Showing posts with label Genetics. Show all posts
Showing posts with label Genetics. Show all posts

Saturday, September 20, 2025

[Botany • 2025] Heteropolygonatum farreri (Asparagaceae: Convallarioideae) • A New Species from the Gaoligongshan in eastern Myanmar and western China


Heteropolygonatum farreri Floden, 

in Floden et Pendry, 2025.

Abstract
A new species of Heteropolygonatum, H. farreri, is described from the easternmost part of Myanmar and western Yunnan in a limestone region of the Gaoligongshan. It is morphologically similar to Heteropolygonatum marmoratum but differs by its shortly scabrous stem, narrowly cylindrical perianth with lanceolate tepals, red-orange fruit, and diploid chromosome count. An illustration of the new species is provided, as is a map of its distribution and that of its closest relative, Heteropolygonatum marmoratum, showing their disjunction. Chromosome counts for Heteropolygonatum farreri (2n = 32) and a second count for H. marmoratum (2n = 4x = 64) are given.

Keywords: Asparagaceae, China, Chromosome, Endemic, Heteropolygonatum, Myanmar

Heteropolygonatum farreri Floden, sp. nov.
A, Habit in the field in Myanmar; B, a leafy stem with fruit; C, the perianth (outer surface; dissected, showing the insertion level of the filaments, and the lengths of the ovary and style; and showing the filament shape and lightly papillose surface ornamentation).
Scale bars in C: 1 mm. All photographs of B.Olsen s.n. (TENN), 
taken by B. Olsen (A and B) and A. J. Floden (C).


A. J. Floden and C. A. Pendry. 2025. A New Species of Heteropolygonatum (ASPARAGACEAE: CONVALLARIOIDEAE, POLYGONATEAE) from the Gaoligongshan in eastern MYANMAR and western CHINA.  Edinburgh Journal of Botany. 82; DOI: doi.org/10.24823/ejb.2025.2057 

Tuesday, December 3, 2024

[Botany • 2024] Rhododendron tyaihyonii & R. kantoense • Unraveling Enigmatic Disjunctions: Population Genetic Analysis Points to Independent Origins of Rare Rhododendrons in the Rhododendron keiskei complex (Ericaceae)

 

  the Rhododendron keiskei complex. B–D, Morphological comparisons of:
B, Rhododendron keiskei Suzuki (1932) R. keiskei var. keiskei;
C, Rhododendron kantoense S.Sakag. & Y.Watan., nom. & stat. nov. R. keiskei var. hypoglaucum;
D, Rhododendron tyaihyonii S.Sakag., H.J.Choi & S.C.Kim, sp. nov. Rhododendron sp.

in Sakaguchi, H.-J. Choi, Yoichi, Takahashi, ..., H.-J. Choi et S.-C. Kim, 2024. 
 — Photos: B, Shota Sakaguchi; C, Watanabe Yoichi; D, J.-C. Yang.
 
Abstract
Unraveling species boundaries is pivotal for evolutionary biology and conservation endeavors. However, it proves challenging in instances where recent speciation is intertwined with complex demographic histories and natural selection processes. The Rhododendron keiskei complex, an evergreen rhododendron distributed in East Asia, consists of a widespread variety (R. keiskei var. keiskei) and a more restricted R. keiskei var. hypoglaucum. Intriguingly, the latter is exceptionally rare yet displays a disjunction that spans approximately 1100 km. This study aimed to elucidate the evolutionary backgrounds of the enigmatic disjunctions of R. keiskei var. hypoglaucum and to propose species delimitation within the species complex. An integrative approach, combining genomic data (MIG-seq and GBS-derived SNPs) with Scanning Electron Microscopy analysis of leaf microstructures was adopted in this study. Phylogenetic analyses revealed significant divergence among the studied rhododendrons. Genetic demographic analyses favored the population models that assumed non-monophyly of two disjunct populations of R. keiskei var. hypoglaucum indicating their independent origins. Recent gene flow between the widespread R. keiskei var. keiskei and “var. hypoglaucum” populations were limited due to geographic and habitat isolation factors, even in areas where their distributions overlap. Detailed morphological assessments detected distinctions between morphologically similar “var. hypoglaucum” populations based on leaf microstructures and flowering habits. Our study has shown that the apparent disjunctions of rare rhododendrons are more likely attributed to morphological convergence, possibly due to similar environmental selections in unrelated taxa. The finding highlights the importance of an integrative approach for resolving taxonomic challenges in plant species complexes.

Keywords: demographic modeling, disjunct distribution, East Asia, endangered species, phylogeny, species delimitation

A) Rhododendron tyaihyonii; B) R. kantoense; C) R. keiskei 

R. keiskei var. keiskei
R. keiskei var. hypoglaucum (R. kantoense nom. & stat. nov.)
Rhododendron sp. (R. tyaihyonii sp. nov.; formerly identified as var. hypoglaucum)


A, The geographic distribution of the Rhododendron keiskei complex.
B–D, Morphological comparisons of: B, R. keiskei var. keiskei; C, R. keiskei var. hypoglaucum; D, Rhododendron sp. 
E, Comparison of leaf blade morphology of three taxa, based on the voucher specimens (suppl. Table S1). Note that the leaf morphological variation of R. keiskei var. hypoglaucum and Rhododendron sp. overlap. — Photos: B, Shota Sakaguchi; C, Watanabe Yoichi; D, J.-C. Yang.

