in south-central Washington State and the Cascade Mountains of Oregon. Morpho-metric study of 20 characters using multiple discriminant function analysis (MDA) showed that frogs from extreme southwestern British Columbia are also of this species. These populations comprise R. pretiosa Baird and Girard, 1853 sensu stricto ("Oregon spotted frog"). Spotted frog populations in the rest of British Columbia, Washington, and Oregon, as well as the Yukon, Idaho, Montana, Wyoming, Nevada, and Utah comprise R. luteiventris Thompson, 1913 n. comb. ("Columbia spotted frog"). Four measurements of the head contribute the greatest weight to distinguish-ing the species by MDA, but qualitative morphological distinctions usable as field characters have not been identified.

Evolutionary Relationships Within the Ensatina Eschscholtzii Complex Confirm the Ring Species Interpretation

Article

Full-text available

Sep 1992

Sequences (644-681 bp) from the mitochondrial cytochrome b gene were obtained for 24 individuals representing the geographic range and morphological diversity of the polytypic salamander ring species Ensatina eschscholtzii. These data were used to estimate the phylogeny of components of the ring to test the biogeographic scenario underlying current interpretations of speciation in this complex. The analysis revealed high levels of nucleotide variation among subspecies. Strong subdivision was evident within the subspecies platensis and oregonensis. The phylogenetic hypothesis of minimum length that is best supported by the data contains one monophyletic group that includes populations from the southern Sierra Nevada and mountains of southern California (croceater, klauberi, and southern platensis) and another that includes populations of the southern and central coastal regions (xanthoptica and eschscholtzii) Samples of oregonensis were typically basal, but their precise branching order was unstable. Both oregonensis and platensis were paraphyletic, with several disparate lineages in oregonensis and a strong northsouth dichotomy in platensis. The data were incompatible with a biogeographic model that required all subspecies to be monophyletic but were compatible with slightly modified predictions of a model assuming stepwise colonizations from north to south down the Sierra Nevada and independently down the coastal ranges. These features provide strong support for the biogeographic scenario central to the interpretation of Ensatina eschscholtzii as a ring species. Division of this complex into separate species on the basis of the observed patterns of monophyly for mitochondrial DNA (mtDNA) is unwarranted because further sampling could reveal additional instances of paraphyly across subspecies and, more generally, because mtDNA alone should not be used to infer species boundaries

Coding Polymorphic Data: Examples from Allozymes and Ontogeny

Article

Full-text available

Jun 1993

Limitations for using polymorphic characters in phylogenetic analysis include the lack of computer algorithms that allow input of complex branched or reticulate character state trees and the inability to use polymorphisms as data in tree building and character optimization. The step matrix option in PAUP version 3.0 and MacClade versions 2.1 and 3.0 provides a solution to these problems, allowing all homology information among character states to be utilized while retaining a biologically realistic definition of characters. For genetic data, this means that the locus can be coded as the character and allelic combinations can be coded as the character states. For ontogenetic data, this means that the entire ontogenetic sequence can be coded as the character and combinations of observed conditions within ontogenies can be coded as the character states. The unity of the locus or character ontogeny is preserved, and homology information from shared electrophoretic or ontogenetic conditions is not lost. Attention has not been called to the loss of homology information that accompanies coding the locus or an entire ontogeny as the character, possibly because of the lack of a coding option through which these data could be retained. The step matrix option allows any and all assumptions of transformation (order) among character states while retaining the unity of the locus or a whole ontogeny as the character and can be utilized for coding these and other polymorphic characters for phylogenetic analysis.

Moritz C, Dowling TE, Brown WM. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst 18: 269-292

Article

Full-text available

Nov 1987
Annu Rev Ecol Systemat

Sequence and organization of the human mitochondrial genome

Article

Full-text available

Apr 1981

The complete sequence of the 16,569-base pair human mitochondrial genome is presented. The genes for the 12S and 16S rRNAs, 22 tRNAs, cytochrome c oxidase subunits I, II and III, ATPase subunit 6, cytochrome b and eight other predicted protein coding genes have been located. The sequence shows extreme economy in that the genes have none or only a few noncoding bases between them, and in many cases the termination codons are not coded in the DNA but are created post-transcriptionally by polyadenylation of the mRNAs.

