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opencc-zeroDec 2012View details →

Data from: Phylogenetic relationships within the lizard clade Xantusiidae: using trees and divergence times to address evolutionary questions at multiple levels

Xantusiidae (night lizards) is a clade of small-bodied, cryptic lizards endemic to the New World. The clade is characterized by several features that would benefit from interpretation in a phylogenetic context, including: (1) monophyletic status of extant taxa Cricosaura, Lepidophyma, and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of disputed age; (3) origins of the parthenogenetic species of Lepidophyma; (4) pronounced micro-habitat differences accompanied by distinct morphologies in both Xantusia and Lepidophyma; and (5) placement of Xantusia riversiana, the only vertebrate species endemic to the California Channel Islands, which is highly divergent from its mainland relatives. This study incorporates extensive new character data from multiple gene regions to investigate the phylogeny of Xantusiidae using the most comprehensive taxonomic sampling available to date. Parsimony and partitioned Bayesian analyses of more than 7 kb of mitochondrial and nuclear sequence data from 11 loci all confirm that Xantusiidae is monophyletic, and comprises three well-supported clades: Cricosaura, Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well supported as the sister to all other xantusiids. Estimates of divergence time indicate that Cricosaura diverged from the (Lepidophyma + Xantusia) clade ∼81 million years ago (Ma), a time frame consistent with the separation of the Antilles from North America. Our results also confirm and extend an earlier study suggesting that parthenogenesis has arisen at least twice within Lepidophyma without hybridization, that rock-crevice ecomorphs evolved numerous times (>9) within Xantusia and Lepidophyma, and that the large-bodied Channel Island endemic X. riversiana is a distinct, early lineage that may form the sister group to the small-bodied congeners of the mainland.

opencc-zeroDec 2023View details →

Phylogenetic relationships and divergence dating of Mantodea using mitochondrial phylogenomics

Mantodea is a predatory insect group, its members occupying a diverse array of widely distributed habitats. Praying mantis species utilize hunting strategies including remarkable mimicry and unique camouflage for hiding from natural enemies while catching their prey. The emergence of a "cyclopean ear" in mantises is thought to be a morphological innovation of the group, and an "arms race" with echolocating bats is one of the hypotheses put forward to account for the emergence of the mantis ear from a coevolutionary perspective. However, this hypothesis has not been rigorously tested because of a lack of robust higher‐level phylogeny and a detailed chronogram of Mantodea. Previous phylogenetic studies found an incongruence between traditional classification and molecular phylogenetics due to the convergent evolution of various ecomorphic strategies of the lineage. Here, we performed a comprehensive phylogenetic analysis of Mantodea based on data from 61 mitogenomes. Our analyses showed that the monophyly of Acanthopidae, Haaniidae, Nanomantidae, Miomantidae and Mantidea was supported. The newly updated Gonypetidae were paraphyletic, whereas Eremiaphilidae, Deroplatyidae and Toxoderidae were polyphyletic. Our molecular dating analyses inferred that Spinomantodea originated at ca. 149 Ma (Late Jurassic), whereas the origin of hearing mantises (Cernomantodea) was inferred as Early Cretaceous (119 Ma, 95% CI: 110–129 Ma). The molecular dating results indicated that the hearing organ in mantises did not arise in response to bat predation. Our study provides a robust framework for further evolutionary comparative studies of mantises.

opencc-zeroApr 2022View details →

Dung beetles maintain phylogenetic divergence but functional convergence across a highly fragmented tropical landscape