Rhododendron tyaihyonii S.Sakag., H.J.Choi & S.C.Kim, sp. nov. 

Distribution: SOUTH KOREA. Jeollanam-do, Yeosu-si, Samseon-myeon. Narrowly endemic to Daesambudo Island.

Ecology: The plants are found on the northern slope of Daesambudo Island. They inhabit coastal rocky places with the evergreen woody species of Rhaphiolepis indica var. umbellata (Thunb.) H.Ohashi, Ligustrum japonicum Thunb., Camellia japonica L, Litsea japonica (Thunb.) Juss.

Etymology: The specific epithet, “tyaihyonii”, is named in honor of Chung Tyaihyon (1883–1971), known as the father of plant taxonomy in Korea and the first curator of Sungkyunkwan University Herbarium (Ha Eun Herbarium, SKK). We have a better understanding of Korean flora thanks to his work in the early to mid-1900s.
Korean name: Seom-Jin-Dal-Rae.
Japanese name: Chosen-Hikage-Tsutsuji.
English name: Tyaihyon's rhododendron.


Rhododendron kantoense S.Sakag. & Y.Watan., nom. & stat. nov. 
≡ Rhododendron keiskei var. hypoglaucum Suto & T.Suzuki in Trans. Nat. Hist. Soc. Formosa 22: 23. 1932 
– Holotype: JAPAN. Kanto District, Tochigi (Shimotsuke), Kanuma, Mt. Ozaku, 1 May 1931, E. Kitamura ST3902 (TAI barcode TAI 119040 [image!] [fl.]; isotype: TNS barcode TNS 55292 [image!]).

Note: Rhododendron kantoense is similar to R. tyaihyonii, the differences being: the latter has petiole 4–7 mm long; stomata type anomocytic; inflorescence with 2–6 flowers.

Distribution: JAPAN. Kanto, Prefectures of Tochigi, Gunma, Saitama and Tokyo. Endemic to the chert and limestone mountain ridges of Kanto District.

Etymology: The specific epithet “kantoense” is derived from the Kanto District, where this species is distributed.
Japanese name: Urajiro-Hikage-Tsutsuji.
Korean name: Il-bon-Huin-Jin-Dal-Rae.
English name: Kanto rhododendron.

 
Shota Sakaguchi, Hee-Joo Choi, Watanabe Yoichi, Daiki Takahashi, Shun K. Hirota, Masayuki Maki, Shoki Murakami, Taichi Harada, Nobuo Kobayashi, Yuji Kurashige, Jun-Ho Song, Hyeok-Jae Choi and Seung-Chul Kim. 2024. Unraveling Enigmatic Disjunctions: Population Genetic Analysis Points to Independent Origins of Rare Rhododendrons in the Rhododendron keiskei complex (Ericaceae). TAXON. DOI: doi.org/10.1002/tax.13288

Saturday, February 12, 2022

[Herpetology • 2022] Pristimantis cryptopictus • Genetics, Bioacoustics, and Morphology Reveal A New Hidden Species in Pristimantis dorsopictus (Anura: Strabomantidae)


Pristimantis dorsopictus (Rivero & Serna, 1988)

[A-H] Pristimantis cryptopictus
 Patiño-Ocampo, Duarte-Marín & Rivera Correa, 2022

Photos: M. Rivera Correa. twitter.com/biodiversitario

Abstract
The phenotypic variation of some species at the geographic level makes them excellent models to evaluate different evolutionary attributes and answer questions related to their diversity. In addition, the constant effort of sampling in high Andean ecosystems that include the type localities of the species, and the integration of a novel data set can lead to unsuspected taxonomic findings. In this study we provide genetic, bioacoustics and morphological evidence to support the delimitation, and description of a new species from the northern Andean forests, historically confused with Pristimantis dorsopictus (Rivero & Serna, 1988). The latter and the new species were not recovered as sister lineages in our phylogenetic analyses, and although they are relatively similar, both differ phenotypically in body size, coloration pattern, skin texture, call duration and dominant frequency, among other attributes. Our phylogenetic inference suggests that the new species is part of the P. boulengeri group and was recovered as sister to the clade that includes P. urani, P. angustilineatus, P. boulengeri, P. brevifrons, and P. dorsopictus. The results suggest that advertisement calls constitute an important source of information for understanding the acoustic diversity of the P. boulengeri group and for delimiting the species of the genus Pristimantis, which despite its great diversity, presents a limited acoustic knowledge in those with distribution in Colombia.

Keywords: Andes, cryptic diversity, haplotype network, geography, phylogenetics.


Holotype of  Pristimantis dorsopictus sp. nov. MHUA-A 12478, SVL 23.5 mm, adult male.
  Photos: Mauricio Rivera Correa.

