scholarly journals How important is it to consider lineage diversification heterogeneity in in macroevolutionary studies: lessons from the lizard family Liolaemidae

2019 ◽  
Author(s):  
Melisa Olave ◽  
Luciano J. Avila ◽  
Jack W. Sites ◽  
Mariana Morando
Keyword(s):  
Diversification Rates ◽  
State Dependent ◽  
The Family ◽  
Problematic Issue ◽  
Speciation Rates ◽  
Potential Risks ◽  
Species Groups ◽  
Extinction Model ◽  
Diversification Pattern ◽  
Lineage Diversification

AbstractMacroevolutionary studies commonly apply multiple models to test state-dependent diversification. These models track the association between states of interest along a phylogeny, but they do not consider whether independent shifts in character states are associated with shifts in diversification rates. This potentially problematic issue has received little theoretical attention, while macroevolutionary studies implementing such models in increasing larger scale studies continue growing. A recent macroevolutionary study has found that Andean orogeny has acted as a species pump driving diversification of the family Liolaemidae, a highly species-rich lizard family native to temperate southern South America.This study approaches a distribution-dependent hypothesis using the Geographic State Speciation and Extinction model (GeoSSE). However, more recent analyses have shown that there is a clear heterogeneous diversification pattern in the Liolaemidae, which likely biased the GeoSSE analysis. Specifically, we show here that there are two shifts to accelered speciation rates involving species groups that were classified as “Andean” in their distributions. We demonstrate that this GeoSSE result is meaningless when heterogeneous diversification rates are included. We use the lizard family Liolaemidae to demonstrate potential risks of ignoring clade-specific differences in diversification rates in macroevolutionary studies.

scholarly journals Detecting hidden diversification shifts in models of trait-dependent speciation and extinction

2015 ◽  
Author(s):  
Jeremy M Beaulieu ◽  
Brian C O'Meara
Keyword(s):  
Empirical Data ◽  
Diversification Rate ◽  
Transition Rates ◽  
Diversification Rates ◽  
Extinction Rates ◽  
State Dependent ◽  
Speciation Rates ◽  
Nuanced Understanding ◽  
Hidden States ◽  
Major Criticism

The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased their extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE methods. Specifically, our model, which we refer to as HiSSE (Hidden-State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification (CID) models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.

scholarly journals Interaction Between Ploidy, Breeding System, and Lineage Diversification

2019 ◽  
Author(s):  
Rosana Zenil-Ferguson ◽  
J. Gordon Burleigh ◽  
William A. Freyman ◽  
Boris Igić ◽  
Itay Mayrose ◽  
...  
Keyword(s):  
Breeding System ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Self Incompatibility ◽  
Evolutionary Pathway ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Biological Hierarchy ◽  
Lineage Diversification

AbstractIf particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

Systematics of reptile-associated scale mites of the genus Pterygosoma (Acariformes: Pterygosomatidae) derived from external morphology

Zootaxa ◽  
2019 ◽  
Vol 4603 (3) ◽  
pp. 401
Author(s):  
MONIKA FAJFER
Keyword(s):  
North Africa ◽  
New Genus ◽  
Arabian Peninsula ◽  
Morphological Characters ◽  
Mite Species ◽  
South American ◽  
The Family ◽  
Outgroup Species ◽  
Tree Lizards ◽  
Species Groups

The phylogeny of the mite genus Pterygosoma Peters, 1849 (Acariformes: Pterygosomatidae), permanent parasites of lizards of the families Agamidae, Gerrhosauridae and Liolaemidae (Reptilia: Squamata), was inferred with maximum parsimony, successive weighting and implied weighting approaches based on 182 characters of 48 ingroup and 12 outgroup species. All undertaken analyses questioned the monophyly of the genus. Based on this research, Pterygosoma includes 56 mite species associated with agamas from Africa and Asia (Sauria: Agamidae). Within the genus seven natural species groups were found: mutabilis, inermis, melanum, caucasica, fimbriata, singularis and foliosetis; 13 species of the genus were not assigned to any of the groups due to their unique morphological characters. For the ligare group of the subgenus Pterygosoma s. str. (7 species) associated with the South American tree lizards from the family Liolaemidae, a new genus, Neopterygosoma gen. nov., is established. The subgenus Gerrhosaurobia Lawrence, 1959 (3 species) associated with the African plated lizards of the family Gerrhosauridae is elevated to the genus rank. Diagnoses for the three genera are presented. Historical associations are reconstructed by fitting the obtained mite tree into the host topology on the family level. Results of coevolutionary analysis highlight the coincidence of both trees. The studies suggest that the ancestor of the genus Pterygosoma switched from the hosts of Gerrhosaurobia i.e. from the plated lizards (Gerrhosauridae) to the agamas (Agamidae), and the genus Pterygosoma has its biogeographic origin in North Africa, and colonized Asia via the Arabian Peninsula, which is congruent with the historical biogeography of its hosts.

