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This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/7766530. Review of the preprint- Effects of phylogenetic variation on prioritization of species for conservation DOI: https://doi.org/10.1101/2023.01.21.525012 Discussion led by: Gohil Prapti (10.03.2023) Notes taken by: Sakshi Ravindra Tripathi Review written by: Journal Club (Prapti Gohil, Sakshi Ravindra Tripathi, Daniel Linke, Mar Repulles, Phil Honle, Petr Klimes, Pavel Matos, Irena Kleckova, Pedro Ribeiro, Karolina Hruba, Alena Suchackova, Kristian Grell) Overview The authors collated nine datasets of multilocus phylogenies from the literature, with a broad taxonomic scope extending from fungi to primates. Their aim was to calculate the Fair Proportion (FP) index as a measure of evolutionary distinctiveness of a species, and to compare how much the FP index rank changes depending on the used molecular dataset (single genes vs. species trees). They have found that for some taxa, there is relatively stronger correlation among the calculation methods (e.g., fungi, mammals), while in other groups the correlation is weaker and results are more variable with regard to the FP index (dolphins, primates). Overall, the paper's message is apparently that the FP index based on single gene trees performs poorer than based on species trees. Although this work is of interest in the field of evolutionary and conservation biology, we have some suggestions for improvement. These are outlined below. Positive feedback We believe that the manuscript is good at providing background for conservation biologists on the subject of phylogenetic diversity indices (specifically, the FP index). The simplicity of the analyses is beneficial for those not familiar in phylogenetics to understand the methods of measuring and ranking of phylogenetic diversity. The authors did a good job in assembling a very broad and interesting dataset, spanning multiple taxa. In addition, they provided a link to the Data and Scripts available in GitHub, which increases the reproducibility of their results. Concerns We provide below both major and minor concerns with the aim of improving the message of the article. We follow the structure of the paper: Title: The title sounds somehow misleading because the article deals with methodological effects of single genes vs species trees, but does not really focus on how to prioritize species in conservation. If the authors prefer to expand the analyses to include for example, correlations among indices, conservation statuses, then the title would be fine. Otherwise, perhaps the title could be edited to something in the lines of: "Effects of gene-tree species-tree discordance on the estimate of unique evolutionary lineages obtained by conservation indexes". Abstract: Overall, the text is fine, but we provide minor feedback to improve clarity of certain passages. For example, we believe that the first section of the abstract, where authors explain the "background", is too long and perhaps it would be better to remove the sentence that goes from "Several" to "input" to make it concise. The FP index apportions the total diversity of a phylogenetic tree among all leaves in such a way that each species receives a "fair proportion" of its ancestry. - this sentence is too methodological and specific for the paragraph, and it is fairly explained in the previous sentence. It would be useful to add more information about methods and results instead of a rather long introductory section with background information. Also, we would suggest rephrasing the last sentence, since starting with "our aim" breaks the flow. Maybe "we conclude" or something similar would increase readability; from results (previous sentence) to conclusion. Introduction: The introduction seems too specific/targeted for a very specific audience. We believe it would gain clarity by broadening the explanation and definition of some terms such as: gene trees and species trees, the FP index based on the target audience (probably people working in conservation). Also, if FP is a "popular" measure, it would be useful to state a few of them with their respective citations to provide a broader background. Perhaps giving it a whole paragraph starting with why you need this index in conservation, then its definition and finally its relation to phylogenetic discordance. The fifth paragraph, starting with "Phylogenetic", might be better positioned at the beginning of the introduction since it contains the gap of the knowledge that the authors are trying to tackle. Methods & Results: In the species tree reconstruction, the molecular clock was enforced (time calibrated) but it is not clear if the authors used calibration points or particular substitution rates. Can the authors test whether those taxa having long branches and stable positions in the phylogeny have more consistent estimates of FP indices across gene trees? If that's the case, then the estimated FP indices should be highly correlated among gene trees and species trees. Are there certain genes for each group which give an overall good resolution for the phylogeny while others might be omitted? What would give conservationists / policy makers the best result for the least effort / cost? Overall, we think the figures are adequate but it might be valuable to provide in the Appendix similar figures for each study group as currently provided in Fig. 2 (dolphins only). It can be useful to add the status of the endangered taxa, where available, to the figure. Importantly, there is no information whether those taxa that converge well in FP and rank high in Fig. 2 contain most of the endangered species, or whether those are the lineages that are most unique in the phylogeny. We are not sure if this is possible to assess, but such a direction would strengthen the conservation focus of the study, and make it more valuable for practical use, beyond a methodological note paper. In addition, we have the following minor notes: Can the authors compare the efficiency and usefulness of the FP index with other indices used in conservation biology? Selection of datasets: Four out of nine datasets are from mammals and there is no representative from invertebrates. We are also confused why the yeast dataset is included, since the paper is focusing on conservation. It'd be informative if the authors could explain their reasons behind selection of these datasets. We believe the figure 1 contains a mistake in the branch leading to taxon x2. The length should be "1". Similarly, the branch leading to taxon x3 should have a length of "2" Discussion: Overall, the authors wrote a good and concise discussion. However, we see a potential for improvement, and we provide some suggestions below. We think that a concrete recommendation should be made by the authors about the use of the FP index - should we avoid entirely using gene trees? - Especially if the target audience is policy makers, whose background might not necessarily be in phylogenetics or evolutionary biology. In general, we recommend supporting crucial information with references. For instance, the first line of the first paragraph "The FP index is a popular tool for prioritizing species for conservation…" is a very broad statement, indicating that the FP index has effectively been employed in species protection, but no studies are provided. At the end of the second paragraph, are there examples of studies or conservation projects specifically using gene trees to delimit species that are in urgent need of conservation? If yes, please add them. Are there cases in which a gene tree would be preferred over a species tree? This point is very important for a critical assessment of the FP index. We suggest providing, if possible, a concrete conservation-relevant example in the conclusion, which will highlight the relevance of the study. Competing interests The author declares that they have no competing interests.