Pristimantis cryptopictus sp. nov. in life:
(A) MHUA-A 12480, SVL 22.9 mm, adult male; (B) MHUA-A 12618, SVL 233 mm, adult male;
(C) MHUA-A 12608, SVL 22.3 mm, adult male; (D) MHUA-A 12476, SVL 23.8 mm, adult male;
(E) MHUA-A 12474, SVL 23.0 mm, adult male; (F) MHUA-A 12475, SVL 21.7 mm, adult male;
(G) MHUA-A 12479, SVL 23.1 mm, adult male; (H) MHUA-A 12481, SVL 9.9 mm, juvenile.
Photos: Mauricio Rivera Correa.



 Pristimantis dorsopictus in life:
(A) MHUA-A 12483, SVL 19.1 mm, adult male; (B) MHUA-A 12482, SVL 20.1 mm, adult male;
(C) MHUA-A 12490, SVL 19.6 mm, adult male; (D) MHUA-A 12499, SVL 20.9 mm, adult male;
(E) MHUA-A 12501, SVL 18.7 mm, adult male; (F) MHUA-A 12502, SVL 20.0 mm, adult male;
(G) MHUA-A 12493, SVL 20.8 mm, adult male; MHUA-A 12494, SVL 30.8 mm, adult female; (H) MHUA-A 12503, SVL 10.1 mm, juvenile.
Photos: Mauricio Rivera Correa.

Pristimantis cryptopictus sp. nov.

 
Eliza Patiño-Ocampo, Sebastián Duarte-Marín and Mauricio Rivera Correa. 2022. GENÉTICA, BIOACÚSTICA Y MORFOLOGÍA REVELAN UNA NUEVA ESPECIE OCULTA EN Pristimantis dorsopictus (ANURA: STRABOMANTIDAE). [Genetics, Bioacoustics, and Morphology Reveal A New Hidden Species in Pristimantis dorsopictus (Anura: Strabomantidae)]. Revista Latinoamericana De Herpetología. 5(1), 60–90. DOI: 10.22201/fc.25942158e.2022.1.305 

Resumen: La variación fenotípica de algunas especies a nivel geográfico, las convierte en excelentes modelos para evaluar los diferentes atributos evolutivos y responder preguntas relacionadas con su diversidad. Sumado a ello, el constante esfuerzo de muestreo en ecosistemas altoandinos que incluyan las localidades tipo de las especies y la integración de un novedoso conjunto de datos, puede conducir a hallazgos taxonómicos insospechados. En este estudio proporcionamos evidencia genética, bioacústica y morfológica para soportar la delimitación y descripción de una nueva especie de los bosques al norte de los Andes, históricamente confundida con Pristimantis dorsopictus (Rivero & Serna, 1988). Esta última y la nueva especie no fueron recuperadas como linajes hermanos en nuestros análisis filogenéticos, y aunque son relativamente similares, ambas se diferencian fenotípicamente en tamaño corporal, patrón de coloración, textura de piel, duración del canto y frecuencia dominante, entre otros atributos. Nuestra inferencia filogenética sugiere que la nueva especie es parte del grupo P. boulengeri, y fue recuperada como hermana del clado que incluye a P. urani, P. angustilineatus P. boulengeri, P. brevifrons y P. dorsopictus. Los resultados sugieren que los cantos de anuncio constituyen una fuente de información importante para comprender la diversidad acústica del grupo de P. boulengeri y para la delimitar la especies del género Pristimantis, que a pesar su gran diversidad, presenta un limitado conocimiento acústico en aquellas con distribución en Colombia.
Palabras clave: Diversidad críptica, acústica, filogenética, morfología


Wednesday, October 30, 2019

[Crustacea • 2019] Phimochirus formani & P. tunnelli • Two New Species of the Phimochirus holthuisi complex (Anomura: Paguridae) from the Gulf of Mexico, supported by Morphology, Color, and Genetics


Phimochirus formani & P. tunnelli 
 Felder, Lemaitre & Craig, 2019


Abstract
Coloration, gene-sequence data (H3, 12s, 16s), and subtle features in morphology support the description of two new species, both formerly regarded to represent accepted variants of Phimochirus holthuisi s.l. While color in life consistently separates these species from P. holthuisi s.s. and from each other, morphological distinctions are subtle and less than absolute in small specimens, being based on ventral spine counts of walking leg dactyls and relative development of the superior crest on the major chela. Molecular phylogenetic analyses clearly support the separation of sister clades, representing two new species, from P. holthuisi s.s. as well as other congeners available for analysis. Both of the new species are presently known to occur widely throughout the northern Gulf of Mexico, though one occurs more commonly in the northeastern and southeastern Gulf, and may range as far south as Suriname. The other has been taken primarily in the northwestern Gulf, and is not known from outside Gulf waters. While both of the new species appear restricted to relatively deep subtidal waters of the continental shelf, Phimochirus holthuisi s.s. is instead more commonly found in shallow nearshore tropical waters on or near coral reefs. Previous literature reports of P. holthuisi usually represent, at least in part, one or both of these two new species.

