scholarly journals Joint Phylogenetic Estimation of Geographic Movements and Biome Shifts during the Global Diversification of Viburnum

2020 ◽  
Vol 70 (1) ◽  
pp. 67-85 ◽  
Author(s):  
Michael J Landis ◽  
Deren A R Eaton ◽  
Wendy L Clement ◽  
Brian Park ◽  
Elizabeth L Spriggs ◽  
...  

Abstract Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy are all lines of evidence that reflect the singular evolutionary history of a clade, but they are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, while incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize in our ongoing worldwide monographic treatment of the group. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia, we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia, we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, whereas the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. It will be critical to take advantage of all available lines of evidence to decipher events in the distant past. The joint estimation approach developed here provides cautious hope even when fossil evidence is limited. [Biogeography; biome; combined evidence; fossil pollen; phylogeny; Viburnum.]

2019 ◽  
Author(s):  
Michael J. Landis ◽  
Deren A. R. Eaton ◽  
Wendy L. Clement ◽  
Brian Park ◽  
Elizabeth L. Spriggs ◽  
...  

AbstractPhylogeny, fossils, biogeography, and biome occupancy provide evidence that reflects the singular evolutionary history of a clade. Despite the connections that bind them together, these lines of evidence are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, while the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. We argue that it will be critical to take advantage of all available lines of evidence to decipher events in the distant past, and the joint estimation approach developed here provides cautious hope even when fossil evidence is limited.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Weizhao Yang ◽  
Nathalie Feiner ◽  
Catarina Pinho ◽  
Geoffrey M. While ◽  
Antigoni Kaliontzopoulou ◽  
...  

AbstractThe Mediterranean basin is a hotspot of biodiversity, fuelled by climatic oscillation and geological change over the past 20 million years. Wall lizards of the genus Podarcis are among the most abundant, diverse, and conspicuous Mediterranean fauna. Here, we unravel the remarkably entangled evolutionary history of wall lizards by sequencing genomes of 34 major lineages covering 26 species. We demonstrate an early (>11 MYA) separation into two clades centred on the Iberian and Balkan Peninsulas, and two clades of Mediterranean island endemics. Diversification within these clades was pronounced between 6.5–4.0 MYA, a period spanning the Messinian Salinity Crisis, during which the Mediterranean Sea nearly dried up before rapidly refilling. However, genetic exchange between lineages has been a pervasive feature throughout the entire history of wall lizards. This has resulted in a highly reticulated pattern of evolution across the group, characterised by mosaic genomes with major contributions from two or more parental taxa. These hybrid lineages gave rise to several of the extant species that are endemic to Mediterranean islands. The mosaic genomes of island endemics may have promoted their extraordinary adaptability and striking diversity in body size, shape and colouration, which have puzzled biologists for centuries.


Author(s):  
Gordon Grigg ◽  
David Kirshner

Biology and Evolution of Crocodylians is a comprehensive review of current knowledge about the world's largest and most famous living reptiles. Gordon Grigg's authoritative and accessible text and David Kirshner's stunning interpretive artwork and colour photographs combine expertly in this contemporary celebration of crocodiles, alligators, caimans and gharials. This book showcases the skills and capabilities that allow crocodylians to live how and where they do. It covers the biology and ecology of the extant species, conservation issues, crocodylian–human interaction and the evolutionary history of the group, and includes a vast amount of new information; 25 per cent of 1100 cited publications have appeared since 2007. Richly illustrated with more than 500 colour photographs and black and white illustrations, this book will be a benchmark reference work for crocodylian biologists, herpetologists and vertebrate biologists for years to come. Winner of the 2015 Whitley Medal.