Macey, J. R., J. A. Schulte II, A. Larson, B. S. Tuniyev, N. Orlov, and T. J. Papenfuss. Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families. Molecular Phylogenetics and Evolution

Article

Full-text available

Sep 1999

Phylogenetic relationships among lizards of the families Anguidae, Anniellidae, Xenosauridae, and Shinisauridae are investigated using 2001 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (OL) between the tRNAAsn and the tRNACys genes. The aligned sequences contain 1013 phylogenetically informative characters. A well-resolved phylogenetic hypothesis is obtained. Because monophyly of the family Xenosauridae (Shinisaurus and Xenosaurus) is statistically rejected, we recommend placing Shinisaurus in a separate family, the Shinisauridae. The family Anniellidae and the anguid subfamilies Gerrhonotinae and Anguinae each form monophyletic groups receiving statistical support. The Diploglossinae*, which appears monophyletic, is retained as a metataxon (denoted with an asterisk) because its monophyly is statistically neither supported nor rejected. The family Anguidae appears monophyletic in analyses of the DNA sequence data, and statistical support for its monophyly is provided by reanalysis of previously published allozymic data. Anguid lizards appear to have had a northern origin in Laurasia. Taxa currently located on Gondwanan plates arrived there by dispersal from the north in two separate events, one from the West Indies to South America and another from a Laurasian plate to Morocco. Because basal anguine lineages are located in western Eurasia and Morocco, formation of the Atlantic Ocean (late Eocene) is implicated in the separation of the Anguinae from its North American sister taxon, the Gerrhonotinae. Subsequent dispersal of anguine lizards to East Asia and North America appears to have followed the Oligocene drying of the Turgai Sea. The alternative hypothesis, that anguine lizards originated in North America and dispersed to Asia via the Bering land bridge with subsequent colonization of Europe and Morocco, requires a phylogenetic tree seven steps longer than the most parsimonious hypothesis. North African, European, and West Asian anguines were isolated from others by the rapid uplift of Tibet in the late Oligocene to Miocene. Phylogenetic analysis of evolutionary changes in the gene encoding tRNACys suggests gradual reduction of dihydrouridine (D) stems by successive deletion of bases in some lineages. This evolutionary pattern contrasts with the one observed for parallel elimination of the D-stem in mitochondrial tRNAs of eight other reptile groups, in which replication slippage produces direct repeats. An unusual, enlarged TψC (T) stem is inferred for tRNACys in most species.

Systematics and Evolution of Western North American Frogs Allied to Rana Aurora and Rana Boylii: Karyological Evidence

Article

Full-text available

Sep 1986
Syst Zool

David M. Green

C-banded karotypes of five species of frogs endemic to western North America were analyzed to investigate the use of such chromosomal data in determining their systematic interrelationships. Morphologically, three of the species (Rana aurora, R. cascadae and R. pretiosa) may be considered generalized "brown frogs," while the other two species (R. boylii and R. muscosa) are morphologically divergent and may be termed "stream frogs." The peculiar karyotype of R. muscosa, with its three pairs of telocentric chromosomes, can be derived from that of R. boylii by postulating a series of chromosomal inversions. Based on karyotypic character analysis, R. boylii and R. muscosa constitute a pair of sister taxa that appears to have arisen from within the western Rana. The chromosomal evidence, while concordant with morphological considerations, conflicts with various systematic hypotheses that have been proposed concerning these frogs based on immunological distance studies and reanalyses. [Anura; Ranidae; Rana; systematics; evolutionary relationships; chromosomes; C-bands; western North America.].

Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics

Article

Full-text available

Nov 1993

Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20-600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor-joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.

Tan, AM, Wake, DB. MtDNA phylogeography of the California newt, Taricha torosa (Caudata, Salamandridae). Molec Phylogenet Evol, 4: 383-394

Article

Full-text available

Jan 1996

Thirty-six individuals of the California newt, Taricha torosa, representing 22 populations from throughout the range of the two currently recognized subspecies, torosa and sierrae, were examined for sequence variation in a segment (375 bp) of the mitochondrial (mt) cytochrome b gene. The maximum sequence divergence within T. torosa is about 9%. Phylogenetic analyses used the sister taxa T. rivularis and T. granulosa as outgroups. Eighteen haploid sequence types found in T. torosa were grouped by parsimony, maximum likelihood, and neighbor-joining analyses into five mitochondrial clusters: two in torosa (the northern and southern clusters) and three in sierrae (the northern, central, and southern clusters). The southern sierrae cluster apparently shared a most recent common ancestor with the northern torosa cluster. The approximate time of sequence divergence within the current species was calibrated using the known fossil record (0.8% divergence per million years or 0.01 maximum likelihood distance per million years). Phylogenetic implications of mtDNA sequence variation for evolution and biogeography of the T. torosa species complex are discussed.