Keywords: Crustacea, Paguroidea, Paguridae, Phimochirus, new species, Gulf of Mexico


FIGURE 2. Phimochirus holthuisi (Provenzano, 1961) s.s.: A, male, sl 3.3 mm (USNM 1542650 = ULLZ 3564), Belize; B, male, sl 2.9 mm (USNM 1558313 = ULLZ 16588), Belize.
Phimochirus formani nov. sp.: C, male paratype, sl 3.1 mm (USNM 1547566 = ULLZ 14352), northeastern Gulf of Mexico; D, male paratype, sl 2.8 mm (USNM 1543170 = ULLZ 7711), northeastern Gulf of Mexico.
Phimochirus tunnelli nov. sp.: E, male paratype, sl 4.1 mm (USNM 1545269 = ULLZ 10611), northwestern Gulf of Mexico; F, ov female paratype, sl 3.9 mm (USNM 1541146 = ULLZ 5789), northwestern Gulf of Mexico.

Taxonomy
 Family Paguridae 

Phimochirus holthuisi (Provenzano, 1961) s.s.

Diagnosis. Carapace shield approximately as long as broad; rostrum broadly subtriangular, rounded. Antennular and antennal peduncles at most reaching to distal margin of corneas; antennal flagella with short setae 1 or less flagellar article in length. Right chela with dorsal surface of fixed finger with small, low nearly obsolete tubercles; palm with dorsal surface smooth, lateral and mesial margins sharply defined by weakly crenulate ridge, mesial margin expanded distally and terminating in strong, blunt spiniform angle. Carpus with dorsomesial margin weakly defined by low ridge armed with 1 proximal spine and 2 or 3 small, blunt spines distally. Dactyls of second and third pereopods approximately 1.7 times longer than propodi; dorsomesial margins each with usually 5 corneous spinules, ventromesial margins each with row of usually 5 or 6 corneous spinules. Anterior lobe of sternite between third pereopods subsemiovate, with simple setae; sternite between fourth and fifth pereopods with simple setae.
 GenBank sequence accession numbers for Belize specimen (USNM 1558313 = ULLZ 16588): (H3) MK830047; (12s) MK848210; (16s) 848227. 
...

Habitat. Occupying variety of medium sized gastropod shells, including faciolariids, turbinids, and muricids; coral reefs, on coralline sand and rubble substrates of spur and groove reef front to backreef lagoon rubble, sands, and seagrass beds; reef crests and shallow adjacent subtidal waters; inner continental shelf; most commonly 2–18 m, to 91 m off North Carolina, perhaps to 291 m off Georgia. 

Distribution. Western Atlantic: East coast of the United States, off North Carolina and Georgia; Caribbean, including Quintana Roo (Cozumel), Belize, Virgin Islands, Jamaica, Guadeloupe, and Colombia; questionably northeastern coast of South America, Suriname to Brazil.


Phimochirus formani nov. sp.

Diagnosis. Carapace shield approximately 1.1 times longer than broad; rostrum acutely triangular, reaching distally beyond lateral projections, terminating in strong spine. Antennular peduncles exceeding distal margins of cornea when fully extended by approximately one-fourth length of ultimate segment. Antennal peduncles reaching to about distal margin of corneas when fully extended, flagellum with alternating long (2 flagellar articles in length) and short setae (less than 1 flagellar article in length). Right chela with dorsal surface of fixed finger with few wellspaced low tubercles; palm smooth dorsally or with few well-spaced low tubercles distally near base of fixed finger, dorsomesial margin sinuous sharply defined as tuberculate or bluntly spinose ridge flaring distally and terminating in spine-like distal angle; carpus with dorsomesial margin sharply defined by spinose ridge including strong, mesially projecting spine. Dactyls of second and third pereopods with ventromesial row of 7–9 corneous spinules (or 4 corneous spinules in very small individuals sl < 2.0 mm). Anterior lobe of sternite between third pereopods semisubovate, distal margin with simple setae; sternites between fourth and fifth pereopods with simple setae.
GenBank sequence accession numbers for paratype (USNM 1547566 = ULLZ 14352): (H3) MK830053; (12s) MK828404; (16s) MK848222.

Etymology. The specific name was selected to honor W. Wayne Forman, a New Orleans based environmental scientist whose talents include an unusually broad grasp of marine biota, and who has over many years brokered access to research sites, acquisition of research specimens, and the securing of financial support for marine scientists working throughout the northern Gulf of Mexico. 

Habitat. Occupying variety of small to medium sized gastropod shells, especially faciolariids, turbinids, and muricids; offshore calcareous banks and deep platforms around coral reefs, especially where richly covered by macroalgae and epifauna, including among rhodoliths; inner to middle continental shelf; 27–62 m. 

Distribution. Western Atlantic: northeastern, northwestern, and southeastern Gulf of Mexico; Suriname.


Phimochirus tunnelli nov. sp.