scholarly journals Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

2010 ◽  
Vol 277 (1700) ◽  
pp. 3587-3592 ◽  
Author(s):  
Soo Hyung Eo ◽  
J. Andrew DeWoody
Keyword(s):  
Species Richness ◽  
Nuclear Data ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Rate Variation ◽  
Substitution Rates ◽  
Diversification Rates ◽  
Extinction Process ◽  
Molecular Evolutionary Rates ◽  
Speciation Rates

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO 3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

Taxonomic review of the genus Meleonoma Meyrick (Lepidoptera: Autostichidae), with a checklist of all the described species

Zootaxa ◽  
2020 ◽  
Vol 4763 (3) ◽  
pp. 371-393 ◽  
Author(s):  
SHUXIA WANG ◽  
XIAOJU ZHU ◽  
BAIXUE ZHAO ◽  
XIAOFEI YANG
Keyword(s):  
Morphological Study ◽  
Molecular Data ◽  
Species Group ◽  
Diagnostic Characters ◽  
Taxonomic Review ◽  
The Family ◽  
Species Groups

Meleonoma Meyrick, 1914 is treated as a genus of the family Autostichidae based on the recent study. Fifty species are transferred from the genus Cryptolechia to Meleonoma, and eight Meleonoma species groups are proposed for the taxonomic convenience based on both molecular data and morphological study. Eight species groups include: the malacobyrsa group, the segregnatha group, the annulignatha group, the fasciptera group, the jigongshanica group, the dentivalvata group, the facialis group, and the acutiuscula group. Diagnostic characters and representative illustrations of each species group are provided. A discussion on the proposed species groups is given, and a checklist of all the 88 described Meleonoma species is provided. 

scholarly journals An analysis of the sessile, structure-forming invertebrates living on California oil and gas platforms

2019 ◽  
Vol 95 (4) ◽  
pp. 583-596
Author(s):  
Milton S Love ◽  
Mary M Nishimoto ◽  
Linda Snook ◽  
Li Kui
Keyword(s):  
Southern California ◽  
Oil And Gas ◽  
Narrow Range ◽  
Depth Range ◽  
Lophelia Pertusa ◽  
The Family ◽  
Species Groups ◽  
Invertebrate Assemblages

Using video transects of oil and gas platform crossbeams off central and southern California, we characterized the structure-forming invertebrates (with a height of at least 20 cm) found around 23 oil and gas platforms at depths between 20 and 363 m. We observed 20,357 individual invertebrates, comprising 19,800 Cnidaria and 557 Porifera of at least 15 species or species groups. Metridium farcimen (Brandt, 1835) was by far the most commonly observed cnidarian, forming 97.6% of all invertebrates catalogued. The alcyonacean, Leptogorgia chilensis (Verrill, 1868), and the scleractinian, Lophelia pertusa (Linnaeus, 1758), were the most commonly observed corals. White vase sponges (most or all in the family Aphrocallistidae) were the most abundant of the sponges (comprising 38.4% observed). We also documented a variety of unidentified foliose, barrel, and other various-shaped sponges. The height of these invertebrates ranged from 20 to 80 cm. Taxa displayed a variety of depth patterns. Some, such as M. farcimen, unidentified white vase sponges, and L. pertusa, were found throughout most or all of the survey depth range, while others (notably the gorgonians L. chilensis, Placogorgia spp., and Acanthogorgia spp.) were found over a relatively narrow range. Invertebrate assemblages tended to be similar among many platforms reflecting species similarities over a broad range of platform depths. Based on these relationships, it is apparent that the assemblages of structure-forming invertebrates varied by depth rather than geography.

A new subfamily, Cydnodromellinae, in the family Phytoseiidae (Acari: Gamasina)

1986 ◽  
Vol 64 (12) ◽  
pp. 2811-2823 ◽  
Author(s):  
D. A. Chant ◽  
E. Yoshida-Shaul
Keyword(s):  
Type Species ◽  
Species Group ◽  
Adult Females ◽  
The Family ◽  
Species Groups ◽  
Lateral Area