Macey JR, Larson A, Ananjeva NB, Fang ZL, Papenfuss TJ. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol Biol Evol 14: 91-104

Article

Full-text available

Feb 1997

Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog. Statistical tests incorporating phylogeny indicate a link between novel vertebrate mitochondrial gene orders and movement of the origin of light-strand replication. A mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of vertebrate mitochondrial genes. A second mechanism involving small direct repeats also is identified. These mechanisms implicate gene order as a reliable phylogenetic character. Shifts in gene order define major lineages without evidence of parallelism or reversal. The loss of the origin of light-strand replication from its typical vertebrate position evolves in parallel and, therefore, is a less reliable phylogenetic character. Gene junctions also evolve in parallel. Sequencing across multigenic regions, in particular transfer RNA genes, should be a major focus of future systematic studies to locate novel gene orders and to provide a better understanding of the evolution of the vertebrate mitochondrial genome.

Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs

Article

Full-text available

Feb 1997

Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNA is unusually variable among lepidosaurian reptiles. Phylogenetic and comparative analyses of cysteine tRNA gene sequences identify eight parallel losses of the D-stem, resulting in D-arm replacement loops. Sampling within the monophyletic Acrodonta provides no evidence for reversal. Slipped-strand mispairing of noncontiguous repeated sequences during replication or direct replication slippage can explain repeats observed within cysteine tRNAs that contain a D-arm replacement loop. These two mechanisms involving replication slippage can account for the loss of the cysteine tRNA D-stem in several lepidosaurian lineages, and may represent general mechanisms by which the secondary structures of mitochondrial tRNAs are altered.

PHYLOGENETIC INFERENCE FROM RESTRICTION ENDONUCLEASE CLEAVAGE SITE MAPS WITH PARTICULAR REFERENCE TO THE EVOLUTION OF HUMANS AND THE APES

Article

Mar 1983
EVOLUTION

Alan R. Templeton

EVOLUTION OF RIBOSOMAL DNA: FIFTY MILLION YEARS OF RECORDED HISTORY IN THE FROG GENUS RANA

Article

Nov 1986
EVOLUTION

Evolution of nuclear ribosomal DNA (rDNA) arrays of frogs of the genus Rana was examined among 32 species that last shared a common ancestor approximately 50 million years ago. Extensive variation in restriction sites exists within the transcribed and nontranscribed rDNA spacer regions among the species, whereas rDNA coding regions exhibit comparatively little interspecific variation in restriction sites. The most parsimonious phylogenetic hypothesis for the evolution of the group was constructed based on variation in restriction sites and internal spacer lengths among the 32 species of Rana and one species of Pyxicephalus (examined for outgroup comparison). This analysis suggests that R. sylvatica of North America is more closely related to the R. temporaria group of Eurasia than to other North American Rana. The hypothesized phylogeny also supports the monophyly of the R. boylii group, the R. catesbeiana group, the R. palmipes group, the R. tarahumarae group, and the R. pipiens complex. Furthermore, the restriction site data provide information about the evolution within and among these species groups. This demonstrates that restriction site mapping of rDNA arrays provides a useful molecular technique for the examination of historical evolutionary questions across considerable periods of time.

The Application of Electrophoretic Data in Systematic Studies

Article

Jan 1984
Annu Rev Ecol Systemat

Donald G. Buth

The comparison of morphological and molecular data in phylogenetic systematics

Chapter

Jan 1994
EXS

A. Larson

Analytical methods facilitating the use of molecular and morphological characters as complementary sources of phylogenetic information are explored. Separation of phyloge-netically useful information from misleading patterns of character variation is most effective when the methods of “taxonomic congruence” and “character congruence” are used together. Statistical approaches for implementing both methods are described and illustrated with an example from the phylogeny of salamanders.

Evolution Of Animal Mitochondrial Dna: Relevance For Population Biology And Systematics

Article

Jan 1987
Annu Rev Ecol Systemat

Examines the form and frequency of 3 types of change in mtDNA: base substitution, length variation and sequence rearrangement. Knowledge of molecular processes allows informed use of mtDNA variation in evolutionary studies.-P.J.Jarvis