Diagnosis. Carapace shield approximately 1.1 times longer than broad; rostrum acutely triangular, reaching distally beyond lateral projections, terminating in strong spine. Antennular peduncles reaching to distal margins of corneas when fully extended. Antennal peduncles reaching to approximately midlevel of corneas when fully extended; flagellum with short setae 1 to < 1 flagellar articles in length. Right chela with dorsal surface of fixed finger covered with well-spaced low tubercles; palm with numerous well-spaced tubercles or blunt spines on distal half, dorsomesial margin sharply defined as straight (in mesial view) crenulate or bluntly spinulose ridge terminating in rounded or spine-like angle; carpus with dorsomesial margin sharply defined by ridge with 3 or 4 sharp proximal spines and 2 or 3 smaller blunt distal spines. Dactyls of second and third pereopods with 3 rows of corneous spinules, one dorsomesial with 10 or 11, one ventromesial with 5–10, and one ventral with 9–11. Anterior lobe of sternite between third pereopods semisubovate, distal margin with simple and often capsulate setae; sternites between fourth and fifth pereopods with simple setae and often short capsulate setae.
 GenBank sequence accession numbers for holotype (USNM 1547302 = ULLZ 13837): (12s) MK848209; (16s) MK848226.

Etymology. The specific name is assigned in recognition of the late John W. (Wes) Tunnell, formerly of Texas A&M University–Corpus Christi, whose deep appreciation for, and professional understanding of, coastal and marine biodiversity in the Gulf of Mexico region is reflected in many books and other publications that he authored or orchestrated over his long and productive career. 

Habitat. Occupying varied medium sized gastropod shells, especially faciolariids, turbinids, and muricids; offshore rhodolith and other calcareous banks, especially where richly covered by macroalgae and epifaunal communities; inner to middle continental shelf; 38–72 m.

 Distribution. Western Atlantic: northeastern, northwestern, and southeastern Gulf of Mexico. 

Darryl L. Felder, Rafael Lemaitre and Catherine Craig. 2019. Two New Species of the Phimochirus holthuisi complex from the Gulf of Mexico, supported by Morphology, Color, and Genetics (Crustacea: Anomura: Paguridae). Zootaxa. 4683(4); 531–551. DOI: 10.11646/zootaxa.4683.4.4

Thursday, April 12, 2018

[Mammalogy • 2018] Ethiopian Highlands as A Cradle of the African Fossorial Root-rats (Genus Tachyoryctes), the Genetic Evidence




Šumbera, Krásová, Lavrenchenko, et al., 2018.

 Highlights
• Six major genetic clades do not correspond to the expected two or 13 root-rat species.
• Ethiopian, and not Kenyan, highlands are the cradle of the genus diversity.
• Root-rat history was shaped by climatic oscillations and complex geomorphology.
• The giant root-rat is an internal lineage of the genus modified for life in the Afroalpine.
• Root-rats and mole-rats represent different specialisations for the subterranean niche.

Abstract
Root-rats of the genus Tachyoryctes (Spalacidae) are subterranean herbivores occupying open humid habitats in the highlands of Eastern Africa. There is strong disagreement about species diversity of the genus, because some authors accept two species, while others more than ten. Species with relatively high surface activity, the giant root-rat Tachyoryctes macrocephalus, which is by far largest member of the genus, and the more fossorial African root-rat Tachyoryctes splendens, which eventually has been divided up to 12-13 species, represent two major morphological forms within the genus. In our study, we carried out a multilocus analysis of root-rats’ genetic diversity based on samples from 41 localities representing most of Tachyoryctes geographic distribution. Using two mitochondrial and three nuclear genes, we found six main genetic clades possibly representing separate species. These clades were organised into three basal groups whose branching is not well resolved, probably due to fast radiation in the late Pliocene and early Pleistocene. Climatic changes in that time, i.e. fast and repeated changes between extremely dry and humid conditions, which both limited root-rat dispersal, probably stimulated their initial genetic diversification. Contrary to expectation based on the largest root-rat diversity in Kenya (up to eight species by some authors), we found the highest diversity in the Ethiopian highlands, because all but one putative species occur there. All individuals outside of Ethiopia belong to a single recently diverged and expanded clade. This species should bear the name T. annectens (Thomas, 1891), and all other names of taxa described from outside of Ethiopia should be considered its junior synonyms. However, to solve taxonomic issues, future detailed morphological analyses should be conducted on all main clades together with genetic analysis of material from areas of their supposed contact. One of the most interesting findings of the study is the internal position of T. macrocephalus in T. splendens sensu lato. This demonstrates the intriguing phenomenon of accelerated morphological evolution of rodents occupying the Afroalpine zone in Ethiopia. Finally, we discuss how the distribution of Tachyoryctes is influenced by competition with another group of subterranean herbivores on the continent, the African mole-rats. We assume that both groups do not compete directly as previously expected, but specialisation to different subterranean niches is the main factor responsible for their spatial segregation.

Keywords: Tachyoryctes; fossorial rodent; Eastern Africa; Plio-Pleistocene climatic changes; Great Rift Valley; multi-species coalescent





 Conclusion: 

Contrary to the expectation that root-rats have their highest species diversity in the Kenyan highlands, our results convincingly demonstrated that the Ethiopian mountains are the centre of genus diversity and the cradle of the whole group. The evolution of extant root-rats took place in the Pleistocene and was affected mainly by the interplay between climate changes and the complex geomorphology, with the presence of high mountain massifs, in Ethiopia. Root-rat genetic structure in Ethiopia suggests several cryptic species that should be explored in future taxonomic work, because it is clear that current taxonomy does not reflect the evolutionary history of the genus at all. Probably all taxa described from outside Ethiopia are descendants of a single relatively recent “out-of-Ethiopia” dispersal event and should be considered as conspecific. The fact that the largest and morphologically most deviating species, T. macrocephalus, is not a sister but an internal lineage of “splendens” is further evidence of a fast morphological evolution in response to strong selection in the Afroalpine environment in Ethiopia. We may expect that more thorough genetic surveys of unique Afroalpine taxa will reveal more such findings not only in mammals, but also in other groups of vertebrates. Finally, ecological, behavioural and physiological studies could reveal how the distribution of root-rats is influenced by competition with the African mole-rats, another group of African rodents with subterranean habits.


