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opencc-by-4.0Aug 2020View details →

Phylogenetic signal in phonotactics: Supplementary materials

Data, code and results for the paper Phylogenetic signal in phonotactics (<a href="https://doi.org/10.1075/dia.20004.mac">Macklin-Cordes, Bowern & Round, 2021</a>). Information and usage instructions are found in the readme.txt file and Section S3 of the paper's Supplementary Information.

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Phylogenetic signals in host-parasite associations for Neotropical bats and Nearctic desert rodents

Hosts and their parasites have strong ecological and evolutionary relationships, with hosts representing habitats and resources for parasites. In the present study, we use approaches developed to evaluate the statistical dependence of species trait values on phylogenetic relationships to determine whether host–parasite relationships (i.e. parasite infections) are contingent on host phylogeny. If host–parasite relationships are contingent on the ability of hosts to provide habitat or resources to parasites, and if host phylogeny is an effective surrogate for among-host variation in habitat and resource quality, host–parasite relationships should evince phylogenetic signals (i.e. be contingent on host phylogeny). Because the strength of ecological relationships between parasites and their hosts may affect the likelihood of phylogenetic signals occurring in host–parasite relationships, we hypothesized that (1) host specificity would be positively correlated with the strength of phylogenetic signals and (2) the strength of phylogenetic signals will be greater for parasites that rely more on their host throughout their life cycle. Analyses were conducted for ectoparasites from tropical bats and for ectoparasites, helminths, and coccidians from desert rodents. Phylogenetic signals were evaluated for parasite presence and for parasite prevalence. The frequency of phylogenetic signal occurrence was similar for parasite presence and prevalence, with a signal detected in 24–27% of cases at the species level and in 67% and 15% of cases at the genus level for parasites of bats and rodents, respectively. No differences in signal strength or the likelihood of detecting a signal existed between groups of parasites. Phylogenetic signal strength was correlated with host specificity, suggesting that mechanisms increasing host specificity also increase the likelihood of a phylogenetic signal in host use by parasites. Differences in the transmission mode did not affect signal strength or the likelihood of detecting a signal, indicating that variation in host switching opportunities associated with the transmission mode does not affect signal strength.

opencc-zeroDec 2014View details →

Fig. 5 in Systematic revision of a Miocene sperm whale from Patagonia, Argentina, and the phylogenetic signal of tympano-periotic bones in Physeteroidea

Fig. 5. Schematic comparisons of the periotic of MLP 76-IX-5-1, "Preaulophyseter gualichensis" Caviglia and Jorge, 1980 (A) with "Aulophyseter" rionegrensis (B), Acrophyseter deinodon (C, modified from Lambert et al. 2016), Zygophyseter varolai (D, modified from Bianucci and Landini 2006), Aulophyseter morricei (E, modified from Kellogg 1927), Orycterocetus crocodilinus (F, modified from Kellogg 1965), and Physeter macrocephalus (G, modified from Kasuya 1973). In dorsal (A1–G1), ventral (A2–G2), medial (A3–G3), and lateral (A4–C4, E4–G4) views. Black areas indicate anatomical foramina. Not to scale.

Fig. 4 in Systematic revision of a Miocene sperm whale from Patagonia, Argentina, and the phylogenetic signal of tympano-periotic bones in Physeteroidea

Fig. 4. Isolated periotics of a sperm whale Physeteroidea indet. from the Miocene of Patagonia. A. MPEF-PV-605, right periotic. B. MPEF-PV-651, right periotic. C. MPEF-PV-6098, left periotic. D. MLP 80-VIII-30-133a, right periotic. E MLP 80-VIII-30-133b, left periotic. F. MLP 52-X-2-8, right periotic. In dorsal (A1–F1), ventral (A2–F2), medial (A3–F3), and lateral (A4–F4) views. G. MLP 56-IX-2-7, fragmentary periotic in dorsal (G1) and medial (G2) views.

Fig. 2 in Systematic revision of a Miocene sperm whale from Patagonia, Argentina, and the phylogenetic signal of tympano-periotic bones in Physeteroidea

Fig. 2. Teeth of a sperm whale Physeteroidea indet. previously described as "Preaulophyseter gualichensis" Caviglia and Jorge, 1980, MLP 76-IX5-1, from the Miocene of Gran Bajo del Gualicho Formation, Patagonia, Argentina; in labial (A1) and lingual (A2) views, and detailed view of the crown (A3) and enamel (A4). I and II refer to the two fragmentary teeth of the MLP 76-IX-5-1 (the best and worst preserved tooth, respectively).

