Discovery of a new species of Anolis lizards from Brazil and its implications for the historical biogeography of montane Atlantic Forest endemics

Abstract Recent biological discoveries have changed our understanding of the distribution and evolution of neotropical biotas. In the Brazilian Atlantic Forest, the discovery of closely related species isolated on distant mountains has led to the hypothesis that the ancestors of montane species occupied and dispersed through lowland regions during colder periods. This process may explain the distribution of an undescribed Anolis lizard species that we recently discovered at a montane site in the Serra dos Órgãos National Park, a popular tourist destination close to the city of Rio de Janeiro. To investigate whether this species is closely related to other Atlantic Forest montane anoles, we implement phylogenetic analyses and divergence time estimation based on molecular data. We infer the new species nested within the Dactyloa clade of Anolis, forming a clade with A. nasofrontalis and A. pseudotigrinus, two species restricted to montane sites about 400 km northeast of Serra dos Órgãos. The new species diverged from its sister A. nasofrontalis around 5.24 mya, suggesting a cold-adapted lowland ancestor during the early Pliocene. Based on the phylogenetic results, we emend the definitions of the series taxa within Dactyloa, recognizing a clade containing the new species and several of its relatives as the nasofrontalis series. Lastly, we provide morphological data supporting the recognition of the new species and give it a formal scientific name. Future studies are necessary to assess how park visitors, pollutants, and shrinking montane habitats due to climate change will affect this previously overlooked anole species.

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Global classification and evolution of brushlegged mayflies (Insecta: Ephemeroptera: Oligoneuriidae): phylogenetic analyses of morphological and molecular data and dated historical biogeography

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz031 ◽

2019 ◽

Vol 187 (2) ◽

pp. 378-412 ◽

Cited By ~ 3

Author(s):

Fabiana Criste Massariol ◽

Daniela Maeda Takiya ◽

Frederico Falcão Salles

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Single Species ◽

Molecular Data ◽

Neotropical Region ◽

Fossil Species ◽

Divergence Time Estimation ◽

The Family ◽

Family Based

AbstractOligoneuriidae is a Pantropical family of Ephemeroptera, with 68 species described in 12 genera. Three subfamilies are recognized: Chromarcyinae, with a single species from East Asia; Colocrurinae, with two fossil species from Brazil; and Oligoneuriinae, with the remaining species distributed in the Neotropical, Nearctic, Afrotropical and Palaearctic regions. Phylogenetic and biogeographical analyses were performed for the family based on 2762 characters [73 morphological and 2689 molecular (COI, 16S, 18S and 28S)]. Four major groups were recovered in all analyses (parsimony, maximum likelihood and Bayesian inference), and they were assigned to tribal level, namely Oligoneuriini, Homoeoneuriini trib. nov., Oligoneuriellini trib. nov. and Elassoneuriini trib. nov. In addition, Yawari and Madeconeuria were elevated to genus level. According to Statistical Dispersal-Vicariance (S-DIVA), Dispersal Extinction Cladogenesis (DEC) and divergence time estimation analyses, Oligoneuriidae originated ~150 Mya in the Gondwanan supercontinent, but was probably restricted to the currently delimited Neotropical region. The initial divergence of Oligoneuriidae involved a range expansion to Oriental and Afrotropical areas, sometime between 150 and 118 Mya. At ~118 Mya, the family started its diversification, reaching the Nearctic through dispersal from the Neotropical region and the Palaearctic and Madagascar from the Afrotropical region.

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Biogeography and divergence time estimation of the relict Cape dragonfly genus Syncordulia: global significance and implications for conservation

Zootaxa ◽

10.11646/zootaxa.2216.1.2 ◽

2009 ◽

Vol 2216 (1) ◽

pp. 22-36 ◽

Cited By ~ 8

Author(s):

JESSICA L. WARE ◽

JOHN P. SIMAIKA ◽

MICHAEL J. SAMWAYS

Keyword(s):

South Africa ◽

New Species ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Cape Floristic Region ◽