Radim Šumbera, Jarmila Krásová, Leonid A. Lavrenchenko, Sewnet Mengistu, Afework Bekele, Ondřej Mikula and Josef Bryja. 2018. Ethiopian Highlands as A Cradle of the African Fossorial Root-rats (Genus Tachyoryctes), the Genetic Evidence. Molecular Phylogenetics and Evolution. In Press.   DOI: 10.1016/j.ympev.2018.04.003

Thursday, February 22, 2018

[Cnidaria • 2018] A Simple Molecular Technique for Distinguishing Species reveals Frequent Misidentification of Hawaiian Corals in the Genus Pocillopora


colonies of Pocillopora spp. from O‘ahu, Hawai‘i;
(B–D) Pocillopora ligulata, (F–I) P. meandrina and (K–M) P. eydouxi. 

Johnston​, Forsman & Toonen, 2018.
 DOI:  10.7717/peerj.4355 

Abstract
Species within the scleractinian genus Pocillopora Lamarck 1816 exhibit extreme phenotypic plasticity, making identification based on morphology difficult. However, the mitochondrial open reading frame (mtORF) marker provides a useful genetic tool for identification of most species in this genus, with a notable exception of P. eydouxi and P. meandrina. Based on recent genomic work, we present a quick and simple, gel-based restriction fragment length polymorphism (RFLP) method for the identification of all six Pocillopora species occurring in Hawai‘i by amplifying either the mtORF region, a newly discovered histone region, or both, and then using the restriction enzymes targeting diagnostic sequences we unambiguously identify each species. Using this approach, we documented frequent misidentification of Pocillopora species based on colony morphology. We found that P. acuta colonies are frequently mistakenly identified as P. damicornis in Kāne‘ohe Bay, O‘ahu. We also found that P. meandrina likely has a northern range limit in the Northwest Hawaiian Islands, above which P. ligulata was regularly mistaken for P. meandrina.



Figure 3: Images of Pocillopora ligulata colonies, (A)–(E); P. meandrina colonies, (F)–(J); and P. eydouxi colonies, (K)–(O) from O‘ahu, Hawai‘i. 

Figure 1: Pocillopora species composition across the Hawaiian Islands for samples collected from colonies demonstrating P. meandrina morphology. The size of the pie chart is proportional to the number of individuals sampled per island. Pocillopora species are represented by different colors, specifically: P. meandrina, light yellow; P. eydouxi, dark yellow; P. ligulata, light blue; and P. verrucosa, dark blue.

Conclusions: 
Here, we present an assay that allows rapid and unambiguous identification of all six species of Pocillopora present in Hawai‘i, which we hope will work anywhere these species are found. We present two cases where samples identified morphologically were misidentified to highlight the utility of this approach. Taxonomic confusion can impact a wide range of studies and the ability to rapidly and cost-effectively distinguish among species of Pocillopora will benefit future studies of population structure, ecology, biodiversity, evolution and conservation in this challenging genus.


Erika C. Johnston​, Zac H. Forsman and Robert J. Toonen. 2018. A Simple Molecular Technique for Distinguishing Species reveals Frequent Misidentification of Hawaiian Corals in the Genus Pocillopora.  PeerJ. 6:e4355.  DOI:  10.7717/peerj.4355
  

Thursday, February 8, 2018

[Botany • 2018] Genomics of the Origin and Evolution of Citrus


Proposed origin of Citrus and ancient dispersal routes. Arrows suggest plausible migration directions of the ancestral citrus species from the centre of origin—the triangle formed by northeastern India, northern Myanmar and northwestern Yunnan. The proposal is compatible with citrus biogeography, phylogenetic relationships, the inferred timing of diversification and the paleogeography of the region, especially the geological history of Wallacea and Japan. The red star marks the fossil location of C. linczangensis. Citrus fruit images in c and d are not drawn to scale.

Wu, Terol, Ibanez, et al., 2018. 

Abstract
The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.