Molecular Cloning: A Laboratory Manual (2nd edn) Cold Spring Harbor, New York

Article

Jan 1982

Ecology, distribution, and systematics of frogs of the Rana boylei group

Article

Jan 1955

R.G. Zweifel

Chapter 8. Fish Biogeography and Molecular Clocks

Chapter

Dec 1997

This chapter highlights the biogeography of fishes with perspectives from the Panamanian isthmus as it provides a rich landscape to study the evolution of fish and molecules. It focuses on fish biogeography, particularly the geography of conspecific populations of tropical marine and freshwater fishes. It provides an insight into the mechanics and reliability of mitochondrial molecular clocks functioning across shallow spans of time. Conspecific populations, if differentiated, can provide historical information about a region. Molecules, particularly mtDNA, are well suited for reconstructing the evolutionary relationships among conspecific populations. For species or species groups demonstrating little or no phylogenetically informative morphological variation, molecules can provide a taxonomy that can be easily and immediately placed in a phylogenetic context. Tabular representations are provided for the geographic scaling of species groups like the Panama Isthmus, the circumtropical Abudefduf, and Neotropical freshwater fishes. A reasonable conclusion follows that molecular and genetic analysis can provide rapid means for surveying regional biotic diversity. Phylogenetic history and/or genetic diversity should be used in biodiversity indices to emphasize the phylogenetic and genetic distinctiveness of some groups compared to others.

Biochemical Identification of Red-Legged Frogs, Rana aurora draytoni (Ranidae) at Duckwater, Nevada

Article

Nov 1985

David M. Green

Phylogenetic Inference From Restriction Endonuclease Cleavage Site Maps with Particular Reference to the Evolution of Humans and the Apes

Article

Mar 1983

Alan R. Templeton

The estimation procedure utilizes a compatibility analysis between enzyme data sets of the most parsimonious trees constructed from the restriction enzyme. Next, a non-parametric test is given for comparing alternative phylogenies. A 2nd non-parametric test is developed for testing the molecular clock hypothesis. To illustrate the power of these procedures, data derived from the mitochondrial DNA and globin DNA of man and the apes are analyzed. Although previous analyses of these data led to the speculation that 10 times more information would be required to resolve the evolutionary relationships between man with chimps and gorillas, this algorithm resolved these relationships at the 5% level of significance. The molecular clock hypothesis was rejected at the 1% level. The implications of this phylogenetic inference when coupled with other types of data lead to the conclusion that knuckle-walking - not bipedalism - is the evolutionary novelty in mode of locomotion in the primates and that many other hominid features are primitive whereas their African ape counterparts are derived.-from Author

Evolution of Ribosomal DNA: Fifty Million Years of Recorded History in the Frog Genus rana

Article

Nov 1986

Studies of the Rana Species Complex in the Pacific Northwest

Article

Mar 1966
COPEIA

Philip C. Dumas

An analysis was made of the taxonomic relationships, ecology, and distribution of five taxa of ranids of the Pacific Northwest. Experimental crosses indicate that four of these taxa should be recognized as species: Rana aurora, R. sylvatica, R. pretiosa, and R. cascadae: however, luteiventris appears to be only a race of R. pretiosa. Studies of water relations, ecology, behavior, electrophoretic separations of blood proteins, and precipitin ring tests indicate that these species belong to two separate ranid stocks, a "wood frog" group composed of R. aurora and R. sylvatica, and a "pond frog" group composed of R. pretiosa and R. cascadae. It is suggested that the speciation of these taxa and their distributions are primarily the result of paleoclimatic changes during and since the last glacial advance.

The Relationships of Rana Sylvatica and the Monophyly of the Rana Boylii Group

Article

Jun 1981
Syst Zool

The Relationships of Rana sylvatica and the Monophyly of the Rana boylii Group. Syst. Zool., 30:170–180.—Reciprocal immunological distances were measured using antisera to the serum albumins of Rana sylvatica and representatives of five groups of Holarctic Rana (R. pipiens, R. catesbeiana, R. temporaria, R. lessonae, and R. muscosa or R. aurora or both). Scaled reciprocal values for three data sets (with R. muscosa, with R. aurora, or with both) were used to generate three sets of Fitch and Margoliash phenograms. The nine lowest percent standard deviations ranged from 6.18 to 8.44, 5.20 to 6.95, and 7.51 to 9.12, respectively. The interspecific distances in both the input and network matrices suggest that R. sylvatica is immunologically most like the eastern North American Rana. Probable cladograms place R. sylvatica either with the eastern North American Rana or in an independent lineage between the brown frogs and the water frogs. Oneway comparisons with antigens representing 12 additional species were made using the first four antisera listed. The R. sylvatica antiserum distinguished two subgroups of eastern North American Rana while the R. temporaria antiserum did not, and the R. temporaria antiserum distinguished two subgroups of both Nearctic (Rana boylii group) and Palearctic brown frogs while the R. sylvatica antiserum did not. Our data support the monophyly of the Rana boylii group, the affinity of the Palearctic brown frogs to the R. boylii group, and a distant association between R. sylvatica and the eastern North American Rana.

PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10

Book

Jan 2002

David L. Swofford

— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.

MacClade: Analysis of Phylogeny and Character Evolution, Version 4.0 PPC

Article

Jan 1992
AM BIOL TEACH

Confidence Limits on Phylogenies With a Molecular Clock

Article

Jun 1985
Syst Zool

Joseph Felsenstein

For three species in the presence of a molecular clock, it is possible to compute how many steps a phylogeny must have to be significantly worse than the most parsimonious phylogeny. This analysis extends the pioneering work of Cavender (1978, 1981) by taking advantage of the constraints imposed by the assumption of a molecular clock. The distribution of two statistics is obtained by direct enumeration of all possible outcomes in a worst-case phylogeny which has a trifurcation. The two statistics are the number of fewer steps in the best tree than in the next best tree, and the number of “phylogenetically informative” characters supporting the best tree. These two statistics prove to be approximately equivalent in statistical power, and tables of 95%-significance values are provided for each. The possible extension of these results to more than three species is discussed. The enumeration of all outcomes also allows us to compute exact tail probabilities for Templeton's (1983) test of one tree against another. His test is not exactly correct, but usually is conservative when used as a two-tailed test.

Analysis of phylogeny and character evolution

Article

Jan 1992

Wp Maddison

Molecular cloning: A laboratory manual, second ed

Article

Jan 1989

The Application of Electrophoretic Data in Systematic Studies

Article

Nov 2003
Annu Rev Ecol Systemat

Donald G. Buth

Provides an historical prespective in demonstrating the development of issues and the refinement of procedures, and assesses the unnecessary limitations that have been imposed on the application of electrophoretic data in systematic studies. Recommendations are presented for the phylogenetic treatment of such data.-from Author

Applications of mitochondrial DNA analysis in conservation: A critical review

Article

Aug 1994
MOL ECOL

Craig Moritz

Patterns of variation in mitochondrial DNA (mtDNA) increasingly are being investigated in threatened or managed species, but not always with clearly defined goals for conservation. In this review I identify uses of mtDNA analysis which fall into two different areas: (i) ‘gene conservation’ - the identification and management of genetic diversity, and (ii) ‘molecular ecology’ - the use of mtDNA variation to guide and assist demographic studies of populations. These two classes of application have different conceptual bases, conservation goals and time-frames. Gene conservation makes extensive use of phylogenetic information and is, in general, most relevant to long-term planning. Appropriate uses here include identification of Evolutionarily Significant Units and assessment of conservation priority of taxa or areas from an evolutionary perspective. Less appropriate are inferences about fitness from within-population diversity and about species boundaries. Molecular ecology makes more use of allele frequencies and provides information useful for short-term management of populations. Powerful applications are to identify Management Units and to define and use naturally occurring genetic tags. Estimating demographic parameters, e.g migration rate and population size, from patterns of mtDNA diversity is fraught with difficulty, particularly where populations are fluctuating, and is unlikely to produce quantitative estimates sufficiently accurate to be useful for practical management of contemporary populations. However, through comparative studies, mtDNA analysis can provide qualitative signals of population changes, allowing efficient targeting of resource-intensive ecological studies. Thus, there are some relatively straightforward uses of mtDNA, preferably in conjunction with assays of nuclear variation, that can make a significant contribution to the long-term planning and short-term execution of species recovery plans.

Branch Support and Tree Stability

Article

Sep 1994
CLADISTICS

Kåre Gunnar Bremer

Abstract— Branch support is quantified as the extra length needed to lose a branch in the consensus of near-most-parsimonious trees. This approach is based solely on the original data, as opposed to the data perturbation used in the bootstrap procedure. If trees have been generated by Farris's successive approximations approach to character weighting, branch support should be examined in terms of weighted extra length needed to lose a branch. The sum of all branch support values over the tree divided by the length of the most parsimonious tree[s] provides a new index, the total support index. This index is a measure of tree stability in terms of supported resolutions, which is of prime importance in cladistic analysis.

Molecular Cloning: A Laboratory Manual

Chapter

Jan 1983

Phylogenetic Relationships among Agamid Lizards of theLaudakia caucasiaSpecies Group: Testing Hypotheses of Biogeographic Fragmentation and an Area Cladogram for the Iranian Plateau

Article

Sep 1998

Phylogenetic relationships within theLaudakia caucasiaspecies group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochromecoxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation ofLaudakiapopulations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north–south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5–10 MYBP (million years before present)]. The shortest tree suggests the latter hypothesis, and statistical tests reject the other two hypotheses. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north–south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61–0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree.

