Tortoise (Reptilia, Testudinidae) radiations in Southern Africa from the Eocene to the present.

Zoologica Scripta 46(4): 389-400

Abstract:

Africa, inclusive of the West Indian Ocean islands, harbours 11 of the world's 16 extant testudinid genera. Fossil records indicate that testudinids originated in Asia and dispersed first to North America and Europe (Early Eocene) and later to Africa (Late Eocene). We used mitochondrial (1870 bp) and nuclear (1416 bp) DNA sequence data to assess whether molecular data support the late cladogenesis of Southern African testudinid lineages. Our results revealed strong support for the monophyly of a clade consisting of Kinixys, the two Malagasy genera and four Southern African genera (Psammobates, Stigmochelys, Homopus and Chersina). Kinixys diverged from this clade in the Late Palaeocene, suggesting that testudinids occupied Africa at an earlier date than indicated by fossil records. The Southern African tortoises consist of three, strongly supported clades: Psammobates + Stigmochelys; the five-toed Homopus + Chersina; and the four-toed Homopus. Due to the paraphyly of Homopus, we propose the taxonomic resurrection of Chersobius for the five-toed Homopus species (boulengeri, signatus and solus). Cladogenesis at the genus level occurred mainly in the Eocene, with Chersina and Chersobius diverging in the Oligocene. The latter divergence coincided with species-level radiations within Homopus (areolatus and femoralis) and Psammobates (oculifer, geometricus and tentorius). Our phylogeny could not resolve relationships within Psammobates, indicating rapid speciation between the Late Oligocene and Early Miocene. The Chersobius species were the last to diverge in the Early to Mid-Miocene. By the Mid-Miocene, P. tentorius started to differentiate into four lineages instead of the three recognized subspecies: P. t. tentorius, P. t. trimeni and two P. t. verroxii subclades occurring north and south of the Orange River, respectively. Terminal radiations in several taxa suggest the existence of cryptic species and a more diverse tortoise fauna than currently recognized. Factors contributing to this diversity may include the early origin of African testudinids and climatic fluctuations over a heterogeneous landscape.

hofmeyr-biblio

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements.

Preprint: doi: https://doi.org/10.1101/717520
Molecular Phylogenetics and Evolution 146: 106731

Volltext (Preprint): https://www.biorxiv.org/content/10.1101/717520v1.full.pdf+html

Abstract:

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread “generalist” clades. This is especially true in the Australasia, where the monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately “derived” parachute geckos of the genus Ptychozoon.

Here we employ sequence capture targeting 5060 ultraconserved elements to infer phylogenomic relationships among 42 representative ingroup gekkonine lizard taxa. We analyzed multiple datasets of varying degrees of completeness (10, 50, 75, 95, and 100 percent complete with 4715, 4051, 3376, 2366, and 772 UCEs, respectively) using concatenated maximum likelihood and multispecies coalescent methods.

Our sampling scheme was designed to address four persistent systematic questions in this group:

(1) Are Luperosaurus and Ptychozoon monophyletic and are any of these named species truly nested within Gekko?

(2) Are prior phylogenetic estimates of Sulawesi’s L. iskandari as sister to Melanesian G. vittatus supported by our genome-scale dataset? (

3) Is the high elevation L. gulat of Palawan Island correctly placed within Gekko? (

4) And, finally, where do the enigmatic taxa P. rhacophorus and L. browni fall in a higher-level gekkonid phylogeny?

We resolve these issues; confirm with strong support some previously inferred findings (placement of Ptychozoon taxa within Gekko; the sister relationship between L. iskandari and G. vittatus); resolve the systematic position of unplaced taxa (L. gulat, and L. browni); and transfer L. iskandari, L. gulat, L. browni, and all members of the genus Ptychozoon to the genus Gekko. Our unexpected and novel systematic inference of the placement of Ptychozoon rhacophorus suggests that this species is not related to Ptychozoon or even Luperosaurus (as previously expected) but may, in fact, be most closely related to several Indochinese species of Gekko. With our final, well-supported topologies, we recognize seven newly defined subgenera to accommodate ∼60 species within the more broadly defined and maximally-inclusive Australasian genus Gekko. The newly defined subgenera will aide taxonomists and systematists in species descriptions by allowing them to only diagnose putatively new species from the most relevant members of the same subgenus, not necessarily the phenotypically variable genus Gekko as a whole, and we argue that it appropriately recognizes geographically circumscribed units (e.g., a new subgenus for a novel clade, entirely endemic to the Philippines) while simultaneously recognizing several of the most systematically controversial, phenotypically distinct, and phylogenetically unique lineages. An added benefit of recognizing the most inclusive definition of Gekko, containing multiple phylogenetically-defined subgenera, is that this practice has the potential to alleviate taxonomic vandalism, if widely adopted, by creating formally available, supraspecific taxa, accompanied by character-based diagnoses and properly assigned type species, such that future, more atomized classifications would necessarily be required to adopt today’s subgenera as tomorrow’s genera under the guidelines of The Code of Zoological Nomenclature. Not only does this simple practice effectively eliminate the nefarious motivation behind taxonomic vandalism, but it also ensures that supraspecific names are created only when accompanied by data, that they are coined with reference to a phylogenetic estimate, and that they explicitly involve appropriate specifiers in the form of type species and, ultimately, type specimens.