Fig. 3. Sperm whale Physeteroidea indet. A in Systematic revision of a Miocene sperm whale from Patagonia, Argentina, and the phylogenetic signal of tympano-periotic bones in Physeteroidea

Fig. 3. Sperm whale Physeteroidea indet. A. Left periotic of nomen dubium "Preaulophyseter gualichensis" Caviglia and Jorge, 1980, MLP 76-IX-5-1, from the Miocene of Gran Bajo del Gualicho Formation, Patagonia, Argentina, in dorsal (A1, A2), ventral (A3, A4), medial (A5, A6), and lateral (A7, A8) views. B, C. Two isolated right periotics from the Miocene of Patagonia, MLP 76-IX-2-3 (B) and MLP 76-IX-2-4 (C), in dorsal (B1, C1), ventral (B2, C2), medial (B3, C3), and lateral (B4, C4) views. Photographs (A1, A3, A5, A7, B, C) and explanatory drawings (A2, A4, A6, A8). Abbreviations: abf, anterior bullar facet; aca, aperture for cochlear aqueduct; ai, anterior incisure; ao, accessory ossicle; ava, aperture for the vestibular aqueduct; eh, epitympanic hiatus; fasu, facial sulcus; fo, fenestra ovalis; fosi, foramen singulare; fr, fenestra rotunda; iam, internal acoustic meatus; lt, lateral tuberosity; mf, mallear fossa; pbf, posterior bulla facet; pofc, proximal opening of facial canal (VII); sct, spiral cribiform tract (VIII).

Fig. 1 in Systematic revision of a Miocene sperm whale from Patagonia, Argentina, and the phylogenetic signal of tympano-periotic bones in Physeteroidea

Fig. 1. Geographic location of studied area in Patagonia, southern Argentina (A) and location of the marine Miocene outcrops (B, stars) where the specimens included in this study were collected: Gran Bajo del Gualicho Formation (1) and Gaiman Formation (2).

opencc-zeroMar 2024View details →

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Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions

Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: "Do closely related hosts interact with closely related symbionts?" and "Do host and symbiont phylogenies mirror one another?". These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other. However, in most situations, a positive answer to the first question, hereafter referred to as "cophylogenetic signal", does not imply a close match between the host and symbiont phylogenies. It suggests only that past evolutionary history has contributed to shaping present-day interactions, which can arise, for example, through present-day trait matching, or from a single ancient vicariance event that increases the probability that closely related species overlap geographically. A positive answer to the second, referred to as "phylogenetic congruence", is more restrictive as it suggests a close match between the two phylogenies, which may happen, for example, if symbiont diversification tracks host diversification or if the diversifications of the two clades were subject to the same succession of vicariance events. Here we apply a set of methods (ParaFit, PACo, and eMPRess), which significance is often interpreted as evidence for phylogenetic congruence, to simulations under three biologically realistic scenarios of trait matching, a single ancient vicariance event, and phylogenetic tracking. The latter is the only scenario that generates phylogenetic congruence, whereas the first two generate a cophylogenetic signal in the absence of phylogenetic congruence. We find that tests of global-fit methods (ParaFit and PACo) are significant under the three scenarios, whereas tests of event-based methods (eMPRess) are only significant under the scenario of phylogenetic tracking. Therefore, significant results from global-fit methods should be interpreted in terms of cophylogenetic signal and not phylogenetic congruence; such significant results can arise under scenarios when hosts and symbionts had independent evolutionary histories. Conversely, significant results from event-based methods suggest a strong form of dependency between hosts and symbionts evolutionary histories. Clarifying the patterns detected by different cophylogenetic methods is key to understanding how interspecific interactions shape and are shaped by evolution.

FIGURE 4 in Exploring the phylogenetic signal in the cranial variation of European populations of grayling (Actinopterygii, Salmonidae)

FIGURE 4 PCA of the grayling dorsal cranium. Wireframe diagrams (magnified 3 times) illustrate shape differences along PC1 and PC2 axes.

FIGURE 1 in Exploring the phylogenetic signal in the cranial variation of European populations of grayling (Actinopterygii, Salmonidae)

FIGURE 1 Grayling populations analyzed. Abbreviations and symbols: filled symbols, wild populations; open symbols, hatchery populations; circles, T. thymallus populations from the Caspian phylogenetic clade (2 – Bugurla and 3 – Kana); square, T. aeliani population from the Adriatic phylogenetic clade (4 – Soča); triangles, T. thymallus populations from the Balkan phylogenetic clade (1 – Lim, 5 – Sava Bohinjka and 6 – Una).

FIGURE 3 in Exploring the phylogenetic signal in the cranial variation of European populations of grayling (Actinopterygii, Salmonidae)

FIGURE 3 Landmarks collected on grayling cranium in A) dorsal, B) ventral, and C) occipital views. See table 2 for definitions of landmarks.