Phylogenetic Relationships of Toads in theBufo bufoSpecies Group from the Eastern Escarpment of the Tibetan Plateau: A Case of Vicariance and Dispersal

Article

Mar 1998

Phylogenetic relationships among Tibetan populations of theBufo bufospecies group are investigated using 1063 bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAIle, tRNAGln, tRNAMet, and ND2. The aligned sequences contain 181 phylogenetically informative characters across all taxa sampled. Two hypotheses for colonization of the Tibetan Plateau are tested. A vicariant hypothesis predicts monophyly of populations from high elevations. A dispersalist hypothesis predicts monophyly of populations in each of two river drainages (Yangtze and Yellow rivers), which requires nonmonophyly of populations from high elevations. Both hypotheses are rejected in favor of a third hypothesis that combines elements of vicariance and dispersal. The most parsimonious phylogenetic tree places the high-elevation species,B. andrewsi,as the sister taxon to the other AsianBufopopulations; these high-elevation populations are postulated to have had a vicariant origin approximately 5 million years before present. The high-elevation population recognized asB. minshanicusis nested within low-elevation populations ofB. gargarizansand is suggested to have dispersed onto the Tibetan Plateau more recently.

Comparative phylogeography and the identification of genetically divergent areas for conservation

Article

Apr 1998

Genetic diversity is recognized as a fundamental component of biodiversity and its protection is incorporated in several conventions and policies. However, neither the concepts nor the methods for assessing conservation value of the spatial distribution of genetic diversity have been resolved. Comparative phylogeography can identify suites of species that have a common history of vicariance. In this study we explore the strengths and limitations of Faith’s measure of ‘Phylogenetic Diversity’ (PD) as a method for predicting from multiple intraspecific phylogeographies the underlying feature diversity represented by combinations of areas. An advantage of the PD approach is that information on the spatial distribution of genetic diversity can be combined across species and expressed in a form that allows direct comparison with patterns of species distributions. It also seeks to estimate the same parameter, feature diversity, regardless of the level of biological organization. We extend the PD approach by using Venn diagrams to identify the components of PD, including those unique to or shared among areas and those which represent homoplasy on an area tree or which are shared across all areas. PD estimation should be complemented by analysis of these components and inspection of the contributing phylogeographies. We illustrate the application of the approach using mtDNA phylogeographies from vertebrates resident in the wet tropical rainforests of north-east Queensland and compare the results to biodiversity assessments based on the distribution of endemic vertebrate species. The genetic vs. species approaches produce different assessments of conservation value, perhaps reflecting differences in the temporal and spatial scale of the determining processes. The two approaches should be seen as complementary and, in this case, conservation planning should incorporate information on both dimensions of biodiversity.

Non Parametric Statistical Methods

Book

Jan 1973

Nuclear integrations: Challenges for mitochondrial DNA markers

Article

Jun 1996
TRENDS ECOL EVOL

The combined use of mitochondrial DNA markers and polymerase chain reaction (PCR) techniques has greatly enhanced evolutionary studies. These techniques have also promoted the discovery of mitochondrial-like sequences in the nuclear genomes of many animals. While the nuclear sequences themselves are interesting, and capable of serving as valuable molecular tools, they can also confound phylogenetic and population genetic studies. Clearly, a better understanding of these phenomena and vigilance towards misleading data are needed.

Albumin Differences Among Ranid Frogs: Taxonomic and Phylogenetic Implications

Article

Mar 1973
Syst Zool

Wallace, D. G., M. C. King and A. C. Wilson (Biochemistry Dept., University of California, Berkeley, California 94720) 1973. Albumin differences among ranid frogs: taxonomic and phylogenetic implications. Syst. Zool., 22:1–13.—Since morphological analysis of living and fossil material has provided little information on taxonomic and phylogenetic relationships among species in the frog family Ranidae, an attempt was made to obtain such information by comparing their serum albumins. Rabbit antisera were prepared against the purified serum albumins of seven ranid species and tested by the microcomplement fixation method for reactivity with the albumins of 36 ranid species. This method provides a measure of the degree of amino acid sequence difference between albumins. The taxonomic and phylogenetic schemes we have derived from the albumin comparisons are generally in agreement with nonmolecular evidence. In some cases, they go beyond it, permitting demarcations among taxa that were previously unresolved. For example, it is proposed that the North American species of Rana are divisible into at least two major subgroups; an eastern subgroup, which includes R. pipiens and R. catesbeiana, and a western cluster, which includes R. aurora. The nearest relatives of the western cluster appear from albumin comparisons to be the R. temporaria cluster of the Palearctic region. The albumin results also permitted the construction of a phylogenetic tree with a very low percent standard deviation. With the aid of this tree and the molecular clock hypothesis we have estimated the approximate divergence times of various groups, subgroups and clusters of Holarctic ranid species. The molecular differences among Rana species are at least as large as those usually found within orders of placental mammals. This raises an important question regarding the ranking of taxonomic categories. If the genus Rana is equivalent in terms of genetic dispersion to an order of mammals, should one elevate the rank of Rana to the ordinal level? We believe that the molecular findings provide taxonomists with a dilemma.