Conservation Action ◽

Divergence Time Estimation ◽

Divergence Time Estimates ◽

Two New Species

Syncordulia (Odonata: Anisoptera: Libelluloidea) inhabits mostly cool mountainous streams in the Cape Floristic Region of South Africa. It is found at low densities in geographically restricted areas. Syncordulia is endemic to South Africa and, until recently, only two species were known, S. venator (Barnard, 1933) and S. gracilis (Burmeister 1839), both considered Vulnerable by the World Conservation Union (IUCN). Two new species, S. serendipator Dijsktra, Samways & Simaika 2007 and S. legator Dijsktra, Samways & Simaika 2007, were described from previously unrecognized museum specimens and new field collections. Here we corroborate the validity of these two new species using multiple genes and propose intergeneric relationships within Syncordulia. Molecular data from two independent gene fragments (nuclear 28S and ribosomal and cytochrome oxidase subunit I mitochondrial data) were sequenced and/or downloaded from GenBank for 7 libelluloid families, including 12 Syncordulia specimens (2 Syncordulia gracilis, 4 S. serendipator, 2 S. legator and 4 S. venator). The lower libelluloid group GSI (sensu Ware et al. 2007), a diverse group of non– corduliine taxa, is strongly supported as monophyletic. Syncordulia is well supported by both methods of phylogenetic analyses as a monophyletic group deeply nested within the GSI clade. A DIVA biogeographical analysis suggests that the ancestor to the genus Syncordulia may have arisen consequent to the break–up of Gondwana (>120 Mya). Divergence time estimates suggest that Syncordulia diverged well after the breakup of Gondwana, approximately 60 million years ago (Mya), which coincides with the divergence of several Cape fynbos taxa, between 86 – 60 Mya. DIVA analyses suggest that the present distributions of Syncordulia may be the result of dispersal events. We relate these phylogenetic data to the historical biogeography of the genus and to the importance of conservation action.

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Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa

Horticulture Research ◽

10.1093/hr/uhab050 ◽

2022 ◽

Vol 9 ◽

Author(s):

Jordan R Brock ◽

Terezie Mandáková ◽

Michael McKain ◽

Martin A Lysak ◽

Kenneth M Olsen

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Diploid Species ◽

Time Estimation ◽

Polyploid Species ◽

Chromosome Counts ◽

Diploid Parent ◽

Divergence Time Estimation ◽

Multiple Origins ◽

Chloroplast Genomes

Abstract The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.

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Molecular and morphological data reveal three new cryptic species ofChiasmocleis(Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil

PeerJ ◽

10.7717/peerj.3005 ◽

2017 ◽

Vol 5 ◽

pp. e3005 ◽

Cited By ~ 6

Author(s):

Mauricio C. Forlani ◽

João F.R. Tonini ◽

Carlos A.G. Cruz ◽

Hussam Zaher ◽

Rafael O. de Sá

Keyword(s):

New Species ◽

Cryptic Species ◽

Atlantic Forest ◽

Morphological Characters ◽

Molecular Data ◽

Sao Paulo ◽

Morphological Data ◽

Congeneric Species ◽

The Third ◽

Coloration Patterns

Three new cryptic species ofChiasmocleisfrom the Atlantic Forest of Brazil are described. Two of these species occur in the northeastern states of Sergipe and Bahia, whereas the third species is found in the southeastern state of São Paulo. The new species can be distinguished from other congeneric species by the molecular data, as evidenced in the phylogeny, and by a combination of morphological characters including: size, foot webbing, dermal spines, and coloration patterns.Chiasmocleisspecies differ in osteological traits, therefore we also provide an osteological description of each new species and comparsions with data reported for other species in the genus.

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The formerly enigmatic Unidentiidae in the limelight again: a new species of the genus Unidentia from Thailand (Gastropoda: Nudibranchia)

Zootaxa ◽

10.11646/zootaxa.4551.5.4 ◽

2019 ◽

Vol 4551 (5) ◽

pp. 556 ◽

Cited By ~ 3

Author(s):

TATIANA KORSHUNOVA ◽

RAHUL MEHROTRA ◽

SPENCER ARNOLD ◽

KENNET LUNDIN ◽

BERNARD PICTON ◽

...