Understanding how human-modified landscapes affect the phylogenetic composition and assembly mechanisms of biological communities is critical for effectively managing and restoring tropical ecosystems. We evaluated how forest coverage loss, fragmentation, and landscape heterogeneity affect the phylogenetic diversity of dung beetles and their assembly mechanisms in Los Tuxtlas Biosphere Reserve, a protected but highly fragmented tropical landscape. We calculated Faith's phylogenetic diversity, mean pairwise phylogenetic distance, and mean nearest taxon distance for 5,388 individuals in 36 species. The standardised effect sizes of these metrics were estimated to control their correlation with species richness. Phylogenetic diversity was also assessed separately for each dung beetle functional group. Finally, we compared the mean functional and phylogenetic pairwise distance and mean nearest taxon distance and measured the phylogenetic signal among dung beetle functional traits to determine the influence of niche conservatism on the phylogenetic structure of species assemblages. Faith's phylogenetic diversity of dung beetles was positively correlated with forest coverage, while their mean phylogenetic and nearest taxon distance values decreased with increasing landscape fragmentation. Necrophagous beetles and forest specialists responded most negatively to forest coverage loss and fragmentation. Alpha and beta diversity values showed phylogenetic overdispersion but functional convergence and weak phylogenetic signals in their functional traits, suggesting low niche conservatism. Landscapes with moderate forest coverage (≥ 40%) favoured higher phylogenetic beta diversity, whereas phylogenetic and functional beta diversity decreased significantly in landscapes with low forest coverage (< 30%). Synthesis and applications: Forest habitats in fragmented landscapes are essential for safeguarding the evolutionary history of dung beetles, reducing biotic homogenisation processes by favouring phylogenetic overdispersion and complementarity between sites. Therefore, to secure the phylogenetic diversity of dung beetles within fragmented tropical reserves, we recommend protecting the existing forests, preventing further fragmentation of continuous forest areas, and increasing matrix quality by implementing biodiversity-friendly production systems. Finally, managers should consider assessing different functional groups in other species, as their response to landscape disturbance may not be phylogenetically similar. The above will allow more effective management practices to protect the species most susceptible to disturbances.

opencc-zeroMay 2022View details →

Phylogenetic divergence and ecophysiological variation in the disjunct Kalmia buxifolia (Sand-myrtle, Ericaceae)

Kalmia buxifolia (sand-myrtle, Ericaceae) is disjunctly distributed across the high-elevation rock outcrops of the southern Appalachians, upper monadnocks and pine savannas of the Carolina Piedmont and Coastal Plain, and the New Jersey Pine Barrens. Here, we sampled plants from each region and reconstructed the phylogeographic history of K. buxifolia to test a rock-outcrop Pleistocene refugium hypothesis, estimate the potential direction(s) and timing of migration, and date divergence from its alpine sister species, K. procumbens. We also assess whether isolation in these different environments has led to variation in intrinsic water-use efficiency (IWUE). Dating analysis challenges the current hypothesis that rock-outcrop species are relics of Pleistocene refugia (<18,000 ybp), placing the divergence of K. buxifolia and K. procumbens much earlier, in the late-Miocene (9.40 Ma). Chloroplast haplotype analysis indicates four potential refugial sites, with the most ancient on Mount LeConte in the Great Smoky Mountains, and point to an Appalachian corridor as the likely Pine Barrens colonization route. The sister species divergence time and population level divergences within K. buxifolia generally coincide with major climatic shifts from the late-Miocene to mid-Pleistocene. Results from CID indicate that plant water-use varies geographically within K. buxifolia, as does leaf morphology, although it is unclear whether this variation is due to genetic adaptation or phenotypic plasticity. These patterns of phylogenetic divergence and resulting ecophysiological diversity within K. buxifolia are significant for clarifying long-held questions about the biogeographic history and trait differentiation within this species. Further, our results suggest that high-elevation rock outcrop communities may have been inhabitated by northern-affinity species for much longer than previously assumed, and that subsequent population disjunction and isolation may have resulted in ecophysioloigcal differentiation in these communities.

opennotspecifiedSep 2017View details →

FIGURE 2 in Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)

FIGURE 2. Phylogenetic trees of the genus Chelonoidis, including the C. chilensis complex, obtained by three different criteria. A: Maximum Parsimony, B: Maximum Likelihood, C: Bayesian Inference. The numbers above the nodes indicate bootstrap support scores (A and B) and posterior probability scores (C). Clade colors refer to the corresponding eco–regions (see Fig. 1).

opennotspecifiedSep 2017View details →

FIGURE 1 in Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)