Overbeckia jambiensis Klimes, sp. nov. (Fig. 4) Etymology Named after the Jambi Province on Sumatra Island (Indonesia) where the type specimen was collected by J. Drescher in the lowland rainforest of Bukit Duabelas National Park (EFForTS project core plot BF2, see Drescher et al. 2016). Material examined Holotype: Worker (MZB): BF2.2/ 7.x.2013 / wet season/canopy fogging/lowland forest / Bukit Duabelas National Park / 01°58′54.2″S, 102°45′02.3″E /leg. J. Drescher (det. R. Nazarreta, P. Klimes) Paratype: Worker (ZMHB):same data as above but marked as paratype. Diagnosis Overbeckia jambiensis workers are the hairiest of the Overbeckia species, with numerous conspicuous erect hairs present on dorsum of petiole, thorax, and also dorsally and ventrally on the head, abdomen and scape; head integument without punctation and with fine lineation; cuticle covered with sparse, short, appressed hairs that are less numerous but longer than in other species and present all over the head except in the area between the eyes and around carinae; integument darker and glossy; frontal carinae less approaching one another anteriorly compared to those of O. subclavata but curvature evenly convex when compared to those of the other species in frontal view (Fig. 4 d). Lineation present on whole lateral sides of mesosoma, including upper part of frontal coxae and the areas above metathoracic spiracle. Description of worker Morphometrics. Holotype ‘BF2.2.’ (one paratype): HL 1.37 (1.29), HW 1.29 (1.30), IOD 0.94 (0.96), CL 0.24 (0.22), CW 0.53 (0.54), ML 0.55 (0.55), EL 0.40 (0.40), EW 0.30 (0.31), FCDp 0.42 (0.43), FCDa 0.31 (0.31), SL 1.30 (1.27), SWmax 0.16 (0.16), SWmin 0.08 (0.08), WL 1.94 (1.94), PW 0.96 (0.97), HFL 1.30 (N.A.), HFT 0.29 (N.A.), HTL 1.24 (N.A.), PetW 0.45 (0.44), PetL 0.24 (0.22), FCDI 137 (141), CI 94 (101), SI 101 (98), MI 40 (42). Head. General morphology as for the genus (see above). Frontal carinae less approaching one another anteriorly (FCDI = 137) and with convex curvature laterally (Fig. 4 d). Mesosoma and metasoma. As for the genus (see above). Pilosity. Tiny appressed hairs (approximately twice the length of ommatidium) present only sparsely over the head and mesosoma; numerous relatively long erect hairs (length ≥ SW) present on the clypeus and head, and all over abdomen; these longer hairs also present on genae and occipital corners of the head and on frons, surpassing the head margin in frontal view (Fig. 4 b); scape with relatively long hairs of both appressed and erect type, the erect hairs not limited to the apical tip but present along most of the scape (Fig. 4 b). Approximately eight erect hairs growing dorsally from apical margin of petiole. Sculpture. Fine shallow lines, joining each other to a cell formation over the glossy cuticle of the head (Fig. 4 b, d). These lines also present dorsolaterally on mesosoma; the lineation very soft and rather curved, except the lateral sites of mesosoma below metathoracic spiracle and towards coxae and on propodeum, where lines are somewhat deeper and straight (Fig. 4 a); soft lineation also present on frontal coxae and petiole. Colouration. Head, thorax and scape of rather glossy metallic appearance and black, except at scape apex where lighter brown; petiole, abdomen, apical parts of femurs and tibiae brown; tarsi, apex of funiculus and palps brown; femurs pale yellow near the joints; trochanters and mid and hind coxae pale yellow (Fig. 4 a, c). Description of male and queen None (no material) Remarks Body size is somewhat larger on average than in the other two Overbeckia species but due to the availability of only two specimens, assessing whether body size is significantly larger is difficult (the size is comparable to the largest workers measured from series of O. papuana)., Published as part of Klimeš, Petr, Drescher, Jochen, Buchori, Damayanti, Hidayat, Purnama, Nazarreta, Rizky, Potocký, Pavel, Rimandai, Maling, Scheu, Stefan & Matos-Maraví, Pável, 2022, Uncovering cryptic diversity in the enigmatic ant genus Overbeckia and insights into the phylogeny of Camponotini (Hymenoptera: Formicidae: Formicinae), pp. 277-288 in Invertebrate Systematics 36 (6) on pages 569-570, DOI: 10.1071/is21067, http://zenodo.org/record/6987297, {"references":["Drescher J, Rembold K, Allen K, Beckschafer P, Buchori D, Clough Y, Faust H, Fauzi AM, Gunawan D, Hertel D, Irawan B, Jaya INS, Klarner B, Kleinn C, Knohl A, Kotowska MM, Krashevska V, Krishna V, Leuschner C, Lorenz W, Meijide A, Melati D, Nomura M, Perez- Cruzado C, Qaim M, Siregar IZ, Steinebach S, Tjoa A, Tscharntke T, Wick B, Wiegand K, Kreft H, Scheu S (2016) Ecological and socioeconomic functions across tropical land use systems after rainforest conversion. Philosophical Transactions of the Royal Society of London - B. Biological Sciences 371 (1694), 20150275. doi: 10.1098 / rstb. 2015.0275"]}

Overbeckia papuana Klimes, sp. nov. (Fig. 5, 6) Etymology Dedicated to all Papua New Guineans, the nation of the country from which the type and nest series were collected (Papua New Guinea). Material examined Holotype. Worker (ZMHB): Morphospecies ‘ CAMP021 ’/Acc.N. ‘HP0177’/ Tree number code ‘WS4D0868’/Secondary forest/ Wanang village / Madang province / Papua New Guinea / 8.iii.2007 / 05°14′S, 145°11′E /leg. M. Rimandai. Paratypes. Five workers (1w ZMHB, 1w IECA, 2w NAIC, 1w MZB), one male (ZMHB), one queen without wings (ZMHB): From the same nest series as holotype (the same data). Additional material examined. Papua New Guinea: Other 30 workers and 2 males, including brood, kept in one vial with ethanol in IECA, all from the same nest as the type specimens (same data). Australia (photos): 1 worker (SAMA): ‘ Camponotus ’/Cairns NQ/on tree/ Parkland/ 2.viii.1975 /leg. B. B. Lowery (frontal and lateral photo on p. 115 in McArthur (2012) and A. McArthur, pers. comm. for coll. information; previously misidentified by the original author for Camponotus janeti). 