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Morphological Data ◽

Sea Slugs ◽

The Family ◽

Molecular Phylogenetic ◽

Morphological Differences ◽

First Time ◽

A New Species

An integrative molecular and morphological study is presented for the family Unidentiidae. Molecular phylogenetic analyses were conducted with the inclusion of all previous and newly obtained molecular data for the family Unidentiidae Millen & Hermosillo 2012. A new species of the genus Unidentia Millen & Hermosillo 2012, U. aliciae sp. nov., is described from Thailand as part of an inventory of sea slugs at Koh Tao. All up-to-date available morphological data for the species of the genus Unidentia is for the first time summarized. Morphological differences among the different species of Unidentia are clarified showing that every species has its own distinguishable morphological traits. According to the new molecular and morphological data, the family Unidentiidae is re-confirmed as a well-supported taxon of the aeolidacean nudibranchs. The taxonomy and phylogeny of the Aeolidacea in the light of the family Unidentiidae is briefly discussed and necessity of a fine-scale and narrowly-defined taxa approach instead of a ‘‘superlumping’’ one is highlighted.

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Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty

BMC Ecology and Evolution ◽

10.1186/s12862-021-01931-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Stephanie J. Spielman ◽

Molly L. Miraglia

Keyword(s):

Model Selection ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Selection Procedure ◽

Evolutionary Model ◽

Time Estimation ◽

Ancestral State ◽

Sequence Alignments ◽

Multiple Sequence ◽

Divergence Time Estimation

Abstract Background Multiple sequence alignments (MSAs) represent the fundamental unit of data inputted to most comparative sequence analyses. In phylogenetic analyses in particular, errors in MSA construction have the potential to induce further errors in downstream analyses such as phylogenetic reconstruction itself, ancestral state reconstruction, and divergence time estimation. In addition to providing phylogenetic methods with an MSA to analyze, researchers must also specify a suitable evolutionary model for the given analysis. Most commonly, researchers apply relative model selection to select a model from candidate set and then provide both the MSA and the selected model as input to subsequent analyses. While the influence of MSA errors has been explored for most stages of phylogenetics pipelines, the potential effects of MSA uncertainty on the relative model selection procedure itself have not been explored. Results We assessed the consistency of relative model selection when presented with multiple perturbed versions of a given MSA. We find that while relative model selection is mostly robust to MSA uncertainty, in a substantial proportion of circumstances, relative model selection identifies distinct best-fitting models from different MSAs created from the same set of sequences. We find that this issue is more pervasive for nucleotide data compared to amino-acid data. However, we also find that it is challenging to predict whether relative model selection will be robust or sensitive to uncertainty in a given MSA. Conclusions We find that that MSA uncertainty can affect virtually all steps of phylogenetic analysis pipelines to a greater extent than has previously been recognized, including relative model selection.

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The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)

Zootaxa ◽

10.11646/zootaxa.4250.6.5 ◽

2017 ◽

Vol 4250 (6) ◽

pp. 577 ◽

Cited By ~ 5

Author(s):

MICHAEL J. GHEDOTTI ◽

MATTHEW P. DAVIS

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Time Estimation ◽

Species Group ◽

Total Evidence ◽

Morphological Data ◽

Fossil Species ◽

Divergence Time Estimation ◽

Biogeographic History ◽

Extant Species

The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53–23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys.

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Four new species, DNA barcode library and pre-Pliocene speciation of the euedaphic Afromontane Clivinini genera Trilophidius and Antireicheia (Coleoptera: Carabidae, Scaritinae)

Fragmenta Entomologica ◽

10.4081/fe.2017.225 ◽

2017 ◽

Vol 49 (1) ◽

pp. 1 ◽

Cited By ~ 2

Author(s):

Vasily V. Grebennikov ◽

Petr Bulirsch ◽

Paolo Magrini

Keyword(s):