Biochemical Systematics of Members of the Genus Rana Native to Western North America

Article

Sep 1978
Syst Zool

Susan M. Case

Case, S. M. (Museum of Vertebrate Zoology and Departments of Zoology and Biochemistry, University of California, Berkeley, California 94720) 1978. Biochemical systematics of members of the genus Rana native to western North America. Syst. Zool. 27:299–311 .—Few supraspecific groups have been defined in North American ranids and the informal groupings which are recognized are often poorly characterized. Two biochemical methods, starch gel electrophoresis and microcomplement fixation, have been used in an examination of the evolutionary relationships among western North American frogs of the genus Rana . Both the electrophoretic and albumin comparisons indicate that the Rana boylii species group presently includes two very different evolutionary lineages. Rana aurora , R. boylii , R. cascadae , R. muscosa , and R. pretiosa are all members of one lineage allied to R. temporaria of Europe. A Mexican species traditionally included in this group, R. tarahumarae , is most closely related to other members of the genus that occur in Mexico and is part of a larger lineage that also includes R. pipiens . Frogs found in eastern North America diverged from western European frogs in mid-Eocene; estimates of divergence time are consistent with the hypothesis that separation of these lineages coincided with the end of a land connection between Europe and North America. The catesbeiana , pipiens , and tarahumarae groups diverged from each other in the Oligocene. Western North American Rana diverged from a Eurasian ancestor in the Oligocene and radiated in this area to form the five members of the boylii group.

Paraphyly of the Rana boylii Species Group

Article

Dec 1979
Syst Zool

Rana temporaria is Not a Member of the Rana boylii Group

Article

Sep 1986
Syst Zool

Systematics and Evolution of Western North American Frogs Allied to Rana Aurora and Rana Boylii: Electrophoretic Evidence

Article

Sep 1986
Syst Zool

David M. Green

Eight species of frogs of the genus Rana, comprising five species endemic to western North America and three related species, were examined electrophoretically in order to investigate their systematic interrelationships. Two morphotypic “stream frogs,” R. boylii and R. muscosa, were found to be sister taxa derived from within an assemblage of “brown frogs” that included R. aurora, R. cascadae and R. pretiosa. Rana cascadae was closely allied to R. aurora. The two subspecies of R. aurora were discernable, but closely related, and exhibited variation conforming to a north-south pattern of allozyme divergence. Allozyme differences indicated considerable divergence in R. pretiosa, both between samples and from other species. The five western species were found to be a monophyletic group exclusive of the Eurasian species R. temporaria and R. dybowskii and the North American R. sylvatica. The 24-chromosome species R. dybowskii was very distant genetically from all other species examined. The electrophoretic evidence agrees with a number of conclusions drawn from karyological investigations, such as the common derivation of R. boylii and R. muscosa, but disputes previous conflicting systematic hypotheses concerning these frogs based on immunological distance studies and reanalyses of existing data. The widespread “brown frog” morphotype may be considered a conserved primitive state in Rana. In certain respects, karyotypic, morphotypic and genotypic evolution in these frogs may have proceeded independently.

Biochemical evolution. Annu Rev Biochem

Article

Feb 1977

Molecular Approaches to Ecology and Evolution

Article

Feb 1994
EXS

Allan Larson

Analytical methods facilitating the use of molecular and morphological characters as complementary sources of phylogenetic information are explored. Separation of phylogenetically useful information from misleading patterns of character variation is most effective when the methods of "taxonomic congruence" and "character congruence" are used together. Statistical approaches for implementing both methods are described and illustrated with an example from the phylogeny of salamanders.