3 workers (WAM): CASENT0872736, CASENT0872753, CASENT0872754 (AntWeb codes; ‘ Overbeckia wam01’): Queensland / Mossman/ 18.ix.2002 /leg, R. Jordan /nest in dead twig in living tree behind sugar mill (thicket near Mossman R.)/det. B. E. Heterick, ii.2018. 1 worker (CASC): CASENT0887749 (AntWeb code; ‘ Overbeckia au01’): Queensland /Mt Peters/ 1. v. 2014 /leg, M. Collis/ det. A. Andersen 30.xi.2020. Australia (physical specimen): 1 worker (ZMHB): n#15720/ AUST Qld/Captain Billy Landing/rainforest, ex. dead hanging twig/ 11°38′S, 142°51′E /leg. P. Ward (the same collection series as CASENT0882197 at AntWeb; ‘ Overbeckia au01’). Diagnosis General appearance of worker and queen as in O. subclavata, but hairier on the head, with erect hairs on dorsum of petiole, thorax and abdomen; a few hairs also present on distal part of scape. Head integument less punctate than in O. subclavata, with many short-erect hairs extending past head margins in frontal view; tiny appressed hairs in high densities all over the head including genae; frontal carinae significantly approaching one another anteriorly (FCDI> 190) (Fig. 5 d). Description of worker Morphometrics. Holotype, ‘HP0177’ nest series (five paratypes; total N = 6, min.–max): HL 1.08 (1.04–1.41), HW 1.10 (1.05–1.43), IOD 0.82 (0.79–1.10), CL 0.17 (0.14–0.23), CW 0.41 (0.39–0.55), ML 0.44 (0.36–0.57), EL 0.28 (0.26–0.34), EW 0.21 (0.19–0.27), FCDp 0.37 (0.35–0.52), FCDa 0.18 (0.15–0.27), SL 1.05 (1.02–1.24), SWmax 0.14 (0.12–0.18), SWmin 0.06 (0.06–0.09), WL 1.58 (1.52–2.02), PW 0.77 (0.69–1.03), HFL 1.09 (0.92–1.24), HFT 0.24 (0.24–0.30), HTL 0.94 (0.82–1.05), PetW 0.39 (0.37–0.47), PetL 0.17 (0.17–0.24), FCDI 208 (193–236), CI 102 (99–105), SI 95 (87–101), MI 40 (30–43). Head. General morphology as for the genus (see above). Frontal carinae relatively more approaching one another anteriorly above the clypeal margin compared to those of the other species (FCDI = 208), with rather straight carinae curvature all along (only slightly convex laterally adjacent to the antennal sockets at frontal view; Fig. 5 d). Mesosoma and metasoma. As for the genus (see above). Pilosity. Tiny appressed hairs (approximately twice the length of ommatidium or smaller) present in high densities over the head, mesosoma and abdomen; relatively long erect hairs (length ≥ SWmin) present on clypeus, head integument and all over abdomen; these longer hairs are also present on genae and occipital corners of the head and on frons (extending past head margins from the frontal view; Fig. 5 b); scape with relatively short, appressed hairs (as in O. subclavata), with a few erect hairs not limited to the apex but present ventrally along the anterior half of the scape. These hairs shorter and less numerous than in O. jambiensis (Fig. 5 b). Approximately six erect hairs growing dorsally from apical margin of petiole. Sculpture. Less dotted, rather covered by short lines joining each other to a cell formation with fine punctation over the glossy cuticle of the head (Fig. 5 d) and mesosoma dorsolaterally, with most of these cells like pits at smaller (b, c). Lateral sites of thorax with soft lineation below mesothoracic spiracle towards mid and hind coxa. The lineation is also present on frontal coxa and petiole, but smoother. Colouration. Head, mesosoma and frontal coxa black; scape dark brown except at apex, where lighter brown; funiculus of antennae brown except the lighter apex; petiole dark brown; abdomen and hind tibiae brown, remaining appendages rather light brown, with mid and hind coxae, trochanters and palps pale yellow (Fig. 5 a, c). Description of queen Morphometrics. Paratype ‘HP0177’ nest series: HL 1.56, HW 1.57, IOD 1.22, CL 0.32, CW 0.59, ML 0.63, EL 0.49, EW 0.37, FCDp 0.50, FCDa 0.24, SL 1.23, SWmax 0.16, SWmin 0.09, WL 2.51, PW 1.14, HFL 1.22, HFT 0.31, HTL 1.27, PetW 0.55, PetL 0.35, FCDI 208, CI 101, SI 78, MI 40. Head, mesosoma and metasoma. Similar to O. subclavata, except frontal carinae significantly approaching one another anteriorly (FCDI = 208; Fig. 6 e). Pilosity. Tiny appressed hairs on scape surface, with three to four longer erect hairs on the lateral sites of the first half of the scape (hair length ≥1 ocellus); presence of many relatively long, erect hairs on the head (length ≥1 ocellus) on genae, above the eyes and over the occipital corners of the head (Fig. 6 e), and on thorax dorsum, apical tip of petiole, and over both ventral and dorsal sites of all five abdominal tergites. Sculpture. Fine punctation over the head, and on mesosoma dorsum and propodeum; and soft lineation on lateral sites of mesosoma (Fig. 6 a). Colouration. Black head, thorax, petiole and frontal coxae; dark brown abdomen and appendages except middle and hind coxae, trochanters, palps and apical tips of antennae and tarsi that are lighter brown (Fig. 6 a). Description of male Morphometrics. Paratype ‘HP0177’ nest series: HL 0.84, HW 1.00, IOD 0.66, CL 0.12, CW 0.35, ML 0.31, EL 0.34, EW 0.29, FCDp 0.27, FCDa 0.10, SL 0.67, SWmax 0.10, SWmin 0.06, WL 1.71, PW 0.96, HFL 1.31, HFT 0.18, HTL 0.99, PetW 0.33, PetL 0.21, FCDI 255, CI 119, SI 67, MI 37. Structures and diagnosis (Fig. 6 b, d, f). No apparent large distinction when compared to the male of O. subclavata, except for the following minor differences: The specimen is ~10% larger than the measured male of O. subclavata, but morphological measures otherwise considerably overlapping between the two species’ males. Frontal carinae relatively more approaching one another anteriorly than in O. subclavata, but this difference not as distinct as between the two species’ workers (FCDI = 