Phytotaxa ◽  
2016 ◽  
Vol 272 (4) ◽  
pp. 235
Author(s):  
JOSEPH MOHAN ◽  
JEFFERY R. STONE ◽  
CHRISTOPHER J CAMPISANO

Paleolake Hadar was an expansive lake in the lower Awash Valley of Ethiopia’s Afar Depression that existed periodically through the Late Pliocene. The sedimentary deposits from this ancient lake (Hadar Formation) have broad importance because a significant number of hominin fossils have been recovered from the formation. Samples of the Hadar Formation lacustrine sequence were collected from sediment cores extracted as part of the Hominin Sites and Paleolakes Drilling Project (HSPDP). A paleoecological study of the HSPDP Northern Awash (Hadar Formation) material has unearthed three novel species of Bacillariophyta (diatoms) from diatomites that appear periodically in the cores. The Hadar Formation assemblage represents a newly revealed excerpt from the evolutionary history of freshwater diatoms in East Africa during the Piacenᴢian age (2.59–3.60 Ma). The HSPDP Northern Awash diatom species are compared to previously reported diatoms from Pliocene outcrops, modern and fossil core material from Lake Malawi, and extant species. Here we describe two new species of Aulacoseira and one of Lindavia. Taxonomic treatment of two diatom varieties reported by previous researchers as Melosira are transferred into Aulacoseira herein.


2015 ◽  
Vol 29 (2) ◽  
pp. 191 ◽  
Author(s):  
James K. Liebherr ◽  
Nick Porch

A late Holocene but prehistoric carabid beetle fauna from the lowland Makauwahi Cave, Kauai, is characterised. Seven extinct species – Blackburnia burneyi, B. cryptipes, B. godzilla, B. menehune, B. mothra, B. ovata and B. rugosa, spp. nov. (tribe Platynini) – represent the first Hawaiian insect species to be newly described from subfossil specimens. Four extant Blackburnia spp. – B. aterrima (Sharp), B. bryophila Liebherr, B. pavida (Sharp), and B. posticata (Sharp) – and three extant species of tribe Bembidiini – Bembidion ignicola Blackburn, B. pacificum Sharp and Tachys oahuensis Blackburn – are also represented. All subfossil fragments are disarticulated, with physical dimensions and cladistic analysis used to associate the major somites – head, prothorax and elytra – for description of the new species. The seven new Makauwahi Cave species support recognition of a lowland area of endemism adjoining Haupu, a low-stature 700 m elevation ridgeline in southern Kauai. Four of the extinct Blackburnia are adelphotaxa to extant species currently found at higher elevations in Kauai. Addition of these lowland specialists to the phylogenetic hypothesis undercuts applicability of the taxon cycle for interpreting evolutionary history of these taxa. Two of the extinct species are Kauai representatives in clades that subsequently colonised younger Hawaiian Islands, enhancing support for the progressive biogeographic colonisation of the archipelago by this lineage. And three of the extinct Blackburnia species comprised larger beetles than those of any extant Kauai Blackburnia, consistent with the evolution of island gigantism in the lowland habitats of Kauai.


Author(s):  
Robert J Kallal ◽  
Dimitar Dimitrov ◽  
Miquel A Arnedo ◽  
Gonzalo Giribet ◽  
Gustavo Hormiga

Abstract We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the family Araneidae paraphyletic. We discuss the importance of monophyly, outgroup selection, and taxon sampling, the subjectivity of ranks, and the implications of the age of origin criterion to assign categorical ranks in biological classifications. We explore the outcome of applying the approach of Kuntner et al. (2019) to the classification of spiders with emphasis on the ecribellate orb-weavers (Araneoidea) using a recently published dated phylogeny. We discuss the implications of including the putative sister group of Nephilinae (the sexually dimorphic genus Paraplectanoides) and the putative sister group of Araneidae (the miniature, monomorphic family Theridiosomatidae). We propose continuation of the phylogenetic classification put forth by Dimitrov et al. (2017), and we formally rank Nephilinae and Phonognathinae as subfamilies of Araneidae. Our classification better reflects the understanding of the phylogenetic placement and evolutionary history of nephilines and phonognathines while maintaining the diagnosability of Nephilinae. It also fulfills the fundamental requirement that taxa must be monophyletic, and thus avoids the paraphyly of Araneidae implied by Kuntner et al. (2019).


Phytotaxa ◽  
2015 ◽  
Vol 219 (2) ◽  
pp. 101 ◽  
Author(s):  
Bin Sun ◽  
Yi-Ming Cui ◽  
Hai-Feng Wang ◽  
David Kay Ferguson ◽  
Qiao-Ping Xiang ◽  
...  