Re: Homology in Phylogenetic Analysis: Alignment of Transfer RNA Genes and the Phylogenetic Position of Snakes

Article

May 1997

Vicariant Patterns of Fragmentation among Gekkonid Lizards of the Genus Teratoscincus Produced by the Indian Collision: A Molecular Phylogenetic Perspective and an Area Cladogram for Central Asia

Article

Sep 1999

A well-supported phylogenetic hypothesis is presented for gekkonid lizards of the genus Teratoscincus. Phylogenetic relationships of four of the five species are investigated using 1733 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase). A single most parsimonious tree depicts T. przewalskii and T. roborowskii as a monophyletic group, with T. scincus as their sister taxon and T. microlepis as the sister taxon to the clade containing the first three species. The aligned sequences contain 341 phylogenetically informative characters. Each node is supported by a bootstrap value of 100% and the shortest suboptimal tree requires 29 additional steps. Allozymic variation is presented for proteins encoded by 19 loci but these data are largely uninformative phylogenetically. Teratoscincus species occur on tectonic plates of Gondwanan origin that were compressed by the impinging Indian Subcontinent, resulting in massive montane uplifting along plate boundaries. Taxa occurring in China (Tarim Block) form a monophyletic group showing vicariant separation from taxa in former Soviet Central Asia and northern Afghanistan (Farah Block); alternative biogeographic hypotheses are statistically rejected. This vicariant event involved the rise of the Tien Shan-Pamir and is well dated to 10 million years before present. Using this date for separation of taxa occurring on opposite sides of the Tien Shan-Pamir, an evolutionary rate of 0.57% divergence per lineage per million years is calculated. This rate is similar to estimates derived from fish, bufonid frogs, and agamid lizards for the same region of the mitochondrial genome ( approximately 0.65% divergence per lineage per million years). Evolutionary divergence of the mitochondrial genome has a surprisingly stable rate across vertebrates.

Phylogeography of the California Mountain Kingsnake, Lampropeltis zonata (Colubridae)

Article

Dec 1999

The phylogeography of the California mountain kingsnake, Lampropeltis zonata, was studied using mitochondrial DNA sequences from specimens belonging to the seven recognized subspecies and collected throughout the range of the species. Maximum parsimony and maximum likelihood methods identified a basal split within L. zonata that corresponds to southern and northern segments of its distribution. The southern clade is composed of populations from southern California (USA) and northern Baja California, Mexico. The northern clade is divided into two subclades, a 'coastal' subclade, consisting of populations from the central coast of California and the southern Sierra Nevada Mountains of eastern California, and a 'northeastern' subclade, mainly comprised of populations north of the San Francisco Bay and from the majority of the Sierra Nevada. We suggest that past inland seaways in southwestern California and the embayment of central California constituted barriers to gene flow that resulted in the two deepest divergences within L. zonata. Throughout its evolutionary history, the northern clade apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. Examination of colour pattern variation in 321 living and preserved specimens indicated that the two main colour pattern characters used to define the subspecies of L. zonata are so variable that they cannot be reliably used to differentiate taxonomic units within this complex, which calls into question the recognition of seven geographical races of this snake.

The genetics of amphibian declines: Population substructure and molecular differentiation in the Yosemite Toad, Bufo canorus (Anura, Bufonidae) based on single-strand conformation polymorphism analysis (SSCP) and mitochondrial DNA sequence data

Article

Apr 2000

We present a comprehensive survey of genetic variation across the range of the narrowly distributed endemic Yosemite toad Bufo canorus, a declining amphibian restricted to the Sierra Nevada of California. Based on 322 bp of mitochondrial cytochrome b sequence data, we found limited support for the monophyly of B. canorus and its closely related congener B. exsul to the exclusion of the widespread western toad B. boreas. However, B. exsul was always phylogenetically nested within B. canorus, suggesting that the latter may not be monophyletic. SSCP (single-strand conformation polymorphism) analysis of 372 individual B. canorus from 28 localities in Yosemite and Kings Canyon National Parks revealed no shared haplotypes among these two regions and lead us to interpret these two parks as distinct management units for B. canorus. Within Yosemite, we found significant genetic substructure both at the level of major drainages and among breeding ponds. Kings Canyon samples show a different pattern, with substantial variation among breeding sites, but no substructure among drainages. Across the range of B. canorus as well as among Yosemite ponds, we found an isolation-by-distance pattern suggestive of a stepping stone model of migration. However, in Kings Canyon we found no hint of such a pattern, suggesting that movement patterns of toads may be quite different in these nearby parklands. Our data imply that management for B. canorus should focus at the individual pond level, and effective management may necessitate reintroductions if local extirpations occur. A brief review of other pond-breeding anurans suggests that highly structured populations are often the case, and thus that our results for B. canorus may be general for other species of frogs and toads.

Molecular Phylogenetics of Western North American Frogs of the Rana boylii Species Group

Abstract

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