255 v. 229 in O. subclavata male). The hairs on clypeus more numerous than on clypeus of O. subclavata; presence of many more small hairs on frons and above ocelli (length near 1/2 of ocellus) over the occipital region (Fig. 6 f). These small, dense hairs are also present dorsolaterally on thorax (on mesoscutum and mesoscutellar disc; Fig. 6 b, d). Colouration as in O. subclavata male. Remarks The arboreal nest of O. papuana sp. nov. in Papua New Guinea was collected at 16.4 m in a dead vine growing along the tree trunk of Trichospermum pleiostigma (F. Muell.) Kosterm. (diameter at breast height = 16.3 cm). The nest consisted of less than one hundred workers, with one wingless gyne, three males, and multiple larvae and pupae enclosed in cocoons. The material from Australia was examined and measured mainly from photographs from the following sources: (i) the book by McArthur (2012), where a worker of Overbeckia was incorrectly assigned to Camponotus janeti (minor worker fits ‘ O. papuana’, whereas major worker presumably fits C. janeti; there is uncertainty as to whether the two individuals are from different localities and pins or are on a single pin at SAMA); (ii) the photos on AntWeb of the three specimens in Heterick (2019) (see above). The Australian specimens appear to be larger in body size based on the measures from the photos (4 workers measured from photos, WL> 1.95 mm) than the Papua New Guinea (PNG) nest series (6w measured, WL O. papuana types in the body size (WL = 1.64; Supplementary Table S1) and morphology.

Overbeckia subclavata Viehmeyer (Fig. 1, 2) Etymology Viehmeyer (1916) does not explain the reasoning for the species name, but this likely refers to the club-shaped anterior part of antennae, mentioned in the original description (‘Geissel gegen Ende verdickt’: funinculus enlarged towards the tip) (Fig. 2 h). Material examined Syntypes. All examined from photos (AntWeb codes): CASENT0101191, CASENT0101192, workers (NHMB; F. Santschi collection); focol0130, worker (DEIC, marked as ‘ Syntypus’); focol2566, alate queen (marked as ‘ Typus’), focol2567 and focol2568, workers, focol2564 and focol2565, males (ZMHB, all marked as ‘ Typus’); CASENT0178502, worker (MCZC, marked as ‘ Paratype 30741’); CASENT0905180, male (MSGN)/coll. H. Overbeck, Indonesia: 5 workers and 1 queen; all leg. J. Drescher, canopy fogging (det. R. Nazarreta & P. Klimes): Worker (ZMHB): HJ3.1/ 5.xi. 2013 /Harapan Rainforest/jungle rubber/dry season/ 01°50′57.7″S, 103°17′59.7″E. Worker (MZB): BJ6.2/ 1.xii.2013 /Bukit Duabelas National Park/jungle rubber/rainy season/ 02°01′48.4″S, 102°46′14.9″E. Worker (IECA): BF3.1/ 5.x.2013 /Bukit Duabelas National Park/jungle rubber/rainy season/ 01°56′34.1″S, 102°34′51.5″E. Worker (MZB): BF1.1/ 8.x.2013 /Bukit Duabelas National Park/forest/dry season/ 01°59′41.4″S, 102°45′08.5″E. Worker (CASC): CASENT0872838 (AntWeb)/HymFrm285 1.xii.2013 /Bukit Duabelas National Park/jungle rubber/rainy season/ 02°00′56.2″S, 102°45′11.5″E. Queen without wings (IECA): HF4.1/ 12.ix.2013 /Harapan Rainforest/forest/dry season/ 02°11′15.4″S, 103°20′34.7″E. Philippines (photos): Acc. No. 3576 (MCZC)/Lot Bu.of Sci., P.I./coll. M. Ramos (further details in General and Alpert 2012). Diagnosis Compared to the other two Overbeckia species described here, Overbeckia papuana sp. nov. and O. jambiensis sp. nov., workers and queens in O. subclavata are less hairy, with a lack of long erect hairs on dorsum of petiole, on thorax and on scape except the apical margin; head integument with fine dense punctation; no erect hairs extending past head margins in frontal view; frontal carinae approaching one another less anteriorly compared to those in O. papuana sp. nov. (FCDI b, 2 h). Longer erect hairs present only on clypeus and ventral abdomen. Fine straight lineation on lateral sides of thorax limited to the basal region below metanotal groove (Fig. 1 a). Description of worker Morphometrics. Non type ‘HJ.3.1’ (six syntypes and further five non-types workers, N.A. = measure not available hereafter; total measured N = 11, min.– max): HL 1.08 (0.87–1.25), HW 1.14 (0.88–1.24), IOD 0.87 (0.67–0.92), CL 0.16 (0.15–0.19), CW 0.49 (0.34–0.54), ML 0.45 (0.33–0.47), EL 0.31 (0.25–0.36), EW 0.22 (0.16–0.26), FCDp 0.38 (0.29–0.44), FCDa 0.28 (0.21–0.29), SL 0.99 (0.70–1.08), SWmax 0.13 (0.11–0.17), SWmin 0.06 (0.05–0.09), WL 1.62 (1.24–1.76), PW 0.79 (0.61–0.88), HFL 1.03 (0.92–1.08), HFT 0.24 (0.20–0.25), HTL N.A. (0.82–1.07), PetW 0.40 (0.32–0.47), PetL 0.22 (0.15–0.24), FCDI 134 (126–165), CI 105 (98–105), SI 87 (80–93), MI 41 (32–42). Head. General morphology as for the genus (see above). Frontal carinae approaching one another less anteriorly (FCDI = 134) and with relatively straight curvature, slightly concave near antennal sockets (Fig. 1 d). Mesosoma and metasoma. As for the genus (see above). Pilosity. Numerous tiny appressed hairs (approximately twice the length of 1 ommatidium or shorter) over scape, head and most of the thorax and abdomen; relatively long erect hairs (length ≥ SW) present only on clypeus, head and ventral abdomen and one pair of hairs present on frons in the middle above the eyes (Fig. 1 a); these longer hairs missing on genae and the occipital corners of the head including region above the eyes (in frontal view none of the longer hairs surpass the head margin); scape also without erect hairs except a tuft of ~8 setae growing from the apical tip (Fig. 1 b). No long erect hairs at the apex of petiole. Sculpture. Fine punctation on dorsal surface of the head, in particular in the area between frontal carinae and above the clypeus (Fig. 1 b, d) and on mesosoma dorsum and lateral sites of thorax above metathoracic spiracle and dorsolaterally on propodeum (Fig. 1 a); this punctuation changes to the