New Species ◽

South African ◽

Dna Barcode ◽

Divergence Time ◽

Time Estimation ◽

Equatorial Guinea ◽

Cytochrome Oxidase Subunit ◽

Divergence Time Estimation ◽

Maximum Likelihood Approach ◽

Likelihood Approach

We describe and extensively illustrate four new species of euedaphic (= dwelling in the soil) Clivinini ground beetles: Trilophidius acastus sp. nov. and T. argus sp. nov. (both from Bioko, Equatorial Guinea), as well as Antireicheia calais sp. nov. and A. zetes sp. nov. (both from the South Pare Mountains, Tanzania). We generate and report all currently available DNA barcode (= cytochrome oxidase subunit I) data for euedaphic Afromontane Clivinini of the genera Trilophidius (2 species, four records) and Antireicheia (13 species, 43 records). We infer a phylogeny for these beetles using a Maximum Likelihood approach based upon a matrix of 53 sequenced specimens (dx.doi.org/10.5883/DS-ANTIREI) with 658 aligned positions. All nominative species represented by two or more sequences are recovered as monophyletic. Both new species of Trilophidius form a weakly supported clade, while all seven species of South African Antireicheia form a moderately supported clade. The genus Antireicheia and the geographical assemblage of its six Tanzanian species are not monophyletic. We perform divergence time estimation in Afrotropical Antireicheia, and our analysis indicates that these lineages diverged predominantly in the middle or late Miocene. We highlight the notable lack of phylogenetic hypothesis linked with the vaguely and variably defined taxon “subfamily Scaritinae” and its subordinated taxa.

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Was species diversification in Tenthredinoidea (Hymenoptera: Symphyta) related to the origin and diversification of angiosperms?

The Canadian Entomologist ◽

10.4039/tce.2014.60 ◽

2014 ◽

Vol 147 (4) ◽

pp. 443-458 ◽

Cited By ~ 6

Author(s):

Y. Isaka ◽

T. Sato

Keyword(s):

Host Plant ◽

Larval Stage ◽

Divergence Time ◽

Time Estimation ◽

Molecular Data ◽

Significant Shift ◽

Divergence Time Estimation ◽

Species Diversification ◽

Insect Order ◽

Molecular Phylogenetic

AbstractThe paraphyletic grouping “Symphyta” (8353 described species) represents the basal lineages of the insect order Hymenoptera. The most species-rich superfamily in Symphyta is Tenthredinoidea (7390 species), with six extant families. Most of tenthredinoids species are phytophagous at the larval stage, and the species using angiosperms as a host are more numerous (6265 species) than those using gymnosperms (140 species) or pteridophytes (985 species). In this study, we investigated whether diversification of Tenthredinoidea could be attributed to their use of angiosperms as hosts by examining host plant usage by lineage. We performed molecular phylogenetic and divergence time estimation analyses using molecular data (~2 kilobase sequence in five DNA regions) and conducted a diversification analysis. Our results suggest that Tenthredinoidea (excluding Blasticotomidae) had used angiosperms since its origin; the phylogeny of Tenthredinoidea showed a significant shift in diversification at two nodes, and those nodes overlap with the periods of origin and diversification of angiosperms.

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Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d190141 ◽

2018 ◽

Vol 19 (1) ◽

pp. 303-310 ◽

Cited By ~ 2

Author(s):

FITRA ARYA DWI NUGRAHA ◽

FATCHIYAH FATCHIYAH ◽

NIA KURNIAWAN ◽

ERIC NELSON SMITH

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Limited Data ◽

Divergence Time Estimation ◽

12S Rdna ◽

The Subject ◽

Molecular Relationships ◽

Inference Methods

Nugraha FAD, Fatchiyah F, Smith EN, Nia Kurniawan N. 2018. Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java. Biodiversitas 19: 303-310. The phylogenetic relationship among the major colubrid snakes, particularly those of the subfamily Colubrinae, has been the subject of much debate. Also, there was limited data on the molecular relationships of Sundaland colubrid snakes. This study aimed to examine the relationships among colubrid snakes from Sumatra and Java based on fragments of 12S rDNA gene. We sequenced 17 specimens of colubrid snakes representing 5 genera and 2 subfamilies: Colubrinae and Ahaetullinae. We used maximum likelihood, maximum parsimony and Bayesian inference methods for inferring phylogenetic relationships. The result of our phylogenetic analyses is in line with the previous findings for the separation between Colubrinae and Ahaetullinae. Interestingly, we found two distinct clades of Dendrelaphis pictus species with the high genetic divergence between them where D. pictus from Sumatra and West Java separated from Central and East Java clade. Our divergence time estimation showed that the differentiation between these clades of D. pictus occurred in the late Miocene epoch (8.9 Ma) when Sumatra and Java separated after being inundated in the early Miocene epoch.

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