Thuja, with 5 extant species, exhibiting a disjunctive distribution between East Asia (3 species) and North America (2 species), was investigated with respect to the morphological characters of foliage and cones by LM and SEM. Here we provide 2 keys to all 5 species of Thuja based on the cones and foliage respectively, which not  only can be used for identifying extant Thuja at the species level, but also have a great potential for recognizing and/or linking the fossil species to living ones, and further tracing the evolutionary history of the genus.


2001 ◽  
Vol 32 (4) ◽  
pp. 381-392 ◽  
Author(s):  
Nils Møller Andersen ◽  
David Grimaldi

AbstractSemiaquatic bugs (Hemiptera: Gerromorpha) comprise about 1,800 extant species classified in eight families. So far, 38 fossil species belonging to six families have been described or recorded, most of Cenozoic age. Knowledge about the evolutionary history of the major groups of Gerromorpha is seriously hampered by the scarcity of well-preserved Mesozoic fossils, especially from the Cretaceous. The present paper reports on a well-preserved semiaquatic bug from amber collected in the northern part of Myanmar (Burma). The source of this fossiliferous amber was previously considered to be Eocene in age, but recent evidence indicates that it originated in the Middle Cretaceous (Turonian-Cenomanian), or 100-90 Ma. The fossil species is described as Carinametra burmensis gen. et sp. n. The presence of three pairs of cephalic trichobothria, a prolonged head, long slender antennae and legs, reduced wing venation, etc., places the fossil in the gerromorphan family Hydrometridae or water measurers. Other characters suggest a close relationship with the two extant genera of the most basal of the hydrometrid subfamilies, Heterocleptinae. We present and discuss the available evidence used in the dating of Burmese amber. Finally, we discuss the phylogenetic, paleobiological, and biogeographic significance of the new fossil.


2020 ◽  
Author(s):  
Anton Suvorov ◽  
Celine Scornavacca ◽  
M. Stanley Fujimoto ◽  
Paul Bodily ◽  
Mark Clement ◽  
...  

SUMMARYIntrogression is arguably one of the most important biological processes in the evolution of groups of related species, affecting at least 10% of the extant species in the animal kingdom. Introgression reduces genetic divergence between species, and in some cases can be highly beneficial, facilitating rapid adaptation to ever-changing environmental pressures. Introgression also significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model, relic insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically “intermediate” species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression probably coming from zygopteran genomes. Additionally, we found evidence for multiple cases of deep inter-familial ancestral introgression. However, weaker evidence of introgression was found within more recently diverged focal clades: Aeshnidae, Gomphidae+Petaluridae and Libellulidae.


2017 ◽  
Author(s):  
Roman Sloutsky ◽  
Kristen M. Naegle

AbstractEvolutionary reconstruction algorithms produce models of the evolutionary history of proteins: the order of duplications and speciations that led to extant homologous proteins observed across species. Although they are regularly used to gain insight into protein function, these models are estimates of an unknowable truth according to the underlying assumptions inherent in each algorithm, its objective function, and the input sequences supplied for reconstruction. In practice, the generated models are highly sensitive to the sequence inputs. In this work, we asked whether we could identify stronger phylogenetic signal by capitalizing on the variance introduced by perturbing the input to evolutionary reconstruction to explore a rich space of possible models that could explain protein evolution. We subsampled from available protein orthologs, “same” proteins across multiple extant species, and produced an ensemble of topologies representing the duplication history which produced related proteins (paralogs) for simulated protein families and in a real protein family – the LacI transcription factor family. We found that two very important phenomena arise from this approach. First, the reproducibility of an all-sequence, single-alignment reconstruction, measured by comparing topologies inferred from 90% subsamples, directly correlates with the accuracy of that single-alignment reconstruction, producing a measurable value for something that has been traditionally unknowable. Second, if we take a large ensemble of trees inferred from 50% subsamples and cast the ensemble into a form that represents the distribution of pairwise leaf distances observed across the ensemble, then trees that capture the most frequently observed relationships are also the most accurate. We propose a new methodology, ASPEN, a meta-algorithm that finds and ranks the trees that are most consistent with observations across the ensemble. Top-ranked ASPEN trees are significantly more accurate than the single-alignment tree produced from all available sequences. Importantly, our findings suggest that the true tree is currently inaccessible for most real protein families. Instead, applications that rely on evolutionary models should integrate across many trees that are equally likely to represent the true evolutionary history of a protein family.


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