sculpturing rather forming a cell structure than individual pits posteriorly towards the occipital region; soft lineation on lateral sites of mesosoma, below the metathoracic spiracle and on propodeum between propodeal spiracle and hind coxae; same cuticular lineation also present on frontal coxae, petiole and anteriorly on the head near clypeus, but here much softer than on thorax (Fig. 1 b, c). Colouration. Black head, thorax and petiole; dark brown scape except at the apex where light brown; brown abdomen and femurs; tarsi, funiculus and palps light brown to yellow; femurs brown in the middle but lighter near the joints (Fig. 1 a, c). Description of queen Morphometrics. Syntype ‘focol2566’: HL 1.43, HW 1.45, IOD 1.08, CL 0.30, CW 0.60, ML 0.67, EL 0.53, EW 0.35, FCDp 0.47, FCDa 0.33, SL 1.17, SWmax 0.16, SWmin 0.08, WL 2.56, PW 1.14, HFL 1.08, HFT 0.36, HTL 1.34, PetW 0.58, PetL 0.28, FCDI 142, CI 101, SI 81, MI 47. Head (Fig. 2 e). Eyes almost twice as large as in worker. Frontal carinae approaching each other anteriorly above the posterior margin of clypeus relatively less when compared to queen of O. papuana (FCDI Mesosoma (Fig. 2 a, c). In lateral view, thorax dorsum flat at mesothorax, otherwise evenly rounded with convex prothoracic and propodeal angle. Overall morphology of thoracic segments and wings as in Camponotus queens, except apical part of the forewing being relatively broader with evenly convex margins laterally towards the tip. Metasoma. Petiole similar to worker but relatively thicker and with less sharp apex. Abdomen as in workers but larger. Pilosity. Numerous tiny appressed (≥1/2 length of ocellus) hairs over scape; erect relatively long hairs (length>1 ocellus) present only on clypeus, ventral head, near ocelli, on mesothorax dorsum and on 3rd to 5th abdominal tergites (Fig. 2 a); these longer hairs missing on genae and the occipital corners of the head including region above the eyes (in frontal view no longer hairs surpass the head margins); scape also lacks erect hairs except five to six setae at the apical tip (Fig. 2 e). No long erect hairs on apex of petiole. Sculpture. Fine punctation on the dorsal surface of the head, and on mesosoma dorsum and propodeum; soft lineation on lateral sites of mesosoma, similar to workers. Colouration. Brown head, thorax, scape (except the tip that is lighter) and petiole; light brown abdomen; legs and funiculus yellow (Fig. 2 a, c). Notes The generally lighter colouring may also reflect either the old age of the museum specimen (>100 years) or a relatively young queen collected from inside nest (alate). Description of male Morphometrics. Syntype ‘CASENT0905180’: HL 0.90, HW 1.08, IOD 0.69, CL 0.17, CW 0.40, ML 0.34, EL 0.46, EW 0.32, FCDp 0.32, FCDa 0.14, SL 0.80, SWmax 0.09, SWmin 0.07, WL 1.95, PW 1.08, HFL 1.31, HFT 0.18, HTL 1.30, PetW N.A., PetL N.A., FCDI 229, CI 120, SI 74, MI 38. Head (Fig. 2 f). Eyes largely surpass the head margins in frontal view, with EL ~1/2 of HL, placed at ~1/2 of HL posteriorly. Frontal carinae approaching relatively less one another anteriorly above the posterior margin of clypeus compared to those in male of O. papuana (FCDI = 229), although this variance is not as distinct as among workers and among queens of the two species. Mandibles blunt without teeth. Three ocelli well developed and relatively larger than in queens (diameter as SWmax). Antennae with 13 segments not broadened towards the tip of funiculus like in the workers and queen (see frontal image of another male from the type series ‘focol2564’ with intact antennae) (AntWeb, see https://www.antweb.org). Scape long, at half of the length passing the head margin in frontal view. Mesosoma. Thorax dorsum flat at mesoscutum, otherwise evenly rounded in lateral view with convex prothoracic and propodeal angle, except the mesoscutellar disc that is placed higher and of more convex shape than the other thoracic parts in lateral view (Fig. 2 b). Suture between pronotum and mesoscutum not visible in dorsal view due to highly convex and enlarged mesoscutum compared to pronotum (Fig. 2 d). Metasoma. Petiole triangular but relatively thicker and blunter at the apex. Pilosity. Tiny appressed hairs present on scape and thorax but less numerous over the head compared to queen and workers; long erect hairs (length = SWmax) present only on clypeus, genae, ventral head, near ocelli (one long seta et each) and on 3rd to 5th abdominal tergites (Fig. 2 b); these longer hairs missing completely on scape, petiole and at the occipital corners of the head including region above the eyes (in frontal view, no long hairs surpass the head margin). Sculpture. Fine punctation on dorsal surface of the head, and on mesosoma dorsum and propodeum. Colouration. Light brown to yellowish body, except brown head, thorax dorsum and antennae. Mandibles and appendages pale. Remarks The specimens of O. subclavata from Indonesia that were examined have the posterior parts of the frontal carinae bent slightly inwards and therefore have slightly smaller FCDI (mean 133) than the type specimens from Singapore (mean 155) (Fig. 1 d, 2 h). However, the difference is small and this could possibly be due to measurement error from photographs. All other morphological parameters and the general appearance of the specimens are consistent between the two regions, therefore we regard this to be only a variation within the species. The specimen from the Philippines has a damaged left upper side of the head and a whitish dirt attached to the carinae. Therefore, we did not consider this for morphological measurements. However, absence of the longer hairs on the scape and the thorax, and the finely punctate head with numerous minute recumbent hairs, clearly fit the general appearance of O. subclavata. Viehmeyer (1916) reported that O. subclavata nested in a hollow bamboo stem and in a hollow branch of a mango tree, therefore there is uncertainty whether the syntype series of the species (six workers, three males and one queen, available from AntWeb) belongs to a single nest. Five vials (samples?) collected in 1913 and two collected in 1914 were reported, therefore several colonies from one or more sites in Singapore might have been pooled for the syntype series (most likely two colonies from two stems, a mango and a bamboo). There is also uncertainty as to whether all specimens collected in 1913–1914 are documented online at AntWeb, therefore more material might be scattered in museums worldwide. Nevertheless, all specimens collected by H. Overbeck illustrated in the AntWeb match O. subclavata. The arboricolous nesting in hollow plant structures of (probably) dead tissues suggests that the species nests in tree canopies, but is rather a generalist; that is, not using living tissues or myrmecophytic plants, as do more specialised arboreal species (Klimes and McArthur 2014). Specimens of O. subclavata were probably collected by H. Overbeck in a human-managed area but collections from Sumatra suggest that the species utilises a variety of habitats (see Distribution and Discussion for further information)., Published as part of Klimeš, Petr, Drescher, Jochen, Buchori, Damayanti, Hidayat, Purnama, Nazarreta, Rizky, Potocký, Pavel, Rimandai, Maling, Scheu, Stefan & Matos-Maraví, Pável, 2022, Uncovering cryptic diversity in the enigmatic ant genus Overbeckia and insights into the phylogeny of Camponotini (Hymenoptera: Formicidae: Formicinae), pp. 277-288 in Invertebrate Systematics 36 (6) on pages 565-569, DOI: 10.1071/is21067, http://zenodo.org/record/6987297, {"references":["Viehmeyer H (1916) Ameisen von Singapore. Beobachtet und gesammelt von H. Overbeck. Archiv fur Naturgeschichte - A 81 (8), 108 - 168.","General DM, Alpert GD (2012) A synoptic review of the ant genera (Hymenoptera, Formicidae) of the Philippines. ZooKeys 200, 1 - 111. doi: 10.3897 / zookeys. 200.2447","Klimes P, McArthur A (2014) Diversity and ecology of arboricolous ant communities of Camponotus (Hymenoptera: Formicidae) in a New Guinea rainforest with descriptions of four new species. Myrmecological News 20, 141 - 158."]}

The uploaded files correspond to .tre files forall the phylogenetic species trees generated with ASTRAL III in our study. Thesetrees were inferred with alignments produced by each of our utilized assembly and loci extraction strategies.Names of phylogenetic trees follow the pattern: Sequencing approach_Assembly(WGS or TC)_Loci extraction strategy(ABySS 21, 33, 55, 77 or multikmer OR SPAdes)_processing of alingments(not processed or processed)_read depth coverage(10X, 5X or 2X).

Article published in the journal Tropical Lepidoptera Research

The files include output files, input data and scripts used for phylogenetic inference, historical biogeography and diversification rate analyses: 1. Morphological matrix --> nexus file containing the morphological character states of Brassolini butterflies. 2. Concatenation-based Total Evidence phylogeny --> nexus file containing the alignment of molecular and morphological data and commands for running MrBayes 3.2.6 (Ronquist et al. 2012). You can also find the resulting 50% majority-rule consensus phylogeny. 3. Multispecies coalescent Total Evidence species tree --> XML file containing the molecular and morphological data, and settings for running BEAST 2.6.3 (Bouckaert et al. 2014). You can also find the resulting maximum clade credibility tree. 4. Georeferenced occurrence data --> csv files containing 7,255 Brassolini records from ATLANTIC BUTTERFLIES (Santos et al. 2018) and GBIF databases, and 7,174 Brassolini vetted records as suggested by CoordinateCleaner 2.0-11 (Zizka et al. 2019). R script containing the code to clean georeferenced records using CoordinateCleaner and a pdf file with vetted records plotted in a map. 5. Geographic range data --> text file containing geographic ranges of all Brassolini butterflies in four Neotropical bioregions (M: Mesoamerica + NW Andes; S: tropical South America including the Amazon basin; C: dry diagonal including Cerrado and Caatinga; F: Brazilian Atlantic Forest). 6. Sampling probabilities --> text file containing the proportions of sampled species per genus in the species tree; sampling proportions were used in diversification rate analyses., FUNDING: Marie Skłodowska-Curie Fellowship (European Commission, Grant No. MARIPOSAS-704035). Grant Agency of the Czech Republic (GAČR grant: GJ20-18566Y). Czech Academy of Sciences' PPLZ programme (Czech Academy of Sciences, Fellowship No. L200961951). FAPESP (2011/50225-3, 2012/50260-6, 2013/50297-0). Brazilian Research Council - CNPq (303834/2015-3). National Science Foundation (DEB-1256742). United States Agency for International Development - USAID / the U.S. National Academy of Sciences (NAS), under the PEER program (Sponsor Grant Award Number: AID-OAA-A-11-00012) (Mapping and Conserving Butterfly Biodiversity in the Brazilian Amazon). Swedish Research Council. Swedish Foundation for Strategic Research. Knut and Alice Wallenberg Foundation. Royal Botanic Gardens, Kew., {"references":["Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA & Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542","Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A & Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537","Santos JP dos, Freitas AVL, Brown KS, Carreira JYO, Gueratto PE, Rosa AHB, Lourenço GM, Accacio GM, Uehara-Prado M, Iserhard CA, Richter A, Gawlinski K, Romanowski HP, Mega NO, Teixeira MO, Moser A, Ribeiro DB, Araujo PF, Filgueiras BKC, Melo DHA, Leal IR, Beirão M do V, Ribeiro SP, Cambuí ECB, Vasconcelos RN, Cardoso MZ, Paluch M, Greve RR, Voltolini JC, Galetti M, Regolin AL, Sobral-Souza T & Ribeiro MC. 2018. Atlantic butterflies: a data set of fruit-feeding butterfly communities from the Atlantic forests. Ecology 99: 2875","Zizka A, Silvestro D, Andermann T, Azevedo J, Duarte Ritter C, Edler D, Farooq H, Herdean A, Ariza M, Scharn R, Svantesson S, Wengström N, Zizka V & Antonelli A. 2019. CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution 10: 744–751"]}

