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opencc-by-4.0Nov 2020View details →

How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree

This repository contains all the scripts and most of the intermediary files necessary to replicate the analyses of the preprint "How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree" submitted to Molecular Ecology and available at: <a href="https://www.biorxiv.org/content/10.1101/2020.11.25.394544v1">https://www.biorxiv.org/content/10.1101/2020.11.25.394544v5</a> Within each of the different zipped folders a readme.txt file briefly explains how the analyses are organized. This version of the dataset has been revised in agreement with the manuscript revision to answer the comments of the first two rounds of reviews in Peer Community In Evolutionary Biolology (PCI-EvolBiol; <a href="https://evolbiol.peercommunityin.org/">https://evolbiol.peercommunityin.org/</a>) by M. Navascues (Recommender), Katharina Budde (reviewer) and Yurena Arjona (reviewer), as well as two rounds of reviews in Molecular Ecology. All PCIevolbiol comments, response and changes are documented on the PCIevolbiol website.

Fig. 12. - Begueo vulgoris G.E in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 12. - Begueo vulgoris G.E. Schatz, Gereau & Lowry. A. Flowering branch; B. Portion of inflorescence axis; C. Detail of flower at anthesis; D. Infructescence axis with fruits. [A-C: Molcomber et ol. 2058, MO; D: Rokotozofy et ol. 174, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 11. – Begueo turkii G.E in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 11. – Begueo turkii G.E. Schatz, Gereau & Lowry. A. Flowering branch; B. Portion of inflorescence axis; C. Detail of flower at anthesis; D. Infructescence axis with fruits; E. Seed. [A-C: Turk & Solo 192, MO; D: Rokotomolozo 492, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 10. - Begueo tsorotononensis G.E in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 10. - Begueo tsorotononensis G.E. Schatz, Gereau & Lowry. A. Flowering branch; B. Portion of inflorescence axis; C. Detail of flower at anthesis. [Antilohimeno 631, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 9. – Begueo golokensis G.E. Schatz & Lowry. A in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 9. – Begueo golokensis G.E. Schatz & Lowry. A. Flowering branch; B. Leaflet (lower surface); C. Leaflet (upper surface); D. Portion of inflorescence axis with two flowers. [Monjoto et ol. 454, P] [Drawing: R.L. Andriamiarisoa]

Fig. 8. – Begueo boreolis G.E. Schatz & Lowry. A in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 8. – Begueo boreolis G.E. Schatz & Lowry. A. Flowering branch; B. Leaflet (lower surface); C. Portion of inflorescence axis; D. Two flowers (one with filaments only partially expanded); E. Detail of flower at anthesis. [Rondrionoivo et ol. 1163, P]. [Drawing: R.L. Andriamiarisoa]

Fig. 7. – Begueo birkinshowii G.E in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 7. – Begueo birkinshowii G.E. Schatz, Gereau & Lowry. A. Flowering branch; B. Detail of flower at anthesis; C. Portion of inflorescence axis. [Birkinshow 159, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 6. – Begueo betomponensis G.E in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 6. – Begueo betomponensis G.E. Schatz, Gereau & Lowry. A. Flowering branch; B. Portion of inflorescence axis; C. Detail of flower at anthesis. [Andrionorisoto et ol. 246, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 4 in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 4. – Geographic distribution of Begueo opetolo Capuron (circles), B. birkinshowii G.E. Schatz, Gereau & Lowry (stars), B. boreolis G.E. Schatz & Lowry (diamond), B. tsorotononensis G.E. Schatz, Gereau & Lowry (squares) and B. turkii G.E. Schatz, Gereau & Lowry (triangles), mapped on the bioclimatic zones of Madagascar (after CORNET, 1974; see SCHATZ, 2000).

Fig. 5. – Begueo oustrolis G.E in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 5. – Begueo oustrolis G.E. Schatz, Gereau & Lowry. A. Fruiting branch; B. Leaflet (lower surface); C. Leaflet (upper surface); D. Fruit (with close-up of surface); E. Section of fruit. [Rondriomompionono 633, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 1. – Begueo onkeronensis G.E. Schatz & Lowry. A in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 1. – Begueo onkeronensis G.E. Schatz & Lowry. A. Flowering branch; B. Detail of flower at anthesis; C. Portion of inflorescence axis; D. Leaflet (lower surface); E. Leaflet (upper surface). [Antilohimeno 7978, MO] [Drawing: R.L. Andriamiarisoa]

Fig. 3 in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 3. – Geographic distribution of Begueo onkeronensis G.E. Schatz & Lowry (square), B. oustrolis G.E. Schatz, Gereau & Lowry (diamond), B. betomponensis G.E. Schatz, Gereau & Lowry (triangle), B. golokensis G.E. Schatz & Lowry (star) and B. vulgoris G.E. Schatz, Gereau & Lowry (circles), mapped on the bioclimatic zones of Madagascar (after CORNET, 1974; see SCHATZ, 2000).

Fig. 2 in A revision of the endemic Malagasy genus Beguea (Sapindaceae)

Fig. 2. – Photographs of Begueo Capuron. A. Begueo onkeronensis G.E. Schatz & Lowry; B. Begueo opetolo Capuron; C. Begueo turkii G.E. Schatz, Gereau & Lowry; D. Begueo vulgoris G.E. Schatz, Gereau & Lowry. [A: Antilohimeno 7978; B: Rovelonorivo 3854; C: Rokotovoo 3648; D: Antilohimeno 5459] [Photos: A, C: P. Antilahimena; B: D. Ravelonarivo; C: C. Rakotovao]

opencc-zeroApr 2024View details →

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Museum genomics reveals the hybrid origin of an extinct crater lake endemic

Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.

