The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management

There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah’s phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah’s whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.info:eu-repo/semantics/publishedVersio

Radiating on Oceanic Islands: Patterns and Processes of Speciation in the Land Snail Genus Theba (Risso 1826)

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors

ES_5_clique_details

Electronic supplement (ES) 5 UPGMA clustering of the dissimilarity values calculated in the pairwise excess index matrix (Fig. 4) showing all character numbers of the morphological data matrix. Clustered characters are indicated by a vertical terminal line. The two cliques and the remaining character subset are indicated by grey boxes

Data from: The identification of concerted convergence in insect heads corroborates Palaeoptera

The relationships of the three major clades of winged insects - Ephemeroptera, Odonata and Neoptera - are still unclear. Many morphologists favor a clade Metapterygota (Odonata+Neoptera), but Chiastomyaria (Ephemeroptera+Neoptera) or Palaeoptera (Ephemeroptera+Odonata) have also been supported in some older and more recent studies. A possible explanation for the difficulties in resolving these relationships is concerted convergence - the convergent evolution of entire character complexes under the same or similar selective pressures. In this study we analyse possible instances of this phenomenon in the context of head structures of Ephemeroptera, Odonata and Neoptera. We apply a recently introduced formal approach to detect the occurrence of concerted convergence. We found that characters of the tentorium and mandibles in particular, but also some other head structures, have apparently not evolved independently, and thus can cause artefacts in tree reconstruction. Our subsequent analyses, which exclude character sets that may be affected by concerted convergence, corroborate the Palaeoptera concept. We show that the analysis of homoplasy and its influence on tree inference can be formally improved with important consequences for the identification of incompatibilities between datasets. Our results suggest that modified weighting (or exclusion of characters) in cases of formally identified correlated cliques of characters may improve morphology based tree reconstruction

AMARE replicate transformation.

<p>This example shows how AMARE transforms replicates into pairs (<i>i,j</i>) representing the observed state 0 (fragment absence) or 1 (fragment presence) within each bin.</p

<i>Ipomoea</i> data set of Holland et al. [31].

<p>The neighbor-joining trees are based on uncorrected genetic distances calculated from A) the original character matrix with 1425 markers and B) the AMARE masked character matrix with 406 markers. Bootstrap support values ≥50% (1000 bootstrap replicates) are labeled with •. Replicated individuals are indicated in green. <i>Ipomoea tiliacea</i> represents the root of the tree. A graphical overview of the replicates character matrix is shown below. In this matrix each row represents a replicate pair of a single individual and each column a bin. Light blue cells specify reproducible (0,0) bin states, dark blue cells reproducible (1,1) bin states and red cells unreproducible (0,1) bin states. Scale bar indicates uncorrected genetic distance.</p

Flow chart of AMARE.

<p>Flow chart of AMARE.</p