Taygetina brocki Lamas & Nakahara, n. sp. (Figs. 1, 2a–b, 3a–g, 4) (Zoobank LSID: urn:lsid:zoobank.org:act: F4180E42-6E12- 4095-B248-C12E826E58F4) Systematic placement and diagnosis (Fig. 1). Taygetina brocki n. sp. is recovered as sister to T. banghaasi with a strong to moderate support (Fig. 1A: SH-aLRT/UFBoot = 93.7/95; Fig. 1B: SH-aLRT/ UFBoot = 90.1/89). The genetic distances among three barcoded T. brocki n. sp. individuals (KW-15-076, 077, and 078) range from 0.104 to 0.23%, and the distances between them and its sister species, T. banghaasi, range from 5.92 to 6.38% (Supp Table 1 [online only]). These two species can be readily recognized by their differing average adult size, with T. brocki n. sp. being smaller (male forewing length 25–27 mm [n = 16]; female forewing length 23–26 mm [n = 7]) than T. banghaasi (forewing length 31–34 mm [n = 3]; syntype male of Taygetis banghaasi in ZSM = 31 mm). Taygetina brocki n. sp. is also distinguished from T. banghaasi by the lack of orange scaling in the discal cell of both VFW and VHW, in addition to its rather whitish/purplish ventral scaling. Furthermore, genitalic characters provide three more diagnostic characters to separate both species, namely: 1) the uncus of T. banghaasi being more strongly curved down compared with T. brocki n. sp.; 2) the sclerotized structure accompanying the plate below the ostium bursae is strongly curved into U-shaped arms with a semicircular plate in the middle of this structure, whereas the sclerotized arms are not curved in and the semicircular plate is reduced in T. brocki n. sp.; 3) the length of the ductus bursae and corpus bursae are similar in length in T. banghaasi, whereas the length of the ductus bursae is twice as great as that of the corpus bursae in T. brocki n. sp.. The female genitalic modifications in T. brocki n. sp. seem to be unique in the genus, except for T. weymeri (Draudt, 1912), which appears to have the lamella antevaginalis similar when viewed from the ventral side. However, the ostium bursae is located closer to the U-shaped arms in T. weymeri, without having a sclerotized plate above as in T. brocki n. sp. Description. MALE Forewing length 25–27 mm (n = 16). Head: Eyes with hair-like setae, white scales at base; first segment of labial palpi short, brownish, adorned with white long hair-like scales and brownish long hair-like scales ventrally, second segment length almost twice as great as eye depth and covered with brownish scales laterally, and with blackish scales along edge of distal two-third of dorsal surface, ventrally adorned with black hair-like scales about 3–4 times as long as segment width, third segment roughly two-fifth of second segment in length and covered with black scales dorsally and ventrally, with brownish-white scales laterally; antennae approximately two-fifth of forewing length, with ca. 37–38 segments (n = 2), distal 13–14 segments composing rather inconspicuous club. Thorax: Dense long light brown hair-like scales anteriorly, sparse white and light brown long hair-like scales present on meso- and metathorax, with some golden scales, ventrally covered with dirty white long hair-like scales with sparse white scales. Legs: Foreleg whitish, tarsus and tibia almost same in length, femur slightly shorter; midleg and hindleg with femur whitish ventrally, tibia and tarsus dorsally grayish, ventrally ochre, tarsus and tibia adorned with spines ventrally, pair of tibial spurs present at distal end of tibia. Abdomen (Fig. 3a): Eighth tergite as sclerotized stripe at base of eighth abdominal segment, in addition to presence of distal broader sclerotized patch; eighth sternite appearing as single broad patch. Wing venation: Basal half of forewing subcostal vein swollen; base of cubitus swollen; forewing recurrent vein absent; hindwing humeral vein developed; origin of M 2 towards M 1 than M 3. Wing shape: Forewing subtriangular, costal margin convex, apex appearing somewhat truncated, outer margin convex, inner margin straight, but rounded towards thorax near base; hindwing slightly elongate, rounded, costal margin convex, outer margin sinuate with distal end of M3 being most pointy, inner margin slightly concave near tornus, anal lobe convex, slightly round. Dorsal forewing: Ground color brownish, distally appearing darker, black androconial scales present in middle of DFW, roughly mirroring area between VFW discal band and postdiscal band, apparently faded near costa. Dorsal hindwing: Ground color similar to forewing, distally darker, no visible androconial scales. Ventral forewing: Ground color grayish chestnut brown, area basal of discal band paler, scattered with whitish scales near discal band; discal band somewhat indistinct, appearing as slightly sinuate brownish band in discal cell and extending below origin of Cu2 (but see also below); area between discal band and postdiscal band scattered with whitish scales mainly between Radius and Cu 2; postdiscal band sinuate, appearing darker and more defined than previous band, extending from Radius towards inner margin, fading in cell Cu 2 and reaching 2A (but see also below); area between postdiscal band and submarginal band scattered with whitish scales, in addition to band-like streak of dense whitish scales from apex towards