FIGURE 1 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan

FIGURE 1. Maps of Kyrgyzstan showing the location of Ortok and important topographical structures. A, Google Earth imagery (accessed May 2018) of the Kochkor and Issyk Kul Basins showing major basins, main bodies of water, Tien Shan mountains, and major fault lines for Kyrgyzstan. The Tien Shan mountains run roughly east to west, leaving high altitude basins infilled with Cenozoic sediments between each sub range. The Kochkor Basin is roughly 80 km long and 24 km wide. Map data: Google, Mapabc.com. Scale equals 96 km; B, additional zoomed in map of Kochkor Basin with fossil localities. Furthest left star is the Ortok site, other fossil collections are from both Tarasov (1970) and McLaughlin (2018). Map data: Google, Digital Globe. Scale equals 16.2 km; C, zoomed in Google Earth map of Kochkor Basin showing main body of water and topographic features. Likely, the Kochkor Basin was connected to the Issyk Kul Basin (the large lake in the figure) until geologically very recently, as shown by the low hills dividing the two basins. Map data: Google, Landsat Copernicus. Scale equals 65 km; D, Google Earth imagery of the Ortok. Base of measured stratigraphic and paleomagnetostratigraphic section (see McLaughlin, 2018) marked with a blue star. Fossiliferous outcrop extends to east and north of the star in the pale tan exposure. To the east, a gorge cut into reddish Paleozoic granite with the thin layer of Chu unconformably resting on it. Strata at Ortok are dipping very gently to the north and are the least deformed structurally of any site included in this study. Additionally, the fossils are the least diagenically altered, indicating little to no diagenic alteration to the site as well. Map data: Google, Digital Globe.Map Scale equals 300 m.

FIGURE 5. Specimen UOMNH F-70508 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan

FIGURE 5. Specimen UOMNH F-70508, Adcrocuta eximia, in occlusal view with insets of morphological features discussed in text. A, occlusal schematic diagram of preserved dentition and p1 alveolus (arrow); B, occlusal view of m1 (anterior to the left) illustrating early stage wear on paraconid and protoconid, respectively; C, occlusal of preserved specimen; D, buccal view of p3 showing examples of transitional acute-angle Hunter-Schreger Bands. These are associated with robust hyaenines (Tseng, 2011); E, detail oblique lingual view of talonid of carnassial (m1) with reduced hypoconid and entoconid. Abbreviations: Encd, entoconid; Hypcd, hypoconid; Ptd, protoconid. Scale bar A and C, equals 5 cm, B, equals 5 mm, D, equals 20 mm, and E, equals 10 mm.

FIGURE 2 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan

FIGURE 2. Stratigraphy, sediment and partially reconstructed fossil from Ortok site. A, Schematic and generalized stratigraphic column for the Cenozoic formations outcropping in the Kochkor Basin. Relative average grainsize is indicated by the X axis, while stratigraphic position is related on the Y axis; B, specimen UOMNH F-70508 in situ prior to removal by W.N.F. McLaughlin to demonstrate fossil completeness and surrounding matrix. Scale bar equals 10 cm; C, cleaned and reconstructed UOMNH F-70508. Note: some diagnostic features were damaged and lost during preparation; see Figure 3 for complete specimen. Scale bar equals 5 cm.

FIGURE 3. Specimen UOMNH F-70508 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan

FIGURE 3. Specimen UOMNH F-70508, Adcrocuta eximia, right partial mandible, pre-breakage and reconstruction. A, annotated line drawing of buccal view, demonstrating two mental foramina and partial preservation of masseteric fossa (light grey). Note alveolus of p1 anterior to p2; B, UOMNH F-70508 after excavation and preliminary reconstruction demonstrating diagnostic features. Abbreviations: aac, anterior accessory cusp; ap, angular process; cp, coronoid process; mc, mandibular condyle; mf, masseteric fossa; mnf, mental foramina; pac, posterior accessory cusp; pad, paraconid; ptd, protoconid; tld, talonid. Scale bar equals 5 cm.

FIGURE 7 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan

FIGURE 7. Time-scaled phylogeny of the Paramachaerodus genus and UOMNH F-70509's placement within it. The depicted tree is a strict consensus of two most-parsimonious trees of score 32. Note the location of UOMNH F-70509 as unresolved relative to "Promegantereon" ogygia at the base of the genus even though it occurs much later in the rock record. Time-scaling was performed in R, version 3.6.1 (R Core Team, 2019) with the Strap package (Bell and Lloyd, 2014) using the "basic" method. Taxa ages derive from Li and Spassov (2017). The outgroup taxon Proailurus lemanensis has an Oligocene occurrence, not shown for clarity, but its basal position in our analysed taxa is depicted with dotted lines.

FIGURE 4. Isolated left P4 in Endemism and migration in the Kochkor Basin? Identification and description of Adcrocuta eximia (Mammalia: Carnivora: Hyaenidae) and c.f. Paramachaerodus (Mammalia: Carnivora: Felidae) fossils at the Miocene locality of Ortok, Kyrgyzstan

FIGURE 4. Isolated left P4 of UOMNH F-70508, Adcrocuta eximia. A, schematic of preserved features in occlusal view; B, occlusal view of specimen displaying minimal wear on metastylar blade; C, lingual view of specimen. Note reduced protocone that does not extend anterior to the anterior face of the parastyle. Scale bar equals 10 mm.