Figure 1: Genetic structure, heterozygosity and phylogeny of Citrus species.  a, Principal coordinate analysis of 58 citrus accessions based on pairwise nuclear genome distances and metric multidimensional scaling. The first two axes separate the three main citrus groups (citrons, pummelos and mandarins) with interspecific hybrids (oranges, grapefruit, lemon and limes) situated at intermediate positions relative to their parental genotypes. b, Violin plots of the heterozygosity distribution in 58 citrus accessions, representing 10 taxonomic groups as well as 2 related genera, Poncirus (Poncirus trifoliata, also known as Citrus trifoliata) and Chinese box orange (Severinia). White dot, median; bar limits, upper and lower quartiles; whiskers, 1.5× interquartile range. The bimodal separation of intraspecies (light blue) and interspecies (light pink) genetic diversity is manifested among the admixed mandarins and across different genotypes including interspecific hybrids. Three-letter codes are listed in parenthesis with additional descriptions in Supplementary Table 2. c, Chronogram of citrus speciation. Two distinct and temporally well-separated phases of species radiation are apparent, with the southeast Asian citrus radiation followed by the Australian citrus diversification. Age calibration is based on the citrus fossil C. linczangensis16 from the Late Miocene (denoted by a filled red circle). The 95% confidence intervals are derived from 200 bootstraps. Bayesian posterior probability is 1.0 for all nodes. d, Proposed origin of citrus and ancient dispersal routes. Arrows suggest plausible migration directions of the ancestral citrus species from the centre of origin—the triangle formed by northeastern India, northern Myanmar and northwestern Yunnan. The proposal is compatible with citrus biogeography, phylogenetic relationships, the inferred timing of diversification and the paleogeography of the region, especially the geological history of Wallacea and Japan. The red star marks the fossil location of C. linczangensis. Citrus fruit images in c and d are not drawn to scale.

Guohong Albert Wu, Javier Terol, Victoria Ibanez, Antonio López-García, Estela Pérez-Román, Carles Borredá, Concha Domingo, Francisco R. Tadeo, Jose Carbonell-Caballero, Roberto Alonso, Franck Curk, Dongliang Du, Patrick Ollitrault, Mikeal L. Roose, Joaquin Dopazo, Frederick G. Gmitter, Daniel S. Rokhsar and Manuel Talon. 2018. Genomics of the Origin and Evolution of Citrus.  Nature.   DOI: 10.1038/nature25447

  

The Citrus Family Tree  on.natgeo.com/2AQGWMo   @NatGeoMag

  

Monday, December 18, 2017

[Herpetology • 2017] Evolutionarily Significant Units of the Critically Endangered Leaf Frog Pithecopus ayeaye (Anura, Phyllomedusidae) are Not Effectively Preserved by the Brazilian Protected Areas Network


Pithecopus ayeaye B. Lutz, 1966

de Magalhães, Lemes, Camargo, et al. 2017. 
Photograph by R. A. Brandão. || DOI: 10.1002/ece3.3261   

Abstract

Protected areas (PAs) are essential for biodiversity conservation, but their coverage is considered inefficient for the preservation of all species. Many species are subdivided into evolutionarily significant units (ESUs) and the effectiveness of PAs in protecting them needs to be investigated. We evaluated the usefulness of the Brazilian PAs network in protecting ESUs of the critically endangered Pithecopus ayeaye through ongoing climate change. This species occurs in a threatened mountaintop ecosystem known as campos rupestres. We used multilocus DNA sequences to delimit geographic clusters, which were further validated as ESUs with a coalescent approach. Ecological niche modeling was used to estimate spatial changes in ESUs’ potential distributions, and a gap analysis was carried out to evaluate the effectiveness of the Brazilian PAs network to protect P. ayeaye in the face of climate changes. We tested the niche overlap between ESUs to gain insights for potential management alternatives for the species. Pithecopus ayeaye contains at least three ESUs isolated in distinct mountain regions, and one of them is not protected by any PA. There are no climatic niche differences between the units, and only 4% of the suitable potential area of the species is protected in present and future projections. The current PAs are not effective in preserving the intraspecific diversity of P. ayeaye in its present and future range distributions. The genetic structure of P. ayeaye could represent a typical pattern in campos rupestres endemics, which should be considered for evaluating its conservation status.

KEYWORD: Sapproximate Bayesian computation, campos rupestres, conservation genetics, ecological niche modeling, niche overlap, statistical phylogeography 


FIGURE 1: An individual of Pithecopus ayeaye B. Lutz, 1966 from type locality, Morro do Ferro, Poços de Caldas—MG.

Photograph by Reuber Albuquerque Brandão. 

Rafael Félix de Magalhães, Priscila Lemes, Arley Camargo, Ubirajara Oliveira, Reuber Albuquerque Brandão, Hans Thomassen, Paulo Christiano de Anchietta Garcia, Felipe Sá Fortes Leite and Fabrício Rodrigues Santos. 2017. Evolutionarily Significant Units of the Critically Endangered Leaf Frog Pithecopus ayeaye (Anura, Phyllomedusidae) are Not Effectively Preserved by the Brazilian Protected Areas Network.  Ecology and Evolution. 7(21); 8812–8828.  DOI: 10.1002/ece3.3261  


Wednesday, November 15, 2017

[Herpetology • 2017] Living Quarters of A Living Fossil - Uncovering the Current Distribution Pattern of the Rediscovered Hula Painted Frog (Latonia nigriventer) using Environmental DNA