tornus, traversing basal of submarginal band and touching some submarginal ocelli; submarginal band undulating, appearing brownish with whitish scaling along distal margin, more sinuate than basal two bands, extending from apex to tornus; marginal band smoothly traversing along outer margin with whitish scaling visible distally; fringe brownish; submarginal ocelli in cells R 5, M 1, M 2, M 3, and Cu 1, all appearing as whitish pupil in somewhat indistinct brownish ‘ring’ without black central area. Ventral hindwing: Ground color similar to forewing; area basal of discal band scattered with whitish scales; discal band similar to that of VFW in appearance except for extending from costa towards inner margin and reaching it, curved inwards below 2A (but see also below); area between discal band and postdiscal band scattered with whitish scales, basally more dense; postdiscal band similar to that of VFW in appearance except for passing origin of M 3, crossing 2A and apparently reaching inner margin where it terminates (but see also below); area between postdiscal band and submarginal band scattered with whitish scales, especially area near postdiscal band and area close to submarginal band; submarginal band similar to that of VFW in appearance except for bent inwards when crossing Cu 2; marginal band similar to that of VFW in appearance; fringe brownish; submarginal ocelli in cells Rs, M 1, M 2, M 3, and Cu 1, similar to those of VFW in appearance except for ocellus in Cu1 being most prominent and occasionally black central area present. Genitalia (Fig. 3a–d): Tegumen semicircular in lateral view, dorsal margin convex and ventral margin straight; uncus broad in lateral view, appearing robust (in contrast with many other euptychiines), slightly curved and posteriorly terminating in single point in lateral view, no visible hair-like setae; brachium tapering towards apex, similar to uncus in length, apical point positioned above uncus in lateral view, parallel to uncus with apical edge curving inwards in dorsal view; combination of ventral arms from tegumen and dorsal arms from saccus rather straight, slightly broadening near saccus; appendices angulares present, curving inwards; saccus straight, anteriorly somewhat angular, similar to tegumen plus uncus in length; juxta present as shallow ‘U-shaped’ plate with apical point rounded (Fig. 3c); valva appearing roughly parallelogram in lateral view and distally setose, ventral margin convex, in addition to presence of concavity distally, dorsal margin distal of costa accompanying ‘hump’ at base of apical process, height of hump similar to width of apical process, apical process about one-third of entire valva length, terminating in rather round blunt end; phallus roughly straight, similar in length to tegumen plus uncus, phallobase occupying about one-fourth of phallus, ductus ejaculatorius visible as illustrated, posterior portion of aedeagus somewhat curved upwards, manica covering less than half of aedeagus, weakly sclerotized region of vesica apparently present as cornuti (Fig. 3d)., Published as part of Nakahara, Shinichi, Matos-Maraví, Pável, Barbosa, Eduardo P., Willmott, Keith R., Lamas, Gerardo & Freitas, André V. L., 2019, Two New Species of Taygetina With a Possible Case of ' Juxta Loss' in Butterflies (Lepidoptera: Nymphalidae: Satyrinae), pp. 1-13 in Insect Systematics and Diversity 3 (6) on pages 5-7, DOI: 10.1093/isd/ixz023, http://zenodo.org/record/5385172

Nakahara, Shinichi, Matos-Maraví, Pável, Barbosa, Eduardo P., Willmott, Keith R., Lamas, Gerardo, Freitas, André V. L. (2019): Two New Species of Taygetina With a Possible Case of 'Juxta Loss' in Butterflies (Lepidoptera: Nymphalidae: Satyrinae). Insect Systematics and Diversity 3 (6), No. 9: 1-13, DOI: 10.1093/isd/ixz023, URL: http://dx.doi.org/10.1093/isd/ixz023

Regional species diversity is ultimately explained by speciation, extinction, and dispersal. Here we estimate dispersal and speciation rates in Neotropical rainforest biomes to propose an explanation for the distribution and diversity of extant butterfly species. We focus on the butterfly tribe Brassolini (Owl butterflies and allies): a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We infer a total-evidence species tree of Brassolini using the multispecies coalescent framework. By applying biogeographical stochastic mapping, we infer ancestral ranges and estimate rates of butterfly dispersal and cladogenesis at the scale of millions of years. We suggest that speciation in Mesoamerica and the northwestern flank of the Andes has only increased within the past 2 million years. In contrast, speciation in the Brazilian Atlantic Forest has been constant throughout the past 10 million years. The disparate species diversification dynamics may be explained by the geological and environmental history of each bioregion: the Central American Arc was likely intermittently inundated by water for most of the Miocene (15 to 3 Ma), thus, reduced landmass area until the Plio-Pleistocene may have hindered species diversification; the Atlantic Forest, in turn, likely went through episodes of expansion and contraction and has probably been biologically connected with the Amazonian forest since at least the early Miocene until the Pliocene, about 5 Ma. Importantly, a longer time for speciation in the Atlantic Forest than in Mesoamerica plus NW Andes is ruled out because the dispersal rates into both regions increased simultaneously in the middle-Miocene. Our results reveal a mosaic of bioregion-specific evolutionary histories within the Neotropics, where species have diversified rapidly (cradles: e.g., Mesoamerica), have accumulated gradually (museums: e.g., Atlantic Forest), or have alternately diversified and accumulated (e.g., Amazonia).