FIGURE 2 in Exploring the phylogenetic signal in the cranial variation of European populations of grayling (Actinopterygii, Salmonidae)

FIGURE 2 Phylogeny of studied grayling populations based on Neighbour-Joining method of A) mtDNA CR haplotypes (indicated in parentheses), including Da23 Sava Bohinjka haplotype – phylogeny mtDNA CR Da23, B) mtDNA CR haplotypes (indicated in parentheses), including Da25 Sava Bohinjka haplotype – phylogeny mtDNA CR Da25, and C) DAS estimated from 12 microsatellite DNA loci – phylogeny microsatellites.

FIGURE 6 in Exploring the phylogenetic signal in the cranial variation of European populations of grayling (Actinopterygii, Salmonidae)

FIGURE 6 PCA of the grayling occipital cranium. Wireframe diagrams (magnified 3 times) illustrate shape differences along PC1 and PC2 axes. Downloaded from Brill.com 06/21/2024 06:29:33PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

FIGURE 5 in Exploring the phylogenetic signal in the cranial variation of European populations of grayling (Actinopterygii, Salmonidae)

FIGURE 5 PCA of the grayling ventral cranium. Wireframe diagrams (magnified 3 times) illustrate shape differences along PC1 and PC2 axes. Downloaded from Brill.com 06/21/2024 06:29:33PM via Open Access. This is an open access article distributed under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/

Fig. 4. Composite phylogenetic hypothesis for 33 in Phylogenetic signal and major ecological shifts in the ecomorphological structure of stream fish in two river basins in Brazil

Fig. 4. Composite phylogenetic hypothesis for 33 stream fish species based on six different studies. Solid circles indicate six taxonomic groups that were significant in the canonical phylogenetic ordination (CPO); they are numerically labeled as follows: 1, Siluriformes/Characiformes; 2, Loricariidae; 3, Farlowella/Rineloricaria; 4, Characidae; 5, Hypostominae; 6, Pimelodella/Rhamdia.

Fig. 3 in Phylogenetic signal and major ecological shifts in the ecomorphological structure of stream fish in two river basins in Brazil

Fig. 3. Projection of the first three PCA axes based on 14 ecomorphological attributes for the following fish species from the upper São Francisco River, Brazil: Apaibi, Apareiodon ibitiensis; Astriv, Astyanax rivularis; Cetihe, Cetopsorhamdia iheringi; Chafas, Characidium fasciatum; Crevar, Creagrutus aff. varii; Harnov, Harttia cf. novalimensis; Micsp, Microlepidogaster sp.; Neofra, Neoplecostomus franciscoensis; Piaarg, Piabina argentea; Tribra, Trichomycterus brasiliensis; Trirei, Trichomycterus reinhardti and Trivar, Trichomycterus variegatus. The figures in black indicate the most representative ecomorphotypes.

Fig. 2 in Phylogenetic signal and major ecological shifts in the ecomorphological structure of stream fish in two river basins in Brazil

Fig. 2. Projection of the first two PCA axes based on 14 ecomorphological attributes for the following fish species from the upper Paraguai River, Brazil: Ancsp, Ancistrus sp.; Astasu, Astyanax asuncionensis; Astlin, A. lineatus; Astsp, Astyanax sp.; Chafas, Characidium fasciatum; Chazeb, C. zebra; Cremer, Creagrutus meridionalis; Farpar, Farlowella paraguayensis; Hyplue, Hyphessobrycon luetkenii; Hypbou, Hypostomus boulengeri; Hypcoc, Hypostomus cochliodon; Hypsp, Hypostomus sp.; Jupaca, Jupiaba acanthogaster; Moebon, Moenkhausia bonita; Moesan, M. sanctaefilomenae; Odopeq, Odontostilbe pequira; Parnas, Parodon nasus; Piator, Piabarchus torrenticola; Pimgra, Pimelodella gracilis; Rhaque, Rhamdia quelen; Rinlan, Rineloricaria lanceolata; and Sercal, Serrapinnus calliurus. The figures in black indicate the most representative ecomorphotypes.

Fig. 1 in Phylogenetic signal and major ecological shifts in the ecomorphological structure of stream fish in two river basins in Brazil

Fig. 1. Study area with the sampling sites at the upper Paraguai and upper São Francisco River basins. BOD: Serra da Bodoquena National Park; CAN: Serra da Canastra National Park; MG: Minas Gerais State; MS: Mato Grosso do Sul State; PG 1-6: sampling locations in the upper Paraguai River basin; SF 1-6: sampling locations in the upper São Francisco River basin.