Latonia nigriventer (Mendelssohn & Steinitz, 1943)

photo: @Roll_Ur   || DOI:  10.1111/mec.14420 

Abstract   
One of the greatest challenges of effective conservation measures is the correct identification of sites where rare and elusive organisms reside. The recently rediscovered Hula painted frog (Latonia nigriventer) has not been seen for many decades, and was therefore categorized extinct. Since its rediscovery in 2011, individuals from the critically endangered species have been found, with great effort, only in four restricted sites. We applied the environmental DNA (eDNA) approach to search for new populations of the Hula painted frog in suitable aquatic habitats. We further used the eDNA data to classify the landscape factors associated with the species distribution and to predict its suitable habitats. We sampled 52 aquatic sites in the Hula valley during the spring of 2015 and 2016, and amplified the samples with a species-specific qPCR assay. DNA of the Hula painted frog was detected in 22 of the sites, all of which clustered within three main areas. A boosting classification model showed that soil type, vegetation cover, and the current and former habitats are all key predictors of the frog's current distribution. Intriguingly, the habitat suitability models reveal a high affinity of the species to its long-lost habitat of the historical wetlands. Our findings encourage a series of informed searches for new populations of this threatened frog, and provide guidance for future conservation management programs. In the era of global conservation crisis of amphibians, developing the eDNA approach, a reliable detection method for many critically endangered and elusive amphibians, is of particularly importance.

Keywords: Conservation genetics; Genetic monitoring; Amphibians; Species distribution modelling (SDM)




Sharon Renan, Sarig Gafny, R. G. Bina Perl, Uri Roll, Yoram Malka, Miguel Vences and Eli Geffen. 2017. Living Quarters of A Living Fossil - Uncovering the Current Distribution Pattern of the Rediscovered Hula Painted Frog (Latonia nigriventer) using Environmental DNA. Molecular Ecology. DOI:  10.1111/mec.14420 

 Using #eDNA analysis we were able to map suitable habitats for the newly re-discovered #Living_fossil -the Hula_painted_frog, and see that it retains its affinity to the now drained Hula lake and swamp. #Molecular_Ecology  || Detection of Hula painted frogs using eDNA

Friday, September 15, 2017

[Herpetology • 2017] Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provide Founders for Species Restoration Program




Abstract
Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 individuals with distinctive morphology sampled from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano’s slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopus tortoises to Floreana Island to serve as engineers of the island’s ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this “lost” species today.


Figure 1: Distribution of tortoises among Galápagos Islands and representative photos of tortoise carapace morphology.
(a) Map of the distribution of tortoises among Galápagos Islands along with cartoons indicating carapace morphology for each. Light grey shading indicates domed morphology, unshaded indicates saddle-backed. Extinct species are noted with †. (b) Larger view of Volcano Wolf on northern Isabela Island. The circle indicates the approximate field location of the current study. Examples of Galápagos giant tortoises with domed (c) saddle-backed (d) morphology.  



Joshua M. Miller, Maud C. Quinzin, Nikos Poulakakis, James P. Gibbs, Luciano B. Beheregaray, Ryan C. Garrick, Michael A. Russello, Claudio Ciofi, Danielle L. Edwards, Elizabeth A. Hunter, Washington Tapia, Danny Rueda, Jorge Carrión, Andrés A. Valdivieso and Adalgisa Caccone. 2017. Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provide Founders for Species Restoration Program. Scientific Reports. 7, Article number: 11471. DOI: 10.1038/s41598-017-11516-2

Back from the dead—how to revive a lost species
 phy.so/424511176 via @physorg_com

  

Wednesday, August 9, 2017

[Entomology • 2017] Ectinogonia cryptica • Genetic and Morphological Evidence for A New Cryptic Species of Ectinogonia (Coleoptera: Buprestidae) from central Chile


Ectinogonia cryptica
Anguita-Salinas, Barahona-Rodrigo, Poulin & Zúñiga-Reinoso, 2017

Abstract

The genus Ectinogonia Spinola, 1837 is a genus mainly found in Chile; it currently contains 17 species. Recent exploration in the Andes Mountain Range of the Bio Bio Region in Chile have resulted in the collection of specimens slightly different morphologically from all previously described species. The aim of this paper is to describe this new species of Ectinogonia using morphological and genetic evidence. To establish differences between species we described the external morphology and compared it to species that are morphologically similar (i.e. E. buqueti Spinola 1837 and E. intermedia Kerremans 1903). We also measured the genetic differences in COI sequences, constructing a distance matrix in which we compared it to species that are morphologically similar (E. buqueti and E. intermedia) and other species found in the same region (E. speciosa oscuripennis Moore 1994). We found that Ectinogonia cryptica sp. n. differs from E. buqueti (which previously contained E. cryptica sp. n.) in pronotum and elytral patterns. The genetic distance matrix shows that E. cryptica sp. n. differs by 4.6% from all other Ectinogonia species compared, supporting the morphological evidence.

Keywords: Coleoptera, Chrysochroinae, Dicercini, Ectinogonia cryptica sp. n., genetic distance, taxonomy


Simón Anguita-Salinas, Rodrigo M. Barahona-Rodrigo, Elie Poulin and Alvaro Zúñiga-Reinoso. 2017. Genetic and Morphological Evidence for A New Cryptic Species of Ectinogonia (Coleoptera: Buprestidae) from central Chile. Zootaxa. 4303(2); 284–292. DOI: 10.11646/zootaxa.4303.2.8