FIGURE 1. Map of Argentina showing the localities from which the tissue samples were taken. Different colors indicate different eco–regions. Legends near sample localities are in accordance with the haplotypes shown in the phylogenetic trees (Fig. 2).

opennotspecifiedSep 2017View details →

FIGURE 3 in Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)

FIGURE 3. Ultrametric trees obtained by the two-step method of McCartney & Barreto (2010), showing the divergence times within the family Testudinidae (A) and the divergence times within the C. chilensis complex (B). Numbers above the nodes indicate median of node ages, red numbers below the nodes indicate the clades belonging to the genus Chelonoidis (see table 5).

opennotspecifiedNov 2022View details →

Fig. 3 in Phylogenetic relationships and divergence times of the poorly known genus Spalerosophis (Serpentes: Colubridae)

Fig. 3 Geographical distribution range of the genus Spalerosophis based on data taken from Marx (1959), Baig and Masroor (2008), www.GBIF.org website, and our study

FIGURE 11 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 11. Illustration of Specklinia pertenuis (C.Schweinf.) Karremans & Gravend by G.C.K. Dunsterville, based on Dunsterville 430 (AMES) from Venezuela. Reproduced with the kind permission of the Orchid Herbarium of Oakes Ames, the Harvard University Herbaria.

FIGURE 14 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 14. Known elevation distribution of the glandulous species of Specklinia. Based on the studied specimens cited. On the X-axis the elevations in meters are depicted.

FIGURE 7 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 7. Specklinia chontalensis (A.H.Heller & A.D.Hawkes) Luer. A. habit. B. flower. C. dissected perianth. D. petal. E. lip. F. column and lip, lateral view. G. column, ventral view. H. anther with pollinaria. I. pollinaria. Drawn by E. Winkel from Pupulin 6543 (JBL-spirit. L-spirit).

FIGURE 4. Specklinia alajuelensis Karremans & Pupulin. A. habit. B. flower. C. dissected perianth. D in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 4. Specklinia alajuelensis Karremans & Pupulin. A. habit. B. flower. C. dissected perianth. D. column and lip, lateral view. E. anther and pollinaria. Drawn by A.P. Karremans & L. Oses from Karremans 3265 (JBL-spirit).

FIGURE 1. The glandulous Specklinia species. A. S. alajuelensis 1 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 1. The glandulous Specklinia species. A. S. alajuelensis 1 (Karremans 3265). B. S. alajuelensis 2 (Bogarín 2895). C. S. chontalensis (Pupulin 6543). D. S. gersonii (Karremans 6025). E. S. glandulosa (Karremans 6306). F. S. vittariifolia (Karremans 2945). Photographs by A.P. Karremans.

FIGURE 13 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 13. Extract of the distribution map of the glandulous species of Specklinia, with emphasis on Nicaragua, Costa Rica and Panama. Edited by D. Bogarín.

FIGURE 12 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 12. Specklinia vittariifolia (Schltr.) Pridgeon & M.W.Chase. A. habit. B. flower. C. dissected perianth. D. column and lip, lateral view. E. lip. F. anther and pollinaria. Drawn by A.P. Karremans & L. Oses from Karremans 2945 (JBL-spirit).

FIGURE 10 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 10. Specklinia glandulosa (Ames) Pridgeon & M.W.Chase. A. habit. B. flower. C. dissected perianth. D. column and lip, lateral view. E. lip. F. anther and pollinaria. Drawn by A.P. Karremans & L. Oses from Karremans 6306 (JBL-spirit).

FIGURE 9 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 9. Type illustration of Specklinia glandulosa (Ames) Pridgeon & M.W.Chase, published by Ames (1923). Reproduced with the kind permission of the Orchid Herbarium of Oakes Ames, the Harvard University Herbaria.

FIGURE 17 in The glandulous Specklinia: morphological convergence versus phylogenetic divergence

FIGURE 17. Comparison of the lip size, shape, ornamentation and color of two species of glandulous Specklinia, in natural position (right) and extended (left). A. S. alajuelensis 1 (Pupulin 8470). B. S. vittariifolia (Chinchilla 1111). Scale bar = 5 mm. Photographs by A.P. Karremans.