A new subfamily, Cydnodromellinae, is proposed in the family Phytoseiidae. Members of the subfamily are characterized by the unique chaetotaxy of the podoscutum, which has five pairs of setae (j3, z2, z4, s4, s6) on its lateral area, with seta z3 absent. There are two genera in this new subfamily. Platyseiella Muma is monotypic, represented by the type-species, P. platypilis (Chant). Cydnodromella Muma includes three species groups and six species: the negevi group (C. negevi (Swirski and Amitai) comb.nov.), the pilosus group (C. pilosus (Chant), type-species of the genus Cydnodromella), and the alveolaris group (C. alveolaris (De Leon) comb.nov., C. borinquensis (De Leon) comb.nov., C. sanictus (De Leon) comb.nov. and C. tunapunensis (De Leon) comb.nov.). Galendromimus Muma and Typhlodromus (Galendromimus) Muma sensu van der Merwe are designated as junior synonyms of the genus Cydnodromella and Cydnoseius cordiae Muma, Typhlodromus medanicus El Badry, and T. zaheri El Badry are designated as junior synonyms of C. negevi. Systematic concepts pertaining to the species in the two genera are reviewed, and descriptions of each genus, species group, and species are given. Keys to the adult females of the species groups in the genus Cydnodromella and to the species in the alveolaris group are provided.

Larvae of the North American Olethreutidae (Lepidoptera)

1959 ◽  
Vol 91 (S10) ◽  
pp. 5-338 ◽  
Author(s):  
Margaret Rae MacKay
Keyword(s):  
North American ◽  
Fruit Trees ◽  
Individual Species ◽  
The North ◽  
The Family ◽  
Late Instar ◽  
Species Groups ◽  
Relationship Of ◽  
Spruce Needles ◽  
The Relationship

AbstractThe late-instar larvae of about 185 species of the North American Olethreutidae are described and most of them illustrated. Included in these are many pests, such as Grapholitha molesta, Carpocapsa pomonella, and Spilonota ocellana on fruit trees, Paralobesia viteana on grapes, Ancylis comptana fragariae on strawberries, Laspeyresia nigricana in pea pods, Laspeyresia caryana in hickory and pecan nuts, Taniva albolineana in spruce needles, and species of Rhyacionia and Petrova on pines. Keys to species groups and to individual species are provided. Of the diagnostic and specialized characters listed, the most useful include the setae, the spinneret, and the shape of the larva, especially of its head and anal shield. The main characters are given for the postulated ancestral larva and for the highly developed larva. Most of the species groups are arranged according to the suggested phylogenetic relationship of their larvae, emphasizing the necessity of a revision of the family. Larvae of some genera previously difficult to classify, such as Pseudogalleria and Hystricophora, indicate the relationship of those genera to other groups; conversely, lack of relationship is clearly shown in other instances, e.g., between Carpocapsa pomonella and Carpocapsa saltitans, and between the two species Epiblema culminana and E. suffusana and other members of the genus Epiblema.

Two new species of the family Pontellidae (Copepoda, Calanoida) from Arguni Bay, Kaimana, West Papua, Indonesia, with notes on their species-groups

Crustaceana ◽  
2014 ◽  
Vol 87 (14) ◽  
pp. 1620-1639 ◽  
Author(s):  
Keyword(s):  
New Species ◽  
Species Group ◽  
West Pacific ◽  
The Family ◽  
West Papua ◽  
Two New Species ◽  
Species Groups ◽  
The Right

Two new species of the family Pontellidae, Labidocera kaimanaensis and Pontella papuaensis, are described and illustrated from specimens collected in Arguni Bay, West Papua, Indonesia. L. kaimanaensis belongs to the L. detruncata species-group, is distinguishable from other species of this group by the very elongated Ur1 (urosomite 1) and the asymmetrical P5 in the female and the Pdg5 (pediger 5) and P5 in the male. P. papuaensis does not belong to any of the known five groups of Indo-West Pacific Pontella, in having Ur1 with a beak-like posterodorsal process and almost symmetrical Re’s (exopods) of P5 in the female, a rostrum with double convex lenses, the chela of the right P5 with a bilobed thumb, and the inner margin of that chela armed with a large process, in the male. The establishment of four new species-sub-groups of L. detruncata, i.e., L. d.-cervi, L. d.-farrani, L. d.-kaimanaensis, and L. d.-sinilobata, as well as the establishment of a P. papuaensis species-group, are proposed.

scholarly journals Mass extinction in tetraodontiform fishes linked to the Palaeocene–Eocene thermal maximum

2017 ◽  
Vol 284 (1866) ◽  
pp. 20171771 ◽  
Author(s):  
Dahiana Arcila ◽  
James C. Tyler
Keyword(s):  
Mass Extinction ◽  
Reef Fishes ◽  
Morphological Data ◽  
Fossil Species ◽  
Thermal Maximum ◽  
Extant Species ◽  
Homogeneous Models ◽  
Speciation Rates ◽  
Mass Extinction Event ◽  
Lineage Diversification

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene–Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic.

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