wood-biblio

Molecular Systematics and Phylogeny of Old and New World Ratnakes, Elaphe AUCT., and Related Genera (Reptilia, Squamata, Colubridae.

Russian J. Herpetology 9(2): 105-124.

Abstract:

The phylogenetic relationships of the Holarctic ratsnakes (Elaphe auct.) are inferred from portions of two
mitochondrial genes, 12S rRNA and COI. Elaphe Fitzinger is made up of ten Palaearctic species. Natrix
longissima Laurenti (type species) and four western Palaearctic species (hohenackeri, lineatus, persicus,
and situla) are assigned to Zamenis Wagler. Its phylogenetic affinities with closely related genera, Coronella and Oocatochus, remain unclear. The East Asian Coluber porphyraceus Cantor is referred to a new genus. This taxon and the western European Rhinechis scalaris have an isolated position among Old World ratsnakes. Another new genus is described for four Oriental species (cantoris, hodgsonii, moellendorffi, and taeniurus). New World ratsnakes and allied genera are monophyletic. Coluber flavirufus Cope is referred to Pseudelaphe Mertens and Rosenberg. Pantherophis Fitzinger is revalidated for Coluber guttatus L. (type species) and further Nearctic species (bairdi, obsoletus, and vulpinus). Senticolis triaspis is the sister taxon of New World ratsnakes including the genera Arizona, Bogertophis, Lampropeltis, Pituophis, and Rhinocheilus. The East Asian Coluber conspicillatus Boie and Coluber mandarinus Cantor form a monophyletic outgroup with respect to other Holarctic ratsnake genera and are referred to Euprepiophis Fitzinger. Three Old World species, viz. Elaphe (sensu lato) bella, E. (s.l.) frenata, and E. (s.l.) prasina remain unassigned. The various groups of ratsnakes (tribe Lampropeltini) show characteristic hemipenis features.

utiger-biblio

Divergent Morphology among Populations of the New Guinea Crocodile, Crocodylus novaeguineae (Schmidt, 1928): Diagnosis of An Independent Lineage and Description of A New Species.

Copeia. 107(3): 517-523.

Abstract:

The New Guinea Crocodile (Crocodylus novaeguineae) is a freshwater species of crocodilian endemic to the island of New Guinea in northern Oceania. The species inhabits both the country of Papua New Guinea in the east and Indonesian West Papua. Crocodylus novaeguineae occurs on both the northern and southern side of the Central Highlands, which span east to west dividing the entire island into northern and southern halves. Like most crocodilians, C. novaeguineae inhabits various grassy and forested swamps in lowland freshwater areas and has maintained both cultural and economic significance in the region for centuries. Neill (1971) and, more recently, Hall (1989) have suggested that Crocodylus novaeguineae on the northern side of the Central Highlands (“NCN”) and those on the southern side (“SCN”) are on independent evolutionary trajectories and should be taxonomically recognized. Hall (1989) attempted to affirm the suspicions of Neill and presented compelling morphological and ecological data to do so. Morphologically, the northern and southern hypothesized lineages differed in proportional premaxillary (PXS) to maxillary (MXS) length (NCN: MXS > PXS; SCN: PXS > MXS) and patterns of cervical squamation (NCN: >4 post-occipital scutes with lateral contiguity between them, anteromedial nuchal scute separation absent; SCN: 4 post-occipital scutes with lateral discontinuity between them, anteromedial nuchal scute separation present). Ecologically, C. novaeguineae south of the Central Highlands nest in the wet season, in synchrony with sympatric Crocodylus porosus, whereas north of the Central Highlands, nesting occurs in the dry season. Additionally, variation in reproductive strategy (clutch size and egg size ratios) was diagnosed between NCN and SCN; however, reproductive strategy is highly plastic, even intraspecifically, among crocodilians. Thus, these character states are not robustly interpretable as diagnostic. Phylogenetic approaches using molecular data were later tested and interpreted in the unpublished thesis of Gratten (2003) in which NCN and SCN were considered distinct operational taxonomic units in light of Hall (1989). A Bayesian analysis of relationships of Indo-Pacific Crocodylus using mtDNA curiously recovered a paraphyletic C. novaeguineae, rendered so by the purported Borneo Crocodile C. raninus, described from a skull and two preserved juveniles with no known extant population (Muller and Schlegel, 1844). NCN was recovered as more closely related to C. raninus than to SCN. This finding was attributed to either extremely recent divergence in NCN or misidentification of a dispersed or introduced NCN to Borneo from which the molecular sample was taken. Oaks (2011) recovered a paraphyletic C. novaeguineae; however, all samples of this species were from captive animals and identification of some samples appeared problematic. Thus, our analyses and comparisons herein only include populations of C. novaeguineae due to the lack of biologically reasonable comparisons. Crocodylus novaeguineae is the only freshwater crocodilian in the region besides the putative C. raninus. Little material with robust locality data exists in collections for this species, and in the absence of more specimens and diverse datasets we are unable to make additional comparisons. An improved analysis of morphological variation among populations of C. novaeguineae is warranted, given the ecological and molecular patterns that have slowly emerged. Here, we use multivariate geometric morphometric approaches to gain clarity on the differentiation of populations north and south of the Central Highlands by assessing cranial shape variation across the distribution. We aim to identify diagnostic characters for populations on independent evolutionary trajectories and test whether cranial shape variation corresponds to the hypothesized lineages (a clade north of the central highlands and one south). We predicted that specimens from drainages on the northern side would more closely resemble each other than specimens from drainages on the southern side of the highlands and that shape-based diagnostic characters would be revealed.

murray-biblio

Molecular phylogenetics and the diversification of hummingbirds.

Current Biology 24 (8): 910–916. doi:10.1016/j.cub.2014.03.016. PMID 24704078.

Summary:

The tempo of species diversification in large clades can reveal fundamental evolutionary mechanisms that operate on large temporal and spatial scales. Hummingbirds have radiated into a diverse assemblage of specialized nectarivores comprising 338 species, but their evolutionary history has not, until now, been comprehensively explored. We studied hummingbird diversification by estimating a time-calibrated phylogeny for 284 hummingbird species, demonstrating that hummingbirds invaded South America by ∼22 million years ago, and subsequently diversified into nine principal clades. Using ancestral state reconstruction and diversification analyses, we (1) estimate the age of the crown-group hummingbird assemblage, (2) investigate the timing and patterns of lineage accumulation for hummingbirds overall and regionally, and (3) evaluate the role of Andean uplift in hummingbird speciation. Detailed analyses reveal disparate clade-specific processes that allowed for ongoing species diversification. One factor was significant variation among clades in diversification rates. For example, the nine principal clades of hummingbirds exhibit ∼15-fold variation in net diversification rates, with evidence for accelerated speciation of a clade that includes the Bee, Emerald, and Mountain Gem groups of hummingbirds. A second factor was colonization of key geographic regions, which opened up new ecological niches. For example, some clades diversified in the context of the uplift of the Andes Mountains, whereas others were affected by the formation of the Panamanian land bridge. Finally, although species accumulation is slowing in all groups of hummingbirds, several major clades maintain rapid rates of diversification on par with classical examples of rapid adaptive radiation.

mcguire-biblio

Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild.

Evol. Appl. 2021 Mar; 14(3): 698–709.

Published online 2020 Nov 7. doi: 10.1111/eva.13149

Abstract:

Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross‐bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population (“Javan Pied Starling”) is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.

bavej-biblio

Molecular diversity among domestic guinea-pigs (Cavia porcellus) and their close phylogenetic relationship with the Andean wild species Cavia tschudii.

Revista Chilena de Historia Natural 77: 243-250

Abstract:

To investigate the origin and diversity of domestic guinea-pigs Cavia porcellus (Linnaeus, 1758; Rodentia, Caviidae), we sequenced the mitochondrial cytochrome b gene of 12 domestic and 10 wild specimens from six species, including the two presumed as ancestral to the domestic one: Cavia tschudii and Cavia aperea. All maximum parsimony and maximum likelihood analyses grouped C. porcellus with C. tschudii (mean K2P distance = 3.2 %); best trees had 609 steps (CI = 0.796; Bremer support Index (SI) = 28), and a –Ln = 4419.52, with 100 % and 97 % bootstrap support respectively. This clade, supported by three substitutions and 96 % bootstrap, is also obtained in the cladistic analysis of corresponding amino acids. When the C. aperea node was forced to join C. porcellus, these trees were consistently longer, less likely and robust, and with less defining characters than the optimal one. All C. porcellus sequences also clustered in a node defined by 15 substitutions. The sub-node containing animals from city markets, pet shops and laboratories was characterized by four substitutions (one non-silent, SI = 7, and 91 % bootstrap). Some South American C. porcellus, called “criollos” (creoles) by local breeders, were more diverse. Probably, a particular clade from southern Peru and Chile may represent a pre-Columbian lineage. Mean K2P distance between C. tschudii and C. aperea was rather large, 7.7 %. Cavia appeared as a robust node (100 % bootstrap). These results indicate that C. tschudii is the species most closely related to C. porcellus.

spotorno-biblio

Natural genetic polymorphism and phylogeography of Siberian sturgeon Acipenser baerii Brandt, 1869.

Russ. J. Genet. 53: 358–368. https://doi.org/10.1134/S1022795417030024

Abstract:

Five populations of Siberian sturgeon Acipenser baerii collected throughout the species distribution range (Lake Baikal, Lena, Yenisei, Kolyma, and Irtysh rivers) were examined for genetic polymorphism using five tetraploid microsatellite loci and the mitochondrial DNA control region. It was demonstrated that Siberian sturgeon was represented by genetically well-differentiated groups that corresponded to hydrographic basins, Ob–Irtysh, Baikal–Yenisei, Lena, and Kolyma. Population assignment of the Siberian sturgeon broodstock should be considered in the restocking programs.

barmintseva-biblio

Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities.

Emu - Austral Ornithology 120 (3): 201–215. doi:10.1080/01584197.2020.1779596. S2CID 222094508.

Abstract:

A well-supported genus-level classification of any group of organisms underpins downstream understanding of its evolutionary biology and enhances the role of phylogenetic diversity in guiding its conservation and management. The lorikeets (Psittaciformes: Loriini) are parrots for which genus-level systematics (phylogenetic relationships and classification) has long been unstable and unsatisfactory. Instability has manifested through frequently changing compositions of some genera (e.g. Trichoglossus and Psitteuteles). Other genera (e.g. Charmosyna, Vini) have become so large that their phenotypic heterogeneity alone at least questions whether they are monophyletic assemblages that genera should comprise. Recent molecular phylogenetic and phenotypic studies have improved the framework with which to rationalise genus-level systematics in lorikeets but some trenchant uncertainty has remained. Here we utilise published genomic data and tetrahedral analysis of plumage colour to develop a full review of the genus-level classification of lorikeets. Using existing phylogenetic relationships and a newly estimated time-calibrated tree for lorikeets, we show where paraphyletic assemblages have misled the classification of genera. We assign six species to three new genera and six other species to four previously described generic names that have been in synonymy in recent literature. Our taxonomic revision brings a new perspective informing and guiding the conservation and management of the lorikeets and their evolutionary biology.

joseph-biblio

A molecular phylogeny of the Australian monitor lizards (Squamata:Varanidae) inferred from mitochondrial DNA sequences.

Australian Journal of Zoology. 54: 253–269.

Volltext: https://www.researchgate.net/publication/248902243_A_molecular_phylogeny_of_the_Australian_monitor_lizards_Squamata_Varanidae_inferred_from_mitochondrial_DNA_sequences

Abstract:

To date no complete phylogeny of all of the currently recognised Indo-Australian varanid species and subspecies has been published. This paper presents a comprehensive mitochondrial gene phylogeny of these lizards. A portion of the mitochondrial genome comprising part of the ND4 gene and three adjacent tRNA genes (hereafter referred to as ND4) was analysed alone and, for a subset of the taxa, combined with previously published mitochondrial data. Similar tree topologies were produced by both datasets although combining the data helped resolve some of the unresolved or weakly supported nodes in the ND4 analyses. The monophyly of the Indo-Australian group was strongly supported in all analyses. This group comprised three major lineages: the gouldii group, the Odatria group and the varius group. Mitochondrial ND4 nucleotide sequences were successfully amplified from all of the Indo-Australian monitor species and subspecies currently recognised and, as such, is the first comprehensive phylogenetic study of the Australian monitor lizards published. Analysis of the tempo of diversification and evolution of preferred habitat use identified six episodes of increased net speciation rate, with two closely adjacent episodes showing the highest rates of diversification and correlating with the appearance of all preferred habitat types. The comprehensive molecular phylogenetic framework will also be useful for the identification of varanid species and traded products derived from monitors and, as such, has important applications for wildlife management and conservation.

fitch-biblio